Protection Of Cells From Alu-rna-induced Degeneration And Inhibitors For Protecting Cells

  *US09453226B2*
  US009453226B2                                 
(12)United States Patent(10)Patent No.: US 9,453,226 B2
  et al. (45) Date of Patent:*Sep.  27, 2016

(54)Protection of cells from Alu-RNA-induced degeneration and inhibitors for protecting cells 
    
(75)Inventor: UNIVERSITY OF KENTUCKY RESEARCH FOUNDATION,  Lexington, KY (US) 
(73)Assignee:University of Kentucky Research Foundation,  Lexington, KY (US), Type: US Company 
(*)Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 U.S.C. 154(b) by 0 days. 
  This patent is subject to a terminal disclaimer. 
(21)Appl. No.: 14/158,357 
(22)Filed: Jan.  17, 2014 
(65)Prior Publication Data 
 US 2014/0178309 A1 Jun.  26, 2014 
 Related U.S. Patent Documents 
(63) .
Continuation-in-part of application No. PCT/US2012/046928, filed on Jul.  16, 2012 .
 
(60)Provisional application No. 61/508,867, filed on Jul.  18, 2011.
 
 Provisional application No. 61/543,038, filed on Oct.  4, 2011.
 
Jan.  1, 2013 C 12 N 15 1136 F I Sep.  27, 2016 US B H C Jan.  1, 2013 A 61 K 31 713 L I Sep.  27, 2016 US B H C Jan.  1, 2013 A 61 K 38 08 L I Sep.  27, 2016 US B H C Jan.  1, 2013 A 61 K 38 1709 L I Sep.  27, 2016 US B H C Jan.  1, 2013 A 61 K 49 005 L I Sep.  27, 2016 US B H C Jan.  1, 2013 A 61 K 49 0008 L I Sep.  27, 2016 US B H C Jan.  1, 2013 C 07 K 7 06 L I Sep.  27, 2016 US B H C Jan.  1, 2013 C 07 K 14 00 L I Sep.  27, 2016 US B H C Jan.  1, 2013 C 07 K 16 244 L I Sep.  27, 2016 US B H C Jan.  1, 2013 G 01 N 33 5023 L I Sep.  27, 2016 US B H C Jan.  1, 2013 G 01 N 33 5041 L I Sep.  27, 2016 US B H C Jan.  1, 2013 G 01 N 33 6869 L I Sep.  27, 2016 US B H C Jan.  1, 2013 C 07 K 2317 76 L A Sep.  27, 2016 US B H C Jan.  1, 2013 G 01 N 2333 54 L A Sep.  27, 2016 US B H C
(51)Int. Cl. A61K 048/00 (20060101); C12N 015/113 (20100101); A61K 031/713 (20060101); A61K 038/08 (20060101); A61K 038/17 (20060101); C07K 007/06 (20060101); C07K 016/24 (20060101); G01N 033/50 (20060101); G01N 033/68 (20060101); A61K 049/00 (20060101); C07K 014/00 (20060101)
(58)Field of Search  514/44

 
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     * cited by examiner
 
     Primary Examiner —Kimberly Chong
     Art Unit — 1674
     Exemplary claim number — 1
 
(74)Attorney, Agent, or Firm — Stites & Harbison PLLC; Mandy Wilson Decker

(57)

Abstract

A method of protecting a cell includes inhibiting an inflammasome, MyD88, IL-18, VDAC1, VDAC2, caspase-8, and/or NFκB of the cell. Administering an inhibitor of MyD88, IL-18, VDAC1, VDAC2, caspase-8, and/or NFκB can protect the cell from Alu-RNA-induced degeneration. Protecting a cell, such as an retinal pigment epithelium (RPE), can be therapeutically useful in the context of age-related macular degeneration and geographic atrophy.
25 Claims, 23 Drawing Sheets, and 28 Figures


RELATED APPLICATIONS

[0001] This application claims priority from International Patent Application No. PCT/US2012/046928 filed Jul. 16, 2012, which claims priority to U.S. Provisional Application Ser. No. 61/508,867 filed Jul. 18, 2011 and U.S. Provisional Application Ser. No. 61/543,038 filed Oct. 4, 2011, the entire disclosures of each of which are incorporated herein by this reference.

GOVERNMENT INTEREST

[0002] This invention was made with government support under R01EY018350, R01EY018836, R01EY020672, R01EY022238, R21EY019778, RC1EY020442 awarded by the National Eye Institute of the National Institutes of Health. The government has certain rights in the invention.

TECHNICAL FIELD

[0003] The presently-disclosed subject matter relates to inhibition of inflammosome, MyD88, IL-18, VDAC1, VDAC2, Caspase-8, and NFκB; inhibitors of inflammosome, MyD88, IL-18, VDAC1, VDAC2, Caspase-8, and NFκB, methods protecting a cell, and screening methods for identifying inhibitors.

INTRODUCTION

[0004] Age-related macular degeneration (AMD), which is as prevalent as cancer in industrialized countries, is a leading cause of blindness worldwide. In contrast to the neovascular form of AMD, for which many approved treatments exist, the far more common atrophic form of AMD remains poorly understood and without effective clinical intervention. Extensive atrophy of the retinal pigment epithelium (RPE) leads to severe vision loss and is termed geographic atrophy, the pathogenesis of which is unclear. Geographic atrophy causes blindness in millions of people worldwide and there is currently no approved treatment.
[0005] The present inventors have shown a dramatic reduction of the RNase DICER1 in the retinal pigmented epithelium (RPE) of human eyes with geographic atrophy (Kaneko et al. Nature 2011, which is incorporated herein by this reference). The present inventors have also demonstrated that DICER1 deficiency leads to an accumulation of Alu RNA transcripts, which is also observed in the RPE of human eyes with geographic atrophy. These Alu RNA transcripts induce cell death of human RPE cells and RPE degeneration in mice. The precise mechanisms of cytotoxicity of Alu transcripts are unknown.
[0006] As described herein the present inventors have now found that DICER1 deficit or Alu RNA exposure activates the NLRP3 inflammasome and triggers toll-like receptor-independent MyD88 signalling via IL-18 both in the RPE of mice and in human and mouse RPE cells.

SUMMARY

[0007] The presently-disclosed subject matter meets some or all of the above-identified needs, as will become evident to those of ordinary skill in the art after a study of information provided in this document.
[0008] This Summary describes several embodiments of the presently-disclosed subject matter, and in many cases lists variations and permutations of these embodiments. This Summary is merely exemplary of the numerous and varied embodiments. Mention of one or more representative features of a given embodiment is likewise exemplary. Such an embodiment can typically exist with or without the feature(s) mentioned; likewise, those features can be applied to other embodiments of the presently-disclosed subject matter, whether listed in this Summary or not. To avoid excessive repetition, this Summary does not list or suggest all possible combinations of such features.
[0009] The presently-disclosed subject matter includes methods for identifying MyD88 inhibitors, and methods and compositions for inhibiting MyD88 and uses thereof. The presently-disclosed subject matter includes methods for identifying inflammasome inhibitors, and methods and compositions for inhibiting an inflammasome and uses thereof. The presently-disclosed subject matter includes methods for identifying inhibitors of components of inflammosome, and methods and compositions for inhibiting a component of inflammasome and uses thereof. Components of inflammasome include, for example, NLRP3, PYCARD, and Caspase-1. The presently-disclosed subject matter includes methods for identifying IL-18 inhibitors, and methods and compositions for inhibiting IL-18 and uses thereof. The presently-disclosed subject matter includes methods for identifying VDAC1 and VDAC2 inhibitors, and methods and compositions for inhibiting VDAC1 and VDAC2 and uses thereof. The presently-disclosed subject matter includes methods for identifying caspase-8 inhibitors, and methods and compositions for inhibiting caspase-8 and uses thereof. The presently-disclosed subject matter includes methods for identifying NFkB inhibitors, and methods and compositions for inhibiting NFkB and uses thereof. Also provided are methods and compositions for imaging activated caspase-1 in an eye of a subject.
[0010] The presently-disclosed subject matter includes methods including inhibiting one or more of an inflammasome, MyD88, and IL-18 of a cell. In some embodiments, the presently-disclosed subject matter includes methods including inhibiting one or more of MyD88, IL-18, VDAC1, VDAC2, NFκB, caspase-8, caspase-1, NLRP-3, PYCARD, and an inflammasome, including a component of an inflammasome (e.g., caspase 1, NLRP-3, PYCARD) of a cell. In some embodiments, the presently-disclosed subject matter includes methods including administering one or more inhibitors selected from inhibitors of MyD88, IL-18, VDAC1, VDAC2, NFκB, caspase-8, caspase-1, NLRP-3, PYCARD, and an inflammasome, including a component of an inflammasome (e.g., caspase 1, NLRP-3, PYCARD).
[0011] In some embodiments of the method, the cell is selected from an RPE cell, a retinal photoreceptor cell, or a choroidal cell. In some embodiments, the cell is an RPE cell. In some embodiments, the cell is the cell of a subject. In some embodiments, the cell is a cell of a subject having, suspected of having, or at risk of having a condition of interest. In some embodiments, the cell is a cell of a subject having, suspected of having, or at risk of having age-related macular degeneration. In some embodiments, the cell is a cell of a subject having, suspected of having, or at risk of having geographic atrophy. In some embodiments, the cell is a cell of a subject having, suspected of having, or at risk of having geographic atrophy and the cell is an RPE cell. In some embodiments, a subject having age-related macular degeneration can be treated using methods and compositions as disclosed herein. In some embodiments of the method the cell is protected against Alu-RNA-induced degeneration.

BRIEF DESCRIPTION OF THE DRAWINGS

[0012] FIG. 1. Alu RNA does not activate or function via toll-like receptors (TLRs) (A-E) pAlu, but not pNull, induces RPE degeneration in WT (A), Tlr3−/− (B), Tlr7−/− (C), Unc93b1 mt mice, which are functionally deficient in TLRs-3,7,9 (D), and Tlr4−/− mice (E). Representative images shown. n=8-12. Fundus photographs, top row; Flat mounts stained for zonula occludens-1 (ZO-1; red), bottom row. Degeneration outlined by blue arrowheads. Scale bars, 20 μm. (F) Stimulation of HEK293 cell lines expressing various TLRs with either of two different Alu RNA sequences does not elicit NF-κB activation. Positive (+) controls using TLR-specific ligands activated NF-κB. n=3. Data are represented as mean+/−SEM. See also FIG. 8.
[0013] FIG. 2. Alu RNA induces RPE degeneration via MyD88 (A) pAlu does not induce RPE degeneration in Myd88−/− mice. (B) pAlu-induced RPE degeneration in WT mice is inhibited by a MyD88 homodimerization peptide inhibitor (MyD88i), but not by a control peptide. (C) pAlu-induced RPE degeneration in WT mice is inhibited by cholesterol-conjugated Myd88 siRNA but not control siRNA. (D and E) siRNA targeting MyD88 (siMyD88) reduces target gene (D) and protein (E) abundance in mouse RPE cells compared to control siRNA. n=3, *p<0.05 by Student t-test. (F) pAlu does not induce RPE degeneration in Myd88 heterozygous (het) mice. (G) Western blot of Alu RNA-induced IRAK1 and IRAK4 phosphorylation in human RPE cells. Image representative of 3 experiments. (H) pAlu reduces cell viability of WT but not Myd88 mouse RPE cells. (I) Loss of human RPE cell viability induced by pAlu is rescued by MyD88i. (J) AAV1-BEST1-Cre, but not AAV1-BEST1-GFP, protected Myd88f/f mice from pAlu-induced RPE degeneration. (K) pAlu induces IL-18 secretion from human RPE cells measured by ELISA. IL-1β secretion is barely detectable. n=3, *p<0.05 by Student t-test. (L) Recombinant IL-18 induces RPE degeneration in WT but not Myd88−/− mice. (M and N) pAlu-induced RPE degeneration in WT mice is rescued by IL-18 neutralizing antibody (N) but not by IL-1β neutralizing antibody (M). Representative images shown. n=8-12. Fundus photographs, top row; ZO-1 stained (red) flat mounts, bottom row. Degeneration outlined by blue arrowheads. Scale bars, 20 μm (A-C,F,J,L-N). n=3, *p<0.05 by Student t-test. Data are represented as mean+/−SEM (D,E,H,I,K). See also FIG. 9.
[0014] FIG. 3. Alu RNA induces RPE degeneration via NLRP3 inflammasome (A) Western blot of Caspase-1 activation (p20 subunit) by Alu RNA in human RPE cells. (B) Western blot of pAlu-induced IL-18 maturation in RPE cell lysates in wild-type mice impaired by Caspase-1 peptide inhibitor. (C) Caspase-1 peptide inhibitor protects WT mice from pAlu-induced RPE degeneration. (D and E) pAlu does not induce RPE degeneration in Casp1−/− mice or (E) cytotoxicity in Casp1−/− mouse RPE cells. (F) Alu RNA and LPS+ATP induce formation of PYCARD clusters in human RPE cells transfected with GFP-PYCARD. (G and H) pAlu does not induce RPE degeneration in Nlrp3−/− (G) or Pycard−/− (H) mice. (I) Nlrp3−/− and Pycard−/− mouse RPE cells are protected against pAlu-induced loss of cell viability. (J) siRNAs targeting NLRP3 or PYCARD rescued human RPE cells from pAlu-induced cytotoxicity, compared to control siRNA. n=3-4, *p<0.05 by Student t-test (A,B,E,F,I,J). Images representative of 3 experiments. Densitometry values normalized to Vinculin are shown in parentheses (A,B). Fundus photographs, top row; ZO-1 stained (red) flat mounts, bottom row. Degeneration outlined by blue arrowheads. n=8-12. Scale bars, 20 μm (C,D,G,H). Representative images shown. See also FIG. 11.
[0015] FIG. 4. Alu RNA induces mitochondrial ROS production and NLRP3 priming (A) pAlu induces NLRP3 and IL18 mRNAs in WT and Myd88−/− mouse RPE cells. (B) pAlu induces generation of reactive oxygen species (ROS) in human RPE cells as monitored with the fluorescent probe H2DCFDA (A.U, arbitrary units). (C) DPI blocks pAlu-induced NLRP3 and IL18 mRNAs in human RPE cells. (D) DPI protects WT mice from pAlu-induced RPE degeneration. (E) pAlu induces generation of mitochondrial reactive oxygen species in human RPE cells as detected by the fluorescence of MitoSOX Red (green pseudocolor), colocalized with respiring mitochondria labeled by MitoTracker Deep Red (red). (F) PMA, but not pAlu, induces phagosomal ROS generation, as assessed by fluorescent Fc OXYBURST Green assay in human RPE cells. (A.U, arbitrary units). (G) MitoTempo and MitoQ, but not vehicle or dTPP controls, prevent Alu RNA-induced RPE degeneration in WT mice. (H) NADPH oxidase inhibitor gp91ds-tat or a scrambled peptide do not prevent Alu RNA-induced RPE degeneration in WT mice. (I) Alu RNA induces RPE degeneration mice deficient in Cybb (which encodes the gp91phox subunit of NADPH oxidase). (J and K) siRNAs targeting VDAC1 and VDAC2, but not VDAC3 or scrambled control, prevent pAlu-induced mROS generation (J) and upregulation of NLRP3 and IL18 mRNAs (K) in human RPE cells. mROS visualized with MitoSox Red dye and cell nuclei with Hoechst stain. n=3-4, *p<0.05 by Student t-test (A-C, K), NS, not significant by Student t-test (F). Representative images shown. n=8-12. ZO-1 stained (red) flat mounts. Scale bars, 20 nm (D, E, G-I), n=3-4. Scale bar, 100 μm (J). See also FIG. 11.
[0016] FIG. 5. RPE degeneration does not occur via pyroptosis (A and B) Glycine inhibits human RPE cell death induced by LPS+ATP (A) but not by pAlu (B). (C) Recombinant IL-18 induces RPE degeneration in Casp1−/− mice. n=3-4 (A,B), *p<0.05 by Student t-test. Representative images shown. n=8-12. Fundus photographs, top row; ZO-1 stained (red) flat mounts, bottom row. Degeneration outlined by blue arrowheads. Scale bars, 20 μm (C).
[0017] FIG. 6. DICER1 loss induces cell death via inflammasome (A) Western blot of Alu RNA-induced Caspase-1 cleavage (p20) inhibited by DICER1 overexpression in human RPE cells. (B and C) DICER1 overexpression reduces Alu RNA-induced Caspase-1 activation in human RPE cells (measured by cleavage (B left panel, green) of Caspalux®1 fluorescent substrate). Fluorescence quantification shown in right panel. (C) Western blot of increased Caspase-1 activation (p20 subunit) in RPE cell lysates of BEST1-Cre; Dicer1f/f mice compared to BEST1-Cre or Dicer1f/f mice. (D) Western blot of increased Caspase-1 activation (p20 subunit) and IL-18 maturation in RPE cell lysates of Dicer1f/f mice treated with AAV1-BEST1-Cre. (E and F) RPE degeneration induced by AAV1-BEST1-Cre in Dicer1f/f mice is rescued by peptide inhibitors of either Caspase-1 (E) or MyD88 (F). (G) MyD88 inhibitor rescues loss of human RPE cell viability induced by DICER1 antisense (AS) treatment. (H) DICER1 antisense (AS) treatment of human RPE cells reduces DICER1 and increases IRAK1 and IRAK4 phosphorylation. (I) MyD88 inhibitor rescues loss of cell viability in Dicer1f/f mouse RPE cells treated with adenoviral vector coding for Cre recombinase (Ad-Cre). (J) Ad-Cre induced global miRNA expression deficits in Dicer1f/f mouse RPE cells compared to Ad-Null. No significant difference in miRNA abundance between MyD88 inhibitor and control peptide-treated Dicer1 depleted cells. n=3 (A,B,F-H). Densitometry values normalized to Vinculin are shown in parentheses (A,C). Degeneration outlined by blue arrowheads. n=8 (E,F). *p<0.05 by Student t-test (G,I). Images representative of 3 experiments (A,B,C,D,H). See also FIG. 12.
[0018] FIG. 7. NLRP3 Inflammasome and MyD88 activation in human GA (A) NLRP3 and IL18 abundance was significantly elevated in macular GA RPE (n=13) compared to normal age-matched controls (n=12). *p<0.05 by Mann-Whitney U-test. There was no significant difference between groups (p=0.32 by Mann-Whitney U-test) in IL1B abundance. (B-D) Increased immunolocalization of NLRP3 (B), PYCARD (C) and Caspase-1 (D) in macular GA RPE compared to age-matched normal controls. Scale bar, 20 μm. (E) Western blots of macular RPE lysates from individual human donor eyes show that abundance of NLRP3, PYCARD, and phosphorylated IRAK1/4, normalized to the levels of the housekeeping protein Vinculin, is reduced in geographic atrophy (GA) compared to age-matched normal controls. Data are represented as mean+/−SEM (A). Representative images shown. n=6 (B-E). See also FIG. 13.
[0019] FIG. 8. Alu RNA does not activate several RNA sensors. (A and B) p7SL (a 7SL expression vector) (A) and in vitro synthesized 7SL RNA (B) do not induce RPE degeneration in wild-type mice. (C) RPE degeneration induced by subretinal injection of pAlu in wild-type mice is not blocked by a TLR4 antagonist. (D-E) Mice deficient in Mda5 (D) or Prkr (E) are susceptible to pAlu-induced RPE degeneration. (F) Dephosphorylated (Dep) Alu RNA induces RPE degeneration in wild-type mice just as well as Alu RNA. (G) Mice deficient in Mays are susceptible to pAlu-induced RPE degeneration. pNull does not induce RPE degeneration in any strain of mice. Degeneration outlined by blue arrowheads. Fundus photographs, top rows; ZO-1 stained (red) RPE flat mounts, bottom rows. n=8 (A-G). (H) A schematic of the innate immune pathways that are not activated by Alu RNA.
[0020] FIG. 9. Alu RNA induces RPE degeneration via MyD88, not TRIF or IFNγ, (A) Subretinal administration of pAlu induces RPE degeneration in Ticam1−/− mice. (B) Alu RNA does not induce RPE degeneration in Myd88−/− mice. (C) Subretinal administration of a different Alu expression plasmid (pAlu(2)) also induces RPE degeneration in wild-type but not Myd88−/− mice. (D) Alu RNA does not induce RPE degeneration in Myd88+/− heterozygous (het) mice. (E) MyD88 inhibitory peptide reduces Alu RNA-induced phosphorylation of IRAK1/4, normalized to Vinculin expression. (F) Subretinal injection of AAV1-BEST1-Cre, but not AAV1-BEST1-GFP, protects Myd88f/f mice from Alu RNA-induced RPE degeneration. (G) pAlu and Alu RNA induces RPE degeneration in wild-type mice receiving Myd88−/− bone marrow (Myd88−/−→wild-type) but did not do so in Myd88−/− mice receiving wild-type bone marrow (wild-type→Myd88−/−). (H-K) Subretinal administration of pAlu induces RPE degeneration in Ifng−/− (H), Ifngr1−/− (I), and Il1r1−1− mice (J) but not in Il18r1−1− mice (K). pNull administration does not induce RPE degeneration in any strain of mice. Degeneration outlined by blue arrowheads. Fundus photographs, top rows; ZO-1 stained (red) RPE flat mounts, bottom rows. n=8 (A-D, F-K).
[0021] FIG. 10. Alu RNA induces RPE degeneration via NLRP3 inflammasome activation, (A) Alu RNA or LPS+ATP induce activation of Caspase-1 in human RPE cells as assessed by increased cleavage of Caspalux®1 (green, left panel), a fluorescent-linked peptide substrate as compared to mock treatment. Fluorescence quantification shown in right panel. (B) Western blot of Alu RNA-induced Caspase-1 activation (p20 subunit) in THP-1 and HeLa cells, normalized to Vinculin expression. (C) Caspase-1 inhibitor peptide blocks Alu RNA-induced substrate cleavage in human RPE cells. n=3. (D) Subretinal injection of Alu RNA does not induce RPE degeneration in Casp1−/− mice. (E) Alu RNA or LPS+ATP induce the appearance of a brightly fluorescent cluster of GFP-PYCARD visible in the cytoplasm of human RPE cells. Area in insets shown in higher magnification. Images representative of 3 experiments. (F and G) Subretinal injection of Alu RNA does not induce RPE degeneration in Nlrp3−/− (F) or Pycard−/− (G) mice. (H) The abundance of NLRP3 in HEK293 cells transfected with an NLRP3 expression vector and of PYCARD in human RPE cells is reduced by transfection of siRNAs targeting these genes, compared to control (Ctrl) siRNAs. n=3, *p<0.05 compared to Ctrl siRNAs by Student t-test. (I) Alu RNA-induced Caspase-1 activation (p20 subunit) in human RPE cells is unaffected by MyD88 inhibitory peptide, normalized to Vinculin expression. (J) MyD88 inhibitory peptide does not reduce Alu RNA-induced cleavage activity of Caspase-1 in human RPE cells (top panel). Fluorescence quantification (bottom panel). (K) Caspase-1 activation (p20 subunit) in RPE cell lysates of wild-type mice treated with subretinal pAlu administration is unimpaired by intravitreous administration of anti-IL-18 neutralizing antibodies. (L) Alu RNA-induced phosphorylation of IRAK1/4 is reduced by Caspase-1 inhibitory peptide in human RPE cells, normalized to Vinculin expression. Vehicle control injections also do not damage the RPE. Fundus photographs, top rows; ZO-1 stained (red) RPE flat mounts, bottom rows. n=8 (D,F,G). Images representative of 3 experiments (A,B,I,J-L).
[0022] FIG. 11. NLRP3 does not physically interact with Alu RNA, and VDAC knockdown by siRNA. (A) RNA-binding protein immunoprecipitation (RIP) assay in human RPE cells transfected with pAlu and pNLRP3-FLAG Immunoprecipitation of protein-RNA complexes with antibodies against NLRP3 or FLAG did not reveal interaction between NLRP3 and Alu RNA. RNA isolated from an equal amount of cell lysate (not subjected to IP) was used as input for Alu PCR. Relative abundance of Alu RNA in the immunoprecipitate, assessed by real-time RT-PCR using Alu-specific primers, was normalized to levels obtained with control IgG immunoprecipitation. N=3. (B) The abundance of VDAC1, VDAC2, and VDAC3 mRNAs in human RPE cells is reduced by transfection of siRNAs targeting these genes compared to control (targeting Luc) siRNA. N=3. *p<0.05 compared to Control siRNA by Student t-test.
[0023] FIG. 12. DICER1 is a negative regulator of Caspase-1 activation by Alu RNA, (A) Knockdown of DICER1 by antisense oligonucleotides (AS) in human RPE cells increases cleavage activity of Caspase-1, as monitored by Caspalux, a fluorescent (green in overlay) reporter of substrate cleavage compared to control AS treatment. (B) Inhibition of Alu RNA by AS treatment reduces Caspalux fluorescence in human RPE cells treated with DICER1 AS. Mean values of Caspalux fluorescence shown in parentheses. Images representative of 3 experiments.
[0024] FIG. 13. Schematic representation of proposed model of NLRP3 inflammasome activation by DICER1 deficit-induced Alu RNA that leads to RPE degeneration and geographic atrophy. Alu RNA induces priming of NLRP3 and IL18 mRNAs via generation of reactive oxygen species (ROS). Activation of the NLRP3 inflammasome triggers cleavage of pro-IL-18 by activated Caspase-1 to mature IL-18. IL-18 signals via MyD88 to phosphorylate IRAK1 and IRAK4, which leads to RPE cell death.
[0025] FIG. 14. Intravitreous administration of Caspase-8 inhibitor protects wild-type mice from pAlu-induced RPE degeneration. Representative images shown. n=8-12. Fundus photographs, top row; ZO-1 stained (red) flat mounts, bottom row.
[0026] FIG. 15. Caspase-8 inhibitor protects human RPE cells from Alu induced cytotoxicity. Caspase-8 inhibitory peptide Z-IETD-FMK (100 μM) but not the control peptide Z-FA-FMK (100 μM) protects human RPE cells from Alu RNA-induced cytotoxicity.
[0027] FIG. 16. Caspase-8 inhibitor protects human RPE cells from pAlu-induced cytotoxicity. Caspase-8 inhibitory peptide Z-IETD-FMK (100 μM) but not the control peptide Z-FA-FMK (100 μM) protects human RPE cells from pAlu-induced cytotoxicity.
[0028] FIG. 17. IL-18 induced caspase-8 activation. Subretinal injection of IL-18 in wild-type mice induced activation of caspase-8, as monitored by fluorometric plate assay.
[0029] FIG. 18. pAlu does not induce RPE degeneration in CD95−/− mice. Representative images shown. n=8-12. Fundus photographs, top row; ZO-1 stained (red) flat mounts, bottom row.
[0030] FIG. 19. Alu RNA does not induce RPE degeneration in CD95−/− mice. Representative images shown. n=8-12. Fundus photographs, top row; ZO-1 stained (red) flat mounts, bottom row.
[0031] FIG. 20. Recombinant IL-18 does not induce RPE degeneration in CD95−/− mice. Representative images shown. n=8-12. Fundus photographs, top row; ZO-1 stained (red) flat mounts, bottom row.
[0032] FIG. 21. pAlu does not induce RPE degeneration in Faslg mice. Representative images shown. n=8-12. Fundus photographs, top row; ZO-1 stained (red) flat mounts, bottom row.
[0033] FIG. 22. Alu RNA does not induce RPE degeneration in Faslg mice. Representative images shown. n=8-12. Fundus photographs, top row; ZO-1 stained (red) flat mounts, bottom row.
[0034] FIG. 23. Recombinant IL-18 does not induce RPE degeneration in Faslg mice. Representative images shown. n=8-12. Fundus photographs, top row; ZO-1 stained (red) flat mounts, bottom row.
[0035] FIG. 24. Alu RNA does not induce RPE degeneration in Nfkb1−/− mice. Representative images shown. n=8-12. Fundus photographs, top row; ZO-1 stained (red) flat mounts, bottom row.
[0036] FIG. 25. Alu RNA or vehicle (PBS) was injected into the subretinal space of fellow eyes of a wild-type mouse. 3-days later, DyeLight782-VAD-FMK3 was injected into the vitreous humor of both eyes. 24-hours later, RPE flat mount preparations were visualized under fluorescent microscopy to visualize areas of bioactive caspase (green fluorescence), which corresponded to the area of Alu RNA injection.
[0037] FIG. 26. Alu RNA or vehicle (PBS) was injected into the subretinal space of fellow eyes of two wild-type mice (left and right panels). 3-days later, DyeLight782-VAD-FMK3 was injected into the vitreous humor of both eyes. From baseline (0 hours) to 8 hours thereafter, photographs of the fundus (retina) were taken through the ICG filter of a Topcon 50IX camera. In the Alu RNA-injected eye, white fluorescent areas corresponding to bioactive caspase generation were observed in the area of Alu RNA injection. No such widespread areas were observed in the vehicle-injected eye.
[0038] FIG. 27. Recombinant IL-18 or vehicle (PBS) was injected into the subretinal space of fellow eyes of a wild-type mouse. 2-days later, DyeLight782-VAD-FMK3 was injected into the vitreous humor of both eyes. From baseline (0 hours) to 24 hours thereafter, photographs of the fundus (retina) were taken through the ICG filter of a Topcon 50IX camera. In the IL-18-injected eye, white fluorescent areas corresponding to bioactive caspase generation were observed in the area of IL-18 injection. No such widespread areas were observed in the vehicle-injected eye.
[0039] FIG. 28. Representative images show that subretinally injected Alu RNA (1 μg)-induced RPE degeneration is blocked by intravitreous administration of the MyD88 peptide inhibitor DRQIKIWFQNRRMKWKKRDVLPGTCVWSIASE (2 μg). Top panels show color fundus photographs. Bottom panels show retinal flat mount preparations stained with an anti-ZO1 antibody (red). Alu RNA-induced RPE degeneration (left panels) is evidenced by depigmentation seen on color photos (top left) and dysmorphic appearing RPE cells (bottom left). Treatment with the MyD88 peptide inhibitor prevents those degenerative changes and preserves normal RPE anatomy.

BRIEF DESCRIPTION OF THE SEQUENCE LISTING

[0040] SEQ ID NO: 1. IMG-2005-1 peptide sequence: DRQIKIWFQNRRMKWKKRDVLPGT, wherein the last 7 amino acids are required for inhibition of MyD88 homodimerization, while the preceding amino acid sequence is an Antennopedia cell permeation sequence that enables the inhibitory peptide to enter the cell, so that it can block MyD88.
[0041] SEQ ID NO: 2. Control peptide sequence: DRQIKIWFQNRRMKWKK
[0042] SEQ ID NO: 3. MyD88 siRNA #1 sense: 5′-GAGAAGCCUUUACAGGUdTdT-3′
[0043] SEQ ID NO: 4. MyD88 siRNA #1 antisense: 5′-ACCUGUAAAGGCUUCUCdTdT-3′
[0044] SEQ ID NO: 5. MyD88 siRNA #2 sense: 5′-CAGAGCAAGGAAUGUGAdTdT-3′
[0045] SEQ ID NO: 6. MyD88 siRNA #2 antisense: 5′-UCACAUUCCUUGCUCUGdTdT-3′
[0046] SEQ ID NO: 7 NLRP3 siRNA—5′-GUUUGACUAUCUGUUCUdTdT-3′
[0047] SEQ ID NO: 8: NLRP3 siRNA—5′-GGAUCAAACUACUCUGUGA-3′
[0048] SEQ ID NO: 9: NLRP3 siRNA—5′-UGCAAGAUCUCUCAGCAAA-3′
[0049] SEQ ID NO: 10: NLRP3 siRNA—5′-GAAGUGGGGUUCAGAUAAU-3′
[0050] SEQ ID NO: 11: NLRP3 siRNA—5′-GCAAGACCAAGACGUGUGA-3′
[0051] SEQ ID NO: 12: PYCARD siRNA—5′-GAAGCUCUUCAGUUUCAdTdT-3′
[0052] SEQ ID NO: 13: PYCARD siRNA—5′-GGCUGCUGGAUGCUCUGUACGGGAA-3′
[0053] SEQ ID NO: 14: PYCARD siRNA—5′-UUCCCGUACAGAGCAUCCAGCAGCC-3′.
[0054] SEQ ID NO: 15: siRNA of the human Pyrin coding sequence: GCTGGAGCAGGTGTACTACTTC.
[0055] SEQ ID NO: 16: siRNA of the human NLRP3 coding sequence CAGGTTTGACTATCTGTTCT.
[0056] SEQ ID NO: 17: siRNA of the 3′ UTR of the human caspase-1 GTGAAGAGATCCTTCTGTA.
[0057] SEQ ID NO: 18: Oligonucleotide primer for human MB, forward 5′-TTAAAGCCCGCCTGACAGA-3′.
[0058] SEQ ID NO: 19: Oligonucleotide primer for human MB, reverse 5′-GCGAATGACAGAGGGTTTCTTAG-3′).
[0059] SEQ ID NO: 20: Oligonucleotide primer for human IL18, forward 5′-ATCACTTGCACTCCGGAGGTA-3′.
[0060] SEQ ID NO: 21: Oligonucleotide primer for human IL18, reverse 5′-AGAGCGCAATGGTGCAATC-3′.
[0061] SEQ ID NO: 22: Oligonucleotide primer for human NLRP3, forward 5′-GCACCTGTTGTGCAATCTGAA-3′.
[0062] SEQ ID NO: 23: Oligonucleotide primer for human NLRP3, reverse 5′-TCCTGACAACATGCTGATGTGA-3′.
[0063] SEQ ID NO: 24: Oligonucleotide primer for human PYCARD, forward 5′-GCCAGGCCTGCACTTTATAGA-3′.
[0064] SEQ ID NO: 25: Oligonucleotide primer for human PYCARD, reverse 5′-GTTTGTGACCCTCGCGATAAG-3′.
[0065] SEQ ID NO: 26: Oligonucleotide primer for human VDAC1, forward 5′-ACTGCAAAATCCCGAGTGAC-3′.
[0066] SEQ ID NO: 27: Oligonucleotide primer for human VDAC1, reverse 5′-CTGTCCAGGCAAGATTGACA-3′.
[0067] SEQ ID NO: 28: Oligonucleotide primer for human VDAC2, forward 5′-CAGTGCCAAATCAAAGCTGA-3′.
[0068] SEQ ID NO: 29: Oligonucleotide primer for human VDAC2, reverse 5′-CCTGATGTCCAAGCAAGGTT-3′).
[0069] SEQ ID NO: 30: Oligonucleotide primer for human VDAC3, forward 5′-TTGACACAGCCAAATCCAAA-3′.
[0070] SEQ ID NO: 31: Oligonucleotide primer for human VDAC3, reverse 5′-GCCAAAACGGGTGTTGTTAC-3′.
[0071] SEQ ID NO: 32: Oligonucleotide primer for human 18S rRNA, forward 5′-CGCAGCTAGGAATAATGGAATAGG-3′.
[0072] SEQ ID NO: 33: Oligonucleotide primer for human 18S rRNA, reverse 5′-GCCTCAGTTCCGAAAACCAA-3′.
[0073] SEQ ID NO: 34: Oligonucleotide primer for mouse Myd88, forward 5′-CACCTGTGTCTGGTCCATTG-3′.
[0074] SEQ ID NO: 35: Oligonucleotide primer for mouse Myd88, reverse 5′-AGGCTGAGTGCAAACTTGGT-3′.
[0075] SEQ ID NO: 36: Oligonucleotide primer for mouse Nlrp3, forward 5′-ATGCTGCTTCGACATCTCCT-3′.
[0076] SEQ ID NO: 37: Oligonucleotide primer for mouse Nlrp3, reverse 5′-AACCAATGCGAGATCCTGAC-3′.
[0077] SEQ ID NO: 38: Oligonucleotide primer for mouse Il18, forward 5′-GACAGCCTGTGTTCGAGGAT-3′.
[0078] SEQ ID NO: 39: Oligonucleotide primer for mouse Il18, reverse 5′-TGGATCCATTTCCTCAAAGG-3′.
[0079] SEQ ID NO: 40: Oligonucleotide primer for mouse 18S rRNA, forward 5′-TTCGTATTGCGCCGCTAGA-3′.
[0080] SEQ ID NO: 41: Oligonucleotide primer for mouse 18S rRNA, reverse 5′-CTTTCGCTCTGGTCCGTCTT-3′.
[0081] SEQ ID NO: 42: Mouse miR-184-5′-TGGACGGAGAACTGATAAGGGT-3;
[0082] SEQ ID NO: 43: Mouse miR-221/222-5′-AGCTACATCTGGCTACTGGGT-3;
[0083] SEQ ID NO: 44: Mouse miR-320a-5′-AAAAGCTGGGTTGAGAGGGCGA-3′, and
[0084] SEQ ID NO: 45: Mouse mouse miR-484-5′-TCAGGCTCAGTCCCCTCCCGAT-3′.
[0085] SEQ ID NO: 46: U6 snRNA-5′-AAATTCGTGAAGCGTTCC-3′.
[0086] SEQ ID NO: 47: VDAC1 siRNA sense-5′-CGGAAUAGCAGCCAAGUdTdT-3′.
[0087] SEQ ID NO: 48: VDAC2 siRNA sense-5′-CCCUGGAGUUGGAGGCUdTdT-3′.
[0088] SEQ ID NO: 49: VDAC3 siRNA sense-5′-GCUUUAAUCGAUGGGAAdTdT-3′.
[0089] SEQ ID NO: 50: DICER1 antisense oligonucleotide (AS)-5′-GCUGACCTTTTTGCTUCUCA-3′.
[0090] SEQ ID NO: 51: Control for DICER1 AS-5′-TTGGTACGCATACGTGTTGACTGTGA-3′.
[0091] SEQ ID NO: 52: Alu AS-5′-CCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCACGAGTAGCTGGGACTACAGGCGCCCGACACCACTCCCGGCTAATTTTTTGTATTTTT-3′.
[0092] SEQ ID NO: 53: Control for Alu AS-5′-GCATGGCCAGTCCATTGATCTTGCACGCTTGCCTAGTACGCTCCTCAACCTATCCTCCTAGCCCGTTACTTGGTGCCACCGGCG-3′.
[0093] SEQ ID NO: 54: Oligopeptide for inhibiting MyD88 homodimerization: RDVLPGT.
[0094] SEQ ID NO: 55: Oligopeptide for inhibiting MyD88 homodimerization: RDVVPGG.
[0095] SEQ ID NO: 56. MyD88 siRNA: UUAUUUCCUAAWGGGUCdTdT.
[0096] SEQ ID NO: 57. VDAC1 siRNA sense (5′-CGGAAUAGCAGCCAAGUdTdT-3′).
[0097] SEQ ID NO: 58. VDAC2 siRNA sense (5′-CCCUGGAGUUGGAGGCUdTdT-3′).
[0098] SEQ ID NO: 59. VDAC3 siRNA sense (5′-GCUUUAAUCGAUGGGAAdTdT-3′).
[0099] SEQ ID NO: 60. MyD88 inhibitor: DRQIKIWFQNRRMKWKKRDVLPGTCVWSIASE.
[0100] SEQ ID NO: 61. MyD88 inhibitor: RDVLPGTCVWSIASE.

DESCRIPTION OF EXEMPLARY EMBODIMENTS

[0101] The presently-disclosed subject matter includes methods for identifying MyD88 inhibitors, and methods and compositions for inhibiting MyD88 and uses thereof. The presently-disclosed subject matter includes methods for identifying inflammasome inhibitors, and methods and compositions for inhibiting an inflammasome and uses thereof. The presently-disclosed subject matter includes methods for identifying inhibitors of components of inflammosome, and methods and compositions for inhibiting a component of inflammasome and uses thereof. Components of inflammasome include, for example, NLRP3, PYCARD, and Caspase-1. The presently-disclosed subject matter includes methods for identifying IL-18 inhibitors, and methods and compositions for inhibiting IL-18 and uses thereof. The presently-disclosed subject matter includes methods for identifying VDAC1 and VDAC2 inhibitors, and methods and compositions for inhibiting VDAC1 and VDAC2 and uses thereof. The presently-disclosed subject matter includes methods for identifying caspase-8 inhibitors, and methods and compositions for inhibiting caspase-8 and uses thereof. The presently-disclosed subject matter includes methods for identifying NFkB inhibitors, and methods and compositions for inhibiting NFkB and uses thereof. Also provided are methods and compositions for imaging activated caspase-1 in an eye of a subject.
[0102] The presently-disclosed subject matter includes methods including inhibiting one or more of an inflammasome, MyD88, and IL-18 of a cell. In some embodiments, the presently-disclosed subject matter includes methods including inhibiting one or more of MyD88, IL-18, VDAC1, VDAC2, NFκB, caspase-8, caspase-1, NLRP-3, PYCARD, and an inflammasome, including a component of an inflammasome (e.g., caspase 1, NLRP-3, PYCARD) of a cell.
[0103] In some embodiments of the method, the cell is selected from an RPE cell, a retinal photoreceptor cell, or a choroidal cell. In some embodiments, the cell is an RPE cell. In some embodiments, the cell is the cell of a subject. In some embodiments, the cell is a cell of a subject having, suspected of having, or at risk of having a condition of interest. In some embodiments, the cell is a cell of a subject having, suspected of having, or at risk of having age-related macular degeneration. In some embodiments, the cell is a cell of a subject having, suspected of having, or at risk of having geographic atrophy. In some embodiments, the cell is a cell of a subject having, suspected of having, or at risk of having geographic atrophy and the cell is an RPE cell. In some embodiments, a subject having age-related macular degeneration can be treated using methods and compositions as disclosed herein.
[0104] As used herein, the term “subject” refers to a target of treatment. The subject of the herein disclosed methods can be a vertebrate, such as a mammal, a fish, a bird, a reptile, or an amphibian. Thus, the subject of the herein disclosed methods can be a human or non human. Thus, veterinary therapeutic uses are provided in accordance with the presently disclosed subject matter.
[0105] In some embodiments, the inhibiting one or more of an inflammasome, MyD88, IL-18, VDAC1, VDAC2, NLRP3, PYCARD, caspase-1, caspase-8, and NFκB of a cell includes administering an inhibitor to the cell, or to a subject wherein the cell is the cell of a subject. Such inhibitors can be administered, for example, by intraocular injection (e.g., localized interocular therapy); intravitreous injection; subretinal injection; episcleral injection; sub-Tenon's injection; retrobulbar injection; peribulbar injection; transscleral administration; topical administration, e.g., topical eye drop application; suprachoroidal administration; release from a sustained release delivery device that is sutured to or attached to or placed on the sclera, or injected into the vitreous humor, or injected into the anterior chamber, or implanted in the lens bag or capsule; oral administration; or intravenous administration.
[0106] As used herein the term “inhibit” or “inhibiting” refers to suppressing, reducing, decreasing, or substantially eliminating the biological activity of a polypeptide, such as MyD88, IL-18, VDAC1, VDAC2, caspase-8, NFκB, or a polypeptide of an inflammasome (e.g., NLRP3, PYCARD, caspase-1). As used herein with reference to a polypeptide being inhibited, “of a cell” refers to a polypeptide that is inside the cell (inside the cell membrane), on the cell (in the cell membrane, presented on the cell membrane, otherwise on the cell), or outside of a cell, but insofar as the polypeptide is outside of the cell, it is in the extracellular mileu such that one of ordinary skill in the art would recognize the polypeptide as being associated with the cell. For example, VDAC1, VDAC2, caspase-8, NFκB, or a polypeptide of an inflammasome (e.g., NLRP3, PYCARD, caspase-1 of a cell could be in the cell. For another example MyD88 could be in the cell or on the cell. For yet another example, IL-18 could be outside the cell because it is secreted, but it would be recognized by one or ordinary skill in the art as being associated with the cell.
[0107] As will be understood by those skilled in the art upon studying this application, inhibition of an inflammasome, MyD88, IL-18, VDAC1, VDAC2, caspase-1, caspase-8, and NFκB of a cell can be achieved in a number of manners. In some embodiments the inhibition can be achieved by affecting the transcription or translation of the polypeptide, by degrading the polypeptide, by scavenging the polypeptide, or otherwise impacting the biological activity of the polypeptide Inhibition comprises administering an inhibitor. An inhibitor is a compound that affects such inhibition of the biological activity of a polypeptide. Such compounds can be, for example, a polypeptide (including oligonucleotide, and including a polypeptide that binds to the polypeptide-of-interest to affect inhibition), a small molecule (including a small chemical compound), a compound for RNA interference (including siRNA, miRNA, shRNA), an antibody (e.g., a neutralizing antibody against polypeptide of interest, an antibody that blocks polypeptide of interest from binding to a receptor), an aptamer, a dominant negative plasmid or vector, or a virus-encoded inflammasome.
[0108] The terms “polypeptide”, “protein”, and “peptide”, which are used interchangeably herein, refer to a polymer of the 20 protein amino acids, or amino acid analogs, regardless of its size. The terms “polypeptide fragment” or “fragment”, when used in reference to a reference polypeptide, refers to a polypeptide in which amino acid residues are deleted as compared to the reference polypeptide itself, but where the remaining amino acid sequence is usually identical to the corresponding positions in the reference polypeptide. Such deletions can occur at the amino-terminus or carboxy-terminus of the reference polypeptide, from internal portions of the reference polypeptide, or a combination thereof. A fragment can also be a “functional fragment,” in which case the fragment retains some or all of the activity of the reference polypeptide as described herein.
[0109] The terms “modified amino acid”, “modified polypeptide”, and “variant” refer to an amino acid sequence that is different from the reference polypeptide by one or more amino acids, e.g., one or more amino acid substitutions. A variant of a reference polypeptide also refers to a variant of a fragment of the reference polypeptide, for example, a fragment wherein one or more amino acid substitutions have been made relative to the reference polypeptide. A variant can also be a “functional variant,” in which the variant retains some or all of the activity of the reference protein as described herein. The term functional variant includes a functional variant of a functional fragment of a reference polypeptide.
[0110] In some embodiments, the methods and compositions of the presently-disclosed subject matter can be used in a subject having, suspected of having, or at risk of having a condition of interest. In some embodiments, methods and compositions of the presently-disclosed subject matter can be used for treating a condition of interest. Examples of conditions of interest include, but are not limited to: Geographic atrophy (Kaneko, Dridi et al. 2011); Macular degeneration (Kaneko, Dridi et al. 2011); Keratitis (Guo, Gao et al. 2011); Gout (Chen, Shi et al. 2006); Acne vulgaris (Terhorst, Kalali et al. 2010); Crohn's disease (Reuter and Pizarro 2004; Abreu, Fukata et al. 2005; Medvedev, Sabroe et al. 2006); Ulcerative colitis (Reuter and Pizarro 2004; Abreu, Fukata et al. 2005; Medvedev, Sabroe et al. 2006); irritable bowel disease/irritable bowel syndrome (McKernan, Nolan et al. 2009); Type I diabetes (Devaraj, Tobias et al. 2011; von Herrath, Filippi et al. 2011); Type 2 diabetes (Hutton, Soukhatcheva et al. 2010; Nogueira-Machado, Volpe et al. 2011); Insulin resistance (Ghanim, Mohanty et al. 2008; Tilich and Arora 2011); Obesity (Fresno, Alvarez et al. 2011); Hemolytic-Uremic Syndrome (Batsford, Duermueller et al. 2011); Polyoma virus infection (Batsford, Duermueller et al. 2011); Immune complex renal disease (Anders, Banas et al. 2004; Anders and Schlondorff 2007); Acute tubular injury (Anders, Banas et al. 2004; Anders and Schlondorff 2007); Lupus nephritis (Anders, Banas et al. 2004; Anders and Schlondorff 2007); Familial cold autoinflammatory syndrome (Mariathasan, Weiss et al. 2006; Meng, Zhang et al. 2009); Muckle-Wells syndrome and neonatal onset multisystem inflammatory disease (Mariathasan, Weiss et al. 2006; Meng, Zhang et al. 2009); Chronic infantile neurologic cutaneous and articular autoinflammatory diseases, Renal ischemia-perfusion injury (El-Achkar and Dagher 2006; Robson 2009); Glomerulonephritis (E1-Achkar and Dagher 2006; Robson 2009); Cryoglobulinemia (Banas, Banas et al. 2008); Systemic vasculitides (Weyand, Ma-Krupa et al. 2005; Hurtado, Jeffs et al. 2008; Summers, Steinmetz et al. 2011); IgA nephropathy (Lim, Lee et al. 2011); Atherosclerosis (Curtiss and Tobias 2009); HIV/AIDS (Brichacek, Vanpouille et al. 2010); Malaria (Franklin, Ishizaka et al. 2011); Helminth parasites (Babu, Blauvelt et al. 2005; Venugopal, Nutman et al. 2009); Sepsis and septic shock (Knuefermann, Nemoto et al. 2002; Opal and Huber 2002; Cristofaro and Opal 2003; Chen, Koustova et al. 2007); Allergic asthma (Slater, Paupore et al. 1998; Park, Gold et al. 2001); Hay fever (Slater, Paupore et al. 1998; Park, Gold et al. 2001); Chronic obstructive pulmonary disease (Geraghty, Dabo et al. 2011); Drug-induced lung inflammation (Liu, Yang et al. 2010); Contact dermatitis (Martin, Dudda et al. 2008; Yokoi, Niizeki et al. 2009); Leprosy (Krutzik, Tan et al. 2005; Terhorst, Kalali et al. 2010); Burkholderia cenocepacia infection (Ventura, Balloy et al. 2009); Respiratory syncitial virus infection (Aeffner, Traylor et al. 2011); Psoriasis (Zuany-Amorim, Hastewell et al. 2002; Barrat and Coffman 2008; Li, Zhou et al. 2009); Systemic lupus erythematosus (Zuany-Amorim, Hastewell et al. 2002; Barrat and Coffman 2008; Li, Zhou et al. 2009); Scleroderma (Zuany-Amorim, Hastewell et al. 2002; Barrat and Coffman 2008; Li, Zhou et al. 2009); Reactive arthritis (Zuany-Amorim, Hastewell et al. 2002; Barrat and Coffman 2008; Li, Zhou et al. 2009); Cystic fibrosis, Syphilis, Sjögren's syndrome (Zuany-Amorim, Hastewell et al. 2002; Barrat and Coffman 2008; Li, Zhou et al. 2009); Rheumatoid arthritis (Zuany-Amorim, Hastewell et al. 2002; Barrat and Coffman 2008; Li, Zhou et al. 2009); Inflammatory joint disease (O'Neill 2008); Non-alcoholic fatty liver disease (Tan, Fiel et al. 2009); Cardiac surgery (peri-/post-operative inflammation) (Cremer, Martin et al. 1996; Taylor 1996; Dybdahl, Wahba et al. 2002); Acute and chronic organ transplant rejection (Alegre, Leemans et al. 2008; Miller, Rossini et al. 2008; Taylor, Ehrhardt et al. 2008; Krams, Wang et al. 2010; Wang, Schmaderer et al. 2010; Shin and Harris 2011; Testro, Visvanathan et al. 2011); Acute and chronic bone marrow transplant rejection (Alegre, Leemans et al. 2008; Miller, Rossini et al. 2008; Taylor, Ehrhardt et al. 2008; Krams, Wang et al. 2010; Wang, Schmaderer et al. 2010; Shin and Harris 2011; Testro, Visvanathan et al. 2011); Alzheimer's disease; and Tumor angiogenesis (Frantz, Vincent et al. 2005; Schmid, Avraamides et al. 2011).
[0111] As used herein, the terms treatment or treating relate to any treatment of a condition of interest, including but not limited to prophylactic treatment and therapeutic treatment. As such, the terms treatment or treating include, but are not limited to: preventing a condition of interest or the development of a condition of interest; inhibiting the progression of a condition of interest; arresting or preventing the development of a condition of interest; reducing the severity of a condition of interest; ameliorating or relieving symptoms associated with a condition of interest; and causing a regression of the condition of interest or one or more of the symptoms associated with the condition of interest.
[0112] In some embodiments, the methods and compositions of the presently-disclosed subject matter are useful for protecting the cell against Alu-RNA-induced degeneration. As such, in some embodiments, a method includes administering an inhibitor, wherein the cell is protected against Alu-RNA-induced degeneration.

Inhibiting Inflammasome

[0113] In some embodiments, the presently-disclosed subject matter includes a method of protecting a cell, comprising: inhibiting an inflammasome of the cell. The method of any one of the prior claims, wherein the inflammasome is selected from NLRP3 inflammasome, NLRP1 inflammasome, NLRC4 inflammasome, AIM2 inflammasome, and IFI16 inflammasome. In some embodiments, the inflammasome is the NLRP3 inflammasome.
[0114] In some embodiments the inhibiting the inflammasome includes inhibiting a component of the inflammasome. In some embodiments the inflammasome components can include a polypeptide encoded by PYCARD. In some embodiments the inflammasomse components can include a caspase. In some embodiments the inflammasome components can include PYCARD, NLRP3, and caspase-1.
[0115] In some embodiments, the inhibiting the inflammasome comprises administering an inflammasome inhibitor. The inflammasome inhibitor can be an inhibitor of a component of the inflammasome. In some embodiments, the inflammosome
[0116] As noted above, in some embodiments, inhibiting a polypeptide of interest to the presently-disclosed subject matter comprises administering an oligonucleotide or a small RNA molecule. Such small RNA molecule can target, for example, NLRP3 and/or PYCARD. Such nucleotides can target and degrade NLRP3 and/or PYCARD. In this regard, the presently-disclosed subject matter includes a isolated double-stranded RNA molecule that inhibits expression of NLRP3 and/or PYCARD, wherein a first strand of the double-stranded RNA comprises a sequence as set forth in Table A, and includes about 14 to 25 nucleotides. As noted above, in some embodiments, inhibiting comprises administering an inflammasome inhibitor that is a dominant negative vector. In some embodiments, inhibiting inflammasome comprises administering an inhibitor of Caspase-1. In some embodiments the inhibitor of Caspase-1 is a peptide inhibitor.
[0117] Examples of inflammasome inhibitors that can be used in accordance with the presently-disclosed subject matter include, but are not limited to those set forth in Table A. As such, embodiments of the presently-disclosed subject matter can include administering an inflammasome inhibitor set forth in Table A.
[0118] 
[00001] [TABLE-US-00001]
  TABLE A
 
  Examples of Inflammasome Inhibitors
 
 
  Ion channel inhibitors, for example, glybenclamide/glyburide (CAS Number: 10238-21-8)
  (Lamkanfi, et al., 2009).
 
  IkB-α inhibitors, for example, BAY11-7082 (CAS Number: 195462-67-7; also known as (E)-
  3-(4-Methylphenylsulfony1)-2-propenenitrile) (Juliana, et al., 2010).
 
  Compounds similar to BAY11-7082, for example, other related vinyl sulfone compounds, as
  set forth in Lamkanfi, et al., 2009; Juliana, et al., 2010; deRivero Vaccari, et al., 2008; and
  Newman, et al., 2011, which are incorporated herein by this reference.
 
  Antibodies, for example, Anti-ASC and Anti-NALP1 and antibodies based on protein
  sequences selected from: ASC: ALR QTQ PYL VTD LEQ S; NALP1: MEE SQS KEE SNT
  EG-cys (deRivero Vaccari, et al., 2008); and Anti-NALP1 (Abcam, Cambridge, MA), anti-
  IL-1β (Cell Signaling Technology, Beverly, MA), anti-IL-18 (R & D Systems, Minneapolis,
  MN), anti-caspase-1 (Millipore, Billerica, MA), anti-caspase-1 (Santa Cruz Biotechnology,
  Santa Cruz, CA), anti-caspase-11 (Alexis Biochemicals, San Diego, CA), anti-caspase-11
  (Santa Cruz Biotechnology).
 
  Direct inhibitors of Caspase-1 and/or NLRP3, for example, parthenolide (Juliana, et al.,
  2010).
 
  Caspase-1 inhibitors, such as estrogen binding B-box protein (Munding et al., 2006); COP
  (Lee, et al., 2001); ICEBERG (Humke, et al., 2000); and Z-WEHD-FMK (R&D Systems).
 
  Caspase 1 and/or 4 inhibitors, for example, Ac-YVAD-CHO (Ac-Tyr-Val-Ala-Asp-CHO)
  and Ac-YVAD-CMK (CAS Number: 178603-78-6; N-acetyl-L-tyrosyl-L-valyl-N-[(1S)-
  1-(carboxymethyl)-3-chloro-2-oxo-propyl]-L-alaninamide) (Hilbi, et al., 1997).
 
  Caspase-12 inhibitors (Saleh, et al., 2006).
 
  Host-derived inhibitors of Caspase-1, for example, cellular PYRIN domain (PYD)-only
  proteins (POP) family: cP0P1 and cPOP2 (Stehlik, et al., 2003; Dorfleutner, et al., 2007);
  serpin proteinase inhibitor 9 (PI-9) (Young, et al., 2000); BCL-2 and BCL-xL (Young, et al.,
  2000).
 
  Inhibitors of Nlrp1b inflammasome, for example, auranofin (Newman, et al., 2011).
 
  Virus expressed inhibitors of the inflammasome, for example, PYD homologs M13L-PYD,
  S013L (Benedict, et al., 2005; Dorfleutner, et al., 2007; Johnston, et al., 2005); SPI-2
  homologs CrmA, Serp2, SPI-2, (Komiyama, et al., 1994; Kettle, et al., 1997; Messud-Petit, et
  al., 1998); NS1 (Stasakova, et al., 2005); Kaposi Sarcoma-associated Herpesvirus Orf63
 
  (Gregory, et al., 2011).
 
  Potassium chloride (KCl) (CAS Number: 7447-40-7 (Schorn, et al. 2011).
 
  Cathepsin-B inhibitors, for example, CA-074 Me (L-3-trans-(Propylcarbamoyl)oxirane-2-
  Carbonyl)-L-Isoleucyl-L-Proline Methyl Ester (Li, et al., 2009).
 
  Cytochalasin D (Dostert, et al., 2008).
 
  ROS inhibitors, for example, N-acetyl-L-cysteine (NAC), and (2R,4R)-4-aminopyrrolidine-
  2,4-dicarboxylate (APDC) (Dostert, et al., 2008).
 
  ASC-1 inhibitors, for example, cellular pyrin domain (PYD) superfamily proteins, also
  known as M013 (Rahman, et al., 2009).
 
  NLRP3 inflammasome pan-caspase inhibitors, for example, Z-VAD-FMK (Dostert, et al.,
  2009).
 
  Microtubules, for example, colchicine (CAS Number: 64-86-8) (Martinon, et al., 2006).
 
  An isolated double-stranded RNA molecule that inhibits expression of NLRP3, and which
  can be conjugated to cholesterol or not, and at least one strand including the sequence:
  GUUUGACUAUCUGUUCUdTdT (SEQ ID NO: 7).
 
  An isolated double-stranded RNA molecule that inhibits expression of NLRP3, at least one
  strand of which includes a sequence selected from: 5′-GGAUCAAACUACUCUGUGA-3′
  (SEQ ID NO: 8); 5′-UGCAAGAUCUCUCAGCAAA-3′ (SEQ ID NO: 9); 5′-
  GAAGUGGGGUUCAGAUAAU-3′ (SEQ ID NO: 10); and 5′-
  GCAAGACCAAGACGUGUGA-3′)(SEQ ID NO: 11) (Wong, et al., 2011).
 
  An isolated double-stranded RNA molecule that inhibits expression of PYCARD, at least one
  strand of which includes the sequence of: 5′-GAAGCUCUUCAGUUUCAdTdT-3′ (SEQ ID
  NO: 12).
 
  An isolated double-stranded RNA molecule that inhibits expression of PYCARD, at least one
  strand of which includes a sequence selected from: 5′-GAAGCUCUUCAGUUUCAdTdT-3′
  (SEQ ID NO: 12); 5′-GGCUGCUGGAUGCUCUGUACGGGAA-3′ (SEQ ID NO: 13); and
  5′-UUCCCGUACAGAGCAUCCAGCAGCC-3′ (SEQ ID NO: 14). (Stealth siRNA oligos
  were designed and obtained with Lipofectamine 2000).
 
[0119] Further information regarding Caspase-1 inhibitors and probes can be found in Table B. Information found at the links set forth in Table B as of the filing date of this application is incorporated herein by this reference.
[0120] 
[00002] [TABLE-US-00002]
  TABLE B
 
  Peptide      
  Sequence   Application   Link   Notes
 
  GWEHDGK   fluorescent    http://www.ncbi.nlm.nih.gov/pmc/articles/   Gly-Trp-Glu-His-Asp-Gly-
    in vivo   PMC1502090/   Lys
 
  YVADAPV   fluorescent   http://www.ncbi.nlm.nih.gov/pubmed/801   DABCYL-Tyr-Val-Ala-
      2123   Asp-Ala-Pro -Val-EDANS
 
  GFEVD   fluorescent   http://www.ncbi.nlm.nih.gov/pmc/articles/   Abz-GXEVD-
      PMC1221285/pdf/10947972.pdf   GVY(NO2)D
 
  GYEVD   fluorescent   http://www.ncbi.nlm.nih.gov/pmc/articles/   Abz-GXEVD-
      PMC1221285/pdf/10947972.pdf   GVY(NO2)D
 
  YVAD   fluorescent   http://www.sciencedirect.com/science/arti-   BFP-YVAD-GFP
      cle/pii/S1074552199800519  
    fluorescent   http://www.jbc.org/content/286/37/   Ac-YVAD-CHO
      32513.full  
    inhibitor   http://www.jbc.org/content/273/49/  
      32608.long  
 
  WEHD   fluorescent   http://jem.rupress.org/content/191/11/1819/KDPC5G-WEHD-
      T1.expansion.htmlGINGC5PKGY
    Inhibitor   http://www.jbc.org/content/273/49/  
      32608.long  
 
  YVHDAP   fluorescent   http://www.funakoshi.co.jp/data/datasheet/   Caspalux
      ONC/CPL1RE-5.pdf  
 
  YVADAP   fluorescent   http://www.ncbi.nlm.nih.gov/pubmed/8012123   DABCYL-YVADAP-
        EDANS
 
  YEVD   fluorescent   http://www.jbc.org/content/272/15/9677.long   Ac-YVED-pNA
 
  YVHDAPVR   Kinetic   http://www.jbc.org/content/272/11/7223/  
    substrate   Tl.expansion.html
 
  Small      
  molecule      
  Sequence   Application   Link   Notes
 
  VX-765   Inhibitor   http://www.medkoo.com/Anticancer-   Vertex Pharmaceuticals,
      trials/VX-765.htm   Reversible, clinical trials
 
  ML132   Inhibitor   http://www.ncbi.nlm.nih.gov/books/NBK   Reversible(?), based on
      56241/   VX-765
 
  VX-740   Inhibitor   http://www.ncbi.nlm.nih.gov/pubmed/173   Vertex Pharmaceuticals,
      93315   common name: Pralnacasan
        clincal trials halted 
        (liver abnormalities)
 
  VRT-   Inhibitor   http://www.ncbi.nlm.nih.gov/pubmed/178   Active metabolite of VX-
  018858     45807   740
 
  CM-269   Reporter   http://www.sciencedirect.com/science/arti-   Luciferase based reporter
      cle/pii/S1074552110003091#sec5.1
 
[0121] The presently-disclosed subject matter further includes compositions useful for inhibiting an inflammasome. Such compositions include an inhibitor. As noted above, such inhibitors can be, for example, a nucleotide, a polypeptide, a small (chemical) molecule, etc. In some embodiments, a composition can include an isolated RNA molecule.
[0122] The presently-disclosed subject matter includes isolated RNA molecules that inhibit expression of a component of inflammasome, e.g., NLRP3, caspase-1 and/or PYCARD. In some embodiments, a first strand of the double-stranded RNA comprises a sequence selected from the following, and including about 14 to 25 nucleotides: 5′-GUUUGACUAUCUGUUCUdTdT-3′ (SEQ ID NO: 7); 5′-GGAUCAAACUACUCUGUGA-3′ (SEQ ID NO: 8); 5′-UGCAAGAUCUCUCAGCAAA-3′ (SEQ ID NO: 9); 5′-GAAGUGGGGUUCAGAUAAU-3′ (SEQ ID NO: 10); 5′-GCAAGACCAAGACGUGUGA-3′ (SEQ ID NO: 11); 5′-GAAGCUCUUCAGUUUCAdTdT-3′ (SEQ ID NO: 12); 5′-GGCUGCUGGAUGCUCUGUACGGGAA-3′ (SEQ ID NO: 13); and 5′-UUCCCGUACAGAGCAUCCAGCAGCC-3′ (SEQ ID NO: 14).
[0123] The presently-disclosed subject matter includes isolated RNA molecules that inhibit expression of an inflammasome component. In some embodiments, the RNA molecule comprises a sequence selected from the following:
[0124] 
[00003] [TABLE-US-00003]
    (SEQ ID NO: 15)
    GCTGGAGCAGGTGTACTACTTC,
   
    (SEQ ID NO: 16)
    CAGGTTTGACTATCTGTTCT,
    and 
   
    (SEQ ID NO: 17)
    GTGAAGAGATCCTTCTGTA.
[0125] The presently-disclosed subject matter further includes methods of screening candidate inhibitors to identify inflammasome inhibitors. In some embodiments, a method of identifying an inflammasome inhibitor makes use of a cultured cell wherein a cell based-system is provided, which measures PYCARD aggregation, Caspase-1 cleavage, or cleavage/secretion of IL-1β or IL-18 in response to an activator of the inflammasome (e.g., Alu RNA, lipopolysaccharide+ATP).
[0126] In some embodiments, a screening method for inflammasome inhibitors includes stimulating cells (e.g., RPE cells) or a cell line (e.g., THP-1 or RAW macrophages) that has been transfected with a plasmid encoding a fluorescent-tagged PYCARD with Alu RNA or LPS+ATP; monitoring the aggregation of fluorescent PYCARD into a “speck”—an aggregosome focus using fluorescent microscopy; and testing the candidate molecules for the degree of inhibition of PYCARD “speck” formation.
[0127] In some embodiments, a screening method for inflammasome inhibitors includes stimulating cells (e.g., RPE cells) or a cell line (e.g., THP-1 or RAW macrophages with Alu RNA or LPS+ATP; monitoring Caspase-1 activity using CaspaLux®1-E2D2 assay (OncoImmunin, Inc.); and testing the candidate molecules for the degree of inhibition of Caspaslux fluorescence.
[0128] In some embodiments, a screening method for inflammasome inhibitors includes stimulating cells (e.g., RPE cells) or a cell line (e.g., THP-1 or RAW macrophages with Alu RNA or LPS+ATP; monitoring Caspase-1 activity by measuring the abundance of cleaved Caspase-1 (p10 or p20 isoforms) by Western blotting using an anti-Caspase-1 antibody; and testing the candidate molecules for the degree of inhibition of Caspase-1 cleaved fragments (p10 or p20).
[0129] In some embodiments, a screening method for inflammasome inhibitors includes stimulating HEK-Blue™ IL-1β Cells (Invivogen) with Alu RNA or LPS+ARP to detect bioactive IL-1β formation using QUANT1-Blue™ (Invivogen); and testing the candidate molecule for degree of inhibition of colometric signal.

Inhibiting MyD88

[0130] In some embodiments, the presently-disclosed subject matter includes a method of protecting a cell, comprising: inhibiting MyD88 of the cell. In some embodiments, the inhibiting MyD88 comprises administering a MyD88 inhibitor.
[0131] As noted above, in some embodiments, inhibiting a polypeptide of interest to the presently-disclosed subject matter comprises administering an oligonucleotide or a small RNA molecule. Such small RNA molecule can target MyD88. Such nucleotides can target and degrade MyD88. In this regard, the presently-disclosed subject matter includes a isolated double-stranded RNA molecule that inhibits expression of MyD88, wherein a first strand of the double-stranded RNA comprises a sequence as set forth in Table C, and includes about 14 to 25 nucleotides. Examples of MyD88 inhibitors that can be used in accordance with the presently-disclosed subject matter include, but are not limited to those set forth in Table C. As such, embodiments of the presently-disclosed subject matter can include administering a MyD88 inhibitor set forth in Table C.
[0132] 
[00004] [TABLE-US-00004]
  TABLE C
 
  Examples of MyD88 Inhibitors
 
 
  A inhibitor comprising the polypeptide sequence of IMG-2005-1 peptide sequence:
  DRQIKIWFQNRRMKWKKRDVLPGT (SEQ ID NO: 1), including about 29 to 100
  nucleotides.
  Oligopeptide for inhibiting MyD88 homodimerization: RDVLPGT (SEQ ID NO: 54
  Oligopeptide for inhibiting MyD88 homodimerization: RDVVPGG (SEQ ID NO: 55
  Loiarro et al. J Biol Chem 2005; 280:15809-14.
 
  DRQIKIWFQNRRMKWKKRDVLPGTCVWSIASE (SEQ ID NO: 60).
 
  RDVLPGTCVWSIASE (SEQ ID NO: 61).
 
  An isolated double-stranded RNA molecule that inhibits expression of MyD88, at least 
  one strand of which is about 14 to 25 nucleotides and includes a sequence selected  
  from: 5′-GAGAAGCCUUUACAGGUdTdT-3′ (SEQ ID NO: 3); 
  5′-ACCUGUAAAGGCUUCUCdTdT-3′ (SEQ ID NO: 4); 
  5′-CAGAGCAAGGAAUGUGAdTdT-3′ (SEQ ID NO: 5); 
  5′-UCACAUUCCUUGCUCUGdTdT-3′ (SEQ ID NO: 6); and 
  5′-UAUUUCCUAAWGGGUCdTdT-3′ (SEQ ID NO: 56).
 
  A homodimerization inhibitor, such as Pepinh-MYD (Invitrogen).
 
  A a dominant negative or splice variant of MyD88, such as a MyD88 splice variants that
  lack exon 2 (also known as the “intermediate domain” (e.g., having sequences set for at
  accession numbers NM_001172566.1 and NM_001172568.1), or other splice variants of MyD88
  (e.g., having sequences set for at accession numbers NM_002468.4 and NM_001172569.1).
 
[0133] As noted above, in some embodiments, inhibiting MyD88 comprises administering an MyD88 inhibitor that is a dominant negative vector against MyD88, e.g., a dominant negative inhibitory form of MyD88 (pMyD88-dn) that contains the truncated ΔMyD88 (amino acids 152-296) lacking the death domain of MyD88 (Muzio et al. IRAK (Pelle) Family Member IRAK-2 and MyD88 as Proximal Mediators of IL-1 Signaling. Science 1997; 278:1612-1615).
[0134] As noted above, in some embodiments, inhibiting MyD88 comprises administering an MyD88 inhibitor that is a small molecule (e.g., (1) hydrocinnamoyl-L-valyl pyrrolidine, referred to as compound 4a in Bartfai et al. “A low molecular weight mimic of the Toll/IL-1 receptor/resistance domain inhibits IL-1 receptor-mediated responses.” PNAS 2003; 100: 7971-7976; or (2) ST2825 as described in Carminati, P., Gallo, G., Ruggiero, V., Sassano, M., Mastroianni, D. “MyD88 homodimerization inhibitors” Patent No. WO2006067091 and characterized in Loiarro et al “Inhibition of MyD88 dimerization and recruitment of IRAK1 and IRAK4 by a novel peptidomimetic compound.” Journal of Leukocyte Biology. 2007; 82:801-810; or (3) 4-[(E)-2-(1-hexylpyridin-1-ium-2-yeethenyl]-N,N-dimethylaniline iodide, also known as 4-[(E)-2-(1-hexylpyridin-6-yl)ethenyl]-N,N-dimethyl-aniline Iodide, also known as Chemical Structure CID 5716367 in PubChem which blocks MyD88 interactions, or (4) the compounds referred to as 50-F12 and 26-J10 in Lee et al. “Application of β-Lactamase Enzyme Complementation to the High-Throughput Screening of Toll-Like Receptor Signaling Inhibitors.” Molecular Pharmacology 2007; 72:868-875), or a natural product (malyngamide F acetate as described in Villa et al. “Selective MyD88-dependent pathway inhibition by the cyanobacterial natural product malyngamide F acetate.” European Journal of Pharmacology 2010; 629:140-146), or a DNA or RNA aptamer generated by SELEX or other screening technology that binds or blocks MyD88.
[0135] The presently-disclosed subject matter further includes compositions useful for inhibiting MyD88. Such compositions include an inhibitor. As noted above, such inhibitors can be, for example, a nucleotide, a polypeptide, a small (chemical) molecule, etc. In some embodiments, a composition can include an isolated RNA molecule.
[0136] The presently-disclosed subject matter includes isolated RNA molecules that inhibit expression of MyD88. In some embodiments, a first strand of the double-stranded RNA comprises a sequence selected from the following, and including about 14 to 25 nucleotides: 5′-GAGAAGCCUUUACAGGUdTdT-3′ (SEQ ID NO: 3); 5′-ACCUGUAAAGGCUUCUCdTdT-3′ (SEQ ID NO: 4); 5′-CAGAGCAAGGAAUGUGAdTdT-3′ (SEQ ID NO: 5); and 5′-UCACAUUCCUUGCUCUGdTdT-3′ (SEQ ID NO: 6).
[0137] The presently-disclosed subject matter includes isolated polypeptide molecules that inhibit expression of MyD88. In some embodiments, the polypeptide molecule comprises a sequence selected from the following: DRQIKIWFQNRRMKWKKRDVLPGT (SEQ ID NO: 1), including about 29 to 100 amino acids. In some embodiments, the polypeptide molecule comprises a sequence selected from the following: RDVLPGT (SEQ ID NO: 54) and RDVVPGG (SEQ ID NO: 55).
[0138] In some embodiments, a method of identifying a MyD88 inhibitor makes use of a cultured cell wherein MyD88 is upregulated. Candidate compounds can be screened using the cultured cell to determine efficacy in modulating MyD88. Candidate compounds include, for example, small molecules, biologics, and combinations thereof, such as compositions including multiple compounds. The term small molecules is inclusive of traditional pharmaceutical compounds. The term biologics is inclusive of polypeptides and nucleotides, and including siRNAs, antibodies, aptamers, and dominant negative plasmids or vectors.
[0139] In some embodiments, the screening method includes providing a cell in culture wherein MyD88 is upregulated; and contacting a candidate compound with the cell. The method can further include identifying a change in MyD88. For example, a measurable change in MyD88 levels can be indicative of efficacy associated with the candidate compound. In some embodiments, wherein the change in the MyD88 is a measurable decrease in MyD88, the change is an indication that the candidate compound is a MyD88 inhibitor. Such MyD88 inhibitors can have utility for therapeutic applications as disclosed herein.
[0140] In some embodiments, the MyD88 can be upregulated using Alu RNA or lipopolysaccharide (LPS), for example, by stimulating cells (macrophages or RPE cells) with Alu RNA or LPS. In some embodiments, the MyD88 can be upregulated using CpG nucleotides, for example, by stimulating cells (macrophages or RPE cells) with synthetic oligonucleotides containing unmethylated CpG dinucleotides, such as 5′-tcg tcg ttt tgt cgt ttt gtc gtt-3′ or 5′-ggG GGA CGA TCG TCg ggg gg-3′. In some embodiments, the MyD88 can be upregulated using interleukin-1 beta or interleukin 18, for example, by stimulating cells (macrophages or RPE cells) with recombinant forms of interleukin-1 beta or interleukin 18.
[0141] In some embodiments of the method for identifying a MyD88 inhibitor, a change in the MyD88 can be monitored by measuring cell viability, measuring the expression of genes known to be induced by MyD88 signaling (e.g., Cox-2, Socs3, TNF-alpha) or using other criteria that would be recognized by one of ordinary skill in the art, using methods known to one of ordinary skill in the art. In some embodiments, the cultured cell is an RPE cell. In some embodiments, the cell is a retinal photoreceptor cell. In some embodiments, the cell is a choroidal cell.
[0142] In some embodiments, a method of identifying a MyD88 inhibitor includes providing a cultured cell wherein MyD88 is upregulated or undergoes oligomerization or induces phosphorylation of IRAK1 or of IRAK4; and contacting the cell with a candidate compound; and determining whether the candidate compound results in a change in the MyD88 levels, or a change in the abundance of dimerized or oligomerized MyD88, or a change in the abundance of phosphorylated IRAK1 or of phosphorylated IRAK4. In some embodiments, the MyD88 is upregulated by: Alu RNA, lipopolysacharide, CpG nucleotides, single-stranded RNA, interleukin-1 beta, or interleukin 18. In some embodiments, the MyD88 is monitored by measuring cell viability, or measuring the expression of a gene known to be induced by MyD88 signaling. In some embodiments, the gene known to be induced by MyD88 signaling is selected from Cox-2, Socs3, and TNF-α.
[0143] In some embodiments of a screening method for MyD88 inhibitors, cells or cell lines can be stimulated with a known activator of MyD88, e.g., Alu RNA, or LPS. The RNA levels of genes such as Cox2, Socs3, or TNF-α can be measured using quantitative real-time RT-PCR. Candidate molecules can be tested for degree of inhibition of these gene transcripts.
[0144] In some embodiments of a screening method for MyD88 inhibitors, cells or cell lines can be stimulated with a known activator of MyD88, e.g., Alu RNA, or LPS. The abundance of dimerized or oligomerized MyD88 can be measured by Western blotting under non-reducing conditions using an anti-MyD88 antibody. The candidate molecule can be tested for degree of inhibition of MyD88 dimerization or oligomerization.
[0145] In some embodiments of a screening method for MyD88 inhibitors, cells or cell lines that have been transfected with plasmids coding for a fusion MyD88 protein tagged to fragments of YFP (yellow fluorescent protein) can be stimulated with a known activator of MyD88, e.g., Alu RNA, or LPS. The fluorescent signal can be measured using bimolecular fluorescence complementation techniques. The candidate molecule can be tested for degree of inhibition of fluorescent signal.
[0146] In some embodiments of a screening method for MyD88 inhibitors, cells or cell lines can be stimulated with a known activator of MyD88, e.g., Alu RNA, or LPS. The abundance of phosphorylated forms of IRAK1 or IRAK4 can be measured by Western blotting under reducing conditions using an anti-phosphoIRAK1 or anti-phosphoIRAK4 antibodies. The candidate molecule can be tested for degree of inhibition of IRAK1 or IRAK4 phosphorylation.

Inhibiting IL-18

[0147] In some embodiments, the presently-disclosed subject matter includes a method of protecting a cell, comprising: inhibiting IL-18 of the cell. In some embodiments, the inhibiting IL-18 comprises administering an IL-18 inhibitor.
[0148] As noted above, in some embodiments, inhibiting a polypeptide of interest to the presently-disclosed subject matter comprises administering a binding protein or an antibody. Such antibodies can include a neutralizing antibody against IL-18, or an antibody that blocks IL-18 binding to the IL-18 receptor. In some embodiments, the IL-18 inhibitor can be an IL-18 binding protein (Novick, et al., 1999).
[0149] Examples of IL-18 inhibitors that can be used in accordance with the presently-disclosed subject matter include, but are not limited to those set forth in Table D. As such, embodiments of the presently-disclosed subject matter can include administering an IL-18 inhibitor set forth in Table D.
[0150] 
[00005] [TABLE-US-00005]
  TABLE D
 
  Examples of IL-18 Inhibitors
 
 
  A neutralizing antibody against IL-18, or an antibody that blocks
  IL-18 binding to the IL-18 receptor, e.g., IL-18 neutralizing antibody
  (MBL International); IL-18 neutralizing antibody (R&D Systems); or
  IL-18R1 neutralizing antibody (R&D Systems); or IL-18R1 neutralizing
  antibody (Genetex).
  An IL-18 binding protein as described by Novick, et al., 1999.
  IL18BP (an endogenous, naturally occurring IL-18 binding protein)
 
[0151] The presently-disclosed subject matter further includes compositions useful for inhibiting IL-18. Such compositions include an inhibitor. As noted above, such inhibitors can be, for example, a nucleotide, a polypeptide, a small (chemical) molecule, etc. In some embodiments, a composition can include an isolated RNA molecule. In some embodiments, a composition can include an antibody or a binding protein.
[0152] The presently-disclosed subject matter further includes methods of screening candidate inhibitors to identify IL-18 inhibitors. In some embodiments, a method of identifying an IL-18 inhibitor includes plating recombinant IL-18R1 on a solid state surface suitable for surface plasmon resonance (SPR); exposing the plated recombinant IL-18R1 to fluorescence-labeled recombinant IL-18; further exposing the system to a putative IL-18 inhibitor which would displace IL-18:IL-18R1 binding; and measuring fluorescence to determine degree of inhibition.
[0153] In some embodiments, a method of identifying an IL-18 inhibitor includes stimulating cells (e.g., RPE cells) or a cell line (e.g., THP-1 or RAW macrophages) with recombinant IL-18; measuring MyD88 activation, e.g., by measuring increased MyD88 dimerization (through Western blotting) or by measuring increased phosphorylation of IRAK1 or of IRAK4.

Inhibiting VDAC1 and/or VDAC2

[0154] In some embodiments, the presently-disclosed subject matter includes a method of protecting a cell, comprising: inhibiting VDAC1 and/or VDAC2 of the cell. In some embodiments, the inhibiting VDAC1 and/or VDAC2 comprises administering an VDAC1 and/or VDAC2 inhibitor.
[0155] As noted above, in some embodiments, inhibiting a polypeptide of interest to the presently-disclosed subject matter comprises administering an oligonucleotide or a small RNA molecule. Such small RNA molecule can target VDAC1 and/or VDAC2. Such nucleotides can target and degrade VDAC1 and/or VDAC2. In this regard, the presently-disclosed subject matter includes a isolated double-stranded RNA molecule that inhibits expression of VDAC1 and/or VDAC2, wherein a first strand of the double-stranded RNA comprises a sequence as set forth in Table E, and includes about 14 to 25 nucleotides. Examples of VDAC1 and/or VDAC2 inhibitors that can be used in accordance with the presently-disclosed subject matter include, but are not limited to those set forth in Table E. As such, embodiments of the presently-disclosed subject matter can include administering a VDAC1 and/or VDAC2 inhibitor set forth in Table E.
[0156] 
[00006] [TABLE-US-00006]
  TABLE E
 
  Examples of VDAC1 and/or VDAC2 Inhibitors
 
 
  An isolated double-stranded RNA molecule that inhibits expression of VDAC1, at least one
  strand of which is about 14 to 25 nucleotides and includes the sequence of: 5′-
  CGGAAUAGCAGCCAAGUdTdT-3′ (SEQ ID NO: 47).
 
  An isolated double-stranded RNA molecule that inhibits expression of VDAC2, at least one
  strand of which is about 14 to 25 nucleotides and includes the sequence of: 5′-
  CCCUGGAGUUGGAGGCUdTdT-3′ (SEQ ID NO: 48).
 
  Any phosphorothioate oligonucleotide randomer (Trilink Industries), which all inhibit VDAC
  (Stein & Marco Colombini. Specific VDAC inhibitors: phosphorothioate oligonucleotides. J
  Bioenerg Biomembr 2008; 40:157-62; Tan et al. Phosphorothioate oligonucleotides block the
  VDAC channel. Biophys J. 2007; 93:1184-91)
 
  Cyclosporin A-blocks VDAC1
 
  Superoxide dismutase 1-blocks VDAC1
 
  4,4′-diisothiocyanatostilbene-2,2′-disulfonic acid (DIDS)-blocks VDAC1
 
  Bcl-x(L) BH4(4-23)-blocks VDAC
 
  TRO19622-blocks VDAC
 
[0157] The presently-disclosed subject matter further includes compositions useful for inhibiting VDAC1 and/or VDAC2. Such compositions include an inhibitor. As noted above, such inhibitors can be, for example, a nucleotide, a polypeptide, a small (chemical) molecule, etc. In some embodiments, a composition can include an isolated RNA molecule.
[0158] The presently-disclosed subject matter includes isolated RNA molecules that inhibit expression of VDAC1 and/or VDAC2. In some embodiments, a first strand of the double-stranded RNA comprises a sequence selected from the following, and including about 14 to 25 nucleotides: 5′-CGGAAUAGCAGCCAAGUdTdT-3′ (SEQ ID NO: 47) and 5′-CCCUGGAGUUGGAGGCUdTdT-3′ (SEQ ID NO: 48).
[0159] The presently-disclosed subject matter further includes methods of screening candidate inhibitors to identify VDAC1 and/or VDAC2 inhibitors. In some embodiments, cell or cell line-based methods are used.

Inhibiting Caspase-8

[0160] In some embodiments, the presently-disclosed subject matter includes a method of protecting a cell, comprising: inhibiting caspase-8 of the cell. In some embodiments, the inhibiting caspase-8 comprises administering a caspase-8 inhibitor.
[0161] Examples of caspase-8 inhibitors that can be used in accordance with the presently-disclosed subject matter include, but are not limited to those set forth in Table F. As such, embodiments of the presently-disclosed subject matter can include administering a caspase 8 inhibitor set forth in Table F.
[0162] 
[00007] [TABLE-US-00007]
  TABLE F
 
  Examples of Caspase-8 Inhibitors
 
 
    Z-IETD-FMK (BD Biosciences)
    Ac-Ala-Ala-Val-Ala-Leu-Leu-Pro-Ala-Val-Leu-Leu-Ala-Leu-Leu-
    Ala-Pro-Ile-Glu-Thr-Asp-
    CHO (EMD Millipore)
  Z-Ile-Glu(OMe)-Thr-Asp(OMe)-CH2F (EMD Millipore)
    Cellular fas-associated death domain-like interleukin-1-β-
    converting enzyme-inhibitory protein (L), i.e. c-FLIP(L), a.k.a.
    FLICE, a.k.a. MACH, a.k.a. Mch5
   
[0163] The presently-disclosed subject matter further includes compositions useful for inhibiting caspase-8. Such compositions include an inhibitor. As noted above, such inhibitors can be, for example, a nucleotide, a polypeptide, a small (chemical) molecule, etc. In some embodiments, a composition can include an isolated RNA molecule.
[0164] The presently-disclosed subject matter further includes methods of screening candidate inhibitors to identify caspase-8 inhibitors. In some embodiments, cell or cell line-based methods are used.

Inhibiting NFκB

[0165] In some embodiments, the presently-disclosed subject matter includes a method of protecting a cell, comprising: inhibiting NFκB of the cell. In some embodiments, the inhibiting NFκB comprises administering a caspase-8 inhibitor.
[0166] Examples of NFκB inhibitors that can be used in accordance with the presently-disclosed subject matter include, but are not limited to those set forth in Table G. As such, embodiments of the presently-disclosed subject matter can include administering a NFκB inhibitor set forth in Table G.
[0167] 
[00008] [TABLE-US-00008]
  TABLE G
 
  Examples of NFKB Inhibitors
  Any one or more of the following NFKB inhibitors
 
 
  Antioxidants that have been shown to inhibit activation of NF-kB
  a-Lipoic acid   Sen et al, 1998; Suzuki et al, 1992
  a-tocopherol   Islam et al, 1998
  Aged garlic extract (allicin)   Ide & Lau, 2001; Lang et al, 2004; Hasan et al, 2007
  2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP)   Yun et al, 2005
  N-acetyldopamine dimers (from P. cicadae)   Xu et al, 2006
  Allopurinol   Gomez-Cabrera et al, 2006
  Anetholdithiolthione   Sen et al, 1996
  Apocynin   Barbieri et al, 2004
  Apple juice/extracts   Shi & Jiang, 2002; Daviset al, 2006; Jung et al, 2009
  Aretemsia p7F (5,6,3′,5′-tetramethoxy 7,4′-hydroxyflavone)   Lee et al, 2004
  Astaxanthin   Lee et al, 2003
  Autumn olive extracts; olive leaf extracts   Wang et al, 2007; Wanget al, 2008
  Avenanthramides (from oats)   Guo et al, 2007; Sur et al, 2008
  Bamboo culm extract   Lee et al, 2008
  Benidipine   Matsubara & Hazegawa, 2004
  bis-eugenol   Murakami et al, 2003
  Bruguiera gymnorrhiza compounds   Homhual et al, 2006
  Butylated hydroxyanisole (BHA)   Israel et al, 1992; Schulze-Osthoff et al, 1993
  Cepharanthine   Okamoto et al, 1994;Tamatani et al, 2007
  Caffeic Acid Phenethyl Ester   Natarajan et al, 1996;Nagasaka et al, 2007
  (3,4-dihydroxycinnamic acid, CAPE)  
  Carnosol   Lo et al, 2002; Huang et al, 2005
  beta-Carotene   Bai et al, 2005;Guruvayoorappan & Kuttan, 2007
  Carvedilol   Yang et al, 2003
  Catechol Derivatives   Suzuki & Packer, 1994;Zheng et al, 2008
  Centaurea L (Asteraceae) extracts   Karamenderes et al, 2007
  Chalcone   Liu et al, 2007
  Chlorogenic acid   Feng et al, 2005
  5-chloroacetyl-2-amnio-1,3-selenazoles   Nam et al, 2008
  Cholestin   Lin et al, 2007
  Chroman-2-carboxylic acid N-substituted phenylamides   Kwak et al, 2008
  Cocoa polyphenols   Lee et al, 2006
  Coffee extract (3-methyl-1,2-cyclopentanedione)   Chung et al, 2007
  Crataegus pinnatifida polyphenols   Kao et al, 2007
  Curcumin (Diferulolylmethane);   Singh & Aggarwal, 1995;Pae et al, 2008; Kasinskiet al, 2008
  dimethoxycurcumin; EF24 analog  
  Dehydroepiandrosterone (DHEA) and   DHEA-sulfate (DHEAS)   Iwasaki et al, 2004; Liu et al, 2005
  Dibenzylbutyrolactone lignans   Cho et al, 2002
  Diethyldithiocarbamate (DDC)   Schreck et al, 1992
  Diferoxamine   Sappey et al, 1995;Schreck et al, 1992
  Dihydroisoeugenol; isoeugenol;   Murakami et al, 1995Tark et al, 2007; Ma et al, 2008
  epoxypseudoisoeugenol-2-methyl butyrate  
  Dihydrolipoic Acid   Suzuki et al, 1992, 1995
  Dilazep + fenofibric acid   Sonoki et al, 2003; Yanget al, 2005
  Dimethyldithiocarbamates (DMDTC)   Pyatt et al, 1998
  Dimethylsulfoxide (DMSO)   Kelly et al, 1994
  Disulfiram   Schreck et al, 1992
  Ebselen   Schreck et al, 1992
  Edaravone   Kokura et al, 2005; Ariiet al, 2007; Yoshida et al, 2007
  EPC-K1 (phosphodiester compound   Hirano et al, 1998
  of vitamin E and vitamin C)  
  Epigallocatechin-3-gallate (EGCG; green tea polyphenols)   Lin & Lin, 1997; Yang et a1,1998; Hou et al, 2007; Jiang et al, 2012
  Ergothioneine   Rahman et al, 2003
  Ethyl Pyruvate (Glutathione depletion)   Song et al, 2004; Tsung et al, 2005; Jimenez-Lopezet al, 2008
  Ethylene Glycol Tetraacetic Acid (EGTA)   Janssen et al, 1999
  Eupatilin   Lee et al, 2008
  Exercise   Goto et al, 2007
  Fisetin   Park et al, 2006; Sung et al, 2007
  Flavonoids (Cmtaegus; Boerhaavia diffusa root; xanthohumol;   Zhang et al, 2004; Chenet al, 2004; Pandey et al, 2005; Albini
  Eupatorium arnottianum; genistein;   et al, 2005;Colgate et al, 2006;Clavin et al, 2007;
  kaempferol; quercetin, daidzein; flavone; isorhamnetin;   Hamalainen et al, 2008;Zheng et al, 2008; Junget al, 2008;
  naringenin; pelargonidin; finestin; Sophora   Mishra et al, 2008
  flavescens; Seabuckthorn fruit berry)  
  Flavonoid-7-glycosides (chamomile flowers extract)   Bulgari et al, 2012
  Folic acid   Au-Yeung et al, 2006
  Gamma-glutamylcysteine synthetase (gamma-GCS)   Manna et al, 1999
  Ganoderma lucidum polysaccharides   Zhang et al, 2003; Ho et al, 2007
  Garcinol (from extract of Garcinia indica fruit rind)   Liao et al, 2004
  Ginkgo biloba extract   Chen et al, 2003
  Glutathione   Cho et al, 1998; Schrecket al, 1992; Wang et al, 2007
  Guaiacol (2-methoxyphenol)   Murakami et al, 2007
  Hematein   Choi et al, 2003
  Hinokitiol   Byeon et al, 2008
  HMCO5 herbal extract   Kim et al, 2007
  Hydroquinone   Pyatt et al, 1998; Yang et al, 2006
  23-hydroxyursolic acid   Shin et al, 2004
  IRFI 042 (Vitamin E-like compound)   Altavilla et al, 2001
  Iron tetrakis   Kang et al, 2001
  Isosteviol   Xu et al, 2008
  Isovitexin   Lin et al, 2005
  Isoliquiritigenin   Kumar et al, 2007; Kimet al, 2008; Kim et al, 2008
  Justicia gendarussa root extract   Kumar et al, 2011
  Kallistatin   Shen et al, 2008
  Kangen-karyu extract   Satoh et al, 2005;Yokozawa et al, 2007
  L-cysteine   Mihm et al, 1991
  Lacidipine   Cominacini et al, 1997
  Lazaroids   Marubayashi et al, 2002
  Ligonberries   Wang et al, 2005
  Lupeol   Saleem et al, 2004; Lee et al, 2007
  Lutein   Kim et al, 2008
  Magnolol   Chen et al, 2002; Ou et al, 2006; Kim et al, 2007
  Maltol   Yang et al, 2006
  Manganese superoxide dismutase (Mn-SOD)   Manna et al, 1998
  Extract of the stem bark of Mangifera indica L.   Leiro et al, 2004; Garridoet al, 2005
  Melatonin   Gilad et al, 1998; Mohanet al, 1995; Li et al, 2005
  21 (alpha, beta)-methylmelianodiol   Zhou et al, 2007
  Mulberry anthocyanins   Chen et al, 2006
  N-acetyl-L-cysteine (NAC)   Schreck et al, 1991
  Nacyselyn (NAL)   Antonicelli et al, 2002
  Nordihydroguaiaritic acid (NDGA)   Brennan & O'Neill, 1998;Israel et a1,1992; Schulze-Osthoff et
  al, 1993; Staalet al, 1993  
  Ochnaflavone   Suh et al, 2006
  Onion extract (2,3-dihydro-3,5-   Ban et al, 2007; Tang et al, 2008
  dihydroxy-6-methyl-4H-pyranone)  
  Orthophenanthroline   Schreck et al, 1992
  N-(3-oxo-dodecanoyl) homoserine lactone   Kravchenko et al, 2008
  Paricalcitol   Tan et al, 2008
  Phenolic antioxidants (Hydroquinone   Ma et al, 2003
  and tert-butyl hydroquinone)  
  Olive oil phenols (extra-virgin olive oil)   Sangiovanni et al, 2012
  alkenylphenols from Piper obliquum   Valdivia et al, 2008
  alpha-phenyl-n-tert-butyl-nitron (PBN)   Kotake et al, 1998;Lin et al, 2006
  Phenylarsine oxide (PAO, tyrosine phosphatase inhibitor)   Arbault et al, 1998
  Phyllanthus urinaria   Chularojmontri et al, 2005; Shen et al, 2007
  Phytosteryl ferulates (rice bran)   Islam et al, 2008; Jung et al, 2008
  Piper longum Linn. extract   Singh et al, 2007
  Pitavastatin   Tounai et al, 2007; Wang& Kitajima, 2007
  Prodelphinidin B2 3, 3′ di-O-gallate   Hou et al, 2007
  Pterostilbene   Cichocki et al, 2008; Panet al, 2009
  Pyrrolinedithiocarbamate (PDTC)   Schreck et al, 1992
  Quercetin   Musonda & Chipman, 1998; Shih et al, 2004;Garcia-
    Mediavilla et al, 2006; Ruiz et al, 2007;Min et al, 2007; Kim et al, 2007
  Red orange extract   Cimini et al, 2008
  Red wine   Blanco-Colio et al, 2000;Cui & He, 2004
  Ref-1 (redox factor 1)   Ozaki et al, 2002
  Rg(3), a ginseng derivative   Keum et al, 2003
  Rotenone   Schulze-Osthoff et al, 1993
  Roxithromycin   Ueno et al, 2005; Ou et al, 2008
  Rutin   Kyung et al, 2008
  S-allyl-cysteine (SAC, garlic compound)   Geng et al, 1997
  Salogaviolide (Centaurea ainetensis)   Ghantous et al, 2008
  Sauchinone   Lee et al, 2003;   Hwang et al, 2003
  Schisandrin B   Giridharan et all, 2011
  Silybin   Gazak et al, 2007
  Spironolactone   Han et al, 2006
  Strawberry extracts   Wang et al, 2005
  Sulfuretin   Lee et al, 2012
  Taxifolin   Wang et al, 2005
  Tempol   Cuzzocrea et al, 2004
  Tepoxaline (5-(4-chlorophenyl)-N-hydroxy-   Kazmi et al, 1995; Ritchieet al, 1995
  (4-methoxyphenyl)-N-methyl-1H-pyrazole-3-propanamide)  
  Thio avarol derivatives   Amigo et al, 2007; Amigoet al, 2008
  Thymoquinone   El Gazzar et al, 2007;1Sethi et al, 2008
  Tocotrienol (palm oil)   Wu et al, 2008
  8-(Tosylamino)quinoline   Jung et al, 2012
  Tomato peel polysaccharide   De Stefano et al, 2007
  UDN glycoprotein (Ulmus davidiana Nakai) Lee & Lim, 2007  
  Vaccinium stamineum (deerberry) extract   Wang et al, 2007
  Vanillin (2-hydroxy-3-methoxybenzaldehyde)   Murakami et al, 2007
  Vitamin C   Staal et al, 1993; Son et al, 2004
  Vitamin B6   Yanaka et al, 2005
  Vitamin E and derivatives   Suzuki & Packer, 1993;Ekstrand-Hammarstrom et al, 2007;
  Glauert, 2007  
  a-torphryl succinate   Staal et al, 1993; Suzuki & Packer, 1993
  a-torphryl acetate   Suzuki & Packer, 1993
  PMC (2,2,5,7,8-pentamethyl-6-hydroxychromane)   Suzuki & Packer, 1993
  Yakuchinone A and B   Chun et al, 2002
  Proteasome and proteases inhibitors that inhibit Rel/NF-kB
  Proteasome inhibitors  
  Peptide Aldehydes:   Palombella et al, 1994; Grisham et al, 1999; Jobin et al, 1998
  ALLnL
  (N-acetyl-leucinyl-leucynil-norleucynal,MG101)
  LLM (N-acetyl-leucinyl-leucynil-methional)
  Z-LLnV
  (carbobenzoxyl-leucinyl-leucynil-norvalinal,MG115)
  Z-LLL
  (carbobenzoxyl-leucinyl-leucynil-leucynal, MG132)
  MG262   Pujois et al, 2012
  Lactacystine, beta-lactone   Fenteany & Schreiber, 1998; Grisham et al, 1999
  Boronic Acid Peptide   Grisham et al, 1999; Iqbal et al, 1995
  Dithiocarbamate complexes with metals   Cvek & Dvorak, 2007
  CEP-18770   Piva et al, 2007
  Ubiquitin Ligase Inhibitors   Yaron et al, 1997
  PS-341 (Bortezomib)   Adams, 2004
  Salinosporamide A (1, NPI-0052)   Macherla et al, 2005; Ahn et al, 2007
  Cyclosporin A   Frantz et al, 1994; Kunz et al, 1995; Marienfeld et al, 1997;
  McCaffrey et al, 1994;Meyer et al, 1997; Wechsler et al, 1994
  FK506 (Tacrolimus)   Okamoto et al, 1994; Venkataraman et al, 1995
  Deoxyspergualin   Tepper et al, 1995
  Disulfiram   Lovborg et al, 2005
  PT-110   Momose et al, 2007
  Protease inhibitors  
  APNE (N-acetyl-DL-phenylalanine-b-naphthylester)   Higuchi et al, 1995
  B IEE (N-benzoyl L-tyrosine-ethylester)   Rossi et al, 1998
  DCIC (3,4-dichloroisocoumarin)   D′Acquisto et al, 1998
  DFP (diisopropyl fluorophosphate)  
  TPCK (N-a-tosyl-L-phenylalanine chloromethyl ketone)  
  TLCK (N-a-tosyl-L-lysine chloromethyl ketone)  
  IkBa phosphorylation and/or degradation inhibitors
  Molecule   Point of Inhibition   References
  Desloratadine; diphenhydramine Histamine H1 receptor   Wu et al, 2004; Scadding, 2005;   Roumestan et al, 2008
  Bikunin   LPS receptor agonists   Kobayashi, 2006;
      Kanayama et al, 2007
  Ron Tyrosine kinase receptor   Suppresses TNF production   Lentsch et al, 2007
  TAK-242   TLR4 intracellular domain   Kawamoto et al, 2008
  Salmeterol, fluticasone propionate   beta2 agonists   Baouz et al, 2005
  CPU0213   Endothelin receptor antagonist   He et al, 2006
  Doxazosin   alpha1-adrenergic receptor antagonist   Hui et al, 2007
  Erbin overexpression   NOD2 inhibitor   McDonald et al, 2005
  Protein-bound polysaccharide from basidiomycetes   LPS-CD14 interaction   Asai et al 2005
  Anti-CD146 antibody AA98   upstream of IKK   Bu et al, 2006
  Calagualine (fern derivative)   upstream of IKK (TRAF2-NIK)   Manna et al, 2003
  NS3/4A (HCV protease)   upstream of IKK   Karayiannis, 2005
  golli BG21 (product of myelin basic protein)   upstream of IKK (PKC)   Feng et al 2004
  NPM-ALK oncoprotein   Traf2 inhibition   Horie et al, 2004
  NS5A (Hepatitis C virus)   Traf2 inhibition   Park et al, 2002
  LY29 and LY30   PI3 Kinase inhibitors   Choi et al, 2004
  Shiga toxin (Enterohemorrhagic E coli)   PI3 Kinase inhibitor   Gobert et al 2007
  Evodiamine (Evodiae Fructus component)   AKT-IKK interaction   Takada et al 2005
  Rituximab (anti-CD20 antibody)   up-regulates Raf-1 kinase inhibitor   Jazirehi et al, 2005
  Kinase suppressor of ras (KSR2)   MEKK3 inhibitor   Channavajhala et al, 2005
  Cholecystokinin ocatpeptide (CCK-8)p38 kinase   Li et al, 2007
  M2L (Vaccinia virus)   ERK2 inhibitor   Gedey et al, 2006;
  Pefabloc (serine protease inhibitor)upstream of IKK   Tando et al, 2002   Hinthong et al, 2008
  Rocaglamides (Aglaia derivatives)   upstream of IKK   Baumann et al, 2002
  Ymer   Binds to Ub-RIP   Bohgaki et al, 2007
  Epoxyquinol B   TAK1 crosslinker   Kamiyama et al, 2008
  Betaine   NIK/IKK   Go et al, 2004, 2007
  TNAP   NIK   Hu et al, 2005
  Selected peptides   NEMO binding to Ub   Wyler et al, 2007
  Biochanin   upstream of IKK/ phosphorylates of IκBα   Manna et al, 2012
  Desflurane   IKK complex formation with TNF-Rl   Li et al, 2008
  Geldanamycin   IKK complex formation   Chen et al, 2002
  Grape seed proanthocyanidins   IKKa activity   Mantena & Katiyar, 2006;
      Sharma et al, 2007;
      Cheng et al, 2007; Xu et al, 2008
  Laretia acaulis azorellane diterpenoids   IKKa activity   Borquez et al, 2007
  MC160 (Molluscum contagiosum virus)   IKKa activity   Nichols & Shisler , 2006
  NS5B (Hepatitis C protein)   IKKa activity   Choi et al, 2006
  Pomegranate fruit extract   IKKa activity   Afaq et al, 2004; Khan et al, 2006
  Tetrandine (plant alkaloid)   IKKa activity   Ho et al, 2004; Xue et al, 2008;
      Lin et al 2008
  BMS-345541 (4(2′-Aminoethyl)amino-1,8-
  dimethylimidazo(1,2-a) quinoxaline)
  and 4-amino derivatives
  IKKa and IKKb kinase activity   Burke et al, 2002; Yang et al, 2006;   Beaulieu et al, 2006
  1-O-acetylbritannilactone   IKKb activity   Liu et al, 2007
  2-amino-3-cyano-4-aryl-6-(2-hydroxy-   IKKb activity   Murata et al, 2003, 2004, 2004
  phenybpyridine derivatives    
  Acrolein   IKKb activity/p50 DNA binding   Lambert et al 2007
    Vallacchi et al, 2005;  
  Anandamide   IKKb activity   Sancho et al, 2003
  AS602868   IKKb activity   Frelin et al, 2003:
      Griessinger et al, 2007
  benzoxathiole(6,6-dimethyl-2-(phenylimino)-6,7-dihydro-   IKKb activity   Venkateswararao et al, 2012
  5H-benzo-[1,3]oxathio1-4-one (and its analogs)    
  Cobrotoxin   IKKb activity/p50 DNA  
    binding Park et al, 2005  
  Core protein (Hepatitis C)   IKKb activity   Joo et al, 2005;
      Shrivastava et al, 1998
  1-[2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole   IKKb activity   Yore et al, 2006
  Dihydroxyphenylethanol   IKKb activity   Guichard et al, 2006
  Heibimycin A   IKKb activity   Iwasaki et al, 1992;
      Mahon & O'Neill, 1995;
      Ogino et al, 2004
  Inhibitor 22   IKKb activity   Baxter et al, 2004
  Isorhapontigenin   IKKb activity   Li et al, 2005
  Manumycin A   IKKb activity   Bernier et al, 2005;
      Frassanito et al, 2005
  6-methyl-2-propolyimino-6,7-dihydro-5   IKKb   Kim et al, 2008
  H-benzo[1,3]oxathiol-4-one    
  MLB120 (small molecule)   IKKb activity   Nagashima et al, 2006
  Naphthopyrones (6-methoxycomaparvin and   IKKb activity   Fulmer et al, 2008
  6-methooxycomaparvin 5-methyl ether)    
  Novel Inhibitor   IKKb activity   Kamon et al, 2004
  vIRF3 (KSHV)   IKKb activity   Seo et al, 2004
  Nitric oxide   IKKb activity/IkB phosphorylation   Katsuyama et al, 1998;
      Matthews et al, 1996;
      Spieker & Liao, 1999;
      Reynaert et al, 2004
  SC-514 (small molecule)   IKKb activity   Kishore et al, 2003
  Thienopyridine   IKKb activity   Morwick et al, 2006
  Acetyl-boswellic acids   IKK activity   Syrovets et al, 2004, 2005
  Amino-pyrimidine derivative   IKK activity   Karin et al, 2004
  Benzoimidazole derivative   IKK activity   Karin et al, 2004
  BMS-345541   IKK activity   Burke et al, 2003
  Butein   IKKb activity   Pandey et al, 2007
  Beta-carboline   IKK activity   Yoon et al, 2005
  CYL-19s and CYL-26z, two synthetic alpha-methylene-   IKK activity   Huang et al, 2004
  gamma-butyrolactone derivatives    
  ACHP (2-amino-6-[2-(cyclopropylmethoxy)-6-   IKKb activity (ATP analog)   Sanda et al, 2006
  hydroxyphenyl]-4-piperidin-4-yl nicotinonitrile    
  Berberine   IKKb activity   Hu et al, 2007; Yi et al, 2008;
      Pandey et al 2008
  Compound A   IKKb activity (ATP analog)   Ziegelbauer et al, 2005
  Flavopiridol   IKK activity and RelA phosphor.   Takada & Aggarwal, 2003
  Cyclopentones   IKKb activity   Bickley et al, 2004
  Dehydroascorbic acid (Vitamin C)   IKKb activity   Carcamo et al, 2004
  Gossypyin or Gossypium extracts   IKKb activity   Kunnumakkara et al, 2007;
      Ji et al, 2008
  M protein (SARS-Cornonavirus protein)   IKKb activity   Fang et al, 2007
  IMD-0354   IKKb activity   Tanaka et al, 2004, 2006;
      Inayama et al 2006
  Jesterone dimer   IKKb activity; DNA binding   Liang et al, 2003, 2006
  KINK-1   IKKb activity   Schon et al, 2008
  LCY-2-CHO   IKKb activity   Ho et al, 2007
  Prolyl hydroxylase-1   IKKb activity   Cummins et al, 2006
  Naphthopyrones (Echinoderm Comanthus parvicirrus)   IKKb activity   Folmer et al, 2007
  Neuropeptides CGRP, PACAP and VIP   IKKb activity   Ding et al, 2007
  PS-1145 (MLN1145)   IKKb activity   Hideshima et al, 2002
  2-[(aminocarbonyl)amino]-5-(4-fluorophenyl)-   IKKb activity   Bonafoux et al, 2005;
  3-thiophenecarboxamides (TPCA-1)     Podolin et al, 2005
  1′-Acetoxychavicol acetate (Languas galanga)   IKK activity   Ichikawa et al, 2005;
      Ito et al, 2005
  17-Acetoxyjolkinolide B   IKK activity   Yan et al, 2008
  Acute alcohol exposure   IKK activity   Mandrekar et al, 2007
  Anacardic acid (6-nonadecyl-salicylic acid)   IKK activity   Sung et al, 2008
  Apigenin (plant flavinoid)   IKK activity   Shukla & Gupta, 2004;
      Yoon et al, 2006
  Asiatic acid   IKK activity   Yun et al, 2008
  Cardamomin   IKK activity   Lee et al, 2005
  CDDO-Me (synthetic triterpenoid)   IKK activity   Shishodia et al, 2006
  CHS 828 (anticancer drug)   IKK activity   Olsen et al, 2004
  CIVIL-1   IKK activity   Mo et al, 2006
  Compound 5 (Uredio-thiophenecarboxamide derivative)   IKK activity   Roshak et al, 2002
  CT20126   IKK activity/NIK   Lee et al, 2008
  Diaylpyridine derivative   IKK activity   Murata et al, 2003
  3,4-dihydroxybenzalacetone (from Chaga)   IKK activity   Sung et al, 2008
  Diosgenin   IKK activity   Shishodia & Aggarwal, 2005;
      Liagre et al 2005
  E3-14.7K (Adenovirus)   IKK activity   Li et al, 1999
  E3-10.4K/14.5K (Adenovirus)   IKK activity   Friedman & Horwitz, 2002
  E7 (human papillomavirus)   IKK activity   Spitkovsky et al, 2002
  Furonaphthoquinone   IKK activity   Shin et al, 2006
  3-Formylchromone   IKKb activity/p65 DNA binding   Yadav et al, 2011
  Guggulsterone   IKK activity   Ichikawa & Aggarwal, 2006;
      Deng, 2007;
      Lv et al, 2008; Lee et al, 2008
  HB-EGF (Heparin-binding epidermal   IKK activity   Mehta & Besner, 2003
  growth factor-like growth factor)    
  Falcarindol   IKK activity   Shiao et al, 2005
  Hammerhead ribozyme to IKKa/b   IKK activity   Yang et al, 2007
  Hepatocyte growth factor   IKK activity   Min et al, 2005; Gong et al, 2006
  Honokiol   IKK activity   Tse et al, 2005; Munroe et al, 2007
  Humulone   IKK activity   Lee et al, 2007
  Hypoestoxide   IKK activity   Ojo-Amaize et al, 2001
  Indolecarboxamide derivative   IKK activity   Karin et al, 2004
  Labdane diterpenoids   IKK activity   Giron et al, 2008
  LF15-0195 (analog of 15-deoxyspergualine)   IKK activity   Yang et al, 2003
  gamma-mangostin (from Garcinia mangostana)   IKK activity   Nakatani et al, 2004
  Garcinone B   IKK activity   Yamakuni et al, 2005
  (Amino)imidazolylcalboxaldehyde derivative   IKK activity   Karin et al, 2004
  Imidazolylquinoline-carboxaldehyde derivative   IKK activity   Karin et al, 2004
  Kahweol   IKK activity   Kim et al, 2004
  Kava (Piper methysticum) derivatives   IKK activity   Folmer et al, 2006
  Lead   IKK activity   Xu et al, 2006
  Marasmius oreades liquid extract   IKK activity   Petrova et al, 2008
  Menatetrenone (vitamin K2 analogue)   IKK activity   Ozaki et al, 2007
  Metformin   IKK activity   Huang et al, 2008
  Mild hypothermia   IKK activity   Han et al, 2003
  ML 120B   IKK activity   Catley et al, 2006
  Morin (3,5,7,2′,4′-Pentahydroxyflavone)   IKK activity   Manna et al, 2007
  Morusin   IKK activity   Lee et al, 2008
  MX781 (retinoid antagonist)   IKK activity   Bayonet al, 2003
  N-acetylcysteine   IKK activity   Oka et al, 2000
  Nitrosylcobalamin (vitamin B12 analog)   IKK activity   Chawla-Sarkar et al 2003
  NSAIDs   IKK activity   Takada et al, 2004
  Hepatits C virus NS5B   IKK activity   Choi et al, 2006
  PAN1 (aka NALP2 or PYPAF2)   IKK activity   Bruey et al, 2004
  Pectin (citrus)   IKK activity   Chen et al, 2006
  Pinitol   IKK activity   Sethi et al, 2008
  PMX464   IKK activity   Callister et al, 2008
  Pyrazolo[4,3-c]quinoline derivative   IKK activity   Karin et al, 2004
  Pyridooxazinone derivative   IKK activity   Karin et al, 2004
  N-(4-hydroxyphenyl) retinamide   IKK activity   Shishodia et al, 2005;
      Kuefer et al, 2007
  Scytonemin   IKK activity   Stevenson et al, 2002
  Semecarpus anacardiu extract   IKK activity   Singh et al, 2006
  SPC-839   IKK activity   Palanki et al, 2002
  Sulforaphane and phenylisothiocyanate   IKK activity   Xu et al, 2005;
      Murakami et al, 2007;
      Liu et al, 2008:
      Hayes et al, 2008
  Survanta (Surfactant product)   IKK activity   Raychaudhuri et al, 2003
  Torque Teno virus ORF2   IKK activity   Zheng et al, 2007
  Piceatannol   IKK activity   Islam et al, 2004
  Plumbagin (5-hydroxy-2-methyl-1,4-naphthoquinone)   IKK activity   Sandur et al, 2006
  IKKb peptide to NEMO binding domain   IKK-NEMO interaction   May et al. 2000
  NEMO CC2-LZ peptide   NEMO oligomerization   Agou et al, 2004
  AGRO100 (G-quadraplex oligodeoxynucleotide)   NEMO binding   Girvan et al, 2006
  PTEN (tumor suppressor)   Activation of IKK   Gustin et al, 2001
  Theaflavin (black tea component)   Activation of IKK   Aneja et al, 2004;
      Ukil et al, 2006;
      Kalra et al, 2007
  Tilianin   Activation of IKK   Nam et al, 2005
  Withanolides   Activation of IKK   Ichikawa et al, 2006
  Zerumbone   Activation of IKK   Takada et al, 2005
  Silibinin   IKKa activity; nuclear translocation   Dhanalakshmi et al, 2002;
      Singh et al, 2004;
      Min et al, 2007
  Sulfasalazine   IKKa and IKKb kinase activity   Wahl et al, 1998:
      Weber et al, 2000
  Sulfasalazine analogs   IKK kinase activity   Habens et al, 2005
  Quercetin   IKK activity   Peet & Li, 1999
  Rosmarinic acid   IKK activity   Lee et al, 2006
  Staurosporine   IKK activity   Peet & Li, 1999
  gamma-Tocotrienol   IKK activity   Shah & Sylvester, 2005;
      Ahn et al, 2006
  Wedelolactone   IKK activity   Kobori et al, 2003
  Betulinic acid   IKKa activity and p65 phosphorylation   Takada & Aggarwal, 2003;
      Rabi et al, 2008
  Ursolic acid   IKKa activity and p65 phosphorylation   Shishodia et al, 2003;
      Manu & Kuttan, 2008
  Thalidomide (and thalidomideanalogs)   IKK activity   Keifer et al, 2001;
      Ge et al, 2006;
      Carcache de-
      Blanco et al, 2007
  Salubrinal   IKK activity/degradation   Huang et al, 2011
  Fas-associated factor-1   IKK assembly   Park et al, 2007
  Interleukin-10   Reduced IKKa and IKKb expression   Tabary et al, 2003
  MC160 (molluscum contagiosum virus)   Reduced IKKa expression   Nichols & Shisler, 2006
  Monochloramine and glycine chloramine (NH2C1)   Oxidizes IkB   Kim et al, 2005;
      Midwinter et al, 2006
  GS143   Blocks IkB ubiquitylation   Nakajima et al, 2008;
      Hirose et al, 2008
  Salmonella Secreted Factor L   Blocks IkB ubiquitylation   Le Negrate et al, 2008
  Anethole   Phosphorylation   Chainy et al, 2000
  Anti-thrombin III   Phosphorylation   Oelschlager et al, 2002
  Artemisia vestita   Phosphorylation   Sun et al, 2006
  Aspirin, sodium salicylate   Phosphorylation, IKKbeta   Frantz & O'Neill, 1995;
      Kopp & Ghosh, 1994;
      Yin et al, 1998
  Azidothymidine (AZT)   Phosphorylation   Ghosh et al, 2003;
      Kurokawa et al, 2005
  Baoganning   Phosphorylation   Tan et al, 2005
  BAY-11-7082    
  (E3((4-methylphenyl)-sulfonyl)-2-propenenitrile)    
  Phosphorylation   Pierce et al, 1997  
  BAY-117083    
  (E3((4-t-butylphenyl)-sulfonyl)-2-propenenitrile)    
  Phosphorylation   Pierce et al, 1997  
  Benzyl isothiocyanate   Phosphorylation   Srivastava & Singh, 2004
  Black raspberry extracts (cyanidin 3-O-glucoside, cyanidin   Phosphorylation   Huang et al, 2002;
  3-O-(2(G)-xylosylrutinoside), cyanidin     Hecht et al, 2006
  3-O-(2(G)-xylosylrutinoside), cyanidin 3-O-rutinoside)    
  Buddlejasaponin IV   Phosphorylation   Won et al, 2006
  Cacospongionolide B   Phosphorylation   Posadas et al, 2003
  Calagualine   Phosphorylation   Manna et al, 2003
  Carbon monoxide   Phosphorylation   Sarady et al, 2002
  Carboplatin   Phosphorylation   Singh & Bhat, 2004
  Cardamonin   Phosphorylation   Israf et al, 2006
  Chorionic gonadotropin   Phosphorylation   Manna et al, 2000
  Cordycepin   Phosphorylation   Kim et al, 2006;
      Huang et al., 2007
  Crassocephalum rabens galactolipid   Phosphorylation   Hou et al., 2007
  Cycloepoxydon; 1-hydroxy-2-   Phosphorylation   Gehrt et al, 1998
  hydroxymethyl-3-pent-1-enylbenzene    
  Cytomegalovirus   Phosphorylation   Jarvis et al, 2006
  Decursin   Phosphorylation   Kim et al, 2006
  Delphinidin   Phosphorylation   Syed et al, 2008
  Dexanabinol   Phosphorylation   Juttler et al, 2004
  Digitoxin   Phosphorylation   Srivastava et al, 2004;
      Jagielska et al, 2009
  Dihydrotestosterone   Phosphorylation   Xu et al, 2011
  Diterpenes (synthetic)   Phosphorylation   Chao et al, 2005
  Docosahexaenoic acid   Phosphorylation   Chen et al, 2005; Zand et al, 2008
  Entamoeba histolytica   Phosphorylation   Kammanadiminti & Chadee, 2006
  Extensively oxidized low density lipoprotein   Phosphorylation   Brand et al, 1997; Page et al, 1999
  (ox-LDL), 4-Hydroxynonenal (HNE)    
  FBD   Phosphorylation   Lin et al, 2008
  FHIT (Fragile histidine triad protein)   Phosphorylation   Nakagawa & Akao, 2006
  Fructus Ligustrum lucidi   Phosphorylation   An et al, 2007
  Gabexate mesilate   Phosphorylation   Uchiba et al, 2003
  [6]-gingerol; casparol   Phosphorylation   Kim et al, 2005; Aktan et al, 2006;
      Ishiguro et al, 2007
  Gleditsia sinensis thorns extract   Phosphorylation   Ha et al, 2008
  Gleevec (Imatanib)   Phosphorylation   Wolf et al, 2005
  Glossogyne tenuifolia   Phosphorylation   Wu et al, 2004; Ha et al, 2006
  Guggulsterone   Phosphorylation   Shishodia & Aggarwal, 2004
  4-hydroxy-3,6,7,8,3′,4′-hexamethoxyflavone   Phosphorylation   Lai et al, 2007
  Hydroquinone   Phosphorylation   Kerzic et al, 2003
  Ibuprofen   Phosphorylation   Palayoor et al, 1998
  Indirubin-3′-oxime   Phosphorylation   Mak et al, 2004
  Inonotus obliquus ethanol extract   Phosphorylation   Kim et al, 2007
  Interferon-alpha   Phosphorylation   Manna et al, 2000
  Inhaled isobutyl nitrite   Phosphorylation   Ponnappan et al, 2004
  Kaempferol   Phosphorylation   Garcia-Mediavilla et al, 2006;
      Kim et al 2007
  Kushen flavonoids and kurarinone   Phosphorylation   Han et al, 2006
  Licorce extracts   Phosphorylation   Kim et al, 2006: Kwon et al, 2007
  Melatonin   Phosphorylation   Alonso et al, 2006;
      Tamura et al, 2009
  Marine natural products (several)   IKKb/proteasome   Folmer et al, 2009
  Methotrexate   Phosphorylation   Majumdar & Aggarwal, 2001;
      Yozai et al 2005
  Monochloramine   Phosphorylation   Omori et al, 2002
  Nafamostat mesilate   Phosphorylation   Noguchi et al, 2003
  Obovatol   Phosphorylation   Lee et al, 2008
  Oleandrin   Phosphorylation   Manna et al, 2000;
      Sreeivasan et al, 2003
  Oleanolic acid (Aralia elata)   Phosphorylation   Suh et al, 2007
  Omega 3 fatty acids   Phosphorylation   Novak et al, 2003
  Panduratin A (from Kaempferia pandurata, Zingiberaceae)   Phosphorylation   Yun et al, 2003
  Petrosaspongiolide M   Phosphorylation   Posadas et al, 2003
  Pinosylvin   Phosphorylation   Lee et al, 2006
  Plagius flosculosus extract polyacetylene spiroketal   Phosphorylation   Calzado et al, 2005
  Phytic acid (inositol hexakisphosphate)   Phosphorylation   Ferry et al, 2002
  Pomegranate fruit extract   Phosphorylation   Ahmed et al, 2005
  Prostaglandin Al   Phosphorylation/IKK   Rossi et al, 1997, 2000
  Protocatechuic Aldehyde   Phosphorylation   Xu et al, 2011
  20(S)-Protopanaxatriol (ginsenoside metabolite)   Phosphorylation   Oh et al, 2004; Lee et al, 2005
  Rengyolone   Phosphorylation   Kim et al, 2006
  Rottlerin   Phosphorylation   Kim et al, 2005;
      Torricelli et al, 2008
  Saikosaponin-d   Phosphorylation;   Dang et al, 2007
    Increased IkBLeung et al, 2005;  
  Saline (low Na+istonic)   Phosphorylation   Tabary et al, 2003
  Salvia miltiorrhizae water-soluble extract   Phosphorylation   Kim et al, 2005
  Sanguinarine (pseudochelerythrine,   Phosphorylation   Chaturvedi et al, 1997
  13-methyl-[1,3]-benzodioxolo-[5,6-c]-    
  1,3-dioxolo-4,5phenanthridinium)    
  Scoparone   Phosphorylation   Jang et al, 2005
  Sesaminol glucosides   Phosphorylation   Lee et al, 2006
  Shikonins   Phosphorylation   Nam et al, 2008
  Silymarin   Phosphorylation   Manna et al, 1999;
      Saliou et al, 1998
  Snake venom toxin (Vipera lebetina turanica)   Phosphorylation   Son et al, 2007
  SOCS1   Phosphorylation   Kinlyo et al, 2002;
      Nakagawa et al, 2002
  Spilanthol   Phosphorylation   Wu et al, 2008
  Statins (several)   Phosphorylation   Hilgendorff et al, 2003;
      Han et al, 2004;
      Planavila et al, 2005
  Sulindac   IKK/Phosphorylation   Yamamato et al, 1999
  THI 52 (1-naphthylethyl-6,7-dihydroxy-   Phosphorylation   Kang et al, 2003
  1,2,3,4-tetrahydroisoquinoline)    
  1,2,4-thiadiazolidine derivatives   Phosphorylation   Manna et al, 2004
  Tomatidine   Phosphorylation   Chiu & Lin, 2008
  Vesnarinone   Phosphorylation   Manna & Aggarwal, 2000;
      Harada et al 2005
  Xanthoangelol D   Phosphorylation   Sugii et al, 2005
  YC-1   Phosphorylation   Huang et al, 2005
  YopJ (encoded by Yersinia pseudotuberculosis)   Deubiquintinase for IkBa;   Schesser et al, 1998;
      Zhou et al, 2005;
    Acetylation of IKKbeta   Mittal et al, 2006;
      Mukherjee & Orth, 2008
  Osmotic stress   IkB ubiquitination   Huangfu et al, 2007
  Acetaminophen   Degradation   Mancini et al, 2003
  Activated Protein C (APC)   Degradation   Yuksel et al, 2002
  Alachlor   Degradation   Shimomura-Shimizu
      et al, 2005
  Allylpyrocatechol   Degradation   Sarkar et al, 2008
  a-melanocyte-stimulating hormone (a-MSH)   Degradation   Manna & Aggarwal, 1998
  Amentoflavone   Degradation   Banerjee et al, 2002;
      Guruvayoorappan &
      Kuttan, 2007
  Angelica dahurica radix extract   Degradation   Kang et al, 2006
  Apple extracts   Degradation/proteasome   Yoon & Liu, 2007
  Artemisia capillaris Thunb extract (capillarisin)   Degradation   Hong et al, 2004;
      Kim et al, 2007;
      Lee et al, 2007
  Artemisia iwayomogi extract   Degradation   Kim et al, 2005
  L-ascorbic acid   Degradation   Han et al, 2004
  Antrodia camphorata   Degradation   Hseu et al, 2005
  Aucubin   Degradation   Jeong et al, 2002
  Baicalein   Degradation   Ma et al, 2004
  N-(quinolin-8-yl)benzenesulfonamindes   Degradation   Xie et al, 2007
  beta-lapachone   Degradation   Manna et al, 1999
  Blackberry extract   Degradation   Pergola et al, 2006
  1-Bromopropane   Degradation   Yoshida et al, 2006
  Buchang-tang   Degradation   Shin et al, 2005
  Capsaicin (8-methyl-N-vanillyl-6-nonenamide)   Degradation   Singh et al, 1996;
      Mori et al, 2006;
      Kang et al, 2007
  Catalposide   Degradation   Kim et al, 2004
  Clerodendron trichotomum Tunberg Leaves   Degradation   Park & Kim, 2007
  Clomipramine/imipramine   Degradation   Hwang et al, 2008
  Coptidis rhizoma extract   Degradation   Kim et al, 2007
  Cyclolinteinone (sponge sesterterpene)   Degradation   D'Acquisto et al, 2000
  DA-9601 (Artemisia asiatica extract)   Degradation   Choi et al, 2006
  Diamide (tyrosine phosphatase inhibitor)   Degradation   Toledano & Leonard, 1991;
      Singh & Aggarwal, 1995
  Dihydroarteanniun   Degradation   Li et al, 2006
  Dobutamine   Degradation   Loop et al, 2004
  Docosahexaenoic acid   Degradation   Weldon et al, 2006
  E-73 (cycloheximide analog)   Degradation   Sugimoto et al, 2000
  Ecabet sodium   Degradation   Kim et al, 2003
  Electrical stimulation of vagus nerve   Degradation   Guarini et al, 2003
  Emodin (3-methyl-1,6,8-trihydroxyanthraquinone)   Degradation   Kumar et al, 1998;
      Huang et al, 2004
  Ephedrae herba (Mao)   Degradation   Aoki et al, 2005
  Equol   Degradation   Kang et al, 2005
  Erbstatin (tyrosine kinase inhibitor)   Degradation   Natarajan et al, 1998
  Estrogen (E2)   Degradation/and various other steps   Sun et al, 1998;
      Kalaitzidis & Gilmore, 2005;
      Steffan et al, 2006
  Ethacrynic acid   Degradation (and DNA binding)   Han et al, 2004
  Fludarabine   Degradation   Nishioka et al, 2007
  Fosfomycin   Degradation   Yoneshima et al, 2003
  Fungal gliotoxin   Degradation   Pahl et al, 1999
  Gabexate mesilate   Degradation   Yuksel et al, 2003
  Gamisanghyulyunbueum   Degradation   Shin et al, 2005
  Genistein (tyrosine kinase inhibitor)   Degradation; caspase cleavage of IkBa   Natarajan et al, 1998;
      Baxa & Yoshimura, 2003
  Genipin   Degradation   Koo et al, 2004
  Glabridin   Degradation   Kang et al, 2004
  Ginsenoside Re   Degradation   Zhang et al, 2007
  Glimepiride   Degradation   Schiekofer et al, 2003
  Glucosamine (sulfate or carboxybutyrylated)   Degradation   Largo et al, 2003; Rafi et al, 2007;
      Rajapakse et al, 2008
  gamma-glutamylcysteine synthetase   Degradation   Manna et al, 1999
  Glutamine   Degradation   Singleton et al, 2005;
      Fillmann et al, 2007;
      Chen et al, 2008
  Glycochenodeoxycholate   Degradation   Bucher et al, 2006
  Guave leaf extract   Degradation   Choi et al, 2008
  Gumiganghwaltang   Degradation   Kim et al, 2005
  Gum mastic   Degradation   He et al, 2007
  Heat shock protein-70   Degradation   Chan et al, 2004; Shi et al, 2006
  Herbal mixture (Cinnamomi ramulus,   Degradation   Jeong et al, 2008
  Anemarrheriae rhizoma, Officinari rhizoma)    
  Hypochlorite   Degradation   Mohri et al, 2002
  Ibudilast   Degradation   Kiebala & Maggirwar, 1998
  IL-13   Degradation   Manna & Aggarwal, 1998
  Incensole acetate   Degradation   Moussaieff et al, 2007
  Intravenous immunoglobulin   Degradation   Ichiyama et al, 2004
  Isomallotochromanol and isomallotochromene   Degradation   Ishii et al, 2003
  K1L (Vaccinia virus protein)   Degradation   Shisler & Jin, 2004
  Kochia scoparia fruit (methanol extract)   Degradation   Shin et al, 2004
  Kummerowia striata (Thunb.) Schindl (ethanol extract)   Degradation   Tao et al, 2008
  Leflunomide metabolite (A77 1726)   Degradation   Manna & Aggarwal, 1999
  Lidocaine   Degradation   Feng et al, 2007; Lahat et al, 2008
  Lipoxin A4   Degradation   Zhang et al, 2007
  Losartan   Degradation/NF-kB expression   Chen et al, 2002; Zhu et al, 2007
  Low level laser therapy   Degradation   Rizzi et al, 2006
  LY294002 (PI3-kinase inhibitor)   Degradation   Park et al 2002
  [2-(4-morpholinyl)-8-phenylchromone]    
  MC159 (Molluscum contagiosum virus)   Degradation of IkBb   Murao & Shisler, 2005
  Melatonin   Degradation   Zhang et al, 2004
  Meloxicam   Degradation   Liu et al, 2007
  5′-methylthioadenosine   Degradation   Hevia et al, 2004
  Midazolam   Degradation   Kim et al, 2006
  Momordin I   Degradation   Hwang et al, 2005
  Morinda officinalis extract   Degradation   Kim et al, 2005
  Mosla dianthera extract   Degradation   Lee et al, 2006
  Mume fructus extract   Degradation   Choi et al, 2007
  Murrl gene product   Degradation   Ganesh et al, 2003
  Neurofibromatosis-2 (NF-2; merlin) protein   Degradation   Kim et al, 2002
  Opuntia ficus indica va saboten extract   Degradation   Lee et al, 2006
  Ozone (aqueous)   Degradation   Huth et al, 2007
  Paeony total glucosides   Degradation   Chen et al, 2007
  Pectenotoxin-2   Degradation   Kim et al, 2008
  Penetratin   Degradation   Letoya et al, 2006
  Pervanadate (tyrosine phosphatase inhibitor)   Degradation   Singh & Aggarwal, 1995;
      Singh et al, 1996
  Phenylarsine oxide (PAO, tyrosine phosphatase inhibitor)   Degradation   Mahboubi et al, 1998;
      Singh & Aggarwal, 1995
  beta-Phenylethyl (PEITC) and 8-methylsulphinyloctyl   Degradation   Rose et al, 2005
  isothiocyanates (MSO) (watercress)    
  Phenytoin   Degradation   Kato et al, 2005
  c-phycocyanin   Degradation   Cherng et al, 2007
  Platycodin saponins   Degradation   Aim et al, 2005; Lee et al, 2008
  Polymeric formula   Degradation   de Jong et al, 2007
  Polymyxin B   Degradation   Jiang et al, 2006
  Poncirus trifoliata fruit extract   Degradation; phosphorylation of IkBa   Shin et al, 2006; Kim et al 2007
  Probiotics   Degradation   Petrof et al, 2004
  Pituitary adenylate cyclase-activating polypeptide (PACAP)   Degradation   Delgado & Ganea, 2001
  Prostaglandin 15-deoxy-Delta(12,14)-PGJ(2)   Degradation   Cuzzocrea et al, 2003;
      Chatterjee et al, 2004
  Prodigiosin (Hahella chejuensis)   Degradation   Huh et al, 2007
  PS-341   Degradation/proteasome   Hideshima et al, 2002
  Radix asari extract   Degradation   Song et al, 2007
  Radix clematidis extract   Degradation   Lee et al, 2009
  Resiniferatoxin   Degradation   Singh et al, 1996
  Sabaeksan   Degradation   Choi et al, 2005
  SAIF (Saccharomyces boulardii anti-inflammatory factor)   Degradation   Sougioultzis et al 2006
  Sanguis Draconis   Degradation   Choy et al, 2007
  San-Huang-Xie-Xin-Tang   Degradation   Shih et al, 2007
  Schisandra fructus extract   Degradation   Kang et al, 2006; Guo et al, 2008
  Scutellarin   Degradation   Tan et al, 2007
  Sesquiterpene lactones (parthenolide; ergolide;   Degradation   Hehner et al, 1998;
      Whan Han et al, 2001;
  guaianolides; alpha-humulene; trans-caryophyllene)     Schorr et al, 2002;
      Medeiros et al, 2007
  Sevoflurane/isoflurane   Degradation   Boost et al, 2009
  Siegeskaurolic acid (from Siegesbeckia pubescens root)   Degradation   Park et al, 2007
  ST2 (IL-1-like receptor secreted form)   Degradation   Takezako et al, 2006
  Synadenium carinatum latex lectin   Degradation   Rogerio et al, 2007
  Taiwanofungus camphoratus   Degradation   Liu et al, 2007
  Taurene bromamine   Degradation   Tokunaga et al, 2007
  Thiopental   Degradation   Loop et al, 2002
  Tipifarnib   Degradation   Xue et al, 2005
  Titanium   Degradation   Yang et al, 2003
  TNP-470 (angiogenesis inhibitor)   Degradation   Mauriz et al, 2003
  Stinging nettle (Urtica dioica) plant extracts   Degradation   Riehemann et al, 1999
  Trichomomas vaginalis infection   Degradation   Chang et al, 2004
  Triglyceride-rich lipoproteins   Degradation   Kumwenda et al, 2002
  Tussilagone (Farfarae fins)   Degradation   Lim et al, 2008
  U0126 (MEK inhibitor)   Degradation   Takaya et al, 2003
  Ursodeoxycholic acid   Degradation   Joo et al, 2004
  Xanthium strumarium L. (methanol extract)   Degradation   Kim et al, 2005; Yoon et al, 2008
 
  Yulda-Hanso-Tang   Degradation   Jeong et al, 2007
  Zinc   Degradation   Uzzo et al, 2006; Bao et al, 2006
  Molluscum contagiosum virus MC159 protein   IkBbeta degradation   Murao & Shisler, 2005
  Vasoactive intestinal peptide   Degradation (and CBP-RelA interaction)   Delgado & Ganea, 2001; Delgado, 2002
  HIV-1 Vpu protein   TrCP ubiquitin ligase inhibitor Bour et al, 2001  
  Epoxyquinone A monomer   IKKb/DNA binding   Liang et al, 2006
  Ro106-9920 (small molecule)   IkBa ubiqutination inhibitor Swinney et al, 2002  
  Furonaphthoquinone   IKK activity   Shin et al, 2006
  β-TrCP   Degradation   Kanarek et al, 2012
  Inhibitors from IMGENEX: NF-kB Pathway Inhibitory Peptides
  Cat.No   Description   Species
  IMG-2009-2   Antennapedia Control Peptide   N/A
  IMG-2009-5   Antennapedia Control Peptide   N/A
  IMG-2000   IKKg NEMO Binding Domain   H, M, R
    (NBD) Inhibitory Peptide Set Functions as an  
    IKKa/IKKb decoy by binding to IKKg NBD,  
    thereby preventing formation of the IKK  
    complex.  
  IMG-2000-5   IKKg NEMO Binding Domain (NBD)   H, M, R
    Inhibitory Peptide Set Functions as an  
    IKKa/IKKb decoy by binding to IKKg  
    NBD, thereby preventing formation of  
    the IKK complex.  
  IMG-2005-5   MyD88 Homodimerization Inhibitory   H, M, R, X, Z
    Peptide Set Functions as a decoy by binding to  
    the MyD88 TIR domain  
  IMG-2005-1   MyD88 Homodimerization Inhibitory Peptide   H, M, R, X, Z
    Set Functions as a decoy by binding to the  
    MyD88 TIR domain  
  IMG-2004   NF-kB p50 (NLS) Inhibitory Peptide Set   B, C, C, D, H, M,
    Functions as a p50 decoy by blocking the   R, X
    intracellular recognition mechanism of  
    p50 NLS.  
  IMG-2004-5   NF-kB p50 (NLS) Inhibitory Peptide Set   B, C, C, D, H, M,
    Functions as a p50 decoy by blocking the   R, X
    intracellular recognition mechanism of  
    p50 NLS.  
  IMG-2001   NF-kB p65 (Ser276) Inhibitory Peptide Set   C, D, H, M, M, R
    Functions as a p65 decoy through  
    phosphorylation of the Ser276 site on  
    the peptide.  
  IMG-2001-5   NF-kB p65 (Ser276) Inhibitory Peptide Set   C, D, H, M, M, R
    Functions as a p65 decoy through  
    phosphorylation of the Ser276 site on the  
    peptide.  
  IMG-2003   NF-kB p65 (Ser529/536) Inhibitory Peptide   C, D, H, M, M, R
    Set Functions as a p65 decoy through  
    phosphorylation of the Ser529/536 sites on  
    the peptide.  
  IMG-2003-5   NF-kB p65 (Ser529/536) Inhibitory Peptide   C, D, H, M, M, R
    Set Functions as a p65 decoy through  
    phosphorylation of the Ser529/536 sites on  
    the peptide.  
  IMG-2006-5   TIRAP Inhibitory Peptide Set Functions as a   H, M
    TIRAP decoy by binding to TIR interacting  
    domains on specific TLR receptors.  
  IMG-2006-1   TIRAP Inhibitory Peptide Set Functions as a   H, M
    TIRAP decoy by binding to TIR interacting  
    domains on specific TLR receptors.  
  IMG-2011 set   TLR4 Peptide Inhibitor Set: VIPER   H, M
  IMG-2002   TRAF6 Inhibitory Peptide Set Functions as a   H, M, R
    TRAF6 decoy by binding to the T6DP motif of  
    RANK, thereby preventing binding of  
    RANK to TRAF6.  
  IMG-2002-5   TRAF6 Inhibitory Peptide Set Functions as a   H, M, R
    TRAF6 decoy by binding to the T6DP motif of  
    RANK, thereby preventing binding of.  
    RANK to TRAF6  
  NF kappa B Inhibitors
  9-Methylstreptimidone    
  Z-VRPR-FMK    
  2-(1,8-naphthyridin-2-y1)-Phenol    
  5-Aminosalicylic acid    
  BAY 11-7082    
  BAY 11-7085    
  Caffeic acid phenethyl ester    
  Diethylmaleate    
  Ethyl 3,4-Dihydroxycinnamate    
  Helenalin    
  NFicB Activation Inhibitor II, JSH-23    
  NFicB Activation Inhibitor III    
  PPM-18    
  Pyrrolidinedithiocarbamic acid ammonium salt    
  (R)-MG-132    
  Rocaglamide    
  Sodium Salicylate
 
[0168] The presently-disclosed subject matter further includes compositions useful for inhibiting NFκB. Such compositions include an inhibitor. As noted above, such inhibitors can be, for example, a nucleotide, a polypeptide, a small (chemical) molecule, etc. In some embodiments, a composition can include an isolated RNA molecule.
[0169] The presently-disclosed subject matter further includes methods of screening candidate inhibitors to identify NFκB inhibitors. In some embodiments, cell or cell line-based methods are used.

Imaging Caspase in an Eye of a Subject

[0170] In some embodiments, a diagnostic composition is provided for imaging activated Caspase in an eye of a subject, comprising a fluorescent molecule conjugated to a substrate of Caspase-1 or a molecule that fluoresces following cleavage by Caspase-1. In some embodiments, a method is provided for imaging activated Caspase-1 in an eye of a subject, including administering (e.g., intraocularly or intravenously) to RPE cells of the subject the diagnostic composition, and optically monitoring the spatial clustering of fluorescence.
[0171] The details of one or more embodiments of the presently-disclosed subject matter are set forth in this document. Modifications to embodiments described in this document, and other embodiments, will be evident to those of ordinary skill in the art after a study of the information provided in this document. The information provided in this document, and particularly the specific details of the described exemplary embodiments, is provided primarily for clearness of understanding and no unnecessary limitations are to be understood therefrom. In case of conflict, the specification of this document, including definitions, will control.
[0172] Some of the polynucleotide and polypeptide sequences disclosed herein are cross-referenced to GENBANK®/GENPEPT® accession numbers. The sequences cross-referenced in the GENBANK®/GENPEPT® database are expressly incorporated by reference as are equivalent and related sequences present in GENBANK®/GENPEPT® or other public databases. Also expressly incorporated herein by reference are all annotations present in the GENBANK®/GENPEPT® database associated with the sequences disclosed herein. Unless otherwise indicated or apparent, the references to the GENBANK®/GENPEPT® database are references to the most recent version of the database as of the filing date of this Application.
[0173] While the terms used herein are believed to be well understood by one of ordinary skill in the art, definitions are set forth to facilitate explanation of the presently-disclosed subject matter.
[0174] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the presently-disclosed subject matter belongs. Although any methods, devices, and materials similar or equivalent to those described herein can be used in the practice or testing of the presently-disclosed subject matter, representative methods, devices, and materials are now described.
[0175] Following long-standing patent law convention, the terms “a”, “an”, and “the” refer to “one or more” when used in this application, including the claims. Thus, for example, reference to “a cell” includes a plurality of such cells, and so forth.
[0176] Unless otherwise indicated, all numbers expressing quantities of ingredients, properties such as reaction conditions, and so forth used in the specification and claims are to be understood as being modified in all instances by the term “about”. Accordingly, unless indicated to the contrary, the numerical parameters set forth in this specification and claims are approximations that can vary depending upon the desired properties sought to be obtained by the presently-disclosed subject matter.
[0177] As used herein, the term “about,” when referring to a value or to an amount of mass, weight, time, volume, concentration or percentage is meant to encompass variations of in some embodiments ±20%, in some embodiments ±10%, in some embodiments ±5%, in some embodiments ±1%, in some embodiments ±0.5%, and in some embodiments ±0.1% from the specified amount, as such variations are appropriate to perform the disclosed method.
[0178] As used herein, ranges can be expressed as from “about” one particular value, and/or to “about” another particular value. It is also understood that there are a number of values disclosed herein, and that each value is also herein disclosed as “about” that particular value in addition to the value itself. For example, if the value “10” is disclosed, then “about 10” is also disclosed. It is also understood that each unit between two particular units are also disclosed. For example, if 10 and 15 are disclosed, then 11, 12, 13, and 14 are also disclosed.
[0179] The presently-disclosed subject matter is further illustrated by the following specific but non-limiting examples. The following examples may include compilations of data that are representative of data gathered at various times during the course of development and experimentation related to the present invention.

EXAMPLES

Example 1

[0180] Alu RNA accumulation due to DICER1 deficiency in the retinal pigmented epithelium (RPE) is implicated in geographic atrophy (GA), an advanced form of age-related macular degeneration that causes blindness in millions of individuals. The mechanism of Alu RNA-induced cytotoxicity is unknown. Here it is shown that DICER1 deficit or Alu RNA exposure activates the NLRP3 inflammasome and triggers TLR-independent MyD88 signaling via IL-18 in the RPE. Genetic or pharmacological inhibition of inflammasome components (NLRP3, Pycard, Caspase-1), MyD88, or IL-18 prevents RPE degeneration induced by DICER1 loss or Alu RNA exposure. These findings, coupled with the observation that human GA RPE contains elevated amounts of NLRP3, PYCARD and IL-18, and evidence of increased Caspase-1 and MyD88 activation, provide a rationale for targeting this pathway in GA. The findings also reveal a novel function of the inflammasome outside the immune system and a surprising immunomodulatory action of mobile elements.
[0181] Age-related macular degeneration (AMD) affects the vision of millions of individuals (Smith et al., 2001). AMD is characterized by degeneration of the retinal pigmented epithelium (RPE), which is situated between the retinal photoreceptors and the choroidal capillaries (Ambati et al., 2003). RPE dysfunction disrupts both photoreceptors and choroidal vasculature (Blaauwgeers et al., 1999; Lopez et al., 1996; McLeod et al., 2009; Vogt et al., 2011). These tissue disruptions lead to atrophic or neovascular disease phenotypes. Although there are therapies for neovascular AMD, there is no effective treatment for the more common atrophic form. GA, the advanced stage of atrophic AMD, is characterized by degeneration of the RPE, and is the leading cause of untreatable vision loss.
[0182] Recently it was shown that a dramatic and specific reduction of the RNase DICER1 leads to accumulation of Alu RNA transcripts in the RPE of human eyes with GA (Kaneko et al., 2011). These repetitive element transcripts, which are non-coding RNAs expressed by the highly abundant Alu retrotransposon (Batzer and Deininger, 2002), induce human RPE cell death and RPE degeneration in mice. DICER1 deficit in GA RPE was not a generic cell death response because DICER1 expression was not dysregulated in other retinal diseases. Likewise, Alu RNA accumulation did not represent generalized retrotransposon activation due to a stress response in dying cells because other retrotransposons were not elevated in GA RPE.
[0183] DICER1 is central to mature microRNA biogenesis (Bernstein et al., 2001). Yet following DICER1 deficit, the accumulation of Alu RNA and not the lack of mature microRNAs was the critical determinant of RPE cell viability (Kaneko et al., 2011). Moreover, 7SL RNA, transfer RNA, and primary microRNAs do not induce RPE degeneration (Kaneko et al., 2011), ruling out a nonspecific toxicity of excess, highly structured RNA. Still, the precise mechanisms of Alu RNA cytotoxicity are unknown.
[0184] Although the retina is exceptional for its immune privilege (Streilein, 2003), insults mediated by innate immune sensors can result in profound inflammation. The three major classes of innate immune receptors include the TLRs, RIG-1-like helicases, and NLR proteins (Akira et al., 2006). Numerous innate immune receptors are expressed in the RPE (Kumar et al., 2004), and several exogenous substances can induce retinal inflammation (Allensworth et al., 2011; Kleinman et al., 2012). However, it is not known whether this surveillance machinery recognizes or responds to host endogenous RNAs. The concept was explored that innate immune machinery, whose canonical function is the detection of pathogen associated molecular patterns and other moieties from foreign organisms, might also recognize Alu RNA.
[0185] Indeed, it was shown that Alu transcripts can hijack innate immunity machinery to induce RPE cell death. Surprisingly, the data show that DICER1 deficit or Alu RNA activates the NLRP3 inflammasome in a MyD88-dependent, but TLR-independent manner. NLRP3 inflammasome activation in vivo has been largely restricted to immune cells, although the data open the possibility that NLRP3 activity may be more widespread, as reflected by examples in cell culture studies of keratinocytes (Feldmeyer et al., 2007; Keller et al., 2008). The data also broaden the scope of DICER1 function beyond microRNA biogenesis, and identify it as a guardian against aberrant accumulation of toxic retrotransposon elements that comprise roughly 50% of the human genome (Lander et al., 2001). In sum, the findings present a novel self-recognition immune response, whereby endogenous non-coding RNA-induced NLRP3 inflammasome activation results from DICER1 deficiency in a non-immune cell.
[0186] Results
[0187] Alu RNA does not Activate a Variety of TLRs or RNA Sensors
[0188] Alu RNA has single-stranded (ss) RNA and double-stranded (ds) RNA motifs (Sinnett et al., 1991). Thus it was tested whether Alu RNA induced RPE degeneration in mice deficient in toll-like receptor-3 (TLR3), a dsRNA sensor (Alexopoulou et al., 2001), or TLR7, a ssRNA sensor (Diebold et al., 2004; Heil et al., 2004). Subretinal delivery of a plasmid coding for Alu RNA (pAlu) induced RPE degeneration in Tlr3−/− and Tlr7−/− mice just as in wild-type (WT) mice (FIGS. 1A-C). It was previously shown that ≧21-nucleotide fully complementary siRNAs activate TLR3 on RPE cells (Kleinman et al., 2011). Lack of TLR3 activation by Alu RNA is likely due to its complex structure containing multiple hairpins and bulges that might preclude TLR3 binding. Neither 7SL RNA, the evolutionary precursor of Alu RNA, nor p7SL induced RPE degeneration in WT mice (FIGS. 8A and 8B), suggesting that Alu RNA cytotoxicity might be due to as yet unclear structural features. pAlu induced RPE degeneration in Unc93b1 mice (FIG. 1D), which lack TLR3, TLR7, and TLR9 signaling (Tabeta et al., 2006), indicating that these nucleic acid sensors are not activated by Alu RNA redundantly. pAlu induced RPE degeneration in Tlr4−/− mice (FIG. 1E), and the TLR4 antagonist Rhodobacter sphaeroides LPS (Qureshi et al., 1991) did not inhibit pAlu-induced RPE degeneration in WT mice (FIG. 8C). Thus the observed RPE cell death is not due to lipopolysaccharide contamination. Further, two different in vitro transcribed Alu RNAs (Kaneko et al., 2011) did not activate multiple TLRs (FIG. 1F).
[0189] Next it was tested whether other dsRNA sensors such as MDA5 (Kato et al., 2006) or PKR (encoded by Prkr, (Yang et al., 1995)) might mediate Alu RNA toxicity. However, pAlu induced RPE degeneration in Mda5−/− and Prkr−/− mice (FIGS. 8D and 8E). It was tested whether the 5′-triphosphate on in vitro transcribed Alu RNA, which could activate RIG-I or IFIT-1 that sense this moiety (Hornung et al., 2006; Pichlmair et al., 2011), was responsible for RPE degeneration. Dephosphorylated Alu RNA induced RPE degeneration in WT mice just as well as Alu RNA not subjected to dephosphorylation (FIG. 8F), indicating that this chemical group is not responsible for the observed cell death. Indeed a 5′-triphosphate ssRNA that activates RIG-I does not induce RPE degeneration in mice (Kleinman et al., 2011). Further, pAlu induced RPE degeneration in mice deficient in MAVS (FIG. 8G), through which RIG-I and MDA-5 signal (Kumar et al., 2006; Sun et al., 2006). Collectively these data pointed to a novel mechanism of Alu RNA-induced RPE degeneration not mediated by a wide range of canonical RNA sensors.
[0190] Alu RNA Cytotoxicity is Mediated Via MyD88 and IL-18
[0191] The involvement of TRIF (encoded by Ticam1), an adaptor for TLR3 and TLR4 (Hoebe et al., 2003; Yamamoto et al., 2003), and MyD88, an adaptor for all TLRs except TLR3 (Akira et al., 2006; Alexopoulou et al., 2001; Suzuki et al., 2003) were then tested. Alu RNA induced RPE degeneration in Ticam1−/− mice (FIG. 9A), consistent with findings in Tlr3−/− and Tlr4−/− mice. Unexpectedly, neither Alu RNA nor two different pAlu plasmids induced RPE degeneration in Myd88−/− mice (FIGS. 2A, 9B, and 9C). Intravitreous delivery of a peptide inhibitor of MyD88 homodimerization (Loiarro et al., 2005) prevented RPE degeneration induced by Alu RNA in WT mice, whereas a control peptide did not do so (FIG. 2B). A MyD88-targeting short interfering RNA (siRNA), which was shorter than 21 nucleotides in length to prevent TLR3 activation and conjugated to cholesterol to enable cell permeation (Kleinman et al., 2008), but not a control siRNA, inhibited RPE degeneration induced by pAlu in WT mice (FIGS. 2C-2E). Myd88+/− heterozygous mice were protected against Alu RNA-induced RPE degeneration (FIGS. 2F and 9D), corroborating the siRNA studies that partial knockdown of MyD88 is therapeutically sufficient.
[0192] MyD88-mediated signal transduction induced by interleukins leads to recruitment and phosphorylation of IRAK1 and IRAK4 (Cao et al., 1996; Kanakaraj et al., 1999; Suzuki et al., 2003; Suzuki et al., 2002). Alu RNA increased IRAK1/4 phosphorylation in human RPE cells (FIG. 2G), supporting the concept that Alu RNA triggers MyD88 signaling. The MyD88 inhibitory peptide reduced Alu RNA-induced IRAK1/4 phosphorylation in human RPE cells (FIG. 9E), confirming its mode of action.
[0193] Next it was assessed whether MyD88 activation mediates Alu RNA-induced cell death in human and mouse RPE cell culture systems. Consonant with the in vivo data, pAlu reduced cell viability in WT but not Myd88−/− mouse RPE cells (FIG. 2H). The MyD88-inhibitory peptide, but not a control peptide, inhibited cell death in human RPE cells transfected with pAlu (FIG. 2I). Together, these data indicate that MyD88 is a critical mediator of Alu RNA-induced RPE degeneration.
[0194] MyD88 is generally considered an adaptor of immune cells (O'Neill and Bowie, 2007). However, Alu RNA induced cell death via MyD88 in RPE monoculture. Thus, it was tested whether Alu RNA-induced RPE degeneration in mice was also dependent solely on MyD88 activation in RPE cells. Conditional ablation of MyD88 in the RPE by subretinal injection of AAV1-BEST1-Cre in Myd88f/f mice protected against Alu RNA-induced RPE degeneration (FIGS. 2J and 9F). Consistent with this finding, Alu RNA induced RPE degeneration in WT mice receiving Myd88−/− bone marrow but did not do so in Myd88−/− mice receiving WT bone marrow (FIG. 9G). Collectively, these results indicate that MyD88 expression in the RPE, and not in circulating immune cells, is critical for Alu RNA-induced RPE degeneration. These findings comport with histopathological studies of human GA tissue that show no infiltration of immune cells in the area of pathology (personal communication, C. A. Curcio, H. E. Grossniklaus, G. S. Hageman, L. V. Johnson).
[0195] Although MyD88 is critical in TLR signaling (O'Neill and Bowie, 2007), MyD88 activation by Alu RNA was independent of TLR activation. Thus, other mechanisms of MyD88 involvement were examined. MyD88 can regulate IFN-γ signaling by interacting with IFN-γ receptor 1 (encoded by Ifngr1) (Sun and Ding, 2006). However, pAlu induced RPE degeneration in both Ifng−/− and Ifngr1−/− mice (FIGS. 9H and 9I). MyD88 is also essential in interleukin-1 signaling (Muzio et al., 1997). Thus, it was tested whether IL-1β and the related cytokine IL-18, both of which activate MyD88 (Adachi et al., 1998), mediated Alu RNA cytotoxicity. Interestingly, whereas Alu RNA overexpression in human RPE cells increased IL-18 secretion, IL-1β secretion was barely detectable (FIG. 2K).
[0196] Recombinant IL-18 induced RPE degeneration in WT but not Myd88−/− mice (FIG. 2L). IL-18 neutralization protected against pAlu-induced RPE degeneration in WT mice, but IL-1β did not (FIGS. 2M and 2N). Also, pAlu induced RPE degeneration in Il1r1−/− mice but not Il18r1−/− mice (FIGS. 9J and 9K). These data indicate that IL-18 is an effector of Alu RNA-induced cytotoxicity.
[0197] Alu RNA Activates the NLRP3 Inflammasome
[0198] It was explored whether Caspase-1 (encoded by Casp1), a protease that induces maturation of interleukins into biologically active forms (Ghayur et al., 1997; Gu et al., 1997; Thornberry et al., 1992), was involved in Alu RNA-induced RPE degeneration. Alu RNA treatment of human RPE cells led to Caspase-1 activation as measured by western blotting and by a fluorescent reporter of substrate cleavage (FIGS. 3A and 10A). Indeed, Alu RNA induced Caspase-1 activation in other cell types such as HeLa and THP-1 monocytic cells (FIG. 10B), suggesting that Alu RNA cytotoxicity has potentially broad implications in many systems. Intravitreous delivery of the Caspase-1-inhibitory peptide Z-WEHD-FMK, but not a control peptide Z-FA-FMK, blocked IL-18 maturation and pAlu-induced RPE degeneration in WT mice (FIGS. 3B and 3C). The Caspase-1-inhibitory peptide blocked Alu RNA-induced substrate cleavage in human RPE cells (FIG. 10C), confirming its mode of action. Similarly, Casp1−/− mice treated with Alu RNA or pAlu did not exhibit RPE degeneration (FIGS. 3D and 10D). Also, pAlu did not induce cell death in Casp1−/− mouse RPE cells (FIG. 3E).
[0199] Caspase-1 can be activated within a multiprotein innate immune complex termed the inflammasome (Tschopp et al., 2003). The best-characterized inflammasome pathway is one that is activated by binding of NLRP3 to the caspase-1 adaptor ASC (encoded by PYCARD). One hallmark of inflammasome assembly is spatial clustering of PYCARD (Fernandes-Alnemri et al., 2007). In human RPE cells transfected with fluorescent tagged PYCARD (GFP-PYCARD), Alu RNA induced the appearance of a brightly fluorescent cytoplasmic cluster similar to treatment with LPS and ATP, which activates the NLRP3 inflammasome (FIGS. 3F and 10E) (Mariathasan et al., 2006).
[0200] Next the functional relevance of NLRP3 and PYCARD to Alu RNA cytotoxicity was tested. Neither pAlu nor Alu RNA induced RPE degeneration in either Nlrp3−/− or Pycard−/− mice (FIGS. 3G, 3H, 10F and 10G), demonstrating the critical importance of the inflammasome in Alu RNA cytotoxicity. Also, pAlu did not induce cell death in Nlrp3−/− or Pycard−/− mouse RPE cells (FIG. 31). Moreover, knockdown of NLRP3 or PYCARD by siRNAs rescued pAlu-induced human RPE cell death (FIGS. 3J and 10H). These findings provide direct evidence that NLRP3 activation in response to Alu RNA occurs in RPE cells and does not require the presence of other immune cells.
[0201] It was determined that IL-18 and MyD88 activation indeed were downstream of Caspase-1 activation by showing (1) that whereas MyD88 inhibition reduced Alu RNA-induced IRAK1/4 phosphorylation in human RPE cells (FIG. 9E), it did not reduce Alu RNA-induced Caspase-1 cleavage or fluorescent substrate cleavage (FIGS. 10I and 10J); (2) that IL-18 neutralization did not inhibit Alu RNA-induced Caspase-1 cleavage (FIG. 10K); and (3) that Caspase-1 inhibition reduced Alu RNA-induced phosphorylation of IRAK1/4 (FIG. 10L).
[0202] Alu RNA Induces Mitochondrial ROS and NLRP3 Priming
[0203] NLRP3 inflammasome function requires two signals, the first of which is termed priming. pAlu induced inflammasome priming as it upregulated both NLRP3 and IL18 mRNAs. This priming occurred equivalently in both WT and Myd88−/− mouse RPE cells (FIG. 4A), further corroborating that MyD88 functions downstream of NLRP3 in this system. Akin to other inflammasome agonists that do not directly interact with NLRP3 (Tschopp and Schroder, 2010), a physical interaction between Alu RNA and NLRP3 was not observed (FIG. 11A). To determine how Alu RNA primed the inflammasome, it was studied whether it induced reactive oxygen species (ROS) production, a signal for priming (Bauernfeind et al., 2011; Nakahira et al., 2011). pAlu induced ROS generation in human RPE cells (FIG. 4B), and the ROS inhibitor diphenyliodonium (DPI) blocked pAlu-induced NLRP3 and IL18 mRNA upregulation and Alu RNA-induced RPE degeneration in WT mice (FIGS. 4C and 4D). As DPI blocks mitochondrial ROS and phagosomal ROS (Li and Trush, 1998), it was tested which pathway was triggered because there is controversy surrounding the source of ROS contributing to NLRP3 responses (Latz, 2010).
[0204] MitoSOX Red was used, which labels ROS-generating mitochondria, in combination with MitoTracker Deep Red, which labels respiring mitochondria. To monitor phagosomal ROS generation, Fc OxyBURST Green was used, which measures activation of NADPH oxidase within the phagosome. A marked increase in ROS-generating mitochondria was observed in human RPE cells transfected with pAlu (FIG. 4E). In contrast, whereas phorbol myristate acetate (PMA) induced phagosomal ROS as expected (Savina et al., 2006), pAlu did not do so (FIG. 4F). These data are consistent with the findings that NLRP3 responses are impaired by mitochondrial ROS inhibitors (Nakahira et al., 2011; Zhou et al., 2011) but are preserved in cells carrying genetic mutations that impair NADPH-oxidase-dependent ROS production (Meissner et al., 2010; van Bruggen et al., 2010).
[0205] Consonant with these reports and the observation that the principal source of cellular ROS is mitochondria (Murphy, 2009), it was found that the mitochondria-targeted antioxidants Mito-TEMPO and MitoQ (Murphy and Smith, 2007; Nakahira et al., 2011) both blocked Alu RNA-induced RPE degeneration in WT mice, whereas dTPP, a structural analog of MitoQ that does not scavenge mitochondrial ROS, did not do so (FIG. 4G). In contrast, gp91ds-tat, a cell-permeable peptide that inhibits association of two essential NADPH oxidase subunits (gp91phox and p47phox) (Rey et al., 2001), did not do so (FIG. 4H). Corroborating these data, Alu RNA induced RPE degeneration in mice deficient in Cybb (which encodes gp91phox) just as in WT mice (FIG. 4I). Next the voltage-dependent anion channels (VDAC) was studied because VDAC1 and VDAC2, but not VDAC3, are important in mitochondrial ROS produced by NLRP3 activators in macrophages (Zhou et al., 2011). Consistent with these observations, siRNA knockdown of VDAC1 and VDAC2, but not VDAC3, impaired pAlu-induced mitochondrial ROS (FIGS. 4J and 11B) and NLRP3 and IL18 mRNA induction in human RPE cells (FIG. 4K). Collectively, these data implicate mitochondrial ROS in Alu RNA-induced NLRP3 inflammasome-mediated RPE degeneration.
[0206] Alu RNA does not Induce RPE Degeneration Via Pyroptosis
[0207] Alu RNA activates Caspase-1, which can trigger pyroptosis, a form of cell death characterized by formation of membrane pores and osmotic lysis (Fink and Cookson, 2006). The cytoprotective agent glycine, which attenuates pyroptosis (Fink et al., 2008; Fink and Cookson, 2006; Verhoef et al., 2005), inhibited human RPE cells death induced by LPS+ATP but not by Alu RNA (FIGS. 5A and 5B). Pyroptosis requires Caspase-1 but can proceed independent of IL-18 (Miao et al., 2010). Thus, the finding that IL-18 induced RPE degeneration in Casp1−/− mice (FIG. 5C), coupled with the lack of rescue by glycine, suggests that Alu RNA-induced RPE degeneration does not occur via pyroptosis.
[0208] DICER1 Loss Induces Cell Death Via Inflammasome
[0209] It was previously demonstrated that the key role of DICER1 in maintaining RPE cell health (Kaneko et al., 2011): DICER1-cleaved Alu RNA did not induce RPE degeneration in vivo; DICER1 overexpression protected against Alu RNA-induced RPE degeneration; and DICER1 loss-induced RPE degeneration was blocked by antagonizing Alu RNA (Kaneko et al., 2011). Also, rescue of DICER1 knockdown-induced RPE degeneration by Alu RNA inhibition was not accompanied by restoration of microRNA deficits (Kaneko et al., 2011). Therefore, it was tested whether DICER1 also prevented NLRP3 inflammasome activation by Alu RNA. Alu RNA-induced Caspase-1 activation in human RPE cells was inhibited by DICER1 overexpression (FIGS. 6A and 6B). Conversely, Caspase-1 cleavage induced by DICER1 knockdown in human RPE cells was inhibited by simultaneous antisense knockdown of Alu RNA (FIGS. 12A and 12B).
[0210] Next the relevance of these pathways was tested in the context of DICER1 loss in vivo. Caspase-1 cleavage was increased in the RPE of BEST1 Cre; Dicer1f/f mice (FIG. 6C), which lose DICER1 expression in the RPE during development and exhibit RPE degeneration (Kaneko et al., 2011). Subretinal delivery of AAV1-BEST1-Cre in Dicer1f/f mice induced Caspase-1 activation and IL-18 maturation in the RPE (FIG. 6D). This treatment also induced RPE degeneration, which was blocked by intravitreous delivery of the Caspase-1-inhibitory peptide but not the control peptide (FIG. 6E). AAV1-BEST1-Cre-induced RPE degeneration in Dicer1f/f mice was also blocked by intravitreous delivery of the MyD88-inhibitory peptide but not a control peptide (FIG. 6F). In addition, MyD88 inhibition prevented cell death in human RPE cells treated with antisense oligonucleotides targeting DICER1 (FIG. 6G). DICER1 knockdown in human RPE cells increased IRAK1/4 phosphorylation, providing further evidence of MyD88 activation upon loss of DICER1 (FIG. 6H). MyD88 inhibition also prevented cell death in Dicer1f/f mouse RPE cells treated with an adenoviral vector coding for Cre recombinase (FIG. 6I). MyD88 inhibition blocked RPE cell death without restoring the microRNA expression deficits induced by Dicer1 knockdown (FIG. 6J). These findings demonstrate that DICER1 is an essential endogenous negative regulator of NLRP3 inflammasome activation, and that DICER1 deficiency leads to Alu RNA-mediated, MyD88-dependent, microRNA-independent RPE degeneration.
[0211] Inflammasome and MyD88 Activation in Human GA
[0212] Next it was tested whether human eyes with GA, which exhibit loss of DICER1 and accumulation of Alu RNA in their RPE (Kaneko et al., 2011), also display evidence of inflammasome activation. The abundance of NLRP3 mRNA in the RPE of human eyes with GA was markedly increased compared to control eyes (FIG. 7A). IL18 and IL1B mRNA abundance also was increased in GA RPE; however, only the disparity in IL18 levels reached statistical significance (FIG. 7A) Immunolocalization studies showed that the expression of NLRP3, PYCARD, and Caspase-1 proteins was also increased in GA RPE (FIGS. 7B-D). Western blot analyses corroborated the increased abundance of NLRP3 and PYCARD in GA RPE, and revealed greatly increased levels of the enzymatically active cleaved Caspase-1 p20 subunit in GA RPE (FIG. 7E). There was also an increase in the abundance of phosphorylated IRAK1 and IRAK4 in GA RPE, indicative of increased MyD88 signal transduction (FIG. 7E). Collectively, these data provide evidence of NLRP3 inflammasome and MyD88 activation in situ in human GA, mirroring the functional data in human RPE cell culture and mice in vivo.
[0213] Discussion
[0214] The data establish a functional role for the subversion of innate immune sensing pathways by Alu RNA in the pathogenesis of GA. Collectively, the findings demonstrate that the NLRP3 inflammasome senses GA-associated Alu RNA danger signals, contributes to RPE degeneration, and potentially vision loss in AMD (FIG. 13). To date, the function of the NLRP3 inflammasome has been largely restricted to immune cells in vivo. The finding that it plays a critical function in RPE cell survival broadens the cellular scope of this inflammasome and raises the possibility that other non-immune cells could employ this platform.
[0215] The NLRP3 inflammasome was originally recognized as a sensor of external danger signals such as microbial toxins (Kanneganti et al., 2006; Mariathasan et al., 2006; Muruve et al., 2008). Subsequently, endogenous crystals, polypeptides, and lipids were reported to activate it in diseases such as gout, atherogenesis, Alzheimer disease, and Type 2 diabetes (Halle et al., 2008; Masters et al., 2010; Muruve et al., 2008; Wen et al., 2011). To the knowledge, Alu RNA is the first endogenous nucleic acid known to activate this immune platform. The findings expand the diversity of endogenous danger signals in chronic human diseases, and comport with the concept that this inflammasome is a sensor of metabolic danger (Schroder et al., 2010).
[0216] Dampening inflammasome activation can be essential to limiting the inflammatory response. Pathogens have evolved many strategies to inhibit inflammasome activation (Martinon et al., 2009). Likewise, host autophagy proteins (Nakahira et al., 2011), Type I interferon (Guarda et al., 2011), and T cell contact with macrophages can inhibit this process (Guarda et al., 2009). The finding that DICER1, through its cleavage of Alu RNA, prevents activation of NLRP3 adds to the repertoire of host inflammasome modulation capabilities and reveals a new facet of how dysregulation of homeostatic anti-inflammatory mechanisms can promote AMD (Ambati et al., 2003; Takeda et al., 2009).
[0217] Added to its recently described anti-apoptotic and tumor-related functions, DICER1 emerges as a multifaceted protein. It remains to be determined how this functional versatility is channeled in various states. As DICER1 dysregulation is increasingly recognized in several human diseases, it is reasonable to imagine that Alu RNA might be an inflammasome activating danger signal in those conditions too. It is also interesting that, at least in adult mice and in a variety of mouse and human cells, the microRNA biogenesis function of DICER1 is not critical for cell survival, at least in a MyD88-deficient environment (data not shown).
[0218] The data that mitochondrial ROS production is involved in Alu RNA-induced RPE degeneration comport with observations of mitochondrial DNA damage (Lin et al., 2011), downregulation of proteins involved in mitochondrial energy production and trafficking (Nordgaard et al., 2008), and reduction in the number and size of mitochondria (Feher et al., 2006) in the RPE of human eyes with AMD. Jointly, these findings suggest a potential therapeutic benefit to interfering with mitochondrial ROS generation.
[0219] Current clinical programs targeting the inflammasome largely focus on IL-1β; presently there are no IL-18 inhibitors in registered clinical trials. However, the data indicate that IL-18 is more important than IL-1β in mediating RPE cell death in GA (similar to selective IL-18 involvement in a colitis model (Zaki et al., 2010)), pointing to the existence of regulatory mechanisms by which inflammasome activation bifurcates at the level of or just preceding the interleukin effectors. Although Caspase-1 inhibition could be an attractive local therapeutic strategy, caspase inhibitors can promote alternative cell death pathways, possibly limiting their utility (Vandenabeele et al., 2006).
[0220] MyD88 is best known for transducing TLR signaling initiated by pathogen associated molecular patterns (O'Neill and Bowie, 2007), although recently it has been implicated in human cancers (Ngo et al., 2011; Puente et al., 2011). The findings introduce an unexpected new function for MyD88 in effecting death signals from mobile element transcripts that can lead to retinal degeneration and blindness, and raise the possibility that MyD88 could be a central integrator of signals from other non-NLRP3 inflammasomes that also employ Caspase-1 (Schroder and Tschopp, 2010). Since non-canonical activation of MyD88 is a critical checkpoint in RPE degeneration in GA (FIG. 13), it represents an enticing therapeutic target. A potential concern is its important anti-microbial function in mice (O'Neill and Bowie, 2007). However, in contrast to Myd88−/− mice, adult humans with MyD88 deficiency are described to be generally healthy and resistant to a wide variety of microbial pathogens (von Bernuth et al., 2008). MyD88-deficient humans have a narrow susceptibility range to pyogenic bacterial infections, and that too only in early childhood and not adult life (Picard et al., 2010). Moreover, as evident from the siRNA and Myd88+/− studies, partial inhibition of MyD88 is sufficient to protect against Alu RNA. Localized intraocular therapy, the current standard of care in most retinal diseases, would further limit the likelihood of adverse infectious outcomes. It is reasonable to foresee development of MyD88 inhibitors for prevention or treatment of GA.
[0221] Experimental Procedures
[0222] Subretinal injection and imaging. Subretinal injections (1 μL) were performed using a Pico-Injector (PLI-100, Harvard Apparatus). Plasmids were transfected in vivo using 10% Neuroporter (Genlantis). Fundus imaging was performed on a TRC-50 IX camera (Topcon) linked to a digital imaging system (Sony). RPE flat mounts were immunolabeled using antibodies against zonula occludens-1 (Invitrogen).
[0223] mRNA Abundance.
[0224] Transcript abundance was quantified by real-time RT-PCR using an Applied Biosystems 7900 HT Fast Real-Time PCR system by the 2−ΔΔCt method.
[0225] Protein Abundance and Activity.
[0226] Protein abundance was assessed by Western blot analysis using antibodies against Caspase-1 (1:500; Invitrogen), pIRAK1 (1:500; Thermo Scientific), pIRAK4 (1:500, Abbomax), PYCARD (1:200, Santa Cruz Biotechnology), NLRP3 (1:500, Enzo Life Sciences) and Vinculin (1:1,000; Sigma-Aldrich). Caspase-1 activity was visualized using Caspalux1 E1D2 (Oncolmmunin) according to manufacturer's instructions.
[0227] Mice.
[0228] All animal experiments were approved by institutional review committees and in accordance with the Association for Research in Vision and Ophthalmology Statement for the Use of Animals in Ophthalmic and Visual Research. Wild-type C57BL/6J, Cybb−/−, Tlr3−1−, Tlr4−/− (C57BL/10ScNJ), Trif−/− (Ticam1Lps2), Ifng−/−, Ifngr1−/−, Il1r1−1−, Il18r1−1−, Myd88f/f, and Dicer1f/f mice were purchased from The Jackson Laboratory. Casp1−1−, Nbp3−/−, and Pycard−/− mice have been previously described (Kanneganti et al., 2006). Unc93b1 mutant mice were generously provided by B. A. Beutler via K. Fitzgerald. Myd88−/− and Tlr7−/− mice were generously provided by S. Akira via T. Hawn and D. T. Golenbock. Mda5−/− mice were generously provided by M. Colonna. mice were generously provided by B. R. Williams and R. L. Silverman. Mavs−/− mice were generously provided by Z. Chen via K. Fitzgerald. For all procedures, anesthesia was achieved by intraperitoneal injection of 100 mg/kg ketamine hydrochloride (Ft. Dodge Animal Health) and 10 mg/kg xylazine (Phoenix Scientific), and pupils were dilated with topical 1% tropicamide (Alcon Laboratories).
[0229] Fundus Photography.
[0230] Retinal photographs of dilated mouse eyes were taken with a TRC-50 IX camera (Topcon) linked to a digital imaging system (Sony).
[0231] Human Tissue.
[0232] Donor eyes or ocular tissues from patients with geographic atrophy due to AMD or age-matched patients without AMD were obtained from various eye banks. These diagnoses were confirmed by dilated ophthalmic examination prior to acquisition of the tissues or eyes or upon examination of the eye globes post mortem. The study followed the guidelines of the Declaration of Helsinki. Institutional review boards granted approval for allocation and histological analysis of specimens.
[0233] Immunolabeling.
[0234] Human eyes fixed in 2-4% paraformaldehyde were prepared as eyecups, cryoprotected in 30% sucrose, embedded in optimal cutting temperature compound (Tissue-Tek OCT; Sakura Finetek), and cryosectioned into 10 μm sections. Depigmentation was achieved using 0.25% potassium permanganate and 0.1% oxalic acid. Immunohistochemical staining was performed with the rabbit antibody against NLRP3 (1:100, Sigma Aldrich) or rabbit antibody against Caspase-1 (prediluted, AbCam). Isotype IgG was substituted for the primary antibody to assess the specificity of the staining. Bound antibody was detected with biotin-conjugated secondary antibodies, followed by incubation with ABC reagent and visualized by Vector Blue (Vector Laboratories). Levamisole (Vector Laboratories) was used to block endogenous alkaline phosphatase activity. Slides were washed in PBS, counterstained with neutral red (Fisher Scientific), rinsed with deionized water, air dried, and then mounted in Vectamount (Vector Laboratories). Fluorescent labeling of human tissue was performed with the rabbit antibody against PYCARD (1:50, Clone N-15, Santa Cruz Biotechnology) Immunolabeling was visualized by fluorescently conjugated anti-rabbit secondary antibody (Invitrogen). Tissue autofluorescence was quenched by incubating the sections in 0.3% Sudan black (Fisher Scientific). Sections were mounted in Vectashield with DAPI (Vector Laboratories). Mouse RPE/choroid flat mounts were fixed with 4% paraformaldehyde or 100% methanol, stained with rabbit antibodies against human zonula occludens-1 (1:100, Invitrogen) and visualized with Alexa594 (Invitrogen). All images were obtained using the Leica SP-5 or Zeiss Axio Observer Z1 microscopes.
[0235] Subretinal Injection.
[0236] Subretinal injections (1 μL) in mice were performed using a Pico-Injector (PLI-100, Harvard Apparatus). In vivo transfection of plasmids coding for two different Alu sequences (pAlu) or empty control vector (pNull) (Bennett et al., 2008; Kaneko et al., 2011; Shaikh et al., 1997) was achieved using 10% Neuroporter (Genlantis). AAV1-BEST1-Cre (Alexander and Hauswirth, 2008) or AAV1-BEST1-GFP were injected at 1.0×1011 pfu/mL and in vitro transcribed Alu RNA was injected at 0.3 mg/mL.
[0237] Drug Treatments.
[0238] siRNAs formulated in siRNA buffer (20 mM KCL, 0.2 mM MgCl2 in HEPES buffer at pH 7.5; Dharmacon) or phosphate buffered saline (PBS; Sigma-Aldrich); the TLR4 antagonist Ultra Pure Rhodobacter sphaeroides LPS (LPS-RS, InvivoGen), a peptide inhibitor of MyD88 homodimerization IMG-2005 (IMGENEX), control inhibitor (IMGENEX), recombinant IL-18 (Medical & Biological Laboratories), neutralizing rat antibodies against mouse IL-1β (IMGENEX), neutralizing rat antibodies against mouse IL-18 (Medical & Biological Laboratories), isotype control IgGs (R&D Systems or eBioscience as appropriate), Caspase-1 inhibitor Z-WEHD-FMK (R&D Systems), Caspase control inhibitor Z-FA-FMK (R&D Systems), DPI (Enzo Life Sciences), Mito-TEMPO (Enzo Life Sciences), MitoQ and dTPP (both adsorbed to cyclodextrin and provided by M.P. Murphy, MRC Mitochondrial Biology Unit), and gp91ds-tat and scrambled gp91 ds-tat (both Anaspec), were dissolved in phosphate buffered saline (PBS; Sigma-Aldrich) or dimethyl sulfoxide (DMSO; Sigma-Aldrich), and injected into the vitreous humor in a total volume of 1 μL with a 33-gauge Exmire microsyringe (Ito Corporation). To assess the effect of MyD88 blockade on pAlu-induced RPE degeneration, 1 μL of cholesterol (chol) conjugated MyD88 siRNA (17+2 nt; 2 μg/μL) was intravitreously injected 1 day after pAlu injection. As a control, Luc siRNA-chol (17+2 nt) was used with identical dosages.
[0239] Bone Marrow Chimeras.
[0240] Bone marrow transplantation was used to create Myd88−/− chimera mice wherein the genetic deficiency of Myd88 was confined to either circulating cells (Myd88−/− →WT) or nonhematopoietic tissue (WT→Myd88−/−). Briefly, bone marrows were collected from femur and tibia of congenic WT or Myd88−/− donor mice by flushing with RPMI1640. After two washing steps, cells were resuspended in RPMI1640. 1×107 cells in 150 μL of RPMI1640 were injected into the tail vein of irradiated donor mice. Two chimera groups were generated: WT→Myd88−/− (WT cells into Myd88−/− mice) and Myd88→WT (Myd88 cells into WT mice). 2 months after bone marrow transfer, mice were injected subretinally with Alu RNA, vehicle, pAlu, or pNull, and monitored for RPE degeneration 7 days later.
[0241] Real-Time PCR.
[0242] Total RNA was extracted from tissues or cells using Trizol reagent (Invitrogen) according to manufacturer's recommendations, DNase treated and reverse transcribed (QuantiTect, Qiagen). The RT products (cDNA) were amplified by real-time quantitative PCR (Applied Biosystems 7900 HT Fast Real-Time PCR system) with Power SYBR green Master Mix. Oligonucleotide primers specific for human IL1B (forward 5′-TTAAAGCCCGCCTGACAGA-3′ and reverse 5′-GCGAATGACAGAGGGTTTCTTAG-3′), human IL18 (forward 5′-ATCACTTGCACTCCGGAGGTA-3′ and reverse 5′-AGAGCGCAATGGTGCAATC-3′), human NLRP3 (forward 5′-GCACCTGTTGTGCAATCTGAA-3′ and reverse 5′-TCCTGACAACATGCTGATGTGA-3′), human PYCARD (forward 5′-GCCAGGCCTGCACTTTATAGA-3′ and reverse 5′-GTTTGTGACCCTCGCGATAAG-3′), human VDAC1 (forward 5′-ACTGCAAAATCCCGAGTGAC-3′ and reverse 5′-CTGTCCAGGCAAGATTGACA-3′), human VDAC2 (forward 5′-CAGTGCCAAATCAAAGCTGA-3′ and reverse 5′-CCTGATGTCCAAGCAAGGTT-3′), human VDAC3 (forward 5′-TTGACACAGCCAAATCCAAA-3′ and reverse 5′-GCCAAAACGGGTGTTGTTAC-3′), human 18S rRNA (forward 5′-CGCAGCTAGGAATAATGGAATAGG-3′ and reverse 5′-GCCTCAGTTCCGAAAACCAA-3′), mouse Myd88 (forward 5′-CACCTGTGTCTGGTCCATTG-3′ and reverse 5′-AGGCTGAGTGCAAACTTGGT-3′), mouse Nlrp3 (forward 5′-ATGCTGCTTCGACATCTCCT-3′ and reverse 5′-AACCAATGCGAGATCCTGAC-3′), mouse Il18 (forward 5′-GACAGCCTGTGTTCGAGGAT-3′ and reverse 5′-TGGATCCATTTCCTCAAAGG-3′), and mouse 18S rRNA (forward 5′-TTCGTATTGCGCCGCTAGA-3′ and reverse 5′-CTTTCGCTCTGGTCCGTCTT-3′) were used. The QPCR cycling conditions were 50° C. for 2 min, 95° C. for 10 min followed by 40 cycles of a two-step amplification program (95° C. for 15 s and 58° C. for 1 min). At the end of the amplification, melting curve analysis was applied using the dissociation protocol from the Sequence Detection system to exclude contamination with unspecific PCR products. The PCR products were also confirmed by agarose gel and showed only one specific band of the predicted size. For negative controls, no RT products were used as templates in the QPCR and verified by the absence of gel-detected bands. Relative expressions of target genes were determined by the 2−ΔΔCt method.
[0243] miRNA Quantification.
[0244] Total RNA containing miRNAs was polyadenylated and reverse transcribed using universal primer using the All-In-One miRNA q-RT-PCR Detection Kit (GeneCopoeia) according to the manufacturer's specifications using a universal reverse primer in combination with the following forward primers: mouse miR-184 (5′-TGGACGGAGAACTGATAAGGGT-3′); mouse miR-221/222 (5′-AGCTACATCTGGCTACTGGGT-3′); mouse miR-320a (5′-AAAAGCTGGGTTGAGAGGGCGA-3′), and mouse miR-484 (5′-TCAGGCTCAGTCCCCTCCCGAT-3′). miRNA levels were normalized to levels of U6 snRNA (5′-AAATTCGTGAAGCGTTCC-3′) using the 2−ΔΔCt method. Detection was achieved by SYBR green qPCR with the following conditions: 95° C. for 10 min followed by 40 cycles of 95° C. for 10 s, 60° C. for 20 s and 72° C. for 20 s. Amplicon specificity was assessed by melt curve analysis and unique bands by agarose gel electrophoresis.
[0245] Western Blotting.
[0246] Tissues or cells were homogenized in lysis buffer (10 mM Tris base, pH 7.4, 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 0.5% NP-40, protease and phosphatase inhibitor cocktail (Roche)). Protein concentrations were determined using a Bradford assay kit (Bio-Rad) with bovine serum albumin as a standard. Proteins (40-100 μg) were run on NuPAGE Bis-Tris gels (Invitrogen) and transferred to Immun-Blot PVDF membranes (Bio-Rad). Cells were scraped in hot Laemmli buffer (62.5 mM Tris base, pH 6.8, 2% SDS, 5% 2-Mercaptoethanol, 10% Glycerol, 0.01% Bromophenol Blue). Samples were boiled and run on 4-20% NuPAGE Tris-Glycine gels (Invitrogen). The transferred membranes were blocked for 1 h at RT and incubated with antibodies against human Caspase-1 (1:500; Invitrogen), mouse Caspase 1 (1:500; MBL), NLRP3 (1:1000; Enzo Life Sciences), PYCARD (1:1000, RayBiotech), phospho-IRAK1 (S376) (1:500, Thermo Scientific), phospho-IRAK4 (T345) (1:500, AbboMax), DICER1 (1:2,000; Bethyl), MyD88 (1:1,000; Cell Signaling), and mouse IL-18 (1:200; MBL) at 4° C. overnight. Protein loading was assessed by immunoblotting using an anti-Vinculin antibody (1:1,000; Sigma-Aldrich). The secondary antibodies were used (1:5,000) for 1 h at RT. The signal was visualized by enhanced chemiluminescence (ECL plus) and captured by VisionWorksLS Image Acquisition and Analysis software (Version 6.7.2, UVP, LLC).
[0247] Cell Culture.
[0248] All cell cultures were maintained at 37° C. and 5% CO2. Primary mouse RPE cells were isolated as previously described (Yang et al., 2009) and grown in Dulbecco Modified Eagle Medium (DMEM) supplemented with 20% FBS and standard antibiotics concentrations. Primary human RPE cells were isolated as previously described (Yang et al., 2008) and maintained in DMEM supplemented with 10% FBS and antibiotics. HeLa cells were maintained in DMEM supplemented with 20% FBS and standard antibiotics concentrations. THP-1 cells were cultured in RPMI 1640 medium supplemented with 10% FBS and antibiotics.
[0249] In vitro transcription of Alu RNAs. Two Alu RNAs were synthesized: a 281 nt Alu sequence originating from the cDNA clone TS 103 (Shaikh et al., 1997) and a 302 nt Alu sequence isolated from the RPE of a human eye with geographic atrophy. Linearized plasmids containing these Alu sequences with an adjacent 5′ T7 promoter were subjected to AmpliScribe™ T7-Flash™ Transcription Kit (Epicentre) according to the manufacturer's instructions. DNase-treated RNA was purified using MEGAclear™ (Ambion), and integrity was monitored by gel electrophoresis. This yields single stranded RNAs that fold into a defined secondary structure identical to Pol III derived transcripts. Where indicated, transcribed RNA was dephosphorylated using calf intestine alkaline phosphatase (Invitrogen) and repurified by Phenol:Chloroform:Isoamyl alcohol precipitation.
[0250] Transient Transfection.
[0251] Human or mouse RPE cells were transfected with pUC19, pAlu, pcDNA3.1/Dicer-FLAG, pcDNA3.1, Alu RNA, NLRP3 siRNA sense (5′-GUUUGACUAUCUGUUCUdTdT-3′), PYCARD siRNA sense (5′-GAAGCUCUUCAGUUUCAdTdT-3′), MyD88 siRNA sense (sense: 5′-CAGAGCAAGGAAUGUGAdTdT-3′), VDAC1 siRNA sense (5′-CGGAAUAGCAGCCAAGUdTdT-3′), VDAC2 siRNA sense (5′-CCCUGGAGUUGGAGGCUdTdT-3′), VDAC3 siRNA sense (5′-GCUUUAAUCGAUGGGAAdTdT-3′), DICER1 antisense oligonucleotide (AS) (5′-GCUGACCTTTTTGCTUCUCA-3′), control (for DICER1) AS (5′-TTGGTACGCATACGTGTTGACTGTGA-3′), Alu AS (5′-CCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCACGAGTAGCTGGGACTACAGGCGCCCGACACCACTCCCGGCTAATTTTTTGTATTTTT-3′), control (for Alu) AS (5′-GCATGGCCAGTCCATTGATCTTGCACGCTTGCCTAGTACGCTCCTCAACCTATCCTCCTAGCCCGTTACTTGGTGCCACCGGCG-3′) using Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions.
[0252] Adenoviral Infection.
[0253] Cells were plated at density of 15×103/cm2 and after 16 h, at approximately 50% confluence, were infected with AdCre or AdNull (Vector Laboratories) with a multiplicity of infection of 1,000.
[0254] Cell Viability.
[0255] MTS assays were performed using the CellTiter 96 AQueous One Solution Cell Proliferation Assay (Promega) according to the manufacturer's instructions. For examining the cytoprotective effect of glycine in Alu RNA induced cell death, human RPE cells were transfected with pNull/pAlu. At 6 h post-transfection the cells were incubated with complete media containing glycine (5 mM) or vehicle, and cell viability was assessed after 24 h. Similarly, human RPE cells primed with LPS (5 μg/ml for 6 h) were treated with ATP (25 μM) in the presence of glycine containing media (5 mM). 30 min post ATP cell viability was assessed as described above.
[0256] Caspase-1 activity. Caspase-1 activity was visualized by incubating cells with Caspalux1E1D2 reagent (Oncolmmunin) according to the manufacturer's instructions. Caspalux1E1D2 signal was quantified reading the fluorescence (excitation 552 nm, emission 580 nm) using a Synergy 4 reader (Biotek). Quantification of fluorescence from images was performed by converting images into grayscale in Adobe Photoshop CSS, and measuring the integrated density of black and white images using ImageJ software (NIH) (Bogdanovich et al., 2008).
[0257] ROS Production.
[0258] Cellular ROS production was assessed using the ROS-specific probe 2′7′-dichlorodihydrofluorescin diacetate (H2DCFDA, BioChemica, Fluka). Mitochondrial ROS production was assessed using MitoSOX™ Red (Invitrogen). Sub-confluent human RPE cells were transfected with pNull or pAlu. After 24 h cells were loaded for 10 min at 37° C. with 10 μM H2DCFDA or MitoSOX™ Red (Invitrogen) mitochondrial superoxide indicator for live-cell imaging and washed twice with PBS. For H2DCFDA, fluorescence was recorded in 96-well plate using with a Synergy 4 reader (Biotek) using a FITC filter (excitation 485 nm, emission 538 nm). To visualize respiring mitochondria for colocalization with the mitochondrial ROS signal, after PBS wash cells were incubated with MitoTracker Deep Red™ (Invitrogen) for 30 min at 37° C. and then washed twice with PBS. The fluorescent signals were detected using Leica SP-5 or Zeiss Axio Observer Z1 microscopes. Phagosomal ROS production was assessed using the Fc-OXYBURST Green™ assay (Invitrogen). Sub-confluent human RPE cells were transfected with pNull or pAlu, or treated with PMA (0.5 μg/ml; Sigma-Aldrich). The cells were incubated with Krebs-Ringer's PBS (KRP) at 37° C. for 20 min before adding Fc-OXYBURST Green™. The total fluorescence from the cells was measured immediately after adding Fc-OXYBURST Green™ with a Synergy 4 reader (Biotek) using FITC filter (excitation 485 nm, emission 538 nm).
[0259] RNA-Binding Protein Immunoprecipitation (RIP):
[0260] The physical interaction between NLRP3 and Alu RNA was examined using RNA ChIP-IT kit following the manufacturer's instructions (Active Motif). Briefly, human RPE cells were transfected with pAlu and pNLRP3-FLAG (provided by G. Núñez) and the protein-RNA complexes were immunoprecipitated with antibodies against NLRP3 (Enzo Life Sciences), FLAG (Sigma-Aldrich) or control IgG (Sigma-Aldrich). RNA isolated from these immunoprecipitates was analyzed by real-time RT-PCR using Alu-specific primers.
[0261] ELISA.
[0262] Secreted cytokine content in conditioned cell culture media was analyzed using the Human IL-1β and IL-18 ELISA Kits (R&D) according to the manufacturer's instructions.
[0263] TLR Screen.
[0264] A custom TLR ligand screen was performed by InvivoGen using HEK293 cells over-expressing individual TLR family members coupled with an AP-1/NF-κB reporter system. Cells were stimulated with each of two Alu RNAs synthesized by in vitro transcription, or a TLR-specific positive control ligand.
[0265] Statistics.
[0266] Results are expressed as mean±SEM, with p<0.05 considered statistically significant. Differences between groups were compared by using Mann-Whitney U test or Student t-test, as appropriate, and 2-tailed p values are reported.

Example 2

[0267] It was shown that both in vitro transcribed Alu RNA and a plasmid encoding Alu (pAlu) both induce RPE cell death by inducing IL-18 secretion, which triggers MyD88-dependent signaling that leads to Caspase-3 activation. Determine the intervening mechanistic steps in this cell death pathway were sought.
[0268] Caspase-8 is known to activate Caspase-3 (Stennicke et al. 1998). Therefore, it was tested whether Caspase-8 inhibition would inhibit RPE cell death or degeneration induced by Alu RNA or pAlu. It was found that the Caspase-8 inhibitory peptide Z-IETD-FMK, but not the control peptide Z-FA-FMK, blocked RPE degeneration induced by pAlu in wild-type mice (FIG. 14). Z-IETD-FMK also inhibited human RPE cell death induced by Alu RNA (FIG. 15) or pAlu (FIG. 16). It was also found that subretinal injection of recombinant IL-18 induced activation of Caspase-8, as monitored by a fluorometric assay, in the RPE of wild-type mice (FIG. 17). These data indicate that Alu RNA- or pAlu-induced IL-18 leads to Caspase-8 activation upstream of Caspase-3 activation.
[0269] MyD88 is known to bind Fas-associated death domain protein (FADD) and induce apoptosis via Caspase 8 (Aliprantis et al. 2000). Therefore, it was tested whether ablation of Fas (encoded by CD95) or FasL (encoded by Faslg) would inhibit RPE cell death or degeneration induced by Alu RNA, pAlu, or IL-18. It was found that neither pAlu (FIG. 18) nor Alu RNA (FIG. 19) induced RPE degeneration in CD95−/− (Faslpr) mice. In addition, recombinant IL-18 also did not induce RPE degeneration in CD95−/− (Faslpr) mice (FIG. 20). Likewise, pAlu (FIG. 21), Alu RNA (FIG. 22), and IL-18 (FIG. 23) did not induce RPE degeneration in Faslg−/− (Faslgld) mice.
[0270] It has been shown that Alu RNA induces RPE degeneration via the NLRP3 inflammasome. Because NF-κB activation is required for NLRP3 activation (Bauernfeind et al. 2009; Qiao et al. 2012), it was tested whether Alu RNA required NF-κB to induce RPE degeneration. Indeed, it was found that Alu RNA did not induce RPE degeneration in Nfkb1−/− mice, confirming that NF-κB activation is a critical step in this cell death pathway.
[0271] Experimental Procedures
[0272] Mice.
[0273] All animal experiments were approved by institutional review committees and in accordance with the Association for Research in Vision and Ophthalmology Statement for the Use of Animals in Ophthalmic and Visual Research. Wild-type C57BL/6J, Fas−/− (a.k.a CD95 or Faslpr) Faslg−/− (a.k.a. Fasgld) and Nfkb1−/− mice were purchased from The Jackson Laboratory. For all procedures, anesthesia was achieved by intraperitoneal injection of 100 mg/kg ketamine hydrochloride (Ft. Dodge Animal Health) and 10 mg/kg xylazine (Phoenix Scientific), and pupils were dilated with topical 1% tropicamide (Alcon Laboratories).
[0274] Fundus Photography.
[0275] Retinal photographs of dilated mouse eyes were taken with a TRC-50 IX camera (Topcon) linked to a digital imaging system (Sony).
[0276] Subretinal Injection.
[0277] Subretinal injections (1 μL) in mice were performed using a Pico-Injector (PLI-100, Harvard Apparatus). In vivo transfection of plasmids coding for two different Alu sequences (pAlu) or empty control vector (pNull) (Bennett et al., 2008; Kaneko et al., 2011; Shaikh et al., 1997) was achieved using 10% Neuroporter (Genlantis). In vitro transcribed Alu RNA was injected at 0.3 mg/mL.
[0278] Drug Treatments.
[0279] Recombinant IL-18 (Medical & Biological Laboratories), Caspase-8 inhibitor Z-IETD-FMK (R&D Systems), Caspase control inhibitor Z-FA-FMK (R&D Systems), IRAK1/4 inhibitor (Calbiochem), were dissolved in phosphate buffered saline (PBS; Sigma-Aldrich) or dimethyl sulfoxide (DMSO; Sigma-Aldrich), and injected into the vitreous humor in a total volume of 1 μL with a 33-gauge Exmire microsyringe (Ito Corporation).
[0280] Cell Culture.
[0281] All cell cultures were maintained at 37° C. and 5% CO2. Primary mouse RPE cells were isolated as previously described (Yang et al., 2009) and grown in Dulbecco Modified Eagle Medium (DMEM) supplemented with 20% FBS and standard antibiotics concentrations. Primary human RPE cells were isolated as previously described (Yang et al., 2008) and maintained in DMEM supplemented with 10% FBS and antibiotics. HeLa cells were maintained in DMEM supplemented with 20% FBS and standard antibiotics concentrations. THP-1 cells were cultured in RPMI 1640 medium supplemented with 10% FBS and antibiotics.
[0282] In Vitro Transcription of Alu RNAs.
[0283] We synthesized a 302 nt Alu sequence isolated from the RPE of a human eye with geographic atrophy. A linearized plasmid containing this Alu sequence with an adjacent 5′ T7 promoter were subjected to AmpliScribe™ T7-Flash™ Transcription Kit (Epicentre) according to the manufacturer's instructions. DNase-treated RNA was purified using MEGAclear™ (Ambion), and integrity was monitored by gel electrophoresis. This yields single stranded RNAs that fold into a defined secondary structure identical to Pol III derived transcripts. Where indicated, transcribed RNA was dephosphorylated using calf intestine alkaline phosphatase (Invitrogen) and repurified by Phenol:Chloroform:Isoamyl alcohol precipitation.
[0284] Transient Transfection.
[0285] Human RPE cells were transfected with pUC19, pAlu, Alu RNA, VDAC1 siRNA sense (5′-CGGAAUAGCAGCCAAGUdTdT-3′), VDAC2 siRNA sense (5′-CCCUGGAGUUGGAGGCUdTdT-3′), VDAC3 siRNA sense (5′-GCUUUAAUCGAUGGGAAdTdT-3′), using Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions.
[0286] Cell Viability.
[0287] MTS assays were performed using the CellTiter 96 AQueous One Solution Cell Proliferation Assay (Promega) according to the manufacturer's instructions.
[0288] Caspase-8 Activity.
[0289] RPE tissues were homogenized in lysis buffer (10 mM Tris base, pH 7.4, 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 0.5% NP-40, protease and phosphatase inhibitor cocktail (Roche)). Protein concentrations were determined using a Bradford assay kit (Bio-Rad) with bovine serum albumin as a standard. The caspase-3 activity was measured using Caspase-8 Fluorimetric Assay (R&D) in according to the manufacturer's instructions.
[0290] Statistics.
[0291] Results are expressed as mean±SEM, with p<0.05 considered statistically significant. Differences between groups were compared by using Mann-Whitney U test or Student t-test, as appropriate, and 2-tailed p values are reported.
[0292] Methods for Caspase Imaging
[0293] Alu RNA or recombinant IL-18 was injected into the subretinal space of wild-type mice on day 0. DyeLight782-VAD-FMK3 (ThermoScientific), a probe that fluoresces in the presence of bioactive caspases, was injected into the vitreous humor of wild-type mice on day 2 or day 3 after injection.
[0294] Flat Mount Imaging.
[0295] At 24 hours after injection of DyeLight782-VAD-FMK3, the eyecup was dissected out of mice, the neural retina was removed, and a flat mount of the RPE was prepared, and viewed under a fluorescent microscope.
[0296] In Vivo Bioimaging in the Living Eye.
[0297] At intervals from 0-24 hours after injection of DyeLight782-VAD-FMK3, fundus photographs were taken with the Topcon 50IX camera using the ICG filter.
[0298] Throughout this document, various references are mentioned. All such references are incorporated herein by reference to the same extent as if each individual reference was specifically and individually indicated to be incorporated by reference, including the references set forth in the following list:

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[0504] It will be understood that various details of the presently disclosed subject matter can be changed without departing from the scope of the subject matter disclosed herein. Furthermore, the foregoing description is for the purpose of illustration only, and not for the purpose of limitation.
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Claims

1. A method of protecting an retinal pigment epithelium (RPE) cell, a retinal photoreceptor cell, or a choroidal cell, comprising:
inhibiting one or more of an inflammasome of the cell; MyD88 of the cell; IL-18 of the cell; VDAC1 of the cell; VDAC2 of the cell; caspase-8 of the cell; and NFκB of the cell;
wherein the cell is protected against Alu-RNA-induced degeneration;
wherein inhibiting the inflammasome consists essentially of administering an inflammasome inhibitor selected from the group consisting of an NLRP3 inhibitor, a PYCARD inhibitor, an inflammosome inhibitor comprising a sequence selected from the sequences of SEQ ID NOS: 7-16, an inhibitor of Caspase-1, a peptide inhibitor of Caspase-1, a Caspase-1 inhibitor comprising the sequence of SEQ ID NO: 17, and the inflammosome inhibitors selected from: ion channel inhibitors; IkB-α inhibitors; antibodies selected from: Anti-ASC, Anti-NALP1, antibodies based on protein sequences selected from: ASC: ALR QTQ PYL VTD LEQ S; NALP1: MEE SQS KEE SNT EG-cys; Anti-NALP1, anti-IL-1β, anti-IL-18, anti-caspase-1, and anti-caspase-11; direct inhibitors of Caspase-1 and/or NLRP3; parthenolide; estrogen binding B-box proteins, COP, ICEBERG, and Z-WEHD-FMK; Caspase 1 and/or 4 inhibitors; Caspase-12 inhibitors; host-derived inhibitors of caspase-1; inhibitors of Nlrp1b inflammasome; virus expressed inhibitors of the inflammasome; potassium chloride; Cathepsin-B-inhibitors; Cytochalsin D; ROS inhibitors; ASC-1 inhibitors; NLRP3 inflammasome pan-caspase inhibitors; Microtubules; an isolated double-stranded RNA molecule that inhibits expression of NLRP3, and which can be conjugated to cholesterol or not, and at least one strand including the sequence: GUUUGACUAUCUGUUCUdTdT (SEQ ID NO: 7); an isolated double-stranded RNA molecule that inhibits expression of PYCARD, at least one strand of which includes the sequence of: 5′-GAAGCUCUUCAGUUUCAdTdT-3′ (SEQ ID NO: 12); and an isolated double-stranded RNA molecule that inhibits expression of PYCARD, at least one strand of which includes a sequence selected from: 5′-GAAGCUCUUCAGUUUCAdTdT-3′ (SEQ ID NO: 12); 5′-GGCUGCUGGAUGCUCUGUACGGGAA-3′ (SEQ ID NO: 13); and 5′-UUCCCGUACAGAGCAUCCAGCAGCC-3′ (SEQ ID NO: 14).
2. The method of claim 1, wherein the inhibiting MyD88 comprises administering a MyD88 inhibitor.
3. The method of claim 2, wherein the inhibitor is selected from the group consisting of a MyD88 inhibitor comprising a polypeptide sequence selected from the sequences of SEQ ID NO: 1, 54, 55, 60, and 61; and a MyD88 inhibitor comprising a double-stranded RNA molecule, at least one strand of which includes a sequence selected from SEQ ID NOS: 3, 4, 5, 6, and 56.
4. The method of claim 2, wherein the My D88 inhibitor is selected from the group consisting of a MyD88 homodimerization inhibitor; Pepinh-MYD; a dominant negative or splice variant of MyD88; a MyD88 splice variants that lack exon 2; and MyD88 inhibitors as set forth in Table C.
5. The method of claim 4, wherein the inhibitor is administered by intravitreous injection; subretinal injection; episcleral injection; sub-Tenon's injection; retrobulbar injection; peribulbar injection; topical eye drop application; release from a sustained release implant device that is sutured to or attached to or placed on the sclera, or injected into the vitreous humor, or injected into the anterior chamber, or implanted in the lens bag or capsule; oral administration; or intravenous administration.
6. A method of protecting an RPE cell, a retinal photoreceptor cell, or a choroidal cell, comprising:
inhibiting one or more of an inflammasome of the cell; MyD88 of the cell; IL-18 of the cell; VDAC1 of the cell; VDAC2 of the cell; caspase-8 of the cell; and NFκB of the cell;
wherein the cell is protected against Alu-RNA-induced degeneration;
wherein inhibiting the inflammasome comprises administering an inflammasome inhibitor selected from the group consisting of an NLRP3 inhibitor, a PYCARD inhibitor, an inflammosome inhibitor comprising a sequence selected from the sequences of SEQ ID NOS: 7-16, an inhibitor of Caspase-1, a peptide inhibitor of Caspase-1, a Caspase-1 inhibitor comprising the sequence of SEQ ID NO: 17, and the inflammosome inhibitors selected from: ion channel inhibitors; IkB-α inhibitors; antibodies selected from: Anti-ASC, Anti-NALP1, antibodies based on protein sequences selected from: ASC: ALR QTQ PYL VTD LEQ S; NALP1: MEE SQS KEE SNT EG-cys; Anti-NALP1, anti-IL-1β, anti-IL-18, anti-caspase-1, and anti-caspase-11; direct inhibitors of Caspase-1 and/or NLRP3; parthenolide; estrogen binding B-box proteins, COP, ICEBERG, and Z-WEHD-FMK; Caspase 1 and/or 4 inhibitors; Caspase-12 inhibitors; host-derived inhibitors of caspase-1; inhibitors of Nlrp1b inflammasome; virus expressed inhibitors of the inflammasome; potassium chloride; Cathepsin-B-inhibitors; Cytochalsin D; ROS inhibitors; ASC-1 inhibitors; NLRP3 inflammasome pan-caspase inhibitors; Microtubules; an isolated double-stranded RNA molecule that inhibits expression of NLRP3, and which can be conjugated to cholesterol or not, and at least one strand including the sequence: GUUUGACUAUCUGUUCUdTdT (SEQ ID NO: 7); an isolated double-stranded RNA molecule that inhibits expression of PYCARD, at least one strand of which includes the sequence of: 5′-GAAGCUCUUCAGUUUCAdTdT-3′ (SEQ ID NO: 12); and an isolated double-stranded RNA molecule that inhibits expression of PYCARD, at least one strand of which includes a sequence selected from: 5′-GAAGCUCUUCAGUUUCAdTdT-3′ (SEQ ID NO: 12); 5′-GGCUGCUGGAUGCUCUGUACGGGAA-3′ (SEQ ID NO: 13); and 5′-UUCCCGUACAGAGCAUCCAGCAGCC-3′ (SEQ ID NO: 14), wherein the inflammasome includes a protein encoded by PYCARD.
7. The method of claim 6, wherein the inflammasome is selected from NLRP3 inflammasome, NLRP1 inflammasome, NLRC4 inflammasome, AIM2 inflammasome, and IFI16 inflammasome.
8. The method of claim 7, wherein the inflammasome is the NLRP3 inflammasome.
9. The method of claim 1, wherein the inflammasome inhibitor is selected from glybenclamide/glyburide; BAY11-7082 (CAS Number: 195462-67-7; also known as (E)-3-(4-Methylphenylsulfonyl)-2-propenenitrile); Anti-ASC and Anti-NALP1 and antibodies based on protein sequences selected from: ASC: ALR QTQ PYL VTD LEQ S; NALP1: MEE SQS KEE SNT EG-cys; Anti-NALP1, anti-IL-1β, anti-IL-18, anti-caspase-1, and anti-caspase-11; parthenolide; estrogen binding B-box proteins, COP, ICEBERG, and Z-WEHD-FMK; Ac-Tyr-Val-Ala-Asp-CHO (Ac-YVAD-CHO) or N-acetyl-L-tyrosyl-L-valyl-N-[(1S)-1-(carboxymethyl)-3-chloro-2-oxo-propyl]-L-alaninamide (Ac-YVAD-CMK); Caspase-12 inhibitors; cellular PYRIN domain (PYD)-ony proteins (POP) family: cPOP1 and cPOP2; serpin proteinase inhibitor 9 (PI-9); BCL-2 and BCL-xL; auranofin; PYD homologs M13L-PYD, S013L, SPI-2 homologs CrmA, Serp2, SPI-2, NS1, Kaposi Sarcoma-associated Herpesvirus Orf63; potassium chloride; L-3-trans-(Propylcarbamoyl)oxirane-2-Carbonyl)-L-Isoleucyl-L-Proline Methyl Ester (“CA-074 Me”); Cytochalsin D; N-acetyl-L-cysteine (NAC), (2R,4R)-4-aminopyrrolidine-2,4-dicarboxylate (APDC); cellular pyrin domain (PYD) superfamily proteins, also known as M013; Z-VAD-FMK; colchicine; an isolated double-stranded RNA molecule that inhibits expression of NLRP3, and which can be conjugated to cholesterol or not, and at least one strand including the sequence: GUUUGACUAUCUGUUCUdTdT (SEQ ID NO: 7); an isolated double-stranded RNA molecule that inhibits expression of PYCARD, at least one strand of which includes the sequence of: 5′-GAAGCUCUUCAGUUUCAdTdT-3′ (SEQ ID NO: 12); and an isolated double-stranded RNA molecule that inhibits expression of PYCARD, at least one strand of which includes a sequence selected from: 5′-GAAGCUCUUCAGUUUCAdTdT-3′ (SEQ ID NO: 12); 5′-GGCUGCUGGAUGCUCUGUACGGGAA-3′ (SEQ ID NO: 13); and 5′-UUCCCGUACAGAGCAUCCAGCAGCC-3′ (SEQ ID NO: 14).
10. The method of claim 1, wherein the inflammasome inhibitor is selected from the group consisting of an inflammosome inhibitor comprising a sequence selected from the sequences of SEQ ID NOS: 7-16; an inhibitor of Caspase-1 selected from VX-765, ML132, VX-740, VRT-018858, YVAD, WEHD; and a Caspase-1 inhibitor comprising the sequence of SEQ ID NO: 17.
11. The method of claim 9, wherein the inhibitor is administered by intravitreous injection; subretinal injection; episcleral injection; sub-Tenon's injection; retrobulbar injection; peribulbar injection; topical eye drop application; release from a sustained release implant device that is sutured to or attached to or placed on the sclera, or injected into the vitreous humor, or injected into the anterior chamber, or implanted in the lens bag or capsule; oral administration; or intravenous administration.
12. The method of claim 1, wherein the inhibiting IL-18 comprises administering an IL-18 inhibitor.
13. The method of claim 12, wherein the IL-18 inhibitor is selected from the group consisting of a neutralizing antibody against IL-18; an antibody that blocks IL-18 binding to the IL-18 receptor, IL-18 neutralizing antibodies; IL-18 binding protein; and IL18BP.
14. The method of claim 13, wherein the inhibitor is administered by intravitreous injection; subretinal injection; episcleral injection; sub-Tenon's injection; retrobulbar injection; peribulbar injection; topical eye drop application; release from a sustained release implant device that is sutured to or attached to or placed on the sclera, or injected into the vitreous humor, or injected into the anterior chamber, or implanted in the lens bag or capsule; oral administration; or intravenous administration.
15. The method of claim 1, wherein the inhibiting VDAC1 comprises administering a VDAC1 inhibitor and inhibiting VDAC2 comprises administering a VDAC2 inhibitor.
16. The method of claim 15, wherein the VDAC1 inhibitor is selected from the group consisting of a VDAC1 inhibitor comprising the sequence of SEQ ID NO: 47; a VDAC2 inhibitor comprising the sequence of SEQ ID NO: 48; phosphorothioate oligonucleotide randomer (Trilink Industries) that inhibits VDAC; cyclosporin A; superoxide dismutase 1; 4,4′-diisothiocyanatostilbene-2,2′-disulfonic acid (DIDS); Bcl-x(L) BH4(4-23); and TRO19622.
17. The method of claim 15, wherein the inhibitor is administered by intravitreous injection; subretinal injection; episcleral injection; sub-Tenon's injection; retrobulbar injection; peribulbar injection; topical eye drop application; release from a sustained release implant device that is sutured to or attached to or placed on the sclera, or injected into the vitreous humor, or injected into the anterior chamber, or implanted in the lens bag or capsule; oral administration; or intravenous administration.
18. The method of claim 1, wherein the inhibiting Caspase-8 comprises administering a Caspase-8 inhibitor.
19. The method of claim 18, wherein the Caspase-8 inhibitor is selected from the group consisting of Z-IETD-FMK, Ac-Ala-Ala-Val-Ala-Leu-Leu-Pro-Ala-Val-Leu-Leu-Ala-Leu-Leu-Ala-Pro-Ile-Glu-Thr-Asp-CHO, Z-Ile-Glu(OMe)-Thr-Asp(OMe)-CH2F, and Cellular fas-associated death domain-like interleukin-1-β-converting enzyme-inhibitory protein (L).
20. The method of any one of claim 18, wherein the inhibitor is administered by intravitreous injection; subretinal injection; episcleral injection; sub-Tenon's injection; retrobulbar injection; peribulbar injection; topical eye drop application; release from a sustained release implant device that is sutured to or attached to or placed on the sclera, or injected into the vitreous humor, or injected into the anterior chamber, or implanted in the lens bag or capsule; oral administration; or intravenous administration.
21. The method of claim 1, wherein the inhibiting NFkB comprises administering a NFkB inhibitor.
22. The method of claim 21, wherein the inhibitor is administered by intravitreous injection; subretinal injection; episcleral injection; sub-Tenon's injection; retrobulbar injection; peribulbar injection; topical eye drop application; release from a sustained release implant device that is sutured to or attached to or placed on the sclera, or injected into the vitreous humor, or injected into the anterior chamber, or implanted in the lens bag or capsule; oral administration; or intravenous administration.
23. The method of claim 1, wherein the cell is in a subject.
24. The method of claim 23, wherein the subject has age-related macular degeneration.
25. An molecule selected from the group consisting of:
an isolated double-stranded RNA molecule that inhibits expression of MyD88, wherein a first strand of the double-stranded RNA comprises a sequence selected from SEQ ID NO: 3, 4, 5, 6, and 56, and including about 11 to 27 nucleotides;
an isolated double-stranded RNA molecule that inhibits expression of NLRP3 and/or PYCARD, wherein a first strand of the double-stranded RNA comprises a sequence selected from SEQ ID NO: 7-14, and including about 11 to 27 nucleotides;
an isolated double-stranded RNA molecule that inhibits expression of Pyrin, comprising the sequence of SEQ ID NO: 15, and including about 11 to 27 nucleotides;
an isolated double-stranded RNA molecule that inhibits expression of NALP3, comprising the sequence of SEQ ID NO: 16, and including about 11 to 27 nucleotides;
an isolated double-stranded RNA molecule that inhibits expression of caspase-1, comprising the sequence of SEQ ID NO: 17, and including about 11 to 27 nucleotides;
an isolated double-stranded RNA molecule that inhibits expression of VDAC1 and/or VDAC2, wherein a first strand of the double-stranded RNA comprises a sequence selected from SEQ ID NO: 47 and 48, and including about 11 to 27 nucleotides;
a polypeptide molecule that inhibits MyD88, comprising a sequence selected from SEQ ID NO: 60 and SEQ ID NO: 61.
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