WO2023133409A2 - Combination therapies including parp1 inhibitors - Google Patents

Combination therapies including parp1 inhibitors Download PDF

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WO2023133409A2
WO2023133409A2 PCT/US2023/060098 US2023060098W WO2023133409A2 WO 2023133409 A2 WO2023133409 A2 WO 2023133409A2 US 2023060098 W US2023060098 W US 2023060098W WO 2023133409 A2 WO2023133409 A2 WO 2023133409A2
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cancer
cells
inhibitors
stromal
olaparib
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WO2023133409A3 (en
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Jorge MOSCAT-GUILLEN
Maria T. DIAZ-MECO CONDE
Juan F. LINARES RODRIGUEZ
Tania Cid DIAZ
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Cornell University
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Cornell University
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/50—Pyridazines; Hydrogenated pyridazines
    • A61K31/502—Pyridazines; Hydrogenated pyridazines ortho- or peri-condensed with carbocyclic ring systems, e.g. cinnoline, phthalazine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
    • A61K31/4418—Non condensed pyridines; Hydrogenated derivatives thereof having a carbocyclic group directly attached to the heterocyclic ring, e.g. cyproheptadine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/47—Quinolines; Isoquinolines
    • A61K31/4709—Non-condensed quinolines and containing further heterocyclic rings
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/47—Quinolines; Isoquinolines
    • A61K31/473—Quinolines; Isoquinolines ortho- or peri-condensed with carbocyclic ring systems, e.g. acridines, phenanthridines
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/535—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines
    • A61K31/5375—1,4-Oxazines, e.g. morpholine
    • A61K31/5377—1,4-Oxazines, e.g. morpholine not condensed and containing further heterocyclic rings, e.g. timolol
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/535—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines
    • A61K31/5375—1,4-Oxazines, e.g. morpholine
    • A61K31/538—1,4-Oxazines, e.g. morpholine ortho- or peri-condensed with carbocyclic ring systems
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • A61K38/177—Receptors; Cell surface antigens; Cell surface determinants
    • A61K38/1793—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/43—Enzymes; Proenzymes; Derivatives thereof
    • A61K38/46—Hydrolases (3)
    • A61K38/47—Hydrolases (3) acting on glycosyl compounds (3.2), e.g. cellulases, lactases
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/24—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against cytokines, lymphokines or interferons
    • C07K16/244—Interleukins [IL]
    • C07K16/248—IL-6
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
    • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
    • C12Y302/01035—Hyaluronoglucosaminidase (3.2.1.35), i.e. hyaluronidase

Definitions

  • the tumor microenvironment can be a driver of tumorigenesis in many types of tumors.
  • Activation of tumor stromal fibroblasts to generate cancer-associated fibroblasts (CAFs) can embolden epithelial cancer cells to progress to more malignant stages and affect disease outcomes (Barron and Rowley, 2012; Cunha et al., 2002; Rowley, 1998; Tuxhorn et al., 2001).
  • Cancer-associated fibroblasts impact the tumor epithelium by modulating many functions through the secretion of stromal growth factors and inflammatory mediators, by reprogramming their metabolism to provide nutrients and survival factors, and by remodeling the extracellular matrix (Hanahan and Weinberg, 2011; Kasashima et al., 2020; Sahai et al., 2020).
  • tumor-secreted lactate activates cancer associated fibroblasts (CAF) through downregulation of p62, a master regulator of CAF. Lactate reduces the NAD+/NADH ratio, which impairs PARP1 activity and inhibits p62. NAD+ supplementation can revert stromal activation.
  • PARP1 inhibitors PARPli
  • Olapanb mimic lactate and activate CAF in vitro and in vivo.
  • Olaparib-induced stroma is rich in hyaluronan.
  • Co-treatment of Olaparib and PEGPH20, a clinical grade hyaluronidase reverts stroma activation and enhances Olaparib anti-tumor activity.
  • compositions and methods that include use of PARP1 inhibitors can be combined with drugs that target the stroma to enhance PARP1 inhibitor efficacy or drugs that block or inhibit TNFalpha, IL-6 or Janus kinase (JAK).
  • PARP1 inhibitors can be combined with drugs that target the stroma to enhance PARP1 inhibitor efficacy or drugs that block or inhibit TNFalpha, IL-6 or Janus kinase (JAK).
  • the PARP1 inhibitors can include olaparib (Lynparza), niraparib (Zejula), rucaparib (Rubraca), talazoparib (Talzenna), veliparib (ABT-888), or a combination thereof.
  • agents that can be used to treat or inhibit activated stromal / activated cancer-associated fibroblasts include but are not limited to hyaluronan (HA) synthase inhibitors, hyaluronan build-up inhibitors (e.g., PEGylated Recombinant Human Hyaluronidase, PEGPH20), autophagy inhibitors (e.g., ULK inhibitors such as SBI-0202965), fibroblast activation protein alpha (FAPa) inhibitors, GW4064 (farnesoid X receptor (FXR) agonists, Pirfenidone (PDF) combined with doxorubicin, SMO-inhibitors (e.g., vismodegib, sonidegib), amphiregulin inhibitors, CXCL12 antagonists (e.g., an E5 antagonistic peptide), DDR2 inhibitors (e.g., WRG-28, which is a small molecule inhibitor of DDR2), or a
  • agents that can inhibit JAK include but are not limited to lesataurtinib, baricitinib, tofacitinib, upadacitinib, filgonitib, delgocitinib, deucravacitinib, LS104, ON044580,NVP-BBT594, or NVP-CHZ868, or a combination thereof.
  • agents that can inhibit IL6 include but are not limited to tocilizumab, sarilumab, siltuximab, olokizumab, elsilimomab, clazakizumab, sirukumab, levimumab, CPSI-2364, ARGX-109, FE301 or FM101, or any combination thereof.
  • agents that can inhibit TNFalpha include but are not limited to adalimumab, certolizumab pegol, etanercept, golimumab, or infliximab, or a combination thereof.
  • FIGs. 1A-1L PCa cells secrete a soluble factor that reduces p62 expression in stromal cells.
  • FIG. 1A shows qPCR of Sqstml, Sdf-1 and Tgf/3 ⁇ & e ⁇ s in mPSC- GFP cells mixed with TRAMPC2 cells and cultured for 7 days and western blot.
  • FIGs. ID and IE provide immunoblot analysis for the indicated proteins (FIG. ID) and qPCR of SQSTM1 (FIG.
  • FIGs. 2A-2L Lactate is sufficient to downregulate p62.
  • FIGs. 2D and 2E show immunoblot analysis for the indicated proteins (FIG. 2D) and qPCR of SQSTM1 and MCT4 levels (FIG.
  • FIGs. 3A-3M API elements control p62 downregulation by lactate.
  • FIG. 3A illustrates four clusters (Cl, C2, C3 and C4) heatmap of ATAC-seq peaks, +/- 2 Kb from TSS in WPMY-1 cells treated or not with lactate for 48 hours.
  • FIG. 3B illustrates HOMER discovery analysis of TFs enriched promoter regions (1-2 Kb) closed in WPMY-1 cells treated with Lactate (Control vs Lactate).
  • FIG. 3C shows genome browser view at SQSTM1 promoter. Chromatin accessibility (ATAC-seq) and RNA-seq profiles are shown in WPMY-1 cells treated or not with Lactate.
  • FIG. 3A illustrates four clusters (Cl, C2, C3 and C4) heatmap of ATAC-seq peaks, +/- 2 Kb from TSS in WPMY-1 cells treated or not with lactate for 48 hours.
  • FIG. 3B illustrates HOMER discovery analysis of TFs
  • FIG. 3F shows immunoblot analysis in sgC and sgAP-lA WPMY-1 cells for the indicated proteins.
  • FIG. 3G shows immunoblot analysis for the indicated proteins
  • FIG. 3H show immunoblot analysis for the indicated proteins (FIG. 3G) and qPCR of SQSTM1 levels (FIG. 3H) in s
  • FIG. 3L and 3M show immunoblot analysis for the indicated proteins (FIG.
  • FIGs. 4A-4G Changes in NAD+/NADH levels by lactate are critical for p62 downregulation.
  • FIGs. 5A-5T PARP-1 is critical for the control of p62 levels in stromal cells.
  • FIG. 5A shows immunoblot analysis for the indicated proteins in WPMY-1 cells transduced with the indicated siRNAs.
  • FIGs. 5B and 5C show immunoblot analysis for the indicated proteins (B) and qPCR of SQSTM1 levels (FIG. 5C) in WPMY-1 cells transduced with the indicated siRNAs.
  • FIGs. 5D and 5E show immunoblot analysis for the indicated proteins and qPCR of PARP-1 (FIG. 5D) and SQSTM1 (FIG. 5E) levels in WPMY-1 cells transduced with the indicated siRNAs.
  • FIGs. 5A shows immunoblot analysis for the indicated proteins in WPMY-1 cells transduced with the indicated siRNAs.
  • FIGs. 5C show immunoblot analysis for the indicated proteins and qPCR of SQSTM1 levels in WPMY-1 cells transduced with the indicated siRNAs.
  • FIGs. 5J and 5K illustrate ChlP-PCR analysis of SQSTM1 promoter (AP-1A) occupancy of c-FOS (FIG. 5 J) or c-JUN (FIG.
  • FIG. 5K shows immunoblot analysis for the indicated proteins and PARylated protein levels in WPMY-1 cells incubated with lactate for the indicated times.
  • FIG. 50 and 5P illustrate PARylation of c-JUN (FIG. 50) or c-FOS (FIG. 5P
  • FIGs. 6A-6M API control of the SQSTM1 promoter in stromal cells is critical for PCa tumor growth and invasion.
  • FIG. 6C illustrates GSEA analysis of “LACTATE UP” and “LACTATE DOWN” gene signatures in CAFs vs. NAFs gene set GSE34312.
  • FIG. 6H and 61 show experimental design (FIG. 6H) and H&E staining (FIG. 61) of organotypic gels combining PC3 cells with sgC and sgAP-lA WPMY-1 cells.
  • Experimental design (FIG. 6J), Tumor weight (FIG. 6K), gross images (FIG. 6L), IHC for Masson Trichrome, HA and aSMA (FIG. 6M), scale bars 50 pm. Results are shown as mean ⁇ SEM *p ⁇ 0.05, **p ⁇ 0.01, ***p ⁇ 0.001, ****p ⁇ 0.0001.
  • FIGs. 7A-7T Olaparib treatment mimics lactate loss of p62 and promotes stromal activation.
  • FIG. 7A illustrates enriched pathways obtained by GSEA preranked analysis using DEG in Olaparib-treated WPMY-1 cells.
  • FIG. 7B illustrates GSEA analysis for stromal activation and CAF phenotype gene signatures in Olaparib-treated WPMY-1 cells.
  • FIG. 7C illustrates GSEA analysis of “Olaparib_UP”, “Olaparib_DN”, “Olaparib_ADT_UP”, “Olaparib_ADT_DN” gene signatures in CAFs vs. NAFs gene set GSE34312.
  • FIG. 7A-7T Olaparib treatment mimics lactate loss of p62 and promotes stromal activation.
  • FIG. 7A illustrates enriched pathways obtained by GSEA preranked analysis using DEG in Olaparib-treated WPMY-1 cells.
  • FIG. 7B illustrates GSEA analysis for stromal activation and CA
  • FIG. 7E shows four clusters (Cl, C2, C3 and C4) heatmap of ATAC-seq peaks, +/- 2 Kb from TSS, upon Olaparib treatment for 96 hours in basal conditions.
  • FIG. 7F shows HOMER discovery analysis of TFs enriched in promoter regions (1-2 Kb) closed upon Olaparib treatment in WPMY-1 cells (DMSO vs Olaparib).
  • FIG. 7G shows integrative Genomics Viewer (IGV) of ATAC-seq peaks in SQSTM1 promoter in Olaparib-treated WPMY-1 cells in basal conditions.
  • FIG. 7H-7J show trans-well migration and invasion assays.
  • Experimental design FIG. 7H
  • FIG. 7H trans-well migration and invasion assay of PC3 PCa cultured with Olaparib pre-treated WPMY-1 cells for 20 hours, scale bar 50 pm.
  • FIG. 7I-7J relative number of migrating and invading cells
  • FIG. 7K and 7L show click-iT EdU incorporation assay.
  • Experimental design (FIG. 7K), left, representative images of EdU incorporation in PC3 PCa cells treated with CM from Olaparib-treated WPMY-1 cells for 24 hours.
  • FIGs. 7M and 7N show survival assay of GFP-labeled PC3 PCa cells cocultured with WPMY-1 cells or alone, treated with DMSO or Olaparib, in basal and ADT conditions.
  • Experimental design (FIG. 70), tumor weight (g) (FIG. 7P), tumor volume (mm 3 ) (FIG.
  • FIGs. 8A-8N Stromal activation upon Olaparib treatment impacts prostate epithelial cells.
  • FIG. 8A and 8B illustrate TRAMP + mice treated with Olaparib 40 mg/Kg, 5 days a week for 4 weeks.
  • Experimental design FIG. 8A
  • IHC for HA IHC for HA
  • aSMA FIG. 8B
  • scale bars 50 pm FIG. 8C and 8D show scRNAseq compartment identification.
  • UMAP plot with clustering results color-coded by compartment types FIGG. 8C).
  • Proportion cell number of the identified cell compartments FIG. 8D).
  • FIG. 8E and 8F show scRNAseq fibroblast subset.
  • UMAP plot with re-clustering of fibroblast showing the main markers of each cluster FIGG.
  • FIG. 8E Feature plot for the expression of indicated genes (FIG. 8F).
  • FIG. 8H shows IHC for SPINK1, scale bars 50 pm.
  • FIG. 8I-8L illustrate scRNAseq epithelial subset. UMAP plot with re-clustering of epithelial cells color-coded by cell type (FIG. 81). Violin plots of specific epithelial cell markers (FIG. 8J). Proportion cell number of the identified epithelial cell populations (FIG. 8K). Violin plots of indicated gene signatures (FIG. 8L).
  • FIG. 8F Feature plot for the expression of indicated genes
  • FIG. 8M shows IHC for pSMAD2, scale bars 50 pm.
  • FIG. 8N illustrates Cellphone DB analysis showing ligand-receptor interactions between identified epithelial and fibroblast populations.
  • FIGs. 9A-9G Stroma activation blockade reduce the tumor supporting effects of Olaparib.
  • FIG. 9A shows IF for HABP in WPMY- cells treated with vehicle (DMSO), Olaparib 10 pM or Olaparib 10 pM +PEGPH202.5 pg/ml for 96- hour, scale bars 50 pm.
  • FIG. 9B and 9C illustrate trans- ell migration assays. Experimental design (FIG.
  • FIG. 9B shows relative number of migrating PC3 PCa cultured with Olaparib 10 pM or Olaparib 10 pM +PEGPH20 2.5 pg/m pre-treated WPMY-1 cells for 20 hours, basal and ADT conditions.
  • FIG. 9D and 9E show Click-iT EdU incorporation assay.
  • Experimental design FIG. 9D
  • left representative images of EdU incorporation in PC3 PCa cells treated with CM from Olaparib 10 pM, Olaparib 10 pM +PEGPH202.5 pg/m or Olaparib lOpM +CM incubation with Galunisertib 10 pM WPMY-1 cells for 24 hours.
  • FIGs. 10A-10F Lactate-driven p62 downregulation is not affected by different degradative mechanisms.
  • FIG. 10B and 10C show immunoblot analysis for indicated proteins in WPMY-1 cells treated or not with lactate and MG132 (FIG. 10B) or Bafilomycin Al (FIG. 10C) for 48 hours.
  • FIG. 10B and 10C show immunoblot analysis for indicated proteins
  • FIG. 10D shows immunoblot analysis for indicated proteins in WPMY-1 cells, treated or not with lactate for 48 hours, and transduced with the indicated siRNAs.
  • FIG. 10E and 10F show immunoblot analysis for indicated proteins in WPMY-1 cells, treated or not with lactate for 48 hours and a dose-response of the Calpain inhibitor (FIG. 10E) or Caspase inhibitor (FIG. 10F).
  • FIG. 11A-11F Selective downregulation of p62 by PARP1 deletion.
  • FIG. 11A and 11B show qPCR analysis of mRNA levels of the indicated genes in WPMY-1 cells, transduced with the indicated siRNAs.
  • FIG. 11C shows qPCR analysis of mRNA levels of the indicated genes and immunoblot analysis for indicated proteins in s PARP-1 and sgC WPMY-1 cells.
  • FIG. 11D-11E illustrate Olaparib induces autophagy. Immunoblot analysis of p62 (FIG. 11D) and LC3 (FIG. HE) in WPMY-1 cells treated with Olaparib in the presence of lysosomal inhibitors (PI).
  • FIG. HF shows treatment with an autophagy inhibitor (ULK inhibitor, SBI-0202965) reverts the stroma activation induced by Olaparib as determined by qPCR of the CAF marker, ACTA2.
  • FIGs. 12A-12D Olaparib induces fibroblast activation in different stromal cells.
  • FIG. 12A-12D show qPCR analysis of mRNA levels of the indicated genes in (FIG. 12A) WPMY-1 cells (FIG. 12B) human normal primary fibroblast cells (FIG. 12C) mouse normal fibroblast cells (FIG. 12D) shows mouse hepatic stellate cells treated with Olaparib.
  • FIGs. 13A-F PARP inhibitors induce stromal activation in different cell lines and in vivo models.
  • FIG. 13A-13D show immunoblot analysis for P62 protein in primary prostate fibroblasts (FIG. 13A), lung primary fibroblasts (FIG. 13B), breast primary fibroblasts (FIG. 13C), and endometrial primary fibroblasts (FIG. 13D), veh-treated or Olaparib-treated, 20 pM, for 4 days.
  • FIG. 13E-13F show GSEA analysis for the indicated stromal activation signatures comparing Talazoparib- (PARP inhibitor) vs veh- treated in mammary gland tumors (GSE 125206) (FIG. 13E) and Niraparib (PARP inhibitor) vs veh-treated in human ovarian cancer PDXs (GSE163854) (FIG. 13F) showing stromal activation in PARP inhibitors treated samples.
  • PARP inhibitor Talazoparib-
  • FIGs. 14A-14F Targeting IL6/JAK/STAT or TNFa signaling decreases stromal activation and rescue the proliferative effect conferred to PC3 prostate tumor epithelial cells.
  • FIG. 14A-14C show GSEA analysis for the indicated signatures in Olaparib 20 pM vs DMSO-treated WPMY-1 cells (FIG. 14A), Talazoparib- (PARP inhibitor) vs saline-treated in mammary gland tumors (GSE 125206, FIG. 14B) and Niraparib- (PARP inhibitor) vs veh-treated in human ovarian cancer PDXs (GSE163854, FIG. 14C), showing increased inflammatory related signatures upon PARP inhibitor treatment.
  • FIG. 14A show GSEA analysis for the indicated signatures in Olaparib 20 pM vs DMSO-treated WPMY-1 cells (FIG. 14A), Talazoparib- (PARP inhibitor) vs saline-treated in
  • FIG. 14D shows experimental design.
  • 14F shows Click-iT EdU incorporation assay, left, representative images of EdU incorporation in PC3 PCa cells treated 24 h with CM from WPMY-1 treated with DMSO, Olaparib lOpM, Olaparib 10 pM + Lestaurtinib 50nM, Olaparib 10 pM + IL-6 capture antibody (2h), Olaparib 10 pM +TNFa neutralizing antibody 1 pg/ml (1 h), Lestaurtinib 50 nM, IL-6 capture antibody (2 h) or TNFa neutralizing antibody 1 pg/m (1 h).
  • FIGs. 15A-15K Olaparib induces stromal activation in vivo both in healthy and metastatic tissues.
  • FIG. 15A-15C shows Olaparib induces stromal activation in tumor-invaded lymph nodes and bones in TRAMP + /FVB castrated mice.
  • FIG. 15D-15E show bone in culture (BICA) assay on femur pieces pre-treated or not with Olaparib 20 pM for 48 h cocultured with RMl-BoMe3 tumor epithelial cells for 48 h.
  • Experimental design FIG. 15D). Left representative images of RFP + RMl-BoMe3 cells attached to the bone. Right, graph or RFP + positive area showing increased tumor homing of RM1- BoMe3 in Olaparib pre-treated bones (FIG. 15E).
  • FIG. 15G shows qPCR analysis of mRNA levels of indicated genes in cultured primary bone marrow cells treated with Olaparib 10 pM or DMSO (96 h).
  • FIG. 15H-15J illustrate caudal artery injection of RMl-BoMe3 mouse metastasis model showing that Olaparib induces HA deposition and activation of TGFP signaling.
  • FIG. 15K shows IHC for HA in pre- and post- Olaparib treatment in a prostate cancer bone metastasis showing increased HA deposition in Olaparib-treated mice, scale bars 100 pm.
  • TEE tumor microenvironment
  • stromal fibroblasts as a driver of tumorigenesis in many types of tumors, including prostate cancer (PCa)
  • PCa prostate cancer
  • CAFs cancer-associated fibroblasts
  • CAFs impact the tumor epithelium by modulating many functions through the secretion of stromal growth factors and inflammatory mediators, by reprogramming their metabolism to provide nutrients and survival factors, and by remodeling the extracellular matrix (Hanahan and Weinberg, 2011; Kasashima et al., 2020; Sahai et al., 2020).
  • This fibroblast-epithelium synergistic crosstalk promotes malignancy and is believed to negatively impact cancer treatment by promoting the accumulation of “persisting” or “resistant” tumor cells, which limit therapy efficacy and promote resistance (Bluemn et al., 2017; Linares et al., 2017; Zhang et al., 2020).
  • the autophagy substrate and signaling adaptor p62 (encoded by SQSTM1 gene) is a regulator of CAF biology (Huang et al., 2018; Linares et al., 2017; Valencia et al., 2014). P62 has a dual role in cancer (Duran et al., 2011; Duran et al., 2016; Duran et al., 2008; Moscat et al., 2016; Umemura et al., 2016).
  • p62 downregulation is a central event in the acquisition of the CAF phenotype and in creating a pro-tumorigenic microenvironment conducive to cancer (Linares et al., 2017; Valencia et al., 2014).
  • the poly (ADP-ribose) polymerase 1 (PARP1) enzyme helps cells repair themselves if they become damaged by serving as a "sensor" for DNA strand breaks. Increased PARP1 expression is sometimes observed in melanomas, breast cancer, lung cancer, and other neoplastic diseases. PARP inhibitors stop PARP from repairing cancer cells.
  • the human PARP1 gene (gene ID: 142) is located on chromosome 1 (NCBI NC_000001.ll (226360691..226408093, complement)).
  • An amino acid sequence for human PARP1 is available in the Umprot database as accession no. P09874 and shown below as SEQ ID NO:1.
  • a cDNA sequence for human PARP1 is available in the NCBI database as accession no. NM_001618.4 and shown below as SEQ ID NO:2.
  • compositions and methods described herein can be effectively treated by the compositions and methods described herein even though those subjects have PARP1 isoforms and variants with somewhat different PARP1 sequences than the examples of PARP1 sequences described herein.
  • Such PARP1 isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein).
  • PARP1 isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window.
  • Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970).
  • Hyaluronan or hyaluronic acid is a high molecular weight unbranched polysaccharide synthesized within a variety of organisms, including mammals.
  • Hyaluronan or hyaluronic acid is a constituent of the extracellular matrix. It consists of alternating glucuronic acid and N-acetylglucosamine residues that are linked by beta- 1-3 and beta- 1-4 glycosidic bonds.
  • Hyaluronic acid is synthesized by membrane-bound synthase at the inner surface of the plasma membrane, and the chains are extruded via ABC-Transporter into the extracellular space. It serves a variety of functions, including space filling, lubrication of joints, and provision of a matrix through which cells can migrate.
  • HAS1 human hyaluronan synthase 1
  • NBCI NC_000019.10 51713112..51723991, complement
  • HAS1 encodes the following human amino acid sequence (NCBI accession no. Q92839.2; SEQ ID NO:3).
  • a cDNA sequence for an HAS 1 polypeptide can have the following human nucleotide sequence (NCBI accession no. NM_001297436.2; SEQ ID NO:4).
  • HAS2 human hyaluronan synthase 2
  • HAS2 encodes the following human amino acid sequence (NCBI accession no.
  • HAS1 or HAS 2 isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein).
  • HAS isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window.
  • Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970).
  • Hyaluronidase is an enzyme that breaks down hyaluronic acid. Although it has been used in medical applications for over 60 years, it is thought exacerbate the spread (metastasis) of cancer. Clinical trials of PEGPH20, a clinical grade hyaluronidase, were discontinued after the investigational drug failed to meet the primary endpoint in a phase 3 trial in metastatic pancreas cancer. However, as illustrated herein, PEGPH20 reverts stroma activation and enhances Olaparib antitumor activity.
  • hyaluronidase sequence is the following hyaluronidase PH20 sequence (Uniprot P38567-1; SEQ ID NO:7).
  • compositions and methods described herein can be effectively treated by the compositions and methods described herein even though those subjects have hyaluronidase isoforms and variants with somewhat different sequences than the examples of hyaluronidase sequences described herein.
  • hyaluronidase isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein).
  • hyaluronidase isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window.
  • Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970).
  • Autophagy is a process of metabolic degradation at the cellular level in which organelles or portions of the cytosol are sequestered by double-membrane autophagosomes and fused with lysosomes for degradation.
  • Unc-51-like kinase 1 (ULK1) is a serine/threonine kinase that participates in the initiation of autophagy.
  • ULK1 is a central kinase of the ULK1 complex involved in autophagy initiation, which promotes autophagosome-lysosome fusion.
  • the human ULK1 gene is on chromosome 12 (NC_000012.12 (131894622..131923150).
  • NC_000012.12 131894622..131923150
  • An example of a human ULK1 amino acid sequence is shown below (Uniprot 075385; SEQ ID NO:9).
  • ULK isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein).
  • ULK isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window.
  • Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970).
  • the p62 protein also referred to as sequestosome-1, is encoded by the human SQSTM1 gene, which is found on chromosome 5 (NC_000005.10 (179806393..179838078).
  • An example of a human p62 amino acid sequence is shown below (Uniprot Q13501-1; SEQ ID NO:11). 10 20 30 40 50
  • a cDNA encoding a human p62 protein is shown below (SEQ ID NO: 12).
  • p62 isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein).
  • p62 isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window.
  • Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970).
  • a cDNA encoding a human TNFa protein is shown below (SEQ ID NO:72).
  • 1 AGCAGACGCT CCCTCAGCAA GGACAGCAGA GGACCAGCTA AGAGGGAGAG AAGCAACTAC 61 AGACCCCCCC TGAAAACAAC CCTCAGACGC CACATCCCCT GACAAGCTGC CAGGCAGGTT 121 CTCTTCCTCT CACATACTGA CCCACGGCTC CACCCTCTCT CCCCTGGAAA GGACACCATG 181
  • AGCACTGAAA GCATGATCCG GGACGTGGAG CTGGCCGAGG AGGCGCTCCC CAAGAAGACA 241 GGGGGGCCCC AGGGCTCCAG GCGGTGCTTG TTCCTCAGCC TCTTCTCCTT CCTGATCGTG 301 GCAGGCCA CCACGCTCTT CTGCCTGCTG CACTTTGGAG TGATCGGCCC CCAGAGGGAA 361 GAGTTCCCCA GGGACCTCTC TCTAATCAGC
  • TNFa isoforms and variants 1621 GTGTCTGTAA TCGCCCTACT ATTCAGTGGC GAGAAATAAA GTTTGCTTAG AAAAGAAA Subjects can be effectively treated by the compositions and methods described herein even though those subjects have TNFa isoforms and variants with somewhat different sequences than the examples of TNFa sequences described herein.
  • TNFa isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein).
  • TNFa isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window.
  • Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970).
  • a cDNA encoding a human IL-6 protein is shown below (SEQ ID NO:74).
  • IL-6 isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein).
  • IL-6 isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window.
  • Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970).
  • a cDNA encoding a human JAK protein is shown below (SEQ ID NO:76).
  • GTCTGTGGTC 1441 AGCATTAACA AGCAGGACAA CAAGAAAATG GAACTGAAGC TCTCTTCCCA
  • JAK isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein).
  • JAK isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window.
  • Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970).
  • hyaluronan synthase can be inhibited, for example by use of an inhibitory nucleic acid that specifically recognizes a nucleic acid that encodes the hyaluronan synthase.
  • An inhibitory nucleic acid can have at least one segment that will hybridize to a hyaluronan synthase nucleic acid, ULK1 nucleic acid, TNFa nucleic acid, IL6 nucleic acid or JAK nucleic acid under intracellular or stringent conditions.
  • the inhibitory nucleic acid can reduce expression of a nucleic acid encoding hyaluronan synthase, ULK1, TNFa, IL6 or JAK.
  • a nucleic acid may hybridize to a genomic DNA, a messenger RNA, or a combination thereof.
  • An inhibitory nucleic acid may be incorporated into a plasmid vector or viral DNA. It may be single stranded or double stranded, circular or linear.
  • An inhibitory nucleic acid is a polymer of ribose nucleotides or deoxyribose nucleotides having more than 13 nucleotides in length.
  • An inhibitory nucleic acid may include naturally occurring nucleotides; synthetic, modified, or pseudonucleotides such as phosphorothiolates; as well as nucleotides having a detectable label such as P 32 , biotin or digoxigenin.
  • An inhibitory nucleic acid can reduce the expression and/or activity of a hyaluronan synthase nucleic acid, ULK1 nucleic acid, TNFa nucleic acid, IL6 nucleic acid or JAK nucleic acid.
  • Such an inhibitory nucleic acid may be completely complementary to a segment of an endogenous hyaluronan synthase nucleic acid (e.g., a hyaluronan synthase RNA) or ULK1 nucleic acid (e.g., an ULK1 mRNA) or TNFa nucleic acid (e.g., a TNFa mRNA) or IL-6 nucleic acid (e.g., a IL-6 mRNA) or JAK nucleic acid (e.g., a JAK mRNA).
  • ULK1 nucleic acid e.g., an ULK1 mRNA
  • TNFa nucleic acid e.g., a TNFa mRNA
  • IL-6 nucleic acid e.g., a IL-6 mRNA
  • JAK nucleic acid e.g., a JAK mRNA
  • some variability is permitted in the inhibitory nucleic acid sequences relative to
  • An inhibitory nucleic acid can hybridize to a hyaluronan synthase nucleic acid or ULK1 nucleic acid or a TNFa nucleic acid or a IL-6 nucleic acid or a JAK nucleic acid under intracellular conditions or under stringent hybridization conditions and is sufficiently complementary to inhibit expression of the endogenous hyaluronan synthase nucleic acid or ULK1 nucleic acid or TNFa nucleic acid or IL-6 nucleic acid or JAK nucleic acid.
  • Intracellular conditions refer to conditions such as temperature, pH and salt concentrations typically found inside a cell, e.g., an animal or mammalian cell.
  • stringent hybridization conditions are selected to be about 5 °C lower than the thermal melting point (T m ) for the specific sequence at a defined ionic strength and pH.
  • stringent conditions encompass temperatures in the range of about 1°C to about 20 °C lower than the thermal melting point of the selected sequence, depending upon the desired degree of stringency as otherwise qualified herein.
  • Inhibitory oligonucleotides can, for example, have 2, 3, 4, or 5 or more stretches of contiguous nucleotides that are precisely complementary to a hyaluronan synthase coding sequence or ULK1 coding sequence or TNFa coding sequence or IL-6 coding sequence or JAK coding sequence, wherein each complementary stretch is separated by one or more contiguous nucleotides that are not complementary to adjacent coding sequences, can inhibit the function of a hyaluronan synthase nucleic acid or ULK1 nucleic acid or TNFa nucleic acid or IL-6 nucleic acid or JAK nucleic acid.
  • each stretch of contiguous nucleotides is at least 4, 5, 6, 7, or 8 or more nucleotides in length.
  • Non-complementary intervening sequences may be 1, 2, 3, or 4 nucleotides in length.
  • One skilled in the art can easily use the calculated melting point of an inhibitory nucleic acid hybridized to a sense nucleic acid to estimate the degree of mismatching that will be tolerated for inhibiting expression of a particular target nucleic acid.
  • Inhibitory nucleic acids of the invention include, for example, a short hairpin RNA, a small interfering RNA, a ribozyme or an antisense nucleic acid molecule.
  • the inhibitory nucleic acid molecule may be single or double stranded (e.g., a small interfering RNA (siRNA)) and may function in an enzyme-dependent manner or by steric blocking.
  • Inhibitory nucleic acid molecules that function in an enzyme-dependent manner include forms dependent on RNase H activity to degrade target mRNA. These include single-stranded DNA, RNA, and phosphorothioate molecules, as well as the double-stranded RNAi/siRNA system that involves target mRNA recognition through sense-antisense strand pairing followed by degradation of the target mRNA by the RNA-induced silencing complex.
  • Steric blocking inhibitory nucleic acids which are RNase-H independent, interfere with gene expression or other mRNA-dependent cellular processes by binding to a target mRNA and getting in the way of other processes.
  • Steric blocking inhibitory nucleic acids include 2'-0 alkyl (usually in chimeras with RNase-H dependent antisense), peptide nucleic acid (PNA), locked nucleic acid (LNA) and morpholino antisense.
  • Small interfering RNAs may be used to specifically reduce translation of hyaluronan synthase or ULK1 or TNFa or IL-6 or JAK nucleic acid such that translation of the encoded hyaluronan synthase, ULKl,TNFa, IL-6 or JAK is inhibited.
  • SiRNAs mediate post-transcriptional gene silencing in a sequencespecific manner. See, for example, website at invitrogen.com/site/us/en/home/Products-and-Services/Applications/rnai.html.
  • siRNA mediate cleavage of the homologous endogenous mRNA transcript by guiding the complex to the homologous mRNA transcript, which is then cleaved by the complex.
  • the siRNA may be homologous and/or complementary to any region of the hyaluronan synthase transcript or to any region of an ULK1 transcript or to any region of a TNFa transcript or any region of a IL-6 transcript or any region of a JAKtranscript.
  • the region of homology may be 30 nucleotides or less in length, e.g., less than 25 nucleotides such as about 21 to 23 nucleotides in length.
  • SiRNA is typically double stranded and may have two-nucleotide 3’ overhangs, for example, 3’ overhanging UU dinucleotides.
  • Methods for designing siRNAs are known to those skilled in the art. See, for example, Elbashir et al. Nature 411: 494-498 (2001); Harborth et al. Antisense Nucleic Acid Drug Dev. 13: 83-106 (2003).
  • the pSuppressorNeo vector for expressing hairpin siRNA can be used to generate siRNA for inhibiting expression of hyaluronan synthase or ULK1.
  • the construction of the siRNA expression plasmid involves the selection of the target region of the mRNA, which can be a trial-and-error process.
  • Elbashir et al. have provided guidelines that appear to work -80% of the time.
  • Elbashir, S.M., et al. Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods, 2002. 26(2): p. 199-213.
  • a target region may be selected, e.g., 50 to 100 nucleotides downstream of the start codon.
  • the 5' and 3' untranslated regions and regions close to the start codon should be avoided as these may be richer in regulatory protein binding sites.
  • siRNA can begin with AA, have 3' UU overhangs for both the sense and antisense siRNA strands, and have an approximate 50 % G/C content.
  • An example of a sequence for a synthetic siRNA is 5'-AA(N19)UU, where N is any nucleotide in the mRNA sequence and the siRNA should be approximately 50% G-C content.
  • the selected sequence(s) can be compared to others in the human genome database to minimize homology to other known coding sequences (e.g., by Blast search, for example, through the NCBI website).
  • SiRNAs may be chemically synthesized, created by in vitro transcription, or expressed from an siRNA expression vector or a PCR expression cassette. See, e.g., website at invitrogen.com/site/us/en/home/Products-and- Services/Applications/rnai.html.
  • the insert encoding the siRNA may be expressed as an RNA transcript that folds into an siRNA hairpin.
  • the RNA transcript may include a sense siRNA sequence that is linked to its reverse complementary antisense siRNA sequence by a spacer sequence that forms the loop of the hairpin as well as a string of U’s at the 3’ end.
  • the loop of the hairpin may be of any appropriate lengths, for example, 3 to 30 nucleotides in length, e.g., , 3 to 23 nucleotides in length, and may be of various nucleotide sequences including, AUG, CCC, UUCG, CCACC, CTCGAG, AAGCUU, CCACACC and UUCAAGAGA.
  • SiRNAs also may be produced in vivo by cleavage of double-stranded RNA introduced directly or via a transgene or virus. Amplification by an RNA-dependent RNA polymerase may occur in some organisms.
  • an inhibitory nucleic acid such as a short hairpin RNA siRNA or an antisense oligonucleotide may be prepared using methods such as by expression from an expression vector or expression cassette that includes the sequence of the inhibitory nucleic acid. Alternatively, it may be prepared by chemical synthesis using naturally occurring nucleotides, modified nucleotides or any combinations thereof.
  • the inhibitory nucleic acids are made from modified nucleotides or non-phosphodiester bonds, for example, that are designed to increase biological stability of the inhibitory nucleic acid or to increase intracellular stability of the duplex formed between the inhibitory nucleic acid and the target hyaluronan synthase nucleic acid.
  • An inhibitory nucleic acid may be generated, for example, by expression from an expression vector encoding a complementarity sequence of the hyaluronan synthase nucleic acid, ULK1 nucleic acid, TNFa nucleic acid, IL-6 nucleic acid or JAK nucleic acid. Alternatively, it may be prepared by chemical synthesis using naturally occurring nucleotides, modified nucleotides or any mixture of combination thereof.
  • the hyaluronan synthase nucleic acids or ULK1 nucleic acids or TNFa nucleic acids or IL-6 nucleic acids or JAK nucleic acids are made from modified nucleotides or non-phosphodiester bonds, for example, that are designed to increase biological stability of the nucleic acids or to increase intracellular stability of the duplex formed between the inhibitory nucleic acids and other (e.g., endogenous) nucleic acids.
  • inhibitory hyaluronan synthase nucleic acids or inhibitory ULK1 nucleic acids or inhibitory TNFa nucleic acids or inhibitory IL-6 nucleic acids or inhibitory JAK nucleic acids can be peptide nucleic acids that have peptide bonds rather than phosphodiester bonds.
  • inhibitory nucleic acids of the hyaluronan synthase or ULK1 or TNFa or IL-6 or JAK described herein may include modified nucleotides, as well as natural nucleotides such as combinations of ribose and deoxyribose nucleotides.
  • Naturally occurring nucleotides that can be employed in the hyaluronan synthase nucleic acids or ULK1 nucleic acids or TNFa nucleic acids or IL-6 nucleic acids or JAK nucleic acids can include the ribose or deoxyribose nucleotides adenosine, guanine, cytosine, thymine and uracil.
  • modified nucleotides that can be employed in the inhibitory hyaluronan synthase nucleic acids or inhibitory ULK1 nucleic acids or inhibitory TNFa nucleic acids or inhibitory IL-6 nucleic acids or inhibitory JAK nucleic acids include 5-fluorouracil, 5 -bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5 -(carboxyhydroxylmethyl) uracil, 5- carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1- methylguanine, 1 -methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2- methylguanine, 3-methylcytosine, 5-methylcytosine, N6-a
  • the inhibitory nucleic acids and may be of same length as wild type hyaluronan synthase or as any isoforms or variants of hyaluronan synthase or ULK1 or TNFa or IL-6 or JAK.
  • the inhibitory nucleic acids of the hyaluronan synthase, ULK1, TNFa, IL-6 or JAK described herein can also be longer and include other useful sequences.
  • the inhibitory nucleic acids of the hyaluronan synthase, ULK1, TNFa, IL-6 or JAK are somewhat shorter.
  • inhibitory nucleic acids of hyaluronan synthase, ULK1, TNFa, IL-6 or JAK can include a segment that has a nucleic acid sequence that can be missing up to 5 nucleotides, or missing up to 10 nucleotides, or missing up to 20 nucleotides, or missing up to 30 nucleotides, or missing up to 50 nucleotides, or missing up to 100 nucleotides from the 5’ or 3’ end.
  • the inhibitory nucleic acids can be introduced via one or more vehicles such as via expression vectors (e.g., viral vectors), via virus like particles, via ribonucleoproteins (RNPs), via nanoparticles, via liposomes, or a combination thereof.
  • the vehicles can include components or agents that can target particular cell types, facilitate cell penetration, reduce degradation, or a combination thereof.
  • Antibodies can be used as inhibitors of hyaluronan synthase, ULK1, TNFa, IL-6 or JAK. Antibodies can be raised against various epitopes of hyaluronan synthase, ULK1, TNFa, IL-6 or JAK. Some antibodies for hyaluronan synthase, ULK1, TNFa, IL-6 or JAK may also be available commercially. However, the antibodies contemplated for treatment pursuant to the methods and compositions described herein are in one embodiment human or humanized antibodies and are highly specific for their targets.
  • the present disclosure relates to use of isolated antibodies that bind specifically to hyaluronan synthase, ULK1, TNFa, IL-6 or JAK.
  • Such antibodies may be monoclonal antibodies.
  • Such antibodies may also be humanized or fully human monoclonal antibodies.
  • the antibodies can exhibit one or more desirable functional properties, such as high affinity binding to hyaluronan synthase, ULK1, TNFa, IL-6 or JAK.
  • Methods and compositions described herein can include antibodies that bind hyaluronan synthase, ULK1, TNFa, IL-6 or JAK, or a combination of antibodies where each antibody type can separately bind hyaluronan synthase, ULK1, TNFa, IL-6 or JAK.
  • antibody as referred to herein includes whole antibodies and any antigen binding fragment (i.e., "antigen-binding portion") or single chains thereof.
  • An “antibody” refers to a glycoprotein comprising at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds, or an antigen binding portion thereof.
  • Each heavy chain is comprised of a heavy chain variable region (abbreviated herein as VH) and a heavy chain constant region.
  • the heavy chain constant region is comprised of three domains, CHI, CH2 and CH3.
  • Each light chain is comprised of a light chain variable region (abbreviated herein as VL) and a light chain constant region.
  • the light chain constant region is comprised of one domain, CL-
  • the VH and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR).
  • CDR complementarity determining regions
  • FR framework regions
  • Each VH and VL is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
  • the variable regions of the heavy and light chains contain a binding domain that interacts with an antigen.
  • the constant regions of the antibodies may mediate the binding of the immunoglobulin to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (Clq) of the classical complement system.
  • antibody portion refers to one or more fragments of an antibody that retain the ability to specifically bind to an antigen (e.g., a peptide or domain of hyaluronan synthase, ULK1, TNFa, IL-6 or JAK). It has been shown that the antigen-binding function of an antibody can be performed by fragments of a full-length antibody.
  • an antigen e.g., a peptide or domain of hyaluronan synthase, ULK1, TNFa, IL-6 or JAK.
  • binding fragments encompassed within the term "antigen-binding portion" of an antibody include (i) a Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CHI domains; (ii) a F(ab')2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the VH and CHI domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al., (1989) Nature 341:544-546), which consists of a VH domain; and (vi) an isolated complementarity determining region (CDR).
  • a Fab fragment a monovalent fragment consisting of the VL, VH, CL and CHI domains
  • F(ab')2 fragment a bivalent fragment comprising two Fab fragments linked by a dis
  • the two domains of the Fv fragment, VL and VH are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv (scFv); see e.g., Bird et al. (1988) Science 242:423-426; and Huston et al. (1988) Proc. Natl. Acad. Sci. USA 85:5879-5883).
  • single chain Fv single chain Fv
  • Such single chain antibodies are also intended to be encompassed within the term "antigen-binding portion" of an antibody.
  • an “isolated antibody,” as used herein, is intended to refer to an antibody that is substantially free of other antibodies having different antigenic specificities (e.g., an isolated antibody that specifically binds hyaluronan synthase, ULK1, TNFa, IL-6 or JAK is substantially free of antibodies that specifically bind antigens other than a hyaluronan synthase, ULK1, TNFa, IL-6 or JAK).
  • an isolated antibody that specifically binds hyaluronan synthase, ULK1, TNFa, IL-6 or JAK may, however, have cross-reactivity to related antigens, such as isoforms or variants of hyaluronan synthase, ULK1, TNFa, IL-6 or JAK from various humans or from other species.
  • an isolated antibody may be substantially free of other cellular material and/or chemicals.
  • the terms “monoclonal antibody” or “monoclonal antibody composition” as used herein refer to a preparation of antibody molecules of single molecular composition.
  • a monoclonal antibody composition displays a single binding specificity and affinity for a particular epitope.
  • human antibody as used herein, is intended to include antibodies having variable regions in which both the framework and CDR regions are derived from human germline immunoglobulin sequences. Furthermore, if the antibody contains a constant region, the constant region also is derived from human germline immunoglobulin sequences.
  • the human antibodies of the invention may include amino acid residues not encoded by human germline immunoglobulin sequences (e.g., mutations introduced by random or site-specific mutagenesis in vitro or by somatic mutation in vivo). However, the term "human antibody,” as used herein, is not intended to include antibodies in which CDR sequences derived from the germline of another mammalian species, such as a mouse, have been grafted onto human framework sequences.
  • human monoclonal antibody refers to antibodies displaying a single binding specificity which have variable regions in which both the framework and CDR regions are derived from human germline immunoglobulin sequences.
  • the human monoclonal antibodies are produced by a hybridoma which includes a B cell obtained from a transgenic nonhuman animal, e.g., a transgenic mouse, having a genome comprising a human heavy chain transgene and a light chain transgene fused to an immortalized cell.
  • recombinant human antibody includes all human antibodies that are prepared, expressed, created or isolated by recombinant means, such as (a) antibodies isolated from an animal (e.g., a mouse) that is transgenic or transchromosomal for human immunoglobulin genes or a hybridoma prepared therefrom (described further below), (b) antibodies isolated from a host cell transformed to express the human antibody, e.g., from a transfectoma, (c) antibodies isolated from a recombinant, combinatorial human antibody library, and (d) antibodies prepared, expressed, created or isolated by any other means that involve splicing of human immunoglobulin gene sequences to other DNA sequences.
  • Such recombinant human antibodies have variable regions in which the framework and CDR regions are derived from human germline immunoglobulin sequences.
  • such recombinant human antibodies can be subjected to in vitro mutagenesis (or, when an animal transgenic for human Ig sequences is used, in vivo somatic mutagenesis) and thus the amino acid sequences of the VL and Vn regions of the recombinant antibodies are sequences that, while derived from and related to human germline VL and Vn sequences, may not naturally exist within the human antibody germline repertoire in vivo.
  • isotype refers to the antibody class (e.g., IgM or IgGl) that is encoded by the heavy chain constant region genes.
  • an antibody recognizing an antigen and "an antibody specific for an antigen” are used interchangeably herein with the term “an antibody which binds specifically to an antigen.”
  • human antibody derivatives refers to any modified form of the human antibody, e.g., a conjugate of the antibody and another agent or antibody.
  • humanized antibody is intended to refer to antibodies in which CDR sequences derived from the germline of another mammalian species, such as a mouse, have been grafted onto human framework sequences. Additional framework region modifications may be made within the human framework sequences.
  • chimeric antibody is intended to refer to antibodies in which the variable region sequences are derived from one species and the constant region sequences are derived from another species, such as an antibody in which the variable region sequences are derived from a mouse antibody and the constant region sequences are derived from a human antibody.
  • an antibody that "specifically binds to human hyaluronan synthase” or an antibody that "specifically binds to human ULK1” or an antibody that “specifically binds to TNFa” or an antibody that “specifically binds to IL-6” or an antibody that “specifically binds to JAK” is intended to refer to an antibody that binds to human hyaluronan synthase or ULK1 or TNFa or IL-6 or JAK with a KD of IxlO -7 M or less, 5xl0 -8 M or less, IxlO -8 M or less, 5xl0 -9 M or less, or between IxlO -8 M and IxlO 10 M or less.
  • K as soc or "K a ,” as used herein, is intended to refer to the association rate of a particular antibody-antigen interaction
  • Kdis or “Kd,” as used herein, is intended to refer to the dissociation rate of a particular antibody-antigen interaction
  • KD is intended to refer to the dissociation constant, which is obtained from the ratio of Kd to Ka (i.e., Kd/ K a ) and is expressed as a molar concentration (M). KD values for antibodies can be determined using methods well established in the art.
  • the antibodies of the invention are characterized by particular functional features or properties of the antibodies.
  • the antibodies bind specifically to human hyaluronan synthase, ULK1, TNFa, IL-6 or JAK.
  • an antibody of the invention binds to hyaluronan synthase, ULK1, TNFa, IL-6 or JAK with high affinity, for example with a KD of IxlO -7 M or less.
  • the antibodies can exhibit one or more of the following characteristics:
  • cancer e.g., metastatic cancer
  • Assays to evaluate the binding ability of the antibodies toward hyaluronan synthase, ULK1, TNFa, IL-6 or JAK can be used, including for example, ELIS As, Western blots and RIAs.
  • the binding kinetics (e.g., binding affinity) of the antibodies also can be assessed by standard assays known in the art, such as by BiacoreTM. analysis.
  • each of the subject antibodies can bind to hyaluronan synthase, ULK1, TNFa, IL-6 or JAK the VL and Vn sequences or the respective antibodies can be "mixed and matched" to create other binding molecules that bind to hyaluronan synthase, ULK1, TNFa, IL-6 or JAK, respectively.
  • the binding properties of such "mixed and matched" antibodies can be tested using the binding assays described above and assessed in assays described in the examples.
  • VL and VH chains are mixed and matched, a Vn sequence from a particular Vn I VL pairing can be replaced with a structurally similar Vn sequence.
  • a VL sequence from a particular Vn I VL pairing may be replaced with a structurally similar VL sequence.
  • the invention provides an isolated monoclonal antibody, or antigen binding portion thereof comprising:
  • the CDR3 domain independently from the CDR1 and/or CDR2 domain(s), alone can determine the binding specificity of an antibody for a cognate antigen and that multiple antibodies can predictably be generated having the same binding specificity based on a common CDR3 sequence. See, for example, Klimka et al., British J.
  • Nucleic acid segments encoding one or more inhibitory nucleic acids, proteins (e.g., hyaluronidase), or antibodies can be inserted into or employed with any suitable expression system.
  • Commercially useful and/or therapeutically effective quantities of one or more inhibitory nucleic acids, proteins (e.g., hyaluronidase), or antibodies can also be generated from such expression systems.
  • the expression systems can be used to express hyaluronidases.
  • the expression systems can be used to express inhibitory nucleic acids that can reduce endogenous hyaluronan synthase levels.
  • Recombinant expression of nucleic acids is usefully accomplished using a vector, such as a plasmid.
  • the vector can include a promoter operably linked to nucleic acid segment encoding one or more of the hyaluronidase or an inhibitory nucleic acid for hyaluronan synthase nucleic acids, or other proteins (e.g., hyaluronidase), or antibodies.
  • vector can also include other elements required for transcription and translation.
  • vector refers to any carrier containing exogenous DNA.
  • vectors are agents that transport the exogenous nucleic acid into a cell without degradation and include a promoter yielding expression of the nucleic acid in the cells into which it is delivered.
  • Vectors include but are not limited to plasmids, viral nucleic acids, viruses, phage nucleic acids, phages, cosmids, and artificial chromosomes.
  • prokaryotic and eukaryotic expression vectors suitable for carrying, encoding and/or expressing hyaluronidase, inhibitory nucleic acids, proteins, or antibodies can be used.
  • a variety of prokaryotic and eukaryotic expression vectors suitable for carrying, encoding and/or expressing hyaluronidase, inhibitory nucleic acids, proteins, or antibodies can be employed.
  • Such expression vectors include, for example, pET, pET3d, pCR2.1, pBAD, pUC, and yeast vectors. The vectors can be used, for example, in a variety of in vivo and in vitro situations.
  • heterologous when used in reference to an expression cassette, expression vector, regulatory sequence, promoter, or nucleic acid refers to an expression cassette, expression vector, regulatory sequence, or nucleic acid that has been manipulated in some way.
  • a heterologous promoter can be a promoter that is not naturally linked to a nucleic acid of interest, or that has been introduced into cells by cell transformation procedures.
  • a heterologous nucleic acid or promoter also includes a nucleic acid or promoter that is native to an organism but that has been altered in some way (e.g.
  • Heterologous nucleic acids may comprise sequences that comprise cDNA forms.
  • Heterologous coding regions can be distinguished from endogenous coding regions, for example, when the heterologous coding regions are joined to nucleotide sequences comprising regulatory elements such as promoters that are not found naturally associated with the coding region, or when the heterologous coding regions are associated with portions of a chromosome not found in nature (e.g., genes expressed in loci where the protein encoded by the coding region is not normally expressed).
  • heterologous promoters can be promoters that at linked to a coding region to which they are not linked in nature.
  • Viral vectors that can be employed include those relating to lentivirus, adenovirus, adeno-associated virus, herpes virus, vaccinia virus, polio virus, AIDS virus, neuronal trophic virus, Sindbis and other viruses. Also useful are any viral families which share the properties of these viruses which make them suitable for use as vectors. Retroviral vectors that can be employed include those described in by Verma, I.M., Retroviral vectors for gene transfer. In Microbiology- 1985, American Society for Microbiology, pp. 229-232, Washington, (1985). For example, such retroviral vectors can include Murine Maloney Leukemia virus, MMLV, and other retroviruses that express desirable properties.
  • viral vectors typically contain, nonstructural early genes, structural late genes, an RNA polymerase III transcript, inverted terminal repeats necessary for replication and encapsidation, and promoters to control the transcription and replication of the viral genome.
  • viruses typically have one or more of the early genes removed and a gene or gene/promoter cassette is inserted into the viral genome in place of the removed viral nucleic acid.
  • a variety of regulatory elements can be included in the expression cassettes and/or expression vectors, including promoters, enhancers, translational initiation sequences, transcription termination sequences and other elements.
  • a “promoter” is generally a sequence or sequences of DNA that function when in a relatively fixed location in regard to the transcription start site.
  • the promoter can be upstream of the nucleic acid segment encoding one or more hyaluronidase, inhibitory nucleic acid, protein, or antibody.
  • a “promoter” contains core elements required for basic interaction of RNA polymerase and transcription factors and can contain upstream elements and response elements.
  • “Enhancer” generally refers to a sequence of DNA that functions at no fixed distance from the transcription start site and can be either 5’ or 3' to the transcription unit.
  • enhancers can be within an intron as well as within the coding sequence itself. They are usually between 10 and 300 by in length, and they function in cis. Enhancers function to increase transcription from nearby promoters. Enhancers, like promoters, also often contain response elements that mediate the regulation of transcription. Enhancers often determine the regulation of expression.
  • Expression vectors used in eukaryotic host cells can also contain sequences for the termination of transcription, which can affect mRNA expression. These regions are transcribed as polyadenylated segments in the untranslated portion of the mRNA encoding tissue factor protein. The 3' untranslated regions also include transcription termination sites.
  • the transcription unit may also contain a polyadenylation region. One benefit of this region is that it increases the likelihood that the transcribed unit will be processed and transported like mRNA.
  • the identification and use of polyadenylation signals in expression constructs is well established. Homologous polyadenylation signals may be used in the transgene constructs.
  • the expression of one or more type of hyaluronidase, inhibitory nucleic acid, protein, or antibody from an expression cassette or expression vector can be controlled by any promoter capable of expression in prokaryotic cells or eukaryotic cells.
  • prokaryotic promoters include, but are not limited to, SP6, T7, T5, tac, bla, trp, gal, lac, or maltose promoters.
  • eukaryotic promoters examples include, but are not limited to, constitutive promoters, e.g., viral promoters such as CMV, SV40 and RSV promoters, as well as regulatable promoters, e.g., an inducible or repressible promoter such as the tet promoter, the hsp70 promoter and a synthetic promoter regulated by CRE.
  • constitutive promoters e.g., viral promoters such as CMV, SV40 and RSV promoters
  • regulatable promoters e.g., an inducible or repressible promoter such as the tet promoter, the hsp70 promoter and a synthetic promoter regulated by CRE.
  • Vectors for bacterial expression include pGEX-5X-3
  • for eukaryotic expression include pCIneo-CMV.
  • the expression cassette or vector can include nucleic acid sequence encoding a marker product.
  • This marker product is used to determine if a vector or expression cassette encoding one or more hyaluronidase, inhibitory nucleic acid, protein, or antibody have been delivered to the cell and once delivered, is being expressed.
  • Marker genes can include the E. coll lacZ gene which encodes P-galactosidase, and green fluorescent protein.
  • the marker can be a selectable marker. When such selectable markers are successfully transferred into a host cell, the transformed host cell can survive if placed under selective pressure. There are two widely used distinct categories of selective regimes.
  • the first category is based on a cell's metabolism and the use of a mutant cell line which lacks the ability to grow independent of a supplemented media.
  • the second category is dominant selection which refers to a selection scheme used in any cell type and does not require the use of a mutant cell line. These schemes typically use a drug to arrest growth of a host cell. Those cells which have a novel gene would express a protein conveying drug resistance and would survive the selection. Examples of such dominant selection use the drugs neomycin (Southern P. and Berg, P., J. Molec. Appl. Genet. 1: 327 (1982)), mycophenolic acid, (Mulligan, R. C. and Berg, P.
  • Gene transfer can be obtained using direct transfer of genetic material, in but not limited to, plasmids, viral vectors, viral nucleic acids, phage nucleic acids, phages, cosmids, and artificial chromosomes, or via transfer of genetic material in cells or carriers such as cationic liposomes.
  • plasmids in but not limited to, viral vectors, viral nucleic acids, phage nucleic acids, phages, cosmids, and artificial chromosomes.
  • Transfer vectors can be any nucleotide construction used to deliver genes into cells (e.g., a plasmid), or as part of a general strategy to deliver genes, e.g., as part of recombinant retrovirus or adenovirus (Ram et al. Cancer Res. 53:83-88, (1993)).
  • Appropriate means for transfection, including viral vectors, chemical transfectants, or physico-mechanical methods such as electroporation and direct diffusion of DNA, are described by, for example, Wolff, J. A., et al., Science, 247, 1465-1468, (1990); and Wolff, J. A. Nature, 352, 815-818, (1991).
  • the nucleic acid molecules, expression cassette and/or vectors encoding one or more hyaluronidase, inhibitory nucleic acid, protein, or antibody can be introduced to a cell by any method including, but not limited to, calcium- mediated transformation, electroporation, microinjection, lipofection, particle bombardment and the like.
  • the cells can also be expanded in culture and then administered to a subject, e.g. a mammal such as a human.
  • the amount or number of cells administered can vary but amounts in the range of about 10 6 to about 10 9 cells can be used.
  • the cells are generally delivered in a physiological solution such as saline or buffered saline.
  • the cells can also be delivered in a vehicle such as a population of liposomes, exosomes or microvesicles.
  • the transgenic cell can produce exosomes or microvesicles that contain nucleic acid molecules, expression cassettes and/or vectors expressing hyaluronidases, inhibitory nucleic acids, proteins, antibodies, or a combination thereof. In some cases, the transgenic cell can produce exosomes or microvesicles that contain nucleic acid molecules that encode one or more hyaluronidases, inhibitory nucleic acids, proteins, or antibodies to particular tissues.
  • Microvesicles can mediate the secretion of a wide variety of proteins (e.g., hyaluronidase), lipids, mRNAs, and micro RNAs, interact with neighboring cells, and can thereby transmit signals, proteins (e.g., hyaluronidase), lipids, and nucleic acids from cell to cell (see, e.g., Shen et al., J Biol Chem. 286(16): 14383-14395 (2011); Hu et al., Frontiers in Genetics 3 (April 2012); Pegtel et al., Proc.
  • proteins e.g., hyaluronidase
  • lipids e.g., mRNAs, and micro RNAs
  • Cells producing such microvesicles can be used to provide one or more hyaluronidase, inhibitory nucleic acid, protein, or antibody.
  • Transgenic vectors or cells with a heterologous expression cassette or expression vector can express one or more hyaluronidase, inhibitory nucleic acid, protein, or antibody. Any of these vectors or cells can be administered to a subject. Exosomes produced by transgenic cells can also be used to administer one or more hyaluronidase, inhibitory nucleic acid, protein, or antibody to the subject.
  • Compositions
  • the invention also relates to compositions containing PARP1 inhibitors and activated stromal I activated cancer-associated fibroblast inhibitors or inhibitors of TNFa, IL-6 or JAK.
  • Such inhibitors can be small molecules, antibodies, polypeptides, inhibitory nucleic acids, nucleic acids encoding inhibitory nucleic acids, nucleic acids encoding a polypeptide (e.g., within an expression cassette or expression vector), or a combination thereof.
  • the compositions can be pharmaceutical compositions.
  • the compositions can include a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable it is meant that a carrier, diluent, excipient, and/or salt is compatible with the other ingredients of the formulation, and not deleterious to the recipient thereof.
  • composition can be formulated in any convenient form.
  • the therapeutic agents of the invention e.g., small molecules, inhibitory nucleic acids, nucleic acids encoding inhibitory nucleic acids, polypeptides, nucleic acid encoding polypeptides (e.g., within an expression cassette or expression vector), a compound identified by a method described herein, or a combination thereof
  • a therapeutically effective amount is an amount sufficient to obtain the desired physiological effect, such a reduction of at least one symptom of cancer.
  • chemotherapeutic agents can reduce cell metastasis by 5%, or 10%, or 15%, or 20%, or 25%, or 30%, or 35%, or 40%, or 45%, or 50%, or 55%, or 60%, or 65%, or %70, or 80%, or 90%, 095%, or 97%, or 99%, or any numerical percentage between 5% and 100%.
  • Symptoms of cancer can also include tumor cachexia, tumor-induced pain conditions, tumor-induced fatigue, tumor growth, and metastatic spread.
  • the chemotherapeutic agents may also reduce tumor cachexia, tumor- induced pain conditions, tumor-induced fatigue, tumor growth, or a combination thereof by 5%, or 10%, or 15%, or 20%, or 25%, or 30%, or 35%, or 40%, or 45%, or 50%, or 55%, or 60%, or 65%, or %70, or 80%, or 90%, 095%, or 97%, or 99%, or any numerical percentage between 5% and 100%.
  • the therapeutic agents may be administered as single or divided dosages.
  • therapeutic agents can be administered in dosages of at least about 0.01 mg/kg to about 500 to 750 mg/kg, of at least about 0.01 mg/kg to about 300 to 500 mg/kg, at least about 0.1 mg/kg to about 100 to 300 mg/kg or at least about 1 mg/kg to about 50 to 100 mg/kg of body weight, although other dosages may provide beneficial results.
  • the amount administered will vary depending on various factors including, but not limited to, the type of small molecules, compounds, polypeptides, antibodies, nucleic acids, or combinations thereof chosen for administration, the disease, the weight, the physical condition, the health, and the age of the mammal. Such factors can be readily determined by the clinician employing animal models or other test systems that are available in the art.
  • Administration of the therapeutic agents in accordance with the present invention may be in a single dose, in multiple doses, in a continuous or intermittent manner, depending, for example, upon the recipient's physiological condition, whether the purpose of the administration is therapeutic or prophylactic, and other factors known to skilled practitioners.
  • the administration of the therapeutic agents and compositions of the invention may be essentially continuous over a preselected period of time or may be in a series of spaced doses. Both local and systemic administration is contemplated.
  • small molecules, compounds, polypeptides, nucleic acids, expression cassettes, and other agents are synthesized or otherwise obtained, purified as necessary or desired.
  • These small molecules, compounds, polypeptides, antibodies, nucleic acids, expression cassettes, and other agents can be suspended in a pharmaceutically acceptable carrier and/or lyophilized or otherwise stabilized.
  • the small molecules, compounds, polypeptides, nucleic acids, expression cassettes, other agents, and combinations thereof can be adjusted to an appropriate concentration, and optionally combined with other agents.
  • the absolute weight of a given small molecule, compound, polypeptide, antibodies, nucleic acid, and/or other agents included in a unit dose can vary widely.
  • the unit dosage can vary from about 0.01 g to about 50 g, from about 0.01 g to about 35 g, from about 0.1 g to about 25 g, from about 0.5 g to about 12 g, from about 0.5 g to about 8 g, from about 0.5 g to about 4 g, or from about 0.5 g to about 2 g.
  • Daily doses of the chemotherapeutic agents of the invention can vary as well. Such daily doses can range, for example, from about 0.1 g/day to about 50 g/day, from about 0.1 g/day to about 25 g/day, from about 0.1 g/day to about 12 g/day, from about 0.5 g/day to about 8 g/day, from about 0.5 g/day to about 4 g/day, and from about 0.5 g/day to about 2 g/day.
  • a pharmaceutical composition can be formulated as a single unit dosage form.
  • one or more suitable unit dosage forms comprising the therapeutic agent(s) can be administered by a variety of routes including parenteral (including subcutaneous, intravenous, intramuscular and intraperitoneal), oral, rectal, dermal, transdermal, intrathoracic, intrapulmonary and intranasal (respiratory) routes.
  • the therapeutic agent(s) may also be formulated for sustained release (for example, using microencapsulation, see WO 94/ 07529, and U.S. Patent No.4,962,091).
  • the formulations may, where appropriate, be conveniently presented in discrete unit dosage forms and may be prepared by any of the methods well known to the pharmaceutical arts.
  • Such methods may include the step of mixing the therapeutic agent with liquid carriers, solid matrices, semi-solid carriers, finely divided solid carriers or combinations thereof, and then, if necessary, introducing or shaping the product into the desired delivery system.
  • the therapeutic agent(s) can be linked to a convenient carrier such as a nanoparticle, albumin, polyalkylene glycol, or be supplied in prodrug form.
  • the therapeutic agent(s), and combinations thereof can be combined with a carrier and/or encapsulated in a vesicle such as a liposome.
  • compositions of the invention may be prepared in many forms that include aqueous solutions, suspensions, tablets, hard or soft gelatin capsules, and liposomes and other slow-release formulations, such as shaped polymeric gels.
  • Administration of inhibitors can also involve parenteral or local administration of the in an aqueous solution or sustained release vehicle.
  • the therapeutic agent(s) and/or other agents can sometimes be administered in an oral dosage form
  • that oral dosage form can be formulated so as to protect the small molecules, compounds, polypeptides, nucleic acids, expression cassettes, and combinations thereof from degradation or breakdown before the small molecules, compounds, antibodies, polypeptides, inhibitory nucleic acids, nucleic acids encoding such polypeptides, and combinations thereof provide therapeutic utility.
  • the small molecules, compounds, inhibitory nucleic acids, polypeptides, nucleic acids encoding such polypeptide, antibodies, and/or other agents can be formulated for release into the intestine after passing through the stomach. Such formulations are described, for example, in U.S. Patent No. 6,306,434 and in the references contained therein.
  • Liquid pharmaceutical compositions may be in the form of, for example, aqueous or oily suspensions, solutions, emulsions, syrups or elixirs, dry powders for constitution with water or other suitable vehicle before use.
  • Such liquid pharmaceutical compositions may contain conventional additives such as suspending agents, emulsifying agents, non-aqueous vehicles (which may include edible oils), or preservatives.
  • the pharmaceutical compositions may take such forms as suspensions, solutions, or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
  • Suitable carriers include saline solution, encapsulating agents (e.g., liposomes), and other materials.
  • the chemotherapeutic agent(s) and/or other agents can be formulated in dry form (e.g., in freeze-dried form), in the presence or absence of a carrier. If a carrier is desired, the carrier can be included in the pharmaceutical formulation, or can be separately packaged in a separate container, for addition to the inhibitor that is packaged in dry form, in suspension or in soluble concentrated form in a convenient liquid.
  • Therapeutic agent(s) and/or other agents can be formulated for parenteral administration (e.g., by injection, for example, bolus injection or continuous infusion) and may be presented in unit dosage form in ampoules, prefilled syringes, small volume infusion containers or multi-dose containers with an added preservative.
  • the compositions can also contain other ingredients such as chemotherapeutic agents, anti-viral agents, antibacterial agents, antimicrobial agents and/or preservatives.
  • additional therapeutic agents include, but are not limited to: alkylating agents, such as nitrogen mustards, alkyl sulfonates, nitrosoureas, ethylenimines, and triazenes; antimetabolites, such as folate antagonists, purine analogues, and pyrimidine analogues; antibiotics, such as anthracy clines, bleomycins, mitomycin, dactinomycin, and plicamycin; enzymes, such as L-asparaginase; farnesyl-protein transferase inhibitors; hormonal agents, such as glucocorticoids, estrogens/antiestrogens, androgens/antiandrogens, progestins, and luteinizing hormone-releasing hormone anatagonists, octreotide acetate; microtubule-disruptor agents, such as ecteinascidins or their analogs and derivatives; microtubule-stabilizing agents
  • the one or more PARP1 inhibitors and inhibitors of activated stromal I activated cancer-associated fibroblasts, TNFa, IE-6 or JAK are useful for selectively targeting tumors or treating cancers.
  • Treatment refers to both therapeutic treatment, and prophylactic or preventative measures. Those in need of treatment include those already with the disorder as well as those prone to have the disorder, or those in whom the disorder is to be prevented.
  • Subject for purposes of treatment refers to any animal classified as a mammal or bird, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, horses, cats, cows, etc. In one embodiment, the subject is human.
  • cancer includes solid animal tumors as well as hematological malignancies.
  • tumor cell(s) and “cancer cell(s)” are used interchangeably herein.
  • Solid animal tumors include cancers of the head and neck, lung, mesothelioma, mediastinum, lung, esophagus, stomach, pancreas, hepatobiliary system, small intestine, colon, colorectal, rectum, anus, kidney, urethra, bladder, prostate, urethra, penis, testis, gynecological organs, ovaries, breast, endocrine system, skin central nervous system; sarcomas of the soft tissue and bone; and melanoma of cutaneous and intraocular origin.
  • a metastatic cancer at any stage of progression can be treated, such as micrometastatic tumors, megametastatic tumors, and recurrent cancers.
  • hematological malignancies includes adult or childhood leukemia and lymphomas, Hodgkin's disease, lymphomas of lymphocytic and cutaneous origin, acute and chronic leukemia, plasma cell neoplasm and cancers associated with AIDS.
  • inventive methods and compositions can also be used to treat cancer of the breast, cancer of the lung, cancer of the adrenal cortex, cancer of the cervix, cancer of the endometrium, cancer of the esophagus, cancer of the head and neck, cancer of the liver, cancer of the pancreas, cancer of the prostate, cancer of the thymus, carcinoid tumors, chronic lymphocytic leukemia, Ewing's sarcoma, gestational trophoblastic tumors, hepatoblastoma, multiple myeloma, non-small cell lung cancer, retinoblastoma, or tumors in the ovaries.
  • a cancer at any stage of progression can be treated or detected, such as primary, metastatic, and recurrent cancers.
  • metastatic cancers are treated but primary cancers are not treated.
  • Information regarding numerous types of cancer can be found, e.g., from the American Cancer Society (cancer.org), or from, e.g., Wilson et al. (1991) Harrison's Principles of Internal Medicine, 12th Edition, McGraw-Hill, Inc.
  • the cancer and/or tumors to be treated are prostate cancers, lung cancers, or breast cancers.
  • Treatment of, or treating, metastatic cancer can include the reduction in cancer cell migration or the reduction in establishment of at least one metastatic tumor.
  • the treatment also includes alleviation or diminishment of more than one symptom of metastatic cancer such as coughing, shortness of breath, hemoptysis, lymphadenopathy, enlarged liver, nausea, jaundice, bone pain, bone fractures, headaches, seizures, systemic pain and combinations thereof.
  • the treatment may cure the cancer, e.g., it may prevent metastatic cancer, it may substantially eliminate metastatic tumor formation and growth, and/or it may arrest or inhibit the migration of metastatic cancer cells.
  • Anti-cancer activity can reduce the progression of a variety of cancers (e.g., breast, lung, or prostate cancer) using methods available to one of skill in the art.
  • Anti-cancer activity for example, can determined by identifying the lethal dose (LD100) or the 50% effective dose (ED50) or the dose that inhibits growth at 50% (GI50) of an agent of the present invention that prevents the migration of cancer cells.
  • anti-cancer activity is the amount of the agent that reduces 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99% or 100% of cancer cell migration, for example, when measured by detecting expression of a cancer cell marker at sites proximal or distal from a primary tumor site, or when assessed using available methods for detecting metastases.
  • PARP1 inhibitors and one or more inhibitors of activated stromal I activated cancer-associated fibroblasts, TNFa, IL-6 or JAK can be administered to sensitize tumor cells to immune therapies.
  • PARP1 inhibitors and one or more inhibitors of activated stromal I activated cancer- associated fibroblasts, TNFa, IL-6 or JAK tumor cells can become more sensitive to the immune system and to various immune therapies.
  • Reduced p62 levels are associated with the induction of the cancer- associated fibroblast (CAF) phenotype, which promotes tumorigenesis in vitro and in vivo through inflammation and metabolic reprogramming.
  • CAF cancer- associated fibroblast
  • how p62 is downregulated in the stroma fibroblasts by tumor cells to drive CAF activation is an unresolved central issue in the field.
  • tumor-secreted lactate downregulate p62 transcriptionally through a mechanism involving reduction of the NAD+/NADH ratio, which impaired poly (ADP-Ribose) -polymerase 1 (PARP1) activity.
  • PARP1 inhibition blocked the poly(ADP-ribosyl)ation of the API transcription factors, c-FOS and c-JUN, which is an obligate step for p62 downregulation. Importantly, restoring p62 levels in CAFs by NAD + rendered CAFs less active.
  • PARP1 inhibitors such as Olaparib, mimicked lactate in the reduction of stromal p62 levels, as well as the subsequent stromal activation both in vitro and in vivo, which suggests that therapies utilizing Olaparib would benefit from strategies aimed at inhibiting CAF activity.
  • the mechanisms whereby cancer cells promote the acquisition of the pro- tumorigenic CAF phenotype was investigated.
  • the lactate secreted by tumor cells downregulates p62 at the transcriptional level to induce stromal activation.
  • Lactate caused a reduction in the NAD + /NADH ratio that impaired Poly(ADP-ribose)polymerase 1 (PARP1) activity.
  • PARP1 Poly(ADP-ribose)polymerase 1
  • TRAMP + mice C57BL/6-Tg(TRAMP)8247Ng/J, stock No: 003135
  • TRAMP + mice were generated in a C57BL/6 background and were born and maintained under pathogen-free conditions. All genotyping was done by PCR. Age- matched mice were used for all experiments.
  • mice 7-week-old male JAX NSG mice (572NCG) were purchased from Charles River Labs (Wilmington, MA, USA). NSG mice were purchased and maintained under pathogen-free conditions. All mice were maintained on food and water ad libitum and were age-matched and co-housed for all experiments. Mice were sacrificed and prostate, tumors or other organs were collected for analysis.
  • WPMY-1 (sex: male), mNAF (sex: male), mHSC (sex: male), hNAF (sex: male), PC3 (sex: male), DU145 (sex: male), TRAMPC2 (sex: male), PrEC (sex: male), RWPE1 (sex: male), LNCAP (sex: male), HEK293T (sex: female) and Phoenix-GP (sex: female) cell lines were purchased from ATCC.
  • WPMY-1, mNAF, mHSC, PC3, DU145, TRAMPC2, HEK293T and Phoenix-GP were cultured in Dulbecco’s Modified Eagles Medium (DMEM, Corning).
  • LNCAP, PrEC and RWPE1 cells were cultured in Roswell Park Memorial Institute Medium (RPMI, Corning), hNAF cells were cultured in Fibroblast media (FM, ScienceCell Research Laboratories). All base mediums were supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine in an atmosphere of 95% air and 5% CO2. Androgen Deprivation Therapy conditions, cells were culture in RPMI media without phenol red (GIBCO) supplemented with 10% charcoal stripped FBS (F6765, Sigma), Glutamax and 100 U/mL penicillin 100 and 100 pg/mL streptomycin. Cultures were tested weekly for mycoplasma contamination.
  • Tumors were measured twice a week. Mice were euthanized 14 days after the initiation of the treatment and tumors were collected and analyzed histologically.
  • WPMY-1 cells were incubated in culture medium with or without lactic acidosis (24 mM of Lactic acid buffered to pH 6.7-6.8 with NaOH) for 48 hours. To avoid fluctuations in extracellular pH during the Lactate treatment, WPMY-1 cells were grown in a bicarbonate-free DMEM with 30 mM of HEPES in absence of CO2.
  • RNA sequences targeting PARP-1 exon2 were purchased from Synthego and transduced into WPMY-1 cells with recombinant Streptococcus pyogenes Cas9 protein (Truecut Cas9 Protein v2, Thermo), using the Neon Transfection System 1 (Invitrogen) following the manufacturer’ s protocol and single clones were expanded and screened by protein immunoblotting.
  • Single-guide RNA sequences targeting the human APl-A binding site was transduced into cells with a Cas9 protein and a single-stranded donor oligonucleotide (ssODN, IDT) using Neon Electroporation System.
  • Single clones were expanded and screened for AP7-A editing by Sanger sequencing.
  • a point mutation to disrupt the API enhancer element in the p62 promoter was introduced by Site Directed Mutagenesis (Stratagene).
  • Knockdown of MCT1, MCT4, FOS, PARP1, PARP2, CD38, ATG5, and SIRT1-7 genes in WPMY-1 cells were achieved by siRNA transfection using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen). Transient overexpression was achieved by transfection using X-tremeGENE HP transfection reagent (Roche). Transfected cells were examined 48 hours after transfection. Establishing stably GFP or RFP expressing cells was achieved by lentivirus-mediated transduction. Lentivirus were produced in HEK293T cells using X-tremeGENE HP transfection reagent (Roche).
  • Viruscontaining supernatants were collected 48, 72 and 96 hours after transfection, filtered to eliminate cells, and supplemented with 8 pg/ml polybrene. Cells were infected with three rounds of viral supernatants and selected with puromycin (3 pg/ml).
  • WPMY-1 cells were treated for 12 hours with 100 nM bafilomycin Al or 12 hours with 20 pM of MG132, respectively, or vehicle (DMSO).
  • DMSO puromycin
  • WPMY-1 cells were treated with PJ34 (2 days) or Olaparib (4 days) at the doses indicated in each experiment.
  • MCT1 inhibition WPMY-1 cells were treated for 48 hours with 10 pM of AZD3965.
  • WPMY-1 cells were treated for 48 hours with 10 pM of SP600125.
  • WPMY-1 cells were treated for 48 hours with 1-20 pM of Calpeptin (Tocris) or z-VAD-FMK (Tocris), respectively.
  • WPMY-1 cells were treated with 50 pg/ml of cycloheximide (Sigma).
  • CM Conditioned media
  • the supernatant was sterile filtered using a 22 mm filter (Millex-GV) with a 10 ml syringe barrel. The samples were stored at 20°C for future experiments. Fractionation of the CM was achieved using Amicon Ultra centrifugal filters (3KUltracel, Millipore). The supernatant was centrifuged at 4000 rpm for 1 hour. The supernatant fraction that was >3 kDa remained above the filter and that which was ⁇ 3kDa passed through to the lower chamber. The >3 -kDa fraction was resuspended in DMEM to the pre-filtration volume.
  • Gel rafts were placed onto collagen-coated nylon sheets and lifted using a sterile supporting steel mesh to set up a raised airliquid culture. Normal medium was changed in alternate days and organotypic cultures were allowed to grow for 14 days. Afterwards, organotypic gels were harvested, fixed in 10% neutral buffered formalin, bisected, and embedded in paraffin. H&E-stained sections were analyzed with a Zeiss light microscope supplemented with Axiovision40 software. Quantification of the invasion assays was performed as described previously (Valencia et al., 2014) using ImageProPlus software.
  • WPMY-1 cells were cultured in DMEN containing 10% FBS (basal conditions) or 10% charcoal stripped FBS (ADT conditions), then the cells were treated with vehicle (DMSO), Olaparib 10 pM, Olaparib 10 pM + PEGPH202.5 pg/ml for 96 hours, refreshing media and stimuli at 48 hours, conditioned media (CM) was generated by collecting supernatant on day 4.
  • PC3 cells were seeded in a black-walled well (Thermo Fisher) and serum starved overnight. CM from WPMY-1 cells was added to PC3 for 24 h. PC3 were exposed to EdU incorporation for the last 2 hours.
  • Proliferating cells were detected using Click-iT EdU Alexa fluor 488 (Thermo Fisher) following the manufacturer’s instructions. Pictures were taken using EVOS M5000 Imaging System and EdU positive were measured using Fiji (Schindelin et al., 2012).
  • Co-culture assays were performed as described previously (Valencia et al., 2014). Briefly, stromal cells were seeded in TC-treated 6-well plates and allowed to attach for 6 hours before PCa cells were seeded on top of Milicell Cell Culture Inserts (Millipore). Inserts were then placed in the pre-seeded 6-well plate.
  • PC3-GFP label 500 PC3 and 1000 WPMY-1 were seeded in a 96 well plate in DMEN containing 10% FBS (basal conditions) or 10% charcoal stripped FBS (ADT conditions) and vehicle (DMSO) or Olaparib 5 pM for 10 days. Media and treatments were refresh every 48 hours. Pictures were taken using EVOS M5000 Imaging System and GFP positive were measured using Fiji (Schindelin et al., 2012).
  • WPMY-1 cells were cultured in DMEM (Cat. #5030, Sigma) medium supplemented with 10% FBS, 4 mM glutamine, 25 mM glucose, 30 mM HEPES, 10% FBS, 100 U/ml penicillin, and 100 pg/ml streptomycin in a humidified cell culture incubator at 37°C with no CO2.
  • DMEM fetal calf serum
  • FBS fetal bovine serum
  • Metabolites were extracted using a modified Bligh and Dyer method and analyzed as previously described in detail (Linares et al., 2017). Briefly, intracellular metabolites were extracted with 0.25 ml -20°C methanol, 0.1 ml 4°C cold water, and 0.25 ml -20°C chloroform. The extracts were vortexed for 10 minutes at 4°C and centrifuged at 16,000xg for 5 minutes at 4°C. The upper aqueous phase was evaporated under vacuum at -4°C, the lower organic phase under airflow.
  • Derivatization for polar metabolites was performed using a Gerstel MPS with 15 pl of 2% (w/v) methoxyamine hydrochloride (Thermo Scientific) in pyridine (incubated for 60 minutes at 45 °C) and 15 pl N-tertbutyldimethylsilyl-N- methyltrifluoroacetamide (MTBSTFA) with 1% tert-butyldimethylchlorosilane (Regis Technologies) (incubated further for 30 minutes at 45°C).
  • Polar derivatives were analyzed by GC-MS using a DB-35MSUI column (30 m x 0.25 i.d.
  • Subconfluent cultures were transfected with Lipofectamine Plus (Invitrogen) with 100 ng of a SQSTM1 -luciferase reporter gene plasmid and 2 ng of the Renilla control reporter pRL-CMV (Promega). After 48 hours, cells were incubated with conditioned medium for 48 hours. The level of promoter activity was evaluated by determining the firefly luciferase activity relative to Renilla luciferase activity using the Dual Luciferase Assay System (Promega) according to the manufacturer’ s instruction.
  • WPMY-1 cells were seeded in coverslides and cultured in DMEN containing 10% FBS (basal conditions) or 10% charcoal stripped FBS (ADT conditions), then the cells were treated with vehicle (DMSO), Olaparib 10 pM, Olaparib 10 pM + PEGPH20 2.5 pg/ml for 96 hours, refreshing media and stimuli at 48 hours.
  • Cells were fixed in PFA 4% for 20 minutes at room temperature, permeabilize and blocked following abeam’ s immunofluorescence protocol. Then, cells were incubated overnight with Hyaluronic acid binding protein (HABP) at 4°C. Cells were incubated with Alexa conjugated streptavidin and mounted in slides with mowiol. Pictures were taken by Zeiss LSM 710 NLO Confocal Microscope. Histological Analysis
  • Tissues from indicated mice were isolated, fixed in zinc buffered formalin overnight at 4°C, dehydrated, and embedded in paraffin. Sections (5 pm) were stained with hematoxylin and eosin (H&E). For immunohistochemistry, sections were deparaffinized, rehydrated, and then treated for antigen retrieval. After blocking in Protein Block Serum-Free solutions (DAKO), tissues were incubated with primary antibody overnight at 4°C followed by incubation with biotinylated secondary antibody. Endogenous peroxidase was quenched in 3% H2O2 in water for 10 minutes at room temperature.
  • H&E hematoxylin and eosin
  • Antibodies were visualized with avidin-biotin complex (Vectastain Elite; Vector Laboratories) using diaminobenzidine as the chromogen. Stained sections were analyzed with a Zeiss light microscope supplemented with Zen 3.3 Bule edition software.
  • Immunoprecipitates were washed three times with lysis buffer, once with high salt (500 mM NaCl), and once more with lysis buffer. Protein concentration in lysates was determined by using Protein Assay Kit (Bio-Rad). Cell extracts and immunoprecipitated proteins were denatured, subjected to SDS-PAGE, transferred to PVDF membranes (GE Healthcare). After blocking with 5% nonfat dry milk in Tris-buffered saline and 0.1% Tween (TBS-T), the membranes were incubated with the specific antibodies (as listed in Key Resources Table) overnight at 4°C. After 2 hours incubation with the appropriate horseradish peroxidase-conjugated antibodies, the immune complexes were detected by chemiluminescence (Thermo Scientific) or Near-infrared fluorescence (LI-COR).
  • chemiluminescence Thermo Scientific
  • LI-COR Near-infrared fluorescence
  • RNA from mouse tissues, cells and cultured organoids was extracted using the TRIZOL reagent (Invitrogen) and the RNeasy Mini Kit (QIAGEN), followed by DNase treatment. After quantification using a Nanodrop 1000 spectrophotometer (Thermo Scientific), RNA was either processed for RNA-seq or reverse-transcribed using random primers and MultiScribe Reverse Transcriptase (Applied Biosystems). Gene expression was analyzed by amplifying 20 ng of the complementary DNA using the CFX96 Real Time PCR Detection System with SYBR Green Master Mix (BioRad) and primers described in Table SI. The amplification parameters were set at 95 °C for 30 seconds, 58°C for 30 seconds, and 72°C for 30 seconds (40 cycles total). Gene expression values for each sample were normalized to the 18s RNA.
  • WPMY-1 cells were fixed by adding directly to the culture medium formaldehyde (HCHO; from a 37% HCHO-10% methanol stock, Calbiochem) to a final concentration of 1%. After, 20 minutes of incubation with 125 mM glycine, cells were washed with ice-cold phosphate-buffered saline (PBS) and lysed with in 50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS and protease inhibitors and incubated 30 minutes at 4 C.
  • HCHO formaldehyde
  • PBS ice-cold phosphate-buffered saline
  • Chromatin was sheared in a COVARIS S220 Focused- ultrasonicator to yield DNA fragment sizes of 200-1000 base pairs, and diluted 10 times in dilution buffer (20 mM Tris pH 8.0, 2 mM EDTA, 1% triton X-100, 150 mM NaCl and protease inhibitors). Immunoprecipitations were carried out overnight at 4°C using the following protein A-antibodies complexes: cFOS, FOSB, cJUN, JUNB.
  • Immunocomplexes were washed three times with buffer TSEI (20 mM Tris pH 8.0, 2 mM EDTA, 1% triton X-100, 150 mM NaCl, 0.1% SDS and protease inhibitors), three washes with buffer TSEII (20 mM Tris pH 8.0, 2 mM EDTA, 1% triton X-100, 500 mM NaCl, 0.1% SDS and protease inhibitors), one wash with buffer TSEIII (10 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Deoxycholate and protease inhibitors) and one wash with TE pH 8.0.
  • buffer TSEI 20 mM Tris pH 8.0, 2 mM EDTA, 1% triton X-100, 150 mM NaCl, 0.1% SDS and protease inhibitors
  • buffer TSEII 20 mM Tris pH
  • the cell pellet was resuspended in 50 pl lysis buffer and then spun down 500 x g for 10 minutes at 4°C.
  • the nuclei pellet was resuspended into 50 pl transposition reaction mixture containing Tn5 transposase from Nextera DNA Library Prep Kit (Illumina) and incubated at 37°C for 30 minutes. Then the transposase-associated DNA was purified using MinElute PCR purification kit (QIAGEN). To amplify the library, the DNA was first amplified for 5 cycles using indexing primer from Nextera kit and NEBNext High-Fidelity 2X PCR master mix.
  • Prostate lobes dissected and washed with cold PBS.
  • Prostate tissue was gently minced with scissors and digested in Advance DMEN/F12 media (Gibco, Thermo Fisher) with 5 mg/ml Collagenase type II (Sigma) supplemented with Y27632 (Tocris) for 1 hour at 37°C.
  • Cells were passed through a 70 pm strainer and centrifuge 5 minutes, 1000 rpm at 4°C. After that, cells were incubated with TrypLE Express (Gibco, Thermo Fisher) supplemented with Y27632 for 20 minutes in agitation at 37 °C to achieve a single cell suspension.
  • TrypLE Express Gibco, Thermo Fisher
  • scRNA-seq libraries were generated using the Chromium Single Cell 30 Reagent Kit v2 (10X Genomics). Cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 2,000 cells per pl (Single Cell 3' library and Gel Bead Kit v.2) as described in the manufacturer’s protocol (lOx User Guide, Revision B). On average, approximately 8,000 cells were loaded.
  • RNA-Seq sequencing Fastq files were uploaded to BaseSpace and processed with RNASeq Alignment App (Illumina) to obtain raw reads counts for each gene.
  • read data was processed with the BlueBee Genomics Platform (BlueBee, San Mateo, CA).
  • GenePattern https://genepattern.broadinstitute.org/gp/pages/index.jsf was used to collapse gene matrix files (CollapseDataset module) or to assess the statistical significance of differential gene expression (ComparativeMarkerSelection module for microarray data and DESeq2 module for RNA-seq data).
  • GSEA Gene Set Enrichment Analysis
  • the Cell Ranger version 2.1.1 software suite from 10X Genomics https://support.10xgenomics.com/single-cell-gene- expression/software/downloads/latest) was used to process, align and summarize unique molecular identifier (UMI) counts against the mouse mmlO assembly reference genome analysis set, obtained from the University of California Santa Cruz (UCSC).
  • UMI unique molecular identifier
  • Raw UMI count matrices were filtered using the Seurat v 3.0 R package (Butler et al., 2018) to remove: barcodes with very low (empty wells) and very high (probably doublets) total UMI counts; matrices for which a high percentage of UMIs originated from mitochondrial features (more than 20%); and matrices for which fewer than 250 genes were expressed.
  • Clustering was performed as follows: The percentage of mitochondrial features was a source of unwanted variation and was regressed out using the Seurat package. Dimensionality reduction was performed by principal component analysis and UMAP embedding with resolution 0.5. Cluster gene markers and differentially expressed genes between groups in each cluster were detected using the Wilcoxon Rank Sum test. CellPhoneDB analysis was performed using Cellphonedb method statistical analysis command.
  • Prostate cancer cells secrete a soluble factor that reduces p62 expression in stromal fibroblasts
  • mPSC mouse GFP-labeled prostate stromal cells
  • TRAMPC2 PCa epithelial cells were incubated.
  • Sqstml coding for p62
  • mRNA levels were reduced upon incubation with tumor cells, which also correlated with an increase in bona-fide CAF markers, such as Tgfbl and Sdf-1 (FIG. 1A).
  • conditioned medium from PC3 cells was size-fractionated to separate molecules that were either less or more than 3 kDa in size, and the ability of either fraction to decrease the amount of stromal p62 was tested.
  • Both the unfractionated tumor-conditioned medium and the ⁇ 3 kDa fraction comparably downregulated p62 at the protein and mRNA levels in stromal fibroblasts (FIGs. 1G and 1H), as well as the activity of the SQSTM1 promoter-driven luciferase reporter (FIG. II).
  • the >3 kDa fraction was totally inactive in these assays (FIGs. 1G-1I).
  • the active soluble factor was heatstable (FIGs. 1J-L), which suggested that it could be a metabolite. Lactate downregulates p62 in stromal fibroblasts
  • lactate could be a good candidate to be the tumor- derived factor responsible for the downregulation of p62 in stroma cells. Consistent with this hypothesis, it was found that the amount of lactate in the media of different PCa cell lines was higher than in the media of normal prostate epithelial cells (FIG. 2A). The cellular uptake of lactate is mediated by different monocarboxylate transporters (MCT1, MCT2, MCT3, and MCT4) (Halestrap, 2013). A prediction would be that blocking these transporters could alleviate the lactate-induced downregulation of p62.
  • MCT1, MCT2, MCT3, and MCT4 monocarboxylate transporters
  • knockdown of MCT1, which controls lactate cellular import in WPMY-1 cells resulted in the inhibition of p62 downregulation induced by CM from PC3 cells (FIGs. 2B and 2C).
  • p62 downregulation in WPMY-1 cells by the same CM was abrogated when MCT4, which controls lactate export, was knocked-down in PC3 cells (FIGs. 2D and 2E).
  • treatment with the MCT1 inhibitor, AZD3965 impaired p62 downregulation in WPMY-1 cells treated with PC3 CM (FIGs. 2F and 2G).
  • Lactate does not affect p62 stability (FIG. 10 A). In agreement with these results, inhibition of the proteasome (FIG. 10B), autophagy (FIGs. 10C and 10D), or cysteine proteases (FIGs. 10E and 10F) did not rescue the reduced p62 protein levels in lactate-treated WPMY-1 cells. API controls p62 downregulation by lactate
  • AP-1A, AP-1B, and AP-1C were individually mutated and the impact of these mutations in the SQSTM1 promoter activity was determined by luciferase assay. Mutation of AP-1A completely inactivates the SQSTM1 promoter to levels comparable to those produced by lactate in the intact SQSTM1 promoter, whereas mutation of AP-1B, or AP-1C had no effect (FIG. 3E).
  • NAD + is a cofactor for three types of transcriptional and posttranslational modulators (Covarrubias et al., 2021). These include the sirtuins (SIRT1 through SIRT7), the cyclic ADP ribose synthases (CD38 and CD157), and the poly-ADP ribose transferases (PARP1/2). Interestingly, only the knockdown of PARP-1 fully mimicked the effect of lactate on p62 expression (FIGs. 5A-5E, FIGs. 11A and 11B). Moreover, treating WPMY-1 cells with the PARP-1 inhibitors PJ34 (FIGs. 5F and 5G) or Olaparib (FIGs.
  • PARP1 in addition to its well-known role in DNA damage repair, also controls many other biological processes including transcription (Feng et al., 2015). Thus, PARP-1 reportedly enhances the DNA binding and transactivation of many transcription factors (Gibson and Kraus, 2012). Of special relevance for this study, both c-FOS and c-JUN have been previously shown to be poly(ADP-ribosyl)ated by PARP-1, which increased their DNA binding activity (Huang et al., 2009). Consistently, Olaparib impaired the recruitment of c-FOS and c-JUN to the AP-1A binding site in the SQSTM1 promoter (FIGs. 5 J and 5K).
  • AP-1 is important for CAF activation driven by p62 loss
  • GSEA Gene set enrichment analysis
  • tumors generated with sgAP-lA fibroblasts showed increased markers of stromal activation, such as the augmented deposition of collagen and hyaluronan (HA), and the enhanced expression of aSMA (FIG. 6M).
  • HA augmented deposition of collagen and hyaluronan
  • FOG. 6M enhanced expression of aSMA
  • PARP-1 inhibitors promote a desmoplastic response in stromal fibroblasts through p62
  • Olaparib treatment reduced SQSTM1 mRNA levels and upregulated CAF markers such as ACTA2, SFRP1, TGF/3, MMP9 and the HA synthases in basal and ADT conditions (FIGs. 7D and 12 A). Similar results were obtained in different human and mouse prostate stromal cell lines and in hepatic stellate cells (FIGs. 12B-D), suggesting that the stromal activation by Olaparib treatment is a general phenotype not linked exclusively to the prostate stroma. Furthermore, ATAC-seq analysis of Olaparib- treated WPMY-1 cells revealed a strong decrease in chromatin accessibility across the genome, like what was observed with lactate treatment (FIGs. 3A and 7E).
  • scRNAseq was performed using 10X Genomics Chromium platform on TRAMP+ prostate tumors after treatment with Olaparib for 4 weeks as compared to vehicle controls (FIG. 8A). Consistent with the results in the xenograft model (FIGs. 7O-7T), in vivo treatment of TRAMP + mice induced a strong desmoplastic response in the prostate (FIG. 8B). Furthermore, unsupervised clustering identified epithelial cells as well as stromal and immune cells with selective markers for each population (FIG. 8C).
  • FIGs. 8C and 8D Consistent with the in vitro data of stromal activation, there was an expansion of the stromal and immune populations in response to Olaparib treatment (FIGs. 8C and 8D). Further re-clustering of the fibroblast compartment identified six clusters, all enriched in CAF signatures (FIG. 8E). Clusters 0 and 2 correspond to the inflammatory CAF subtype (iCAF), whereas clusters 3 and 5 express myofibroblast markers (myCAF). Cluster 3 displayed high levels of two CD44 ligands, Collal and Sppl, while cluster 5 expresses Acta2.
  • cluster 1 has features of both iCAF and myCAF and is enriched in growth factors and inflammatory cytokines as well as EMT markers and constitutes the subpopulation with the lowest levels of p62/ Sqstml.
  • Cluster 4 is enriched in Rspo3 and resembled the mesenchymal cell population termed Mes2, previously described in scRNAseq analysis of normal mouse and human prostates (Karthaus et al., 2020).
  • differential expressed gene analysis identified Hasl, Spinkl and Tgfb2 among the most upregulated transcripts in the Olaparib-treated fibroblast population (FIG. 8F).
  • Hasl is a hyaluronan (HA) synthase, one of the three enzymes that synthesize HA, which has been linked to tumor promotion, therapy resistance, and poor outcomes in various tumors, including PCa (Aaltomaa et al., 2002; Lipponen et al., 2001; Toole, 2004; Toole and Slomiany, 2008). Also, recent reports point to a role of HAS- expressing fibroblasts in the promotion of metastatic spreading (Affo et al., 2021). These data are in good agreement with the results in human prostate stromal cells and in in vivo mouse models, in which increased deposition of HA upon Olaparib treatment was found.
  • HA hyaluronan
  • Hasl and Has3 were upregulated in Olaparib-treated WPMY in both basal and ADT conditions (FIG. 8G).
  • SPINK1 Serine Peptidase Inhibitor, Kazal type 1 expression in PCa has been associated with poor response to ADT, faster progression to the castrate-resistant stage and cancer-associated mortalities (Johnson et al., 2016; Leinonen et al., 2010; Tomlins et al., 2008).
  • recent reports showed increased tumor Spinkl levels in response to AR-targeted therapies (Tiwari et al., 2020) and in prostate stroma after chemotherapy (Chen et al., 2018).
  • Tgfb2 is one of the ligands of the TGFP pathway, which has been long recognized to exert opposing roles in cancer progression but that it is an important component of reactive stromas (Lu et al., 2017; Massague, 2008).
  • TGFP signaling blocks tumorigenesis in primary PCa (Bjerke et al., 2014), it can promote PCa bone metastasis (Fournier et al., 2015) and has been recently associated with resistance to enzalutamide in scRNAseq studies of metastatic CRPC patients (He et al., 2021).
  • anti-TGFP therapies have been proposed to reduce the development and progression of bone metastasis and to enhance the efficacy of immune checkpoint therapy in metastatic CRPC (Jiao et al., 2019). Consistent with enhanced TGFP markers in our scRNAseq data, increased levels of Tgfbl were found in both basal and ADT conditions in WPMY cells (FIG. 8G).
  • Cluster 0 is a luminal population
  • cluster 1 is a basal population
  • clusters 3 and 4 that are luminal but express high levels of EMT markers such as Vimentin (Vim) and Acta 2
  • cluster 5 is a new neuroendocrine population that, in contrast to cluster 2, highly expresses the neuronal marker Synaptophysin (Syp), in addition to luminal and EMT markers (FIGs. 81 and 8J).
  • the Olaparib-treated tumor epithelium showed increased AR, EMT and TGFP signaling, which suggests potential mechanisms of resistance to Olaparib therapy (FIG. 8L). Consistent with enrichment in TGFP signaling signature in Olaparib-treated epithelial cells, there was an increased pSMAD2 staining, an established marker of TGFP activation, in Olaparib-treated prostates (FIG. 8M). Moreover, identification of ligand-receptor interactions between the stromal and epithelial populations by CellPhoneDB analysis revealed changes in receptors for HAS 1/2 in Olaparib-treated populations (FIG. 8N); these included gaining novel CD44-mediated pairs between the stromal populations and the different clusters of tumor cells.
  • CD44 is a receptor of HA that integrates extracellular matrix cues with growth factor and cytokine signals (Misra et al., 2015; Orian-Rousseau and Sleeman, 2014; Ponta et al., 2003).
  • the data showed that Olaparib increased the HAS1/2-CD44 pairs, but also promoted the interaction of CD44 with other growth-factor receptors, such as FGFR2 or HBEGF (FIG. 8N).
  • FGFR2 or HBEGF FIG. 8N
  • TGFP receptor family and their ligands FIG. 8N
  • binding of HA induces clustering of CD44 and the complex formation with other receptors (including the receptors for TGFP), which serve to further reinforce the activation of these pathways.
  • PEGPH20 efficiently degraded HA deposition in response to Olaparib treatment in WPMY-1 cells, in basal and ADT conditions (FIG. 9A). More importantly, PEGPH20 completely blocked the enhanced migration of PC3 cells in response to conditioned media from Olaparib-treated WPMY-1 cells under basal and ADT conditions (FIGs. 9B and 9C). Moreover, PEGPH20 also blocked Olaparib-induced proliferation in stromal cells (FIGs. 9D and 9E). Likewise, treatment with Galunisertib, a TGFPR inhibitor, completely abolished the stromal proliferation induced by Olaparib (FIGs. 9D and 9E).
  • tumor-secreted lactate was identified as the main signal from the epithelium that activates tumor fibroblasts by downregulating p62.
  • p62 is a stromal tumor suppressor whose downregulation in fibroblasts is a key event for CAF activation (Duran et al., 2016; Goruppi and Dotto, 2013; Linares et al., 2017; Valencia et al., 2014).
  • p62 has been shown to be regulated by several transcription factors including API, NRF2, NF-kB and TFEB under different conditions (Duran et al., 2008; Jain et al., 2010; Ling et al., 2012; Park et al., 2019).
  • the AP-1 binding site in the p62 promoter was identified as the element accounting for lactate-mediated p62 downregulation.

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Abstract

Described herein are methods and compositions that include use of one or more PARP1 inhibitors and one or more inhibitors of activated stromal / activated cancer-associated fibroblasts. Such methods and compositions are useful for treating cancer.

Description

COMBINATION THERAPIES INCLUDING PARP1 INHIBITORS
Cross-Reference to Related Applications
This application claims the benefit of the filing date of U.S. application No. 63/296,266, filed on January 4, 2022, the disclosure of which is incorporated by reference herein.
Government Funding
This invention was made with government support under RO 1CA218254 awarded by the National Institutes of Health. The government has certain rights in the invention.
Incorporation by Reference of Sequence Listing
A Sequence Listing is provided herewith as an xml file, “22987 lO.xml” created on January 3, 2023, 2022 and having a size of 95,728 bytes. The content of the xml file is incorporated by reference herein in its entirety.
Background
The tumor microenvironment (TME), including stromal fibroblasts, can be a driver of tumorigenesis in many types of tumors. Activation of tumor stromal fibroblasts to generate cancer-associated fibroblasts (CAFs) can embolden epithelial cancer cells to progress to more malignant stages and affect disease outcomes (Barron and Rowley, 2012; Cunha et al., 2002; Rowley, 1998; Tuxhorn et al., 2001). Cancer-associated fibroblasts impact the tumor epithelium by modulating many functions through the secretion of stromal growth factors and inflammatory mediators, by reprogramming their metabolism to provide nutrients and survival factors, and by remodeling the extracellular matrix (Hanahan and Weinberg, 2011; Kasashima et al., 2020; Sahai et al., 2020).
However, the master regulators of the acquisition of the CAF phenotype, as well as the molecular mechanisms whereby the tumor epithelium drives this process, are currently unknown.
Summary
As described herein, tumor-secreted lactate activates cancer associated fibroblasts (CAF) through downregulation of p62, a master regulator of CAF. Lactate reduces the NAD+/NADH ratio, which impairs PARP1 activity and inhibits p62. NAD+ supplementation can revert stromal activation. PARP1 inhibitors (PARPli) such as Olapanb, mimic lactate and activate CAF in vitro and in vivo. Olaparib-induced stroma is rich in hyaluronan. Co-treatment of Olaparib and PEGPH20, a clinical grade hyaluronidase reverts stroma activation and enhances Olaparib anti-tumor activity.
Combinatorial therapies are described herein that can improve the efficacy of currently available cancer treatments. For example, compositions and methods that include use of PARP1 inhibitors can be combined with drugs that target the stroma to enhance PARP1 inhibitor efficacy or drugs that block or inhibit TNFalpha, IL-6 or Janus kinase (JAK).
The PARP1 inhibitors can include olaparib (Lynparza), niraparib (Zejula), rucaparib (Rubraca), talazoparib (Talzenna), veliparib (ABT-888), or a combination thereof.
Examples of agents that can be used to treat or inhibit activated stromal / activated cancer-associated fibroblasts include but are not limited to hyaluronan (HA) synthase inhibitors, hyaluronan build-up inhibitors (e.g., PEGylated Recombinant Human Hyaluronidase, PEGPH20), autophagy inhibitors (e.g., ULK inhibitors such as SBI-0202965), fibroblast activation protein alpha (FAPa) inhibitors, GW4064 (farnesoid X receptor (FXR) agonists, Pirfenidone (PDF) combined with doxorubicin, SMO-inhibitors (e.g., vismodegib, sonidegib), amphiregulin inhibitors, CXCL12 antagonists (e.g., an E5 antagonistic peptide), DDR2 inhibitors (e.g., WRG-28, which is a small molecule inhibitor of DDR2), or a combination thereof.
Examples of agents that can inhibit JAK include but are not limited to lesataurtinib, baricitinib, tofacitinib, upadacitinib, filgonitib, delgocitinib, deucravacitinib, LS104, ON044580,NVP-BBT594, or NVP-CHZ868, or a combination thereof.
Examples of agents that can inhibit IL6 include but are not limited to tocilizumab, sarilumab, siltuximab, olokizumab, elsilimomab, clazakizumab, sirukumab, levimumab, CPSI-2364, ARGX-109, FE301 or FM101, or any combination thereof.
Examples of agents that can inhibit TNFalpha include but are not limited to adalimumab, certolizumab pegol, etanercept, golimumab, or infliximab, or a combination thereof. Brief Description of the Figures
FIGs. 1A-1L. PCa cells secrete a soluble factor that reduces p62 expression in stromal cells. FIG. 1A shows qPCR of Sqstml, Sdf-1 and Tgf/3\& e\s in mPSC- GFP cells mixed with TRAMPC2 cells and cultured for 7 days and western blot. FIGs. IB and 1C show immunoblot analysis for the indicated proteins (FIG. IB) and qPCR of SQSTM1 (FIG. 1C) in WPMY-1 cells co-cultured with PCa cells during 48 h (n= 3). FIGs. ID and IE provide immunoblot analysis for the indicated proteins (FIG. ID) and qPCR of SQSTM1 (FIG. IE) in WPMY-1 cells incubated 48 hours with conditioned media (CM) from PrEC, RWEP1, PC3, DU145, TRAMPC2 and LNCAP cells (n= 3). FIG. IF illustrates SQSTM1 promoter-driven luciferase in WPMY-1 incubated 48 hours with conditioned media from PrEC, RWEP1, PC3, DU145, TRAMPC2 and LNCAP cells (n= 3). FIGs. 1G and 1H show immunoblot analysis for the indicated proteins (FIG. 1G) and qPCR of SQSTM1 levels (FIG. 1H) in WPMY-1 cells incubated 48 h with fractionated CM from PC3 cells (n= 3). FIG. II shows SQSTM1 promoter-driven luciferase in WPMY-1 cells incubated 48 hours with fractionated CM from PC3 cells (n= 3). FIGs. 1J and IK show immunoblot analysis for the indicated proteins (FIG. 1J) and qPCR of SQSTM1 levels (FIG. IK) in WPMY-1 cells incubated 48 hours with normal or boiled CM from PC3 cells (n= 3). FIG. IL) SQSTM1 promoter-driven luciferase in WPMY-1 cells incubated 48 hours with normal or boiled CM from PC3 cells (n= 3). Results are shown as mean ± SEM *p < 0.05, **p< 0.01, ***p < 0.001, ****p < 0.0001.
FIGs. 2A-2L. Lactate is sufficient to downregulate p62. FIG. 2A shows lactate secretion was determined by YSI2950 analyzer from PCa cells for 72 hours. Results are normalized to total protein content (n= 3). FIGs. 2B and 2C show immunoblot analysis for the indicated proteins (FIG. 2B) and qPCR of SQSTM1 and MCT1 levels (FIG. 2C) in WPMY-1 cells, transduced with the indicated siRNAs, incubated with CM from PC3 cells for 48 hours (n= 3). FIGs. 2D and 2E show immunoblot analysis for the indicated proteins (FIG. 2D) and qPCR of SQSTM1 and MCT4 levels (FIG. 2E) in WPMY-1 cells incubated with CM from PC3 cells, transduced with the indicated siRNAs, for 48 hours (n= 3). FIGs. 2F and 2G show immunoblot analysis for the indicated proteins (FIG. 2F) and qPCR of SQSTM1 levels (FIG. 2G) in WPMY-1 cells, treated with AZD3965, and incubated with CM from PC3 cells for 48 hours (n= 3). FIGs. 2H and 21 show immunoblot analysis for the indicated proteins (FIG. 2H) and qPCR of SQSTM1 levels (FIG. 21) in WPMY- 1 cells incubated with Lactate (24 mM) at different times (n= 3). FIGs. 2 J and 2K provide immunoblot analysis for the indicated proteins (FIG. 2J) and qPCR of SQSTM1 levels (FIG. 2K) in WPMY-1 cells incubated with different dose of Lactate for 48 hours (n= 3). FIG. 2L provides immunoblot analysis for the indicated proteins in WPMY-1 cells incubated with Lactate 24 mM (pH 6.5) or DMEM at different pH for 48 hours (n = 3). Results are shown as mean ± SEM *p < 0.05, **p< 0.01, ***p < 0.001, ****p < 0.0001.
FIGs. 3A-3M. API elements control p62 downregulation by lactate. FIG. 3A illustrates four clusters (Cl, C2, C3 and C4) heatmap of ATAC-seq peaks, +/- 2 Kb from TSS in WPMY-1 cells treated or not with lactate for 48 hours. FIG. 3B illustrates HOMER discovery analysis of TFs enriched promoter regions (1-2 Kb) closed in WPMY-1 cells treated with Lactate (Control vs Lactate). FIG. 3C shows genome browser view at SQSTM1 promoter. Chromatin accessibility (ATAC-seq) and RNA-seq profiles are shown in WPMY-1 cells treated or not with Lactate. FIG. 3D illustrates API-driven luciferase in WPMY-1 cells treated with lactate for 48 hours (n= 3). FIG. 3E shows SQSTM1 promoter-driven luciferase in WPMY-1 cells, transduced with the indicated plasmids, and treated with lactate for 48 hours (n= 3). FIG. 3F shows immunoblot analysis in sgC and sgAP-lA WPMY-1 cells for the indicated proteins. FIGs. 3G and 3H show immunoblot analysis for the indicated proteins (FIG. 3G) and qPCR of SQSTM1 levels (FIG. 3H) in sgC and sgAP-lA WPMY-lcells incubated with lactate (n= 3). FIG. 31 illustrates ChlP-PCR analysis of SQSTM1 promoter (AP-1A) occupancy of c-JUN, c-FOS, FOSB or JUNB in WPMY-1 cells treated or not with lactate (24 mM) for 48 hours (n= 3). FIGs. 3J and 3K show immunoblot analysis for the indicated proteins (FIG. 3J) and qPCR of SQSTM1 levels (FIG. 3K) in WPMY-1 cells incubated with lactate and transduced with the indicated siRNAs (n= 3). FIG. 3L and 3M show immunoblot analysis for the indicated proteins (FIG. 3L) and qPCR of SQSTM1 levels in WPMY-1 cells incubated with lactate and treated with 10 pM of SP600125 (n= 3). Results are shown as mean ± SEM *p < 0.05, **p< 0.01, ***p < 0.001, ****p < 0.0001.
FIGs. 4A-4G. Changes in NAD+/NADH levels by lactate are critical for p62 downregulation. FIGs. 4A and 4B show immunoblot analysis for the indicated proteins (FIG. 4E) and qPCR of SQSTM1 levels (FIG. 4F) in WPMY-1 incubated with Lactate or Pyruvate for 48 hours (n= 3). FIG. 4C illustrates intracellular NAD levels in WPMY-1 cells treated or not with lactate (n= 3). FIGs. 4D and 4E show immunoblot analysis for the indicated proteins and qPCR of SQSTM1 levels in WPMY-1 cells incubated with Lactate and NAD (150 pM) for 48 hours (n= 3). FIGSs. 4F and 4G show immunoblot analysis for the indicated proteins and qPCR of SQSTM1 levels in WPMY-1 cells incubated with Lactate or NR (200 pM) for 48 hours (n= 3). Results are shown as mean ± SEM **p< 0.01, ***p < 0.001, ****p < 0.0001.
FIGs. 5A-5T. PARP-1 is critical for the control of p62 levels in stromal cells. FIG. 5A shows immunoblot analysis for the indicated proteins in WPMY-1 cells transduced with the indicated siRNAs. FIGs. 5B and 5C show immunoblot analysis for the indicated proteins (B) and qPCR of SQSTM1 levels (FIG. 5C) in WPMY-1 cells transduced with the indicated siRNAs. FIGs. 5D and 5E show immunoblot analysis for the indicated proteins and qPCR of PARP-1 (FIG. 5D) and SQSTM1 (FIG. 5E) levels in WPMY-1 cells transduced with the indicated siRNAs. FIGs. 5F and 5G show immunoblot analysis for the indicated proteins (FIG. 5F) and qPCR of SQSTM1 levels (FIG. 5G) in WPMY-1 cells incubated with PJ34 for 24 hours (n= 3). FIGs. 5H and 51 show immunoblot analysis for the indicated proteins (FIG. 5H) and qPCR of SQSTM1 levels (FIG. 51) in WPMY-1 cells incubated with Olaparib for 48 hours (n= 3). FIGs. 5J and 5K illustrate ChlP-PCR analysis of SQSTM1 promoter (AP-1A) occupancy of c-FOS (FIG. 5 J) or c-JUN (FIG. 5K) in WPMY-1 cells treated or not with Olaparib (20 pM) for 48 hours (n= 3). FIG. 5L shows immunoblot analysis for the indicated proteins and PARylated protein levels in WPMY-1 cells incubated with lactate for the indicated times. FIGs. 5M and 5N illustrate PARylation of c-JUN (FIG. 5M) or c-FOS (FIG. 5N) in WPMY-1 treated or not with lactate for 48 h (n= 2). FIGs. 50 and 5P illustrate PARylation of c-JUN (FIG. 50) or c-FOS (FIG. 5P) in WPMY-1 treated or not with lactate and NAD for 48 hours (n= 2). FIG. 5Q and 5R illustrate ChlP-PCR analysis of SQSTM1 promoter (AP-1A) occupancy of c-FOS (FIG. 5Q) or c-JUN (FIG. 5R) in WPMY-1 cells treated or not with lactate and NAD for 48 hours (n= 3). FIGs. 5S and 5T illustrate ChlP-PCR analysis of SQSTM1 promoter (AP-1A) occupancy of c-FOS (FIG. 5S) or c-JUN (FIG. 5T) in WPMY-1 cells treated or not with lactate and NR for 48 hours (n= 3). Results are shown as mean ± SEM *p < 0.05, **p< 0.01, ***p < 0.001, ****p < 0.0001.
FIGs. 6A-6M. API control of the SQSTM1 promoter in stromal cells is critical for PCa tumor growth and invasion. FIG. 6A shows qPCR analysis of mRNA levels of the indicated genes in WPMY-1 cells incubated with Lactate (24 mM) for 48 hours (n = 3). FIG. 6B shows qPCR analysis of mRNA levels of the indicated genes in WPMY-1 cells treated or not with lactate and NAD for 48 hours (n = 3). FIG. 6C illustrates GSEA analysis of “LACTATE UP” and “LACTATE DOWN” gene signatures in CAFs vs. NAFs gene set GSE34312. FIG. 6D illustrates qPCR analysis of mRNA levels of indicated genes in sgC and sgAP-lA WPMY-1 cells (n= 3). FIG. 6E-6G show experimental design (FIG. 6E), Migration (FIG. 6F), and Invasion (FIG. 6G) of PC3 cells co-cultured with sgC or sgAP-lA WPMY-1 cells for 16 h. Representative images and quantification (n= 3). FIG. 6H and 61 show experimental design (FIG. 6H) and H&E staining (FIG. 61) of organotypic gels combining PC3 cells with sgC and sgAP-lA WPMY-1 cells. Quantification of PC3 cells invasion and proliferation of experiments shown in (FIG. 61). FIG. 6J-6M illustrate subcutaneous xenograft co-implantation in castrated NSG mice (male, 7 weeks old) of PC3 PCa cells with sgC or sgAP-lA WPMY-1 cells (PC3 + sgC WPMY-1 n=8; PC3 + sgAP-lA WPMY-1 n=8). Experimental design (FIG. 6J), Tumor weight (FIG. 6K), gross images (FIG. 6L), IHC for Masson Trichrome, HA and aSMA (FIG. 6M), scale bars 50 pm. Results are shown as mean ± SEM *p < 0.05, **p< 0.01, ***p < 0.001, ****p < 0.0001.
FIGs. 7A-7T. Olaparib treatment mimics lactate loss of p62 and promotes stromal activation. FIG. 7A illustrates enriched pathways obtained by GSEA preranked analysis using DEG in Olaparib-treated WPMY-1 cells. FIG. 7B illustrates GSEA analysis for stromal activation and CAF phenotype gene signatures in Olaparib-treated WPMY-1 cells. FIG. 7C illustrates GSEA analysis of “Olaparib_UP”, “Olaparib_DN”, “Olaparib_ADT_UP”, “Olaparib_ADT_DN” gene signatures in CAFs vs. NAFs gene set GSE34312. FIG. 7D shows qPCR analysis of mRNA levels of indicated genes in Olaparib-treated WPMY-1 cells (n= 3). FIG. 7E shows four clusters (Cl, C2, C3 and C4) heatmap of ATAC-seq peaks, +/- 2 Kb from TSS, upon Olaparib treatment for 96 hours in basal conditions. FIG. 7F shows HOMER discovery analysis of TFs enriched in promoter regions (1-2 Kb) closed upon Olaparib treatment in WPMY-1 cells (DMSO vs Olaparib). FIG. 7G shows integrative Genomics Viewer (IGV) of ATAC-seq peaks in SQSTM1 promoter in Olaparib-treated WPMY-1 cells in basal conditions. FIGs. 7H-7J show trans-well migration and invasion assays. Experimental design (FIG. 7H), left, trans-well migration and invasion assay of PC3 PCa cultured with Olaparib pre-treated WPMY-1 cells for 20 hours, scale bar 50 pm. Right, relative number of migrating and invading cells (FIGs. 7I-7J). FIG. 7K and 7L show click-iT EdU incorporation assay. Experimental design (FIG. 7K), left, representative images of EdU incorporation in PC3 PCa cells treated with CM from Olaparib-treated WPMY-1 cells for 24 hours. Right, percentage of Edu positive cells (n= 3) (FIG. 7L), scale bar 50 pm. FIG. 7M and 7N show survival assay of GFP-labeled PC3 PCa cells cocultured with WPMY-1 cells or alone, treated with DMSO or Olaparib, in basal and ADT conditions. Experimental design (FIG. 7M), relative GFP positive area after 10 days of culture (n= 6) (FIG. 7N). FIGs. 7O-7T illustrate subcutaneous xenograft co-implantation in NSG mice (male, 7 weeks old) of PC3 PCa cells with WPMY-1 cells (PC3 + WPMY-1 n= 20). Mouse were treated twice a week with Olaparib 40 mg/Kg for 2 weeks. Experimental design (FIG. 70), tumor weight (g) (FIG. 7P), tumor volume (mm3) (FIG. 7Q), gross images (FIG. 7R), IHC for Masson Trichrome, HA, and aSMA (FIG. 7S). Immunofluorescence (IF) for aSMA, p62, and DAPI. scale bars 50 pm (FIG. 7T). Results are shown as mean ± SEM *p < 0.05, **p< 0.01, ***p < 0.001, ****p < 0.0001.
FIGs. 8A-8N. Stromal activation upon Olaparib treatment impacts prostate epithelial cells. FIG. 8A and 8B illustrate TRAMP+ mice treated with Olaparib 40 mg/Kg, 5 days a week for 4 weeks. Experimental design (FIG. 8A), IHC for HA, and aSMA (FIG. 8B), scale bars 50 pm. FIG. 8C and 8D show scRNAseq compartment identification. UMAP plot with clustering results color-coded by compartment types (FIG. 8C). Proportion cell number of the identified cell compartments (FIG. 8D). FIG. 8E and 8F show scRNAseq fibroblast subset. UMAP plot with re-clustering of fibroblast showing the main markers of each cluster (FIG. 8E). Feature plot for the expression of indicated genes (FIG. 8F). (FIG. 8G shows qPCR analysis of mRNA levels of indicated genes in Olaparib- treated WPMY-1 cells (n= 3). FIG. 8H shows IHC for SPINK1, scale bars 50 pm. FIG. 8I-8L illustrate scRNAseq epithelial subset. UMAP plot with re-clustering of epithelial cells color-coded by cell type (FIG. 81). Violin plots of specific epithelial cell markers (FIG. 8J). Proportion cell number of the identified epithelial cell populations (FIG. 8K). Violin plots of indicated gene signatures (FIG. 8L). FIG. 8M shows IHC for pSMAD2, scale bars 50 pm. FIG. 8N illustrates Cellphone DB analysis showing ligand-receptor interactions between identified epithelial and fibroblast populations. FIGs. 9A-9G. Stroma activation blockade reduce the tumor supporting effects of Olaparib. FIG. 9A shows IF for HABP in WPMY- cells treated with vehicle (DMSO), Olaparib 10 pM or Olaparib 10 pM +PEGPH202.5 pg/ml for 96- hour, scale bars 50 pm. FIG. 9B and 9C illustrate trans- ell migration assays. Experimental design (FIG. 9B), relative number of migrating PC3 PCa cultured with Olaparib 10 pM or Olaparib 10 pM +PEGPH20 2.5 pg/m pre-treated WPMY-1 cells for 20 hours, basal and ADT conditions (FIG. 9C). FIG. 9D and 9E show Click-iT EdU incorporation assay. Experimental design (FIG. 9D), left, representative images of EdU incorporation in PC3 PCa cells treated with CM from Olaparib 10 pM, Olaparib 10 pM +PEGPH202.5 pg/m or Olaparib lOpM +CM incubation with Galunisertib 10 pM WPMY-1 cells for 24 hours. Right, percentage of Edu positive cells (n= 3) (FIG. 9E), scale bar 50 pm. FIG. 9F and 9G illustrate subcutaneous xenograft co-implantation in NSG mice (male, 7 weeks old) of PC3 PCa cells with WPMY-1 cells (PC3 + WPMY-1 n= 20). Mouse were treated twice a week with Olaparib 40 mg/Kg or Olaparib + PEGPH20 0.0375 mg/Kg for 2 weeks. Experimental design (FIG. 9F), tumor volume (mm3) (FIG. 9G).
FIGs. 10A-10F. Lactate-driven p62 downregulation is not affected by different degradative mechanisms. FIG. 10A shows WPMY-1 cells, incubated or not with lactate for 48 hours, were incubated with 50 ug/ml of cycloheximide (CHX) and protein stability was determined by immunoblotting at indicated time points. P62 levels were normalized to actin (n = 3). FIG. 10B and 10C show immunoblot analysis for indicated proteins in WPMY-1 cells treated or not with lactate and MG132 (FIG. 10B) or Bafilomycin Al (FIG. 10C) for 48 hours. FIG. 10D shows immunoblot analysis for indicated proteins in WPMY-1 cells, treated or not with lactate for 48 hours, and transduced with the indicated siRNAs. FIG. 10E and 10F show immunoblot analysis for indicated proteins in WPMY-1 cells, treated or not with lactate for 48 hours and a dose-response of the Calpain inhibitor (FIG. 10E) or Caspase inhibitor (FIG. 10F).
FIG. 11A-11F. Selective downregulation of p62 by PARP1 deletion. FIG. 11A and 11B show qPCR analysis of mRNA levels of the indicated genes in WPMY-1 cells, transduced with the indicated siRNAs. FIG. 11C shows qPCR analysis of mRNA levels of the indicated genes and immunoblot analysis for indicated proteins in s PARP-1 and sgC WPMY-1 cells. FIG. 11D-11E illustrate Olaparib induces autophagy. Immunoblot analysis of p62 (FIG. 11D) and LC3 (FIG. HE) in WPMY-1 cells treated with Olaparib in the presence of lysosomal inhibitors (PI). FIG. HF shows treatment with an autophagy inhibitor (ULK inhibitor, SBI-0202965) reverts the stroma activation induced by Olaparib as determined by qPCR of the CAF marker, ACTA2.
FIGs. 12A-12D. Olaparib induces fibroblast activation in different stromal cells. FIG. 12A-12D show qPCR analysis of mRNA levels of the indicated genes in (FIG. 12A) WPMY-1 cells (FIG. 12B) human normal primary fibroblast cells (FIG. 12C) mouse normal fibroblast cells (FIG. 12D) shows mouse hepatic stellate cells treated with Olaparib.
FIGs. 13A-F. PARP inhibitors induce stromal activation in different cell lines and in vivo models. FIG. 13A-13D show immunoblot analysis for P62 protein in primary prostate fibroblasts (FIG. 13A), lung primary fibroblasts (FIG. 13B), breast primary fibroblasts (FIG. 13C), and endometrial primary fibroblasts (FIG. 13D), veh-treated or Olaparib-treated, 20 pM, for 4 days. FIG. 13E-13F show GSEA analysis for the indicated stromal activation signatures comparing Talazoparib- (PARP inhibitor) vs veh- treated in mammary gland tumors (GSE 125206) (FIG. 13E) and Niraparib (PARP inhibitor) vs veh-treated in human ovarian cancer PDXs (GSE163854) (FIG. 13F) showing stromal activation in PARP inhibitors treated samples.
FIGs. 14A-14F. Targeting IL6/JAK/STAT or TNFa signaling decreases stromal activation and rescue the proliferative effect conferred to PC3 prostate tumor epithelial cells. FIG. 14A-14C show GSEA analysis for the indicated signatures in Olaparib 20 pM vs DMSO-treated WPMY-1 cells (FIG. 14A), Talazoparib- (PARP inhibitor) vs saline-treated in mammary gland tumors (GSE 125206, FIG. 14B) and Niraparib- (PARP inhibitor) vs veh-treated in human ovarian cancer PDXs (GSE163854, FIG. 14C), showing increased inflammatory related signatures upon PARP inhibitor treatment. FIG. 14D shows experimental design. FIG. 14E shows qPCR analysis of mRNA levels of indicated genes in WPMY-1 cells treated with DMSO, Olaparib 10 pM, Lestaurtinib (JAKi) 50nM or Olaparib + Lestaurtinib 50nM (n= 3). FIG. 14F shows Click-iT EdU incorporation assay, left, representative images of EdU incorporation in PC3 PCa cells treated 24 h with CM from WPMY-1 treated with DMSO, Olaparib lOpM, Olaparib 10 pM + Lestaurtinib 50nM, Olaparib 10 pM + IL-6 capture antibody (2h), Olaparib 10 pM +TNFa neutralizing antibody 1 pg/ml (1 h), Lestaurtinib 50 nM, IL-6 capture antibody (2 h) or TNFa neutralizing antibody 1 pg/m (1 h). Right, percentage of Edu positive cells (n= 3) scale bars 50 pm.
FIGs. 15A-15K. Olaparib induces stromal activation in vivo both in healthy and metastatic tissues. FIG. 15A-15C shows Olaparib induces stromal activation in tumor-invaded lymph nodes and bones in TRAMP+/FVB castrated mice. Experimental design (FIG. 15A). IHC for HA and aSMA in tumor- invaded lymph nodes from Olaparib- or Veh-treated mice (n=16) showing increased stromal content upon Olaparib treatment, scale bars 50 pm FIG. 15B shows IHC for HA in bone from Olaparib- or Veh-treated mice (n=3) showing increased HA deposition in the growth plate and stromal areas, scale bars 100 pm (C). FIG. 15D-15E show bone in culture (BICA) assay on femur pieces pre-treated or not with Olaparib 20 pM for 48 h cocultured with RMl-BoMe3 tumor epithelial cells for 48 h. Experimental design (FIG. 15D). Left representative images of RFP+RMl-BoMe3 cells attached to the bone. Right, graph or RFP+ positive area showing increased tumor homing of RM1- BoMe3 in Olaparib pre-treated bones (FIG. 15E). FIG. 15F shows qPCR analysis of mRNA levels of indicated genes in isolated bone marrow cells from Olaparib- 40mg/kg or veh-treated mice (n=3). FIG. 15G shows qPCR analysis of mRNA levels of indicated genes in cultured primary bone marrow cells treated with Olaparib 10 pM or DMSO (96 h). FIG. 15H-15J illustrate caudal artery injection of RMl-BoMe3 mouse metastasis model showing that Olaparib induces HA deposition and activation of TGFP signaling. Experimental design (FIG. 15H). IHC for HA showing increased HA deposition in Olaparib-treated liver metastasis (n=3), scale bars 100 pm (FIG. 151). IHC for pSMAD2 showing an increased pSMAD2 staining in bone metastasis in Olaparib- treated mice (n=3), scale bars 100 pm (FIG. 15J). FIG. 15K shows IHC for HA in pre- and post- Olaparib treatment in a prostate cancer bone metastasis showing increased HA deposition in Olaparib-treated mice, scale bars 100 pm.
Detailed Description
Mounting evidence identifies the tumor microenvironment (TME), including stromal fibroblasts, as a driver of tumorigenesis in many types of tumors, including prostate cancer (PCa) (Klemm and Joyce, 2015; Nakanishi et al., 2018; Zhang et al., 2013; Zhang et al., 2020). It is well accepted now that the activation of tumor stromal fibroblasts to a state commonly known as cancer-associated fibroblasts (CAFs) can embolden epithelial cancer cells to progress to more malignant stages and affect disease outcomes (Barron and Rowley, 2012; Cunha et al., 2002; Rowley, 1998; Tuxhorn et al., 2001). CAFs impact the tumor epithelium by modulating many functions through the secretion of stromal growth factors and inflammatory mediators, by reprogramming their metabolism to provide nutrients and survival factors, and by remodeling the extracellular matrix (Hanahan and Weinberg, 2011; Kasashima et al., 2020; Sahai et al., 2020). This fibroblast-epithelium synergistic crosstalk promotes malignancy and is believed to negatively impact cancer treatment by promoting the accumulation of “persisting” or “resistant” tumor cells, which limit therapy efficacy and promote resistance (Bluemn et al., 2017; Linares et al., 2017; Zhang et al., 2020). The renewed interest in the study of CAFs has resulted in the extensive characterization of their cell heterogeneity as well as the establishment of a complex catalogue of the myriad of secreted intermediates that likely impact tumor progression and response to therapy. However, a major gap in the field is the identification of the key master regulators of the acquisition of the CAF phenotype, as well as the molecular mechanisms whereby the tumor epithelium drives this process.
The autophagy substrate and signaling adaptor p62 (encoded by SQSTM1 gene) is a regulator of CAF biology (Huang et al., 2018; Linares et al., 2017; Valencia et al., 2014). P62 has a dual role in cancer (Duran et al., 2011; Duran et al., 2016; Duran et al., 2008; Moscat et al., 2016; Umemura et al., 2016). Thus, while it plays an important oncogenic function in the tumor epithelium, it is a suppressor of tumor progression by restraining CAF activation (Duran et al., 2016; Goruppi and Dotto, 2013; Linares et al., 2017; Reina-Campos et al., 2018; Valencia et al., 2014). It is well established that p62 is upregulated in the epithelium of many types of tumors, which invariably associates with more aggressive cancer and poorer overall survival (Moscat and Diaz-Meco, 2009; Moscat et al., 2016). However, many tumors display reduced levels of p62 in their stroma, especially in CAFs (Duran et al., 2016; Goruppi and Dotto, 2013; Linares et al., 2017; Valencia et al., 2014). p62 downregulation is a central event in the acquisition of the CAF phenotype and in creating a pro-tumorigenic microenvironment conducive to cancer (Linares et al., 2017; Valencia et al., 2014). From a mechanistic point of view, p62 inactivation in prostate stromal fibroblasts impairs their metabolic detoxification capacity and leads to the accumulation of reactive oxygen species, which in turn results in the release of pro-survival inflammatory cytokines (Valencia et al., 2014). Interestingly, under nutrient stress conditions, the downregulation of p62 in fibroblasts also promotes tumorigenesis by enabling their own survival and that of tumor epithelial cells (Linares et al., 2017). Specifically, under conditions of glutamine deprivation, a common situation in the TME of highly aggressive cancers, the loss of p62 in stromal fibroblasts reprograms their metabolism to produce and secrete asparagine to maintain protein synthesis in the tumor epithelium (Linares et al., 2017). These studies highlight the pivotal role of p62 as a tumor suppressor in the stroma by activating pro-survival pathways and the cellular adaptation to nutrient deprivation.
Therefore, whereas the genetic inactivation of p62 selectively in the tissue epithelium impairs tumorigenesis, that in the stromal fibroblasts has the opposite effect by impacting several metabolic and inflammatory pathways (Moscat et al., 2016). The fact that whole body genetic inactivation of p62 results in increased tumorigenesis, mimicking the phenotype of mice with p62 deficiency in the fibroblast stromal compartment, strongly suggests that the stromal role of p62 as a tumor suppressor is what determines the global impact of p62 in cancer (Valencia et al., 2014). This indicates that the tumor-promoting signals produced by the loss of p62 in CAFs override the requirement for p62 in the tumor epithelium, which highlights the importance of studying how p62 is lost in the tumor’ s fibroblast compartment. In this regard, a key pending question is to determine how tumors downregulate p62 in the stroma to promote the CAF phenotype. Identifying this mechanism is of paramount importance because, given the role of p62 in CAF activation and function, this will provide a paradigm for understanding of the master regulators of stromal activation, which will be more amenable to therapeutic intervention than trying to affect the complex downstream effectors unleashed upon stromal activation.
PARP1
The poly (ADP-ribose) polymerase 1 (PARP1) enzyme helps cells repair themselves if they become damaged by serving as a "sensor" for DNA strand breaks. Increased PARP1 expression is sometimes observed in melanomas, breast cancer, lung cancer, and other neoplastic diseases. PARP inhibitors stop PARP from repairing cancer cells.
The human PARP1 gene (gene ID: 142) is located on chromosome 1 (NCBI NC_000001.ll (226360691..226408093, complement)). An amino acid sequence for human PARP1 is available in the Umprot database as accession no. P09874 and shown below as SEQ ID NO:1.
10 20 30 40 50
MAESSDKLYR VEYAKSGRAS CKKCSES IPK DSLRMAIMVQ SPMFDGKVPH 60 70 80 90 100
WYHFSCFWKV GHSIRHPDVE VDGFSELRWD DQQKVKKTAE AGGVTGKGQD 110 120 130 140 150
GIGSKAEKTL GDFAAEYAKS NRSTCKGCME KIEKGQVRLS KKMVDPEKPQ 160 170 180 190 200
LGMIDRWYHP GCFVKNREEL GFRPEYSASQ LKGFSLLATE DKEALKKQLP 210 220 230 240 250
GVKSEGKRKG DEVDGVDEVA KKKSKKEKDK DSKLEKALKA QNDLIWNIKD 260 270 280 290 300
ELKKVCSTND LKELLIFNKQ QVP SGESAIL DRVADGMVFG ALLPCEECSG 310 320 330 340 350
QLVFKSDAYY CTGDVTAWTK CMVKTQTPNR KEWVTPKEFR EI SYLKKLKV 360 370 380 390 400
KKQDRIFPPE TSASVAATPP P STASAPAAV NS SASADKPL SNMKILTLGK 410 420 430 440 450
LSRNKDEVKA MIEKLGGKLT GTANKASLCI STKKEVEKMN KKMEEVKEAN 460 470 480 490 500
IRVVSEDFLQ DVSASTKSLQ ELFLAHILSP WGAEVKAEPV EWAPRGKSG 510 520 530 540 550
AALSKKSKGQ VKEEGINKSE KRMKLTLKGG AAVDPDSGLE HSAHVLEKGG 560 570 580 590 600
KVFSATLGLV DIVKGTNSYY KLQLLEDDKE NRYWIFRSWG RVGTVIGSNK 610 620 630 640 650
LEQMP SKEDA IEHFMKLYEE KTGNAWHSKN FTKYPKKFYP LEIDYGQDEE 660 670 680 690 700
AVKKLTVNPG TKSKLPKPVQ DLIKMIFDVE SMKKAMVEYE IDLQKMPLGK 710 720 730 740 750
LSKRQIQAAY SILSEVQQAV SQGSSDSQIL DLSNRFYTLI PHDFGMKKPP 760 770 780 790 800
LLNNADSVQA KVEMLDNLLD IEVAYSLLRG GSDDSSKDPI DVNYEKLKTD 810 820 830 840 850
IKVVDRDSEE AEI IRKYVKN THATTHNAYD LEVIDIFKIE REGECQRYKP 860 870 880 890 900
FKQLHNRRLL WHGSRTTNFA GILSQGLRIA PPEAPVTGYM FGKGIYFADM 910 920 930 940 950
VSKSANYCHT SQGDPIGLIL LGEVALGNMY ELKHASHI SK LPKGKHSVKG 960 970 980 990 1000
LGKTTPDPSA NI SLDGVDVP LGTGI SSGVN DTSLLYNEYI VYDIAQVNLK 1010 YLLKLKFNFK TSLW
A cDNA sequence for human PARP1 is available in the NCBI database as accession no. NM_001618.4 and shown below as SEQ ID NO:2.
1 AGCAATCTAT CAGGGAACGG CGGTGGCCGG TGCGGCGTGT
41 TCGGTGGCGG CTCTGGCCGC TCAGGCGCCT GCGGCTGGGT
81 GAGCGCACGC GAGGCGGCGA GGCGGCAGCG TGTTTCTAGG
121 TCGTGGCGTC GGGCTTCCGG AGCTTTGGCG GCAGCTAGGG 161 GAGGATGGCG GAGTCTTCGG ATAAGCTCTA TCGAGTCGAG 201 TACGCCAAGA GCGGGCGCGC CTCTTGCAAG AAATGCAGCG 241 AGAGCATCCC CAAGGACTCG CTCCGGATGG CCATCATGGT 281 GCAGTCGCCC ATGTTTGATG GAAAAGTCCC ACACTGGTAC 321 CACTTCTCCT GCTTCTGGAA GGTGGGCCAC TCCATCCGGC 361 ACCCTGACGT TGAGGTGGAT GGGTTCTCTG AGCTTCGGTG
401 GGATGACCAG CAGAAAGTCA AGAAGACAGC GGAAGCTGGA
441 GGAGTGACAG GCAAAGGCCA GGATGGAATT GGTAGCAAGG
481 CAGAGAAGAC TCTGGGTGAC TTTGCAGCAG AGTATGCCAA
521 GTCCAACAGA AGTACGTGCA AGGGGTGTAT GGAGAAGATA
561 GAAAAGGGCC AGGTGCGCCT GTCCAAGAAG ATGGTGGACC
601 CGGAGAAGCC ACAGCTAGGC ATGATTGACC GCTGGTACCA
641 TCCAGGCTGC TTTGTCAAGA ACAGGGAGGA GCTGGGTTTC
681 CGGCCCGAGT ACAGTGCGAG TCAGCTCAAG GGCTTCAGCC
721 TCCTTGCTAC AGAGGATAAA GAAGCCCTGA AGAAGCAGCT
761 CCCAGGAGTC AAGAGTGAAG GAAAGAGAAA AGGCGATGAG
801 GTGGATGGAG TGGATGAAGT GGCGAAGAAG AAATCTAAAA
841 AAGAAAAAGA CAAGGATAGT AAGCTTGAAA AAGCCCTAAA
881 GGCTCAGAAC GACCTGATCT GGAACATCAA GGACGAGCTA
921 AAGAAAGTGT GTTCAACTAA TGACCTGAAG GAGCTACTCA
961 TCTTCAACAA GCAGCAAGTG CCTTCTGGGG AGTCGGCGAT
1001 CTTGGACCGA GTAGCTGATG GCATGGTGTT CGGTGCCCTC
1041 CTTCCCTGCG AGGAATGCTC GGGTCAGCTG GTCTTCAAGA
1081 GCGATGCCTA TTACTGCACT GGGGACGTCA CTGCCTGGAC
1121 CAAGTGTATG GTCAAGACAC AGACACCCAA CCGGAAGGAG
1161 TGGGTAACCC CAAAGGAATT CCGAGAAATC TCTTACCTCA
1201 AGAAATTGAA GGTTAAAAAA CAGGACCGTA TATTCCCCCC
1241 AGAAACCAGC GCCTCCGTGG CGGCCACGCC TCCGCCCTCC
1281 ACAGCCTCGG CTCCTGCTGC TGTGAACTCC TCTGCTTCAG
1321 CAGATAAGCC ATTATCCAAC ATGAAGATCC TGACTCTCGG
1361 GAAGCTGTCC CGGAACAAGG ATGAAGTGAA GGCCATGATT
1401 GAGAAACTCG GGGGGAAGTT GACGGGGACG GCCAACAAGG
1441 CTTCCCTGTG CATCAGCACC AAAAAGGAGG TGGAAAAGAT
1481 GAATAAGAAG ATGGAGGAAG TAAAGGAAGC CAACATCCGA
1521 GTTGTGTCTG AGGACTTCCT CCAGGACGTC TCCGCCTCCA
1561 CCAAGAGCCT TCAGGAGTTG TTCTTAGCGC ACATCTTGTC
1601 CCCTTGGGGG GCAGAGGTGA AGGCAGAGCC TGTTGAAGTT
1641 GTGGCCCCAA GAGGGAAGTC AGGGGCTGCG CTCTCCAAAA
1681 AAAGCAAGGG CCAGGTCAAG GAGGAAGGTA TCAACAAATC
1721 TGAAAAGAGA ATGAAATTAA CTCTTAAAGG AGGAGCAGCT
1761 GTGGATCCTG ATTCTGGACT GGAACACTCT GCGCATGTCC
1801 TGGAGAAAGG TGGGAAGGTC TTCAGTGCCA CCCTTGGCCT
1841 GGTGGACATC GTTAAAGGAA CCAACTCCTA CTACAAGCTG
1881 CAGCTTCTGG AGGACGACAA GGAAAACAGG TATTGGATAT
1921 TCAGGTCCTG GGGCCGTGTG GGTACGGTGA TCGGTAGCAA
1961 CAAACTGGAA CAGATGCCGT CCAAGGAGGA TGCCATTGAG
2001 CACTTCATGA AATTATATGA AGAAAAAACC GGGAACGCTT
2041 GGCACTCCAA AAATTTCACG AAGTATCCCA AAAAGTTCTA
2081 CCCCCTGGAG ATTGACTATG GCCAGGATGA AGAGGCAGTG
2121 AAGAAGCTGA CAGTAAATCC TGGCACCAAG TCCAAGCTCC
2161 CCAAGCCAGT TCAGGACCTC ATCAAGATGA TCTTTGATGT
2201 GGAAAGTATG AAGAAAGCCA TGGTGGAGTA TGAGATCGAC
2241 CTTCAGAAGA TGCCCTTGGG GAAGCTGAGC AAAAGGCAGA
2281 TCCAGGCCGC ATACTCCATC CTCAGTGAGG TCCAGCAGGC
2321 GGTGTCTCAG GGCAGCAGCG ACTCTCAGAT CCTGGATCTC
2361 TCAAATCGCT TTTACACCCT GATCCCCCAC GACTTTGGGA 2401 TGAAGAAGCC TCCGCTCCTG AACAATGCAG ACAGTGTGCA 2441 GGCCAAGGTG GAAATGCTTG ACAACCTGCT GGACATCGAG 2481 GTGGCCTACA GTCTGCTCAG GGGAGGGTCT GATGATAGCA 2521 GCAAGGATCC CATCGATGTC AACTATGAGA AGCTCAAAAC 2561 TGACATTAAG GTGGTTGACA GAGATTCTGA AGAAGCCGAG 2601 ATCATCAGGA AGTATGTTAA GAACACTCAT GCAACCACAC 2641 ACAATGCGTA TGACTTGGAA GTCATCGATA TCTTTAAGAT 2681 AGAGCGTGAA GGCGAATGCC AGCGTTACAA GCCCTTTAAG 2721 CAGCTTCATA ACCGAAGATT GCTGTGGCAC GGGTCCAGGA 2761 CCACCAACTT TGCTGGGATC CTGTCCCAGG GTCTTCGGAT 2801 AGCCCCGCCT GAAGCGCCCG TGACAGGCTA CATGTTTGGT 2841 AAAGGGATCT ATTTCGCTGA CATGGTCTCC AAGAGTGCCA 2881 ACTACTGCCA TACGTCTCAG GGAGACCCAA TAGGCTTAAT 2921 CCTGTTGGGA GAAGTTGCCC TTGGAAACAT GTATGAACTG 2961 AAGCACGCTT CACATATCAG CAAGTTACCC AAGGGCAAGC 3001 ACAGTGTCAA AGGTTTGGGC AAAACTACCC CTGATCCTTC 3041 AGCTAACATT AGTCTGGATG GTGTAGACGT TCCTCTTGGG 3081 ACCGGGATTT CATCTGGTGT GAATGACACC TCTCTACTAT 3121 ATAACGAGTA CATTGTCTAT GATATTGCTC AGGTAAATCT 3161 GAAGTATCTG CTGAAACTGA AATTCAATTT TAAGACCTCC 3201 CTGTGGTAAT TGGGAGAGGT AGCCGAGTCA CACCCGGTGG 3241 CTCTGGTATG AATTCACCCG AAGCGCTTCT GCACCAACTC 3281 ACCTGGCCGC TAAGTTGCTG ATGGGTAGTA CCTGTACTAA 3321 ACCACCTCAG AAAGGATTTT ACAGAAACGT GTTAAAGGTT 3361 TTCTCTAACT TCTCAAGTCC CTTGTTTTGT GTTGTGTCTG 3401 TGGGGAGGGG TTGTTTTGGG GTTGTTTTTG TTTTTTCTTG 3441 CCAGGTAGAT AAAACTGACA TAGAGAAAAG GCTGGAGAGA 3481 GATTCTGTTG CATAGACTAG TCCTATGGAA AAAACCAAGC 3521 TTCGTTAGAA TGTCTGCCTT ACTGGTTTCC CCAGGGAAGG 3561 AAAAATACAC TTCCACCCTT TTTTCTAAGT GTTCGTCTTT 3601 AGTTTTGATT TTGGAAAGAT GTTAAGCATT TATTTTTAGT 3641 TAAAAATAAA AACTAATTTC ATACTATTTA GATTTTCTTT 3681 TTTATCTTGC ACTTATTGTC CCCTTTTTAG TTTTTTTTGT 3721 TTGCCTCTTG TGGTGAGGGG TGTGGGAAGA CCAAAGGAAG 3761 GAACGCTAAC AATTTCTCAT ACTTAGAAAC AAAAAGAGCT 3801 TTCCTTCTCC AGGAATACTG AACATGGGAG CTCTTGAAAT 3841 ATGTAGTATT AAAAGTTGCA TTTGAAATTC TTGACTTTCT 3881 TATGGGCACT TTTGTCTTCC AAATTAAAAC TCTACCACAA 3921 ATATACTTAC CCAAGGGCTA ATAGTAATAC TCGATTAAAA 3961 ATGCAGATGC CTTCTCTA
Subjects can be effectively treated by the compositions and methods described herein even though those subjects have PARP1 isoforms and variants with somewhat different PARP1 sequences than the examples of PARP1 sequences described herein. Such PARP1 isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein). For example, PARP1 isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window. Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970).
Hyaluronan Synthase
Hyaluronan or hyaluronic acid is a high molecular weight unbranched polysaccharide synthesized within a variety of organisms, including mammals. Hyaluronan or hyaluronic acid is a constituent of the extracellular matrix. It consists of alternating glucuronic acid and N-acetylglucosamine residues that are linked by beta- 1-3 and beta- 1-4 glycosidic bonds. Hyaluronic acid is synthesized by membrane-bound synthase at the inner surface of the plasma membrane, and the chains are extruded via ABC-Transporter into the extracellular space. It serves a variety of functions, including space filling, lubrication of joints, and provision of a matrix through which cells can migrate.
For example, a human hyaluronan synthase 1 (HAS1) gene is on chromosome 19 (NBCI NC_000019.10 (51713112..51723991, complement), and HAS1 encodes the following human amino acid sequence (NCBI accession no. Q92839.2; SEQ ID NO:3).
1 MRQQDAPKPT PAACRCSGLA RRVLTIAFAL LILGLMTWAY
41 AAGVPLASDR YGLLAFGLYG AFLSAHLVAQ SLFAYLEHRR
81 VAAAARGPLD AATARSVALT ISAYQEDPAY LRQC LASARA
121 LLYPRARLRV LMWDGNRAE DLYMVDMFRE VFADEDPATY
161 VWDGNYHQPW EPAAAGAVGA GAYREVEAED PGRLAVEALV
201 RTRRCVCVAQ RWGGKREVMY TAFKALGDSV DYVQVCDSDT
241 RLDPMALLEL VRVLDEDPRV GAVGGDVRIL NPLDSWVSFL
281 SSLRYWVAFN VERACQSYFH CVSCI SGPLG LYRNNLLQQF
321 LEAWYNQKFL GTHCTFGDDR HLTNRMLSMG YATKYTSRSR
361 CYSETPSSFL RWLSQQTRWS KSYFREWLYN ALWWHRHHAW
401 MTYEAWSGL FPFFVAATVL RLFYAGRPWA LLWVLLCVQG
441 VALAKAAFAA WLRGCLRMVL LSLYAPLYMC GLLPAKFLAL
481 VTMNQSGWGT SGRRKLAANY VPLLPLALWA LLLLGGLVRS
521 VAHEARADWS GPSRAAEAYH LAAGAGAYVG YWVAMLTLYW
561 VGVRRLCRRR TGGYRVQV
A cDNA sequence for an HAS 1 polypeptide can have the following human nucleotide sequence (NCBI accession no. NM_001297436.2; SEQ ID NO:4).
1 ACAGAGAGGC TGGGAGAGCA AGCCGGAGAG AAGAGAGAGC 41 CCGGCCAGAC CCACTGCGAT GAGACAGGAC GCGCCCAAGC
81 CCACTCCTGC AGCCTGCCGC TGCTCCGGCC TGGCCCGGAG
121 GGTGCTGACC ATCGCCTTCG CCCTGCTCAT CCTGGGCCTC
161 ATGACCTGGG CCTACGCCGC CGGGGTGCCG CTGGCCTCCG
201 ATCGCTACGG CCTCCTGGCC TTCGGCCTCT ACGGGGCCTT
241 CCTTTCAGCG CACCTGGTGG CGCAGAGCCT CTTCGCGTAC
281 CTGGAGCACC GGCGGGTGGC GGCGGCGGCG CGGGGGCCGC
321 TGGATGCAGC CACCGCGCGC AGTGTGGCGC TGACCATCTC
361 CGCCTACCAG GAGGACCCCG CGTACCTGCG CCAGTGCCTG
401 GCGTCCGCCC GCGCCCTGCT GTACCCGCGC GCGCGGCTGC
441 GCGTCCTCAT GGTGGTGGAT GGCAACCGCG CCGAGGACCT
481 CTACATGGTC GACATGTTCC GCGAGGTCTT CGCTGACGAG
521 GACCCCGCCA CGTACGTGTG GGACGGCAAC TACCACCAGC
561 CCTGGGAACC GGCGGCGGCG GGCGCGGTGG GCGCCGGAGC
601 CTATCGGGAG GTGGAGGCGG AGGATCCTGG GCGGCTGGCA
641 GTGGAGGCGG TGGTGAGGAC TCGCAGGTGC GTGTGCGTGG
681 CGCAGCGCTG GGGCGGCAAG CGCGAGGTCA TGTACACAGC
721 CTTCAAGGCG CTCGGAGATT CGGTGGACTA CGTGCAGGTC
761 TGTGACTCGG ACACAAGGTT GGACCCCATG GCACTGCTGG
801 AGCTCGTGCG GGTACTGGAC GAGGACCCCG GGGTAGGGGC
841 TGTTGGTGGG GACGTGCGGA TCCTTAACCC TCTGGACTCC
881 TGGGTCAGCT TCCTAAGCAG CCTGCGATAC TGGGTAGCCT
921 TCAATGTGGA GCGGGCTTGT CAGAGCTACT TCCACTGTGT
961 ATCCTGCATC AGCGGTCCTC TAGGCCTATA TAGGAATAAC
1001 CTCTTGCAGC AGTTTCTTGA GGCCTGGTAC AACCAGAAGT
1041 TCCTGGGTAC CCACTGTACT TTTGGGGATG ACCGGCACCT
1081 CACCAACCGC ATGCTCAGCA TGGGTTATGC TACCAAGTAC
1121 ACCTCCAGGT CCCGCTGCTA CTCAGAGACG CCCTCGTCCT
1161 TCCTGCGGTG GCTGAGCCAG CAGACACGCT GGTCCAAGTC
1201 GTACTTCCGT GAGTGGCTGT ACAACGCGCT CTGGTGGCAC
1241 CGGCACCATG CGTGGATGAC CTACGAGGCG GTGGTCTCCG
1281 GCCTGTTCCC CTTCTTCGTG GCGGCCACTG TGCTGCGTCT
1321 GTTCTACGCG GGCCGCCCTT GGGCGCTGCT GTGGGTGCTG
1361 GTGTGCGTGG AGGGCGTGGC ACTGGCCAAG GCGGCCTTCG
1401 CGGCCTGGCT GCGGGGCTGC CTGCGCATGG TGCTTCTGTC
1441 GCTCTACGCG CCCCTCTACA TGTGTGGCCT CCTGCCTGCC
1481 AAGTTCCTGG CGCTAGTCAC CATGAACCAG AGTGGCTGGG
1521 GCACCTCGGG CCGGCGGAAG CTGGCCGCTA ACTACGTCCC
1561 TCTGCTGCCC CTGGCGCTCT GGGCGCTGCT GCTGCTTGGG
1601 GGCCTGGTCC GCAGCGTAGC ACACGAGGCC AGGGCCGACT
1641 GGAGCGGCCC TTCCCGCGCA GCCGAGGCCT ACCACTTGGC
1681 CGCGGGGGCC GGCGCCTACG TGGGCTACTG GGTGGCCATG
1721 TTGACGCTGT ACTGGGTGGG CGTGCGGAGG CTTTGCCGGC
1761 GGCGGACCGG GGGCTACCGC GTCCAGGTGT GAGTCCAGCC
1801 ACGCGGATGC CGCCTCAAGG GTCTTCAGGG GAGGCCAGAG
1841 GAGAGCTGCT GGGCCCCGAG CCACGAACTT GCTGGGTGGT
1881 TCTCTGGGCC TCAGTTTCCC TCCTCTGCAA AACGAGGGGG
1921 TCAGCCCAAG ATTCTTCAGT CTGGACTATA TTGGGACTGG
1961 GACTTCTGGG TCTCCAGGGA GGGTATTTAT TGGTCAGGGT
2001 GTGGGATCTG AGGAGTGGAG GGAAAGGGTC CTGCTTTCTC
2041 CTCGTTCTTA TTTAATCTCC ATTTCTACTG TGTGATCAGG 2081 ATGTAATAAA GAATTTTATT TATTTTC
In another example, a human hyaluronan synthase 2 (HAS2) gene is on chromosome 8 (NBCI NC_000008.l l (121612116..121641440, complement), and HAS2 encodes the following human amino acid sequence (NCBI accession no.
NP_005319.1; SEQ ID NO:5).
1 MHCERFLCIL RI IGTTLFGV SLLLGITAAY IVGYQFIQTD
41 NYYFSFGLYG AFLASHLI IQ SLFAFLEHRK MKKSLETPIK
81 LNKTVALCIA AYQEDPDYLR KCLQSVKRLT YPGIKWMVI
121 DGNSEDDLYM MDIFSEVMGR DKSATYIWKN NFHEKGPGET
161 DESHKESSQH VTQLVLSNKS ICIMQKWGGK REVMYTAFRA
201 LGRSVDYVQV CDSDTMLDPA SSVEMVKVLE EDPMVGGVGG
241 DVQILNKYDS WISFLSSVRY WMAFNIERAC QSYFGCVQCI
281 SGPLGMYRNS LLHEFVEDWY NQEFMGNQCS FGDDRHLTNR
321 VLSLGYATKY TARSKCLTET PIEYLRWLNQ QTRWSKSYFR
361 EWLYNAMWFH KHHLWMTYEA I ITGFFPFFL IATVIQLFYR
401 GKIWNILLFL LTVQLVGLIK SSFASCLRGN IVMVFMSLYS
441 VLYMSSLLPA KMFAIATINK AGWGTSGRKT IWNFIGLIP
481 VSVWFTILLG GVIFTIYKES KRPFSESKQT VLIVGTLLYA
521 CYWVMLLTLY VVLINKCGRR KKGQQYDMVL DV
A cDNA encoding this HAS2 amino acid sequence is shown below as SEQ ID NO:6 (NCBI accession no. NM_005328.3)
1 AGACCCCCTT AAGTTGGAGG AGGCAGAAGG GCAACAACGG
41 CGGGGAAGGA GAAGTCAAGA CGTCTGGAAA GAATTACCCA
81 GTCCTGGCTT CGAGCAGCCC ATTGAACCAG AGACTTGAAA
121 CAGCCCCAGC CAAAGACTTT TCTCCCAATT CTGCGCTTCC
161 TGGGTTCTGC TGAGTCTTCC ACAGGCTTTT TTTTTTTTTT
201 TTTTTTTTTT TAAGACGAAA AAGAGATTTT CTGTTATCGG
241 GGGCAGAAAG ACTGAAGCCC AAAAAAAAAA AAAAAAAAAA
281 AAGAAAAGAA AAGAAAAAAG AAAAGTTAAT TTATTTTTAA
321 AGCATAATTT TTTTAAGAAT TAGACTGAAG TGCAACGGAA
361 ACATAAAGAG AATATTAGTG AAATTATTTT TTAAAGTGGG
401 GAAGAATCAA ACATTTAAGA CTCCCCTATC CTTTTTAAAT
441 GTTGTTTTTA AATTTCTTAT TTTTTTTGGC CGGTCGTCTC
481 AAATTCATCT GATCTCTTAT TACCTCAATT TTGGAAACTG
521 CCCGCCACCG ACCCTCCGGG ACCACACAGA CAGGCTGAGG
561 ACGACTTTAT GACCAAGAGC TGAACAAGAT GCATTGTGAG
601 AGGTTTCTAT GTATCCTGAG AATAATTGGA ACCACACTCT
641 TTGGAGTCTC TCTCCTCCTT GGAATCACAG CTGCTTATAT
681 TGTTGGCTAC CAGTTTATCC AAACGGATAA TTACTATTTC
721 TCTTTTGGAC TGTATGGTGC CTTTTTGGCA TCACACCTCA
761 TCATCCAAAG CCTGTTTGCC TTTTTGGAGC ACCGAAAAAT
801 GAAAAAATCC CTAGAAACCC CCATAAAGTT GAACAAAACA
841 GTTGCCCTTT GCATCGCTGC CTATCAAGAA GATCCAGACT
881 ACTTAAGGAA ATGTTTGCAA TCTGTGAAAA GGCTAACCTA
921 CCCTGGGATT AAAGTTGTCA TGGTCATAGA TGGGAACTCA 961 GAAGATGACC TTTACATGAT GGACATCTTC AGTGAAGTCA
1001 TGGGCAGAGA CAAATCAGCC ACTTATATCT GGAAGAACAA
1041 CTTCCACGAA AAGGGTCCCG GTGAGACAGA TGAGTCACAT
1081 AAAGAAAGCT CGCAACACGT AACGCAATTG GTCTTGTCCA
1121 ACAAAAGTAT CTGCATCATG CAAAAATGGG GTGGAAAAAG
1161 AGAAGTCATG TACACAGCCT TCAGAGCACT GGGACGAAGT
1201 GTGGATTATG TACAGGTTTG TGATTCAGAC ACTATGCTTG
1241 ACCCAGCCTC ATCTGTGGAG ATGGTAAAAG TTTTAGAAGA
1281 AGATCCCATG GTTGGAGGTG TTGGGGGAGA TGTCCAGATT
1321 TTAAACAAGT ACGATTCCTG GATCTCATTC CTCAGCAGTG
1361 TAAGATATTG GATGGCTTTT AATATAGAAA GGGCCTGTCA
1401 GTCTTATTTT GGGTGTGTTC AGTGCATTAG TGGACCTCTG
1441 GGAATGTACA GAAACTCCTT GTTGCATGAG TTTGTGGAAG
1481 ATTGGTACAA TCAAGAATTT ATGGGCAACC AATGTAGCTT
1521 TGGTGATGAC AGGCATCTCA CGAACCGGGT GCTGAGCCTG
1561 GGCTATGCAA CAAAATACAC AGCTCGATCT AAGTGCCTTA
1601 CTGAAACACC TATAGAATAT CTCAGATGGC TAAACCAGCA
1641 GACCCGTTGG AGCAAGTCCT ACTTCCGAGA ATGGCTGTAC
1681 AATGCAATGT GGTTTCACAA ACATCACTTG TGGATGACCT
1721 ACGAAGCGAT TATCACTGGA TTCTTTCCTT TCTTTCTCAT
1761 TGCCACAGTA ATCCAGCTCT TCTACCGGGG TAAAATTTGG
1801 AACATTCTCC TCTTCTTGTT AACTGTCCAG CTAGTAGGTC
1841 TCATAAAATC ATCTTTTGCC AGCTGCCTTA GAGGAAATAT
1881 CGTCATGGTC TTCATGTCTC TCTACTCAGT GTTATACATG
1921 TCGAGTTTAC TTCCCGCCAA GATGTTTGCA ATTGCAACAA
1961 TAAACAAAGC TGGGTGGGGC ACATCAGGAA GGAAAACCAT
2001 TGTTGTTAAT TTCATAGGAC TCATTCCAGT ATCAGTTTGG
2041 TTTACAATCC TCCTGGGTGG TGTGATTTTC ACCATTTATA
2081 AGGAGTCTAA AAGGCCATTT TCAGAATCCA AACAGACAGT
2121 TCTAATTGTT GGAACGTTGC TCTATGCATG CTATTGGGTC
2161 ATGCTTTTGA CGCTGTATGT AGTTCTCATC AATAAGTGTG
2201 GCAGGCGGAA GAAGGGACAA CAATATGACA TGGTGCTTGA
2241 TGTATGATCT TCCATGTTTT GACGTTTGCA GTGAGACAGA
2281 ACACCTTAGT TCCTCTAGGG GCTGTACAGT ATTGTGGCAT
2321 CAGATAATGC CACCAAAGGA GACATATCAC TGCTGCTGGG
2361 ACTTGAACAA AGACATTTAT ATGGGTTTAT TTTCATTCTG
2401 CCAAAGTAAA ACAATACATC AACAAGAAGA AACTCAGATT
2441 TAACCTGTTA TTTCTATGAA AATGGGATGA ATTCTTTGTT
2481 TATGCACTTT TTCCTTACTG TGCATCCGCC TGAAAGTGTT
2521 TTGCCCTATA TACCTCACTA GCCATGCTTT ATGTGGGTTA
2561 TCATGGAAGA AAAGGATTTT GGAAACTCAA GGAAAAGTTC
2601 TTTCAACCTA TACAACCTAA CTTATGGACT GTTTTGATAG
2641 ATGATAATTT TTTTTTTTTA GGAAGGATTT TCTTTTTAAC
2681 TTTACCAAAT GAAATGCCAA AGGAAGTTTT AAAGGCCGTT
2721 GGCTGTGCTG TATTTTGATA TAATTGTACT GTGTTTTTAA
2761 ATTTTGTATG CCAATCTTAA AGACAAATTT TGCATATTCT
2801 CTATTTTACT TTTCTGCCAA AATAAACCTG TTCTTCCTTT
2841 TTTAAAATAA AATAAGTTCT TAAAAAATTT ATACTTAAAA
2881 AATCCTGCCC AAAATGTGAA GCTTGGTTGA CTGATGTTCA
2921 TGATAGAAAG AATAAAATGT TTCTCTCTCT CTACCTTTTA
2961 AAATTGAATA GTTTATTTCT GTGAAAGAAG TATTTAAACT 3001 TTCAATATTT TAACTTTTTG TTTTTATTTC TTTTAGAAAA 3041 GGCCAATATA CCTATCACAC TTTGGAAGTA AAAATACACA 3081 CTTTCGTGTG TACCTAAAAA AAAAATCGTT GAAAATCAAG 3121 GCCAAAGGTA GTGCAATTTT TTCATTAAGA TTTAAAAAAA 3161 AGGGAATGAT AGTCTTTGAA AGAAAACAGT AGGCATCCAG 3201 CACTGGACAA AACATGGGTA TCAAAGATGA ATAATCTTTG 3241 GAGATTCTGG CAGTGTTTTC CCAGAACAAG TCAAGTGGAA 3281 AGTGGAGAAA TTATCTGTAT AATTTTGGAC ACATACAATG 3321 CAGTTTATCA AAGGTTTTGT TCTGTGGCCT GAATTTACTG 3361 GGTCCTACCT ACACATTGAA CATGTTTTGC CTGTCTTTTT 3401 TTTTTTTTTC AACTTGCCAG TTCACTTTAC ATGTTAGTAT 3441 AATGTTTACA CGGGTGAGTT GGATAAATTA TAAAACATAT 3481 AAATTCAAAA TTGGCAGATA GAATCACCAA GTATCTATCC 3521 TCTTTTACTT TCAAATGAGG AATTTTGTTT TTCTGAATTA 3561 CACAGATCAT CACTTCCTAT TTCCTGTTCT GGACCTGTAT 3601 AAAAATGTCT ACACAGTAGA AGTGACATCA AGGTTTAATA 3641 AGTATATCAA TGATTGGCAC ATATAAAAAT TGTTGAACCA 3681 CATACTCTGA ACTTGGCTAA TTTAGTTACT GCAAGGCCTC 3721 CATTATCCAG TTTTATTTTT TACACGATTG ACCTTGCCTT 3761 GTAGCTGGTG CTGTGTAGAC CTGTGTTGAA AACACAATCG 3801 GAATATATGA ATAATTGAAT AAACAGCATT ATGGTGAGGC 3841 AGAGACACAT GGAGAAGTGT TAAAAAAAAA ATGGGCTTCC 3881 TGCCTTTCTG CCTCTTTTTT ATGCAGTCAT CTATGTTACA 3921 TCTATCCTGC CTAAGAAAAA GCTGCACATC CTACCTTCAG 3961 AGTACAAAAA GGTACATCTG AGACTCAAGA CTCTCACTGA 4001 TTGGAGAGCT TGTGGAAAAC AAAACACACC ATGCCAATAA 4041 ATGAGATGAA AACTTGAGTT TGCCTTTTTA ACTATTTATG 4081 TTCTAAGTTA AGCTTTGATA ACATTCAAAT GTCAAATTCT 4121 CTCATTCTTA TAAAAAGTTG AATTAATTGC CTGTATTTAT 4161 TTTAGCAATT ATTCAATGTA TTTCCAGTAT AGGATGTATA 4201 GTATAATTAA TTTTTTGTAA ATAAAATATT TTTGATAAGA
Subjects can be effectively treated by the compositions and methods described herein even though those subjects have HAS1 or HAS 2 isoforms and variants with somewhat different sequences than the examples of HAS sequences described herein. Such HAS isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein). For example, HAS isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window. Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970).
Hyaluronidase Hyaluronidase is an enzyme that breaks down hyaluronic acid. Although it has been used in medical applications for over 60 years, it is thought exacerbate the spread (metastasis) of cancer. Clinical trials of PEGPH20, a clinical grade hyaluronidase, were discontinued after the investigational drug failed to meet the primary endpoint in a phase 3 trial in metastatic pancreas cancer. However, as illustrated herein, PEGPH20 reverts stroma activation and enhances Olaparib antitumor activity.
An example of a hyaluronidase sequence is the following hyaluronidase PH20 sequence (Uniprot P38567-1; SEQ ID NO:7).
10 20 30 40
50 MGVLKFKHIF FRSFVKSSGV SQIVFTFLLI PCCLTLNFRA PPVIPNVPFL
60 70 80 90
100
WAWNAPSEFC LGKFDEPLDM SLFSFIGSPR INATGQGVTI FYVDRLGYYP
110 120 130 140
150
YIDSITGVTV NGGIPQKISL QDHLDKAKKD ITFYMPVDNL GMAVIDWEEW
160 170 180 190
200 RPTWARNWKP KDVYKNRSIE LVQQQNVQLS LTEATEKAKQ EFEKAGKDFL
210 220 230 240
250 VETIKLGKLL RPNHLWGYYL FPDCYNHHYK KPGYNGSCFN VEIKRNDDLS
260 270 280 290
300
WLWNESTALY PSIYLNTQQS PVAATLYVRN RVREAIRVSK IPDAKSPLPV
310 320 330 340
350
FAYTRIVFTD QVLKFLSQDE LVYTFGETVA LGASGIVIWG TLSIMRSMKS
360 370 380 390
400 CLLLDNYMET ILNPYI INVT LAAKMCSQVL CQEQGVCIRK NWNSSDYLHL
410 420 430 440
450
NPDNFAIQLE KGGKFTVRGK PTLEDLEQFS EKFYCSCYST LSCKEKADVK
460 470 480 490
500 DTDAVDVCIA DGVCIDAFLK PPMETEEPQI FYNASPSTLS ATMFIVS ILF
LI ISSVASL
A cDNA sequence for such a hyaluronidase is shown below (NCBI L13781.1; SEQ
ID NO:8).
1 ATTCCATTCC CTTTCATCTG TGCTCATACT TTGCATCAGA
41 TATTGGGTAA ACCAAAGTGT GTAGGAAGAA ATAAATGTTT
81 TCATAGTCAT TACTCTTTAC AATGGGAGTG CTAAAATTCA
121 AGCACATCTT TTTCAGAAGC TTTGTTAAAT CAAGTGGAGT
161 ATCCCAGATA GTTTTCACCT TCCTTCTGAT TCCATGTTGC
201 TTGACTCTGA ATTTCAGAGC ACCTCCTGTT ATTCCAAATG
241 TGCCTTTCCT CTGGGCCTGG AATGCCCCAA GTGAATTTTG
281 TCTTGGAAAA TTTGATGAGC CACTAGATAT GAGCCTCTTC
321 TCTTTCATAG GAAGCCCCCG AATAAACGCC ACCGGGCAAG
361 GAGTTACAAT ATTTTATGTT GATAGACTTG GCTACTATCC
401 TTACATAGAT TCAATCACAG GAGTAACTGT GAATGGAGGA
441 ATCCCCCAGA AGATTTCCTT ACAAGACCAT CTGGACAAAG
481 CTAAGAAAGA CATTACATTT TATATGCCAG TAGACAATTT
521 GGGAATGGCT GTTATTGACT GGGAAGAATG GAGACCCACT
561 TGGGCAAGAA ACTGGAAACC TAAAGATGTT TACAAGAATA
601 GGTCTATTGA ATTGGTTCAG CAACAAAATG TACAACTTAG
641 TCTCACAGAG GCCACTGAGA AAGCAAAACA AGAATTTGAA
681 AAGGCAGGGA AGGATTTCCT GGTAGAGACT ATAAAATTGG
721 GAAAATTACT TCGGCCAAAT CACTTGTGGG GTTATTATCT
761 TTTTCCGGAT TGTTACAACC ATCACTATAA GAAACCCGGT
801 TACAATGGAA GTTGCTTCAA TGTAGAAATA AAAAGAAATG
841 ATGATCTCAG CTGGTTGTGG AATGAAAGCA CTGCTCTTTA
881 CCCATCCATT TATTTGAACA CTCAGCAGTC TCCTGTAGCT
921 GCTACACTCT ATGTGCGCAA TCGAGTTCGG GAAGCCATCA
961 GAGTTTCCAA AATACCTGAT GCAAAAAGTC CACTTCCGGT
1001 TTTTGCATAT ACCCGCATAG TTTTTACTGA TCAAGTTTTG
1041 AAATTCCTTT CTCAAGATGA ACTTGTGTAT ACATTTGGCG
1081 AAACTGTTGC TCTGGGTGCT TCTGGAATTG TAATATGGGG
1121 AACCCTCAGT ATAATGCGAA GTATGAAATC TTGCTTGCTC
1161 CTAGACAATT ACATGGAGAC TATACTGAAT CCTTACATAA
1201 TCAACGTCAC ACTAGCAGCC AAAATGTGTA GCCAAGTGCT
1241 TTGCCAGGAG CAAGGAGTGT GTATAAGGAA AAACTGGAAT
1281 TCAAGTGACT ATCTTCACCT CAACCCAGAT AATTTTGCTA
1321 TTCAACTTGA GAAAGGTGGA AAGTTCACAG TACGTGGAAA
1361 ACCGACACTT GAAGACCTGG AGCAATTTTC TGAAAAATTT
1401 TATTGCAGCT GTTATAGCAC CTTGAGTTGT AAGGAGAAAG
1441 CTGATGTAAA AGACACTGAT GCTGTTGATG TGTGTATTGC
1481 TGATGGTGTC TGTATAGATG CTTTTCTAAA ACCTCCCATG
1521 GAGACAGAAG AACCTCAAAT TTTCTACAAT GCTTCACCCT
1561 CCACACTATC TGCCACAATG TTCATTGTTA GTATTTTGTT
1601 TCTTATCATT TCTTCTGTAG CGAGTTTGTA ATTGCGCAGG
1641 TTAGCTGAAA TGAACAATAT GTCCATCTTA AAGTGTGCTT
1681 CCC Subjects can be effectively treated by the compositions and methods described herein even though those subjects have hyaluronidase isoforms and variants with somewhat different sequences than the examples of hyaluronidase sequences described herein. Such hyaluronidase isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein). For example, hyaluronidase isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window. Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970).
ULK
Autophagy plays a crucial role in several cellular functions, and its dysregulation is associated with both tumorigenesis and drug resistance. Autophagy is a process of metabolic degradation at the cellular level in which organelles or portions of the cytosol are sequestered by double-membrane autophagosomes and fused with lysosomes for degradation. Unc-51-like kinase 1 (ULK1) is a serine/threonine kinase that participates in the initiation of autophagy. Some studies have indicated that compounds that directly or indirectly target ULK1 could be used for tumor therapy. However, reports of the therapeutic effects of these compounds have come to conflicting conclusions.
ULK1 is a central kinase of the ULK1 complex involved in autophagy initiation, which promotes autophagosome-lysosome fusion. The human ULK1 gene is on chromosome 12 (NC_000012.12 (131894622..131923150). An example of a human ULK1 amino acid sequence is shown below (Uniprot 075385; SEQ ID NO:9).
10 20 30 40 50
MEPGRGGTET VGKFEFSRKD LI GHGAFAW FKGRHREKHD LEVAVKCINK 60 70 80 90 100
KNLAKSQTLL GKEIKILKEL KHENIVALYD FQEMANSVYL VMEYCNGGDL 110 120 130 140 150
ADYLHAMRTL SEDTIRLFLQ QIAGAMRLLH SKGI IHRDLK PQNILLSNPA 160 170 180 190 200
GRRANPNS IR VKIADFGFAR YLQSNMMAAT LCGSPMYMAP EVIMSQHYDG 210 220 230 240 250
KADLWS IGTI VYQCLTGKAP FQASSPQDLR LFYEKNKTLV PTIPRETSAP 260 270 280 290 300
LRQLLLALLQ RNHKDRMDFD EFFHHPFLDA SPSVRKSPPV PVP SYPSSGS 310 320 330 340 350
GSSS SSSSTS HLASPPSLGE MQQLQKTLAS PADTAGFLHS SRDSGGSKDS 360 370 380 390 400
SCDTDDFVMV PAQFPGDLVA EAPSAKPPPD SLMCSGSSLV ASAGLESHGR 410 420 430 440 450
TPSP SPPCSS SPSPSGRAGP FS SSRCGASV P IPVPTQVQN YQRIERNLQS 460 470 480 490 500
PTQFQTPRSS AIRRSGSTSP LGFARASP SP PAHAEHGGVL ARKMSLGGGR 510 520 530 540 550
PYTP SPQVGT IPERPGWSGT PSPQGAEMRG GRSPRPGSSA PEHSPRTSGL 560 570 580 590 600
GCRLHSAPNL SDLHVVRPKL PKPPTDPLGA VFSPPQASPP QPSHGLQSCR 610 620 630 640 650
NLRGSPKLPD FLQRNPLPP I LGSPTKAVPS FDFPKTPSSQ NLLALLARQG 660 670 680 690 700
VVMTPPRNRT LPDLSEVGPF HGQPLGPGLR PGEDPKGPFG RSFSTSRLTD 710 720 730 740 750
LLLKAAFGTQ APDPGSTESL QEKPMEIAPS AGFGGSLHPG ARAGGTSSP S 760 770 780 790 800
PWFTVGSPP SGSTPPQGPR TRMFSAGPTG SAS SSARHLV PGPCSEAPAP 810 820 830 840 850
ELPAPGHGCS FADPI TANLE GAVTFEAPDL PEETLMEQEH TEI LRGLRFT 860 870 880 890 900
LLFVQHVLEI AALKGSASEA AGGPEYQLQE SWADQISLL SREWGFAEQL 910 920 930 940 950
VLYLKVAELL SSGLQSAIDQ IRAGKLCLSS TVKQWRRLN ELYKASWSC 960 970 980 990 1000
QGLSLRLQRF FLDKQRLLDR IHSITAERLI FSHAVQMVQS AALDEMFQHR 1010 1020 1030 1040 1050
EGCVPRYHKA LLLLEGLQHM LSDQADIENV TKCKLC IERR LSALLTGICA
An example of a human ULK1 cDNA is shown below (NCBI ; SEQ ID NO: 10).
1 GGATCCGGAT TCGGATTAGC AGCCCGGGAA GAGTGCCGTG
41 GCACAGGCGC CGGAGGGAGC GCGACCCTCG GACCCCGCCT
81 GGCCCGCGGG GCTGGGACCC GGCCCCGGCC TGCCCGATGG 121 GGCGCGCGGC CCCGGAGATG CGCCCTCGCC CGGCCCCGCG 161 CCCCCGGCCC CGCGCCCCCG GCCCGCCCGC CCCGGCCCGC 201 GCCTCCGCCT GAGTCCCCCG CGCCTTGGCC CGCCACCCCC 241 CGCCCCGCGC CCCCGGCCCG CCTGCGCCAT GGAGCCCGGC 281 CGCGGCGGCA CAGAGACCGT GGGCAAGTTC GAGTTCTCCC 321 GCAAGGACCT GATCGGCCAC GGCGCCTTCG CGGTGGTCTT 361 CAAGGGCCGC CACCGCGAGA AGCACGATTT GGAGGTCGCC 401 GTCAAGTGCA TTAACAAGAA GAACCTCGCC AAGTCTCAGA 441 CGCTGCTGGG GAAGGAAATC AAAATCCTGA AGGAACTGAA 481 ACATGAAAAC ATCGTGGCCC TGTACGACTT CCAGGAAATG 521 GCTAATTCTG TCTACCTGGT TATGGAGTAC TGCAACGGTG 561 GGGACCTGGC CGACTACCTG CACGCCATGC GCACGCTGAG 601 CGAGGACACC ATCAGGCTCT TCCTGCAGCA GATCGCGGGC 641 GCCATGCGGC TTCTGCACAG CAAAGGCATC ATCCACCGCG 681 ACCTGAAACC GCAGAACATC CTGCTGTCCA ACCCCGCCGG 721 CCGCCGCGCC AACCCCAACA GCATCCGCGT CAAGATCGCT 761 GACTTCGGCT TCGCGCGGTA CCTCCAGAGC AACATGATGG
801 CGGCCACACT CTGCGGCTCC CCCATGTACA TGGCCCCCGA
841 GGTCATCATG TCCCAGCACT ACGACGGGAA GGCGGACCTG
881 TGGAGCATCG GCACCATCGT CTACCAGTGC CTGACGGGGA
921 AGGCGCCCTT CCAGGCCAGC AGCCCCCAGG ACCTGCGCCT
961 GTTCTACGAG AAGAACAAGA CGTTGGTCCC CACCATCCCC
1001 CGGGAGACCT CGGCCCCGCT GCGGCAGCTG CTCCTGGCCC
1041 TACTGCAACG CAACCACAAG GACCGCATGG ACTTCGATGA
1081 GTTTTTTCAT CACCCTTTCC TCGATGCCAG CCCCTCGGTC
1121 AGGAAATCCC CACCCGTGCC TGTGCCCTCG TACCCAAGCT
1161 CGGGGTCCGG CAGCAGCTCC AGCAGCAGCT CCACCTCCCA
1201 CCTGGCCTCC CCGCCGTCCC TGGGCGAGAT GCAGCAGCTG
1241 CAGAAGACCC TGGCCTCCCC GGCTGACACC GCTGGCTTCC
1281 TGCACAGCTC CCGGGACTCT GGTGGCAGCA AGGACTCTTC
1321 CTGTGACACA GACGACTTCG TCATGGTCCC CGCGCAGTTT
1361 CCAGGTGACC TGGTGGCTGA GGCGCCCAGT GCCAAACCCC
1401 CGCCAGACAG CCTGATGTGC AGTGGGAGCT CACTGGTGGC
1441 CTCTGCGGGC TTGGAGAGCC ACGGCCGGAC CCCATCTCCA
1481 TCCCCACCCT GCAGCAGCTG CCCCAGTCCC TCAGGCCGGG
1521 CTGGCCCGTT CTCCAGCAGC AGGTGCGGCG CCTCTGTCCC
1561 CATCCCAGTC CCCACGCAGG TGCAGAACTA CCAGCGCATT
1601 GAGCGAAACC TGCAGTCACC CACCCAGTTC CAAACACCTC
1641 GGTCCTCTGC CATCCGCAGG TCAGGCAGCA CCAGCCCCCT
1681 GGGCTTTGCA AGGGCCAGCC CCTCGCCCCC TGCCCACGCT
1721 GAGCATGGAG GCGTCCTGGC CAGGAAGATG TCTCTGGGTG
1761 GAGGCCGGCC CTACACGCCA TCTCCTCAAG TTGGAACCAT
1801 CCCTGAGCGG CCAGGCTGGA GCGGGACGCC CTCCCCACAG
1841 GGAGCTGAGA TGCGGGGTGG CAGGTCCCCT CGTCCAGGCT
1881 CCTCTGCACC CGAGCACTCT CCCCGCACTT CCGGGCTGGG
1921 CTGCCGCCTG CACAGCGCCC CCAACCTGTC TGACTTGCAC
1961 GTCGTCCGCC CCAAGCTGCC CAAACCCCCC ACGGACCCCC
2001 TGGGAGCTGT GTTCAGCCCA CCACAGGCCA GCCCTCCCCA
2041 GCCGTCCCAC GGCCTGCAGT CCTGCCGGAA CCTGCGGGGC
2081 TCACCCAAGC TGCCCGACTT CCTGCAGCGA AACCCCCTGC
2121 CCCCCATCCT GGGCTCCCCC ACCAAGGCTG TGCCCTCCTT
2161 TGACTTCCCG AAGACCCCCA GCTCCCAGAA CCTGCTGGCC
2201 CTCCTAGCCC GGCAGGGCGT GGTGATGACG CCCCCTCGAA
2241 ACCGGACGCT GCCCGACCTC TCGGAGGTGG GACCCTTCCA
2281 TGGTCAGCCG TTGGGCCCTG GCCTGCGGCC AGGCGAGGAC
2321 CCCAAGGGCC CCTTTGGCCG GTCTTTCAGC ACCAGCCGCC
2361 TCACTGACCT GCTCCTTAAG GCGGCGTTTG GGACACAAGC
2401 CCCGGACCCG GGCAGCACGG AGAGCCTGCA GGAGAAGCCC
2441 ATGGAGATCG CACCCTCAGC TGGCTTTGGA GGGAGCCTGC
2481 ACCCAGGAGC CCGTGCTGGG GGCACCAGCA GCCCCTCCCC
2521 GGTGGTCTTC ACCGTGGGCT CTCCCCCGAG CGGGAGCACG
2561 CCCCCCCAGG GCCCCCGCAC CAGGATGTTC TCAGCGGGCC
2601 CCACTGGCTC TGCCAGCTCT TCTGCCCGCC ACCTGGTGCC
2641 TGGGCCCTGC AGCGAGGCCC CAGCCCCTGA GCTCCCTGCT
2681 CCAGGACACG GCTGCAGCTT TGCCGACCCC ATTGCTGCGA
2721 ACCTGGAGGG GGCTGTGACC TTCGAGGCCC CCGACCTCCC
2761 TGAGGAGACC CTCATGGAGC AAGAGCACAC GGAGATCCTG 2801 CGTGGCCTGC GCTTCACGCT GCTGTTCGTG CAGCACGTCC
2841 TGGAGATCGC AGCCCTGAAG GGCAGCGCCA GTGAGGCGGC
2881 GGGGGGCCCT GAGTACCAGC TGCAGGAGAG TGTGGTGGCC
2921 GACCAGATCA GCCTGCTGAG CCGAGAATGG GGCTTCGCGG
2961 AACAGCTGGT GCTGTACCTG AAGGTGGCCG AGCTACTGTC
3001 CTCCGGCCTG CAAAGTGCCA TCGACCAGAT CCGGGCCGGC
3041 AAGCTCTGCC TGTCGTCCAC TGTGAAGCAG GTGGTGCGCA
3081 GGCTGAATGA GCTGTACAAG GCCAGCGTGG TGTCCTGCCA
3121 GGGCCTGAGC CTGCGGCTGC AGCGCTTCTT CCTGGACAAG
3161 CAGCGGCTCC TGGACCGCAT TCACAGCATC ACTGCCGAGA
3201 GGCTCATCTT CAGCCACGCT GTGCAGATGG TGCAGTCGGC
3241 TGCCCTGGAC GAGATGTTCC AGCACCGTGA GGGCTGCGTC
3281 CCACGCTACC ACAAGGCCCT GCTGCTCCTG GAGGGGCTGC
3321 AGCACATGCT CTCGGACCAG GCCGACATCG AGAACGTCAC
3361 CAAGTGCAAG CTGTGCATTG AGCGGAGACT CTCGGCGCTG
3401 CTGACTGGCA TCTGTGCCTG ACCTTTCTGG CCTGGCTGGG
3441 CCCCCCGTCC TGCCGAGCCC TGCAGAGTGG GCTCTGTGTG
3481 CTGGCTGGAC TCCTCGGGAC AAGCCCATGG CGCTGATCGC
3521 TGGTGCTGAG CCCTGCCCTG GGCCCCACGG ACAGTCAGCC
3561 TGCCGGCCTC CCTGCAGCTC ACGGGGCAGA ACCAGCACAT
3601 CTGGAGCCAC ACAGCTTGGG GGGTGTCTCC CATCTTTTAC
3641 AGGTGGGGAT CACAGAATTT CTGCCCCTCC AGCTGCCTGG
3681 CTCAGCAGGC GTGGGTGCCA CCACCCTCTA GCCCCAGGGC
3721 AGCCCCGGAG GACAGGCAAG GGCCTGAGAC CACTGCCGAC
3761 TCAAAGCCAA AGCGAGCTCC TGCTTAGGGC AGGTCAGCAG
3801 GCACTGTGCC CAGGAAGAGC CTGCGGCCTC GGCGTCCCCC
3841 AGTCTCCAGG AGCCTCTCCC TCCGAGATAC CCACCCAGCT
3881 TTGTCAATCA CCCAAGCACT TTATGCATAT AGAGACAGAA
3921 CCTGGACCTC ACCAGGGACT GCTGGGCAGC GATTCCTGGC
3961 AGTGGCCTGG TGTTTGTACA TACACATATG CAGACACATG
4001 CCAGGGCCCC CCAAGCCCGA GCACCGGACC ACGTTGCTGC
4041 CCAGGTCTGG ACCTCAGCGG GAGAACTGGC TCCGGGGGGA
4081 GTGGGGCCCT GCGCTAGAGG CAGAGGCAGT TCTTTGTTCA
4121 AGCGTTCCTC TGGGGACCGG CAGCAGAGGC ACCGTGTTCT
4161 CTCAGCCCTG GATACGTCTT GTAATCTTTC ACACTTTATT
4201 CCTAAAACGT GTCTTATTTT TATGCAGCTC ATTTTTTCTT
4241 TAAAGGAGAA AACTTGTAGG TGTTTAAGAA TTGGTTTTGG
4281 GAGGGCGAGG ACTGGGCCAG GTTAGAGGCA GATGGCACAG
4321 GGGCGTGTGG CGGGCGGGTG AGGCTGCTTT GCACACCTGT
4361 GTTGGTGGCT GTCCCCTGCC GCCCCTCCCT GTGGCAGCAG
4401 CAGGACAGGT GTGTGCCCAG CACCCTCCCT ACCTGGGCCT
4441 GGAAGCAGAT GAGGGGAATA CTTCATGCAA AGAAAAAAGT
4481 AACATGTGCA AAAGCTCCCC GTCCAGCTTT GACAGTCAGT
4521 TTTGATGTCA GCTCCTCGGC AGGGTAGGCC TGATGACAGC
4561 CCTGTCCCTC CCTGCCTCCG CCTTGCCCAA GGCCACGGAG
4601 GGCGTCTGCA GAGAGGCCTG CCTTCCGGAT TCCAGGCGGG
4641 CATGCCCTGC AAACCCCGCC TGGGCCTCCC TTGGTCTGCC
4681 CAGCCCTCGG TTAGCCCTGC CTGAATCAGT AGATACTTGA
4721 ACGAGTCCCC AGTCTGCGGG AGGCAGTGGT GGGGCCATGG
4761 ACCCATGCGG GGGGTTCCAG GGTCACACGC CACATAACAG
4801 ACAAAAATAC ACACACGTGT GTTTTTCTTT GCAATACTTG 4841 AAATATTGCC ACTGTGCTTG GACTTAGAAG AAGAAAATCC 4881 CCGTGACTTC TTCCTCATCA CCTTGATGGC TTTATTCTCA 4921 CCTTGTGGGG CATGTTTGAA TTTATTGCTT CATGGCCGAC 4961 TGGAATCCTG AGTCCTGGGA AGCTGGCACT GCGGGGATCT 5001 TGCCCGGTGT CCTGGTCCTC TTGCTTCCGT CGCGGCCGCA 5041 TGTGCGTGTG TCCAAGCAGG TCCTGGGCGC CTCAACTGCT 5081 GCCCCTGGTT GAATGTTCTC TTGATAGTGC TGGACCCTTT 5121 GTCTATTTTA AAGCGAATTT TGTGTGATTT CCTGCCCTTT 5161 GCGTTATATT GTATAATACC AACGTAAGGA AATAAACCTT 5201 TGGAATTGTT GAAAAAAAAA AAAAAAAA
Subjects can be effectively treated by the compositions and methods described herein even though those subjects have ULK isoforms and variants with somewhat different sequences than the examples of ULK sequences described herein. Such ULK isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein). For example, ULK isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window. Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970). p62
The p62 protein, also referred to as sequestosome-1, is encoded by the human SQSTM1 gene, which is found on chromosome 5 (NC_000005.10 (179806393..179838078). An example of a human p62 amino acid sequence is shown below (Uniprot Q13501-1; SEQ ID NO:11). 10 20 30 40 50
MASLTVKAYL LGKEDAAREI RRFSFCCSPE PEAEAEAAAG PGPCERLLSR
60 70 80 90 100
VAALFPALRP GGFQAHYRDE DGDLVAFS SD EELTMAMSYV KDD IFRIYIK
110 120 130 140 150
EKKECRRDHR PPCAQEAPRN MVHPNVICDG CNGPWGTRY KCSVCPDYDL
160 170 180 190 200
CSVCEGKGLH RGHTKLAFPS PFGHLSEGFS HSRWLRKVKH GHFGWPGWEM
210 220 230 240 250
GPPGNWSPRP PRAGEARPGP TAESASGP SE DPSVNFLKNV GESVAAALSP
260 270 280 290 300
LGIEVDIDVE HGGKRSRLTP VSPESSSTEE KSS SQP SSCC SDP SKPGGNV
310 320 330 340 350
EGATQSLAEQ MRKIALESEG RPEEQMESDN CSGGDDDWTH LSSKEVDPST
360 370 380 390 400 GELQSLQMPE SEGPS SLDPS QEGPTGLKEA ALYPHLPPEA DPRLIESLSQ
410 420 430 440
MLSMGFSDEG GWLTRLLQTK NYDIGAALDT IQYSKHPPPL
A cDNA encoding a human p62 protein is shown below (SEQ ID NO: 12).
1 GAATTCCCTC GCCGCTCGCT ATGGCGTCGC TCACCGTGAA
41 GGCCTACCTT CTGGGCAAGG AGGACGCGGC GCGCGAGATT
81 CGCCGCTTCA GCTTCTGCTG CAGCCCCGAG CCTGAGGCGG
121 AAGCCGAGGC TGCGGCGGGT CCGGGACCCT GCGAGCGGCT
161 GCTGAGCCGG GTGGCCGCCC TGTTCCCCGC GCTGCGGCCT
201 GGCGGCTTCC AGGCGCACTA CCGCGATGAG GACGGGGACT
241 TGGTTGCCTT TTCCAGTGAC GAGGAATTGA CAATGGCCAT
281 GTCCTACGTG AAGGATGACA TCTTCCGAAT CTACATTAAA
321 GAGAAAAAAG AGTGCCGGCG GGACCACCGC CCACCGTGTG
361 CTCAGGAGGC GCCCCGCAAC ATGGTGCACC CCAATGTGAT
401 CTGCGATGGC TGCAATGGGC CTGTGGTAGG AACCCGCTAC
441 AAGTGCAGCG TCTGCCCAGA CTACGACTTG TGTAGCGTCT
481 GCGAGGGAAA GGGCTTGCAC CGGGGGCACA CCAAGCTCGC
521 ATTCCCCAGC CCCTTCGGGC ACCTGTCTGA GGGCTTCTCG
561 CACAGCCGCT GGCTCCGGAA GGTGAAACAC GGACACTTCG
601 GGTGGCCAGG ATGGGAAATG GGTCCACCAG GAAACTGGAG
641 CCCACGTCCT CCTCGTGCAG GGGAGGCCCG CCCTGGCCCC
681 ACGGCAGAAT CAGCTTCTGG TCCATCGGAG GATCCGAGTG
721 TGAATTTCCT GAAGAACGTT GGGGAGAGTG TGGCAGCTGC
761 CCTTAGCCCT CTGGGCATTG AAGTTGATAT CGATGTGGAG
801 CACGGAGGGA AAAGAAGCCG CCTGACCCCC GTCTCTCCAG
841 AGAGTTCCAG CACAGAGGAG AAGAGCAGCT CACAGCCAAG
881 CAGCTGCTGC TCTGACCCCA GCAAGCCGGG TGGGAATGTT
921 GAGGGCGCCA CGCAGTCTCT GGCGGAGCAG ATGAGGAAGA
961 TCGCCTTGGA GTCCGAGGGG GCCCCTGAGG AACAGATGGA
1001 GTCGGATAAC TGTTCAGGAG GAGATGATGA CTGGACCCAT
1041 CTGTCTTCAA AAGAAGTGGA CCCGTCTACA GGTGAACTCC
1081 AGTCCCTACA GATGCCAGAA TCCGAAGGGC CAAGCTCTCT
1121 GGACCCCTCC CAGGAGGGAC CCACAGGGCT GAAGGAAGCT
1161 GCCTTGTACC CACATCTCCC GCCAGAGGCT GACCCGCGGC
1201 TGATTGAGTC CCTCTCCCAG ATGCTGTCCA TGGGCTTCTC
1241 TGATGAAGGC GGCTGGCTCA CCAGGCTCCT GCAGACCAAG
1281 AACTATGACA TCGGAGCGGC TCTGGACACC ATCCAGTATT
1321 CAAAGCATCC CCCGCCGTTG TGACCACTTT TGCCCACCTC
1361 TTCTGCGTGC CCCTCTTCTG TCTCATAGTT GTGTTAAGCT
1401 TGCGTAGAAT TGGCAGGTCT CTGTACGGGC CAGTTTCTCT
1441 GCCTTCTTCC AGGATCAGGG GTTAGGGTGC AAGAAGCCAT
1481 TTAGGGCAGC AAAACAAGTG ACATGAAGGG AGGGTCCCTG
1521 TGTGTGTGTG TGCTGATGTT TCCTGGGTGC CCTGGCTCCT
1561 TGCAGCAGGG CTGGGCCTGC GAGACCCAAG GCTCACTGCA
1601 GCGCGCTCCT GACCCCTCCC TGCAGGGGCT ACGTTAGCAG
1641 CCCAGCACAT AGCTTGCCTA ATGGCTTTCA CTTTCTCTTT
1681 TGTTTTAAAT GACTCATAGG TCCCTGACAT TTAGTTGATT
1721 ATTTTCTGCT ACAGACCTGG TACACTCTGA TTTTAGATAA
1761 AGTAAGCCTA GGTGTTGTCA GCAGGCAGGC TGGGGAGGCC
1801 AGTGTTGTGG GCCTCCTGCT GGGACTGAGA AGGCCCACGA 1841 AGGCGTCCGC AATGTTGGTT TCACTGAGAG CTGCCTCCTG
1881 GTCTCTTCAC CACTGTAGTT CTCTCATTTC CAAACCATCA
1921 GCTGCTTTTA AAATAAGATC TCTTTGTAGC CATCCTGTTA
1961 AATTTGTAAA CAATCTAATT AAATGGCATG CGCAG
Subjects can be effectively treated by the compositions and methods described herein even though those subjects have p62 isoforms and variants with somewhat different sequences than the examples of p62 sequences described herein. Such p62 isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein). For example, p62 isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window. Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970). TNFa
An example of a human TNFa amino acid sequence is shown below (SEQ ID NO:71).
1 MSTESMIRDV ELAEEALPKK TGGPQGSRRC LFLSLFSFLI VAGATTLFCL LHFGVIGPQR 61 EEFPRDLSLI SPLAQAVRSS SRTPSDKPVA HWANPQAEG QLQWLNRRAN ALLANGVELR 121 DNQLVVPSEG LYLIYSQVLF KGQGCPSTHV LLTHTI SRIA VSYQTKVNLL SAIKSPCQRE 181 TPEGAEAKPW YEPIYLGGVF QLEKGDRLSA EINRPDYLDF AESGQVYFGI IAL
A cDNA encoding a human TNFa protein is shown below (SEQ ID NO:72). 1 AGCAGACGCT CCCTCAGCAA GGACAGCAGA GGACCAGCTA AGAGGGAGAG AAGCAACTAC 61 AGACCCCCCC TGAAAACAAC CCTCAGACGC CACATCCCCT GACAAGCTGC CAGGCAGGTT 121 CTCTTCCTCT CACATACTGA CCCACGGCTC CACCCTCTCT CCCCTGGAAA GGACACCATG 181 AGCACTGAAA GCATGATCCG GGACGTGGAG CTGGCCGAGG AGGCGCTCCC CAAGAAGACA 241 GGGGGGCCCC AGGGCTCCAG GCGGTGCTTG TTCCTCAGCC TCTTCTCCTT CCTGATCGTG 301 GCAGGCGCCA CCACGCTCTT CTGCCTGCTG CACTTTGGAG TGATCGGCCC CCAGAGGGAA 361 GAGTTCCCCA GGGACCTCTC TCTAATCAGC CCTCTGGCCC AGGCAGTCAG ATCATCTTCT 421 CGAACCCCGA GTGACAAGCC TGTAGCCCAT GTTGTAGCAA ACCCTCAAGC TGAGGGGCAG 481 CTCCAGTGGC TGAACCGCCG GGCCAATGCC CTCCTGGCCA ATGGCGTGGA
GCTGAGAGAT
541 AACCAGCTGG TGGTGCCATC AGAGGGCCTG TACCTCATCT ACTCCCAGGT
CCTCTTCAAG
601 GGCCAAGGCT GCCCCTCCAC CCATGTGCTC CTCACCCACA CCATCAGCCG
CATCGCCGTC
661 TCCTACCAGA CCAAGGTCAA CCTCCTCTCT GCCATCAAGA GCCCCTGCCA
GAGGGAGACC
721 CCAGAGGGGG CTGAGGCCAA GCCCTGGTAT GAGCCCATCT ATCTGGGAGG
GGTCTTCCAG
781 CTGGAGAAGG GTGACCGACT CAGCGCTGAG ATCAATCGGC CCGACTATCT
CGACTTTGCC
841 GAGTCTGGGC AGGTCTACTT TGGGATCATT GCCCTGTGAG GAGGACGAAC
ATCCAACCTT
901 CCCAAACGCC TCCCCTGCCC CAATCCCTTT ATTACCCCCT CCTTCAGACA
CCCTCAACCT
961 CTTCTGGCTC AAAAAGAGAA TTGGGGGCTT AGGGTCGGAA CCCAAGCTTA
GAACTTTAAG
1021 CAACAAGACC ACCACTTCGA AACCTGGGAT TCAGGAATGT GTGGCCTGCA
CAGTGAAGTG
1081 CTGGCAACCA CTAAGAATTC AAACTGGGGC CTCCAGAACT CACTGGGGCC
TACAGCTTTG
1141 ATCCCTGACA TCTGGAATCT GGAGACCAGG GAGCCTTTGG TTCTGGCCAG
AATGCTGCAG
1201 GACTTGAGAA GACCTCACCT AGAAATTGAC ACAAGTGGAC CTTAGGCCTT
CCTCTCTCCA
1261 GATGTTTCCA GACTTCCTTG AGACACGGAG CCCAGCCCTC CCCATGGAGC
CAGCTCCCTC
1321 TATTTATGTT TGCACTTGTG ATTATTTATT ATTTATTTAT TATTTATTTA
TTTACAGATG
1381 AATGTATTTA TTTGGGAGAC CGGGGTATCC TGGGGGACCC AATGTAGGAG
CTGCCTTGGC
1441 TCAGACATGT TTTCCGTGAA AACGGAGCTG AACAATAGGC TGTTCCCATG
TAGCCCCCTG
1501 GCCTCTGTGC CTTCTTTTGA TTATGTTTTT TAAAATATTT ATCTGATTAA
GTTGTCTAAA
1561 CAATGCTGAT TTGGTGACCA ACTGTCACTC ATTGCTGAGC CTCTGCTCCC
CAGGGGAGTT
1621 GTGTCTGTAA TCGCCCTACT ATTCAGTGGC GAGAAATAAA GTTTGCTTAG AAAAGAAA Subjects can be effectively treated by the compositions and methods described herein even though those subjects have TNFa isoforms and variants with somewhat different sequences than the examples of TNFa sequences described herein. Such TNFa isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein). For example, TNFa isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window. Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970).
IL-6
An example of a human IL-6 amino acid sequence is shown below (SEQ ID NO:73).
1 MNSFSTSAFG PVAFSLGLLL VLPAAFPAPV PPGEDSKDVA APHRQPLTSS ERIDKQIRYI 61 LDGI SALRKE TCNKSNMCES SKEALAENNL NLPKMAEKDG CFQSGFNEET CLVKI ITGLL 121 EFEVYLEYLQ NRFESSEEQA RAVQMSTKVL IQFLQKKAKN LDAITTPDPT TNASLLTKLQ 181 AQNQWLQDMT THLILRSFKE FLQSSLRALR QM
A cDNA encoding a human IL-6 protein is shown below (SEQ ID NO:74). 1 ATTCTGCCCT CGAGCCCACC GGGAACGAAA GAGAAGCTCT ATCTCCCCTC CAGGAGCCCA 61 GCTATGAACT CCTTCTCCAC AAGCGCCTTC GGTCCAGTTG CCTTCTCCCT GGGGCTGCTC 121 CTGGTGTTGC CTGCTGCCTT CCCTGCCCCA GTACCCCCAG GAGAAGATTC CAAAGATGTA 181 GCCGCCCCAC ACAGACAGCC ACTCACCTCT TCAGAACGAA TTGACAAACA AATTCGGTAC 241 ATCCTCGACG GCATCTCAGC CCTGAGAAAG GAGACATGTA ACAAGAGTAA CATGTGTGAA 301 AGCAGCAAAG AGGCACTGGC AGAAAACAAC CTGAACCTTC CAAAGATGGC TGAAAAAGAT 361 GGATGCTTCC AATCTGGATT CAATGAGGAG ACTTGCCTGG TGAAAATCAT CACTGGTCTT 421 TTGGAGTTTG AGGTATACCT AGAGTACCTC CAGAACAGAT TTGAGAGTAG TGAGGAACAA 481 GCCAGAGCTG TGCAGATGAG TACAAAAGTC CTGATCCAGT TCCTGCAGAA AAAGGCAAAG 541 AATCTAGATG CAATAACCAC CCCTGACCCA ACCACAAATG CCAGCCTGCT GACGAAGCTG 601 CAGGCACAGA ACCAGTGGCT GCAGGACATG ACAACTCATC TCATTCTGCG CAGCTTTAAG 661 GAGTTCCTGC AGTCCAGCCT GAGGGCTCTT CGGCAAATGT AGCATGGGCA CCTCAGATTG 721 TTGTTGTTAA TGGGCATTCC TTCTTCTGGT CAGAAACCTG TCCACTGGGC ACAGAACTTA 781 TGTTGTTCTC TATGGAGAAC TAAAAGTATG AGCGTTAGGA CACTATTTTA ATTATTTTTA 841 ATTTATTAAT ATTTAAATAT GTGAAGCTGA GTTAATTTAT GTAAGTCATA TTTATATTTT 901 TAAGAAGTAC CACTTGAAAC ATTTTATGTA TTAGTTTTGA AATAATAATG GAAAGTGGCT 961 ATGCAGTTTG AATATCCTTT GTTTCAGAGC CAGATCATTT CTTGGAAAGT GTAGGCTTAC 1021 CTCAAATAAA TGGCTAACTT ATACATATTT TTAAAGAAAT ATTTATATTG TATTTATATA 1081 ATGTATAAAT GGTTTTTATA CCAATAAATG GCATTTTAAA AAATTCA
Subjects can be effectively treated by the compositions and methods described herein even though those subjects have IL-6 isoforms and variants with somewhat different sequences than the examples of IL-6 sequences described herein. Such IL-6 isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein). For example, IL-6 isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window. Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970).
JAK
An example of a human JAK amino acid sequence is shown below (SEQ ID NO:75).
1 MQYLNIKEDC NAMAFCAKMR SSKKTEVNLE APEPGVEVIF YLSDREPLRL GSGEYTAEEL 61 CIRAAQACRI SPLCHNLFAL YDENTKLWYA PNRTITVDDK MSLRLHYRMR FYFTNWHGTN 181 DGHDIENECL GMAVLAISHY AMMKKMQLPE LPKDISYKRY IPETLNKSIR QRNLLTRMRI
241 NNVFKDFLKE FNNKTICDSS VSTHDLKVKY LATLETLTKH YGAEIFETSM LLI SSENEMN
301 WFHSNDGGNV LYYEVMVTGN LGIQWRHKPN WSVEKEKNK LKRKKLENKH KKDEEKNKIR
361 EEWNNFSYFP EITHIVIKES VVSINKQDNK KMELKLSSHE EALSFVSLVD GYFRLTADAH
421 HYLCTDVAPP LIVHNIQNGC HGPICTEYAI NKLRQEGSEE GMYVLRWSCT DFDNILMTVT
481 CFEKSEQVQG AQKQFKNFQI EVQKGRYSLH GSDRSFPSLG DLMSHLKKQI LRTDNISFML
541 KRCCQPKPRE ISNLLVATKK AQEWQPVYPM SQLSFDRILK KDLVQGEHLG RGTRTHIYSG
601 TLMDYKDDEG TSEEKKIKVI LKVLDPSHRD ISLAFFEAAS MMRQVSHKHI VYLYGVCVRD
661 VENIMVEEFV EGGPLDLFMH RKSDVLTTPW KFKVAKQLAS ALSYLEDKDL VHGNVCTKNL
721 LLAREGIDSE CGPFIKLSDP GIPITVLSRQ ECIERIPWIA PECVEDSKNL SVAADKWSFG
781 TTLWEICYNG EIPLKDKTLI EKERFYESRC RPVTPSCKEL ADLMTRCMNY DPNQRPFFRA
841 IMRDINKLEE QNPDIVSEKK PATEVDPTHF EKRFLKRIRD LGEGHFGKVE LCRYDPEGDN
901 TGEQVAVKSL KPESGGNHIA DLKKEIEILR NLYHENIVKY KGICTEDGGN GIKLIMEFLP
961 SGSLKEYLPK NKNKINLKQQ LKYAVQICKG MDYLGSRQYV HRDLAARNVL VESEHQVKIG
1021 DFGLTKAIET DKEYYTVKDD RDSPVFWYAP ECLMQSKFYI ASDVWSFGVT LHELLTYCDS
1081 DSSPMALFLK MIGPTHGQMT VTRLVNTLKE GKRLPCPPNC PDEVYQLMRK CWEFQPSNRT
1141 SFQNLIEGFE ALLK
A cDNA encoding a human JAK protein is shown below (SEQ ID NO:76).
1 GCGTCGCTGA GCGCAGGCCG CGGCGGCCGC GGAGTATCCT GGAGCTGCAG ACAGTGCGGG 61 CCTGCGCCCA GTCCCGGCTG TCCTCGCCGC GACCCCTCCT CAGCCCTGGG CGCGCGCACG
121 CTGGGGCCCC GCGGGGCTGG CCGCCTAGCG AGCCTGCCGG TCGACCCCAG CCAGCGCAGC
181 GACGGGGCGC TGCCTGGCCC AGGCGCACAC GGAAGTGCGC TTCTCTGAAG TAGCTTTGGA 241 AAGTAGAGAA GAAAATCCAG TTTGCTTCTT GGAGAACACT GGACAGCTGA
ATAAATGCAG
301 TATCTAAATA TAAAAGAGGA CTGCAATGCC ATGGCTTTCT GTGCTAAAAT
GAGGAGCTCC
361 AAGAAGACTG AGGTGAACCT GGAGGCCCCT GAGCCAGGGG TGGAAGTGAT
CTTCTATCTG
421 TCGGACAGGG AGCCCCTCCG GCTGGGCAGT GGAGAGTACA CAGCAGAGGA
ACTGTGCATC
481 AGGGCTGCAC AGGCATGCCG TATCTCTCCT CTTTGTCACA ACCTCTTTGC
CCTGTATGAC
541 GAGAACACCA AGCTCTGGTA TGCTCCAAAT CGCACCATCA CCGTTGATGA
CAAGATGTCC
601 CTCCGGCTCC ACTACCGGAT GAGGTTCTAT TTCACCAATT GGCATGGAAC
CAACGACAAT
661 GAGCAGTCAG TGTGGCGTCA TTCTCCAAAG AAGCAGAAAA ATGGCTACGA
GAAAAAAAAG
721 ATTCCAGATG CAACCCCTCT CCTTGATGCC AGCTCACTGG AGTATCTGTT
TGCTCAGGGA
781 CAGTATGATT TGGTGAAATG CCTGGCTCCT ATTCGAGACC CCAAGACCGA
GCAGGATGGA
841 CATGATATTG AGAACGAGTG TCTAGGGATG GCTGTCCTGG CCATCTCACA
CTATGCCATG
901 ATGAAGAAGA TGCAGTTGCC AGAACTGCCC AAGGACATCA GCTACAAGCG
ATATATTCCA
961 GAAACATTGA ATAAGTCCAT CAGACAGAGG AACCTTCTCA CCAGGATGCG
GATAAATAAT
1021 GTTTTCAAGG ATTTCCTAAA GGAATTTAAC AACAAGACCA TTTGTGACAG
CAGCGTGTCC
1081 ACGCATGACC TGAAGGTGAA ATACTTGGCT ACCTTGGAAA CTTTGACAAA
ACATTACGGT
1141 GCTGAAATAT TTGAGACTTC CATGTTACTG ATTTCATCAG AAAATGAGAT
GAATTGGTTT
1201 CATTCGAATG ACGGTGGAAA CGTTCTCTAC TACGAAGTGA TGGTGACTGG
GAATCTTGGA
1261 ATCCAGTGGA GGCATAAACC AAATGTTGTT TCTGTTGAAA AGGAAAAAAA
TAAACTGAAG
1321 CGGAAAAAAC TGGAAAATAA ACACAAGAAG GAT GAGGAGA AAAACAAGAT
CCGGGAAGAG
1381 TGGAACAATT TTTCTTACTT CCCTGAAATC ACTCACATTG TAATAAAGGA
GTCTGTGGTC 1441 AGCATTAACA AGCAGGACAA CAAGAAAATG GAACTGAAGC TCTCTTCCCA
CGAGGAGGCC
1501 TTGTCCTTTG TGTCCCTGGT AGATGGCTAC TTCCGGCTCA CAGCAGATGC
CCATCATTAC
1561 CTCTGCACCG ACGTGGCCCC CCCGTTGATC GTCCACAACA TACAGAATGG
CTGTCATGGT
1621 CCAATCTGTA CAGAATACGC CATCAATAAA TTGCGGCAAG AAGGAAGCGA
GGAGGGGATG
1681 TACGTGCTGA GGTGGAGCTG CACCGACTTT GACAACATCC TCATGACCGT
CACCTGCTTT
1741 GAGAAGTCTG AGCAGGTGCA GGGTGCCCAG AAGCAGTTCA AGAACTTTCA
GATCGAGGTG
1801 CAGAAGGGCC GCTACAGTCT GCACGGTTCG GACCGCAGCT TCCCCAGCTT
GGGAGACCTC
1861 ATGAGCCACC TCAAGAAGCA GATCCTGCGC ACGGATAACA TCAGCTTCAT
GCTAAAACGC
1921 TGCTGCCAGC CCAAGCCCCG AGAAATCTCC AACCTGCTGG TGGCTACTAA
GAAAGCCCAG
1981 GAGTGGCAGC CCGTCTACCC CATGAGCCAG CTGAGTTTCG ATCGGATCCT
CAAGAAGGAT
2041 CTGGTGCAGG GCGAGCACCT TGGGAGAGGC ACGAGAACAC ACATCTATTC
TGGGACCCTG
2101 ATGGATTACA AGGATGACGA AGGAACTTCT GAAGAGAAGA AGATAAAAGT
GATCCTCAAA
2161 GTCTTAGACC CCAGCCACAG GGATATTTCC CTGGCCTTCT TCGAGGCAGC
CAGCATGATG
2221 AGACAGGTCT CCCACAAACA CATCGTGTAC CTCTATGGCG TCTGTGTCCG
CGACGTGGAG
2281 AATATCATGG TGGAAGAGTT TGTGGAAGGG GGTCCTCTGG ATCTCTTCAT
GCACCGGAAA
2341 AGCGATGTCC TTACCACACC ATGGAAATTC AAAGTTGCCA AACAGCTGGC
CAGTGCCCTG
2401 AGCTACTTGG AGGATAAAGA CCTGGTCCAT GGAAATGTGT GTACTAAAAA
CCTCCTCCTG
2461 GCCCGTGAGG GCATCGACAG TGAGTGTGGC CCATTCATCA AGCTCAGTGA
CCCCGGCATC
2521 CCCATTACGG TGCTGTCTAG GCAAGAATGC ATTGAACGAA TCCCATGGAT
TGCTCCTGAG
2581 TGTGTTGAGG ACTCCAAGAA CCTGAGTGTG GCTGCTGACA AGTGGAGCTT
TGGAACCACG 2641 CTCTGGGAAA TCTGCTACAA TGGCGAGATC CCCTTGAAAG ACAAGACGCT
GATTGAGAAA
2701 GAGAGATTCT ATGAAAGCCG GTGCAGGCCA GTGACACCAT CATGTAAGGA
GCTGGCTGAC
2761 CTCATGACCC GCTGCATGAA CTATGACCCC AATCAGAGGC CTTTCTTCCG
AGCCATCATG
2821 AGAGACATTA ATAAGCTTGA AGAGCAGAAT CCAGATATTG TTTCAGAAAA
AAAACCAGCA
2881 ACTGAAGTGG ACCCCACACA TTTTGAAAAG CGCTTCCTAA AGAGGATCCG
TGACTTGGGA
2941 GAGGGCCACT TTGGGAAGGT TGAGCTCTGC AGGTATGACC CCGAAGGGGA
CAATACAGGG
3001 GAGCAGGTGG CTGTTAAATC TCTGAAGCCT GAGAGTGGAG GTAACCACAT
AGCTGATCTG
3061 AAAAAGGAAA TCGAGATCTT AAGGAACCTC TATCATGAGA ACATTGTGAA
GTACAAAGGA
3121 ATCTGCACAG AAGACGGAGG AAATGGTATT AAGCTCATCA TGGAATTTCT
GCCTTCGGGA
3181 AGCCTTAAGG AATATCTTCC AAAGAATAAG AACAAAATAA ACCTCAAACA
GCAGCTAAAA
3241 TATGCCGTTC AGATTTGTAA GGGGATGGAC TATTTGGGTT CTCGGCAATA
CGTTCACCGG
3301 GACTTGGCAG CAAGAAATGT CCTTGTTGAG AGTGAACACC AAGTGAAAAT
TGGAGACTTC
3361 GGTTTAACCA AAGCAATTGA AACCGATAAG GAGTATTACA CCGTCAAGGA
TGACCGGGAC
3421 AGCCCTGTGT TTTGGTATGC TCCAGAATGT TTAATGCAAT CTAAATTTTA
TATTGCCTCT
3481 GACGTCTGGT CTTTTGGAGT CACTCTGCAT GAGCTGCTGA CTTACTGTGA
TTCAGATTCT
3541 AGTCCCATGG CTTTGTTCCT GAAAATGATA GGCCCAACCC ATGGCCAGAT
GACAGTCACA
3601 AGACTTGTGA ATACGTTAAA AGAAGGAAAA CGCCTGCCGT GCCCACCTAA
CTGTCCAGAT
3661 GAGGTTTATC AACTTATGAG GAAATGCTGG GAATTCCAAC CATCCAATCG
GACAAGCTTT
3721 CAGAACCTTA TTGAAGGATT TGAAGCACTT TTAAAATAAG AAGCATGAAT
AACATTTAAA
3781 TTCCACAGAT TATCAAGTCC TTCTCCTGCA ACAAATGCCC AAGTCATTTT
TTAAAAATTT 3841 CTAATGAAAG AAGTTTGTGT TCTGTCCAAA AAGTCACTGA ACTCATACTT CAGTACATAT
3901 ACATGTATAA GGCACACTGT AGTGCTTAAT ATGTGTAAGG ACTTCCTCTT TAAATTTGGT
3961 ACCAGTAACT TAGTGACACA TAATGACAAC CAAAATATTT GAAAGCACTT AAGCACTCCT
4021 CCTTGTGGAA AGAATATACC ACCATTTCAT CTGGCTAGTT CACCATCACA ACTGCATTAC
4081 CAAAAGGGGA TTTTTGAAAA CGAGGAGTTG ACCAAAATAA TATCTGAAGA TGATTGCTTT
4141 TCCCTGCTGC CAGCTGATCT GAAATGTTTT GCTGGCACAT TAATCATAGA TAAAGAAAGA
4201 TTGATGGACT TAGCCCTCAA ATTTCAGTAT CTATACAGTA CTAGACCATG CATTCTTAAA
4261 ATATTAGATA CCAGGTAGTA TATATTGTTT CTGTACAAAA ATGACTGTAT TCTCTCACCA
4321 GTAGGACTTA AACTTTGTTT CTCCAGTGGC TTAGCTCCTG TTCCTTTGGG TGATCACTAG
4381 CACCCATTTT TGAGAAAGCT GGTTCTACAT GGGGGGATAG CTGTGGAATA GATAATTTGC
4441 TGCATGTTAA TTCTCAAGAA CTAAGCCTGT GCCAGTGCTT TCCTAAGCAG TATACCTTTA
4501 ATCAGAACTC ATTCCCAGAA CCTGGATGCT ATTACACATG CTTTTAAGAA ACGTCAATGT
4561 ATATCCTTTT ATAACTCTAC CACTTTGGGG CAAGCTATTC CAGCACTGGT TTTGAATGCT
4621 GTATGCAACC AGTCTGAATA CCACATACGC TGCACTGTTC TTAGAGGGTT TCCATACTTA
4681 CCACCGATCT ACAAGGGTTG ATCCCTGTTT TTACCATCAA TCATCACCCT GTGGTGCAAC
4741 ACTTGAAAGA CCCGGCTAGA GGCACTATGG ACTTCAGGAT CCACTAGACA GTTTTCAGTT
4801 TGCTTGGAGG TAGCTGGGTA ATCAAAAATG TTTAGTCATT GATTCAATGT GAACGATTAC
4861 GGTCTTTATG ACCAAGAGTC TGAAAATCTT TTTGTTATGC TGTTTAGTAT TCGTTTGATA
4921 TTGTTACTTT TCACCTGTTG AGCCCAAATT CAGGATTGGT TCAGTGGCAG CAATGAAGTT
4981 GCCATTTAAA TTTGTTCATA GCCTACATCA CCAAGGTCTC TGTGTCAAAC CTGTGGCCAC
5041 TCTATATGCA CTTTGTTTAC TCTTTATACA AATAAATATA CTAAAGACTT TA Subjects can be effectively treated by the compositions and methods described herein even though those subjects have JAK isoforms and variants with somewhat different sequences than the examples of JAK sequences described herein. Such JAK isoforms and variants can have polypeptide or nucleic acid sequences with between 55-100% sequence identity to a reference sequence (e.g., a sequence described herein). For example, JAK isoforms and variants can have at least 55% sequence identity, e.g., at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97% sequence, at least 98%, at least 99% identity to a reference sequence (e.g., a sequence described herein) over a specified comparison window. Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-53 (1970).
Inhibitory Nucleic Acids
The expression of hyaluronan synthase can be inhibited, for example by use of an inhibitory nucleic acid that specifically recognizes a nucleic acid that encodes the hyaluronan synthase.
An inhibitory nucleic acid can have at least one segment that will hybridize to a hyaluronan synthase nucleic acid, ULK1 nucleic acid, TNFa nucleic acid, IL6 nucleic acid or JAK nucleic acid under intracellular or stringent conditions. The inhibitory nucleic acid can reduce expression of a nucleic acid encoding hyaluronan synthase, ULK1, TNFa, IL6 or JAK. A nucleic acid may hybridize to a genomic DNA, a messenger RNA, or a combination thereof. An inhibitory nucleic acid may be incorporated into a plasmid vector or viral DNA. It may be single stranded or double stranded, circular or linear.
An inhibitory nucleic acid is a polymer of ribose nucleotides or deoxyribose nucleotides having more than 13 nucleotides in length. An inhibitory nucleic acid may include naturally occurring nucleotides; synthetic, modified, or pseudonucleotides such as phosphorothiolates; as well as nucleotides having a detectable label such as P32, biotin or digoxigenin. An inhibitory nucleic acid can reduce the expression and/or activity of a hyaluronan synthase nucleic acid, ULK1 nucleic acid, TNFa nucleic acid, IL6 nucleic acid or JAK nucleic acid. Such an inhibitory nucleic acid may be completely complementary to a segment of an endogenous hyaluronan synthase nucleic acid (e.g., a hyaluronan synthase RNA) or ULK1 nucleic acid (e.g., an ULK1 mRNA) or TNFa nucleic acid (e.g., a TNFa mRNA) or IL-6 nucleic acid (e.g., a IL-6 mRNA) or JAK nucleic acid (e.g., a JAK mRNA). Alternatively, some variability is permitted in the inhibitory nucleic acid sequences relative to hyaluronan synthase, ULK1, TNFa, IL6 or JAK. An inhibitory nucleic acid can hybridize to a hyaluronan synthase nucleic acid or ULK1 nucleic acid or a TNFa nucleic acid or a IL-6 nucleic acid or a JAK nucleic acid under intracellular conditions or under stringent hybridization conditions and is sufficiently complementary to inhibit expression of the endogenous hyaluronan synthase nucleic acid or ULK1 nucleic acid or TNFa nucleic acid or IL-6 nucleic acid or JAK nucleic acid. Intracellular conditions refer to conditions such as temperature, pH and salt concentrations typically found inside a cell, e.g., an animal or mammalian cell. One example of such an animal or mammalian cell is a stromal or epithelial cell. Another example of such an animal or mammalian cell is a cancer cell. Generally, stringent hybridization conditions are selected to be about 5 °C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. However, stringent conditions encompass temperatures in the range of about 1°C to about 20 °C lower than the thermal melting point of the selected sequence, depending upon the desired degree of stringency as otherwise qualified herein. Inhibitory oligonucleotides can, for example, have 2, 3, 4, or 5 or more stretches of contiguous nucleotides that are precisely complementary to a hyaluronan synthase coding sequence or ULK1 coding sequence or TNFa coding sequence or IL-6 coding sequence or JAK coding sequence, wherein each complementary stretch is separated by one or more contiguous nucleotides that are not complementary to adjacent coding sequences, can inhibit the function of a hyaluronan synthase nucleic acid or ULK1 nucleic acid or TNFa nucleic acid or IL-6 nucleic acid or JAK nucleic acid. In general, each stretch of contiguous nucleotides is at least 4, 5, 6, 7, or 8 or more nucleotides in length. Non-complementary intervening sequences may be 1, 2, 3, or 4 nucleotides in length. One skilled in the art can easily use the calculated melting point of an inhibitory nucleic acid hybridized to a sense nucleic acid to estimate the degree of mismatching that will be tolerated for inhibiting expression of a particular target nucleic acid. Inhibitory nucleic acids of the invention include, for example, a short hairpin RNA, a small interfering RNA, a ribozyme or an antisense nucleic acid molecule. The inhibitory nucleic acid molecule may be single or double stranded (e.g., a small interfering RNA (siRNA)) and may function in an enzyme-dependent manner or by steric blocking. Inhibitory nucleic acid molecules that function in an enzyme-dependent manner include forms dependent on RNase H activity to degrade target mRNA. These include single-stranded DNA, RNA, and phosphorothioate molecules, as well as the double-stranded RNAi/siRNA system that involves target mRNA recognition through sense-antisense strand pairing followed by degradation of the target mRNA by the RNA-induced silencing complex. Steric blocking inhibitory nucleic acids, which are RNase-H independent, interfere with gene expression or other mRNA-dependent cellular processes by binding to a target mRNA and getting in the way of other processes. Steric blocking inhibitory nucleic acids include 2'-0 alkyl (usually in chimeras with RNase-H dependent antisense), peptide nucleic acid (PNA), locked nucleic acid (LNA) and morpholino antisense.
Small interfering RNAs, for example, may be used to specifically reduce translation of hyaluronan synthase or ULK1 or TNFa or IL-6 or JAK nucleic acid such that translation of the encoded hyaluronan synthase, ULKl,TNFa, IL-6 or JAK is inhibited. SiRNAs mediate post-transcriptional gene silencing in a sequencespecific manner. See, for example, website at invitrogen.com/site/us/en/home/Products-and-Services/Applications/rnai.html. Once incorporated into an RNA-induced silencing complex, siRNA mediate cleavage of the homologous endogenous mRNA transcript by guiding the complex to the homologous mRNA transcript, which is then cleaved by the complex. The siRNA may be homologous and/or complementary to any region of the hyaluronan synthase transcript or to any region of an ULK1 transcript or to any region of a TNFa transcript or any region of a IL-6 transcript or any region of a JAKtranscript. The region of homology may be 30 nucleotides or less in length, e.g., less than 25 nucleotides such as about 21 to 23 nucleotides in length. SiRNA is typically double stranded and may have two-nucleotide 3’ overhangs, for example, 3’ overhanging UU dinucleotides. Methods for designing siRNAs are known to those skilled in the art. See, for example, Elbashir et al. Nature 411: 494-498 (2001); Harborth et al. Antisense Nucleic Acid Drug Dev. 13: 83-106 (2003).
The pSuppressorNeo vector for expressing hairpin siRNA, commercially available from IMGENEX (San Diego, California), can be used to generate siRNA for inhibiting expression of hyaluronan synthase or ULK1. The construction of the siRNA expression plasmid involves the selection of the target region of the mRNA, which can be a trial-and-error process. However, Elbashir et al. have provided guidelines that appear to work -80% of the time. Elbashir, S.M., et al., Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods, 2002. 26(2): p. 199-213. Accordingly, for synthesis of synthetic siRNA, a target region may be selected, e.g., 50 to 100 nucleotides downstream of the start codon. The 5' and 3' untranslated regions and regions close to the start codon should be avoided as these may be richer in regulatory protein binding sites. As siRNA can begin with AA, have 3' UU overhangs for both the sense and antisense siRNA strands, and have an approximate 50 % G/C content. An example of a sequence for a synthetic siRNA is 5'-AA(N19)UU, where N is any nucleotide in the mRNA sequence and the siRNA should be approximately 50% G-C content. The selected sequence(s) can be compared to others in the human genome database to minimize homology to other known coding sequences (e.g., by Blast search, for example, through the NCBI website).
SiRNAs may be chemically synthesized, created by in vitro transcription, or expressed from an siRNA expression vector or a PCR expression cassette. See, e.g., website at invitrogen.com/site/us/en/home/Products-and- Services/Applications/rnai.html. When an siRNA is expressed from an expression vector or a PCR expression cassette, the insert encoding the siRNA may be expressed as an RNA transcript that folds into an siRNA hairpin. Thus, the RNA transcript may include a sense siRNA sequence that is linked to its reverse complementary antisense siRNA sequence by a spacer sequence that forms the loop of the hairpin as well as a string of U’s at the 3’ end. The loop of the hairpin may be of any appropriate lengths, for example, 3 to 30 nucleotides in length, e.g., , 3 to 23 nucleotides in length, and may be of various nucleotide sequences including, AUG, CCC, UUCG, CCACC, CTCGAG, AAGCUU, CCACACC and UUCAAGAGA. SiRNAs also may be produced in vivo by cleavage of double-stranded RNA introduced directly or via a transgene or virus. Amplification by an RNA-dependent RNA polymerase may occur in some organisms.
An inhibitory nucleic acid such as a short hairpin RNA siRNA or an antisense oligonucleotide may be prepared using methods such as by expression from an expression vector or expression cassette that includes the sequence of the inhibitory nucleic acid. Alternatively, it may be prepared by chemical synthesis using naturally occurring nucleotides, modified nucleotides or any combinations thereof. In some embodiments, the inhibitory nucleic acids are made from modified nucleotides or non-phosphodiester bonds, for example, that are designed to increase biological stability of the inhibitory nucleic acid or to increase intracellular stability of the duplex formed between the inhibitory nucleic acid and the target hyaluronan synthase nucleic acid.
An inhibitory nucleic acid may be generated, for example, by expression from an expression vector encoding a complementarity sequence of the hyaluronan synthase nucleic acid, ULK1 nucleic acid, TNFa nucleic acid, IL-6 nucleic acid or JAK nucleic acid. Alternatively, it may be prepared by chemical synthesis using naturally occurring nucleotides, modified nucleotides or any mixture of combination thereof. In some embodiments, the hyaluronan synthase nucleic acids or ULK1 nucleic acids or TNFa nucleic acids or IL-6 nucleic acids or JAK nucleic acids are made from modified nucleotides or non-phosphodiester bonds, for example, that are designed to increase biological stability of the nucleic acids or to increase intracellular stability of the duplex formed between the inhibitory nucleic acids and other (e.g., endogenous) nucleic acids.
For example, the inhibitory hyaluronan synthase nucleic acids or inhibitory ULK1 nucleic acids or inhibitory TNFa nucleic acids or inhibitory IL-6 nucleic acids or inhibitory JAK nucleic acids can be peptide nucleic acids that have peptide bonds rather than phosphodiester bonds.
The inhibitory nucleic acids of the hyaluronan synthase or ULK1 or TNFa or IL-6 or JAK described herein may include modified nucleotides, as well as natural nucleotides such as combinations of ribose and deoxyribose nucleotides.
Naturally occurring nucleotides that can be employed in the hyaluronan synthase nucleic acids or ULK1 nucleic acids or TNFa nucleic acids or IL-6 nucleic acids or JAK nucleic acids can include the ribose or deoxyribose nucleotides adenosine, guanine, cytosine, thymine and uracil.
Examples of modified nucleotides that can be employed in the inhibitory hyaluronan synthase nucleic acids or inhibitory ULK1 nucleic acids or inhibitory TNFa nucleic acids or inhibitory IL-6 nucleic acids or inhibitory JAK nucleic acids include 5-fluorouracil, 5 -bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5 -(carboxyhydroxylmethyl) uracil, 5- carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1- methylguanine, 1 -methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2- methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5 -methylaminomethyluracil, 5 -methoxyaminomethyl-2-thiouracil, beta-D- mannosylqueosine, 5 ’-methoxycarboxymethyluracil, 5 -methoxyuracil, 2-methythio- N6-isopentenyladeninje, uracil-5oxyacetic acid, wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5- methyluracil, uracil-5-oxacetic acid methylester, uracil-5-oxacetic acid, 5-methyl-2- thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and 2,6- diaminopurine.
The inhibitory nucleic acids and may be of same length as wild type hyaluronan synthase or as any isoforms or variants of hyaluronan synthase or ULK1 or TNFa or IL-6 or JAK. The inhibitory nucleic acids of the hyaluronan synthase, ULK1, TNFa, IL-6 or JAK described herein can also be longer and include other useful sequences. In some embodiments, the inhibitory nucleic acids of the hyaluronan synthase, ULK1, TNFa, IL-6 or JAK are somewhat shorter. For example, inhibitory nucleic acids of hyaluronan synthase, ULK1, TNFa, IL-6 or JAK can include a segment that has a nucleic acid sequence that can be missing up to 5 nucleotides, or missing up to 10 nucleotides, or missing up to 20 nucleotides, or missing up to 30 nucleotides, or missing up to 50 nucleotides, or missing up to 100 nucleotides from the 5’ or 3’ end.
The inhibitory nucleic acids can be introduced via one or more vehicles such as via expression vectors (e.g., viral vectors), via virus like particles, via ribonucleoproteins (RNPs), via nanoparticles, via liposomes, or a combination thereof. The vehicles can include components or agents that can target particular cell types, facilitate cell penetration, reduce degradation, or a combination thereof. Antibodies
Antibodies can be used as inhibitors of hyaluronan synthase, ULK1, TNFa, IL-6 or JAK. Antibodies can be raised against various epitopes of hyaluronan synthase, ULK1, TNFa, IL-6 or JAK. Some antibodies for hyaluronan synthase, ULK1, TNFa, IL-6 or JAK may also be available commercially. However, the antibodies contemplated for treatment pursuant to the methods and compositions described herein are in one embodiment human or humanized antibodies and are highly specific for their targets.
In one aspect, the present disclosure relates to use of isolated antibodies that bind specifically to hyaluronan synthase, ULK1, TNFa, IL-6 or JAK. Such antibodies may be monoclonal antibodies. Such antibodies may also be humanized or fully human monoclonal antibodies. The antibodies can exhibit one or more desirable functional properties, such as high affinity binding to hyaluronan synthase, ULK1, TNFa, IL-6 or JAK.
Methods and compositions described herein can include antibodies that bind hyaluronan synthase, ULK1, TNFa, IL-6 or JAK, or a combination of antibodies where each antibody type can separately bind hyaluronan synthase, ULK1, TNFa, IL-6 or JAK.
The term "antibody" as referred to herein includes whole antibodies and any antigen binding fragment (i.e., "antigen-binding portion") or single chains thereof. An "antibody" refers to a glycoprotein comprising at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds, or an antigen binding portion thereof. Each heavy chain is comprised of a heavy chain variable region (abbreviated herein as VH) and a heavy chain constant region. The heavy chain constant region is comprised of three domains, CHI, CH2 and CH3. Each light chain is comprised of a light chain variable region (abbreviated herein as VL) and a light chain constant region. The light chain constant region is comprised of one domain, CL- The VH and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR). Each VH and VL is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4. The variable regions of the heavy and light chains contain a binding domain that interacts with an antigen. The constant regions of the antibodies may mediate the binding of the immunoglobulin to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (Clq) of the classical complement system.
The term "antigen-binding portion" of an antibody (or simply "antibody portion"), as used herein, refers to one or more fragments of an antibody that retain the ability to specifically bind to an antigen (e.g., a peptide or domain of hyaluronan synthase, ULK1, TNFa, IL-6 or JAK). It has been shown that the antigen-binding function of an antibody can be performed by fragments of a full-length antibody. Examples of binding fragments encompassed within the term "antigen-binding portion" of an antibody include (i) a Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CHI domains; (ii) a F(ab')2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the VH and CHI domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al., (1989) Nature 341:544-546), which consists of a VH domain; and (vi) an isolated complementarity determining region (CDR). Furthermore, although the two domains of the Fv fragment, VL and VH, are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv (scFv); see e.g., Bird et al. (1988) Science 242:423-426; and Huston et al. (1988) Proc. Natl. Acad. Sci. USA 85:5879-5883). Such single chain antibodies are also intended to be encompassed within the term "antigen-binding portion" of an antibody. These antibody fragments are obtained using available techniques, and the fragments are screened for utility in the same manner as are intact antibodies.
An "isolated antibody," as used herein, is intended to refer to an antibody that is substantially free of other antibodies having different antigenic specificities (e.g., an isolated antibody that specifically binds hyaluronan synthase, ULK1, TNFa, IL-6 or JAK is substantially free of antibodies that specifically bind antigens other than a hyaluronan synthase, ULK1, TNFa, IL-6 or JAK). An isolated antibody that specifically binds hyaluronan synthase, ULK1, TNFa, IL-6 or JAK may, however, have cross-reactivity to related antigens, such as isoforms or variants of hyaluronan synthase, ULK1, TNFa, IL-6 or JAK from various humans or from other species. Moreover, an isolated antibody may be substantially free of other cellular material and/or chemicals.
The terms "monoclonal antibody" or "monoclonal antibody composition" as used herein refer to a preparation of antibody molecules of single molecular composition. A monoclonal antibody composition displays a single binding specificity and affinity for a particular epitope. The term human antibody, as used herein, is intended to include antibodies having variable regions in which both the framework and CDR regions are derived from human germline immunoglobulin sequences. Furthermore, if the antibody contains a constant region, the constant region also is derived from human germline immunoglobulin sequences. The human antibodies of the invention may include amino acid residues not encoded by human germline immunoglobulin sequences (e.g., mutations introduced by random or site-specific mutagenesis in vitro or by somatic mutation in vivo). However, the term "human antibody," as used herein, is not intended to include antibodies in which CDR sequences derived from the germline of another mammalian species, such as a mouse, have been grafted onto human framework sequences.
The term "human monoclonal antibody" refers to antibodies displaying a single binding specificity which have variable regions in which both the framework and CDR regions are derived from human germline immunoglobulin sequences. In one embodiment, the human monoclonal antibodies are produced by a hybridoma which includes a B cell obtained from a transgenic nonhuman animal, e.g., a transgenic mouse, having a genome comprising a human heavy chain transgene and a light chain transgene fused to an immortalized cell.
The term "recombinant human antibody," as used herein, includes all human antibodies that are prepared, expressed, created or isolated by recombinant means, such as (a) antibodies isolated from an animal (e.g., a mouse) that is transgenic or transchromosomal for human immunoglobulin genes or a hybridoma prepared therefrom (described further below), (b) antibodies isolated from a host cell transformed to express the human antibody, e.g., from a transfectoma, (c) antibodies isolated from a recombinant, combinatorial human antibody library, and (d) antibodies prepared, expressed, created or isolated by any other means that involve splicing of human immunoglobulin gene sequences to other DNA sequences. Such recombinant human antibodies have variable regions in which the framework and CDR regions are derived from human germline immunoglobulin sequences. In certain embodiments, however, such recombinant human antibodies can be subjected to in vitro mutagenesis (or, when an animal transgenic for human Ig sequences is used, in vivo somatic mutagenesis) and thus the amino acid sequences of the VL and Vn regions of the recombinant antibodies are sequences that, while derived from and related to human germline VL and Vn sequences, may not naturally exist within the human antibody germline repertoire in vivo.
As used herein, "isotype" refers to the antibody class (e.g., IgM or IgGl) that is encoded by the heavy chain constant region genes.
The phrases "an antibody recognizing an antigen" and "an antibody specific for an antigen" are used interchangeably herein with the term "an antibody which binds specifically to an antigen."
The term "human antibody derivatives" refers to any modified form of the human antibody, e.g., a conjugate of the antibody and another agent or antibody.
The term "humanized antibody" is intended to refer to antibodies in which CDR sequences derived from the germline of another mammalian species, such as a mouse, have been grafted onto human framework sequences. Additional framework region modifications may be made within the human framework sequences.
The term "chimeric antibody" is intended to refer to antibodies in which the variable region sequences are derived from one species and the constant region sequences are derived from another species, such as an antibody in which the variable region sequences are derived from a mouse antibody and the constant region sequences are derived from a human antibody.
As used herein, an antibody that "specifically binds to human hyaluronan synthase" or an antibody that "specifically binds to human ULK1" or an antibody that “specifically binds to TNFa” or an antibody that “specifically binds to IL-6” or an antibody that “specifically binds to JAK” is intended to refer to an antibody that binds to human hyaluronan synthase or ULK1 or TNFa or IL-6 or JAK with a KD of IxlO-7 M or less, 5xl0-8 M or less, IxlO-8 M or less, 5xl0-9 M or less, or between IxlO-8 M and IxlO 10 M or less.
The term "Kassoc" or "Ka," as used herein, is intended to refer to the association rate of a particular antibody-antigen interaction, whereas the term "Kdis" or "Kd," as used herein, is intended to refer to the dissociation rate of a particular antibody-antigen interaction. The term "KD," as used herein, is intended to refer to the dissociation constant, which is obtained from the ratio of Kd to Ka (i.e., Kd/ Ka) and is expressed as a molar concentration (M). KD values for antibodies can be determined using methods well established in the art. One method for determining the KD of an antibody is by using surface plasmon resonance, e.g., using a biosensor system such as a Biacore™ system. The antibodies of the invention are characterized by particular functional features or properties of the antibodies. For example, the antibodies bind specifically to human hyaluronan synthase, ULK1, TNFa, IL-6 or JAK. In one embodiment, an antibody of the invention binds to hyaluronan synthase, ULK1, TNFa, IL-6 or JAK with high affinity, for example with a KD of IxlO-7 M or less. The antibodies can exhibit one or more of the following characteristics:
(a) binds to human hyaluronan synthase, ULK1, TNFa, IL-6 or JAK with a KD of IxlO-7 M or less;
(b) inhibits the function or activity of hyaluronan synthase, ULK1, TNFa, IL-6 or JAK;
(c) inhibits cancer (e.g., metastatic cancer); or
(d) a combination thereof.
Assays to evaluate the binding ability of the antibodies toward hyaluronan synthase, ULK1, TNFa, IL-6 or JAK can be used, including for example, ELIS As, Western blots and RIAs. The binding kinetics (e.g., binding affinity) of the antibodies also can be assessed by standard assays known in the art, such as by Biacore™. analysis.
Given that each of the subject antibodies can bind to hyaluronan synthase, ULK1, TNFa, IL-6 or JAK the VL and Vn sequences or the respective antibodies can be "mixed and matched" to create other binding molecules that bind to hyaluronan synthase, ULK1, TNFa, IL-6 or JAK, respectively. The binding properties of such "mixed and matched" antibodies can be tested using the binding assays described above and assessed in assays described in the examples. When VL and VH chains are mixed and matched, a Vn sequence from a particular Vn I VL pairing can be replaced with a structurally similar Vn sequence. Likewise, a VL sequence from a particular Vn I VL pairing may be replaced with a structurally similar VL sequence.
Accordingly, in one aspect, the invention provides an isolated monoclonal antibody, or antigen binding portion thereof comprising:
(a) a heavy chain variable region comprising an amino acid sequence; and
(b) a light chain variable region comprising an amino acid sequence; wherein the antibody specifically binds hyaluronan synthase, ULK1, TNFa, IL-6 or JAK. In some cases, the CDR3 domain, independently from the CDR1 and/or CDR2 domain(s), alone can determine the binding specificity of an antibody for a cognate antigen and that multiple antibodies can predictably be generated having the same binding specificity based on a common CDR3 sequence. See, for example, Klimka et al., British J. of Cancer 83(2):252-260 (2000) (describing the production of a humanized anti-CD30 antibody using only the heavy chain variable domain CDR3 of murine anti-CD30 antibody Ki-4); Beiboer et al., J. Mol. Biol. 296:833- 849 (2000) (describing recombinant epithelial glycoprotein-2 (EGP-2) antibodies using only the heavy chain CDR3 sequence of the parental murine MOC-31 anti- EGP-2 antibody); Rader et al., Proc. Natl. Acad. Sci. U.S.A. 95:8910-8915 (1998) (describing a panel of humanized anti-integrin alphavbeta3 antibodies using a heavy and light chain variable CDR3 domain. Hence, in some cases a mixed and matched antibody or a humanized antibody contains a CDR3 antigen binding domain that is specific for hyaluronan synthase, ULK1, TNFa, IL-6 or JAK.
Expression Systems
Nucleic acid segments encoding one or more inhibitory nucleic acids, proteins (e.g., hyaluronidase), or antibodies can be inserted into or employed with any suitable expression system. Commercially useful and/or therapeutically effective quantities of one or more inhibitory nucleic acids, proteins (e.g., hyaluronidase), or antibodies can also be generated from such expression systems. In some cases, the expression systems can be used to express hyaluronidases. In some cases, the expression systems can be used to express inhibitory nucleic acids that can reduce endogenous hyaluronan synthase levels.
Recombinant expression of nucleic acids is usefully accomplished using a vector, such as a plasmid. The vector can include a promoter operably linked to nucleic acid segment encoding one or more of the hyaluronidase or an inhibitory nucleic acid for hyaluronan synthase nucleic acids, or other proteins (e.g., hyaluronidase), or antibodies.
The vector can also include other elements required for transcription and translation. As used herein, vector refers to any carrier containing exogenous DNA. Thus, vectors are agents that transport the exogenous nucleic acid into a cell without degradation and include a promoter yielding expression of the nucleic acid in the cells into which it is delivered. Vectors include but are not limited to plasmids, viral nucleic acids, viruses, phage nucleic acids, phages, cosmids, and artificial chromosomes.
A variety of prokaryotic and eukaryotic expression vectors suitable for carrying, encoding and/or expressing hyaluronidase, inhibitory nucleic acids, proteins, or antibodies can be used. A variety of prokaryotic and eukaryotic expression vectors suitable for carrying, encoding and/or expressing hyaluronidase, inhibitory nucleic acids, proteins, or antibodies can be employed. Such expression vectors include, for example, pET, pET3d, pCR2.1, pBAD, pUC, and yeast vectors. The vectors can be used, for example, in a variety of in vivo and in vitro situations.
The expression cassette, expression vector, and sequences in the cassette or vector can be heterologous. As used herein, the term "heterologous" when used in reference to an expression cassette, expression vector, regulatory sequence, promoter, or nucleic acid refers to an expression cassette, expression vector, regulatory sequence, or nucleic acid that has been manipulated in some way. For example, a heterologous promoter can be a promoter that is not naturally linked to a nucleic acid of interest, or that has been introduced into cells by cell transformation procedures. A heterologous nucleic acid or promoter also includes a nucleic acid or promoter that is native to an organism but that has been altered in some way (e.g. , placed in a different chromosomal location, mutated, added in multiple copies, linked to a non-native promoter or enhancer sequence, etc.). Heterologous nucleic acids may comprise sequences that comprise cDNA forms. Heterologous coding regions can be distinguished from endogenous coding regions, for example, when the heterologous coding regions are joined to nucleotide sequences comprising regulatory elements such as promoters that are not found naturally associated with the coding region, or when the heterologous coding regions are associated with portions of a chromosome not found in nature (e.g., genes expressed in loci where the protein encoded by the coding region is not normally expressed). Similarly, heterologous promoters can be promoters that at linked to a coding region to which they are not linked in nature.
Viral vectors that can be employed include those relating to lentivirus, adenovirus, adeno-associated virus, herpes virus, vaccinia virus, polio virus, AIDS virus, neuronal trophic virus, Sindbis and other viruses. Also useful are any viral families which share the properties of these viruses which make them suitable for use as vectors. Retroviral vectors that can be employed include those described in by Verma, I.M., Retroviral vectors for gene transfer. In Microbiology- 1985, American Society for Microbiology, pp. 229-232, Washington, (1985). For example, such retroviral vectors can include Murine Maloney Leukemia virus, MMLV, and other retroviruses that express desirable properties. Typically, viral vectors contain, nonstructural early genes, structural late genes, an RNA polymerase III transcript, inverted terminal repeats necessary for replication and encapsidation, and promoters to control the transcription and replication of the viral genome. When engineered as vectors, viruses typically have one or more of the early genes removed and a gene or gene/promoter cassette is inserted into the viral genome in place of the removed viral nucleic acid.
A variety of regulatory elements can be included in the expression cassettes and/or expression vectors, including promoters, enhancers, translational initiation sequences, transcription termination sequences and other elements. A “promoter” is generally a sequence or sequences of DNA that function when in a relatively fixed location in regard to the transcription start site. For example, the promoter can be upstream of the nucleic acid segment encoding one or more hyaluronidase, inhibitory nucleic acid, protein, or antibody.
A “promoter” contains core elements required for basic interaction of RNA polymerase and transcription factors and can contain upstream elements and response elements. “Enhancer” generally refers to a sequence of DNA that functions at no fixed distance from the transcription start site and can be either 5’ or 3' to the transcription unit. Furthermore, enhancers can be within an intron as well as within the coding sequence itself. They are usually between 10 and 300 by in length, and they function in cis. Enhancers function to increase transcription from nearby promoters. Enhancers, like promoters, also often contain response elements that mediate the regulation of transcription. Enhancers often determine the regulation of expression.
Expression vectors used in eukaryotic host cells (yeast, fungi, insect, plant, animal, human or nucleated cells) can also contain sequences for the termination of transcription, which can affect mRNA expression. These regions are transcribed as polyadenylated segments in the untranslated portion of the mRNA encoding tissue factor protein. The 3' untranslated regions also include transcription termination sites. The transcription unit may also contain a polyadenylation region. One benefit of this region is that it increases the likelihood that the transcribed unit will be processed and transported like mRNA. The identification and use of polyadenylation signals in expression constructs is well established. Homologous polyadenylation signals may be used in the transgene constructs.
The expression of one or more type of hyaluronidase, inhibitory nucleic acid, protein, or antibody from an expression cassette or expression vector can be controlled by any promoter capable of expression in prokaryotic cells or eukaryotic cells. Examples of prokaryotic promoters that can be used include, but are not limited to, SP6, T7, T5, tac, bla, trp, gal, lac, or maltose promoters. Examples of eukaryotic promoters that can be used include, but are not limited to, constitutive promoters, e.g., viral promoters such as CMV, SV40 and RSV promoters, as well as regulatable promoters, e.g., an inducible or repressible promoter such as the tet promoter, the hsp70 promoter and a synthetic promoter regulated by CRE. Vectors for bacterial expression include pGEX-5X-3, and for eukaryotic expression include pCIneo-CMV.
The expression cassette or vector can include nucleic acid sequence encoding a marker product. This marker product is used to determine if a vector or expression cassette encoding one or more hyaluronidase, inhibitory nucleic acid, protein, or antibody have been delivered to the cell and once delivered, is being expressed. Marker genes can include the E. coll lacZ gene which encodes P-galactosidase, and green fluorescent protein. In some embodiments the marker can be a selectable marker. When such selectable markers are successfully transferred into a host cell, the transformed host cell can survive if placed under selective pressure. There are two widely used distinct categories of selective regimes. The first category is based on a cell's metabolism and the use of a mutant cell line which lacks the ability to grow independent of a supplemented media. The second category is dominant selection which refers to a selection scheme used in any cell type and does not require the use of a mutant cell line. These schemes typically use a drug to arrest growth of a host cell. Those cells which have a novel gene would express a protein conveying drug resistance and would survive the selection. Examples of such dominant selection use the drugs neomycin (Southern P. and Berg, P., J. Molec. Appl. Genet. 1: 327 (1982)), mycophenolic acid, (Mulligan, R. C. and Berg, P. Science 209: 1422 (1980)) or hygromycin, (Sugden, B. et al., Mol. Cell. Biol. 5: 410-413 (1985)). Gene transfer can be obtained using direct transfer of genetic material, in but not limited to, plasmids, viral vectors, viral nucleic acids, phage nucleic acids, phages, cosmids, and artificial chromosomes, or via transfer of genetic material in cells or carriers such as cationic liposomes. Such methods are available in the art and readily adaptable for use in the method described herein. Transfer vectors can be any nucleotide construction used to deliver genes into cells (e.g., a plasmid), or as part of a general strategy to deliver genes, e.g., as part of recombinant retrovirus or adenovirus (Ram et al. Cancer Res. 53:83-88, (1993)). Appropriate means for transfection, including viral vectors, chemical transfectants, or physico-mechanical methods such as electroporation and direct diffusion of DNA, are described by, for example, Wolff, J. A., et al., Science, 247, 1465-1468, (1990); and Wolff, J. A. Nature, 352, 815-818, (1991).
For example, the nucleic acid molecules, expression cassette and/or vectors encoding one or more hyaluronidase, inhibitory nucleic acid, protein, or antibody can be introduced to a cell by any method including, but not limited to, calcium- mediated transformation, electroporation, microinjection, lipofection, particle bombardment and the like. The cells can also be expanded in culture and then administered to a subject, e.g. a mammal such as a human. The amount or number of cells administered can vary but amounts in the range of about 106 to about 109 cells can be used. The cells are generally delivered in a physiological solution such as saline or buffered saline. The cells can also be delivered in a vehicle such as a population of liposomes, exosomes or microvesicles.
In some cases, the transgenic cell can produce exosomes or microvesicles that contain nucleic acid molecules, expression cassettes and/or vectors expressing hyaluronidases, inhibitory nucleic acids, proteins, antibodies, or a combination thereof. In some cases, the transgenic cell can produce exosomes or microvesicles that contain nucleic acid molecules that encode one or more hyaluronidases, inhibitory nucleic acids, proteins, or antibodies to particular tissues. Microvesicles can mediate the secretion of a wide variety of proteins (e.g., hyaluronidase), lipids, mRNAs, and micro RNAs, interact with neighboring cells, and can thereby transmit signals, proteins (e.g., hyaluronidase), lipids, and nucleic acids from cell to cell (see, e.g., Shen et al., J Biol Chem. 286(16): 14383-14395 (2011); Hu et al., Frontiers in Genetics 3 (April 2012); Pegtel et al., Proc. NatT Acad Sci 107(14): 6328-6333 (2010); WG/2013/084000; each of which is incorporated herein by reference in its entirety. Cells producing such microvesicles can be used to provide one or more hyaluronidase, inhibitory nucleic acid, protein, or antibody.
Transgenic vectors or cells with a heterologous expression cassette or expression vector can express one or more hyaluronidase, inhibitory nucleic acid, protein, or antibody. Any of these vectors or cells can be administered to a subject. Exosomes produced by transgenic cells can also be used to administer one or more hyaluronidase, inhibitory nucleic acid, protein, or antibody to the subject. Compositions
The invention also relates to compositions containing PARP1 inhibitors and activated stromal I activated cancer-associated fibroblast inhibitors or inhibitors of TNFa, IL-6 or JAK. Such inhibitors can be small molecules, antibodies, polypeptides, inhibitory nucleic acids, nucleic acids encoding inhibitory nucleic acids, nucleic acids encoding a polypeptide (e.g., within an expression cassette or expression vector), or a combination thereof. The compositions can be pharmaceutical compositions. In some embodiments, the compositions can include a pharmaceutically acceptable carrier. By "pharmaceutically acceptable" it is meant that a carrier, diluent, excipient, and/or salt is compatible with the other ingredients of the formulation, and not deleterious to the recipient thereof.
The composition can be formulated in any convenient form. In some embodiments, the therapeutic agents of the invention (e.g., small molecules, inhibitory nucleic acids, nucleic acids encoding inhibitory nucleic acids, polypeptides, nucleic acid encoding polypeptides (e.g., within an expression cassette or expression vector), a compound identified by a method described herein, or a combination thereof), are administered in a “therapeutically effective amount.” Such a therapeutically effective amount is an amount sufficient to obtain the desired physiological effect, such a reduction of at least one symptom of cancer. For example, chemotherapeutic agents can reduce cell metastasis by 5%, or 10%, or 15%, or 20%, or 25%, or 30%, or 35%, or 40%, or 45%, or 50%, or 55%, or 60%, or 65%, or %70, or 80%, or 90%, 095%, or 97%, or 99%, or any numerical percentage between 5% and 100%. Symptoms of cancer can also include tumor cachexia, tumor-induced pain conditions, tumor-induced fatigue, tumor growth, and metastatic spread. Hence, the chemotherapeutic agents may also reduce tumor cachexia, tumor- induced pain conditions, tumor-induced fatigue, tumor growth, or a combination thereof by 5%, or 10%, or 15%, or 20%, or 25%, or 30%, or 35%, or 40%, or 45%, or 50%, or 55%, or 60%, or 65%, or %70, or 80%, or 90%, 095%, or 97%, or 99%, or any numerical percentage between 5% and 100%.
To achieve the desired effect(s), the therapeutic agents may be administered as single or divided dosages. For example, therapeutic agents can be administered in dosages of at least about 0.01 mg/kg to about 500 to 750 mg/kg, of at least about 0.01 mg/kg to about 300 to 500 mg/kg, at least about 0.1 mg/kg to about 100 to 300 mg/kg or at least about 1 mg/kg to about 50 to 100 mg/kg of body weight, although other dosages may provide beneficial results. The amount administered will vary depending on various factors including, but not limited to, the type of small molecules, compounds, polypeptides, antibodies, nucleic acids, or combinations thereof chosen for administration, the disease, the weight, the physical condition, the health, and the age of the mammal. Such factors can be readily determined by the clinician employing animal models or other test systems that are available in the art.
Administration of the therapeutic agents in accordance with the present invention may be in a single dose, in multiple doses, in a continuous or intermittent manner, depending, for example, upon the recipient's physiological condition, whether the purpose of the administration is therapeutic or prophylactic, and other factors known to skilled practitioners. The administration of the therapeutic agents and compositions of the invention may be essentially continuous over a preselected period of time or may be in a series of spaced doses. Both local and systemic administration is contemplated.
To prepare the composition, small molecules, compounds, polypeptides, nucleic acids, expression cassettes, and other agents are synthesized or otherwise obtained, purified as necessary or desired. These small molecules, compounds, polypeptides, antibodies, nucleic acids, expression cassettes, and other agents can be suspended in a pharmaceutically acceptable carrier and/or lyophilized or otherwise stabilized. The small molecules, compounds, polypeptides, nucleic acids, expression cassettes, other agents, and combinations thereof can be adjusted to an appropriate concentration, and optionally combined with other agents. The absolute weight of a given small molecule, compound, polypeptide, antibodies, nucleic acid, and/or other agents included in a unit dose can vary widely. For example, about 0.01 to about 2 g, or about 0.1 to about 500 mg, of at least one molecule, compound, polypeptide, nucleic acid, and/or other agent, or a plurality of molecules, compounds, polypeptides, nucleic acids, and/or other agents can be administered. Alternatively, the unit dosage can vary from about 0.01 g to about 50 g, from about 0.01 g to about 35 g, from about 0.1 g to about 25 g, from about 0.5 g to about 12 g, from about 0.5 g to about 8 g, from about 0.5 g to about 4 g, or from about 0.5 g to about 2 g.
Daily doses of the chemotherapeutic agents of the invention can vary as well. Such daily doses can range, for example, from about 0.1 g/day to about 50 g/day, from about 0.1 g/day to about 25 g/day, from about 0.1 g/day to about 12 g/day, from about 0.5 g/day to about 8 g/day, from about 0.5 g/day to about 4 g/day, and from about 0.5 g/day to about 2 g/day.
It will be appreciated that the amount of therapeutic agent for use in treatment will vary not only with the particular carrier selected but also with the route of administration, the nature of the cancer condition being treated and the age and condition of the patient. Ultimately the attendant health care provider can determine proper dosage. In addition, a pharmaceutical composition can be formulated as a single unit dosage form.
Thus, one or more suitable unit dosage forms comprising the therapeutic agent(s) can be administered by a variety of routes including parenteral (including subcutaneous, intravenous, intramuscular and intraperitoneal), oral, rectal, dermal, transdermal, intrathoracic, intrapulmonary and intranasal (respiratory) routes. The therapeutic agent(s) may also be formulated for sustained release (for example, using microencapsulation, see WO 94/ 07529, and U.S. Patent No.4,962,091). The formulations may, where appropriate, be conveniently presented in discrete unit dosage forms and may be prepared by any of the methods well known to the pharmaceutical arts. Such methods may include the step of mixing the therapeutic agent with liquid carriers, solid matrices, semi-solid carriers, finely divided solid carriers or combinations thereof, and then, if necessary, introducing or shaping the product into the desired delivery system. For example, the therapeutic agent(s) can be linked to a convenient carrier such as a nanoparticle, albumin, polyalkylene glycol, or be supplied in prodrug form. The therapeutic agent(s), and combinations thereof can be combined with a carrier and/or encapsulated in a vesicle such as a liposome.
The compositions of the invention may be prepared in many forms that include aqueous solutions, suspensions, tablets, hard or soft gelatin capsules, and liposomes and other slow-release formulations, such as shaped polymeric gels. Administration of inhibitors can also involve parenteral or local administration of the in an aqueous solution or sustained release vehicle.
Thus, while the therapeutic agent(s) and/or other agents can sometimes be administered in an oral dosage form, that oral dosage form can be formulated so as to protect the small molecules, compounds, polypeptides, nucleic acids, expression cassettes, and combinations thereof from degradation or breakdown before the small molecules, compounds, antibodies, polypeptides, inhibitory nucleic acids, nucleic acids encoding such polypeptides, and combinations thereof provide therapeutic utility. For example, in some cases the small molecules, compounds, inhibitory nucleic acids, polypeptides, nucleic acids encoding such polypeptide, antibodies, and/or other agents can be formulated for release into the intestine after passing through the stomach. Such formulations are described, for example, in U.S. Patent No. 6,306,434 and in the references contained therein.
Liquid pharmaceutical compositions may be in the form of, for example, aqueous or oily suspensions, solutions, emulsions, syrups or elixirs, dry powders for constitution with water or other suitable vehicle before use. Such liquid pharmaceutical compositions may contain conventional additives such as suspending agents, emulsifying agents, non-aqueous vehicles (which may include edible oils), or preservatives. The pharmaceutical compositions may take such forms as suspensions, solutions, or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Suitable carriers include saline solution, encapsulating agents (e.g., liposomes), and other materials. The chemotherapeutic agent(s) and/or other agents can be formulated in dry form (e.g., in freeze-dried form), in the presence or absence of a carrier. If a carrier is desired, the carrier can be included in the pharmaceutical formulation, or can be separately packaged in a separate container, for addition to the inhibitor that is packaged in dry form, in suspension or in soluble concentrated form in a convenient liquid.
Therapeutic agent(s) and/or other agents can be formulated for parenteral administration (e.g., by injection, for example, bolus injection or continuous infusion) and may be presented in unit dosage form in ampoules, prefilled syringes, small volume infusion containers or multi-dose containers with an added preservative. The compositions can also contain other ingredients such as chemotherapeutic agents, anti-viral agents, antibacterial agents, antimicrobial agents and/or preservatives. Examples of additional therapeutic agents that may be used include, but are not limited to: alkylating agents, such as nitrogen mustards, alkyl sulfonates, nitrosoureas, ethylenimines, and triazenes; antimetabolites, such as folate antagonists, purine analogues, and pyrimidine analogues; antibiotics, such as anthracy clines, bleomycins, mitomycin, dactinomycin, and plicamycin; enzymes, such as L-asparaginase; farnesyl-protein transferase inhibitors; hormonal agents, such as glucocorticoids, estrogens/antiestrogens, androgens/antiandrogens, progestins, and luteinizing hormone-releasing hormone anatagonists, octreotide acetate; microtubule-disruptor agents, such as ecteinascidins or their analogs and derivatives; microtubule-stabilizing agents such as paclitaxel (Taxol®), docetaxel (Taxotere®), and epothilones A-F or their analogs or derivatives; plant-derived products, such as vinca alkaloids, epipodophyllotoxins, taxanes; and topoisomerase inhibitors; prenyl-protein transferase inhibitors; and miscellaneous agents such as, hydroxyurea, procarbazine, mitotane, hexamethylmelamine, platinum coordination complexes such as cisplatin and carboplatin; and other agents used as anti-cancer and cytotoxic agents such as biological response modifiers, growth factors; immune modulators, and monoclonal antibodies. The compositions can also be used in conjunction with radiation therapy.
Treatment
The one or more PARP1 inhibitors and inhibitors of activated stromal I activated cancer-associated fibroblasts, TNFa, IE-6 or JAK are useful for selectively targeting tumors or treating cancers.
“Treatment” or “treating” refers to both therapeutic treatment, and prophylactic or preventative measures. Those in need of treatment include those already with the disorder as well as those prone to have the disorder, or those in whom the disorder is to be prevented.
“Subject” for purposes of treatment refers to any animal classified as a mammal or bird, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, horses, cats, cows, etc. In one embodiment, the subject is human. As used herein, the term “cancer includes solid animal tumors as well as hematological malignancies. The terms “tumor cell(s)” and “cancer cell(s)” are used interchangeably herein.
"Solid animal tumors" include cancers of the head and neck, lung, mesothelioma, mediastinum, lung, esophagus, stomach, pancreas, hepatobiliary system, small intestine, colon, colorectal, rectum, anus, kidney, urethra, bladder, prostate, urethra, penis, testis, gynecological organs, ovaries, breast, endocrine system, skin central nervous system; sarcomas of the soft tissue and bone; and melanoma of cutaneous and intraocular origin. In addition, a metastatic cancer at any stage of progression can be treated, such as micrometastatic tumors, megametastatic tumors, and recurrent cancers.
The term "hematological malignancies" includes adult or childhood leukemia and lymphomas, Hodgkin's disease, lymphomas of lymphocytic and cutaneous origin, acute and chronic leukemia, plasma cell neoplasm and cancers associated with AIDS.
The inventive methods and compositions can also be used to treat cancer of the breast, cancer of the lung, cancer of the adrenal cortex, cancer of the cervix, cancer of the endometrium, cancer of the esophagus, cancer of the head and neck, cancer of the liver, cancer of the pancreas, cancer of the prostate, cancer of the thymus, carcinoid tumors, chronic lymphocytic leukemia, Ewing's sarcoma, gestational trophoblastic tumors, hepatoblastoma, multiple myeloma, non-small cell lung cancer, retinoblastoma, or tumors in the ovaries. A cancer at any stage of progression can be treated or detected, such as primary, metastatic, and recurrent cancers. In some cases, metastatic cancers are treated but primary cancers are not treated. Information regarding numerous types of cancer can be found, e.g., from the American Cancer Society (cancer.org), or from, e.g., Wilson et al. (1991) Harrison's Principles of Internal Medicine, 12th Edition, McGraw-Hill, Inc.
In some embodiments, the cancer and/or tumors to be treated are prostate cancers, lung cancers, or breast cancers.
Treatment of, or treating, metastatic cancer can include the reduction in cancer cell migration or the reduction in establishment of at least one metastatic tumor. The treatment also includes alleviation or diminishment of more than one symptom of metastatic cancer such as coughing, shortness of breath, hemoptysis, lymphadenopathy, enlarged liver, nausea, jaundice, bone pain, bone fractures, headaches, seizures, systemic pain and combinations thereof. The treatment may cure the cancer, e.g., it may prevent metastatic cancer, it may substantially eliminate metastatic tumor formation and growth, and/or it may arrest or inhibit the migration of metastatic cancer cells.
Anti-cancer activity can reduce the progression of a variety of cancers (e.g., breast, lung, or prostate cancer) using methods available to one of skill in the art. Anti-cancer activity, for example, can determined by identifying the lethal dose (LD100) or the 50% effective dose (ED50) or the dose that inhibits growth at 50% (GI50) of an agent of the present invention that prevents the migration of cancer cells. In one aspect, anti-cancer activity is the amount of the agent that reduces 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99% or 100% of cancer cell migration, for example, when measured by detecting expression of a cancer cell marker at sites proximal or distal from a primary tumor site, or when assessed using available methods for detecting metastases.
In another example, PARP1 inhibitors and one or more inhibitors of activated stromal I activated cancer-associated fibroblasts, TNFa, IL-6 or JAK can be administered to sensitize tumor cells to immune therapies. By administering PARP1 inhibitors and one or more inhibitors of activated stromal I activated cancer- associated fibroblasts, TNFa, IL-6 or JAK, tumor cells can become more sensitive to the immune system and to various immune therapies.
The invention will be further described by the following non-limiting examples.
Example 1
Reduced p62 levels are associated with the induction of the cancer- associated fibroblast (CAF) phenotype, which promotes tumorigenesis in vitro and in vivo through inflammation and metabolic reprogramming. However, how p62 is downregulated in the stroma fibroblasts by tumor cells to drive CAF activation is an unresolved central issue in the field. As disclosed herein, tumor-secreted lactate downregulate p62 transcriptionally through a mechanism involving reduction of the NAD+/NADH ratio, which impaired poly (ADP-Ribose) -polymerase 1 (PARP1) activity. PARP1 inhibition blocked the poly(ADP-ribosyl)ation of the API transcription factors, c-FOS and c-JUN, which is an obligate step for p62 downregulation. Importantly, restoring p62 levels in CAFs by NAD+ rendered CAFs less active. PARP1 inhibitors, such as Olaparib, mimicked lactate in the reduction of stromal p62 levels, as well as the subsequent stromal activation both in vitro and in vivo, which suggests that therapies utilizing Olaparib would benefit from strategies aimed at inhibiting CAF activity.
The mechanisms whereby cancer cells promote the acquisition of the pro- tumorigenic CAF phenotype was investigated. As disclosed herein, the lactate secreted by tumor cells downregulates p62 at the transcriptional level to induce stromal activation. Lactate caused a reduction in the NAD+/NADH ratio that impaired Poly(ADP-ribose)polymerase 1 (PARP1) activity. The results demonstrate that NAD+ supplementation restored p62 levels and impaired CAF activation established the functional relevance of the lactate-PARPl axis for p62 downregulation and the generation of a reactive stroma conducive to malignancy. Furthermore, the fact that, PARP1 inhibitors used in the clinic, such as Olaparib, mimicked the effect of lactate in downregulating p62 and promoting CAF activity, reveals an unanticipated potential weakness of therapies based on PARP1 inhibitors, and suggest that reprogramming the stroma would enhance the anti-cancer effects of Olaparib.
Experimental Model and Subject Details Mice
Animal handling and experimental procedures conformed to institutional guidelines and were approved by the Sanford-Burnham-Prebys Medical Discovery Institute Institutional Animal Care and Use Committee, and by the Weill Cornell Medicine Institutional Animal Care and Use Committee. For Olaparib treatment experiments, 13 week-old male TRAMP+ mice (C57BL/6-Tg(TRAMP)8247Ng/J, stock No: 003135) were purchased from The Jackson Laboratory, (Bar Harbor, ME, USA). TRAMP+ mice were generated in a C57BL/6 background and were born and maintained under pathogen-free conditions. All genotyping was done by PCR. Age- matched mice were used for all experiments. For xenograft experiments, 7-week-old male JAX NSG mice (572NCG) were purchased from Charles River Labs (Wilmington, MA, USA). NSG mice were purchased and maintained under pathogen-free conditions. All mice were maintained on food and water ad libitum and were age-matched and co-housed for all experiments. Mice were sacrificed and prostate, tumors or other organs were collected for analysis.
Cell Lines WPMY-1 (sex: male), mNAF (sex: male), mHSC (sex: male), hNAF (sex: male), PC3 (sex: male), DU145 (sex: male), TRAMPC2 (sex: male), PrEC (sex: male), RWPE1 (sex: male), LNCAP (sex: male), HEK293T (sex: female) and Phoenix-GP (sex: female) cell lines were purchased from ATCC. WPMY-1, mNAF, mHSC, PC3, DU145, TRAMPC2, HEK293T and Phoenix-GP were cultured in Dulbecco’s Modified Eagles Medium (DMEM, Corning). LNCAP, PrEC and RWPE1 cells were cultured in Roswell Park Memorial Institute Medium (RPMI, Corning), hNAF cells were cultured in Fibroblast media (FM, ScienceCell Research Laboratories). All base mediums were supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine in an atmosphere of 95% air and 5% CO2. Androgen Deprivation Therapy conditions, cells were culture in RPMI media without phenol red (GIBCO) supplemented with 10% charcoal stripped FBS (F6765, Sigma), Glutamax and 100 U/mL penicillin 100 and 100 pg/mL streptomycin. Cultures were tested weekly for mycoplasma contamination.
Method Details
Xenograft Experiments
For mouse xenografts using PC3 PCa cells and sgC or sgAP-1 WPMY-1 stromal cells. 7 weeks old NSG mice were surgical castrated and let androgen levels drop for 10 days. Cells were trypsinized washed two times in PBS and resuspend in DMEN. IxlO6 PC3 and IxlO6 sgC or sgAP7-A WPMY-1 for each mouse were resuspended in 100 pl DMEM:Matrigel (1:1) and injected subcutaneously into both flanks of immunocompromised NSG mice (PC3 + sgC WPMY-1 n=4; PC3 + sgAP- 1 WPMY-1 n=4). Tumors were allowed to grow for 1 month. Mice were euthanized and tumors were collected and analyzed histologically. For Olaparib treatment in mouse xenografts. PC3 PCa cells and WPMY-1 stromal cells were trypsinized washed two times in PBS and resuspend in DMEN. IxlO6 PC3 and IxlO6 WPMY-1 for each mouse were resuspended in 100 pl DMEM:Matrigel (1:1) and injected subcutaneously into both flanks of immunocompromised NSG mice. Tumors were allowed to grow for 14 days, and mouse were randomly divided to receive vehicle, n=10, Olaparib (40 mg/kg, 2 days each week, i.p.), n=10 or Olaparib (40 mg/kg, 2 days each week, i.p.) +_PEGPH20 ( 0.0375 mg/Kg, 2 days each week, retroorbital injection) n=10. Tumors were measured twice a week. Mice were euthanized 14 days after the initiation of the treatment and tumors were collected and analyzed histologically. For Olaparib treatment in mice, 13 weeks-old male TRAMP+, n=18, were randomly distributed to receive vehicle, n=9, or Olapanb (40 mg/kg/, 5 days each week, i.p.), n=9. Mice were euthanized 1 month after the initiation of the treatment. Prostate and other organs were collected and analyzed histologically. Cell Culture Experiments
To simulate the amounts of lactate that accumulates in the tumor microenvironment as consequence of the Warburg effect, WPMY-1 cells were incubated in culture medium with or without lactic acidosis (24 mM of Lactic acid buffered to pH 6.7-6.8 with NaOH) for 48 hours. To avoid fluctuations in extracellular pH during the Lactate treatment, WPMY-1 cells were grown in a bicarbonate-free DMEM with 30 mM of HEPES in absence of CO2. To knock out PARP-1 in WPMY-1 cells, single-guide RNA sequences targeting PARP-1 exon2 were purchased from Synthego and transduced into WPMY-1 cells with recombinant Streptococcus pyogenes Cas9 protein (Truecut Cas9 Protein v2, Thermo), using the Neon Transfection System 1 (Invitrogen) following the manufacturer’ s protocol and single clones were expanded and screened by protein immunoblotting. To perform AP7 -A binding site editing in the SQSTM1 promoter in WPMY-1 cells, single-guide RNA sequences targeting the human APl-A binding site (Synthego) was transduced into cells with a Cas9 protein and a single-stranded donor oligonucleotide (ssODN, IDT) using Neon Electroporation System. Single clones were expanded and screened for AP7-A editing by Sanger sequencing. A point mutation to disrupt the API enhancer element in the p62 promoter was introduced by Site Directed Mutagenesis (Stratagene). Knockdown of MCT1, MCT4, FOS, PARP1, PARP2, CD38, ATG5, and SIRT1-7 genes in WPMY-1 cells were achieved by siRNA transfection using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen). Transient overexpression was achieved by transfection using X-tremeGENE HP transfection reagent (Roche). Transfected cells were examined 48 hours after transfection. Establishing stably GFP or RFP expressing cells was achieved by lentivirus-mediated transduction. Lentivirus were produced in HEK293T cells using X-tremeGENE HP transfection reagent (Roche). Viruscontaining supernatants were collected 48, 72 and 96 hours after transfection, filtered to eliminate cells, and supplemented with 8 pg/ml polybrene. Cells were infected with three rounds of viral supernatants and selected with puromycin (3 pg/ml). For autophagy or proteasome inhibition, WPMY-1 cells were treated for 12 hours with 100 nM bafilomycin Al or 12 hours with 20 pM of MG132, respectively, or vehicle (DMSO). For PARP1 inhibition, WPMY-1 cells were treated with PJ34 (2 days) or Olaparib (4 days) at the doses indicated in each experiment. For MCT1 inhibition, WPMY-1 cells were treated for 48 hours with 10 pM of AZD3965. For cJUN inhibition, WPMY-1 cells were treated for 48 hours with 10 pM of SP600125. For calpains and caspases inhibition, WPMY-1 cells were treated for 48 hours with 1-20 pM of Calpeptin (Tocris) or z-VAD-FMK (Tocris), respectively. For protein synthesis inhibition, WPMY-1 cells were treated with 50 pg/ml of cycloheximide (Sigma). Conditioned media (CM) was generated by collecting supernatant on day 3. CM was transferred to a 15 ml BD Falcon tube and centrifuged at 1300 rpm for 10 minutes. The supernatant was sterile filtered using a 22 mm filter (Millex-GV) with a 10 ml syringe barrel. The samples were stored at 20°C for future experiments. Fractionation of the CM was achieved using Amicon Ultra centrifugal filters (3KUltracel, Millipore). The supernatant was centrifuged at 4000 rpm for 1 hour. The supernatant fraction that was >3 kDa remained above the filter and that which was <3kDa passed through to the lower chamber. The >3 -kDa fraction was resuspended in DMEM to the pre-filtration volume.
Organotypic Cultures
Organotypic cultures were performed as described previously (Valencia et al., 2014). Briefly, gels were composed of one ml of a mixture of 1.75 volumes of Matrigel, 5.25 volumes of collagen type I, 1 volume of lx DMEM, 1 volume of lOx DMEM, and 1 volume of filtered FBS. The mixture was plated onto 24-well plates coated with diluted collagen type I. Gels were allowed to equilibrate with 1 ml of lx DMEM overnight at 37°C. 5 x 105 cells PCa cells and prostate stromal cells (50:50) were then seeded on top of the matrix. Gel rafts were placed onto collagen-coated nylon sheets and lifted using a sterile supporting steel mesh to set up a raised airliquid culture. Normal medium was changed in alternate days and organotypic cultures were allowed to grow for 14 days. Afterwards, organotypic gels were harvested, fixed in 10% neutral buffered formalin, bisected, and embedded in paraffin. H&E-stained sections were analyzed with a Zeiss light microscope supplemented with Axiovision40 software. Quantification of the invasion assays was performed as described previously (Valencia et al., 2014) using ImageProPlus software.
Migration and Invasion Assay For co-culture migration and invasion assays, 8xl04 WPMY-1 cells were plated onto the lower chamber of a 24 well plate in DMEN containing 10% FBS (basal conditions) or 10% charcoal stripped FBS (ADT conditions) and vehicle (DMSO) or Olaparib 10 pM or Olaparib 10 pM + PEGPH202.5 pg/ml for 48 hours. 5xl04 PC3 were seeded in a transwell chamber (Corning Biocoat control inserts) or in a transwell invasion chamber (Corning BioCoat Matrigel Invasion Chambers), both with 8 pm membrane. PC3 were allowed to migrate or invade for 20 hours at 37°C, 5% CO2. Cells were fixed in cold methanol and stained with crystal violet. Proliferation assay
WPMY-1 cells were cultured in DMEN containing 10% FBS (basal conditions) or 10% charcoal stripped FBS (ADT conditions), then the cells were treated with vehicle (DMSO), Olaparib 10 pM, Olaparib 10 pM + PEGPH202.5 pg/ml for 96 hours, refreshing media and stimuli at 48 hours, conditioned media (CM) was generated by collecting supernatant on day 4. PC3 cells were seeded in a black-walled well (Thermo Fisher) and serum starved overnight. CM from WPMY-1 cells was added to PC3 for 24 h. PC3 were exposed to EdU incorporation for the last 2 hours. Proliferating cells were detected using Click-iT EdU Alexa fluor 488 (Thermo Fisher) following the manufacturer’s instructions. Pictures were taken using EVOS M5000 Imaging System and EdU positive were measured using Fiji (Schindelin et al., 2012).
Co-culture assays
Co-culture assays were performed as described previously (Valencia et al., 2014). Briefly, stromal cells were seeded in TC-treated 6-well plates and allowed to attach for 6 hours before PCa cells were seeded on top of Milicell Cell Culture Inserts (Millipore). Inserts were then placed in the pre-seeded 6-well plate. For coculture experiments of PC3-GFP label with WPMY-1 cells, 500 PC3 and 1000 WPMY-1 were seeded in a 96 well plate in DMEN containing 10% FBS (basal conditions) or 10% charcoal stripped FBS (ADT conditions) and vehicle (DMSO) or Olaparib 5 pM for 10 days. Media and treatments were refresh every 48 hours. Pictures were taken using EVOS M5000 Imaging System and GFP positive were measured using Fiji (Schindelin et al., 2012).
Isotopic Labeling
WPMY-1 cells were cultured in DMEM (Cat. #5030, Sigma) medium supplemented with 10% FBS, 4 mM glutamine, 25 mM glucose, 30 mM HEPES, 10% FBS, 100 U/ml penicillin, and 100 pg/ml streptomycin in a humidified cell culture incubator at 37°C with no CO2. For isotopic tracing, cells were cultured for 48 hours in growth medium, medium was then changed to growth medium containing 10 mM [3-13C]lactate (Cat. # CLM-1578, Cambridge Isotopes) or 10 mM [2-2H]lactate (Cat. #693987, Sigma). Cells were cultured in tracer media for 24 hours. All media was adjusted to pH = 6.8.
Gas Chromatography-Mass Spectrometry (GC/MS)
Metabolites were extracted using a modified Bligh and Dyer method and analyzed as previously described in detail (Linares et al., 2017). Briefly, intracellular metabolites were extracted with 0.25 ml -20°C methanol, 0.1 ml 4°C cold water, and 0.25 ml -20°C chloroform. The extracts were vortexed for 10 minutes at 4°C and centrifuged at 16,000xg for 5 minutes at 4°C. The upper aqueous phase was evaporated under vacuum at -4°C, the lower organic phase under airflow. To determine labeling on lactate in cell culture media, 10 pl of medium was extracted with 90 pl of extraction buffer consisting of 8 parts (v/v) methanol and 1 part (v/v) water, centrifuged at 16,000xg for 5 minutes at 4°C, and 60 pl was dried under vacuum. Derivatization for polar metabolites was performed using a Gerstel MPS with 15 pl of 2% (w/v) methoxyamine hydrochloride (Thermo Scientific) in pyridine (incubated for 60 minutes at 45 °C) and 15 pl N-tertbutyldimethylsilyl-N- methyltrifluoroacetamide (MTBSTFA) with 1% tert-butyldimethylchlorosilane (Regis Technologies) (incubated further for 30 minutes at 45°C). Polar derivatives were analyzed by GC-MS using a DB-35MSUI column (30 m x 0.25 i.d. x 0.25 pm) installed in an Agilent 7890B gas chromatograph (GC) interfaced with an Agilent 5977B mass spectrometer (MS) operating under electron impact ionization at 70 eV. The MS source was held at 230°C, the quadrupole at 150°C, helium was used as carrier gas and the GC oven was held at 100°C for 1 minute, increased to 300°C at 10°C/minute, and held at 325°C for 3 minutes. Intracellular labeling on metabolites (corrected for natural abundance using in-house software) is depicted as 1-M0. YSI (yellow springs instrument) was used to quantify the concentration of media lactate and GC/MS to determine lactate labeling in cell culture media at 0 hours and after 24 hours of culture.
Measurement of NAD levels Quantification was carried out using the NAD/NADH quantification colorimetric kit (Cat. No. MAK037, Sigma) according to the manufacturer’s protocol. At least three independent measurements were carried out. Luciferase assay
Subconfluent cultures were transfected with Lipofectamine Plus (Invitrogen) with 100 ng of a SQSTM1 -luciferase reporter gene plasmid and 2 ng of the Renilla control reporter pRL-CMV (Promega). After 48 hours, cells were incubated with conditioned medium for 48 hours. The level of promoter activity was evaluated by determining the firefly luciferase activity relative to Renilla luciferase activity using the Dual Luciferase Assay System (Promega) according to the manufacturer’ s instruction.
Immunofluorescence analysis
WPMY-1 cells were seeded in coverslides and cultured in DMEN containing 10% FBS (basal conditions) or 10% charcoal stripped FBS (ADT conditions), then the cells were treated with vehicle (DMSO), Olaparib 10 pM, Olaparib 10 pM + PEGPH20 2.5 pg/ml for 96 hours, refreshing media and stimuli at 48 hours. Cells were fixed in PFA 4% for 20 minutes at room temperature, permeabilize and blocked following abeam’ s immunofluorescence protocol. Then, cells were incubated overnight with Hyaluronic acid binding protein (HABP) at 4°C. Cells were incubated with Alexa conjugated streptavidin and mounted in slides with mowiol. Pictures were taken by Zeiss LSM 710 NLO Confocal Microscope. Histological Analysis
Tissues from indicated mice were isolated, fixed in zinc buffered formalin overnight at 4°C, dehydrated, and embedded in paraffin. Sections (5 pm) were stained with hematoxylin and eosin (H&E). For immunohistochemistry, sections were deparaffinized, rehydrated, and then treated for antigen retrieval. After blocking in Protein Block Serum-Free solutions (DAKO), tissues were incubated with primary antibody overnight at 4°C followed by incubation with biotinylated secondary antibody. Endogenous peroxidase was quenched in 3% H2O2 in water for 10 minutes at room temperature. Antibodies were visualized with avidin-biotin complex (Vectastain Elite; Vector Laboratories) using diaminobenzidine as the chromogen. Stained sections were analyzed with a Zeiss light microscope supplemented with Zen 3.3 Bule edition software.
Immunoblotting Analysis Cells for protein analysis were lysed in RIPA buffer (20 mM Tns-HCl, 37 mM NaCh, 2 mM EDTA, 1% Triton-X, 10% glycerol, 0.1% SDS, and 0.5% sodium deoxycholate) with phosphatase and protease inhibitors. For immunoprecipitations, cells were lysed in IP lysis buffer (100 mM NaCl, 25 mM Tris, 1% Triton-X, 10% glycerol, with phosphatase and protease inhibitors) and immunoprecipitated with 25 pl of 50% slurry of protein Glutathione-Sepharose 4B beads (Bioworld). Immunoprecipitates were washed three times with lysis buffer, once with high salt (500 mM NaCl), and once more with lysis buffer. Protein concentration in lysates was determined by using Protein Assay Kit (Bio-Rad). Cell extracts and immunoprecipitated proteins were denatured, subjected to SDS-PAGE, transferred to PVDF membranes (GE Healthcare). After blocking with 5% nonfat dry milk in Tris-buffered saline and 0.1% Tween (TBS-T), the membranes were incubated with the specific antibodies (as listed in Key Resources Table) overnight at 4°C. After 2 hours incubation with the appropriate horseradish peroxidase-conjugated antibodies, the immune complexes were detected by chemiluminescence (Thermo Scientific) or Near-infrared fluorescence (LI-COR).
RNA extraction and Analysis
Total RNA from mouse tissues, cells and cultured organoids was extracted using the TRIZOL reagent (Invitrogen) and the RNeasy Mini Kit (QIAGEN), followed by DNase treatment. After quantification using a Nanodrop 1000 spectrophotometer (Thermo Scientific), RNA was either processed for RNA-seq or reverse-transcribed using random primers and MultiScribe Reverse Transcriptase (Applied Biosystems). Gene expression was analyzed by amplifying 20 ng of the complementary DNA using the CFX96 Real Time PCR Detection System with SYBR Green Master Mix (BioRad) and primers described in Table SI. The amplification parameters were set at 95 °C for 30 seconds, 58°C for 30 seconds, and 72°C for 30 seconds (40 cycles total). Gene expression values for each sample were normalized to the 18s RNA.
Chromatin immunoprecipitation Analysis
WPMY-1 cells were fixed by adding directly to the culture medium formaldehyde (HCHO; from a 37% HCHO-10% methanol stock, Calbiochem) to a final concentration of 1%. After, 20 minutes of incubation with 125 mM glycine, cells were washed with ice-cold phosphate-buffered saline (PBS) and lysed with in 50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS and protease inhibitors and incubated 30 minutes at 4 C. Chromatin was sheared in a COVARIS S220 Focused- ultrasonicator to yield DNA fragment sizes of 200-1000 base pairs, and diluted 10 times in dilution buffer (20 mM Tris pH 8.0, 2 mM EDTA, 1% triton X-100, 150 mM NaCl and protease inhibitors). Immunoprecipitations were carried out overnight at 4°C using the following protein A-antibodies complexes: cFOS, FOSB, cJUN, JUNB.
Immunocomplexes were washed three times with buffer TSEI (20 mM Tris pH 8.0, 2 mM EDTA, 1% triton X-100, 150 mM NaCl, 0.1% SDS and protease inhibitors), three washes with buffer TSEII (20 mM Tris pH 8.0, 2 mM EDTA, 1% triton X-100, 500 mM NaCl, 0.1% SDS and protease inhibitors), one wash with buffer TSEIII (10 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Deoxycholate and protease inhibitors) and one wash with TE pH 8.0. Immunocomplexes were extracted in TE containing 1% SDS, and protein-DNA cross-links were reverted by heating at 65 °C overnight. DNA was extracted by using a PCR purification kit (Qiagen). One-tenth of the immunoprecipitated DNA was used in each PCR, for which the promoter-specific primers were used. RNA-seq Preparation and Sequencing
Total RNA was extracted using Quick-RNA MiniPrep kit (Zymo Research). Libraries were prepared from 200 ng of total RNA using the QuantSeq 3’ mRNA- Seq Library Prep Kit FWD for Illumina from Lexogen, and optional UMIs (Vienna, Austria). Barcoded libraries were pooled, and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego CA). ATAC-Seq Library Preparation and Sequencing
The cell pellet was resuspended in 50 pl lysis buffer and then spun down 500 x g for 10 minutes at 4°C. The nuclei pellet was resuspended into 50 pl transposition reaction mixture containing Tn5 transposase from Nextera DNA Library Prep Kit (Illumina) and incubated at 37°C for 30 minutes. Then the transposase-associated DNA was purified using MinElute PCR purification kit (QIAGEN). To amplify the library, the DNA was first amplified for 5 cycles using indexing primer from Nextera kit and NEBNext High-Fidelity 2X PCR master mix. To reduce the PCR amplification bias, 5 pl of amplified DNA after the first 5 cycles was used to do qPCR of 20 cycles to decide the number of cycles for the second round of PCR. Usually, the maximum cycle of the second round of PCR is 5 cycles. Then the total amplified DNA was size selected to fragments less than 800 bp using SPRI beads. Quantification of the ATAC-seq library was done with QuBit. The size of the pooled library was examined by TapeStation. Barcoded ATAC-seq libraries were pooled and paired end sequenced (sX75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego, CA).
Prostate tissue digestion and IQx Library Preparation and Sequencing
Prostate lobes dissected and washed with cold PBS. Prostate tissue was gently minced with scissors and digested in Advance DMEN/F12 media (Gibco, Thermo Fisher) with 5 mg/ml Collagenase type II (Sigma) supplemented with Y27632 (Tocris) for 1 hour at 37°C. Cells were passed through a 70 pm strainer and centrifuge 5 minutes, 1000 rpm at 4°C. After that, cells were incubated with TrypLE Express (Gibco, Thermo Fisher) supplemented with Y27632 for 20 minutes in agitation at 37 °C to achieve a single cell suspension. TrypLE Express was quenched and washed with Advance DMEN/F12 media and then cells were centrifuged for 5 minutes, 1000 rpm at 4°C. Dead cells were removed by Annexin V (STEMCELL technologies). scRNA-seq libraries were generated using the Chromium Single Cell 30 Reagent Kit v2 (10X Genomics). Cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 2,000 cells per pl (Single Cell 3' library and Gel Bead Kit v.2) as described in the manufacturer’s protocol (lOx User Guide, Revision B). On average, approximately 8,000 cells were loaded. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were all performed as per the manufacturer’ s protocol. Individual sample quality was checked using a Bioanalyzer Tapestation (Agilent). Qubit was used for library quantification before pooling. The final library pool was sequenced on an Illumina NovaSeq6000 instrument using a S 1 flow cell. Bioinformatics Analysis
For RNA-Seq, sequencing Fastq files were uploaded to BaseSpace and processed with RNASeq Alignment App (Illumina) to obtain raw reads counts for each gene. For 3 ’RNA-Seq, read data was processed with the BlueBee Genomics Platform (BlueBee, San Mateo, CA). GenePattern (https://genepattern.broadinstitute.org/gp/pages/index.jsf) was used to collapse gene matrix files (CollapseDataset module) or to assess the statistical significance of differential gene expression (ComparativeMarkerSelection module for microarray data and DESeq2 module for RNA-seq data). Gene Set Enrichment Analysis (GSEA) was performed using GSEA v4.1.0 software (http://www.broadinstitute.org/gsea/index.jsp) using the default parameters, with customized signatures, using the default parameters with customized signatures. Preranked GSEA analysis was performed using default parameters with MSigDB c2.all.v7.0.symbols (C2) and c5.all.v7.0.symbols (C5) collections. Briefly, differential express genes between Olaparib treated cells and vehicle were obtain using DESeq2, genes were sorted by log2FC>±0.5 and padj>0.05. Ranked genes were used as input for GSEA Preranked analysis. For ATACSeq, FASTQ files from ATAC-seq reads were aligned to UCSC mmlO with Bowtie2 (bowtie2 -very- sensitive -x mmlO -1 FILE_merged_Rl.fastq -2 FILE_merged_R2.fastq -X 1000 -p 12 I samtools view -u - 1 samtools sort - > FILE.bam). Peak calling was performed with MACS2 with a threshold of q<0.05. Peaks were annotated with ChipSeeker R package. For motif enrichment analysis in the differential peaks between vehicle and Olaparib-treated cells, p-values were calculated using findMotifsGenome.pl with - size given, -len 6,8,10,12 and -mask program of HOMER v4.10.3. (Heinz et al., 2010) within 1-2 Kb from the TSS. Preranked GSEA analysis was performed using default parameters with MSigDB c2.all.v7.0.symbols (C2) and c5.all.v7.0.symbols (C5) collections. Briefly, differential express genes between Olaparib treated cells and vehicle were obtain using DESeq2, genes were sorted by log2FC>±0.5 and padj>0.05. Ranked genes were used as input for GSEA Preranked analysis. For ATACSeq, FASTQ files from ATAC-seq reads were aligned to UCSC mmlO with Bowtie2 (bowtie2 -very- sensitive -x mmlO -1 FILE_merged_Rl.fastq - 2 FILE_merged_R2.fastq -X 1000 -p 12 I samtools view -u - 1 samtools sort - > FILE.bam). Peak calling was performed with MACS2 with a threshold of q<0.05. Peaks were annotated with ChlPSeeker R package. For motif enrichment analysis in the differential peaks between vehicle and Olaparib-treated cells, p-values were calculated using findMotifsGenome.pl with -size given, -len 6,8,10,12 and -mask program of HOMER v4.10.3. (Heinz et al., 2010) within 1-2 Kb from the TSS. For scRNA-seq, raw sequence reads were quality-checked using FastQC software. The Cell Ranger version 2.1.1 software suite from 10X Genomics (https://support.10xgenomics.com/single-cell-gene- expression/software/downloads/latest) was used to process, align and summarize unique molecular identifier (UMI) counts against the mouse mmlO assembly reference genome analysis set, obtained from the University of California Santa Cruz (UCSC). Raw, unfiltered count matrices were imported into R for further processing. Raw UMI count matrices were filtered using the Seurat v 3.0 R package (Butler et al., 2018) to remove: barcodes with very low (empty wells) and very high (probably doublets) total UMI counts; matrices for which a high percentage of UMIs originated from mitochondrial features (more than 20%); and matrices for which fewer than 250 genes were expressed. Clustering was performed as follows: The percentage of mitochondrial features was a source of unwanted variation and was regressed out using the Seurat package. Dimensionality reduction was performed by principal component analysis and UMAP embedding with resolution 0.5. Cluster gene markers and differentially expressed genes between groups in each cluster were detected using the Wilcoxon Rank Sum test. CellPhoneDB analysis was performed using Cellphonedb method statistical analysis command.
Quantification and Statistical Analysis
All the statistical tests were justified for every figure. All samples represent biological replicates. Data are presented as the mean ± SEM. Statistical analysis was performed using GraphPad Prism 8 or R software environment (http://www.r- project.org/). Significant differences between groups were determined using a Student’s t-test (two-tailed) when the data met the normal distribution tested by D’Agostino test. If the data did not meet this test, a Mann- Whitney [/-test was used. Differences between more than 3 groups were determined using one-way ANOVA test (parametric) or Brown-Forsythe and Welch ANOVA tests (nonparametric) followed by Dunnett post hoc test. If the data did not meet this test, a Mann-Whitney test was used. Differences in Kaplan Meier plots were analyzed by Gehan-Breslow- Wilcoxon test. The chi-square test or Fisher’ s exact test was used to determine the significance of differences between covariates. Eogistic regression analysis was employed to estimate univariate and multivariate odds ratio and 95% confidence interval (CI). Values of p < 0.05 were considered as significantly different.
Table 1. Fist of primers used.
Figure imgf000073_0001
Figure imgf000074_0001
Figure imgf000075_0001
Table 2. List of siRNA oligonucleotides and guides.
Figure imgf000075_0002
Figure imgf000076_0001
Results
Prostate cancer cells secrete a soluble factor that reduces p62 expression in stromal fibroblasts To investigate how p62 expression is downregulated in the tumor stroma, an in vitro cell system was generated in which mouse GFP-labeled prostate stromal cells (mPSC) mixed with TRAMPC2 PCa epithelial cells were incubated. Analysis of GFP-positive stromal cells isolated by FACS sorting showed reduced Sqstml (coding for p62) mRNA levels in stromal cells upon incubation with tumor cells, which also correlated with an increase in bona-fide CAF markers, such as Tgfbl and Sdf-1 (FIG. 1A). To test whether the downregulation of p62 required cell contact between tumor and stromal cells, human prostate stromal fibroblasts (WPMY-1) were co-cultured with different PCa cell lines (PC3, TRAMPC2, and DU145) in a double-chamber setting. p62 was also downregulated at the protein and mRNA levels in stromal cells under these conditions (FIGs. IB and 1C), indicating that a soluble factor secreted by PCa epithelial cells was sufficient to downregulate p62 in stromal cells. In fact, incubation of stromal cells with conditioned media (CM) from PCa cells (PC3, TRAMPC2, DU145 or LNCAP) effectively reduced p62 protein and mRNA levels in stromal cells, without any effect by the CM from normal prostate epithelial cells (PrEC or RWEP1) (FIGs. ID and IE). To determine if the reduction in the mRNA amount of SQSTM1 was due to inhibited transcriptional activity, cells transfected with a luciferase reporter under the control of the SQSTM1 promoter (Duran et al., 2008) were used. PCa-conditioned media reduced the activity of the luciferase reporter (FIG. IF), strongly suggesting that the downregulation of stromal p62 by PCa epithelial cells is mediated through the repression of the SQSTM1 promoter in the stroma by a soluble factor secreted by epithelial tumor cells.
To identify this putative tumor-derived soluble factor, conditioned medium from PC3 cells was size-fractionated to separate molecules that were either less or more than 3 kDa in size, and the ability of either fraction to decrease the amount of stromal p62 was tested. Both the unfractionated tumor-conditioned medium and the <3 kDa fraction comparably downregulated p62 at the protein and mRNA levels in stromal fibroblasts (FIGs. 1G and 1H), as well as the activity of the SQSTM1 promoter-driven luciferase reporter (FIG. II). However, the >3 kDa fraction was totally inactive in these assays (FIGs. 1G-1I). The active soluble factor was heatstable (FIGs. 1J-L), which suggested that it could be a metabolite. Lactate downregulates p62 in stromal fibroblasts
Since cancer cells secrete large amounts of lactate that accumulates in the tumor microenvironment as a consequence of the Warburg effect (Vander Heiden et al., 2009), it was speculated that lactate could be a good candidate to be the tumor- derived factor responsible for the downregulation of p62 in stroma cells. Consistent with this hypothesis, it was found that the amount of lactate in the media of different PCa cell lines was higher than in the media of normal prostate epithelial cells (FIG. 2A). The cellular uptake of lactate is mediated by different monocarboxylate transporters (MCT1, MCT2, MCT3, and MCT4) (Halestrap, 2013). A prediction would be that blocking these transporters could alleviate the lactate-induced downregulation of p62. Notably, knockdown of MCT1, which controls lactate cellular import in WPMY-1 cells resulted in the inhibition of p62 downregulation induced by CM from PC3 cells (FIGs. 2B and 2C). Likewise, p62 downregulation in WPMY-1 cells by the same CM was abrogated when MCT4, which controls lactate export, was knocked-down in PC3 cells (FIGs. 2D and 2E). Furthermore, treatment with the MCT1 inhibitor, AZD3965, impaired p62 downregulation in WPMY-1 cells treated with PC3 CM (FIGs. 2F and 2G).
Together these results demonstrate that secretion of lactate by PCa cells and its uptake by stromal cells is a step in the stromal downregulation of p62. To demonstrate that lactate is sufficient to downregulate p62 in stromal cells, WPMY-1 cells were incubated with different concentrations of lactate for 24 hours or 48 hours, which resulted in the downregulation of p62 in a time (FIGs. 2H and 21) and dose-dependent (FIGs. 2J and 2K) manner. The amount of lactate necessary to downregulate p62 in stromal cells (FIGs. 2J and 2K) was similar to the secreted by PCa cells (FIG. 2A), and consistent with reported data from tumors in vivo (Walenta et al., 2000). MCTs are proton-coupled symporters, which explains why lactate- mediated downregulation of p62 was dependent on an acidic pH (FIG. 2L). However, the simple acidification of the culture media was not sufficient to downregulate p62 in stromal cells (FIG. 2L). These results demonstrated that lactate secreted by epithelial PCa cells impaired p62 expression in stromal cells at the transcriptional level. To rule out the potential contribution of a hypothetical role of p62 protein stability in the response to lactate, cycloheximide-treated cells were incubated with lactate and p62 protein levels analyzed. Lactate does not affect p62 stability (FIG. 10 A). In agreement with these results, inhibition of the proteasome (FIG. 10B), autophagy (FIGs. 10C and 10D), or cysteine proteases (FIGs. 10E and 10F) did not rescue the reduced p62 protein levels in lactate-treated WPMY-1 cells. API controls p62 downregulation by lactate
To unravel the mechanisms whereby lactate downregulates stromal p62, the chromatin accessibility landscape of WPMY-1 cells treated or not with lactate by genome-wide ATAC-seq (assay for transposase-accessible chromatin with high- throughput sequencing) was investigated. This analysis revealed a widespread decrease in chromatin accessibility in lactate-treated WPMY-1 cells (FIGs. 3A). HOMER (Hypergeometric Optimization of Motif EnRichment) analysis showed a significant enrichment of AP-1 transcription factors in the closed chromatin regions of lactate-treated cells (FIG. 3B). Analysis of the SQSTM1 promoter demonstrated the presence of three AP-1 regulatory sites that also showed reduced chromatin accessibility under lactate-treated conditions (FIG. 3C). Consistently lactate repressed an AP-1 -driven luciferase reporter (FIG. 3D), which collectively indicated that the repression of AP-1 sites in the SQSTM1 promoter could account for lactate effects in stromal p62 expression.
To establish the contribution of the different AP-1 sites in the SQSTM1 promoter, AP-1A, AP-1B, and AP-1C) were individually mutated and the impact of these mutations in the SQSTM1 promoter activity was determined by luciferase assay. Mutation of AP-1A completely inactivates the SQSTM1 promoter to levels comparable to those produced by lactate in the intact SQSTM1 promoter, whereas mutation of AP-1B, or AP-1C had no effect (FIG. 3E). These results demonstrate that AP-1 A is the important enhancer element in the SQSTM1 promoter and the most likely target of lactate-induced repressive effects. To test this hypothesis, in a more physiologically relevant system, the AP-1A element in the endogenous SQSTM1 promoter was selectively deleted using CRISPR/Cas9 editing to generate four independent WPMY-1 cell cultures (sgAP-lA), which resulted in the inhibition of mRNA and protein p62 expression (FIGs. 3F-H). These results establish the relevance of AP-1 A for the regulation of p62 expression in stromal cells. In keeping with this notion, chromatin immunoprecipitation (ChIP) analysis demonstrated that the recruitment of c-FOS and c-JUN, but not of FOSB or JUNB, to the AP-1A regulatory site was significantly decreased in stromal fibroblasts stimulated with lactate (FIG. 31). Consistently, the downregulation of c-FOS (FIGs. 3J and 3K) or the inhibition of c-JUN phosphorylation with a pharmacological inhibitor of JNK (FIGs. 3L and 3M), mimicked the effect of lactate on p62 expression both at the protein and mRNA levels. Overall, these data indicate that the impaired recruitment of a c-JUN/c-FOS AP-1 transcriptional complex plays a role in p62 downregulation by lactate in the stroma.
Reduction in NAD+ levels by lactate metabolism mediates p62 downregulation Lactate can be reversibly converted into pyruvate with the subsequent depletion of NAD+ levels in favor of the generation of NADH (Covarrubias et al., 2021). Importantly, increasing the levels of pyruvate in the culture media, which drives this reaction in the opposite direction, clearly impairs the ability of lactate to downregulate p62 (FIGs. 4A and 4B). Therefore, changes in the NAD /NADH ratio could be instrumental for the mechanisms of action of lactate on the regulation of p62 levels. Consistent with this hypothesis, NAD+ levels in stromal fibroblasts treated with lactate are lower than in untreated cells (FIG. 4C). Treatment with NAD+ or with the NAD+ precursor, nicotinamide riboside (NR), completely rescued the lactate-induced reduction in p62 (FIGs. 4D-4G).
PARP-1 inhibition by lactate downregulates p62 in stromal cells
NAD+ is a cofactor for three types of transcriptional and posttranslational modulators (Covarrubias et al., 2021). These include the sirtuins (SIRT1 through SIRT7), the cyclic ADP ribose synthases (CD38 and CD157), and the poly-ADP ribose transferases (PARP1/2). Interestingly, only the knockdown of PARP-1 fully mimicked the effect of lactate on p62 expression (FIGs. 5A-5E, FIGs. 11A and 11B). Moreover, treating WPMY-1 cells with the PARP-1 inhibitors PJ34 (FIGs. 5F and 5G) or Olaparib (FIGs. 5H and 51) also reduced the expression of p62 in a dose-dependent manner. Of note, Olaparib also induced autophagy activation as determined by LC3 lipidation (FIGs. 11D and HE). Since p62 is a substrate of autophagy, Olaparib impaired p62 expression at the mRNA and protein levels. Interestingly, co-treatment with the autophagy inhibitors (ULKi, SBI-0202965) reverted the Olaparib-induced activation of stroma in a dose dependent manner (Figure S2F), which suggest the use of autophagy inhibitors to overcome the stromal activation in response to PARP1 inhibitors.
PARP1, in addition to its well-known role in DNA damage repair, also controls many other biological processes including transcription (Feng et al., 2015). Thus, PARP-1 reportedly enhances the DNA binding and transactivation of many transcription factors (Gibson and Kraus, 2012). Of special relevance for this study, both c-FOS and c-JUN have been previously shown to be poly(ADP-ribosyl)ated by PARP-1, which increased their DNA binding activity (Huang et al., 2009). Consistently, Olaparib impaired the recruitment of c-FOS and c-JUN to the AP-1A binding site in the SQSTM1 promoter (FIGs. 5 J and 5K). Taken together, these results suggest that the regulation of PARP-1 activity by changes in the levels of NAD+ triggered by lactate metabolism in stromal cells is instrumental for p62 downregulation. Therefore, it was posited that lactate could affect the activation of PARP-1 and, consequently, the poly(ADP-ribosyl)ation of c-JUN and c-FOS. Consistently, lactate-treated cells have reduced total poly(ADP-ribosyl)ation levels (FIG. 5L), and immunoprecipitation experiments demonstrated that lactate impaired the poly(ADP-ribosyl)ation of c-JUN and c-FOS (FIGs. 5M and 5N). Adding NAD+ to lactate-treated cells rescued the poly(ADP-ribosyl)ation of both transcription factors (FIGs. 50 and 5P) and, importantly, their recruitment to the AP-1 regulatory site in the SQSTM1 promoter (FIGs. 5Q and 5R). Similar results were obtained by treating these cells with NR (FIGs. 5S and 5T). Taken together, these data demonstrate that depletion of NAD+ by lactate metabolism and the subsequent impairment of the poly(ADP-ribosyl)ation of c-FOS and c-JUN, underlies the mechanism whereby lactate triggers the downregulation of p62 in stromal fibroblasts.
AP-1 is important for CAF activation driven by p62 loss
The loss of p62 drives a CAF phenotype in stromal cells, which promoted tumor progression (Linares et al., 2017; Valencia et al., 2014). Because lactate secretion by PCa cells is necessary and sufficient to downregulate p62 in stromal cells, we next determined whether treating WPMY-1 cells with lactate drives them to a CAF phenotype. Treatment of WPMY-1 cells with lactate increased the expression of bona fide markers of CAF activation such as ACTA2 and TGF- (FIG. 6A), whose expression was reverted by NAD+ addition (FIG. 6B). Gene set enrichment analysis (GSEA) of genes differentially expressed in lactate-treated WPMY-1 cells showed enrichment in CAF signatures from a human stroma PCa data set (GSE34312) (FIG. 6C), validating the human relevance of these observations. Importantly, sgAP-lA fibroblasts in which the SQSTM1 promoter was endogenously inactivated (FIG. 3F) also showed increased expression of CAF markers (FIG. 6D). Consistently, experiments in a two-chamber co-culture system demonstrated that sgAP-lA but not sgC fibroblasts promoted the migration and invasion of PC3 cells (FIGs. 6E-6G). Similar results were obtained using a previously described 3D organotypic model that recapitulates key aspects of epithelial-stromal crosstalk in the tumor microenvironment (Valencia et al., 2014) (FIGs. 6H and 61). In keeping with the in vitro data, subcutaneous xenograft coimplantation of PC3 cells with sgAP-lA in immunodeficient mice (NSG), resulted in increased tumor growth when compared with those co-implanted with sgC fibroblasts (FIGs. 6J-6L). Notably, tumors generated with sgAP-lA fibroblasts showed increased markers of stromal activation, such as the augmented deposition of collagen and hyaluronan (HA), and the enhanced expression of aSMA (FIG. 6M). Collectively, these results establish that the AP-1 -regulatory site in the SQSTM1 promoter, which is the target of lactate-driven signals and has a pivotal role in the control of endogenous p62 levels in stromal cells, is important for the induction of the CAF phenotype.
PARP-1 inhibitors promote a desmoplastic response in stromal fibroblasts through p62
According to the model, lactate triggers the downregulation of p62 in stromal fibroblasts through PARP-1 inhibition. Therefore, it was hypothesized that PARP-1 inhibitors such as Olaparib would be sufficient to induce stromal activation. In agreement with this hypothesis, GSEA of RNAseq data from WPMY-1 fibroblasts, treated or not with Olaparib under basal or androgen deprivation (ADT) conditions, demonstrated enrichment of signatures corresponding to extracellular matrix remodeling, indicative of CAF activation (FIG. 7A), in Olaparib-treated cells, which correlated with well-established gene signatures for stromal activation in several types of cancers, including PCa (FIGs. 7B-7C). Consistently, Olaparib treatment reduced SQSTM1 mRNA levels and upregulated CAF markers such as ACTA2, SFRP1, TGF/3, MMP9 and the HA synthases in basal and ADT conditions (FIGs. 7D and 12 A). Similar results were obtained in different human and mouse prostate stromal cell lines and in hepatic stellate cells (FIGs. 12B-D), suggesting that the stromal activation by Olaparib treatment is a general phenotype not linked exclusively to the prostate stroma. Furthermore, ATAC-seq analysis of Olaparib- treated WPMY-1 cells revealed a strong decrease in chromatin accessibility across the genome, like what was observed with lactate treatment (FIGs. 3A and 7E). Also, consistent with previous findings in lactate-treated fibroblasts, motif enrichment analysis using HOMER showed a significant loss of chromatin accessibility in regions with consensus motifs for AP-1 transcription factors (FIGs. 3B and 7F). Close inspection of ATAC-seq data demonstrated reduce accessibility of the SQSTM1 promoter (FIG. 7G).
Interestingly, co-culture of PC3 cells with Olaparib-pretreated WPMY-1 cells resulted in increased migration and invasion of PCa cells under basal conditions that was even more pronounced in ADT conditions (FIGs. 7H-7J). Moreover, Olaparib-treated WPMY-1 CM led to increased PC3 proliferation (FIGs. 7K and 7L). Based on these observations, it was posited that stromal activation in response to Olaparib treatment could hamper its anti-tumor activity. To test this hypothesis, PC3 cells that were labelled with GFP (PC3GFP) were cultured either with (co-culture) or without (monoculture) WPMY-1 cells in basal or ADT conditions and treated or not with Olaparib for 10 days (FIG. 7M). Interestingly, coculture with WPMY-1 cells rendered PC3GFP cells more resistant to Olaparib as compared to treatment under monoculture conditions (FIG. 7N). This effect was even more apparent under ADT conditions (FIG. 7N). To investigate the pro-CAF phenotype of Olaparib in vivo, PC3 and WPMY-1 cells were co-implanted in NSG mice and then treated either with vehicle or Olaparib (FIG. 70). In vivo Olaparib treatment efficiently reduced tumor growth (FIGs. 7P-7R), consistent with previous reports (Li et al., 2017; Zhang et al., 2018), but also produced a strong desmoplastic response, characterized by enhanced collagen and HA deposition and increased expression of aSMA and reduced p62 levels (FIGs. 7S and 7T).
Single cell analysis of stromal activation and epithelial remodeling in response to Olaparib in vivo
To investigate how the treatment with Olaparib triggered the creation of a more activated, protumorigenic microenvironment in PCa, scRNAseq was performed using 10X Genomics Chromium platform on TRAMP+ prostate tumors after treatment with Olaparib for 4 weeks as compared to vehicle controls (FIG. 8A). Consistent with the results in the xenograft model (FIGs. 7O-7T), in vivo treatment of TRAMP+ mice induced a strong desmoplastic response in the prostate (FIG. 8B). Furthermore, unsupervised clustering identified epithelial cells as well as stromal and immune cells with selective markers for each population (FIG. 8C). Consistent with the in vitro data of stromal activation, there was an expansion of the stromal and immune populations in response to Olaparib treatment (FIGs. 8C and 8D). Further re-clustering of the fibroblast compartment identified six clusters, all enriched in CAF signatures (FIG. 8E). Clusters 0 and 2 correspond to the inflammatory CAF subtype (iCAF), whereas clusters 3 and 5 express myofibroblast markers (myCAF). Cluster 3 displayed high levels of two CD44 ligands, Collal and Sppl, while cluster 5 expresses Acta2. Interestingly, cluster 1 has features of both iCAF and myCAF and is enriched in growth factors and inflammatory cytokines as well as EMT markers and constitutes the subpopulation with the lowest levels of p62/ Sqstml. Cluster 4 is enriched in Rspo3 and resembled the mesenchymal cell population termed Mes2, previously described in scRNAseq analysis of normal mouse and human prostates (Karthaus et al., 2020). Importantly, differential expressed gene analysis identified Hasl, Spinkl and Tgfb2 among the most upregulated transcripts in the Olaparib-treated fibroblast population (FIG. 8F). Hasl is a hyaluronan (HA) synthase, one of the three enzymes that synthesize HA, which has been linked to tumor promotion, therapy resistance, and poor outcomes in various tumors, including PCa (Aaltomaa et al., 2002; Lipponen et al., 2001; Toole, 2004; Toole and Slomiany, 2008). Also, recent reports point to a role of HAS- expressing fibroblasts in the promotion of metastatic spreading (Affo et al., 2021). These data are in good agreement with the results in human prostate stromal cells and in in vivo mouse models, in which increased deposition of HA upon Olaparib treatment was found. Notably, Hasl and Has3 were upregulated in Olaparib-treated WPMY in both basal and ADT conditions (FIG. 8G). Of great relevance, SPINK1 (Serine Peptidase Inhibitor, Kazal type 1) expression in PCa has been associated with poor response to ADT, faster progression to the castrate-resistant stage and cancer-associated mortalities (Johnson et al., 2016; Leinonen et al., 2010; Tomlins et al., 2008). Moreover, recent reports showed increased tumor Spinkl levels in response to AR-targeted therapies (Tiwari et al., 2020) and in prostate stroma after chemotherapy (Chen et al., 2018). The present results show that SPINK1 levels were highly upregulated in human prostate cells under ADT conditions (FIG. 8G) and, more importantly, in tumor stroma in vivo in Ola-treated mice (FIG. 8H). Tgfb2 is one of the ligands of the TGFP pathway, which has been long recognized to exert opposing roles in cancer progression but that it is an important component of reactive stromas (Lu et al., 2017; Massague, 2008). While TGFP signaling blocks tumorigenesis in primary PCa (Bjerke et al., 2014), it can promote PCa bone metastasis (Fournier et al., 2015) and has been recently associated with resistance to enzalutamide in scRNAseq studies of metastatic CRPC patients (He et al., 2021). Furthermore, anti-TGFP therapies have been proposed to reduce the development and progression of bone metastasis and to enhance the efficacy of immune checkpoint therapy in metastatic CRPC (Jiao et al., 2019). Consistent with enhanced TGFP markers in our scRNAseq data, increased levels of Tgfbl were found in both basal and ADT conditions in WPMY cells (FIG. 8G). Altogether these results are of great significance for PCa therapy since they identified regulators in the stroma whose therapeutic targeting impairs Ola-induced stromal activation and increases Ola anti-tumor efficacy. A question that is still to be determined is the precise impact that Olaparib- mediated stromal activation has in the tumor epithelium. To address this question, the scRNAseq data of the PCa tumor epithelial compartment (FIGs. 8I-8K) was interrogated. Of potential relevance, Olaparib treatment completely abolished the neuroendocrine cluster 2 (NE1; FIGs. 8I-8K), supporting the concept that neuroendocrine tumors display enhanced sensitivity to the treatment with Olaparib (Liu et al., 2019; Zhang et al., 2018). However, Olaparib also expanded several other epithelial clusters: Cluster 0 is a luminal population; cluster 1 is a basal population; clusters 3 and 4 that are luminal but express high levels of EMT markers such as Vimentin (Vim) and Acta 2; and cluster 5 is a new neuroendocrine population that, in contrast to cluster 2, highly expresses the neuronal marker Synaptophysin (Syp), in addition to luminal and EMT markers (FIGs. 81 and 8J). Importantly, the Olaparib-treated tumor epithelium showed increased AR, EMT and TGFP signaling, which suggests potential mechanisms of resistance to Olaparib therapy (FIG. 8L). Consistent with enrichment in TGFP signaling signature in Olaparib-treated epithelial cells, there was an increased pSMAD2 staining, an established marker of TGFP activation, in Olaparib-treated prostates (FIG. 8M). Moreover, identification of ligand-receptor interactions between the stromal and epithelial populations by CellPhoneDB analysis revealed changes in receptors for HAS 1/2 in Olaparib-treated populations (FIG. 8N); these included gaining novel CD44-mediated pairs between the stromal populations and the different clusters of tumor cells. Of note, CD44 is a receptor of HA that integrates extracellular matrix cues with growth factor and cytokine signals (Misra et al., 2015; Orian-Rousseau and Sleeman, 2014; Ponta et al., 2003). The data showed that Olaparib increased the HAS1/2-CD44 pairs, but also promoted the interaction of CD44 with other growth-factor receptors, such as FGFR2 or HBEGF (FIG. 8N). There was also gain of multiple interactions of the TGFP receptor family and their ligands (FIG. 8N) that could account for the increased TGFP signaling and EMT phenotype observed in tumor cells in Olaparib conditions. In this regard, binding of HA induces clustering of CD44 and the complex formation with other receptors (including the receptors for TGFP), which serve to further reinforce the activation of these pathways.
Co-targeting the stroma increases Olaparib anti-tumor activity Based on the data that Olapanb induces stromal activation, it was hypothesized that strategies targeting the stroma could improve the efficacy of Olaparib as an anti-tumor therapy. Since treatment with Olaparib induces an HA- rich stroma, and HA can be degraded by PEGPH20, a clinical-grade recombinant hyaluronidase (provided by Halozyme Therapeutics), it was tested whether treatment with PEGPH20 could revert Olaparib-induced stroma activation and enhance its anti-tumor activity. As shown in FIG. 9A, PEGPH20 efficiently degraded HA deposition in response to Olaparib treatment in WPMY-1 cells, in basal and ADT conditions (FIG. 9A). More importantly, PEGPH20 completely blocked the enhanced migration of PC3 cells in response to conditioned media from Olaparib-treated WPMY-1 cells under basal and ADT conditions (FIGs. 9B and 9C). Moreover, PEGPH20 also blocked Olaparib-induced proliferation in stromal cells (FIGs. 9D and 9E). Likewise, treatment with Galunisertib, a TGFPR inhibitor, completely abolished the stromal proliferation induced by Olaparib (FIGs. 9D and 9E). These results indicate that strategies aimed at targeting the stroma could normalize the stromal activation promoted by Olaparib. Consistent with this notion, the in vivo data showed that co-treatment with PEGPH20 enhanced Olaparib antitumor activity (FIGs. 9F and 9G). Collectively, these results demonstrate that combination therapies co-targeting the activated stroma could increase the efficacy of PARP inhibitor therapies such as Olaparib. Discussion
Despite recent advances in the characterization of the heterogeneity of fibroblast populations in the tumor stroma and the mounting evidence on their role in tumor progression, the molecular mechanisms that control stromal activation by the tumor epithelium remain largely unknown. Here, tumor-secreted lactate was identified as the main signal from the epithelium that activates tumor fibroblasts by downregulating p62. Previous work has shown that p62 is a stromal tumor suppressor whose downregulation in fibroblasts is a key event for CAF activation (Duran et al., 2016; Goruppi and Dotto, 2013; Linares et al., 2017; Valencia et al., 2014). However, the mechanisms whereby p62 is downregulated by the tumor in the stroma were not understood. p62 regulation is subjected to a fine-tune balance between transcription and post-translational mechanisms that control its degradation by autophagy or the proteosome machinery (Moscat and Diaz-Meco, 2009; Moscat et al., 2016). Herein, it was shown that lactate modulates p62 at the transcriptional level. Thus, although lactate reportedly induces autophagy (Brisson et al., 2016), which can contribute to lactate effects in tumor cells and the stroma, we show here that blocking autophagy or the proteosome failed to prevent p62-downregulation by lactate. At the transcriptional level, p62 has been shown to be regulated by several transcription factors including API, NRF2, NF-kB and TFEB under different conditions (Duran et al., 2008; Jain et al., 2010; Ling et al., 2012; Park et al., 2019). The AP-1 binding site in the p62 promoter was identified as the element accounting for lactate-mediated p62 downregulation. Interestingly, these findings are reminiscent of previously published data showing that AP-1 was also the major transcription factor for Ras-induced p62 mRNA expression in the tumor epithelium (Duran et al., 2008), which suggests that AP-1 is a hot spot for the upregulation of p62 by oncogenic transformation in the epithelium and its downregulation in the stroma. Regarding the composition of the AP-1 transcription factors mediating this effect in the stroma, the data demonstrate that c-FOS and c-JUN complexes are important since their recruitment to the p62 promoter was impaired in lactate-treated cells, whereas no changes were observed in the binding of FOSB and JUNB. This is interesting because JUNB has recently been shown to be key in the repression of p62 in keratinocytes (Sukseree et al., 2021), which suggests that different AP-1 proteins play distinct roles in p62 regulation under different cellular contexts.
Lactate has been considered for years as just the end product of glycolysis and as such, a metabolic waste (Ippolito et al., 2019). However more recent evidence has recognized many new roles for lactate including its relevance as a carbon source for cellular metabolism, and potential new functions as a signaling molecule in the TME (Brooks, 2018; Ippolito et al., 2019). Lactate is produced from pyruvate and is exported to the TME, where it can reach high concentrations of up to 40 rnM, especially in tumor tissues (Walenta et al., 2000). Most tumor cells can engage in secretion and utilization of lactate depending on the context and extracellular microenvironment (Brooks, 2018). In addition to the shuttling that can take place among different tumor cells, lactate accumulation in the TME has significant effects on the non-malignant compartment, including, as shown here, on the activation of the fibroblasts surrounding the tumor, which results in their acquisition of the CAF phenotype (Bhagat et al., 2019). Therefore, targeting lactate metabolism as a potential therapeutic approach needs to integrate its effects not only on the tumor cell but also in the TME. Lactate dehydrogenase catalyzes the conversion of lactate into pyruvate. This results in the reduction of NAD+ cellular levels, which is an important metabolic and signaling cofactor that impacts multiple functions, often dysregulated in cancer (Chini et al., 2021; Fang et al., 2017). Herein it was shown that low NAD+ levels, as consequence of lactate conversion to pyruvate, is central to the ability of lactate to downregulate p62 in fibroblasts and their subsequent conversion into CAF. Our data demonstrating that supplementation with NAD+ precursors, such as NR, rescued p62 levels and reverted the CAF phenotype, established that altering the cell NAD+/NADH ratio could be a mechanism to modulate stromal activation. In keeping with this notion, downregulation of nicotinamide phosphoribosyl transferase (NAMPT), a rate-limiting enzyme in NAD+ synthesis, has been shown to promote renal and lung fibrosis with increased collagen deposition and ECM remodeling (Muraoka et al., 2019). Furthermore, recent evidence demonstrated that stromal nicotinamide N-methyl transferase (NNMT), an enzyme that impairs NAD+ biosynthesis by depleting its precursor N-nicotinamide, induces CAF differentiation and cancer progression (Eckert et al., 2019). All these evidences are of potential relevance because they strongly suggest that the stromal activation promoted by NAD+ inhibition could limit the efficacy of anti-cancer therapies targeting NAD+ biosynthesis, such as NAMPT inhibitors, and could explain their reported limited efficacy in vivo (Galli et al., 2020). Supplementation with NR has been studied extensively and its dietary administration is considered safe and effective to increase NAD+ levels (Martens et al., 2018). NR supplements are proposed to ameliorate inflammation and metabolic dysfunction in aging, and there is a renewed interest in the potential of NAD-boosting therapies to treat human diseases (Chini et al., 2021; Fang et al., 2017). Based on the present data, an additional benefit of increasing NAD+ levels might be to reprogram the stroma back to a less activated phenotype by restoring p62 levels. However, the role of NAD+ in cancer is complex and manipulating its levels could be a double-edged sword (Chini et al., 2021; Fang et al., 2017). Thus, increasing the NAD+/NADH ratio by administering nicotinamide mononucleotide (NMN), another NAD+ precursor, has been shown to have a protumorigenic effect in K-Ras-driven pancreatic cancer (Nacarelli et al., 2019), unveiling the complexity of these therapeutic approaches.
The work herein identified PARP-1 inhibition as the key target of the reduced NAD+ levels in the transcriptional downregulation of p62 by lactate. PARP1 is the major isoform of the PARP enzyme family and, like the other PARPs, its PARylation activity impacts multiple biological processes with a main dual function in DNA damage repair (DDR) and transcriptional regulation (Feng et al., 2015; Gibson and Kraus, 2012). Most of the therapeutic strategies using PARP inhibitors rely on their blockade of DDR and the creation of synthetic lethality in combination with genetic defects in homologous recombination-mediated repair (Farmer et al., 2005; Lord and Ashworth, 2017; McCabe et al., 2006), which are the basis for the treatment of patients with BRCA1- and BRCA2-associated cancers (Mateo et al., 2019). The use of PARP inhibitors has been most successfully exploited in BRCAl/2-deficient breast and ovarian cancers (Sonnenblick et al., 2015), and recently Olaparib has been approved for the treatment of mCRPC in patients with DDR gene mutations (de Bono et al., 2020; Hussain et al., 2020). However, the fact that the percentage of mCRPC patients with these mutations that could benefit from that type of therapy is a minority has led to new efforts for combinatorial strategies by chemically inducing DDR (Li et al., 2017; Zhang et al., 2018). Most of these efforts have been focused on the direct effect of PARP inhibitors on the tumor cell, and much less is known on how the tumor stroma responds to this type of treatment. The present data, showing that lactate inhibits PARP activity, and that PARP-1 knockdown downregulates p62 through the impaired PARylation of AP-1 transcription factors, resulting in CAF activation, might have important therapeutic implications. The results also highlight the increasingly recognized role of PARP1 in transcriptional regulation as a key mechanism of action beyond its role in DDR (Feng et al., 2015; Liu et al., 2019), and identify an unanticipated function for these inhibitors in the activation of the pro-tumorigenic potential of the tumor stroma. These data are consistent with the previously reported protumorigenic phenotype of PARP 1 KO mice in the context of the TRAMP+ model, indicating the dominant protumorigenic role of the TME in PCa progression under conditions of PARP1 deficiency (Pu et al., 2014). This is an important finding because CAF activation in the TME by PARP inhibitors might limit or even blunt their therapeutic efficacy. Therefore, a better understanding of the fundamental mechanisms controlling the activation of the stromal has the potential to identify vulnerabilities that can improve cancer therapies.
Example 2
Methods In vivo experiments
For Olaparib treatment in mice, 13 weeks-old male TRAMP+/FVB were surgical castrated, after 10 days n=16, were randomly distributed to receive vehicle, n=8, or Olaparib n=8 (5 mg/kg/, 5 days each, i.p.). Mice were euthanized 3 weeks after the initiation of the treatment. Prostate and other organs were collected and analyzed histologically.
For the metastasis model, caudal artery injection was performed with 500000 RMl-BoMe3 -RFP-Luc prostate cancer epithelial cells in 150 pl of PBS n=10 in 8- week-old C57B16 male mice. After 1-week luciferase was visualized using IVIS to detect signal in the lower limbs and in less frequently in visceral organs, mice with signal were randomly distributed to receive vehicle, n=5, or Olaparib n=5 (40 mg/kg/, 5 days each, i.p.). After 3 weeks, mice were euthanized and ex-vivo IVIS was performed in lower limbs, vertebrae, and visceral organs to detect metastasis sites. Tissues were collected and analyzed histologically.
Bone in culture
8-week-old C57B16 male mice were euthanized, and lower limb bone were collected. Femur epiphyses were dissected and fragmented in 4 pieces by sterilized micro dissecting scissors. Bone pieces were aligned into low-attachment 96-well plates pre-loaded with 200 pL DMEM/F12 supplemented with 5% charcoal striped FBS for ADT conditions. Bone pieces were treated with DMSO or Olaparib 20 pM for 48 h and then 5000 RMl-BoMe3 -RFP-Luc cells were seed on top of the bone pieces. After 48 hours, pictures were taken using EVOS M5000 Imaging System and RFP+ positive areas were measured using Fiji.
Stromal-induced activation by PARP inhibitors in other cancers beyond prostate cancer
Olaparib (Ola) downregulated p62 expression, a master regulator of CAFs activation, in stromal cell lines from different tissue origins, including prostate, lung, breast or endometrium (FIGs. 13A-13D). These results demonstrate that the stromal activation induced by PARP inhibitors is a general mechanism taking place not only in the prostate stroma but also in stromal cells from other types of cancer. Consistent with these results, gene set enrichment analysis (GSEA) of RNAseq data of BRCA deficient breast tumors treated with the PARP inhibitor Talazoparib (gene dataset GEO:GSE125206) showed significant enrichment of signatures of stromal activation (FIG. 13E). Similar enrichment in signatures of stromal activation was observed in GSEA of RNAseq data from a PDX model of high grade serous ovarian cancer treated with niraparib (FIG. 13F). These results support the notion that co-targeting the stroma enhances the efficacy of PARP inhibitors in other types of cancer beyond prostate cancer, such as breast and ovarian cancer, where this therapy is approved especially for BRCA deficient tumors.
Blocking inflammatory signals reverts stromal activation by PARP inhibitors
To further characterize the molecular mechanisms involved in the stromal activation by PARP inhibitors, RNAseq data of human prostate fibroblasts treated with Ola was analyzed by GSEA. Interestingly, a significant enrichment was found in inflammatory signaling pathways mediated by inflammatory cytokines such as TNFa and IL-6 and the activation of the JAK-STAT cascade (FIG. 11A). Importantly, similar results were found in the analysis of other datasets of two different in vivo models of breast and ovarian tumors, treated with two different PARP inhibitors, Talazoparib and Niraparib (FIG. 11B). These results indicate that the activation of these inflammatory pathways is a general signaling mechanism in response to PARP inhibitors, regardless the tumor type. Therefore, it was investigated whether blocking these inflammatory pathways could revert the stromal activation mediated by PARP inhibitors. To do that, fibroblasts were treated with Ola in the presence or absence of a JAK inhibitor, Lestaurtinib (FIG. 11C). Of note, incubation with Lestaurtinib and Ola reduces the expression of HAS3, HAS2 and IL6 induced by Ola (FIG. 11D). More importantly, conditioned media from fibroblasts treated with the Lestaurtinib and Ola combination completely blocks the proliferation of cancer cells induced by Ola-treated stromal cells, as determined by Edu (5-ethynyl-2'-deoxyuridine) incorporation (FIG. HE). Similar results were obtained with conditioned media was incubated with anti-IL6 or anti-TNFa antibodies. These results demonstrate that the inflammatory response mediated by TNFa, IL-6 and JAK activation are important events for the stromal activation by PARP inhibitors and that strategies to therapeutically target these signaling cascades could enhance the efficacy of PARP inhibitors. Therefore, the data support the clinical use of combinations of PARP inhibitors and therapies blocking TNFa, IL6 or JAK to improve the clinical response to PARP inhibition in cancer.
PARP inhibitors induce stromal activation in metastatic sites
Since Ola is approved for the treatment of human metastatic castrationresistant prostate cancer (mCRPC), it was investigated whether Ola was able to induce stromal activation not only in the prostate but also in metastatic sites. Treatment with Ola of castrated TRAMP+/FVB Fl mice, which have a high incidence of spontaneous metastasis in lymph nodes, showed increased aS MA expression and higher hyaluronan (HA) deposition in metastatic lymph nodes from Ola-treated mice as compared to those from vehicle-treated mice (FIGs. 15A and 15B). Furthermore, analysis of bones from these mice demonstrated higher levels of HA in surrounding bone marrow stromal cells and in the growth plate of Ola-treated mice (FIG. 15C). These in vivo mouse data demonstrate that Ola treatment remodels the stromal niche not only in the prostate but also in metastatic sites such as lymph nodes or bone. This remodeling of the metastatic niche could support metastatic growth and predispose these sites to further metastasis seeding. To test this hypothesis, bone-in-culture- arrays (BICA) were used to model bone colonization of cancer cells in ex vivo cultures. Mouse fragmented epiphysis and metaphysis of hindlimb bones were treated with Ola in androgen-deprivation conditions (ADT) prior to the seed of luciferase-modified RM1 prostate cancer cells. Of note, Ola significantly increased the seeding of cancer cells onto the bone (FIGs. 15D and 15E). In addition, analysis of mouse bone marrow stromal cell cultures isolated from in vivo Ola-treated TRAMP+ mice showed enhanced expression of markers of stromal activation such as Acta2 and of the HA synthase Has2, which is important for HA production (FIG. 15F). Likewise, in vitro Ola treatment of bone marrow stromal cells also showed increased expression of markers of TGFP family (Tgfb3 and Tgfb2) and Has3 (FIG. 15G). These results demonstrate that Ola treatment promotes stromal activation in the bone, which predisposes the bone niche to the seed of metastatic cancer cells. Moreover, deposition of HA was observed in other metastatic sites such as liver after treatment with Ola of mice in an in vivo metastasis model of injection via caudal artery of metastatic cancer cells (FIG. 151). Also, analysis of bone metastasis treated with Ola demonstrated an increased activation of TGFP signaling as shown by enhanced nuclear pSMAD2 in cancer cells (FIG. 15J). These observations support clinical studies of combinatorial therapy of PARP inhibitors with TGFP inhibition. To further strengthen the human relevance of these observations, paired biopsies of bone metastasis from a mCRPC patient pre- and post-treatment with Ola were analyzed. Importantly, there was a robust increase in HA deposition in the Ola-treated bone metastasis consistent with our mouse data (FIG. 15K). References
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All patents and publications referenced or mentioned herein are indicative of the levels of skill of those skilled in the art to which the invention pertains, and each such referenced patent or publication is hereby specifically incorporated by reference to the same extent as if it had been incorporated by reference in its entirety individually or set forth herein in its entirety. Applicants reserve the right to physically incorporate into this specification any and all materials and information from any such cited patents or publications.
The following statements are intended to describe and summarize various embodiments of the invention according to the foregoing description in the specification.
Statements:
1. A method comprising administering to a subject in need thereof a composition comprising one or more PARP1 inhibitors and one or more inhibitors of activated stromal I activated cancer-associated fibroblasts or one or more inhibitors of TNFalpha, IL6 or JAK.
2. The method of statement 1, wherein the subject has cancer or is suspected of a having cancer.
3. The method of statement 1 or 2, wherein the subject has primary cancer, metastatic cancer, or recurrent cancer.
4. The method of statement 1, 2 or 3, wherein the subject has cancer of the breast, cancer of the lung, cancer of the adrenal cortex, cancer of the cervix, cancer of the endometrium, cancer of the esophagus, cancer of the head, cancer of the neck, cancer of the liver, cancer of the pancreas, cancer of the prostate, cancer of the thymus, carcinoid tumors, chronic lymphocytic leukemia, Ewing's sarcoma, gestational trophoblastic tumors, hepatoblastoma, multiple myeloma, non-small cell lung cancer, retinoblastoma, or tumor in the ovaries.
5. The method of any of statements 1-4, wherein the one or more PARP1 inhibitors are olaparib (Lynparza), niraparib (Zejula), rucaparib (Rubraca), talazoparib (Talzenna), veliparib (ABT-888), or a combination thereof.
6. The method of any of statements 1-5, wherein the one or more inhibitors of activated stromal I activated cancer-associated fibroblasts include hyaluronan (HA) synthase inhibitors, hyaluronan build-up inhibitors (e.g., PEGylated Recombinant Human Hyaluronidase, PEGPH20), autophagy inhibitors (e.g., ULK inhibitors), fibroblast activation protein alpha (FAPa) inhibitors, GW4064 (farnesoid X receptor (FXR) agonists, Pirfenidone (PDF) combined with doxorubicin, SMO-inhibitors (e.g., vismodegib, sonidegib), amphiregulin inhibitors, CXCE12 antagonists (e.g., an E5 antagonistic peptide), DDR2 inhibitors (e.g., WRG-28, which is a small molecule inhibitor of DDR2), or a combination thereof.
7. The method of any of statements 1-6, wherein the composition comprises Olaparib and PEGPH20.
The specific methods and compositions described herein are representative of preferred embodiments and are exemplary and not intended as limitations on the scope of the invention. Other objects, aspects, and embodiments will occur to those skilled in the art upon consideration of this specification and are encompassed within the spirit of the invention as defined by the scope of the claims. It will be readily apparent to one skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention.
The invention illustratively described herein suitably may be practiced in the absence of any element or elements, or limitation or limitations, which is not specifically disclosed herein as essential. The methods and processes illustratively described herein suitably may be practiced in differing orders of steps, and the methods and processes are not necessarily restricted to the orders of steps indicated herein or in the claims.
As used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to “a nucleic acid” or “a protein” or “a cell” includes a plurality of such nucleic acids, proteins, or cells (for example, a solution or dried preparation of nucleic acids or expression cassettes, a solution of proteins, or a population of cells), and so forth. In this document, the term “or” is used to refer to a nonexclusive or, such that “A or B” includes “A but not B,” “B but not A,” and “A and B,” unless otherwise indicated.
Under no circumstances may the patent be interpreted to be limited to the specific examples or embodiments or methods specifically disclosed herein. Under no circumstances may the patent be interpreted to be limited by any statement made by any Examiner or any other official or employee of the Patent and Trademark Office unless such statement is specifically and without qualification or reservation expressly adopted in a responsive writing by Applicants.
The terms and expressions that have been employed are used as terms of description and not of limitation, and there is no intent in the use of such terms and expressions to exclude any equivalent of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention as claimed. Thus, it will be understood that although the present invention has been specifically disclosed by preferred embodiments and optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the appended claims and statements of the invention.
The invention has been described broadly and generically herein. Each of the narrower species and subgeneric groupings falling within the generic disclosure also form part of the invention. This includes the generic description of the invention with a proviso or negative limitation removing any subject matter from the genus, regardless of whether or not the excised material is specifically recited herein. In addition, where features or aspects of the invention are described in terms of Markush groups, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group.

Claims

WHAT IS CLAIMED IS:
1. A method comprising administering to a subject in need thereof one or more PARP1 inhibitors and one or more inhibitors of activated stromal/activated cancer- associated fibroblasts or one or more modulators of TNFalpha, IL6 or JAK.
2. The method of claim 1 wherein the subject is a human.
3. The method of claim 1 or 2, wherein the subject has cancer or is suspected of a having cancer.
4. The method of claim 1, 2 or 3, wherein the subject has primary cancer, metastatic cancer, or recurrent cancer.
5. The method of any one of claims 1 to 4, wherein the subject has cancer of the breast, cancer of the lung, cancer of the adrenal cortex, cancer of the cervix, cancer of the endometrium, cancer of the esophagus, cancer of the head, cancer of the neck, cancer of the liver, cancer of the pancreas, cancer of the prostate, cancer of the thymus, carcinoid tumors, chronic lymphocytic leukemia, Ewing's sarcoma, gestational trophoblastic tumors, hepatoblastoma, multiple myeloma, non-small cell lung cancer, retinoblastoma, or tumor in the ovaries.
6. The method of any one of claims 1 to 5, wherein the one or more PARP1 inhibitors are olaparib (Lynparza), niraparib (Zejula), rucaparib (Rubraca), talazoparib (Talzenna), veliparib (ABT-888), or a combination thereof.
7. The method of any one of claims 1 to 6, wherein the one or more inhibitors of activated stromal I activated cancer-associated fibroblasts include hyaluronan (HA) synthase inhibitors, hyaluronan build-up inhibitors, autophagy inhibitors, fibroblast activation protein alpha (FAPa) inhibitors, GW4064 (farnesoid X receptor (FXR) agonists, Pirfenidone (PDF) combined with doxorubicin, SMO-inhibitors, amphiregulin inhibitors, CXCL12 antagonists, DDR2 inhibitors, or a combination thereof.
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8. The method of claim 7, wherein the DDR2 inhibitor comprises WRG-28.
9. The method of claim 7, wherein the hyaluronan build-up inhibitor comprises PEGylated Recombinant Human Hyaluronidase, PEGPH20.
10. The method of claim 7, wherein the autophagy inhibitor comprises a ULK inhibitor.
11. The method of claim 7, wherein the SMO inhibitor comprises vismodegib or sonidegib.
12. The method of claim 7, wherein the CXCL12 antagonist comprises an E5 antagonistic peptide.
13. The method of any one of claims 1 to 6, wherein the Olaparib and PEGPH20 are administered.
14. The method of any one of claims 1 to 13, wherein the one or more PARP1 inhibitors are administered before the one or more inhibitors of activated stromal/activated cancer-associated fibroblasts or one or more modulators of TNFalpha, IL6 or JAK.
15. The method of any one of claims 1 to 13, wherein the one or more PARP1 inhibitors are administered after the one or more inhibitors of activated stromal/activated cancer-associated fibroblasts or one or more modulators of TNFalpha, IL6 or JAK.
16. The method of any one of claims 1 to 13, wherein the one or more PARP1 inhibitors are administered concurrently with the one or more inhibitors of activated stromal/activated cancer-associated fibroblasts or one or more modulators of TNFalpha, IE6 or JAK.
17. The method of any one of claims 1 to 13, wherein a composition comprises the one or more PARP1 inhibitors are administered before the one or more inhibitors
99 of activated stromal/activated cancer-associated fibroblasts or one or more modulators of TNFalpha, IL6 or JAK.
18. The method of any one of claims 1 to 17, wherein the one or more PARP1 inhibitors are injected.
19. The method of any one of claims 1 to 18, wherein the one or more inhibitors of activated stromal/activated cancer-associated fibroblasts or one or more modulators of TNFalpha, IL6 or JAK are injected.
20. The method of any one of claims 1 to 17, wherein the one or more PARP1 inhibitors are systemically administered.
21. The method of any one of claims 1 to 17 or 20, wherein the one or more inhibitors of activated stromal/activated cancer-associated fibroblasts or one or more modulators of TNFalpha, IL6 or JAK are systemically administered.
22. The method of any one of claims 1 to 21, wherein the JAK inhibitor comprises lesataurtinib, baricitinib, tofacitinib, upadacitinib, filgonitib, delgocitinib, deucravacitinib, LS104, ON044580,NVP-BBT594, or NVP-CHZ868.
23. The method of any one of claim 1 to 22, wherein the IL6 inhibitor comprises an antibody or an antigen binding portion thereof.
24. The method of claim 23, wherein the antibody comprises tocilizumab, sarilumab, siltuximab, olokizumab, elsilimomab, clazakizumab, sirukumab, levimumab, CPS 1-2364.
25. The method of any one of claim 1 to 24, wherein the IL6 inhibitor comprises ARGX-109, FE301 or FMlOl.
26. The method of any one of claim 1 to 25, wherein the TNFalpha inhibitor comprises adalimumab, certolizumab pegol, etanercept, golimumab, or infliximab.
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27. A composition comprising one or more PARP1 inhibitors and one or more inhibitors of activated stromal/activated cancer-associated fibroblasts or one or more modulators of TNFalpha, IL6 or JAK.
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