Compounds For Inducing Anti-tumor Immunity And Methods Thereof

  *US09957506B2*
  US009957506B2                                 
(12)United States Patent(10)Patent No.: US 9,957,506 B2
  et al. (45) Date of Patent:May  1, 2018

(54)Compounds for inducing anti-tumor immunity and methods thereof 
    
(75)Inventor: Cornell University,  Ithaca, NY (US) 
(73)Assignee:Cornell University,  Ithaca, NY (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. 
(21)Appl. No.: 15/024,215 
(22)PCT Filed:Sep.  25, 2014 
(86)PCT No.: PCT/US2014/057525 
 § 371 (c)(1), (2), (4) Date: Sep.  25, 2014 
(87)PCT Pub. No.:WO20/15/048331 
 PCT Pub. Date:Apr.  2, 2015 
(65)Prior Publication Data 
 US 2016/0237429 A1 Aug.  18, 2016 
 Related U.S. Patent Documents 
(60)Provisional application No. 61/882,461, filed on Sep.  25, 2013.
 
Jan.  1, 2013 C 12 N 15 113 F I May  1, 2018 US B H C Jan.  1, 2013 A 61 K 31 713 L I May  1, 2018 US B H C Jan.  1, 2013 A 61 K 45 06 L I May  1, 2018 US B H C Jan.  1, 2013 C 12 N 15 1137 L I May  1, 2018 US B H C Jan.  1, 2013 C 12 Y 207 11 L I May  1, 2018 US B H C Jan.  1, 2013 C 12 N 2310 11 L A May  1, 2018 US B H C Jan.  1, 2013 C 12 N 2310 14 L A May  1, 2018 US B H C Jan.  1, 2013 C 12 N 2320 31 L A May  1, 2018 US B H C
(51)Int. Cl. A61K 048/00 (20060101); C12N 015/113 (20100101); A61K 031/713 (20060101); A61K 045/06 (20060101)

 
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     * cited by examiner
 
     Primary Examiner —Kimberly Chong
     Art Unit — 1674
     Exemplary claim number — 1
 
(74)Attorney, Agent, or Firm — Schwegman Lundberg & Woessner, P.A.

(57)

Abstract

Described herein is a previously unknown function of XBP1 in controlling anti-tumor immunity. It is shown that inhibiting XBP1 in tumor-associated dendritic cells inhibits tumor growth and induces protective anti-tumor immune responses.
10 Claims, 36 Drawing Sheets, and 15 Figures


RELATED APPLICATIONS

[0001] This application is a 35 U.S.C. § 371 national stage filing of PCT Application No. PCT/US2014/057525 filed on Sep. 25, 2014, which claims priority to, and the benefit of U.S. Provisional Patent Application Ser. No. 61/882,461, filed Sep. 25, 2013. The entire content of the above-referenced patent applications is incorporated herein by this reference.

FEDERALLY SPONSORED RESEARCH

[0002] This invention was made with U.S. Government support under Grant No. RO1 AI089967 awarded by the National Institutes of Health. The U.S. government has certain rights in this invention.

STATEMENT REGARDING SEQUENCE LISTING

[0003] The instant application contains a Sequence Listing which has been submitted in computer readable form (CRF) via EFS-Web and is hereby incorporated by reference in its entirety. Said CRF, created on Mar. 23, 2016, is named CUY_014US_Sequence_Listing.txt and is 10900 Kilobytes in size. The Sequence Listing is being submitted by EFS Web and is hereby incorporated by reference into the specification.

BACKGROUND OF THE INVENTION

[0004] The Endoplasmic Reticulum (ER) functions primarily to process newly synthesized secretory and transmembrane proteins. However, abnormal accumulation of unfolded proteins in this compartment causes a state of “ER stress”, which is a hallmark feature of secretory cells and many diseases, including diabetes, neurodegeneration and cancer (Hetz et al., Nature Reviews Drug Discover 2013: 12, 703-719). Adaptation to protein-folding stress is mediated by the activation of an integrated signal transduction pathway known as the ER stress response, or the unfolded protein response (UPR). This coordinated pathway signals through three distinct stress sensors located at the ER membrane: IRE-1α, ATF6, and PERK (Hetz et al., Nature Reviews Drug Discover 2013; 12, 703-719). The most conserved arm of the UPR involves IRE-1α. During ER stress, this kinase oligomerizes, autophosphorylates, and uses its endoribonuclease activity to excise a 26-nucleotide fragment from the unspliced XBP1 mRNA (Yoshida et al., Cell 2001; 107; 881-891). These events give rise to functional XBP1, a potent multitasking transcription factor that promotes the expression of ER chaperones and regulates distinct sets of target genes in a cell type-specific manner (Acosta-Alvear et al., Mol Cell 2007; 27, 53-66; Lee et al., Mol Cell Biol 2003; 23, 7448-7459; Yoshida et al., Cell 2001; 107; 881-891). Importantly, while XBP1 has been shown to control the maintenance of various immune cells under non-pathological conditions, a role for this transcription factor as a negative regulator of anti-tumor responses and normal immune function in cancer has never been reported.
[0005] Aggressive tumors have evolved strategies to thrive in adverse conditions such as hypoxia, nutrient starvation and high metabolic demand. Cancer cells constantly undergo ER stress, but they ensure survival by adjusting the ER protein folding capacity via the UPR (Hetz et al., Nature Reviews Drug Discover 2013; 12, 703-719). In malignant cells, XBP1 confers drug resistance by preventing drug-induced cell-cycle arrest and mitochondrial permeability and apoptosis (Gomez et al., FASEB J 2007; 21, 4013-4027). XBP1 drives the pathogenesis of multiple myeloma (Carrasco et al., Cancer Cell 2007; 11, 349-360; Lee et al., Proc Natl Acad Sci USA 2003; 100, 9446-9951) and of chronic lymphocytic leukemia (Sriburi et al., J Cell Biol 2004; 167, 35-41). Further, it was recently demonstrated that XBP1 fosters triple-negative breast cancer progression by promoting tumor cell survival and metastatic capacity under hypoxic conditions (Chen et al., Nature 2014; 508, 103-107). While XBP1 expression in cancer cells has been shown to directly support tumorigenesis, the role of this ER stress sensor in sculpting a tumor-permissive immune milieu has not been established.
[0006] In most solid cancers, nonmalignant cells such as leukocytes, vascular cells and fibroblasts, stimulate tumor development and progression (Bhowmick et al., Nature 2004; 432, 332-337; Whiteside, Oncogene 2008; 27, 5904-5912). Leukocyte recruitment to established cancers results in diverse pro-tumoral effects including the secretion of growth factors that enhance tumor cell proliferation and metastasis (Coussens et al., Cell 2000; 103, 481-490; Coussens and Werb, Nature 2002; 420, 860-867; Mantovani et al., Nature 2008; 454, 436-444); the induction of tumor vascularization via paracrine mechanisms (De Palma et al., Trends Immunol 2007; 28, 519-524); and the orchestration of immunosuppressive networks (Zou, Nat Rev Cancer 2005; 5, 263-274) that restrain the protective role of the scarce leukocyte subsets with inherent anti-tumor capacity. Ovarian tumors subvert the normal activity of infiltrating dendritic cells (DCs) to inhibit the function of otherwise protective anti-tumor T cells (Cubillos-Ruiz et al., J Clin Invest 2009; 119, 2231-2244; Curiel et al., Nat Med 2003; 9, 562-567; Huarte et al., Cancer Res 2008; 68, 7684-7691; Scarlett et al., Cancer Res 2009; 69, 7329-7337; Scarlett et al., J Exp Med 2012). Eliminating or “re-programming” tumor-associated DCs (tDCs) in vivo has been demonstrated to abrogate ovarian cancer progression (Cubillos-Ruiz et al., J Clin Invest 2009; 119, 2231-2244; Curiel et al., Nat Med 2003; 9, 562-567; Huarte et al., Cancer Res 2008; 68, 7684-7691; Nesbeth et al., Cancer Res 2009; 69, 6331-6338; Nesbeth et al., J Immunol 2010; 184, 5654-5662; Scarlett et al., Cancer Res 2009; 69, 7329-7337; Scarlett et al., J Exp Med 2012), but the precise molecular pathways that tumors exploit in DCs to co-opt their normal activity remain poorly understood, and therefore available therapeutics are limited.

SUMMARY OF THE INVENTION

[0007] Dendritic cells (DCs) are required to initiate and sustain anti-cancer immunity. However, tumors efficiently manipulate DC function to evade immune control. The Endoplasmic Reticulum (ER) stress response has been shown to operate in malignant cells to support tumor growth, but prior to the discovery of the present invention, its role in sculpting the immune response to cancer was elusive. The present invention is based, at least in part, on the new finding that constitutive activation of the ER stress sensor XBP1 in tumor-associated DCs (tDCs) drives ovarian cancer progression. Here, it is reported that, XBP1-deficient tDCs showed reduced intracellular lipid accumulation and demonstrated improved antigen-presenting capacity, leading to enhanced intra-tumoral T cell activation and increased host survival. The present invention is also based, at least in part, on the new finding that therapeutic XBP1 silencing using siRNA-loaded nanoparticles restored proper tDC function in situ and extended host survival by inducing protective anti-tumor immunity. In particular, the instant inventors have discovered that tumors rely on DC-intrinsic XBP1 to elude immune control. These findings, for the first time, reveal a key function for XBP1 in anti-tumor immunity, opening new avenues for therapeutics that target the ER stress response. Such therapeutics could potentially inhibit tumor growth directly while simultaneously inducing robust anti-tumor immunity.
[0008] In one embodiment, the present invention pertains to the unexpected discovery that the ER stress sensor, XBP1 functions as a crucial driver of DC dysfunction in the tumor microenvironment. In another embodiment, the present invention provides that the ER stress sensor XBP1 is constitutively active in ovarian cancer associated dendritic cells (DCs). In another embodiment, the present invention provides that the lipid peroxidation byproduct 4-HNE triggers ER stress and XBP1 activation in DCs. In another embodiment, the present invention provides that XBP1 regulates lipid metabolism and antigen presentation by tumor-associated DCs. In other embodiments, the invention provides that targeting XBP1 in tumor-associated DCs (tDCs) extends host survival by enhancing anti-tumor immunity.
[0009] Accordingly, in one aspect, the invention pertains to a method for enhancing or inducing an anti-tumor immune response in a subject, including administering to the subject an effective amount of a direct or indirect inhibitor of XBP1, thereby enhancing or inducing the anti-tumor immune response in the subject.
[0010] In another aspect, the invention pertains to a method for treating or reducing the progression of ovarian cancer in a subject, including administering to the subject an effective amount of a direct or indirect inhibitor of XBP1, thereby treating or reducing the progression of ovarian cancer in the subject.
[0011] In another aspect, the invention pertains to a method for inducing, enhancing or promoting the immune response of cancer-associated dendritic cells in a subject including administering to the subject an effective amount of a direct or indirect inhibitor of XBP1, thereby inducing, enhancing or promoting the immune response of cancer-associated dendritic cells in the subject.
[0012] In one embodiment, the subject has ovarian cancer. In another embodiment, the subject has primary ovarian cancer or metastatic ovarian cancer. In another embodiment, the subject has a carcinoma, an adenocarcinoma, an epithelial cancer, a germ cell cancer or a stromal tumor.
[0013] In another embodiment, the anti-tumor immune response is induced or enhanced in T cells in the subject. For example, intra-tumoral T cells may be activated in the subject. In certain embodiments, the anti-tumor immune response may be antigen presentation by T cells. In other embodiments, the anti-tumor immune response may be an immunogenic function.
[0014] In one embodiment, the inhibitor of XBP1 is a direct inhibitor. In another embodiment, the inhibitor of XBP1 is an indirect inhibitor.
[0015] For example, the inhibitor of XBP1 may be a nucleic acid molecule that is antisense to an XBP1-encoding nucleic acid molecule, an XBP1 shRNA, and XBP1 siRNA, a microRNA that targets XBP1, a nanoparticle-encapsulated XBP1 siRNA, an XBP1 siRNA-PEI nanoparticle, a dominant negative XBP1 molecule, an XBP1-specific antibody or a small molecule inhibitor of XBP1.
[0016] In certain embodiments, the inhibitor of XBP1 is an agent that inhibits IRE-1α or an agent that inhibits the generation of functional XBP1. For example, the inhibitor of IRE-1α may be an IRE-1α shRNA, an IRE-1αsiRNA, or a nanoparticle-encapsulated IRE-1α siRNA. For example, an agent that inhibits the generation of functional XBP1 may be an agent that inhibits an endonuclease that produces functional XBP1.
[0017] In one embodiment, the inhibitor of XBP1 is administered systemically, parenterally, or at tumor locations in the subject. For example, the inhibitor of XBP1 may be administered at the site of the ovarian cancer or ovarian tumor.
[0018] In another embodiment, the inhibitor of XBP1 targets tumor-associated dendritic cells (tDCs)
[0019] In certain embodiments, the inhibitor of XBP1 is administered in combination with a second cancer therapeutic agent. For example, the inhibitor of XBP1 may be administered in combination with a chemotherapeutic agent.
[0020] In another embodiment, treatment of the subject with a direct or indirect inhibitor of XBP1 induces extended survival of the subject.
[0021] In another aspect, the invention pertains to a method for enhancing or inducing an anti-tumor immune response in a subject including administering to the subject an effective amount of a direct or indirect inhibitor of IRE-1α, thereby enhancing or inducing the anti-tumor response in the subject.
[0022] In one embodiment, the subject has ovarian cancer. In another embodiment, the subject has a carcinoma, an adenocarcinoma, an epithelial cancer, a germ cell cancer or a stromal tumor.
[0023] In another embodiment, the anti-tumor immune response is induced or enhanced in T cells in the subject. For example, intra-tumoral T cells may be activated in the subject.
[0024] In one embodiment, the inhibitor of IRE-1α is a direct inhibitor. In another embodiment, the inhibitor of IRE-1α is an indirect inhibitor.
[0025] For example, the inhibitor of IRE-1α may be a nucleic acid molecule that is antisense to an IRE-1α-encoding nucleic acid molecule, an IRE-1α shRNA, and IR-E1α siRNA, a microRNA that targets IRE-1α, a nanoparticle-encapsulated IRE-1α siRNA, an IRE-1α siRNA-PEI nanoparticle, a dominant negative IRE-1α molecule, an IRE-1α-specific antibody and a small molecule inhibitor of IRE-1α.
[0026] In one embodiment, the inhibitor of IRE-1α is administered systemically, parenterally, or at tumor locations in the subject. For example, the inhibitor of IRE-1α may be administered at the site of the ovarian cancer or ovarian tumor.
[0027] In another embodiment, the inhibitor of IRE-1α targets tumor-associated dendritic cells (tDCs)
[0028] In certain embodiments, the inhibitor of IRE-1α is administered in combination with a second cancer therapeutic agent. For example, the inhibitor of IRE-1α may be administered in combination with a chemotherapeutic agent.
[0029] In another embodiment, treatment of the subject with a direct or indirect inhibitor of IRE-1α induces extended survival of the subject.
[0030] In another aspect, the invention pertains to a method for activating or enhancing Type 1 immunity in ovarian cancer-infiltrating T cells in a subject including administering to the subject an effective amount of a direct or indirect inhibitor of XBP1, thereby activating or enhancing Type 1 immunity in ovarian cancer-infiltrating T cells in the subject.
[0031] In yet another aspect, the invention pertains to a method for reducing ER stress in tumor-associated dendritic cells (tDCs) in a subject including administering to the subject an effective amount of a direct or indirect inhibitor of 4-HNE to inhibit XBP1 activation, thereby reducing ER stress in tumor-associated dendritic cells in the subject.
[0032] In a further aspect, the invention pertains to a method for reducing or preventing intracellular lipid accumulation in tumor-associated dendritic cells (DCs) including administering to the subject an effective amount of a direct or indirect inhibitor of XBP1, thereby reducing or preventing intracellular lipid accumulation in tumor-associated dendritic cells in the subject.
[0033] In one embodiment, the number of cytosolic lipid droplets in the dendritic cell is reduced. In another embodiment, the intracellular levels of total triglycerides is reduced.
[0034] In another aspect, the invention pertains to a method for enhancing or inducing T cell activation at a tumor site in a subject including administering to the subject an effective amount of a direct or indirect inhibitor of XBP1, thereby enhancing or including T cell activation at the tumor site in the subject.
[0035] In yet another aspect, the invention pertains to a method for inducing, enhancing or promoting the antigen presenting capacity of tumor-associated dendritic cells (DCs) in a subject including administering to the subject an effective amount of a direct or indirect inhibitor of XBP1, thereby inducing, enhancing or promoting the antigen presenting capacity of tumor-associated dendritic cells in the subject.
[0036] In yet another aspect, the invention pertains to a method for inducing, enhancing or promoting the antigen presenting capacity of tumor-associated dendritic cells (tDCs) in a subject including contacting dendritic cells with an effective amount of a direct or indirect inhibitor of XBP1 and then administering the dendritic cells to the subject, thereby inducing, enhancing or promoting the antigen presenting capacity of tumor-associated dendritic cells in the subject.
[0037] In a further aspect, the invention pertains to a method of identifying a compound useful in enhancing or inducing anti-tumor immunity in a subject, including providing an indicator composition comprising XBP1, or biologically active portions thereof; contacting the indicator composition with each member of a library of test compounds; selecting from the library of test compounds a compound of interest that interacts with XBP1, or biologically active portions thereof; and contacting ovarian cancer cells with the compound of interest, wherein the ability of the compound to enhance or induce anti-tumor immunity in the subject is indicated by the ability of the compound to inhibit growth of ovarian cancer cells as compared to the growth of ovarian cancer cells in the absence of the compound.

BRIEF DESCRIPTION OF THE DRAWINGS

[0038] FIG. 1A-F: Shows the gating strategy used for FACS analysis
[0039] FIG. 1A: depicts the gating strategy used to isolate human ovarian cancer-associated DCs present in solid tumors.
[0040] FIG. 1B: depicts the gating strategy used to isolate human ovarian cancer-associated DCs present in malignant ascites specimens.
[0041] FIG. 1C: depicts the gating strategy used to isolate tDCs from p53-Kras-driven primary ovarian tumors of mice bearing advanced metastatic ID8-Defb29-VegfA ovarian tumors.
[0042] FIG. 1D: depicts the gating strategy used to isolate tDCs from malignant ovarian ascites of mice bearing advanced metastatic ID8-Defb29-VegfA ovarian tumors.
[0043] FIG. 1E: graphically depicts robust expression of Clec9A/DNGR-1 and Zbtb46 by murine CD45+CD11c+MHC-II+CD11b+CD8α tumor-infiltrating myeloid cells, reinforcing their identity as genuine classical DCs (cDCs). These two markers distinguish cDCs and their committed progenitors from other closely related mononuclear phagocytic lineages.
[0044] FIG. 1F: depicts the gating strategy to isolate control CD45+CD11c+MHC-II+CD11b+CD8α DCs from the spleen (sDCs).
[0045] FIG. 2A-F: Shows constitutive XBP1 activation in human and mouse ovarian cancer-associated DCs.
[0046] FIG. 2A: depicts PCR analysis of Xbp1 mRNA splicing in ovarian cancer tDCs from human (1-12) and mouse (p53/K-ras and ID8-Def29/Vegf-A) origin. XBP1u, unspliced form; XBP1s, spliced form; Actb, β-actin.
[0047] FIG. 2B: graphically depicts expression of total XBP1 mRNA (Left) and spliced XBP1 (XBP1s) mRNA (Right). Expression of the indicated transcript was determined by RT-qPCR. sDC, splenic DCs.
[0048] FIG. 2C: depicts a western blot of XBP1s protein expression in nuclear extracts obtained from the indicated DCs. Lamin B was used as loading control. In all cases data are representative of 3 independent experiments with similar results.
[0049] FIG. 2D: graphically depicts expression of ERdj4 mRNA (Left) and Sec61a1 mRNA (Right). Expression of the indicated transcript was determined by RT-qPCR.
[0050] FIG. 2E: graphically depicts expression of BiP mRNA (Left) and CHOP mRNA (Right). Expression of the indicated transcript was determined by RT-qPCR.
[0051] FIG. 2F: graphically depicts the expression of CHOP in tDCs sorted from human patient ovarian cancer specimens (determined by RT-qPCR) correlated with the percentage of CD45+CD3+T cells present in each individual tumor (circle) or ascites (square) sample. r, Spearman's Rank correlation coefficient.
[0052] FIG. 3A-F: Shows the effect of diverse cytokines and hypoxia mimicking conditions on XBP1 activation by DCs
[0053] FIGS. 3A-D: graphically depict the effect of diverse cytokines on XBP1 activation by DCs. Splicing and upregulation of XBP1 was determined by RT-qPCR analysis.
[0054] FIGS. 3E-F: graphically depict the effect of hypoxia-mimicking conditions on XBP1 activation by DCs.
[0055] FIG. 4A-J: Provides lipid peroxidation byproduct 4-HNE triggers ER stress in DCs.
[0056] FIG. 4A: depicts increased intracellular lipid content in tDCs compared with control sDCs from naïve or tumor-bearing mice (Ovca). Representative FACS analysis of lipid staining for DCs from the indicated sources (Left). Intracellular lipid quantification expressed as mean fluorescence intensity (MFI) of Bodipy 493/503 staining (Right).
[0057] FIG. 4B: graphically depicts the quantification of intracellular ROS levels in DCs expressed as geometric MFI (gMFI) of DCFDA staining.
[0058] FIG. 4C: graphically depicts the levels of 4-HNE-protein adducts in cell-free malignant ascites obtained from hosts bearing metastatic ovarian cancer.
[0059] FIG. 4D: graphically depicts the quantification of total intracellular 4-HNE-protein adducts in tDCs isolated from metastatic ovarian cancer ascites samples of human and mouse origin.
[0060] FIG. 4E: graphically depicts the intracellular levels of 4-HNE-protein adducts in tDCs isolated from mice with advanced ID8-Defb29-VegfA ovarian tumors and exposed to cell-free malignant ascites in the presence or absence of Vitamin E (VitE).
[0061] FIG. 4F: graphically depicts the rapid generation of intracellular 4-HNE-protein adducts in naïve sDCs incubated with increasing concentrations of purified 4-HNE.
[0062] FIGS. 4G-H: depict the quantification of XBP1s gene expression in sDCs exposed for 3 h to increasing amounts of purified 4-HNE. Data are representative of at least two independent experiments with similar results.
[0063] FIG. 4I: depict the quantification of total XBP1 (left) and ERdj4 (right) gene expression in sDCs exposed for 3 h to increasing amounts of purified 4-HNE. Data are representative of at least two independent experiments with similar results.
[0064] FIG. 4J: depict the quantification of total BiP (left) and CHOP (right) gene expression in sDCs exposed for 3 h to increasing amounts of purified 4-HNE. Data are representative of at least two independent experiments with similar results.
[0065] FIG. 5A-C: Shows the efficient and selective XBP1 deletion in DCs via CD11c-controlled Cre expression.
[0066] FIG. 5A: depicts a Schematic of Xbp1 exon 2 deletion.
[0067] FIG. 5B: graphically depicts deletion efficiency of XBP1, which was determined by RT-qPCR using primers that selectively amplify exon 2 of Xbp1 (see methods).
[0068] FIG. 5C: depicts induction of canonical XBP1 target genes ERdj4 (Left) and Sec61 (Right) upon stimulation (determined via RT-qPCR). Data were normalized to endogenous Actb expression in each sample. Data are representative of at least three independent experiments with similar results.
[0069] FIG. 6A-I: Shows the assessment of immune cell population in conditional knockout mice
[0070] FIGS. 6A-C: depict representative FACS analysis of DC populations in the spleen.
[0071] FIG. 6D-E: depict representative FACS analysis of DC populations in infiltrating p53/K-ras ovarian tumors.
[0072] FIG. 6F-G: depict representative FACS analysis of DC populations in malignant ID8-Defb29/Vegf-A ovarian cancer ascites of XBP1f/f (top) or XBP1f/f CD11c-Cre (bottom) mice.
[0073] FIG. 6H-I: depicts the proportions (FIG. 6H) and absolute numbers (FIG. 6I) of depicted immune cell populations in the spleen of wild type or conditional knockout mice. pDC, plasmacytoid DCs. Data are representative of 3 mice per group. *P<0.05
[0074] FIG. 7A-I: Shows ovarian cancer progression in hosts lacking XBP1 in DCs.
[0075] FIG. 7A: depicts p53/K-ras-driven ovarian tumors generated in hosts reconstituted with bone marrow from either XBP1f/f (top) or XBP1f/f CD11c-Cre (bottom) donor mice as described in the methods and primary tumors were resected 48 days after intrabursal injection of Cre-expressing adenovirus (ADV-Cre).
[0076] FIG. 7B: graphically depicts growth kinetics of p53/K-ras-driven ovarian tumors in hosts reconstituted with bone marrow from the indicated genotypes.
[0077] FIG. 7C: graphically depicts the proportion of hosts presenting p53/K-ras-derived metastatic lesions in the peritoneal cavity 48 days after tumor induction.
[0078] FIG. 7D: depicts mice of the indicated genotypes implanted with ID8-Defb29-VegfA ovarian cancer cells via intraperitoneal (i.p.) injection.
[0079] FIG. 7E: graphically depicts peritoneal metastases evaluated 3-4 weeks after tumor implantation (n=3 mice per group). **P<0.001.
[0080] FIG. 7F: graphically depicts malignant ascites generation in tumor-bearing mice expressed as percent weight gain due to progressive accumulation of peritoneal fluid. *P<0.05.
[0081] FIG. 7G: depicts reduced splenomegaly in tumor-bearing mice deficient for XBP1 in CD11c+ DCs.
[0082] FIG. 7H: depicts overall survival rates in mice bearing aggressive ID8-Defb29-VegfA tumors. Data are representative of at least two independent experiments with similar results using 4-6 mice per group. **P<0.001.
[0083] FIG. 7I: depicts overall survival rates in mice bearing parental ID8 tumors. Data are representative of at least two independent experiments with similar results using 4-6 mice per group. **P<0.001.
[0084] FIG. 8A-D: Shows transcriptional analysis of ovarian cancer-associated DCs devoid of XBP1.
[0085] FIG. 8A: depicts the top transcriptional regulators associated with differentially expressed gene signatures in wild type vs. XBP1-deficient DCs isolated from mice bearing ID8-Defb29/Vegf-A ovarian tumors for 3 weeks.
[0086] FIG. 8B: depicts the main ER stress-related gene network controlled by XBP1 in tDCs based on Ingenuity Pathway Analysis (IPA).
[0087] FIG. 8C: depicts the expression levels of previously reported RIDD targets in XBP1-deficient tDCs.
[0088] FIG. 8D: depicts the top significantly affected biological processes identified in tDCs devoid of XBP1 (see methods).
[0089] FIG. 9A-G: Shows that XBP1 disrupts lipid homeostasis in ovarian cancer-associated DCs.
[0090] FIG. 9A: depicts the downregulation of genes involved in the UPR/ER stress response in tDCs devoid of XBP1. WT, XBP1f/f tDC. XBP1def, XBP1f/f CD11c-Cre tDC (n=3/group). FDR, false discovery rate. RPKM, transcript abundance expressed as reads per kilobase per million reads.
[0091] FIG. 9B: depicts the downregulation of genes involved in the lipid metabolism in tDCs devoid of XBP1. WT, XBP1f/f tDC. XBP1def, XBP1f/f CD11c-Cre tDC (n=3/group). FDR, false discovery rate. RPKM, transcript abundance expressed as reads per kilobase per million reads.
[0092] FIG. 9C: depicts decreased intracellular lipid content in XBP1f/f CD11c-Cre tDCs (n=3 mice per group) from mice bearing ID8-Defb29-VegfA tumors for 3 weeks evidenced by Bodipy493/503 staining.
[0093] FIG. 9D: depicts electron micrographs (12,000×) demonstrating large intracellular lipid bodies in XBP1-sufficient, but not XBP1-deficient tDC.
[0094] FIG. 9E: graphically depicts quantification of lipid bodies in tDCs sorted from mice bearing ID8-Defb29-VegfA ovarian tumors for 3-4 weeks.
[0095] FIG. 9F: graphically depicts quantification of intracellular triglycerides (TAG) in tDCs sorted from mice bearing ID8-Defb29-VegfA ovarian tumors for 3-4 weeks.
[0096] FIG. 9G: graphically depicts the intracellular lipid content of tDCs incubated in vitro with 25% cell-free ovarian cancer ascites supernatants in the presence of the indicated inhibitors. Intracellular lipid content was assessed 24 h later via Bodipy493/503 staining. Data are representative of 3 independent experiments with similar results. #P<0.05 compared with control tDC incubated in the absence of cell-free ascites supernatants. *P<0.05 compared with ascites-exposed tDC but left untreated.
[0097] FIG. 10A-F: Shows ER stress and lipid accumulation in tDCs.
[0098] FIG. 10A: depicts increased expression of XBP1-controlled lipid biosynthetic genes (Agpat6, Fasn, Lpar1) in tDCs isolated from mice bearing ID8-Defb29-Vegf-A ovarian tumors for 4-5 weeks compared with the indicated control sDCs.
[0099] FIG. 10B: graphically depicts rapid upregulation of XBP1s, ERdj4 and XBP1-controlled lipid biosynthetic genes (Agpat6, Fasn, Lpar1) in naïve sDCs stimulated for 3 h with increasing concentrations of purified 4-HNE. Data are normalized to endogenous levels of β-actin in each sample, and are representative of three independent experiments with similar results.
[0100] FIG. 10C: graphically depicts the lipidomic profile of tDCs obtained from mice bearing ID8-Defb29/Vegf-A ovarian tumors for 4 weeks.
[0101] FIG. 10D: graphically depicts the lipidomic profile of cell-free ascites supernatants obtained from mice bearing ID8-Defb29/Vegf-A ovarian tumors for 4 weeks.
[0102] FIG. 10E: graphically depicts relative expression of genes encoding scavenger receptors (Cd36, Cd68, Msr1) in XBP1-deficient vs. wild type tDCs.
[0103] FIG. 10F: depicts representative FACS analysis of Bodipy 493/503 staining in tDCs exposed to cell-free ovarian cancer ascites in the presence or absence of inhibitory compounds.
[0104] FIG. 11A-F: Shows that XBP1 promotes immune tolerance by DCs in the ovarian cancer microenvironment.
[0105] FIG. 11A: shows a representative histogram analysis of surface molecule expression on tDCs from peritoneal wash samples of XBP1f/f (striped) or XBP1f/f CD11c-Cre (black) mice bearing ID8-Defb29-VegfA tumors for 3-4 weeks. Dotted histograms indicate isotype control staining.
[0106] FIG. 11B: graphically depicts quantification of the data shown in FIG. 5A expressed as geometric mean fluorescence intensity (gMFI) of staining (n=3 mice per group).
[0107] FIG. 11C: depicts CFSE-dilution analysis of OT-1 T cells cocultured with full-length OVA-pulsed tDCs isolated from the peritoneal cavity of XBP1f/f or XBP1f/f CD11c-Cre mice bearing ID8-Defb29-VegfA ovarian tumors for 4 weeks (see methods for details).
[0108] FIG. 11D: graphically depicts the proportion of proliferating OT-1 T cells described in FIG. 5C.
[0109] FIGS. 11E and 11F: depict enhanced endogenous T cell activation at tumor sites in mice devoid of XBP1 in CD11c+ tDCs. Peritoneal wash samples from wild type (XBP1f/f, black bars) or XBP1-deficient (XBP1f/f CD11c-Cre, gray bars) mice were collected 2-3 weeks after peritoneal implantation of ID8-Defb29-VegfA cancer cells. Surface expression of CD44 and intracellular levels of tumoricidal IFN-γ were analyzed on CD3+CD4+ (FIG. 11E) or CD3+CD8+ (FIG. 11F) tumor-infiltrating T cells (TILs). In all cases, data are representative of at least two independent experiments using 3-4 mice group.
[0110] FIG. 12A-B: Shows antigen presentation by XBP1-deficient sDCs
[0111] FIG. 12A: depicts CFSE-dilution analysis of OT-1 T cells cocultured with full length OVA-pulsed CD11c+MHC-II+CD11b+CD8αDCs isolated from the spleen (sDC) of XBP1f/f or XBP1f/f CD11c-Cre mice.
[0112] FIG. 12B: graphically depicts the proportion of proliferating OT-1 T cells described in FIG. 12A. Data are representative of two independent experiments with similar results.
[0113] FIG. 13A-C: shows biodistributin and silencing activity of Intraperitoneally injected sRNA-PEI nanoparticles
[0114] FIG. 13A: depicts the selective uptake of rhodamine-labeled nanoparticles by CD11c+ tDC in the peritoneal cavity. Top, control untreated mice. Bottom, representative data from mice receiving Rhodamine-labeled siRNA-PEI nanocomplexes.
[0115] FIG. 13B-C: graphically depicts the biodistribution and silencing activity of intraperitoneally injected siRNA-PEI nanoparticles. CD45+CD11c+Rhodamine+tDCs were FACS-sorted from peritoneal wash samples 3 days after nanoparticle injection and gene expression levels were determined via RT-qPCR. Data are representative of three independent silencing experiments with 2-3 mice per group and all data were normalized to endogenous Acthb expression.
[0116] FIG. 14A-J: Shows therapeutic silencing of XBP1 improves tDC function and triggers protective anti-tumor immunity.
[0117] FIG. 14A: shows representative CFSE dilution of OT-1 T cells proliferating in vivo at tumor sites in full-length OVA-pulsed untreated mice or after administration of immunostimulatory nanocomplexes carrying luciferase-matching (siLuc-PEI) or XBP1-specific (siXBP1-PEI) siRNA (see methods for details).
[0118] FIG. 14B: graphically depicts the proportion of OT-1 T cells in the ascites of treated mice (n=3/group) three days after transfer.
[0119] FIG. 14C: graphically depicts the division (Left) and proliferation (Right) index of transferred OT-1 T cells shown in FIG. 6B.
[0120] FIGS. 14D-H: show enhanced anti-tumor immune responses in mice treated with DC-targeting, XBP1-silencing nanocomplexes. ID8-Defb29/Vegf-A tumor-bearing mice (n=3/group) were treated at days 8, 13, 18 and 23 post-tumor injection and peritoneal lavage samples were analyzed at day 27. FIG. 14D graphically depicts the proportion of metastatic spheroid tumor cells (CD45SSChi) found in the peritoneal cavity of treated mice. FIG. 14E shows representative pictures of peritoneal lavages obtained from treated mice. FIG. 14F graphically depicts the proportion of antigen-experienced (CD44+), activated (CD69+) CD4+ (Left) and CD8+ (Right) T cells infiltrating tumor locations determined by FACS analyses (gated on CD3+ cells). FIG. 14G-H show representative ELISA-based analysis showing increased IFN-γ and Granzyme B secretion by peritoneal (FIG. 14G) and splenic (FIG. 14H) T cells isolated from mice treated with XBP1-silencing nanoparticles.
[0121] FIGS. 14I-J: depict overall survival rates in wild type (FIG. 14I) or Rag2-deficient (FIG. 14J) ovarian cancer-bearing mice (n=6/group) treated with nanocomplexes at days 12, 16, 20, 24, 28 and 32 after implantation of ID8-Defb29/Vegf-A cancer cells. In all cases, data are representative of at least two independent experiments with similar results. ***P<0.001. Log-Rank Test.

DETAILED DESCRIPTION OF THE INVENTION

Definitions

[0122] Terms used in the claims and specification are defined as set forth below unless otherwise specified.
[0123] “Polypeptide,” “peptide”, and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymer.
[0124] “Nucleic acid” refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogs of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions can be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081, 1991: Ohtsuka et al. Biol. Chem. 260:2605-2608, 1985); and Cassol et al, 1992; Rossolini et al, Mol. Cell. Probes 8:91-98, 1994). For arginine and leucine, modifications at the second base can also be conservative. The term nucleic acid is used interchangeably with gene, cDNA, and mRNA encoded by a gene. Polynucleotides used herein can be composed of any polyribonucleotide or polydeoxribonucleotide, which can be unmodified RNA or DNA or modified RNA or DNA. For example, polynucleotides can be composed of single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that can be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions. In addition, the polynucleotide can be composed of triple-stranded regions comprising RNA or DNA or both RNA and DNA. A polynucleotide can also contain one or more modified bases or DNA or RNA backbones modified for stability or for other reasons. “Modified” bases include, for example, tritylated bases and unusual bases such as inosine. A variety of modifications can be made to DNA and RNA: thus, “polynucleotide” embraces chemically, enzymatically, or metabolically modified forms.
[0125] As used herein, the term “ER stress” refers to a perturbation in ER function and dysregulation of ER homeostasis due to an internal or external cellular insult. ER stress elicits a signaling cascade (i.e., the unfolded protein response) to mitigate stress.
[0126] The term “Unfolded Protein Response” (UPR) or the “Unfolded Protein Response pathway” refers to an adaptive response to the accumulation of unfolded proteins in the ER and includes the transcriptional activation of genes encoding chaperones and folding catalysts and protein degrading complexes as well as translational attenuation to limit further accumulation of unfolded proteins. Both surface and secreted proteins are synthesized in the endoplasmic reticulum (ER) where they need to fold and assemble prior to being transported.
[0127] As used herein, the term “dendritic cell” refers to a type of specialized antigen presenting cell (APC) involved in innate and adaptive immunity. Also referred to as “DC.” Dendritic cells may be present in the tumor microenvironment and these are referred to as “tumor-associated dendritic cells” or “tDCs.”
[0128] As used herein, the term “anti-tumor immunity” refers to an immune response induced upon recognition of cancer antigens by immune cells.
[0129] As used herein, the term “T cell activation” refers to cellular activation of resting T cells manifesting a variety of responses (For example, T cell proliferation, cytokine secretion and/or effector function). T cell activation may be induced by stimulation of the T cell receptor (TCR) with antigen/MHC complex.
[0130] As used herein, the term “antigen presenting capacity” refers to the ability of antigen presenting cells (APCs) to present antigen to T lymphocytes to elicit an immune response. In certain embodiments, the immune response is a type I immunity response. In certain embodiments, the antigen presenting capacity is determined by measuring infiltration and activation of T cells at tumor locations and/or secretion of IFN-γ and Granzyme B ex vivo by APCs (i.e., dendritic cells).
[0131] As used herein, the term “anti-tumor T cells” refers to T lymphocytes that have been activated by APCs, wherein the antigen is a tumor-associated antigen. These T lymphocytes will subsequently induce the killing of malignant cells.
[0132] As used herein, the term “anti-tumor response” refers to at least one of the following: tumor necrosis, tumor regression, tumor inflammation, tumor infiltration by activated T lymphocytes, or activation of tumor infiltrating lymphocytes. In certain embodiments, activation of lymphocytes is due to presentation of a tumor-associated antigen by APCs.
[0133] As used herein, the term “extended survival” refers to increasing overall or progression free survival in a treated subject relative to an untreated control.
[0134] As used herein, the term “test sample” is a sample isolated, obtained or derived from a subject, e.g., a human subject. The term “subject” or “host” is intended to include living organisms, but preferred subjects or hosts are mammals, and in particular, humans or murines. The term “subject” or “host” also includes cells, such as prokaryotic or eukaryotic cells. In particularly preferred embodiments, the “test sample” is a sample isolated, obtained or derived from a subject, e.g., a female human.
[0135] The term “sufficient amount” or “amount sufficient to” means an amount sufficient to produce a desired effect. e.g., an amount sufficient to reduce the size of a tumor.
[0136] The term “therapeutically effective amount” is an amount that is effective to ameliorate a symptom of a disease. A therapeutically effective amount can be a “prophylactically effective amount” as prophylaxis can be considered therapy.
[0137] As used herein, “combination therapy” embraces administration of each agent or therapy in a sequential manner in a regiment that will provide beneficial effects of the combination and co-administration of these agents or therapies in a substantially simultaneous manner. Combination therapy also includes combinations where individual elements may be administered at different times and/or by different routes but which act in combination to provide a beneficial effect by co-action or pharmacokinetic and pharmacodynamics effect of each agent or tumor treatment approaches of the combination therapy. For example, the agents or therapies may be administered simultaneously, sequentially, or in a treatment regimen in a predetermined order.
[0138] As used herein, “about” will be understood by persons of ordinary skill and will vary to some extent depending on the context in which it is used. If there are uses of the term which are not clear to persons of ordinary skill given the context in which it is used, “about” will mean up to plus or minus 10% of the particular value.
[0139] It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise.
[0140] Various aspects described herein are described in further detail in the following subsections.

ER Stress and UPR

[0141] The “Unfolded Protein Response” (UPR) or the “Unfolded Protein Response pathway” is initiated when there is an accumulation of unfolded proteins in the ER. This results in the transcriptional activation of genes encoding chaperones, folding catalysts, and protein degrading complexes, as well as translational attenuation to limit further accumulation of unfolded proteins.
[0142] Since the ER and the nucleus are located in separate compartments of the cell, the unfolded protein signal must be sensed in the lumen of the ER and transferred across the ER membrane and be received by the transcription machinery in the nucleus. The UPR performs this function for the cell. Activation of the UPR can be caused by treatment of cells with reducing agents like DTT, by inhibitors of core glycosylation like tunicamycin or by Ca-ionophores that deplete the ER calcium stores. First discovered in yeast, the UPR has now been described in C. elegans as well as in mammalian cells. In mammals, the UPR signal cascade is mediated by three ER transmembrane proteins: the protein-kinase and site-specific endoribonuclease IRE-1 alpha; the eukaryotic translation initiation factor 2 kinase, PERK/PEK; and the transcriptional activator ATF6. If the UPR cannot adapt to the presence of unfolded proteins in the ER, an apoptotic response is initiated leading to the activation of JNK protein kinase and caspases 7, 12, and 3. The most proximal signal from the lumen of the ER is received by a transmembrane endoribonuclease and kinase called IRE-1. Following ER stress, IRE-1 is essential for survival because it initiates splicing of the XBP1 mRNA, the spliced version of which activates the UPR.
[0143] The unfolded protein response (UPR) is a major cellular stress response pathway activated in tumors that allows them to adapt to the stresses of the tumor microenvironment. Similarly, the ER stress response has been shown to operate in malignant cells to support tumor growth. The present invention provides the novel discovery that constitutive activation of the ER stress sensor, XBP1, in cancer-associated DCs drives cancer progression (e.g., ovarian cancer progression). In certain embodiments, the ER stress response is dysregulated in cells present in the tumor microenvironment. In certain embodiments, the ER stress response is activated through signaling of the IRE-1/XBP1 pathway. In certain embodiments, the IRE-1/XBP1 pathway is constitutively active in cells present in the tumor microenvironment.
[0144] Accordingly, in one aspect, the invention pertains to a method for treating or reducing the progression of ovarian cancer in a subject, the method comprising administering to the subject a direct or indirect inhibitor of XBP1 or a direct or indirect inhibitor of IRE-1α such that progression of the ovarian cancer in the subject is inhibited. Non-limiting examples of direct inhibitors of XBP1 include a nucleic acid molecule that is antisense to an XBP1-encoding nucleic acid molecule, an XBP1 shRNA, an XBP siRNA, a nanoparticle-encapsulated XBP1 siRNA (e.g., polyethylenimine (PEI)-based nanoparticles encapsulating siRNA), a microRNA that targets XBP1, a dominant negative XBP1 molecule, an XBP1-specific antibody and small molecule inhibitors of XBP1. Non-limiting examples of indirect inhibitors of XBP1 include agents that target IRE-1, an endonuclease essential for proper splicing and activation of XBP1, such that inhibition of IRE-1 leads to inhibition of the production of the spliced, active form of XBP1. Non-limiting examples of IRE-1 inhibitors include a nucleic acid molecule that is antisense to an IRE-1-encoding nucleic acid molecule, an IRE-1 shRNA, an IRE-1 siRNA, a nanoparticle-encapsulated IRE-1 siRNA, a microRNA that targets IRE-1, a dominant negative IRE-1 molecule, an IRE-1-specific antibody and small molecule inhibitors of IRE-1.

XBP1

[0145] X-box binding protein-1 (XBP1) is a transcription factor that acts as an ER stress sensor by promoting the expression of ER chaperones and regulating distinct sets of target genes in a cell type-specific manner (Acosta-Alvear et al., 2007; Lee et al., 2003; Yoshida et al., 2001). In certain embodiments, XBP1 is spliced via IRE-1 activation. In certain embodiments, spliced XBP1 enhances transcription of ER chaperones.
[0146] The X-box binding human protein (“XBP1”) is a DNA binding protein and has an amino acid sequence as described in, for example, Liou, H. C., et. al. 1990. Science 247, 1581-1584 and Yoshimura, T., et al. 1990. EMBO J. 9, 2537-2542, and other mammalian homologs thereof, such as described in Kishimoto T., et al. 1996. Biochem. Biophys. Res. Commun. 223, 746-751 (rat homologue). Exemplary proteins intended to be encompassed by the term “XBP1” include those having amino acid sequences disclosed in GenBank with accession numbers A36299 [gi: 105867], NP_005071 [gi:4827058], P17861 [gi: 139787], CAA39149 [gi:287645], and BAA82600 [gi:5596360] or e.g., encoded by nucleic acid molecules such as those disclosed in GenBank with accession numbers AF027963 [gi:13752783]; NM_013842 [gi: 13775155]; or M31627 [gi: 184485]. XBP1 is also referred to in the art as TREB5 or HTF (Yoshimura, T., et al. 1990. EMBO Journal. 9, 2537; Matsuzaki, Y., et al. 1995. J. Biochem. 117, 303). Like other members of the b-zip family, XBP1 has a basic region that mediates DNA-binding and an adjacent leucine zipper structure that mediates protein dimerization.
[0147] There are two forms of XBP-1 protein, unspliced and spliced, which differ in their sequence and activity. Unless the form is referred to explicitly herein, the term “XBP1” as used herein includes both the spliced and unspliced forms. Spliced XBP1 (“XBP1s”) directly controls the activation of the UPR, while unspliced XBP1 functions to negatively regulate spliced XBP1.
[0148] “Spliced XBP1” (“XBP1s”) refers to the spliced, processed form of the mammalian XBP1 mRNA or the corresponding protein. Human and murine XBP1 mRNA contain an open reading frame (ORF1) encoding bZIP proteins of 261 and 267 amino acids, respectively. Both mRNA's also contain another ORF, ORF2, partially overlapping but not in frame with ORF1. ORF2 encodes 222 amino acids in both human and murine cells. Human and murine ORF1 and ORF2 in the XBP1 mRNA share 75% and 89% identity respectively. In response to ER stress, XBP1 mRNA is processed by the ER transmembrane endoribonuclease and kinase IRE-1 which excises an intron from XBP1 mRNA. In murine and human cells, a 26 nucleotide intron is excised. The boundaries of the excised introns are encompassed in an RNA structure that includes two loops of seven residues held in place by short stems. The RNA sequences 5′ to 3′ to the boundaries of the excised introns form extensive base-pair interactions. Splicing out of 26 nucleotides in murine and human cells results in a frame shift at amino acid 165 (the numbering of XBP1 amino acids herein is based on GenBank accession number NM.sub.-013842 [gi: 13775155] and one of skill in the art can determine corresponding amino acid numbers for XBP1 from other organisms, e.g., by performing a simple alignment). This causes removal of the C-terminal 97 amino acids from the first open reading frame (ORF1) and addition of the 212 amino from ORF2 to the N-terminal 164 amino acids of ORF1 containing the b-ZIP domain. In mammalian cells, this splicing event results in the conversion of a 267 amino acid unspliced XBP1 protein to a 371 amino acid spliced XBP1 protein. The spliced XBP1 then translocates into the nucleus where it binds to its target sequences to induce their transcription.
[0149] “Unspliced XBP1” (“XBP1u”) refers to the unprocessed XBP1 mRNA or the corresponding protein. As set forth above, unspliced murine XBP1 is 267 amino acids in length and spliced murine XBP1 is 371 amino acids in length. The sequence of unspliced XBP1 is known in the art and can be found, e.g., Liou, H. C., et. al. 1990. Science 247, 1581-1584 and Yoshimura, T., et al. 1990. EMBO J. 9, 2537-2542, or at GenBank accession numbers NM_005080 [gi: 14110394] or NM_013842 [gi: 13775155].
[0150] As used herein, the term “functional XBP1” refers to the spliced form of XBP1, which acts as a transcription factor to activate the UPR.
[0151] As used herein, the term “ratio of spliced to unspliced XBP1” refers to the amount of spliced XBP1 present in a cell or a cell-free system, relative to the amount or of unspliced XBP1 present in the cell or cell-free system. “The ratio of unspliced to spliced XBP1” refers to the amount of unspliced XBP1 compared to the amount of unspliced XBP1. “Increasing the ratio of spliced XBP1 to unspliced XBP1” encompasses increasing the amount of spliced XBP1 or decreasing the amount of unspliced XBP1 by, for example, promoting the degradation of unspliced XBP1. Increasing the ratio of unspliced XBP1 to spliced XBP1 can be accomplished, e.g., by decreasing the amount of spliced XBP1 or by increasing the amount of unspliced XBP1. Levels of spliced and unspliced XBP1 an be determined as described herein, e.g., by comparing amounts of each of the proteins which can be distinguished on the basis of their molecular weights or on the basis of their ability to be recognized by an antibody. In another embodiment described in more detail below, PCR can be performed employing primers which span the splice junction to identify unspliced XBP1 and spliced XBP1 and the ratio of these levels can be readily calculated.
[0152] The present invention pertains to the novel discovery that XBP1 is constitutively active in cancer-associated DCs, such as ovarian cancer-associated DCs. In one embodiment, the present invention is directed to the novel discovery that anti-tumor immunity is enhanced or increased in a subject by directly or indirectly inhibiting XBP1. In another embodiment, the present invention is directed to the discovery that ovarian cancer can be treated or reduced in a subject by administering an effective amount of a direct or indirect inhibitor of XBP1 to the subject.

IRE-1α

[0153] The term “IRE-1” or “IRE-1α” refers to an ER transmembrane endoribonuclease and kinase called “Serine/threonine-protein kinase/endoribonuclease,” or alternatively, “Inositol-requiring protein 1”, which oligomerizes and is activated by autophosphorylation upon sensing the presence of unfolded proteins, see, e.g., Shamu et al., (1996) EMBO J. 15: 3028-3039. In Saccharomyces cerevisiae, the UPR is controlled by IREp. In the mammalian genome, there are two homologs of IRE-1, IRE-1α and IRE-1β. IRE-1α is expressed in all cells and tissue whereas IRE-1β is primarily expressed in intestinal tissue. The endoribonucleases of either IRE-1α and IRE-1β are sufficient to activate the UPR. Accordingly, as used herein, the term “IRE-1” includes, e.g., IRE-1α, IRE-1β and IREp. In a preferred embodiment, IRE-1 refers to IRE-1α.
[0154] IRE-1 is a large protein having a transmembrane segment anchoring the protein to the ER membrane. A segment of the IRE-1 protein has homology to protein kinases and the C-terminal has some homology to RNAses. Over-expression of the IRE-1 gene leads to constitutive activation of the UPR. Phosphorylation of the IRE-1 protein occurs at specific serine or threonine residues in the protein.
[0155] IRE-1 senses the overabundance of unfolded proteins in the lumen of the ER. The oligomerization of this kinase leads to the activation of a C-terminal endoribonuclease by trans-autophosphorylation of its cytoplasmic domains. IRE-1 uses its endoribonuclease activity to excise an intron from XBP1 mRNA. Cleavage and removal of a small intron is followed by re-ligation of the 5′ and 3′ fragments to produce a processed mRNA that is translated more efficiently and encodes a more stable protein (Calfon et al. (2002) Nature 415(3): 92-95). The nucleotide specificity of the cleavage reaction for splicing XBP1 is well documented and closely resembles that for IRE-p mediated cleavage of HAC1 mRNA (Yoshida et al. (2001) Cell 107:881-891). In particular, IRE-1 mediated cleavage of murine XBP1 cDNA occurs at nucleotides 506 and 532 and results in the excision of a 26 base pair fragment. IRE-1 mediated cleavage of XBP1 derived from other species, including humans, occurs at nucleotides corresponding to nucleotides 506 and 532 of murine XBP1 cDNA, for example, between nucleotides 502 and 503 and 528 and 529 of human XBP1.
[0156] As used interchangeably herein. “IRE-1 activity,” “biological activity of IRE-1” or “functional activity IRE-1,” includes an activity exerted by IRE-1 on an IRE-1 responsive target or substrate, as determined in vivo, or in vitro, according to standard techniques (Tirasophon et al. 2000. Genes and Development Genes Dev. 2000 14: 2725-2736), IRE-1 activity can be a direct activity, such as a phosphorylation of a substrate (e.g., autokinase activity) or endoribonuclease activity on a substrate e.g., XBP1 mRNA. In another embodiment, IRE-1 activity is an indirect activity, such as a downstream event brought about by interaction of the IRE-1 protein with a IRE-1 target or substrate. As IRE-1 is in a signal transduction pathway involving XBP1, modulation of IRE-1 modulates a molecule in a signal transduction pathway involving XBP1. Modulators which modulate an XBP1 biological activity indirectly modulate expression and/or activity of a molecule in a signal transduction pathway involving XBP1, e.g., IRE-1, PERK, eIF2α, or ATF6α.
[0157] The present invention provides the novel discovery that targeting the IRE-1α/XBP1 branch of the ER stress response in tumor-associated DCs induces protective immune responses against cancer (e.g., ovarian cancer). In some embodiment, the invention provides that inhibiting IRE-1α in tumor-associated DCs extends host survival by enhancing anti-tumor immunity.

Anti-Tumor Immunity

[0158] The immune system plays a critical role in protecting the host from cancer. Notably, the tumor microenvironment is an important aspect of cancer biology that contributes to tumor initiation, tumor progression, and responses to therapy. Cells and molecules of the immune system are a fundamental component of the tumor microenvironment.
[0159] Since tumor tissue is characterized by a variety of antigens not typically found in normal tissue, the immune system may mount a protective response. In certain embodiments, these antigens are referred to as “tumor-associated antigens (TAAs).” Innate immunity against the tumor is invoked very quickly. Macrophages, which are programmed to attack and destroy tumor cells in the similar fashion that they eliminate invading pathogens, are drawn to the tumor (Mantovani et al., Nature Reviews Immunology 2011; 11, 519-531). With time, adaptive anti-tumor immune responses develop. Dendritic cells migrate to the tumor as part of the innate immune response and serve as a link between innate and adaptive immunity. In certain embodiments, dendritic cells process tumor antigens and then directly interact with T and B cells, subsequently stimulating specific immune responses. The initial response of the immune system to a tumor is to recruit lymphocytes in an attempt to clear the tumor. Tumor-infiltrating lymphocytes (TILs) include cytotoxic T lymphocytes (CTLs), helper T cells, and natural killer (NK) cells. Proteins associated with tumorigenesis or malignant growth may also stimulate humoral immunity (Suckow, The Veterinary Journal 2013; 198, 28-33).
[0160] Coordination of the anti-tumor immune response requires communication between cells of the immune system, mostly carried out by cytokines (Dranoff, Nature Reviews Cancer 2004; 4, 11-22). For example, interleukin (IL)-6 produced by T lymphocytes and macrophages enhances the proliferation of both T and B lymphocytes. Likewise, interferon-gamma (IFNγ) is produced by NK cells, T lymphocytes, macrophages, and B lymphocytes and enhances tumor antigen presentation along with cell-mediated cytotoxicity.
[0161] The predominant cell type within tumor stroma is the fibroblast. Cancer-associated fibroblasts produce a variety of factors that promote proliferation and progression of cancer, including osteonectin, vascular endothelial growth factor (VEGF), and matrix metalloproteinases (MMPs). Many of these factors are widely produced by normal cells and therefore the immune system restricts itself from attacking these targets (Rasanen and Vaheri, Experimental Cell Research 2010; 316, 2713-2722).
[0162] In certain embodiments, the presence of a tumor serves as evidence that cancerous cells have successfully avoided immune elimination. This may occur due to immune selection pressure that favors growth of tumors that are less immunogenic (Dunn et. al, Nature Immunology 2002; 3, 991-998). Tumors may also escape through the expression of anti-apoptotic molecules (Reed, Current Opinion in Oncology 1999; 11, 68-75). Factors such as VEGF, soluble Fas, and transforming growth factor (TGF)-β, which are produced by tumor cells and tumor stroma, can suppress anti-tumor immune response (Ben-Baruch, Seminars in Cancer Biology 2006; 16, 38-52; Whiteside, Seminars in Cancer Biology 2006; 16, 3-15). Tumor stromal cells create an environment in which cancerous cells are exposed to growth factors while avoiding immune recognition. For example, thrombospondin-1 is produced by stromal cells and leads to immune suppression via activation of TGF-β (Silze et. al, International Journal of Cancer 2004; 108, 173-180).
[0163] Harnessing the inherent ability of T cells to eliminate tumor cells represents the most promising anti-cancer strategy since the development of chemotherapy, as demonstrated most recently by the dramatic shrinkage of melanoma in response to checkpoint blockers anti-CTLA4 and anti-PD1. In addition, recent reports demonstrate that adoptively transferred anti-tumor T cells (expanded from resected tumor specimens or genetically manipulated) can elicit robust and long-lasting anti-tumor responses (Bollard et al., 2007; Dudley et al., 2002; Leen et al., 2006; Morgan et al., 2006). However, in most cases, the optimal cytotoxic activity of such tumor-reactive T cells is drastically reduced because cancer-associated DCs are unable to support T cell function. (Barnett et al., 2005; Conejo-Garcia et al., 2004; Cubillos-Ruiz et al., 2009; Curiel et al., 2003; Huarte et al., 2008). The present invention reveals for the first time that DC-specific deletion of XBP1 can extend host survival by converting immunosuppressive tDCs into potent activators of Type 1 immunity in ovarian cancer-infiltrating T cells. Indeed, therapeutic silencing of XBP1 in tDCs using siRNA-encapsulating nanocarriers reversed their immunosuppressive phenotype and significantly prolonged host survival by inducing protective anti-tumor immune responses. Novel and more effective therapeutic strategies are needed to improve the dismal prognosis of metastatic ovarian cancer patients. The present invention demonstrates for the first time the feasibility and significant immunotherapeutic potential of targeting ER stress-driven XBP1 in tDCs using a safe and effective nanotechnology-based system that may slow or prevent the usually inevitable recurrence observed in metastatic ovarian cancer patients who have been “optimally” debulked. The present invention also provides that targeting the aberrant ER stress response in innate immune cells of the tumor microenvironment may also represent a viable therapeutic strategy to confront other lethal cancers that normally co-opt the immune response to promote malignant progression. Hence, the present invention provides for the first time that targeting the IRE-1α/XBP1 arm of the ER stress response in cancer-bearing hosts could be used to inhibit tumor growth while simultaneously inducing robust anti-tumor immunity.
[0164] In one embodiment, the present invention is directed to the novel discovery that constitutive activation of XBP1 in tumor-associated dendritic cells allows tumors to manipulate DC function and elude immune control. In another embodiment, the present invention is directed to the discovery that ablaiting XBP1 expression in tumor-associated dendritic cells enhances or induces anti-tumor immunity and extends host survival. In certain embodiments, inhibition of XBP1 enhances infiltration of activated T cells at tumor locations. In certain embodiments, inhibition of XBP1 enhances the capacity of infiltrating T cells to respond to tumor antigens.

Dendritic Cells

[0165] Dendritic cells (DC) are key regulators of both innate and adaptive immunity, and the array of immunoregulatory functions exhibited by these cells is dictated by their differentiation, maturation, and activation status. A major role of these cells is the induction of immunity to pathogens, however, recent data demonstrates that DCs are also critical regulators of anti-tumor immune responses. In certain embodiments, the generation of protective anti-tumor immunity depends on the presentation of tumor antigens by DCs to T cells. The control of DC survival plays an important role in regulating T cell activation and function.
[0166] DCs initiate an immune response by presenting a captured antigen, in the form of peptide-major histocompatability complex (MHC) molecule complexes, to naïve T cells in lymphoid tissues. Upon interaction with DCs, naïve CD4+ and CD8+ T cells can differentiate into antigen-specific effector cells. DCs also play a direct role in humoral immunity by interacting with B cells and indirectly by inducing the expansion and differentiation of CD4+ helper T cells.
[0167] Presentation of antigens to mount an immune response is one of the primary functions of dendritic cells. Tumor-associated DCs have the same function but the antigens are typically tumor-associated (TAA). Tumors can prevent antigen presentation and the establishment of tumor-specific immune responses through a variety of mechanisms. For example, tumors switch the differentiation of monocytes into macrophages and not DCs, or prevent the priming of tumor-specific T cells by DCs, through the mediation of IL-2 and macrophage colony-stimulating factor. In certain embodiments, tumors can interfere with DC maturation. For example, tumor cells can secrete IL-10 which leads to antigen-specific anergy of DCs. In certain embodiments, DCs are tumor-associated DCs (tDCs). These tDCs are present in the tumor microenvironment. The present invention, provides the novel discovery that tumors rely on DC-intrinsic XBP1 to elude immune control. The present invention also provides the novel discovery that inhibiting XBP1 in tumor-associated DCs extends host survival by enhancing anti-tumor immunity.
[0168] In one embodiment, the present invention is directed to the novel discovery that the ER stress sensor XBP1 is constitutively active in cancer-associated DCs, such as ovarian cancer-associated DCs. In another embodiment, the present invention pertains to the discovery that the lipid peroxidation byproduct 4-HNE triggers ER stress and XBP1 activation in DCs. In another embodiment, the present invention pertains to the discovery that XBP1 regulates lipid metabolism and antigen presentation by tumor-associated DCs.

XBP1 and Dendritic Cells

[0169] XBP1 is a transcription factor expressed in dendritic cells and activated by IRE-1α, an ER transmembrane kinase and endoribonuclease. XBP1 functions to regulate the ER stress response by maintaining ER homeostasis and preventing activation of cell death pathways caused by sustained ER stress. The ER stress response, or unfolded protein response (UPR) is activated when unfolded proteins accumulate in the ER and functions to regulate the balance between homeostasis and apoptosis. In certain embodiments, XBP1 plays a role in DC differentiation and survival. For example, XBP1-deficient cells are more sensitive to apoptosis (Iwakoshi 2007).
[0170] The instant inventors have discovered that XBP1 is constitutively active in tumor-associated dendritic cells.
[0171] In one embodiment, the present invention provides the novel discovery that XBP1 is a driver of dendritic cell dysfunction in the tumor microenvironment. In another embodiment, the present invention provides that XBP1 is constitutively active in cancer-associated dendritic cells, such as ovarian cancer-associated dendritic cells. In certain embodiments, XBP1-deficient tDCs demonstrate enhanced antigen-presenting capacity. In certain embodiments, silencing or inhibiting XBP1 improves host survival and induces anti-tumor immunity. In certain embodiments, the induction of anti-tumor immunity is carried out by activated infiltrating T cells that respond to tumor antigens.

XBP1 and Ovarian Cancer

[0172] During tumor development and progression, cancer cells encounter cytotoxic conditions such as hypoxia, nutrient deprivation, and low pH due to inadequate vascularization (Hanahan, D., et al. 2011. Cell 144, 646-74). To maintain survival and growth in the face of these physiologic stressors, a set of adaptive response pathways are induced. One adaptive pathway well studied in other contexts is the unfolded protein response (UPR), which is induced by factors affecting the endoplasmic reticulum (ER) such as changes in glycosylation, redox status, glucose availability, calcium homeostasis or the accumulation of unfolded or misfolded proteins (Hetz, C, et al. 2011. Physiol Rev 91, 1219-43). Notably, features of the tumor microenvironment, such as hypoxia and nutrient deprivation, can disrupt ER homeostasis by the perturbation of aerobic processes such as oligosaccharide modification, disulphide bond formation, isomerization, and protein quality control and export (Wouters. B. G., et al. 2008. Nat Rev Cancer 8, 851-64). In mammalian cells, the UPR is mediated by three ER-localized transmembrane protein sensors: Inositol-requiring transmembrane kinase/endonuclease-1 (IRE-1), PKR-like ER kinase (PERK) and activating transcription factor 6 (ATF6) (Walter, P., et al. 2011. Science 334, 1081-6). Of these, IRE-1 is the most evolutionarily conserved branch. An increase in the load of folding proteins in the ER activates IRE-1, an ER-resident kinase and endoribonuclease that acts as an ER-stress sensor. Activated IRE-1 removes a 26 bp intron from XBP1 mRNA and results in a frame shift in the coding sequence, with the spliced form encoding a 226 amino acid transcriptional activation domain (Calfon, M., et al. 2002. Nature 415, 92-6: Yoshida, H., et al. 2001. Cell 107, 881-91). In contrast to the unspliced XBP1 (XBP1u), which is unstable and quickly degraded, spliced XBP1 (XBP1s) is stable and is a potent inducer of target genes that orchestrate the cellular response to ER stress (Hetz, C, et al. 2011. Physiol Rev 91, 1219-43).
[0173] As described in detail above, the UPR is a major cellular stress response pathway activated in tumors that allows them to adapt to the stresses of the tumor microenvironment. Several studies have reported on the activation of the UPR in various human tumors and its relevance to combinatorial therapy (Carrasco, D. R., et al. 2007. Cancer Cell 11, 349-36; De Raedt, T., et al. 2011. Cancer Cell 20, 400-413; Healy, S. J., et al. 2009. Eur J Pharmacol 625, 234-246; Ma, Y., et al. 2004. Nat Rev Cancer 4, 966-977; Mahoney, D. J., et al. 2011. Cancer Cell 20, 443-456). However, the role of the UPR and XBP1 in anti-tumor immunity is largely unknown. Here, the instant inventors have identified a previously unknown function of XBP1 in anti-tumor immunity and ovarian cancer. Here, it is demonstrated that constitutive activation of XBP1, a key component of the most evolutionarily conserved branch of the UPR, allows tumors to evade immune control by crippling normal DC function. Furthermore, XBP1 deletion and/or silencing inhibits tumor growth and/or progression and induces robust anti-tumor immunity.
[0174] Tumors progress when the host fails to provide an effective anti-tumor immune response. Prior to the discovery of the present invention, the role of XBP1 in anti-tumor immunity was unknown. Herein the instant inventors have identified a role for XBP1 in eluding immune control and therefore inducing the progression of tumor development, such as ovarian tumor development. In certain embodiments, the present invention provides that XBP1 is constitutively active in tumor-associated dendritic cells present in ovarian tumors compared to normal dendritic cells. In certain embodiments, the present invention provides that constitutive activation of XBP1 is critical for the initiation and rapid progression of ovarian tumors. Notably, XBP1 deficient tDCs fail to initiate or progress tumor development (e.g., ovarian tumors). In certain embodiments, the rapid progression of ovarian tumors is a result of constitutively active XBP1 in tumor-associated dendritic cells. In certain embodiments, the present invention provides that tumor progression and/or tumor burden is reduced in XBP1-deficient tDCs, indicating an important role for XBP1 in the development and progression of ovarian tumors.

Lipid Metabolism and Peroxidation

[0175] Cancer-associated DCs accumulate substantial amounts of oxidized lipids, and this abnormal process negatively regulates their antigen-presenting capacity (Herber et al., 2010; Ramakrishnan et al., 2014). As provided by the instant invention, transcriptional and functional analyses of tDCs devoid of XBP1 suggest that this conserved ER stress sensor facilitates the aberrant lipid accumulation commonly observed in dysfunctional cancer-associated DCs.
[0176] Lipid oxidation by reactive oxygen species (ROS) generates reactive byproducts such as the unsaturated aldehyde 4-hydroxy-trans-2-nonenal (4-HNE), which has been shown to induce protein-folding stress by forming stable adducts with ER-resident chaperones (Vladykovskaya et al., 2012). For the first time, the present invention provides that 4-HNE, a lipid peroxidation byproduct available in the human and mouse ovarian cancer microenvironment, can rapidly trigger robust ER stress and XBP1 activation in naïve DCs. Interestingly, 4-HNE has been demonstrated to induce the unfolded protein response in endothelial cells by forming covalent adducts with ER resident chaperones, a process that promotes vascular inflammation (Vladykovskaya et al., 2012). The ER stress response has been linked to lipid biosynthesis (Lee et al., 2008; Sriburi et al., 2004). However, the present invention indicates that enhanced intracellular lipid accumulation by tDCs required ROS generation and IRE-1α/XBP1 activation. Interestingly, exposure to XBP1-activating 4-HNE has been shown to promote fat accumulation in worms and mice (Singh et al., 2008; Singh et al., 2009). Thus, in some embodiments, the present invention provides that reactive metabolic byproducts in the tumor microenvironment, like 4-HNE, can perpetuate ER stress in infiltrating immune cells such as tDCs. Constitutive activation of the IRE-1α/XBP1 arm through this process subsequently promotes abnormal intracellular lipid accumulation in tDCs via upregulation of lipid biosynthetic genes, which ultimately inhibits their natural capacity to support T cell-mediated anti-tumor responses.
[0177] In one embodiment, the present invention provides that XBP1-deficient tDCs display marked downregulation of genes involved in lipid metabolic pathways. These lipid biosynthetic genes are rapidly upregulated in naïve DCs exposed to 4-HNE, an XBP1-activation lipid peroxidation byproduct. This aberrant lipid accumulation by tDCs obstructs their normal antigen processing and presentation capacity (Herber et al., 2010; Ramakrisnan et al., 2014).
[0178] In one embodiment, the present invention provides that the lipid peroxidation byproduct 4-HNE triggers ER stress and XBP1 activation in DCs. In another embodiment, the present invention provides that XBP1 regulates lipid metabolism and antigen presentation by tumor-associated DCs. In one embodiment, the present invention provides that XBP1 deficient tDCs have reduced intracellular lipid accumulation and improved antigen presenting capacity, leading to enhanced intra-tumoral T cell activation and increased host survival.

Therapeutic Targeting of the UPR

[0179] In the present invention, an unexpected role for the ER stress sensor XBP1 as a central driver of DC malfunction in the tumor microenvironment has been discovered. These findings unveil a new mechanistic paradigm whereby a lethal cancer exploits the most conserved arm of the ER stress response in tumor-resident DCs to disrupt their lipid homeostasis, alter their local antigen-presenting capacity and ultimately evade T cell-mediated immune control. While the ER stress response, and especially XBP1 activation, has been previously shown to operate in cancer cells to promote tumorigenesis, the present invention now reveals that this integrated cellular pathway further supports malignant progression by inhibiting the development of protective anti-tumor immunity via manipulation of normal DC function.
[0180] The upstream kinase and endoribonuclease IRE-1, which drives the splicing of XBP1 mRNA, is a viable drug target. Recently, two groups have identified specific IRE-1 endoribonuclease inhibitors (Papandreou, I., et al. 2011. Blood 117, 1311-1314; Volkmann, K., et al. 2011. J Biol Chem 286, 12743-12755). Intriguingly, these compounds efficiently inhibit XBP1 splicing in vivo and dramatically impair tumor growth in a xenograft model (Mahoney, D. J., et al. 2011. Cancer Cell 20, 443-456; Papandreou, I., et al. 2011. Blood 117, 1311-1314; Volkmann, K., et al. 2011. J Biol Chem 286, 12743-12755). While large-scale small molecule screens have provided potentially promising candidates that target the IRE-1/XBP1 pathway, attention needs to be paid to the specificity and cytotoxity of these compounds in vivo. Recent advances in solving the crystal structure of IRE-1 (Korennykh, A. V., et al. 2009. Nature 457, 687-693; Lee, K. P., et al. 2008. Cell 132, 89-100; Zhou, J., et al. 2006. Proc Natl Acad Sci USA 103, 14343-14348) should accelerate the design of more potent and specific IRE-1 inhibitors. The use of UPR inhibitors in combination with standard chemotherapy may greatly enhance the effectiveness of anti-tumor therapies.
[0181] The methods of the invention using inhibitory compounds which inhibit the expression, processing, post-translational modification, or activity of XBP1 or a molecule in a biological pathway involving XBP1, such as IRE-1α, can be used to induce anti-tumor immunity or in the treatment of cancer (e.g., ovarian cancer). In one embodiment of the invention, an inhibitory compound can be used to inhibit (e.g., specifically inhibit) the expression, processing, post-translational modification, or activity of spliced XBP1. In another embodiment, an inhibitory compound can be used to inhibit (e.g., specifically inhibit) the expression, processing, post-translational modification, or activity of unspliced XBP1.
[0182] Inhibitory compounds of the invention can be, for example, intracellular binding molecules that act to directly or indirectly inhibit the expression, processing, post-translational modification, or activity of XBP1 or a molecule in a biological pathway involving XBP1, for example, IRE-1α. As used herein, the term “intracellular binding molecule” is intended to include molecules that act intracellularly to inhibit the processing expression or activity of a protein by binding to the protein or to a nucleic acid (e.g., an mRNA molecule) that encodes the protein. Examples of intracellular binding molecules, described in further detail below, include antisense nucleic acids, intracellular antibodies, peptidic compounds that inhibit the interaction of XBP1 or a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) and a target molecule and chemical agents that specifically or directly inhibit XBP1 activity or the activity of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α).
[0183] In one embodiment, an inhibitory compound of the invention is an antisense nucleic acid molecule that is complementary to a gene encoding XBP1 or a molecule in a signal transduction pathway involving XBP1, (e.g., IRE-1α or a molecule with which XBP1 interacts), or to a portion of said gene, or a recombinant expression vector encoding said antisense nucleic acid molecule. The use of antisense nucleic acids to downregulate the expression of a particular protein in a cell is well known in the art (see e.g., Weintraub, H. et al., Antisense RNA as a molecular tool for genetic analysis, Reviews—Trends in Genetics, Vol. 1(1) 1986; Askari, F. K. and McDonnell, W. M. (1996) N. Eng. J. Med. 334:316-318; Bennett, M. R. and Schwartz, S. M. (1995) Circulation 92:1981-1993; Mercola, D. and Cohen, J. S. (1995) Cancer Gene Ther. 2:47-59; Rossi, J. J. (1995) Br. Med. Bull. 51:217-225; Wagner, R. W. (1994) Nature 372:333-335). An antisense nucleic acid molecule comprises a nucleotide sequence that is complementary to the coding strand of another nucleic acid molecule (e.g., an mRNA sequence) and accordingly is capable of hydrogen bonding to the coding strand of the other nucleic acid molecule. Antisense sequences complementary to a sequence of an mRNA can be complementary to a sequence found in the coding region of the mRNA, the 5′ or 3′ untranslated region of the mRNA or a region bridging the coding region and an untranslated region (e.g., at the junction of the 5′ untranslated region and the coding region). Furthermore, an antisense nucleic acid can be complementary in sequence to a regulatory region of the gene encoding the mRNA, for instance a transcription initiation sequence or regulatory element. Preferably, an antisense nucleic acid is designed so as to be complementary to a region preceding or spanning the initiation codon on the coding strand or in the 3′ untranslated region of an mRNA. Given the known nucleotide sequence for the coding strand of the XBP1 gene and thus the known sequence of the XBP1 mRNA, antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick base pairing. For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of an XBP1. An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length. Similarly, antisense nucleic acids targeting IRE-1α can also be designed according to the rules of Watson and Crick base pairing. An antisense nucleic acid of the invention can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art. To inhibit expression in cells, one or more antisense oligonucleotides can be used.
[0184] Alternatively, an antisense nucleic acid can be produced biologically using an expression vector into which all or a portion of a cDNA has been subcloned in an antisense orientation (i.e., nucleic acid transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest). The antisense expression vector can be in the form of, for example, a recombinant plasmid, phagemid or attenuated virus. The antisense expression vector can be introduced into cells using a standard transfection technique.
[0185] The antisense nucleic acid molecules of the invention are typically administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a protein to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation. An example of a route of administration of an antisense nucleic acid molecule of the invention includes direct injection at a tissue site (e.g. a tumor site). Alternatively, an antisense nucleic acid molecule can be modified to target selected cells (for example, tumor-associated dendritic cells) and then administered systemically. For example, for systemic administration, an antisense molecule can be modified such that it specifically binds to a receptor or an antigen expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecule to a peptide or an antibody which binds to a cell surface receptor or antigen. The antisense nucleic acid molecule can also be delivered to cells using the vectors described herein.
[0186] In yet another embodiment, an antisense nucleic acid molecule of the invention is an α-anomeric nucleic acid molecule. An α-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual β-units, the strands run parallel to each other (Gaultier et al. (1987) Nucleic Acids. Res. 15:6625-6641). The antisense nucleic acid molecule can also comprise a 2′-o-methylribonucleotide (Inoue et al. (1987) Nucleic Acids Res. 15:6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215:327-330).
[0187] In certain embodiments, an antisense nucleic acid molecule of the invention is a ribozyme. Ribozymes are catalytic RNA molecules with ribonuclease activity which are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334:585-591)) can be used to catalytically cleave mRNA transcripts to thereby inhibit translation mRNAs. Alternatively, gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of a gene (e.g., an XBP1 promoter and/or enhancer) to form triple helical structures that prevent transcription of a gene in target cells. See generally, Helene, C. (1991) Anticancer Drug Des. 6(6):569-84; Helene, C. et al. (1992) Ann. N.Y. Acad. Sci. 660:27-36; and Maher, L. J. (1992) Bioassays 14(12):807-15.
[0188] In another embodiment, a compound that promotes RNAi can be used to inhibit expression of XBP1 or a molecule in a biological pathway involving XBP1. The term “RNA interference” or “RNAi”, as used herein, refers generally to a sequence-specific or selective process by which a target molecule (e.g., a target gene, protein or RNA) is downregulated. In certain embodiments, the process of “RNA interference” or “RNAi” features degradation of RNA molecules, e.g., RNA molecules within a cell, said degradation being triggered by an RNA agent. Degradation is catalyzed by an enzymatic, RNA-induced silencing complex (RISC). RNAi occurs in cells naturally to remove foreign RNAs (e.g., viral RNAs). Natural RNAi proceeds via fragments cleaved from free dsRNA which direct the degradative mechanism to other similar RNA sequences. Alternatively, RNAi can be initiated by the hand of man, for example, to silence the expression of target genes. RNA interference (RNAi) is a post-transcriptional, targeted gene-silencing technique that uses double-stranded RNA (dsRNA) to degrade messenger RNA (mRNA) containing the same sequence as the dsRNA (Sharp, P. A. and Zamore, P. D. 287, 2431-2432 (2000); Zamore, P. D., et al. Cell 101, 25-33 (2000). Tuschl, T. et al. Genes Dev. 13, 3191-3197 (1999); Cottrell T R, and Doering T L. 2003. Trends Microbiol. 11:37-43; Bushman F.2003. Mol Therapy. 7:9-10; McManus M T and Sharp P A. 2002. Nat Rev Genet. 3:737-47). The process occurs when an endogenous ribonuclease cleaves the longer dsRNA into shorter, e.g., 21-23-nucleotide-long RNAs, termed small interfering RNAs or siRNAs. As used herein, the term “small interfering RNA” (“siRNA”) (also referred to in the art as “short interfering RNAs”) refers to an RNA agent, preferably a double-stranded agent, of about 10-50 nucleotides in length (the term “nucleotides” including nucleotide analogs), preferably between about 15-25 nucleotides in length, more preferably about 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length, the strands optionally having overhanging ends comprising, for example 1, 2 or 3 overhanging nucleotides (or nucleotide analogs), which is capable of directing or mediating RNA interference. Naturally-occurring siRNAs are generated from longer dsRNA molecules (e.g., >25 nucleotides in length) by a cell's RNAi machinery (e.g., Dicer or a homolog thereof). The smaller RNA segments then mediate the degradation of the target mRNA. Nanoparticle-encapsulated siRNA can also be used to downregulate a target molecule. Kits for synthesis of RNAi are commercially available from, e.g. New England Biolabs or Ambion. In one embodiment one or more of the chemistries described above for use in antisense RNA can be employed in molecules that mediate RNAi.
[0189] Alternatively, a compound that promotes RNAi can be expressed in a cell, e.g., a cell in a subject, to inhibit expression of XBP1 or a molecule in a biological pathway involving XBP1, such as IRE-1α. In contrast to siRNAs, shRNAs mimic the natural precursors of micro RNAs (miRNAs) and enter at the top of the gene silencing pathway. For this reason, shRNAs are believed to mediate gene silencing more efficiently by being fed through the entire natural gene silencing pathway. The term “shRNA”, as used herein, refers to an RNA agent having a stem-loop structure, comprising a first and second region of complementary sequence, the degree of complementarity and orientation of the regions being sufficient such that base pairing occurs between the regions, the first and second regions being joined by a loop region, the loop resulting from a lack of base pairing between nucleotides (or nucleotide analogs) within the loop region. shRNAs may be substrates for the enzyme Dicer, and the products of Dicer cleavage may participate in RNAi. shRNAs may be derived from transcription of an endogenous gene encoding a shRNA, or may be derived from transcription of an exogenous gene introduced into a cell or organism on a vector, e.g., a plasmid vector or a viral vector. An exogenous gene encoding an shRNA can additionally be introduced into a cell or organism using other methods known in the art, e.g., lipofection, nucleofection, etc.
[0190] The requisite elements of a shRNA molecule include a first portion and a second portion, having sufficient complementarity to anneal or hybridize to form a duplex or double-stranded stem portion. The two portions need not be fully or perfectly complementary. The first and second “stem” portions are connected by a portion having a sequence that has insufficient sequence complementarity to anneal or hybridize to other portions of the shRNA. This latter portion is referred to as a “loop” portion in the shRNA molecule. The shRNA molecules are processed to generate siRNAs. shRNAs can also include one or more bulges, i.e., extra nucleotides that create a small nucleotide “loop” in a portion of the stem, for example a one-, two- or three-nucleotide loop. The stem portions can be the same length, or one portion can include an overhang of, for example, 1-5 nucleotides.
[0191] In certain embodiments, shRNAs of the invention include the sequences of a desired siRNA molecule described supra. In such embodiments, shRNA precursors include in the duplex stem the 21-23 or so nucleotide sequences of the siRNA, desired to be produced in vivo.
[0192] Another type of inhibitory compound that can be used to inhibit the expression and/or activity of XBP1 or a molecule in a biological pathway involving XBP1 (for example, IRE-1α) is an intracellular antibody specific for said protein. The use of intracellular antibodies to inhibit protein function in a cell is known in the art (see e.g., Carlson, J. R. (1988) Mol. Cell. Biol. 8:2638-2646: Biocca, S. et al. (1990) EMBO J. 9:101-108; Werge, T. M. et al. (1990) FEBS Letters 274:193-198; Carlson, J. R. (1993) Proc. Natl. Acad. Sci. USA 90:7427-7428; Marasco, W. A. et al. (1993) Proc. Natl. Acad. Sci. USA 90:7889-7893: Biocca, S. et al. (1994) Bio/Technology 12:396-399; Chen, S-Y. et al. (1994) Human Gene Therapy 5:595-601; Duan, L et al. (1994) Proc. Natl. Acad. Sci. USA 91:5075-5079; Chen, S-Y. et al. (1994) Proc. Natl. Acad. Sci. USA 91:5932-5936; Beerli, R. R. et al. (1994) J. Biol. Chem. 269:23931-23936; Beerli, R. R. et al. (1994) Biochem. Biophys. Res. Commun. 204:666-672; Mhashilkar, A. M. et al. (1995) EMBO J. 14:1542-1551; Richardson, J. H. et al. (1995) Proc. Natl. Acad. Sci. USA 92:3137-3141; PCT Publication No. WO 94/02610 by Marasco et al.; and PCT Publication No. WO 95/03832 by Duan et al.).
[0193] To inhibit protein activity using an intracellular antibody, a recombinant expression vector is prepared which encodes the antibody chains in a form such that, upon introduction of the vector into a cell, the antibody chains are expressed as a functional antibody in an intracellular compartment of the cell.
[0194] In another embodiment, an inhibitory compound of the invention is a peptidic compound derived from the XBP1 amino acid sequence or the amino acid sequence of a molecule in a biologicalon pathway involving XBP1.
[0195] The peptidic compounds of the invention can be made intracellularly in cells by introducing into the cells an expression vector encoding the peptide. Such expression vectors can be made by standard techniques using oligonucleotides that encode the amino acid sequence of the peptidic compound. The peptide can be expressed in intracellularly as a fusion with another protein or peptide (e.g., a GST fusion). Alternative to recombinant synthesis of the peptides in the cells, the peptides can be made by chemical synthesis using standard peptide synthesis techniques. Synthesized peptides can then be introduced into cells by a variety of means known in the art for introducing peptides into cells (e.g., liposome and the like).
[0196] In addition, dominant negative proteins (e.g., of XBP1 or IRE-1α) can be made which include XBP1 or IRE-1α(e.g., portions or variants thereof) that compete with native (i.e., wild-type) molecules, but which do not have the same biological activity. Such molecules effectively decrease, e.g., XBP1 IRE-1α activity in a cell.
[0197] Other inhibitory agents that can be used to specifically inhibit the activity of XBP1 or a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) are chemical compounds that directly inhibit expression, processing, post-translational modification, and/or activity of XBP1. Such compounds can be identified using screening assays that select for such compounds, as described in detail above as well as using other art recognized techniques.
[0198] In certain embodiments, targeting XBP1 inhibits tumor growth. In certain embodiments, targeting XBP1 inhibits ovarian tumor growth.
[0199] The present invention provides that constitutive activation of the UPR in dendritic cells prevents a proper anti-tumor immune response. In certain embodiments, targeting XBP1 results in an anti-tumor immune response. In certain embodiments, the anti-tumor immune response is the proliferation and infiltration of T cells targeted for a specific tumor-associated antigen.

Screening Assays

[0200] In one aspect, the invention features methods for identifying compounds useful in enhancing or inducing anti-tumor immunity in a subject, such compounds have the potential for therapeutic use in the treatment of cancer, such as ovarian cancer. In other aspects, the invention features methods for identifying compounds useful in inhibiting the growth of ovarian cancer cells, such compounds having potential therapeutic use in the treatment of ovarian cancer. As described herein, the instant invention is based, at least in part, on the discovery of a previously unknown role for XBP1 in anti-tumor immunity and ovarian cancer, such a role being linked to anti-tumor immunity directed by tumor-associated dendritic cells. In exemplary aspects the invention features methods for identifying compounds useful for inducing or enhancing anti-tumor immunity and inhibiting the growth of ovarian cancer cells, the methods featuring screening or assaying for compounds that modulate, e.g., activate or increase, or inhibit or decrease, the activation of IRE-1/XBP1. In exemplary aspects, the methods comprise: providing an indicator composition comprising XBP1, or biologically active portions thereof; contacting the indicator composition with each member of a library of test compounds; selecting from the library of test compounds a compound of interest that interacts with XBP1, or biologically active portions thereof; and contacting ovarian cancer cells with the compound of interest, wherein the ability of the compound to enhance or induce anti-tumor immunity in the subject is indicated by the ability of the compound to inhibit growth of ovarian cancer cells as compared to the growth of ovarian cancer cells in the absence of the compound.
[0201] In another exemplary aspect, the methods comprise: providing an indicator composition comprising XBP1, or biologically active portions thereof; contacting the indicator composition with each member of a library of test compounds: and selecting from the library of test compounds a compound of interest that decreases the activity of XBP1, or biologically active portions thereof, wherein the ability of a compound to induce anti-tumor immunity or inhibit growth of ovarian cancer cells is indicated by a decrease in the activation as compared to the amount of activation in the absence of the compound.
[0202] As used herein, the term “contacting” (i.e., contacting a cell e.g. a cell, with a compound) includes incubating the compound and the cell together in vitro (e.g., adding the compound to cells in culture) as well as administering the compound to a subject such that the compound and cells of the subject are contacted in vivo. The term “contacting” does not include exposure of cells to an XBP1 modulator that may occur naturally in a subject (i.e., exposure that may occur as a result of a natural physiological process).
[0203] As used herein, the term “test compound” refers to a compound that has not previously been identified as, or recognized to be, a modulator of the activity being tested. The term “library of test compounds” refers to a panel comprising a multiplicity of test compounds.
[0204] As used herein, the term “indicator composition” refers to a composition that includes a protein of interest (e.g., XBP1 or a molecule in a biological pathway involving XBP1, such as IRE-1α), for example, a cell that naturally expresses the protein, a cell that has been engineered to express the protein by introducing one or more of expression vectors encoding the protein(s) into the cell, or a cell free composition that contains the protein(s) (e.g., purified naturally-occurring protein or recombinantly-engineered protein(s)).
[0205] As used herein, the term “cell” includes prokaryotic and eukaryotic cells. In one embodiment, a cell of the invention is a bacterial cell. In another embodiment, a cell of the invention is a fungal cell, such as a yeast cell. In another embodiment, a cell of the invention is a vertebrate cell, e.g., an avian or mammalian cell. In a preferred embodiment, a cell of the invention is a murine or human cell. As used herein, the term “engineered” (as in an engineered cell) refers to a cell into which a nucleic acid molecule e.g., encoding an XBP1 protein (e.g., a spliced and/or unspliced form of XBP1) has been introduced.
[0206] As used herein, the term “cell free composition” refers to an isolated composition, which does not contain intact cells. Examples of cell free compositions include cell extracts and compositions containing isolated proteins.
[0207] The cells used in the instant assays can be eukaryotic or prokaryotic in origin. For example, in one embodiment, the cell is a bacterial cell. In another embodiment, the cell is a fungal cell, e.g., a yeast cell. In another embodiment, the cell is a vertebrate cell, e.g., an avian or a mammalian cell. In a preferred embodiment, the cell is a human cell. The cells of the invention can express endogenous XBP1 or can be engineered to do so. For example, a cell that has been engineered to express the XBP1 protein can be produced by introducing into the cell an expression vector encoding the protein. Recombinant expression vectors can be used for expression of XBP1.
[0208] In another embodiment, the indicator composition is a cell free composition. XBP1 expressed by recombinant methods in a host cells or culture medium can be isolated from the host cells, or cell culture medium using standard methods for protein purification. For example, ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffinity purification with antibodies can be used to produce a purified or semi-purified protein that can be used in a cell free composition. Alternatively, a lysate or an extract of cells expressing the protein of interest can be prepared for use as cell-free composition.

Pharmaceutical Compositions and Modes of Administration

[0209] Pharmaceutical compositions of the invention can be administered in combination therapy, i.e., combined with other agents. Agents include, but are not limited to, in vitro synthetically prepared chemical compositions, antibodies, antigen-binding regions, and combinations and conjugates thereof. In certain embodiments, an agent can act as an agonist, antagonist, allosteric modulator, or toxin.
[0210] In certain embodiments, the invention provides for pharmaceutical compositions comprising an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) with a pharmaceutically acceptable diluent, carrier, solubilizer, emulsifier, preservative and/or adjuvant. In certain embodiments, acceptable formulation materials preferably are nontoxic to recipients at the dosages and concentrations employed. In certain embodiments, the formulation material(s) are for s.c. and/or I.V. administration. In certain embodiments, the pharmaceutical composition can contain formulation materials for modifying, maintaining or preserving, for example, the pH, osmolality, viscosity, clarity, color, isotonicity, odor, sterility, stability, rate of dissolution or release, adsorption or penetration of the composition. In certain embodiments, suitable formulation materials include, but are not limited to, amino acids (such as glycine, glutamine, asparagine, arginine or lysine): antimicrobials; antioxidants (such as ascorbic acid, sodium sulfite or sodium hydrogen-sulfite); buffers (such as borate, bicarbonate, Tris-HCl, citrates, phosphates or other organic acids); bulking agents (such as mannitol or glycine); chelating agents (such as ethylenediamine tetraacetic acid (EDTA)); complexing agents (such as caffeine, polyvinylpyrrolidone, beta-cyclodextrin or hydroxypropyl-beta-cyclodextrin); fillers; monosaccharides; disaccharides; and other carbohydrates (such as glucose, mannose or dextrins); proteins (such as serum albumin, gelatin or immunoglobulins); coloring, flavoring and diluting agents; emulsifying agents; hydrophilic polymers (such as polyvinylpyrrolidone); low molecular weight polypeptides; salt-forming counteriorns (such as sodium); preservatives (such as benzalkonium chloride, benzoic acid, salicylic acid, thimerosal, phenethyl alcohol, methylparaben, propylparaben, chlorhexidine, sorbic acid or hydrogen peroxide); solvents (such as glycerin, propylene glycol or polyethylene glycol); sugar alcohols (such as mannitol or sorbitol); suspending agents: surfactants or wetting agents (such as pluronics, PEG, sorbitan esters, polysorbates such as polysorbate 20, polysorbate 80, triton, tromethamine, lecithin, cholesterol, tyloxapal); stability enhancing agents (such as sucrose or sorbitol); tonicity enhancing agents (such as alkali metal halides, preferably sodium or potassium chloride, mannitol sorbitol); delivery vehicles: diluents; excipients and/or pharmaceutical adjuvants. (Remington's Pharmaceutical Sciences, 18th Edition, A. R. Gennaro, ed., Mack Publishing Company (1995). In certain embodiments, the formulation comprises PBS; 20 mM NaOAC, pH 5.2, 50 mM NaCl; and/or 10 mM NAOAC, pH 5.2, 9% Sucrose. In certain embodiments, the optimal pharmaceutical composition will be determined by one skilled in the art depending upon, for example, the intended route of administration, delivery format and desired dosage. See, for example, Remington's Pharmaceutical Sciences, supra. In certain embodiments, such compositions may influence the physical state, stability, rate of in vivo release and rate of in vivo clearance of an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α).
[0211] In certain embodiments, the primary vehicle or carrier in a pharmaceutical composition can be either aqueous or non-aqueous in nature. For example, in certain embodiments, a suitable vehicle or carrier can be water for injection, physiological saline solution or artificial cerebrospinal fluid, possibly supplemented with other materials common in compositions for parenteral administration. In certain embodiments, the saline comprises isotonic phosphate-buffered saline. In certain embodiments, neutral buffered saline or saline mixed with serum albumin are further exemplary vehicles. In certain embodiments, pharmaceutical compositions comprise Tris buffer of about pH 7.0-8.5, or acetate buffer of about pH 4.0-5.5, which can further include sorbitol or a suitable substitute therefore. In certain embodiments, a composition comprising an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) can be prepared for storage by mixing the selected composition having the desired degree of purity with optional formulation agents (Remington's Pharmaceutical Sciences, supra) in the form of a lyophilized cake or an aqueous solution. Further, in certain embodiments, a composition comprising an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) can be formulated as a lyophilizate using appropriate excipients such as sucrose.
[0212] In certain embodiments, the pharmaceutical composition can be selected for parenteral delivery. In certain embodiments, the compositions can be selected for inhalation or for delivery through the digestive tract, such as orally. The preparation of such pharmaceutically acceptable compositions is within the ability of one skilled in the art.
[0213] In certain embodiments, the formulation components are present in concentrations that are acceptable to the site of administration. In certain embodiments, buffers are used to maintain the composition at physiological pH or at a slightly lower pH, typically within a pH range of from about 5 to about 8.
[0214] In certain embodiments, when parenteral administration is contemplated, a therapeutic composition can be in the form of a pyrogen-free, parenterally acceptable aqueous solution comprising a desired XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) in a pharmaceutically acceptable vehicle. In certain embodiments, a vehicle for parenteral injection is sterile distilled water in which an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) is formulated as a sterile, isotonic solution, properly preserved. In certain embodiments, the preparation can involve the formulation of the desired molecule with an agent, such as injectable microspheres, bio-erodible particles, polymeric compounds (such as polylactic acid or polyglycolic acid), beads or liposomes, that can provide for the controlled or sustained release of the product which can then be delivered via a depot injection. In certain embodiments, hyaluronic acid can also be used, and can have the effect of promoting sustained duration in the circulation. In certain embodiments, implantable drug delivery devices can be used to introduce the desired molecule.
[0215] In certain embodiments, a pharmaceutical composition can be formulated for inhalation. In certain embodiments, an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) can be formulated as a dry powder for inhalation. In certain embodiments, an inhalation solution comprising an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) can be formulated with a propellant for aerosol delivery. In certain embodiments, solutions can be nebulized. Pulmonary administration is further described in PCT application No. PCT/US94/001875, which describes pulmonary delivery of chemically modified proteins.
[0216] In certain embodiments, it is contemplated that formulations can be administered orally. In certain embodiments, an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) that is administered in this fashion can be formulated with or without those carriers customarily used in the compounding of solid dosage forms such as tablets and capsules. In certain embodiments, a capsule can be designed to release the active portion of the formulation at the point in the gastrointestinal tract when bioavailability is maximized and pre-systemic degradation is minimized. In certain embodiments, at least one additional agent can be included to facilitate absorption of an XBP1 inhibitor or absorption of an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α). In certain embodiments, diluents, flavorings, low melting point waxes, vegetable oils, lubricants, suspending agents, tablet disintegrating agents, and binders can also be employed.
[0217] In certain embodiments, a pharmaceutical composition can involve an effective quantity of an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) in a mixture with non-toxic excipients, which are suitable for the manufacture of tablets. In certain embodiments, by dissolving the tablets in sterile water, or another appropriate vehicle, solutions can be prepared in unit-dose form. In certain embodiments, suitable excipients include, but are not limited to, inert diluents, such as calcium carbonate, sodium carbonate or bicarbonate, lactose, or calcium phosphate; or binding agents, such as starch, gelatin, or acacia or lubricating agents such as magnesium stearate, stearic acid, or talc.
[0218] Additional pharmaceutical compositions will be evident to those skilled in the art, including formulations involving an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) in sustained- or controlled-delivery formulations. In certain embodiments, techniques for formulating a variety of other sustained- or controlled-delivery means, such as liposome carriers, bio-erodible microparticles or porous beads and depot injections, are also known to those skilled in the art. See for example, PCT Application No. PCT/US93/00829, which describes the controlled release of porous polymeric microparticles for the delivery of pharmaceutical compositions. In certain embodiments, sustained-release preparations can include semipermeable polymer matrices in the form of shaped articles, e.g. films, or microcapsules. Sustained release matrices can include polyesters, hydrogels, polylactides (U.S. Pat. No. 3,773,919 and EP 058,481), copolymers of L-glutamic acid and gamma ethyl-L-glutamate (Sidman et al., Biopolymers. 22:547-556 (1983)), poly (2-hydroxyethyl-methacrylate) (Langer et al., J. Biomed. Mater. Res., 15: 167-277 (1981) and Langer, Chem. Tech., 12:98-105 (1982)), ethylene vinyl acetate (Langer et al., supra) or poly-D(−)-3-hydroxybutyric acid (EP 133,988). In certain embodiments, sustained release compositions can also include liposomes, which can be prepared by any of several methods known in the art. See, e.g., Eppstein et al, Proc. Natl. Acad. Sci. USA, 82:3688-3692 (1985); EP 036,676, EP 088,046 and EP 143,949.
[0219] The pharmaceutical composition to be used for in vivo administration typically is sterile. In certain embodiments, this can be accomplished by filtration through sterile filtration membranes. In certain embodiments, where the composition is lyophilized, sterilization using this method can be conducted either prior to or following lyophilization and reconstitution. In certain embodiments, the composition for parenteral administration can be stored in lyophilized form or in a solution. In certain embodiments, parenteral compositions generally are placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle.
[0220] In certain embodiments, once the pharmaceutical composition has been formulated, it can be stored in sterile vials as a solution, suspension, gel, emulsion, solid, or as a dehydrated or lyophilized powder. In certain embodiments, such formulations can be stored either in a ready-to-use form or in a form (e.g., lyophilized) that is reconstituted prior to administration.
[0221] In certain embodiments, kits are provided for producing a single-dose administration unit. In certain embodiments, the kit can contain both a first container having a dried protein and a second container having an aqueous formulation. In certain embodiments, kits containing single and multi-chambered pre-filled syringes (e.g., liquid syringes and lyosyringes) are included.
[0222] In certain embodiments, the effective amount of a pharmaceutical composition comprising an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α), to be employed therapeutically will depend, for example, upon the therapeutic context and objectives. One skilled in the art will appreciate that the appropriate dosage levels for treatment, according to certain embodiments, will thus vary depending, in part, upon the molecule delivered, the indication for which an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) is being used, the route of administration, and the size (body weight, body surface or organ size) and/or condition (the age and general health) of the patient. In certain embodiments, the clinician can titer the dosage and modify the route of administration to obtain the optimal therapeutic effect.
[0223] In certain embodiments, the frequency of dosing will take into account the pharmacokinetic parameters of an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) in the formulation used. In certain embodiments, a clinician will administer the composition until a dosage is reached that achieves the desired effect. In certain embodiments, the composition can therefore be administered as a single dose, or as two or more doses (which may or may not contain the same amount of the desired molecule) over time, or as a continuous infusion via an implantation device or catheter. Further refinement of the appropriate dosage is routinely made by those of ordinary skill in the art and is within the ambit of tasks routinely performed by them. In certain embodiments, appropriate dosages can be ascertained through use of appropriate dose-response data.
[0224] In certain embodiments, the route of administration of the pharmaceutical composition is in accord with known methods, e.g. orally, systemically, locally, through injection by intravenous, intraperitoneal, intracerebral (intra-parenchymal), intracerebroventricular, intratumoral, intramuscular, subcutaneously, intra-ocular, intraarterial, intraportal, or intralesional routes; by sustained release systems or by implantation devices. In certain embodiments, the compositions can be administered by bolus injection or continuously by infusion, or by implantation device. In certain embodiments, individual elements of the combination therapy may be administered by different routes.
[0225] In certain embodiments, the composition can be administered locally via implantation of a membrane, sponge or another appropriate material onto which the desired molecule has been absorbed or encapsulated. In certain embodiments, where an implantation device is used, the device can be implanted into any suitable tissue or organ, and delivery of the desired molecule can be via diffusion, timed-release bolus, or continuous administration. In certain embodiments, it can be desirable to use a pharmaceutical composition comprising an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) in an ex vivo manner. In such instances, cells, tissues and/or organs that have been removed from the patient are exposed to a pharmaceutical composition comprising an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α), after which the cells, tissues and/or organs are subsequently implanted back into the patient.
[0226] In certain embodiments, an XBP1 inhibitor or an inhibitor of a molecule in a biological pathway involving XBP1 (e.g., IRE-1α) can be delivered by implanting certain cells that have been genetically engineered, using methods such as those described herein, to express and secrete the polypeptides. In certain embodiments, such cells can be animal or human cells, and can be autologous, heterologous, or xenogeneic. In certain embodiments, the cells can be immortalized. In certain embodiments, in order to decrease the chance of an immunological response, the cells can be encapsulated to avoid infiltration of surrounding tissues. In certain embodiments, the encapsulation materials are typically biocompatible, semi-permeable polymeric enclosures or membranes that allow the release of the protein product(s) but prevent the destruction of the cells by the patient's immune system or by other detrimental factors from the surrounding tissues.
[0227] In other embodiments, ex vivo treatment of dendritic cells with an inhibitor of XBP1 (e.g., siRNA) can be used to activate, induce, enhance or promote the antigen presenting capacity of dendritic cells. The activated dendritic cells can then be administered to a subject. In some embodiments, the dendritic cells may be tumor-associated dendritic cells.
[0228] This invention is further illustrated by the following examples which should not be construed as limiting. The contents of all references, patents, and published patent applications cited throughout this application, as well as the figures and the sequence listing, are hereby incorporated by reference.

EXAMPLES

Experimental Procedures

Tissues, Mice and Cell Lines

[0229] Stage III-IV human ovarian carcinoma specimens and malignant ascites samples were procured through Surgical Pathology at Weill Cornell Medical College/New York-Presbyterian Hospital under an approved protocol where research samples remained totally unidentified. Tumor single cell suspensions were generated as previously described (Conejo-Garcia et al., 2005). Malignant peritoneal ascites samples from patients with metastatic ovarian cancer were centrifuged for 10 min at 1300 rpm and red blood cells were lysed prior to FACS analysis. Mice were housed at the animal facilities of Harvard School of Public School, Weill Cornell Medical College, or The Wistar Institute. The Institutional Animal Care and Use Committee approved all animal experiments described in this study. XBP1f/f mice were generated as previously described (Lee et al., 2008) and have been backcrossed at least 15 generations onto C57BL/6 mice. Wild type, OT-1 transgenic, Itgax-Cre (CD11c-Cre) and Rag2-deficient mice, all in a full C57BL/6 background, were purchased from Jackson Laboratories (Bar Harbor, Me.).
[0230] Double transgenic LSL-K-rasG12D/+p53loxp/loxp (p53/K-ras) mice were generated by obtaining LSL-K-rastm4Tyj (Jackson et al., 2001) and Trp53tm1Brn (Jonkers et al., 2001) from the NCI mouse models of human cancer consortium and bred to a full C57BL/6 background as previously reported (Scarlett et al., 2012). p53/K-ras mice were irradiated two consecutive days with 650 rads followed by reconstitution with bone marrow from XBP1f/f or XBP1f/f CD11c-Cre mice. 8 weeks post bone-marrow reconstitution autochthonous ovarian tumors were initiated by delivery of adenovirus-expressing Cre recombinase (ADV-Cre) into the ovarian bursa as previously reported (Dinulescu et al., 2005; Flesken-Nikitin et al., 2003; Scarlett et al., 2012). Seven weeks after tumor initiation, mice were sacrificed. Tumors, approximately 2-3 cm in diameter, were resected under sterile conditions after euthanizing the mouse. Specimens were then minced into pieces <3 mm in diameter and digested for 1 hour at 37° C. in RPMI containing 2 mg/mL collagenase Type D and 1 mg/ml DNAse I. The digested tissue pieces were then pressed through a 70 μm strainer to create a single cell suspension. Red blood cells were lysed using ACK lysis buffer and pellets from single-cell suspensions were resuspended to 50-100×106 cells/ml in freezing media (FBS containing 10% DMSO) and incubated on ice for 30 minutes. Tubes were then transferred to −80° C. for long-term storage.
[0231] Parental ID8 or aggressive ID8-Defb29/Vegf-A intraperitoneal ovarian tumors were generated as previously described (Conejo-Garcia et al., 2004; Roby et al., 2000). Briefly, 1-2×106 tumor cells were injected into wild type C57BL/6 mice or conditional XBP1-deficient mice. Implanted animals progressively developed multiple peritoneal masses and eventually massive ascites in ˜35 days (ID8-Defb29/Vegf-A) or in ˜2 months (parental ID8). Mice were weighted weekly to monitor malignant ascites accumulation and animals with severe abdominal distension were humanely euthanized.

Isolation of Human and Mouse DCs

[0232] Human patient ovarian cancer-associated DCs (CD45+CD3CD20CD11c+DEC205+) were sorted from tumor single cell suspensions or malignant ascites using flow cytometry, following the gating strategy described in FIG. 1. During sorting, viable cells were identified using the LIVE/DEAD Fixable Yellow Dead Cell Stain Kit (Life Technologies). Mouse ovarian cancer-associated DCs (CD45+CD11c+CD11b+MHC-II+CD8α) were sorted from single-cell suspensions of p53/K-ras-driven ovarian tumors or from peritoneal wash (10 ml 1×PBS) or total malignant ascites samples from mice bearing aggressive ID8-Defb29/Vegf/A intraperitoneal ovarian cancer, following the gating strategy described in FIG. 1. All fluorescently-labeled antibodies were from BioLegend. Control sDCs (CD45+CD11c+CD11b+MHC-II+CD8α) were FACS sorted from spleens of naïve or ovarian cancer-bearing mice using Collagenase D and DNAse I treatment followed by incubation with the indicated antibodies.

Reagents and In Vitro Cellular Treatments

[0233] Murine recombinant cytokines were purchased from Peprotech. Cobalt chloride, Tunicamycin (used at 1 μg/ml), Tiron (used at 100-500 μM) and Vitamin E (α-tocopherol, used at 50-100 μM) were from Sigma. DCFDA staining was utilized for intracellular ROS detection (Abcam). Purified 4-HNE was obtained from Cayman Chemical and 4-HNE-protein adducts in ascites samples and DCs were detected and quantified through competitive ELISA (Cell Biolabs). TOFA (Cayman Chemical) was used at a final concentration of 5 μg/ml to inhibit fatty acid synthesis in DCs by blocking the synthesis of malonyl-CoA by acetyl-CoA carboxylase. The IRE-1α-specific inhibitor 4μ8c (Millipore) was used at a final concentration of 10 μM.

Conventional and Quantitative RT-PCR

[0234] Total RNA from human samples was isolated using the miRVANA miRNA isolation Kit (Life Technologies). RNA from mouse samples was isolated using the Qiazol reagent (Qiagen). 0.1-1 μg of RNA were used to generate cDNA using the High Capacity cDNA Reverse Transcription Kit (Life Technologies). Human and mouse Xbp1 splicing assays were performed as described (Lee et al., 2003a; Martinon et al., 2010) using conventional Reverse Transcription PCR (RT-PCR) and primers shown in Table 1. Gene expression analysis was done via Reverse Transcription quantitative PCR (RT-qPCR) using a Stratagene Mx3005 instrument and SYBR green I (Life Technologies). Murine XBP1s transcript expression was determined using a probe that spans the spliced-out version as previously demonstrated (Reimold et al., 2001). All primers used in this study are described in Table 1.

Western Blot

[0235] 5×106 sDC or tDC were washed twice in 1× cold PBS and nuclear proteins were purified using the Nuclear Extraction Kit (Life Technologies). Proteins were quantified using the BCA method (Pierce) and 15-20 μg of nuclear proteins were separated via SDS-PAGE and transferred onto nitrocellulose membranes following standard procedures. Anti-mouse XBP1s (GL Biochem) was raised in rabbit using a peptide corresponding to the XBP1s C-terminus, and was used at a 1:500 dilution for immunoblotting. Goat anti-mouse Lamin B (Santa Cruz) was used at 1:2000. HRP-conjugated secondary antibodies to rabbit and mouse (Santa Cruz) were used at a 1:2000 dilution. SuperSignal West Femto (Pirce) was used as Chemiluminescent Substrate and blots were imaged using a FluorChemE instrument (ProteinSimple).

RNA-Seq and DC Transcriptional Profile

[0236] tDCs were sorted from peritoneal wash samples of XBP1f/f or XBP1f/f CD11c-Cre female mice (n=3/group) bearing aggressive ID8-Defb29/Vegf-A ovarian tumors for 3 weeks. Total RNA was isolated using the miRVANA miRNA isolation Kit (Life Technologies) and further concentrated via RNeasy MinElute columns (Qiagen). RNA quality and integrity was confirmed in an Agilent Bioanalyzer 2100. In all cases RINs were 9.50 or higher. mRNA libraries were generated and sequenced at the Epigenomics Facility of Weill Cornell Medical College. Reads produced from 51 bp single end sequencing run were aligned against mouse genome (mm9) using Bowtie v0.12.8 (Langmead et al., 2009) algorithm. Mouse mm9 transcriptome information was obtained from UCSC Genome Browser and RSEM algorithm (Li and Dewey, 2011) was used to calculate number of aligned tags for each gene. Differential expression between two groups were tested by EdgeR (Robinson and Oshlack, 2010) and significance was defined using a False Discovery Rate (FDR) cutoff of 0.15. The most up-to-date gene information (official symbol and description) was obtained from NCBI Entrez information on May 15th 2014. Normalized expression RPKM values (Reads Per Kilobase of transcript per Million mapped reads) values were generated by EdgeR and used to demonstrate gene expression across samples as color-coded fold change of expression in a sample versus average expression across all samples. Functional enrichment analysis was done using QIAGEN's Ingenuity Pathway Analysis (IPA®, QIAGEN Redwood City, www.qiagen.com/ingenuity). For IPA upstream analysis, only regulators significant at p<10−6 with predicted activation/inhibition states (Z-score>2) were considered. Significantly affected biological processes were tested by using NCBI DAVID (Huang da et al., 2009) software using level 3 of GO biological processes and considering only FDR<0.15 results that showed at least 20 genes that constitute at least ⅔ of all involved in the process genes specifically up or down-regulated.

Flow Cytometry and Lipid Staining

[0237] Intracellular lipid content in DCs was evaluated via flow cytometry using 4,4-Difluoro-1,3,5,7,8-Pentamethyl-4-Bora-3a,4a-Diaza-s-Indacene (BODIPY 493/503. Life Technologies) as previously reported (Herber et al., 2010). Briefly, 5×106 cells from total spleen single cell suspensions or malignant peritoneal wash samples were conventionally stained for surface markers using fluorescently-labeled antibodies that do not overlap with BODIPY 493/503, namely CD11c-APC, CD45-APC-Cy7 and CD11b-Pacific Blue. Cells were washed twice with 1×PBS and stained with 500 μl of BODIPY 493/503 at 0.5 mg/ml in PBS for 15 min at room temperature in the dark. Cells were washed twice and analyzed by flow cytometry. BODIPY 493/503 staining was detected in the PE channel. For intracellular cytokine staining, 5×106 cells isolated from malignant peritoneal wash samples of ovarian cancer-bearing mice were stimulated for 6 h in 10% FBS complete RPMI containing PMA (Calbiochem), lonomycin (Calbiochem) and Brefeldin A (BioLegend). Cells were collected and stained for surface markers and intracellular cytokines following the FoxP3/Transcription Factor Staining buffer set (eBioscience). All antibodies were from BioLegend. Flow cytometry was performed on a LSRII instrument (BD Biosciences). Cell populations were sorted from peritoneal washes (10 ml 1×PBS) of ovarian carcinoma-bearing mice or from human ascites or tumor single-cell suspensions using a FACSAria sorter (BD Biosciences). Flow cytometry data was analyzed using FlowJo version 9 or 10.

Transmission Electron Microscopy and Lipidomics

[0238] tDC were sorted from the peritoneal cavity of XBP1f/f or XBP1f/f CD11c-Cre female mice bearing ID8-Defb29/Vegf-A ovarian tumors for 3 to 4 weeks as shown in FIG. 1. Cells were washed twice with 1×PBS and pellets were fixed and sectioned for electron microscopy analysis (performed at the Electron Microscopy and Histology Core Facility of Weill Cornell Medical College) following standard methods. Alternatively, cell pellets from 0.5-1×106 sorted tDCs were frozen and total intracellular lipids were extracted and quantitatively analyzed via LC-MS at the Lipidomics Core Facility of Wayne State University School of Medicine.

Antigen Processing and Presentation

[0239] For in vitro antigen presentation experiments, tDC or sDC were sorted from the peritoneal cavity or spleen of XBP1f/f or XBP1f/fCD11c-Cre female mice bearing ID8-Defb29/Vegf-A ovarian tumors for 4 weeks (FIG. 1). tDCs were pulsed for overnight 50 μg/ml of full-length endotoxin-free OVA (SIGMA, Grade VII) in the presence or absence of Vitamin E (50 μg/ml) in media containing 25% cell-free ovarian cancer ascites supernatants. DCs were washed twice and cocultured for 3 days with CFSE-labeled CD8+ T cells immunopurified from OT-1 mice at a 1:10 (DC to T cell) ratio, as previously described (Scarlett et al., 2009).
[0240] For in vivo antigen presentation experiments, wild type C57BL/6 female mice bearing ID8-Defb29/Vegf-A ovarian tumors for three weeks were intraperitoneally injected with 0.6 mg of full length endotoxin-free OVA (SIGMA, grade VII) and 3 hours later, mice were left untreated or injected with siRNA-PEI nanoparticles (see below). 18 hours later, mice were transferred intraperitoneally with 2×106 CFSE-labeled T cells negatively purified from OT-1 transgenic mice. Peritoneal wash samples (10 mL) were collected after 72 hours and analyzed for CFSE dilution via FACS. Data were analyzed using FlowJo version 10. Division Index determines the average number of cell divisions that a cell in the original population has undergone. Proliferation Index shows the total number of divisions of only responding (proliferating) cells. Replication Index is the fold-expansion of the responding cells, thus indicating the expansion capability of the replicating cells.

Preparation of siRNA-PEI Nanoparticles and Therapeutic In Vive Silencing

[0241] Endotoxin-free rhodamine-labeled and unconjugated polyethylenimine (PEI) for in vivo experiments “in vivo-jetPEI” was purchased from PolyPlus Transfection. To generate siRNA-PEI nanocomplexes, 50 μg of siRNA were complexed with “in vivo-jetPEI” at N/P ratio of 6, following the recommendations of the manufacturer and previously optimized conditions (Cubillos-Ruiz et al., 2009). All siRNA oligonucleotides were from IDT and included 2′-OMe modified nucleotides and specific phosphorothioate linkages, as previously reported (Piret et al., 2002). Sequences for the sense and antisense strands are as follows: siLuc sense: 5′-CuUACgcUGAguaCUUcGAdTsdT-3′, siLuc antisense: 5′-UCgAAGUACUCAGCgUAAGdTdsT-3′, siXBP1 sense: 5′-cAcccuGAAuucAuuGucudTsdT-3′, siXBP1 antisense: 5′-AGAcAAUGAAUUcAGGGUGdTsdT-3′. siIRE1a sense: 5′-AuGccGAAGuucAGAuGGAdTsdT-3′, siIRE1a antisense: 5′-UCcAUCUGAACUUCGGcAUdTsdT-3′. 2′-OMe modified nucleotides are in lower case. Phosphorothioate linkages are represented by “s” and “d” indicates DNA bases.
[0242] For in vivo biodistribution, phenotypic and silencing experiments, mice bearing ID8-Defb29/Vegf-A tumors for 3-4 weeks were intraperitoneally injected with rhodamine-labeled siXBP1-PEI or siLuc-PEI nanoparticles (50 μg of siRNA complexed with rhodamine-labeled “in vivo-jetPEI” at N/P 6, per mouse). Rhodamine+CD45+CD11c+CD11b+MHC-II+ tDC were sorted after 3 days for downstream molecular biology analysis. For repeated siRNA treatments, wild-type C57BL/6 female mice were intraperitoneally injected with 1×106 aggressive ID8-Defb29/Vegf-A ovarian carcinoma cells, and mice received nanocomplexes (50 μg of siRNA complexed with “in vivo-jetPEI” at N/P 6, per mouse) at days 12, 16, 20, 24, 28 and 32 after tumor implantation.

Anti-tumor immune responses and ELISA

[0243] Mice were intraperitoneally injected with ID8-Defb29/Vegf-A ovarian cancer cells and treated with siRNA-PEI nanoparticles (n=3/group) at days 8, 13, 18, and 23 after challenge. Total splenic T cells or Ficoll-enriched leukocytes (2-3×105) from peritoneal wash samples were obtained 4 days after the last treatment (day 27) and cocultured in 10% FBS RPMI with 2-3×104 bone marrow-derived DCs previously pulsed overnight with irradiated ID8-Defb29/Vegf-A ovarian cancer cells. Supernatants were collected after 48-72 h of stimulation. IFN-γ and Granzyme B secretion cells was determined by ELISA using the Ready-SET-Go Kit (eBioscience).

Statistical Analysis

[0244] Unless noted otherwise, all experiments were repeated at least two times and results were similar between repeats. The correlation between CHOP expression in tDC and human intra-tumoral T cell infiltration was analyzed using the Spearman's Rank coefficient. Animal experiments used between 3 and 6 mice per group. A P value<0.05 was considered to be statistically significant. All statistical analyses were done using Graph Pad Prism 5.0. Differences between the means of experimental groups were calculated using a two-tailed unpaired Student's/test. Error bars represent standard error of the mean from independent samples assayed within the represented experiments. Survival rates were compared using the Log-Rank test. All survival experiments used at least 6 mice/group. This number provides a 5% significance level and 95% power to detect differences in survival of 20% or greater.

Example 1: Constitutive XBP1 Activation in Ovarian Cancer-Associated DCs

[0245] Innate myeloid cells with phenotypic and functional attributes of regulatory DCs commonly infiltrate ovarian tumors (Conejo-Garcia et al., 2004; Huarte et al., 2008; Scarlett et al., 2012). Rather than inducing anti-cancer immunity, these dysfunctional DCs facilitate malignant progression by preventing the activation and expansion of tumor-reactive T cells (Cubillos-Ruiz et al., 2010). To analyze XBP1 activation in human and mouse ovarian cancer-associated DCs, CD45+CD3CD20CD11c+DEC205+ tDCs were isolated via FACS from human patient ovarian tumors or metastatic ovarian cancer ascites samples. Murine CD45+CD11c+MHC-II+ CD11b+CD8α tDCs were isolated from advanced p53/K-ras-driven ovarian tumors or from malignant ascites of mice bearing aggressive ID8-Defb29/Vegf-A ovarian carcinoma for 4-5 weeks and their identity as bona fide classical DCs was confirmed by quantifying Clec9A/DNGR-1 and Zbtb46 expression (FIG. 1). Splicing of the Xbp1 mRNA was evaluated using conventional PCR.
[0246] Malignant peritoneal fluid samples from patients with metastatic ovarian cancer were centrifuged for 10 min at 1300 rpm and total cells were used for FACS analysis. Solid primary or metastatic ovarian tumors were mechanically dissociated as described above. In both cases, CD45+CD3CD20CD11c+DEC205+ tDCs were sorted via FACS for RNA extraction and gene expression quantification via RT-qPCR. The percentage of CD45+CD3+ T cells present in each sample was correlated with CHOP mRNA expression levels in sorted tDCs from the same specimen (FIG. 2F).
[0247] Notably, tumor-associated DCs (tDCs) isolated from multiple human patient ovarian cancer specimens (FIGS. 1A and 1B) or from preclinical models of aggressive primary and metastatic ovarian cancer (FIGS. 1C-1E) (Conejo-Garcia et al., 2004; Scarlett et al., 2012) exhibited constitutive splicing of the Xbp1 mRNA (FIG. 2A), a molecular event essential for generating fully functional XBP1 (Yoshida et al., 2001).
[0248] Expression of the indicated transcripts was determined by RT-qPCR (FIG. 2B, 2D, 2E) (data are normalized to endogenous levels of Actb in each sample. CD45+CD11c+MHC-II+CD11b+CD8α sDCs were isolated from spleens of naïve or tumor-bearing mice), and quantitative analyses demonstrated increased expression of total and spliced Xbp1 mRNA in tDCs, compared with closely related CD8α-splenic DCs (sDCs) (FIG. 1E) isolated either from naïve or ovarian cancer-bearing mice (FIG. 2B).
[0249] Western blot analysis was used to assay the spliced form of XBP1 (XBP1s) protein expression in nuclear extracts obtained from the indicated DCs. Consistently, tDCs exhibited augmented XBP1 protein levels in the nucleus compared with control DCs obtained from non-tumor sites (FIG. 2C). Further confirming these findings, RT-PCR analysis showed marked upregulation of canonical XBP1 target genes ERdj4 and Sec61a1 (Acosta-Alvear et al., 2007; Lee et al., 2003b) (FIG. 2D), as well as increased expression of general ER stress response markers Hspa5 (BiP) and Ddit3 (CHOP) was evidenced only in tDCs (FIG. 2E).
[0250] The expression of CHOP in tDCs sorted from human patient ovarian cancer specimens was determined using RT-qPCR. Interestingly, CHOP expression levels in tDCs negatively correlated with T cell infiltration in several human ovarian cancer specimens analyzed, suggesting a potential role for ER-stressed tDCs in regulating anti-tumor immune responses (FIG. 2F). Together, these data indicate that DCs in the ovarian cancer microenvironment exhibit severe ER stress and robust XBP1 activation.

Example 2: Byproducts of Lipid Peroxidation Trigger ER Stress in DCs

[0251] One goal of the present invention was to investigate how the tumor microenvironment influences the functional status of XBP1 in DCs. In particular, one aim of the present invention was to investigate whether cancer-derived factors could participate in triggering ER stress and XBP1 activation in tumor-infiltrating DCs, and determine whether this process could impact the detrimental function of these innate immune cells in hosts with ovarian cancer. Interestingly, neither tumorigenic/immunosuppressive cytokines commonly enriched at tumor sites nor hypoxia-mimicking conditions caused robust XBP1 activation in DCs (FIG. 3). In particular, naïve sDCs were isolated and stimulated for 24 h with cytokines (e.g., IL-10. TGF-β, VEGFα, KC, CCL3, IL-6) at concentrations ranging from 5 ng/ml to 25 ng/ml (FIG. 3A-D). Cells were also exposed for 24 hours to increasing concentrations of cobalt chloride (CoCl2), a chemical inducer of the HIF1α pathway that mimics low oxygen conditions (Piret et al. 2002) (FIG. 3E-F). Splicing and upregulation of XBP1 was determined by RT-qPCR analysis (FIG. 3).
[0252] Recent reports demonstrate that abnormal intracellular accumulation of peroxided lipids is a common feature of dysfunctional DCs infiltrating multiple human and mouse cancers (Herber et al., 2010; Ramakrishnan et al., 2014). Importantly, lipid oxidation by reactive oxygen species (ROS) generates reactive byproducts such as the unsaturated aldehyde 4-hydroxy-trans-2-nonenal (4-HNE), which has been shown to induce protein-folding stress by forming stable adducts with ER-resident chaperones (Vladykovskaya et al., 2012). Whether these reactive aldehyde byproducts could trigger ER stress in DCs was investigated. Ovarian cancer-associated DCs demonstrated significantly higher amounts of intracellular lipids and augmented ROS levels in comparison with control non-malignant sDCs isolated from the same host or from naïve mice (FIGS. 4A and 4B). Consistent with active lipid peroxidation taking place at tumor sites, cell-free ovarian cancer ascites of human and mouse origin exhibited high levels of 4-HNE-protein adducts (FIG. 4C). Accordingly, intracellular 4-HNE-protein adducts were also readily found in tDCs isolated from these malignant samples (FIG. 4D). 4-HNE generation in mouse tDCs exposed to cell-free ovarian cancer ascites decreased upon exposure to the common antioxidant Vitamin E (FIG. 4E). Incubation of naïve sDCs with increasing concentrations of purified 4-HNE efficiently formed covalent adducts with intracellular proteins (FIG. 4F) and rapidly triggered splicing of the Xbp1 mRNA in an IRE-1α-dependent manner (FIGS. 4G and 4H). Consistently, upregulation of the canonical XBP1-dependent, ER-resident chaperone ERdj4 (FIG. 4I) as well as robust induction of the general ER stress response markers BiP and CHOP (FIG. 4J) was rapidly evidenced in 4-HNE treated DCs.
[0253] These data demonstrate that 4-HNE, a lipid peroxidation byproduct readily available in the ovarian cancer microenvironment, triggers strong ER stress and XBP1 activation in DCs.

Example 3: DC-Intrinsic XBP1 is Necessary for Optimal Ovarian Cancer Progression

[0254] To determine how sustained XBP1 activity in tDCs might influence malignant progression, aggressive orthotopic ovarian tumors in conditional knockout female mice lacking functional XBP1 in DCs were developed (FIG. 5). To this end, mice whose exon 2 of Xbp1 is flanked by two loxP sites (Lee et al., 2008) were crossed with mice expressing Cre recombinase under control of the integrin alpha X (Itgax) promoter (hereafter referred to as CD11c-Cre) (FIG. 5). In this system. Cre-mediated recombination is predominant in conventional DCs, while low amounts of recombination are detected in lymphocytes, NK cells and other myeloid cells (Caton et al., 2007).
[0255] tDCs were sorted from the peritoneal cavity of mice bearing metastatic ID8-VegfA-Def29b ovarian tumors for 4-5 weeks as described in FIG. 1. Total CD11c+ DCs were magnetically immunopurified from spleens (sDC) or from GMCSF-polarized bone marrow cultures obtained from XBP1f/f (wild type) or XBP1f/f CD11c-Cre (conditional knockout) mice. Total splenic T cells and CD11b+F4/80+ macrophages (M0) were also isolated as control populations. Deletion efficiency was determined by RT-qPCR using primers that selectively amplify exon 2 of Xbp1 (see methods) (FIG. 5B). sDCs from naïve XBP1f/f or XBP1f/f CD11c-Cre mice were left untreated or stimulated for 12 h with the ER stressor Tunicamycin at 1 g/ml. Induction of canonical XBP1 target genes ERdj4 and Sec61 upon stimulation was determined via RT-qPCR. In all cases, data were normalized to endogenous Actb expression in each sample. Data are representative of at least three independent experiments with similar results (FIG. 5C).
[0256] It had been previously been reported that overall DC survival was compromised upon extensive ablation of XBP1 in early hematopoietic precursors (Iwakoshi et al., 2007). In contrast, conditional deletion of XBP1 through CD11c-controlled Cre expression solely affected the proportion and number of splenic CD8α+ DCs (FIG. 6). Other immune cell populations in the spleen remained unaffected (FIG. 6) and the frequency of tumor-infiltrating DCs, which are mainly CD8α (FIGS. 1 and 6), was not altered in conditional knockout mice bearing orthotopic ovarian cancers (FIG. 6). These data suggest that XBP1 is dispensable for the optimal survival of DCs in the ovarian cancer microenvironment. Strikingly, the development and metastatic capacity of p53/K-ras-driven primary ovarian tumors (Scarlett et al., 2012) was profoundly compromised in irradiated hosts reconstituted with bone marrow from XBP1-deficient (XBP1f/f CD11c-Cre) donors, compared with control hosts transplanted with bone marrow from XBP1-sufficient (XBP1f/f) littermates (FIGS. 7A-7C). These data demonstrate that XBP1 expression in CD11c+ DCs is crucial for the initiation and rapid progression of ovarian tumors.
[0257] Since the vast majority of ovarian cancers are diagnosed at advanced stages, when the disease has spread throughout the peritoneal cavity, the next goal was to define how DC-derived XBP1 impacts the progression of orthotropic tumors that closely recapitulate the physiopathology of human metastatic ovarian cancer (Conejo-Garcia et al., 2004). Notably, ovarian cancer-bearing female mice lacking functional XBP1 in DCs demonstrated reduced peritoneal tumor burden (FIGS. 7D and 7E), impaired ascites accumulation (FIG. 7F), and diminished tumor-induced splenomegaly (FIG. 7G) compared with control gene-sufficient (XBP1f/f) littermates. Consequently, tumor-bearing mice deficient for XBP1 in DCs showed a marked increase in survival compared with control littermates (FIG. 7H). Similar survival results were observed in XBP1f/f CD11c-Cre mice developing parental orthotopic ovarian tumors (Roby et al., 2000) that do not ectopically express Defb29 and Vegf-A (FIG. 7I). Together, these results demonstrate for the first time that XBP1 expression in DCs is necessary for the aggressive and accelerated progression of primary and metastatic ovarian cancers in preclinical models of disease.

Example 4: XBP1 Activation Disrupts Lipid Homeostasis in DCs

[0258] To elucidate how XBP1 confers pro-tumorigenic activity in ovarian cancer-associated DCs, a comparison of the transcriptional profile of wild type vs. XBP1-deficient DCs residing in malignant ovarian cancer ascites was performed. 416 genes that were significantly downregulated were identified, while 237 genes showed significantly higher expression due to XBP1 deficiency (Table 2). Significantly altered gene subsets were analyzed to identify transcriptional regulators that may explain the observed mRNA changes. Several predicted affected regulators were identified (FIG. 8A) with the expected XBP1 as a top hit. Additionally, XBP1 was a key node in the top gene network found from the data (FIG. 8B). Confirming sustained ER stress in DCs infiltrating ovarian cancer, multiple direct XBP1 target genes and genes implicated in the unfolded protein response (Acosta-Alvear et al., 2007; Lee et al., 2003b) were markedly repressed in XBP1-deficient tDCs (FIG. 9A). Expression of known Regulated IRE-1α-dependent Decay (RIDD) target mRNAs (Hetz et al., 2013; Hollien et al., 2009) was indistinguishable between wild type and XBP1-deficient tDCs (FIG. 8C), indicating that IRE-1α is not artificially overactivated in this cell type due to the absence of functional XBP1 (So et al., 2012). A search was then performed for any biological processes affected by XBP1-deficiency and 4 significantly enriched functional categories were found (FIG. 8D). Of particular interest, tDCs devoid of XBP1 displayed marked downregulation of multiple genes involved in lipid metabolic pathways (FIG. 9B). In light of the strong association between enhanced lipid accumulation and DC dysfunction in cancer (Herber et al., 2010; Ramakrishnan et al., 2014), the role of XBP1 as a potential mediator of this process was investigated. Consistent with sustained ER stress at tumor locations, ovarian cancer-associated DCs exhibited severe upregulation of multiple XBP1-controlled lipid metabolism genes (FIG. 9B), including Agpat6, Fasn and Lpar1, compared with control DCs in lymphoid tissue (FIG. 10A). Of note, these lipid biosynthetic genes were rapidly upregulated in naïve sDCs exposed to the XBP1-activating lipid peroxidation byproduct 4-HNE (FIG. 10B). Most importantly, ovarian cancer-associated DCs lacking XBP1 showed reduced intracellular lipid content compared with their wild type counterparts (FIG. 9C). Further supporting these findings, XBP1-deficient tDC demonstrated a marked decrease in the number of cytosolic lipid droplets (FIGS. 9D and 9E) as well as reduced intracellular levels of total triglycerides (FIG. 9F) compared with XBP1-sufficient tDC. Other lipid classes remained unaffected in tDCs lacking XBP1 (FIG. 10C) and these observations were confirmed by analyzing cell-free ascites supernatants (FIG. 10D). Decreased intracellular lipid content in XBP1-deficient tDCs did not occur due to defective expression of genes encoding scavenger receptors implicated in extracellular lipid uptake, including Cd36, Cd68 and Msr1 (FIG. 10E). Notably, exposure to cell-free ovarian cancer ascites augmented the intracellular lipid content of tDCs and this process that was prevented by treatment with TOFA, an inhibitor of fatty acid synthesis blocking the synthesis of malonyl-CoA by acetyl-CoA carboxylase (FIGS. 9G and 10F). Pharmacological inhibition of IRE-1α/XBP1 activation using 4μ8c also restricted the observed ascites-induced lipid biogenesis in tDCs (FIGS. 9G and 10F). In addition, consistent with the function of ROS as key generator of XBP1-activating 4-HNE (FIG. 4), reduced intracellular lipid content was also evidenced in tDCs treated with the global ROS scavenger Vitamin E, but not with the superoxide-specific scavenger Tiron (FIGS. 9G and 10F). Taken together, the transcriptional and functional data indicate that sustained activation of ER stress sensor XBP1 disrupts intracellular lipid homeostasis in ovarian cancer-associated DCs.

Example 5: XBP1-Deficient tDCs Support T Cell Activation

[0259] Aberrant lipid accumulation by cancer-associated DCs has been demonstrated to obstruct their normal antigen processing and presentation capacity (Herber et al., 2010; Ramakrishnan et al., 2014). Whether XBP1-deficient tDCs with reduced levels of intracellular lipids might support rather than repress T cell activation and function at tumor sites was investigated. While surface expression of MHC molecules and CD80 remained unaltered, tDCs devoid of XBP1 demonstrated higher levels of costimulatory receptors CD40, CD83 and CD86 (FIGS. 11A and 11B). XBP1-deficiency did not alter the antigen-presenting capacity of control CD8α sDCs (FIG. 12). However, XBP1-deficient tDCs pulsed with full-length OVA in the presence of cell-free malignant ascites more efficiently induced the expansion of OT-1 T cells compared with wild type tDCs (FIGS. 11C and 11D). Consistent with impaired lipid accumulation upon global ROS scavenging and IRE-1α/XBP1 inhibition (FIG. 9G), pre-treatment of regulatory wild type tDC with Vitamin E phenocopied the enhanced antigen-presenting capacity exhibited by XBP1-deficient tDCs in this in vitro assay (FIGS. 11C and 11D). Further supporting these findings, conditional knockout mice developing aggressive orthotopic ovarian tumors demonstrated a marked increase in the proportion of infiltrating CD44+IFNγ-secreting CD8+ and CD4+ T cells at tumor sites compared with XBP1-sufficient control littermates (FIGS. 11E and 11F). Together, these data indicate that constitutive XBP1 activation promotes intracellular lipid accumulation in and immune tolerance by ovarian cancer-associated DCs.

Example 6: Therapeutic XBP1 Silencing in tDCs Extends Host Survival by Inducing Anti-Tumor Immunity

[0260] T cells are the only immune population known to exert significant pressure against ovarian cancer progression (Callahan et al., 2008: Curiel et al., 2003; Hamanishi et al., 2007: Han et al., 2008; Sato et al., 2005; Zhang et al., 2003). Indeed, it has been demonstrated that the magnitude of intra-tumoral T cell infiltration strongly correlates with a better outcome in ovarian cancer patients (Zhang et al., 2003). To investigate whether targeting XBP1 function in vivo and in situ could be used to restore the immunogenic attributes of ovarian cancer-associated DCs and hence, promote the function of anti-tumor T cells, polyethylenimine (PEI)-based nanoparticles encapsulating siRNA were utilized (Cubillos-Ruiz et al., 2012: Cubillos-Ruiz et al., 2009). Wild type C57BL/6 female mice were injected with 1-2×10^6 ID8-Defb29/Vegf/A ovarian cancer cells and mice received a single injection of control (luciferase-specific) or XBP1-targeting siRNA encapsulated in rhodamine-labeled PEI-based nanocomplexes 3-4 weeks later (FIG. 13). These nanocomplexes are preferentially and avidly engulfed by abundant phagocytic tDCs upon intraperitoneal (i.p.) injection, a process that enables selective in vivo gene silencing in this leukocyte subset (Cubillos-Ruiz et al., 2009). Importantly. PEI-based nanoparticles inherently activate ovarian cancer-associated DCs by triggering TLR signaling and therefore exhibit potent immunoadjuvant activity against tumors (Cubillos-Ruiz et al., 2009). Confirming our previous findings (Cubillos-Ruiz et al., 2012; Cubillos-Ruiz et al., 2009), nanoparticles were selectively taken-up by tDCs present in malignant ascites of mice bearing metastatic ovarian cancer (FIG. 13A). PEI-based nanocomplexes delivering Xbp1-specific siRNA induced 50-60% gene silencing in target tDC compared with control nanoparticles encapsulating luciferase-targeting siRNA (FIG. 13B). The functional effects of gene silencing were confirmed by the decreased expression of the canonical XBP1 target ERdj4, as well as lipid biosynthesis-related Fasn and Scd2 in tDCs engulfing Xbp1-specific nanocomplexes (FIG. 13C). Due to selective tDC targeting in vivo, Xbp1 mRNA levels remained unaltered in non-DC leukocytes or cancer cells of the tumor microenvironment after nanoparticle injection (not shown). Supporting the findings using tDC from conditional XBP1 knockout mice, the in vivo proliferation of adoptively transferred CFSE-labeled OT-1 T cells in the ovarian cancer microenvironment was significantly enhanced in mice pulsed i.p. with full-length OVA when XBP1 expression was specifically silenced in tDCs (FIGS. 14A-14C). Therapeutic administration of siRNA-PEI nanocomplexes selectively targeting tDC-derived XBP1 further reduced the total number of metastatic cancer cells in the peritoneal cavity (FIG. 14D) and consequently diminished the accumulation of malignant ascites (FIG. 14E). Importantly, these effects occurred concomitantly with the enhanced infiltration of endogenous antigen-experienced/activated T cells at tumor locations compared with treatments using control nanoparticles (FIG. 14F). Indeed, silencing XBP1 expression in ovarian cancer-associated DCs markedly enhanced the capacity of infiltrating T cells to respond to tumor antigens, as evidenced by er vivo IFN-γ and Granzyme B secretion assays using bone marrow-derived DCs pulsed with tumor antigens (FIG. 14G). These data reinforce the concept that abrogating XBP1 function in tDCs drives the activation and expansion of endogenous anti-tumor T cells at tumor sites. Splenic T cells isolated from mice treated with XBP1-silencing nanocomplexes also demonstrated improved responses upon exposure to tumor antigens in similar re-call assays (FIG. 14H), indicating development of enhanced anti-tumor memory responses after targeting XBP1 in tDCs. Together, these results demonstrate that therapeutic silencing of XBP1 in ovarian cancer-associated DCs can boost endogenous anti-tumor immune responses in vivo.
[0261] To determine whether selective abrogation of the IRE-1α/XBP1 pathway in tDCs had significant therapeutic effects, mice bearing aggressive orthotopic ovarian tumors were i.p. treated with saline, non-targeting or gene-specific siRNA-PEI nanocomplexes. Treatments started 12 days after tumor implantation and injections were administered every 4 days for a period of 3 weeks. Strikingly, wild type mice treated with either XBP1- or IRE-1α-silencing nanoparticles demonstrated a remarkable increase in survival compared with control groups (FIG. 14I). Most importantly, Rag2-deficient hosts bearing ovarian tumors were totally unable to respond to this treatment, demonstrating that an intact adaptive immune system is necessary for the observed therapeutic benefit (FIG. 14J). Together, these data demonstrate that targeting the IRE-1α/XBP1 branch of the ER stress response in tDCs induces protective anti-tumor immune responses against otherwise lethal ovarian cancer.
[0262] 
[00001] [TABLE-US-00001]
  TABLE 1
 
  Primers
  Spe-     Oligo    
  cies   Gene   Name   Sequence 5′-3′   Purpose
 
  HUMAN   ACTB   hAct-F   GCGAGAAGATGA   RT-qPCR
        CCCAGATC  
      hAct-R   CCAGTGGTACGG  
        CCAGAGG  
 
  HUMAN   DDII3/   hCHOP-   CTGCTTCTCTGG   RT-qPCR
    CHOP   F   CTTGGCTG  
      hCHOP-   GCTCTGGGAGGT  
      R   GCTTGTGA  
 
  HUMAN   XBP1   hXBP1-   CCTGGTTGCTGA   Splicing
      SA-F   AGAGGAGG   Assay
      hXBP1-   CCATGGGGAGTT  
      SA-R   CTGGAG  
 
  Mouse   Xbp1   Xbp1-   ACACGTTTGGGA   Splicing
      SA-F   ATGGACAC   Assay
      Xbp1-   CCATGGGAAGAT  
      SA-F   GTTCTGGG  
 
  Mouse   Actb   actb   CTCAGGAGGAGC   RT-qPCR
      1083   AATGATCTTGAT  
      actb   TACCACCATGTA  
      987   CCCAGGCA  
 
  Mouse   Xbp1   Xbp1.   GACAGAGAGTCA   RT-qPCR
      total-F   AACTAACGTGG  
      Xbp1.   GTCCAGCAGGCA  
      total-R   AGAAGGT  
 
  Mouse   Xbp1s   XBPsA   AAGAACACGCTT   RT-qPCR
      406F   GGGAATGG  
      XBPsAa   CTGCACCTGCTG  
      518R   CGGAC  
 
  Mouse   Xbp1   XBP1WT   CCTGAGCCCGGA   RT-qPCR
    (exon 2)   205-F   GGAGAA  
      XBP1WT   CTCGAGCAGTCT   (does not
      272-R   GCGCTG   amplify
          deleted
          exon 2
 
  Mouse   Dnajb9/   ERdj4-F   TAAAAGCCCTGA   RT-qPCR
    Erdj4     TGCTGAAGC  
      ERdj4-R   TCCGACTATTGG  
        CATCCGA  
 
  Mouse   Sec61a1   Sec61a1-   CTATTTCCAGGG   RT-qPCR
      F   CTTCCGAGT  
      Sec61a1-   AGGTGTTGTACT  
      R   GGCCTCGGT  
 
  Mouse   Hspa5/   Grp78-F   TCATCGGACGCA   RT-qPCR
        CTTGGAA  
    BiP   Grp78-R   CAACCACCTTGA  
        ATGGCAAGA  
 
  Mouse   Ddit3/   CHOP-F   GTCCCTAGCTTG   RT-qPCR
    CHOP     GCTGACAGA  
      CHOP-R   TGGAGAGCGAGG  
        GCTTTG  
 
  Mouse   Agpat6   Agpat6-F   AGCTTGATTGTC   RT-qPCR
        AACCTCCTG  
      Agpat6-R   CCGTTGGTGTAG  
        GGCTTGT  
 
  Mouse   Sed2   Sed2-F   GCATTTGGGAGC   RT-qPCR
        CTTGTACG  
      Sed2-R   AGCCGTGCCTTG  
        TATGTTCTG  
 
  Mouse   Fasn   Fasn-F   GGAGGTGGTGAT   RT-qPCR
        AGCCGGTAT  
      Fasn-R   TGGGTAATCCAT  
        AGAGCCCAG  
 
  Mouse   Lpar1   Lpar1.F   GACCTAGCAGGC   RT-qPCR
        TTACAGTTCC  
      Lpar1.R   GCTGTAGTTTGG  
        GGCGATGA  
 
  Mouse   Clec9a   Clec9a.F   GAGCATGGTGTG   RT-qPCR
        TTGTGACG  
      Clec9a.R   TACCTGGAAGAA  
        CTTGATGCCC  
 
  Mouse   Zbtb46   Zbtb46.F   CTCACATACTGG   RT-qPCR
        AGAGCGGC  
      Zbtb46.R   TGCTGTGGACCA  
        GAGTATGTC
 
[0263] 
[00002] [TABLE-US-00002]
  TABLE 2
 
      KO/WT
  Symbol   Description   fold
 
 
  Fut7   fucosyltransferase 7   −2.32
  Slc5a3   solute carrier family 5 (inositol transporters), member 3   −2.22
  Gm2a   GM2 ganglioside activator protein   −1.99
  Stt3a   STT3, subunit of the oligosaccharyltransferase complex,   −1.94
  homolog A (S. cerevisiae)
  Uggt1   UDP-glucose glycoprotein glucosyltransferase 1   −1.81
  Gfpt1   glutamine fructose-6-phosphate transaminase 1   −1.77
  Mlec   malectin   −1.73
  Glce   glucuronyl C5-epimerase   −1.68
  Hk1   hexokinase 1   −1.59
  Aldoc   aldolase C, fructose-bisphosphate   −1.58
  Rpn1   ribophorin I   −1.58
  Mgat1   mannoside acetylglucosaminyltransferase 1   −1.56
  Pfkp   phosphofructokinase, platelet   −1.56
  Gaa   glucosidase, alpha, acid   −1.55
  Phkb   phosphorylase kinase beta   −1.55
  Ogdh   oxoglutarate (alpha-ketoglutarate) dehydrogenase   −1.52
    (lipoamide)
  Ptafr   platelet-activating factor receptor   −1.52
  Pgm3   phosphoglucomutase 3   −1.52
  Pygb   brain glycogen phosphorylase   −1.51
  Idua   iduronidase, alpha-L-   −1.49
  Acly   ATP citrate lyase   −1.48
  Ppip5k2   diphosphoinositol pentakisphosphate kinase 2   −1.47
  Cpt1a   carnitine palmitoyltransferase 1a, liver   −1.47
  Pkm   pyruvate kinase, muscle   −1.46
  St3gal4   ST3 beta-galactoside alpha-2,3-sialyltransferase 4   −1.45
  Ganab   alpha glucosidase 2 alpha neutral subunit   −1.45
  Man2b1   mannosidase 2, alpha B1   −1.43
  Rpn2   ribophorin II   −1.40
  Tram2   translocating chain-associating membrane protein 2   −6.39
  Zfp781   zinc finger protein 781   −4.18
  Apol9b   apolipoprotein L 9b   −4.08
  Tlr12   toll-like receptor 12   −4.06
  Zfp791   zinc finger protein 791   −3.93
  9530036M11Rik   RIKEN cDNA 9530036M11 gene   −3.71
  Leprel1   leprecan-like 1   −3.29
  Il12b   interleukin 12b   −3.12
  Scn4b   sodium channel, type IV, beta   −3.08
  Tuba1c   tubulin, alpha 1C   −3.00
  Dkk3dickkopf homolog 3 (Xenopus laevis)   −2.98
  Sardh   sarcosine dehydrogenase   −2.96
  Cd226   CD226 antigen   −2.90
  Synpo2   synaptopodin 2   −2.87
  Fbxo10   F-box protein 10   −2.79
  Rtkn   rhotekin   −2.75
  Fam13c   family with sequence similarity 13, member C   −2.72
  Itgb2   integrin beta 2   −2.62
  Ptgir   prostaglandin I receptor (IP)   −2.61
  Bcorl1   BCL6 co-repressor-like 1   −2.54
  Rnase2a   #N/A   −2.53
  Fcrls   Fc receptor-like S, scavenger receptor   −2.47
  Hyou1   hypoxia up-regulated 1   −2.47
  Pdia5   protein disulfide isomerase associated 5   −2.45
  Sdc1   syndecan 1   −2.42
  Tmem25   transmembrane protein 25   −2.40
  Ctnna2   catenin (cadherin associated protein), alpha 2   −2.39
  F7   coagulation factor VII   −2.37
  Itgae   integrin alpha E, epithelial-associated   −2.35
  Extl1   exostoses (multiple)-like 1   −2.28
  Spryd3   SPRY domain containing 3   −2.26
  Rps6kc1   ribosomal protein S6 kinase polypeptide 1   −2.26
  Ear2   eosinophil-associated, ribonuclease A family, member 2   −2.24
  Fn1   fibronectin 1   −2.23
  Tenm4   teneurin transmembrane protein 4   −2.22
  Gfra2   glial cell line derived neurotrophic factor family receptor alpha 2   −2.21
  Plekhn1   pleckstrin homology domain containing, family N member 1   −2.21
  Lrrc18   leucine rich repeat containing 18   −2.20
  Nucb2   nucleobindin 2   −2.20
  Cacna1d   calcium channel, voltage-dependent, L type, alpha 1D   −2.16
    subunit
  Kctd12b   potassium channel tetramerisation domain containing 12b   −2.16
  Hspa14   heat shock protein 14   −2.16
  Galnt9   UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-   −2.13
    acetylgalactosaminyltransferase 9
  Hdlbp   high density lipoprotein (HDL) binding protein   −2.11
  Snx22   sorting nexin 22   −2.10
  Dnmbp   dynamin binding protein   −2.05
  Gm8221   apolipoprotein L 7c pseudogene   −2.04
  Lpar1   lysophosphatidic acid receptor 1   −2.04
  Sec61a1Sec61 alpha 1 subunit (S. cerevisiae)   −2.03
  Nlrx1   NLR family member X1   −2.03
  Capn5   calpain 5   −2.03
  Retnla   resistin like alpha   −2.02
  Sec24dSec24 related gene family, member D (S. cerevisiae)   −2.02
  Atg9b   autophagy related 9B   −2.00
  Mpzl2   myelin protein zero-like 2   −1.97
  Slc13a3   solute carrier family 13 (sodium-dependent dicarboxylate   −1.97
    transporter), member 3
  Plce1   phospholipase C, epsilon 1   −1.97
  Otof   otoferlin   −1.96
  F10   coagulation factor X   −1.96
  Unc45bunc-45 homolog B (C. elegans)   −1.96
  Hspa13   heat shock protein 70 family, member 13   −1.93
  Madd   MAP-kinase activating death domain   −1.92
  Nbas   neuroblastoma amplified sequence   −1.92
  Sec24cSec24 related gene family, member C (S. cerevisiae)   −1.91
  Ercc6l   excision repair cross-complementing rodent repair deficiency   −1.90
    complementation group 6 like
  1700021K19Rik   RIKEN cDNA 1700021K19 gene   −1.88
  Abca3   ATP-binding cassette, sub-family A (ABC1), member 3   −1.88
  Kctd11   potassium channel tetramerisation domain containing 11   −1.88
  Agpat4   1-acylglycerol-3-phosphate O-acyltransferase 4   −1.87
    (lysophosphatidic acid acyltransferase, delta)
  Ambra1   autophagy/beclin 1 regulator 1   −1.87
  Xdh   xanthine dehydrogenase   −1.86
  Surf4   surfeit gene 4   −1.86
  Pltp   phospholipid transfer protein   −1.86
  Itgam   integrin alpha M   −1.86
  Cldn1   claudin 1   −1.85
  Atg13   autophagy related 13   −1.84
  Xbp1   X-box binding protein 1   −1.83
  P4hb   prolyl 4-hydroxylase, beta polypeptide   −1.83
  Cdk5rap3   CDK5 regulatory subunit associated protein 3   −1.83
  Gmppb   GDP-mannose pyrophosphorylase B   −1.83
  Zfp872   zinc finger protein 872   −1.82
  Zfp949   zinc finger protein 949   −1.82
  Psd4   pleckstrin and Sec7 domain containing 4   −1.81
  Pidd1   #N/A   −1.80
  Dock2   dedicator of cyto-kinesis 2   −1.80
  Sidt2   SID1 transmembrane family, member 2   −1.80
  4931406H21Rik   RIKEN cDNA 4931406H21 gene   −1.79
  Abca9   ATP-binding cassette, sub-family A (ABC1), member 9   −1.79
  Ppm1f   protein phosphatase 1F (PP2C domain containing)   −1.79
  Abcg3   ATP-binding cassette, sub-family G (WHITE), member 3   −1.79
  Crat   carnitine acetyltransferase   −1.78
  Gpr56   G protein-coupled receptor 56   −1.78
  Bub1bbudding uninhibited by benzimidazoles 1 homolog, beta (S. cerevisiae)   −1.77
  Ticam1   toll-like receptor adaptor molecule 1   −1.77
  Il27ra   interleukin 27 receptor, alpha   −1.77
  Fam129a   family with sequence similarity 129, member A   −1.77
  Dnase1l3   deoxyribonuclease 1-like 3   −1.76
  Ptger2   prostaglandin E receptor 2 (subtype EP2)   −1.75
  Gm1966   predicted gene 1966   −1.75
  Tmem167b   transmembrane protein 167B   −1.75
  Nup188   nucleoporin 188   −1.75
  Tyk2   tyrosine kinase 2   −1.75
  Asb4   ankyrin repeat and SOCS box-containing 4   −1.74
  Tom1l2   target of myb1-like 2 (chicken)   −1.74
  Ascc2   activating signal cointegrator 1 complex subunit 2   −1.74
  Clec4a2   C-type lectin domain family 4, member a2   −1.73
  Polr3b   polymerase (RNA) III (DNA directed) polypeptide B   −1.73
  Igj   immunoglobulin joining chain   −1.73
  Acot11   acyl-CoA thioesterase 11   −1.73
  Ankrd23   ankyrin repeat domain 23   −1.73
  Mis12   MIS12 homolog (yeast)   −1.73
  Rfwd3   ring finger and WD repeat domain 3   −1.73
  Ccpg1   cell cycle progression 1   −1.72
  F2rl2   coagulation factor II (thrombin) receptor-like 2   −1.71
  Arfgap3   ADP-ribosylation factor GTPase activating protein 3   −1.71
  Mmp25   matrix metallopeptidase 25   −1.71
  Ap1g1   adaptor protein complex AP-1, gamma 1 subunit   −1.70
  Cenpi   centromere protein I   −1.70
  Tlr8   toll-like receptor 8   −1.70
  Pdcd1   programmed cell death 1   −1.69
  Tmem127   transmembrane protein 127   −1.69
  Plau   plasminogen activator, urokinase   −1.69
  Tut1   terminal uridylyl transferase 1, U6 snRNA-specific   −1.69
  Mical1   microtubule associated monooxygenase, calponin and LIM   −1.69
    domain containing 1
  Mrc1   mannose receptor, C type 1   −1.69
  Pdia4   protein disulfide isomerase associated 4   −1.69
  Zfp738   zinc finger protein 738   −1.69
  Kat6a   K(lysine) acetyltransferase 6A   −1.69
  Mela   melanoma antigen   −1.69
  Mettl14   methyltransferase like 14   −1.68
  Copg1   coatomer protein complex, subunit gamma 1   −1.68
  Rassf4   Ras association (RalGDS/AF-6) domain family member 4   −1.68
  Klhl18   kelch-like 18   −1.68
  Gorab   golgin, RAB6-interacting   −1.68
  Rab8b   RAB8B, member RAS oncogene family   −1.67
  Spcs3signal peptidase complex subunit 3 homolog (S. cerevisiae)   −1.67
  Btd   biotinidase   −1.67
  Pias3   protein inhibitor of activated STAT 3   −1.67
  Lysmd3   LysM, putative peptidoglycan-binding, domain containing 3   −1.67
  Vps8vacuolar protein sorting 8 homolog (S. cerevisiae)   −1.67
  Calu   calumenin   −1.67
  Sdccag8   serologically defined colon cancer antigen 8   −1.66
  Gpr68   G protein-coupled receptor 68   −1.66
  Kcnab2   potassium voltage-gated channel, shaker-related subfamily,   −1.66
    beta member 2
  Tlr11   toll-like receptor 11   −1.66
  Slc39a7   solute carrier family 39 (zinc transporter), member 7   −1.66
  Fasn   fatty acid synthase   −1.65
  E2f1   E2F transcription factor 1   −1.65
  Zc3h12c   zinc finger CCCH type containing 12C   −1.65
  Fosl2   fos-like antigen 2   −1.65
  Mcph1   microcephaly, primary autosomal recessive 1   −1.64
  Tgoln2   trans-golgi network protein 2   −1.64
  Dpp7   dipeptidylpeptidase 7   −1.64
  Golga3   golgi autoantigen, golgin subfamiiy a, 3   −1.63
  Far1   fatty acyl CoA reductase 1   −1.63
  Pank4   pantothenate kinase 4   −1.63
  Ncapd3   non-SMC condensin II complex, subunit D3   −1.63
  Ddb1   damage specific DNA binding protein 1   −1.62
  Map3k14   mitogen-activated protein kinase kinase kinase 14   −1.62
  Surf6   surfeit gene 6   −1.62
  Sulf1   sulfatase 1   −1.62
  Samd9l   sterile alpha motif domain containing 9-like   −1.62
  Slc41a2   solute carrier family 41, member 2   −1.62
  Tnip2   TNFAIP3 interacting protein 2   −1.62
  Klhl28   kelch-like 28   −1.62
  Lclat1   lysocardiolipin acyltransferase 1   −1.62
  Peg13   paternally expressed 13   −1.61
  Crem   cAMP responsive element modulator   −1.61
  Mmp19   matrix metallopeptidase 19   −1.61
  Copa   coatomer protein complex subunit alpha   −1.61
  Rin3   Ras and Rab interactor 3   −1.61
  Ldlr   low density lipoprotein receptor   −1.61
  Nxpe4   neurexophilin and PC-esterase domain famiiy, member 4   −1.61
  Dock10   dedicator of cytokinesis 10   −1.61
  Leprot   leptin receptor overlapping transcript   −1.61
  Sept9   septin 9   −1.61
  Fbxo38   F-box protein 38   −1.61
  Myo1f   myosin IF   −1.60
  Znfx1   zinc finger, NFX1-type containing 1   −1.60
  Ddi2   DNA-damage inducible protein 2   −1.60
  Anpep   alanyl (membrane) aminopeptidase   −1.60
  Lifr   leukemia inhibitory factor receptor   −1.60
  Utp20   UTP20, small subunit (SSU) processome component,   −1.60
    homolog (yeast)
  Lpin1   lipin 1   −1.60
  Eps8   epidermal growth factor receptor pathway substrate 8   −1.60
  Zfyve16   zinc finger, FYVE domain containing 16   −1.60
  Arhgap18   Rho GTPase activating protein 18   −1.60
  Elmo2   engulfment and cell motility 2   −1.60
  Daglb   diacylglycerol lipase, beta   −1.59
  Elmod2   ELMO/CED-12 domain containing 2   −1.59
  Abcd1   ATP-binding cassette, sub-family D (ALD), member 1   −1.59
  Alpk1   alpha-kinase 1   −1.59
  Ncs1   neuronal calcium sensor 1   −1.59
  Ticam2   toll-like receptor adaptor molecule 2   −1.59
  Clasp1   CLIP associating protein 1   −1.59
  Atxn3   ataxin 3   −1.59
  Depdc5   DEP domain containing 5   −1.58
  Cnnm4   cyclin M4   −1.58
  Steap3   STEAP family member 3   −1.58
  Kit   kit oncogene   −1.58
  1110037F02Rik   RIKEN cDNA 1110037F02 gene   −1.58
  Supt5   suppressor of Ty 5   −1.58
  Socs6   suppressor of cytokine signaling 6   −1.58
  Gm5431   predicted gene 5431   −1.57
  Nup160   nucleoporin 160   −1.57
  Atf6   activating transcription factor 6   −1.57
  Net1   neuroepithelial cell transforming gene 1   −1.57
  Dhdh   dihydrodiol dehydrogenase (dimeric)   −1.57
  Dapk1   death associated protein kinase 1   −1.57
  Taf1   TAF1 RNA polymerase II, TATA box binding protein (TBP)-   −1.57
    associated factor
  Arhgap11a   Rho GTPase activating protein 11A   −1.57
  Supt16   suppressor of Ty 16   −1.57
  Dnajc3   DnaJ (Hsp40) homolog, subfamily C, member 3   −1.57
  Ddx10   DEAD (Asp-Glu-Ala-Asp) box polypeptide 10   −1.56
  Gm8995   predicted gene 8995   −1.56
  Bsdc1   BSD domain containing 1   −1.56
  Gpr108   G protein-coupled receptor 108   −1.56
  Inpp5d   inositol polyphosphate-5-phosphatase D   −1.56
  Snrnp200   small nuclear ribonucleoprotein 200 (U5)   −1.56
  Asb6   ankyrin repeat and SOCS box-containing 6   −1.56
  Mfn2   mitofusin 2   −1.56
  Ccr2   chemokine (C-C motif) receptor 2   −1.56
  Cbl   Casitas B-lineage lymphoma   −1.56
  Mrvi1   MRV integration site 1   −1.56
  Tap2   transporter 2, ATP-binding cassette, sub-family B   −1.56
    (MDR/TAP)
  Mcm3minichromosome maintenance deficient 3 (S. cerevisiae)   −1.56
  Nol8   nucleolar protein 8   −1.56
  Gltpd1   glycolipid transfer protein domain containing 1   −1.56
  Plekho2   pleckstrin homology domain containing, family O member 2   −1.56
  Il1rl1   interleukin 1 receptor-like 1   −1.56
  Ankfy1   ankyrin repeat and FYVE domain containing 1   −1.56
  Gpatch8   G patch domain containing 8   −1.55
  Nap1l4   nucleosome assembly protein 1-like 4   −1.55
  Tmed9   transmembrane emp24 protein transport domain containing 9   −1.55
  Arhgap26   Rho GTPase activating protein 26   −1.55
  Uspl1   ubiquitin specific peptidase like 1   −1.55
  Pdia6   protein disulfide isomerase associated 6   −1.55
  Arrb1   arrestin, beta 1   −1.55
  Mkl1   MKL (megakaryoblastic leukemia)/myocardin-like 1   −1.55
  Zfml   zinc finger, matrin-like   −1.55
  Fchsd2   FCH and double SH3 domains 2   −1.54
  Cnr2   cannabinoid receptor 2 (macrophage)   −1.54
  Ccdc47   coiled-coil domain containing 47   −1.54
  Dok2   docking protein 2   −1.54
  Taok3   TAO kinase 3   −1.54
  Tti1   TELO2 interacting protein 1   −1.54
  Smc5   structural maintenance of chromosomes 5   −1.54
  Pbxip1   pre B cell leukemia transcription factor interacting protein 1   −1.54
  Prr5l   proline rich 5 like   −1.54
  Stat6   signal transducer and activator of transcription 6   −1.54
  Hepacam2   HEPACAM family member 2   −1.54
  2700049A03Rik   RIKEN cDNA 2700049A03 gene   −1.54
  Pkd1   polycystic kidney disease 1 homolog   −1.54
  Lrrk1   leucine-rich repeat kinase 1   −1.54
  Pan2PAN2 polyA specific ribonuclease subunit homolog (S. cerevisiae)   −1.54
  Magt1   magnesium transporter 1   −1.53
  Armcx3   armadillo repeat containing, X-linked 3   −1.53
  Cd1d1   CD1d1 antigen   −1.53
  Plekhb2   pleckstrin homology domain containing, family B (evectins)   −1.53
    member 2
  Bcl2l14   BCL2-like 14 (apoptosis facilitator)   −1.53
  Lmf2   lipase maturation factor 2   −1.53
  Nhsl2   NHS-like2   −1.53
  Timp3   tissue inhibitor of metalloproteinase 3   −1.53
  Casp3   caspase 3   −1.53
  Naaa   N-acylethanolamine acid amidase   −1.52
  Nfam1   Nfat activating molecule with ITAM motif 1   −1.52
  Dcp1aDCP1 decapping enzyme homolog A (S. cerevisiae)   −1.52
  Eif3a   eukaryotic translation initiation factor 3, subunit A   −1.52
  Mtmr6   myotubularin related protein 6   −1.52
  Top2a   topoisomerase (DNA) II alpha   −1.52
  Dnajc14   DnaJ (Hsp40) homolog, subfamily C, member 14   −1.52
  Pde4dip   phosphodiesterase 4D interacting protein (myomegalin)   −1.52
  Evi2a   ecotropic viral integration site 2a   −1.52
  Npat   nuclear protein in the AT region   −1.51
  Sil1endoplasmic reticulum chaperone SIL1 homolog (S. cerevisiae)   −1.51
  Hltf   helicase-like transcription factor   −1.51
  Stim2   stromal interaction molecule 2   −1.51
  Baz2a   bromodomain adjacent to zinc finger domain, 2A   −1.51
  Ell   elongation factor RNA polymerase II   −1.51
  R3hcc1l   R3H domain and coiled-coil containing 1 like   −1.51
  Mybbp1a   MYB binding protein (P160) 1a   −1.51
  Myo1c   myosin IC   −1.50
  Zfp260   zinc finger protein 260   −1.50
  Adam19   a disintegrin and metallopeptidase domain 19 (meltrin beta)   −1.50
  Tkt   transketolase   −1.50
  Exoc2   exocyst complex component 2   −1.50
  Sft2d2   SFT2 domain containing 2   −1.50
  Tuba1a   tubulin, alpha 1A   −1.50
  Oat   ornithine aminotransferase   −1.50
  Baz2b   bromodomain adjacent to zinc finger domain, 2B   −1.50
  Ltn1   listerin E3 ubiquitin protein ligase 1   −1.50
  Copb2   coatomer protein complex, subunit beta 2 (beta prime)   −1.50
  Cyp51   cytochrome P450, family 51   −1.50
  Acin1   apoptotic chromatin condensation inducer 1   −1.50
  Hivep2   human immunodeficiency virus type I enhancer binding   −1.50
    protein 2
  Tmem170b   transmembrane protein 170B   −1.49
  Stom   stomatin   −1.49
  Sec16aSEC16 homolog A (S. cerevisiae)   −1.49
  Krt80   keratin 80   −1.49
  Malat1   metastasis associated lung adenocarcinoma transcript 1   −1.49
    (non-coding RNA)
  Rabgap1   RAB GTPase activating protein 1   −1.49
  Pja2   praja 2, RING-H2 motif containing   −1.49
  Slamf8   SLAM family member 8   −1.49
  Tnpo3   transportin 3   −1.48
  Tmx3   thioredoxin-related transmembrane protein 3   −1.48
  Rbbp6   retinoblastoma binding protein 6   −1.48
  Ilf3   interleukin enhancer binding factor 3   −1.48
  Ctr9   Ctr9, Paf1/RNA polymerase II complex component, homolog   −1.48
  (S. cerevisiae)
  Anapc1   anaphase promoting complex subunit 1   −1.48
  Svil   supervillin   −1.48
  Ptrf   polymerase I and transcript release factor   −1.48
  Tox4   TOX high mobility group box family member 4   −1.48
  Abi2   abl-interactor 2   −1.48
  Atp7a   ATPase, Cu++ transporting, alpha polypeptide   −1.48
  Cnppd1   cyclin Pas1/PHO80 domain containing 1   −1.48
  Zc3h7a   zinc finger CCCH type containing 7 A   −1.48
  Zfp263   zinc finger protein 263   −1.48
  Ipo5   importin 5   −1.48
  Pggt1b   protein geranylgeranyltransferase type I, beta subunit   −1.48
  Ptplad2   protein tyrosine phosphatase-like A domain containing 2   −1.48
  Usp8   ubiquitin specific peptidase 8   −1.48
  Coro7   coronin 7   −1.47
  Sept3   septin 3   −1.47
  Spop   speckle-type POZ protein   −1.47
  Aco1   aconitase 1   −1.47
  Nucb1   nucleobindin 1   −1.47
  Prpf6   PRP6 pre-mRNA splicing factor 6 homolog (yeast)   −1.47
  Mavs   mitochondrial antiviral signaling protein   −1.47
  Cd209c   CD209c antigen   −1.47
  Atp8b4   ATPase, class I, type 8B, member 4   −1.47
  Myof   myoferlin   −1.47
  Sec23bSEC23B (S. cerevisiae)   −1.46
  Nckap1l   NCK associated protein 1 like   −1.46
  Pum1   pumilio RNA-binding family member 1   −1.46
  Fgl2   fibrinogen-like protein 2   −1.46
  Sec31aSec31 homolog A (S. cerevisiae)   −1.46
  Txndc16   thioredoxin domain containing 16   −1.46
  Pdxk   pyridoxal (pyridoxine, vitamin B6) kinase   −1.46
  Gga3   golgi associated, gamma adaptin ear containing, ARF   −1.46
    binding protein 3
  Kitl   kit ligand   −1.46
  Tmcc3   transmembrane and coiled coil domains 3   −1.46
  Gmppa   GDP-mannose pyrophosphorylase A   −1.46
  Ppp1r21   protein phosphatase 1, regulatory subunit 21   −1.46
  Os9   amplified in osteosarcoma   −1.46
  4930506M07Rik   RIKEN cDNA 4930506M07 gene   −1.45
  Smc1a   structural maintenance of chromosomes 1A   −1.45
  Kansl3   KAT8 regulatory NSL complex subunit 3   −1.45
  2900097C17Rik   RIKEN cDNA 2900097C17 gene   −1.45
  Tmem181b-ps   transmembrane protein 181B, pseudogene   −1.45
  Nup210   nucleoporin 210   −1.45
  Entpd7   ectonucleoside triphosphate diphosphohydrolase 7   −1.45
  Stag2   stromal antigen 2   −1.45
  Narf   nuclear prelamin A recognition factor   −1.45
  Tmem39a   transmembrane protein 39a   −1.45
  Rnf41   ring finger protein 41   −1.45
  Agpat6   1-acylglycerol-3-phosphate O-acyltransferase 6   −1.44
    (lysophosphatidic acid acyltransferase, zeta)
  Zfp445   zinc finger protein 445   −1.44
  lkbkg   inhibitor of kappaB kinase gamma   −1.44
  Gripap1   GRIP1 associated protein 1   −1.44
  Chd2   chromodomain helicase DNA binding protein 2   −1.44
  Ankrd27   ankyrin repeat domain 27 (VPS9 domain)   −1.44
  Ppp1r15b   protein phosphatase 1, regulatory (inhibitor) subunit 15b   −1.44
  Golgb1   golgi autoantigen, golgin subfamily b, macrogolgin 1   −1.44
  Tmed3   transmembrane emp24 domain containing 3   −1.44
  Psap   prosaposin   −1.44
  Ctnna1   catenin (cadherin associated protein), alpha 1   −1.44
  Ptbp1   polypyrimidine tract binding protein 1   −1.43
  Csf2rb   colony stimulating factor 2 receptor, beta, low-affinity   −1.43
    (granulocyte-macrophage)
  Ssrp1   structure specific recognition protein 1   −1.43
  Cyth4   cytohesin 4   −1.43
  Tug1   taurine upregulated gene 1   −1.43
  Scd2   stearoyl-Coenzyme A desaturase 2   −1.43
  Arhgef6   Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6   −1.43
  Tbc1d15   TBC1 domain family, member 15   −1.42
  Mbnl1muscleblind-like 1 (Drosophila)   −1.42
  Eif4g2   eukaryotic translation initiation factor 4, gamma 2   −1.42
  Rp2h   retinitis pigmentosa 2 homolog (human)   −1.42
  Adam8   a disintegrin and metallopeptidase domain 8   −1.41
  Neat1   nuclear paraspeckle assembly transcript 1 (non-protein   −1.41
    coding)
  Themis2   thymocyte selection associated family member 2   −1.41
  Gosr2   golgi SNAP receptor complex member 2   −1.40
  Idi1   isopentenyl-diphosphate delta isomerase   −1.40
  Psmd2   proteasome (prosome, macropain) 26S subunit, non-   −1.40
    ATPase, 2
  Hmgcr   3-hydroxy-3-methylglutaryl-Coenzyme A reductase   −1.40
  Eef2   eukaryotic translation elongation factor 2   −1.40
  Myo1g   myosin IG   −1.40
  Msn   moesin   −1.39
  Cfh   complement component factor h   −1.38
  C1qc   complement component 1, q subcomponent, C chain   1.42
  A630089N07Rik   RIKEN cDNA A630089N07 gene   1.43
  Traf5   TNF receptor-associated factor 5   1.44
  Zfp353-ps   zinc finger protein 352   1.45
  Fam110b   family with sequence similarity 110, member B   1.48
  Wfdc17   WAP four-disulfide core domain 17   1.48
  Fam213b   family with sequence similarity 213, member B   1.48
  Trem2   triggering receptor expressed on myeloid cells 2   1.50
  Snx18   sorting nexin 18   1.51
  1500012F01Rik   RIKEN cDNA 1500012F01 gene   1.51
  Tctex1d2   Tctex1 domain containing 2   1.52
  Icam2   intercellular adhesion molecule 2   1.53
  Gngt2   guanine nucleotide binding protein (G protein), gamma   1.53
    transducing activity polypeptide 2
  Lst1   leukocyte specific transcript 1   1.54
  Itsn1   intersectin 1 (SH3 domain protein 1A)   1.54
  Ltbp1   latent transforming growth factor beta binding protein 1   1.55
  Blvrb   biliverdin reductase B (flavin reductase (NADPH))   1.57
  HscbHscB iron-sulfur cluster co-chaperone homolog (E. coli)   1.57
  Acot2   acyl-CoA thioesterase 2   1.57
  Gimap8   GTPase, IMAP family member 8   1.59
  Sept1   septin 1   1.60
  C5ar2   complement component 5a receptor 2   1.60
  Ifga6   integrin alpha 6   1.61
  Dcxr   dicarbonyl L-xylulose reductase   1.61
  Mmp12   matrix metallopeptidase 12   1.61
  Tmem243   transmembrane protein 243, mitochondrial   1.63
  Pou2f2   POU domain, class 2, transcription factor 2   1.63
  Ly6c2   lymphocyte antigen 6 complex, locus C2   1.63
  Hnmt   histamine N-methyltransferase   1.64
  Asns   asparagine synthetase   1.64
  Emp1   epithelial membrane protein 1   1.65
  Ets1   E26 avian leukemia oncogene 1, 5′ domain   1.65
  Cirbp   cold inducible RNA binding protein   1.65
  Cbr2   carbonyl reductase 2   1.68
  Serpinb10   serine (or cysteine) peptidase inhibitor, clade B (ovalbumin),   1.68
    member 10
  Vsig4   V-set and immunoglobulin domain containing 4   1.69
  Fam20c   family with sequence similarity 20, member C   1.69
  Irf2bpl   interferon regulatory factor 2 binding protein-like   1.71
  Cd93   CD93 antigen   1.71
  Med17   mediator complex subunit 17   1.71
  Apoe   apolipoprotein E   1.72
  Cd28   CD28 antigen   1.72
  Ms4a1   membrane-spanning 4-domains, subfamily A, member 1   1.73
  Lpcat2   lysophosphatidylcholine acyltransferase 2   1.73
  Plac8   placenta-specific 8   1.73
  Rab28   RAB28, member RAS oncogene family   1.74
  Mzb1   marginal zone B and B1 cell-specific protein 1   1.74
  Dok3   docking protein 3   1.75
  Arg1   arginase, liver   1.75
  Cd19   CD19 antigen   1.76
  Fcna   ficolin A   1.77
  Cd79b   CD79B antigen   1.77
  Tspan4   tetraspanin 4   1.78
  Mmp9   matrix metallopeptidase 9   1.80
  Itk   IL2 inducible T cell kinase   1.81
  Dppa3   developmental pluripotency-associated 3   1.81
  Ninj1   ninjurin 1   1.81
  Cxcr5   cbemokine (C—X—C motif) receptor 5   1.82
  Spry2sprouty homolog 2 (Drosophila)   1.82
  Prtn3   proteinase 3   1.82
  Snx24   sorting nexing 24   1.83
  Ccl3   chemokine (C-C motif) ligand 3   1.83
  Gdf3   growth differentiation factor 3   1.86
  Ly6d   lymphocyte antigen 6 complex, locus D   1.86
  Cd69   CD89 antigen   1.86
  Selp   selectin, platelet   1.86
  Apoc2   apolipoprotein C-II   1.86
  Gimap3   GTPase, IMAP family member 3   1.88
  Speer7-ps1   spermatogenesis associated glutamate (E)-rich protein 7,   1.89
    pseudogene 1
  Dusp1   dual specificity phosphatase 1   1.89
  Clec4d   C-type lectin domain family 4, member d   1.90
  Cd27   CD27 antigen   1.90
  Sh2d2a   SH2 domain protein 2A   1.91
  Ly6a   lymphocyte antigen 6 complex, locus A   1.92
  Nt5e   5′ nucleotidase, ecto   1.94
  Txk   TXK tyrosine kinase   1.96
  Saa3   serum amyloid A 3   1.96
  Gimap9   GTPase, IMAP family member 9   1.98
  Ndufb2   NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2   1.99
  Tfec   transcription factor EC   2.02
  Cxcl13   chemokine (C—X—C motif) ligand 13   2.03
  Igfbp4   insulin-like growth factor binding protein 4   2.04
  Asb1   ankyrin repeat and SOCS box-containing 1   2.07
  Pf4   platelet factor 4   2.07
  Xkrx   X Kell blood group precursor related X linked   2.09
  Ypel3yippee-like 3 (Drosophila)   2.09
  Ppp3cc   protein phosphatase 3, catalytic subunit, gamma isoform   2.10
  Fam101b   family with sequence similarity 101, member B   2.10
  Slc40a1   solute carrier family 40 (iron-regulated transporter), member 1   2.10
  Samd3   sterile alpha motif domain containing 3   2.11
  Il2rb   interleukin 2 receptor, beta chain   2.12
  Fam169b   family with sequence similarity 169, member B   2.12
  Mri1methylthioribose-1-phosphate isomerase homolog (S. cerevisiae)   2.15
  Gimap6   GTPase, IMAP family member 6   2.15
  Alox15   arachidonate 15-lipoxygenase   2.17
  Tpsb2   tryptase beta 2   2.18
  Lef1   lymphoid enhancer binding factor 1   2.18
  Tcf7   transcription factor 7, T cell specific   2.21
  Skap1   src family associated phosphoprotein 1   2.22
  Tmprss13   transmembrane protease, serine 13   2.22
  Marco   macrophage receptor with collagenous structure   2.23
  Cd79a   CD79A antigen (immunoglobulin-associated alpha)   2.26
  Apoc1   apolipoprotein C-I   2.26
  Ikzf3   IKAROS family zinc finger 3   2.27
  Cd3d   CD3 antigen, delta polypeptide   2.29
  Id1   inhibitor of DNA binding 1   2.29
  Gzmb   granzyme B   2.29
  Satb1   special AT-rich sequence binding protein 1   2.29
  Lax1   lymphocyte transmembrane adaptor 1   2.32
  Gimap4   GTPase, IMAP family member 4   2.34
  Cpa3   carboxypeptidase A3, mast cell   2.36
  Ccr3   chemokine (C-C motif) receptor 3   2.37
  Fam189b   family with sequence similarity 189, member B   2.38
  Wnt2   wingless-related MMTV integration site 2   2.38
  Vmn2r26   vomeronasal 2, receptor 26   2.39
  Ppbp   pro-platelet basic protein   2.40
  Pou2af1   POU domain, class 2, associating factor 1   2.41
  Lck   lymphocyte protein tyrosine kinase   2.42
  Gm11346   X-linked lymphocyte-regulated 5 pseudogene   2.42
  Cma1   chymase 1, mast cell   2.42
  Ctsw   cathepsin W   2.43
  Gm684   predicted gene 684   2.45
  Serpinb2   serine (or cysteine) peptidase inhibitor, clade B, member 2   2.47
  Trav3n-3   T cell receptor alpha variable 3N-3   2.48
  Prg4   proteoglycan 4 (megakaryocyte stimulating factor, articular   2.48
    superficial zone protein)
  Slpi   secretory leukocyte peptidase inhibitor   2.49
  Tmem51os1   Tmem51 opposite strand 1   2.50
  Ccl4   chemokine (C-C motif) ligand 4   2.50
  Klre1   killer cell lectin-like receptor family E member 1   2.51
  Pear1   platelet endothelial aggregation receptor 1   2.52
  Lat   linker for activation of T cells   2.53
  Ptchd4   patched domain containing 4   2.53
  Pard6g   par-6 family cell polarity regulator gamma   2.55
  Prf1   perforin 1 (pore forming protein)   2.57
  Stc1   stanniocalcin 1   2.59
  Scn1a   sodium channel, voltage-gated, type I, alpha   2.60
  Plcb4   phospholipase C, beta 4   2.63
  Cd3g   CD3 antigen, gamma polypeptide   2.67
  Gpr174   G protein-coupled receptor 174   2.69
  Pik3c2b   phosphoinositide-3-kinase, class 2, beta polypeptide   2.71
  Crtam   cytotoxic and regulatory T cell molecule   2.71
  Eomeseomesodermin homolog (Xenopus laevis)   2.72
  Ebf1   early B cell factor 1   2.72
  Tnfsf15   tumor necrosis factor (ligand) superfamily, member 15   2.77
  Gimap7   GTPase, IMAP family member 7   2.81
  Ifitm10   interferon induced transmembrane protein 10   2.82
  Trem3   triggering receptor expressed on myeloid cells 3   2.83
  Fasl   Fas ligand (TNF superfamily, member 6)   2.83
  Epha2   Eph receptor A2   2.83
  Sh2d1a   SH2 domain protein 1A   2.85
  Tdgf1   teratocarcinoma-derived growth factor 1   2.86
  Ncr1   natural cytotoxicity triggering receptor 1   2.88
  Fbxl21   F-box and leucine-rich repeat protein 21   2.88
  Zdhhc15   zinc finger, DHHC domain containing 15   2.89
  Gimap5   GTPase, IMAP family member 5   2.91
  Gzma   granzyme A   2.94
  A630023P12Rik   RIKEN cDNA A630023P12 gene   2.96
  Ms4a4b   membrane-spanning 4-domains, subfamily A, member 4B   2.99
  Mgst2   microsomal glutathione S-fransferase 2   2.99
  Thy1   thymus cell antigen 1, theta   2.99
  2900011O08Rik   RIKEN cDNA 2900011O08 gene   3.01
  Cd3e   CD3 antigen, epsilon polypeptide   3.02
  A730060N03Rik   RIKEN cDNA A730060N03 gene   3.03
  Klrc2   killer cell lectin-like receptor subfamily C, member 2   3.04
  Phactr3   phosphatase and actin regulator 3   3.10
  Retnlg   resistin like gamma   3.11
  Tsix   X (inactive)-specific transcript, opposite strand   3.12
  Rgcc   regulator of cell cycle   3.13
  Dapl1   death associated protein-like 1   3.14
  Slitrk4   SLIT and NTRK-like family, member 4   3.20
  Cyp28a1   cytochrome P450, family 26, subfamily a, polypeptide 1   3.20
  Cd96   CD96 antigen   3.21
  Mrgpra2b   MAS-related GPR, member A2B   3.25
  Lynx1   Ly6/neurotoxin 1   3.25
  Pou1f1   POU domain, class 1, transcription factor 1   3.25
  Klrg1   killer cell lectin-like receptor subfamily G, member 1   3.25
  S100a9   S100 calcium binding protein A9 (calgranulin B)   3.25
  Tlr5   toll-like receptor 5   3.26
  Klra21   killer cell lectin-like receptor subfamily A, member 21   3.27
  Mrgpra2a   MAS-related GPR, member A2A   3.28
  Ptprcap   protein tyrosine phosphatase, receptor type, C polypeptide-   3.29
    associated protein
  I830127L07Rik   RIKEN cDNA I830127L07 gene   3.30
  9530053A07Rik   RIKEN cDNA 9530053A07 gene   3.31
  Olfr288   olfactory receptor 288   3.37
  Ly6c1   lymphocyte antigen 6 complex, locus C1   3.40
  Nkg7   natural killer cell group 7 sequence   3.41
  Folr4   folate receptor 4 (delta)   3.44
  Ctsk   cathepsin K   3.46
  Gpr83   G protein-coupled receptor 83   3.47
  Unc5clunc-5 homolog C (C. elegans)-like   3.47
  Fcer1a   Fc receptor, IgE, high affinity I, alpha polypeptide   3.58
  Klra7   killer cell lectin-like receptor, subfamily A, member 7   3.60
  1810041L15Rik   RIKEN cDNA 1810041L15 gene   3.62
  Nsg2   neuron specific gene family member 2   3.62
  G0s2   G0/G1 switch gene 2   3.68
  Sall3sal-like 3 (Drosophila)   3.68
  S100a8   S100 calcium binding protein A8 (calgranulin A)   3.70
  Klrc1   killer cell lectin-iike receptor subfamily C, member 1   3.71
  Gm13363   predicted gene 13363   3.77
  Slc2a13   solute carrier family 2 (facilitated glucose transporter),   3.77
    member 13
  Upp1   uridine phosphorylase 1   3.78
  Tnik   TRAF2 and NCK interacting kinase   3.82
  Klra1   killer cell lectin-like receptor, subfamily A, member 1   3.85
  Tcrd-V1   T cell receptor delta, variable 1   3.86
  Lrrn4   leucine rich repeat neuronal 4   3.89
  Mycn   v-myc myelocytomatosis viral related oncogene,   3.92
    neuroblastoma derived (avian)
  Fam155a   family with sequence similarity 155, member A   3.93
  Myo16   myosin XVI   3.96
  Xcl1   chemokine (C motif) ligand 1   4.01
  Lcn2   lipocalin 2   4.10
  Gzmk   granzyme K   4.11
  A530013C23Rik   RIKEN cDNA A530013C23 gene   4.20
  Krt75   keratin 75   4.23
  1100001G20Rik   RIKEN cDNA 1100001G20 gene   4.24
  Efna2   ephrin A2   4.24
  C330013E15Rik   RIKEN cDNA C330013E15 gene   4.27
  Hecw2   HECT, C2 and WW domain containing E3 ubiquitin protein   4.31
    ligase 2
  March11   membrane-associated ring finger (C3HC4) 11   4.35
  4930588J15Rik   RIKEN cDNA 4930588J15 gene   4.37
  Sucnr1   succinate receptor 1   4.64
  Smok4a   sperm motility kinase 4A   4.85
  I730030J21Rik   RIKEN cDNA I730030J21 gene   5.14
  Slc15a2   solute carrier family 15 (H+/peptide transporter), member 2   5.21
  Penk   preproenkephalin   5.25
  1700034I23Rik   FUN14 domain containing 2 pseudogene   5.30
  Tnfsf18   tumor necrosis factor (ligand) superfamily, member 18   5.64
  Cox6a2   cytochrome c oxidase subunit VIa polypeptide 2   5.68
  Csf2   colony stimulating factor 2 (granulocyte-macrophage)   5.81
  Actg1   actin, gamma, cytoplasmic 1   5.85
  Apold1   apolipoprotein L domain containing 1   6.06
  Ip6k2   inositol hexaphosphate kinase 2   7.27
  Baiap3   BAI1-associated protein 3   7.29
  Hsd3b1   hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid   9.34
    delta-isomerase 1
  Sec14l4SEC14-like 4 (S. cerevisiae)   10.28
  Itgad   integrin, alpha D   10.29
 

EQUIVALENTS

[0264] Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

REFERENCES

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Claims

1. A method for enhancing or inducing an anti-tumor immune response in a subject, comprising administering to the subject an effective amount of a direct inhibitor of IRE1α for enhancing or inducing an anti-tumor immune response in the subject, wherein the effective amount of the direct inhibitor IRE1α increases antigen presentation in antigen presenting cells, wherein the tumor is a solid tumor, and wherein the solid tumor is from an ovarian cancer, epithelial cancer, germ cell cancer, a stromal tumor.
2. The method of claim 1, wherein the epithelial cancer is a carcinoma or an adenocarcinoma.
3. The method of claim 1, wherein the direct inhibitor of IRE-1α is an IRE-1α-specific antibody or a small molecule inhibitor of IRE-1α.
4. The method of claim 1, wherein the direct inhibitor of IRE-1α is administered systemically or at tumor locations in the subject.
5. The method of claim 1, wherein the direct inhibitor of IRE-1α targets tumor-associated dendritic cells (tDCs).
6. The method of claim 1, wherein the direct inhibitor of IRE-1α is administered in combination with a second cancer therapeutic agent.
7. The method of claim 6, wherein the second cancer therapeutic agent is a chemotherapeutic agent.
8. The method of claim 1, wherein the treatment induces extended survival of the subject.
9. The method of claim 1, wherein the anti-tumor immune response is mediated by adaptive immune cells.
10. The method of claim 9, wherein the adaptive immune cells comprise T cells.
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