WO2024103313A1 - Thérapie anticancéreuse basée sur le ciblage d'irg1 - Google Patents

Thérapie anticancéreuse basée sur le ciblage d'irg1 Download PDF

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WO2024103313A1
WO2024103313A1 PCT/CN2022/132360 CN2022132360W WO2024103313A1 WO 2024103313 A1 WO2024103313 A1 WO 2024103313A1 CN 2022132360 W CN2022132360 W CN 2022132360W WO 2024103313 A1 WO2024103313 A1 WO 2024103313A1
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combination
binding antagonist
irg1
monocytes
macrophages
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PCT/CN2022/132360
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English (en)
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Yue Xiong
Dan YE
Leilei Chen
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Fudan University
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    • 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 [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/40—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against enzymes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
    • C12N5/06—Animal cells or tissues; Human cells or tissues
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
    • C12N5/10—Cells modified by introduction of foreign genetic material
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies

Definitions

  • the instant application contains a Sequence Listing which has been submitted electronically in XML format.
  • the . xml file contains a sequence listing entitled "P2022-2424xlb. xml” created on Nov 16, 2022 and having a size of 133 KB.
  • the sequence listing contained in this . xml file is part of the specification and is herein incorporated by reference in its entirety.
  • the present invention relates to combinations and therapeutic methods comprising genetically modified macrophages, monocytes, or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown, in combination with a PD-1 axis binding antagonist.
  • the invention further provides combinations and therapeutic methods comprising an aconitate decarboxylase 1 (ACOD1) inhibitor, in combination with a PD-1 axis binding antagonist.
  • ACOD1 aconitate decarboxylase 1
  • the invention further provides associated methods of treatment, pharmaceutical compositions and uses thereof.
  • Macrophages are important immunoregulatory cells in the tumor microenvironment (TME) and play a key role in tumor immunity and response to immunotherapy. Macrophages undergo metabolic reprogramming and perform a multitude of functions in response to microenvironmental signals, which drive the acquisition of polarized programs containing two extreme forms: the “classical” (or M1-polarized) macrophages that produce pro-inflammatory mediators and are involved in the responses of type I helper T (Th1) cells, and the “alternative” (or M2-polarized) macrophages that produce anti-inflammatory mediators to support angiogenesis and are involved in Th2-type responses (S.K. Biswas &A. Mantovani, Macrophage plasticity and interaction with lymphocyte subsets: cancer as a paradigm, Nat Immunol. 11 (10) : 889-96 (2010) ) .
  • Tumor-associated macrophages are the most abundant leukocytes in tumor stroma and are derived from recruited inflammatory monocytes or tissue-resident macrophages (R. A. Franklin, et al., The cellular and molecular origin of tumor-associated macrophages, Science 344 (6186) : 921-5 (2014) ; Q. Lahmar, et al., Tissue-resident versus monocyte-derived macrophages in the tumor microenvironment, Biochim Biophys Acta. 1865 (1) : 23-34 (2016) ) . Beyond the classical “M1-M2” binary system, TAMs exhibit strong dynamics and plasticity and influence nearly all stages of tumor development, including angiogenesis (C.
  • TAMs Both the numbers of TAMs and their phenotype influences tumorigenesis. More insight into the molecular and functional diversity of the tumor macrophage compartment is required to identify distinct subsets and to define pro-tumorigenic TAMs in specific tumors. This has primed interest in developing function-based therapies targeting TAM-reprogramming, including eliciting M1-like polarization (M. De Palma, et al., Tumor-targeted interferon-alpha delivery by Tie2-expressing monocytes inhibits tumor growth and metastasis, Cancer Cell. 14 (4) : 299-311 (2008) ; Z.
  • Macrophages undergo dramatic metabolic reprogramming in the presence of pathogens and under inflammatory conditions.
  • itaconic acid ITA
  • ACOD1 aconitate decarboxylase responsible for the decarboxylation of the Kreb cycle intermediate cis-aconitate
  • IRG1 immune responsive gene 1
  • IRG1/ITA anti-inflammatory function of IRG1/ITA has been implicated in preclinical models of sepsis, viral infections, psoriasis, gout, ischemia/reperfusion injury, and pulmonary fibrosis
  • L.L. Chen, et al. Itaconate inhibits TET DNA dioxygenases to dampen inflammatory responses, Nat Cell Biol. 24 (3) : 353-363 (2022) ;
  • B. P. Daniels, et al. The Nucleotide Sensor ZBP1 and Kinase RIPK3 Induce the Enzyme IRG1 to Promote an Antiviral Metabolic State in Neurons, Immunity 50 (1) : 64-76. e4 (2019) ; C.J.
  • ITA acts an SDH inhibitor, which results in succinate accumulation and metabolic reprogramming (T. Cordes, et al., Immunoresponsive Gene 1 and Itaconate Inhibit Succinate Dehydrogenase to Modulate Intracellular Succinate Levels, J Biol Chem. 291 (27) : 14274-14284 (2016) ; V. Lampropoulou, et al., Itaconate Links Inhibition of Succinate Dehydrogenase with Macrophage Metabolic Remodeling and Regulation of Inflammation, Cell Metab. 24 (1) : 158-66 (2016) ) .
  • ITA can also alkylate protein cysteine residues, which induces the electrophilic stress response mediated by NRF2 and I ⁇ B ⁇ (M. Bambouskova, et al., (2016) ; E.L. Mills, et al., Itaconate is an anti-inflammatory metabolite that activates Nrf2 via alkylation of KEAP1, Nature 556 (7699) : 113-117 (2016) ) and impairs aerobic glycolysis (W. Qin, et al., S-glycosylation-based cysteine profiling reveals regulation of glycolysis by itaconate, Nat Chem Biol. 15 (10) : 983-991 (2019) ) .
  • IRG1/Irg1 knockout was reported to impair the antibacterial ability of macrophages in vitro, suggesting itaconate may be useful in treating bacterial infections.
  • Itaconate is a lysosomal inducer that promotes antibacterial innate immunity. Mol Cell, (2022) ) .
  • ITA which is structurally similar to ⁇ -ketoglutaric acid ( ⁇ KG) , binds to and inhibits ⁇ KG-dependent TET DNA demethylases, thereby downregulating NF- ⁇ B and STAT target genes to dampen the inflammatory response in macrophages and restricts M1-like TAM polarization (L.L. Chen, et al., (2022) ) .
  • IRG1/ITA was also induced in peritoneal tissue-resident macrophages from peritoneal tumors (J.M. Weiss, et al., Itaconic acid mediates crosstalk between macrophage metabolism and peritoneal tumors, J Clin Invest. 128 (9) : 3794-3805 (2016) ) .
  • GEMs genetically engineered macrophages
  • Macrophages in which metabolic pathway genes KEAP1 (Kelch-like ECH-associated protein 1) and ACOD1 were knocked out have been recently reported as regulating macrophage polarization and tumor killing efficiency (Chinese Patent Application No. 114657212A) .
  • CAR-Ms Human chimeric antigen receptor macrophages
  • iPSC induced pluripotent stem cell
  • CAR-iMACs induced pluripotent stem cell-derived engineered CAR-macrophages
  • CAR-iMACs reportedly demonstrated anti-tumor activity in ovarian cancer models in NSG TM mice.
  • L. Zhang, et al. Pluripotent stem cell-derived CAR-macrophage cells with antigen-dependent anti-cancer cell functions. J Hematol Oncol 13: 153 (2020) ) .
  • the Programmed Death 1 receptor is a key checkpoint receptor expressed by activated T and B cells and mediates immunosuppression.
  • PD-1 is a member of the CD28 family of receptors, which includes CD28, CTLA-4, ICOS, PD-1, and BTLA.
  • Two cell surface glycoprotein ligands for PD-1 have been identified, Programmed Death Ligand-1 (PD-L1) and Programmed Death Ligand-2 (PD-L2) , that are expressed on antigen-presenting cells as well as many human cancers and have been shown to dampen T cell activation and cytokine secretion upon binding to PD-1. Inhibition of the PD-1/PD-L1 interaction mediates potent anti-tumor activity in certain cancers.
  • the present invention relates to Irg1-deficent macrophages and monocytes, and to methods of making and using such Irg1-deficent macrophages and monocytes, including in combinations and methods of treatment or immunotherapy with PD1-axis binding antagonists.
  • the present invention further relates to combinations and methods of treatment or immunotherapy comprising an ACOD1 inhibitor and a PD-1 axis binding antagonist. Such combinations and methods may be useful in treating cancer or inducing or potentiating an immune response in a subject in need thereof.
  • the invention provides a method of treating cancer in a subject in need thereof, the method comprising administering to the subject an effective amount of: (a) a population of genetically engineered, chemically modified, differentiated, and/or isolated immune cells, wherein the cells have been transiently or permanently modified to reduce or eliminate immune responsive gene 1 (Irg1) activity or expression, and (b) a PD-1 axis binding antagonist.
  • a population of genetically engineered, chemically modified, differentiated, and/or isolated immune cells wherein the cells have been transiently or permanently modified to reduce or eliminate immune responsive gene 1 (Irg1) activity or expression
  • Irg1 immune responsive gene 1
  • the invention provides a method of treating cancer in a subject in need thereof, the method comprising: (a) providing a population of genetically engineered, chemically modified, differentiated, and/or isolated immune cells, wherein the cells have been transiently or permanently modified to reduce or eliminate immune responsive gene 1 (Irg1) activity or expression, and (b) administering the population to the subject in combination with a PD-1 axis binding antagonist.
  • a population of genetically engineered, chemically modified, differentiated, and/or isolated immune cells wherein the cells have been transiently or permanently modified to reduce or eliminate immune responsive gene 1 (Irg1) activity or expression
  • Irg1 immune responsive gene 1
  • the invention provides a method of treating cancer in a subject in need thereof, the method comprising administering to the subject an amount of genetically modified macrophages, monocytes, or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown, in combination with an amount of a PD-1 axis binding antagonist, wherein the amounts together are effective in treating cancer.
  • the subject is administered genetically modified macrophages.
  • the subject is administered genetically modified monocytes.
  • the subject is administered genetically modified stem cell-derived macrophages or monocytes.
  • the invention provides a method of inducing or potentiating an immune response in a subject in need thereof, the method comprising administering to the subject an amount of a composition comprising genetically modified macrophages, monocytes, or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown, in combination with an amount of a PD-1 axis binding antagonist, wherein the amounts together are effective in inducing or potentiating an immune response.
  • a composition comprising genetically modified macrophages, monocytes, or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown
  • the invention provides a combination comprising: (a) genetically modified macrophages, monocytes, or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown; and (b) a PD-1 axis binding antagonist.
  • the combination is for use in the treatment of cancer.
  • the combination is for use in inducing or potentiating an immune response.
  • the invention provides a method of treating cancer in a subject in need thereof, the method comprising administering to the subject an amount of an aconitate decarboxylase 1 (ACOD1) inhibitor, in combination with an amount of a PD-1 axis binding antagonist, wherein the amounts together are effective in treating cancer.
  • ACOD1 aconitate decarboxylase 1
  • the invention provides a method of inducing or potentiating an immune response in a subject in need thereof, the method comprising administering to the subject an effective amount of an aconitate decarboxylase 1 (ACOD1) inhibitor, wherein the subject is undergoing treatment with a PD-1 axis binding antagonist.
  • ACOD1 aconitate decarboxylase 1
  • the invention provides a combination comprising an ACOD1 inhibitor and a PD-1 axis binding antagonist.
  • the combination is for use in the treatment of cancer.
  • the combination is for use in inducing or potentiating an immune response.
  • FIG. 1 shows that Irg1 deletion inhibits tumor growth in immune competent mice.
  • A mRNA expression of IRG1 was compared across 18 distinct solid tumors and corresponding normal tissues from The TCGA Pan-Cancer Dataset. Asterisks denote statistical significance with Wilcoxon rank sum test t.
  • the mRNA expression of Irg1 and intracellular levels of ITA were determined by qRT-PCR and LC-MS, respectively. Data are the mean ⁇ s.d., and the p values were calculated by an unpaired, two-tailed Student’s t test.
  • B16-F10-TCM with indicated inhibitors were used to stimulate BMDMs for 6 hours.
  • the mRNA expression of Irg1 was determined by qRT-PCR. Data are the mean ⁇ s.d. of four independent experiments and p values were calculated by one-way ANOVA.
  • D RelA occupancy at the promoter region of Irg1 was determined by ChIP-qPCR. Data are the mean ⁇ s.d. of four independent experiments. The p values were calculated by two-way ANOVA.
  • E, B16-F10 (left) , MC38 (middle) and E0771 (right) were subcutaneously (s. c.
  • Data are mean ⁇ s.e.m., and the p values were calculated by two-way ANOVA.
  • F Overall survival of mice inoculated with B16-F10, MC38, and E0771 tumor cells. The p values were calculated using Log-rank (Mantel-Cox) test. *p ⁇ 0.05; **p ⁇ 0.01; ***p ⁇ 0.001; ****p ⁇ 0.0001 and n.s. denotes non-significant.
  • FIG. 2. shows that Irg1 deletion reverses the immunosuppressive tumor microenvironment.
  • B Expression of Irg1 and macrophage marker genes was illustrated in the UMAP plots.
  • C Annotated clusters of intratumoral monocytes/macrophages in Irg1 +/+ or Irg1 -/- mice are shown by t-SNE plots (left) . Cell numbers of each cluster are listed (right) .
  • D Normalized expression of select genes in each TAM subtype is shown by heatmap.
  • Percentages of myeloid cells (Cd45 + Cd11b + ) , Monocytes (Cd45 + Cd11b + Ly6c + ) , MDSC (Cd45 + Cd11b + Gr1 + ) , macrophages (Cd11b + F4/80 + ) , M1-like macrophages (Cd45 + Cd11b + F4/80 + iNos + ) , M2-like macrophages (Cd45 + Cd11b + F4/80 + iNos + ) , lymphocytes (Cd45 + Cd11b - ) , T cells (Cd45 + Cd3 + ) , Cd8 + T cells (Cd3 + Cd8 + ) , CD4 + T cells (Cd3 + Cd4 + ) and NK cells (Cd45 + Cd11b + Nk1.1 + ) are shown by violin plot.
  • FIG. 3 shows that Irg1-deficient macrophages acquire more M1-like features and promote antigen presentation and T cell chemotaxis.
  • A The enrichment score of indicated pathways intratumoral monocytes/macrophages in Irg1 +/+ or Irg1 -/- mice, according to scRNA-seq results in FIG. 2A.
  • B Volcano plots of log 2 fold change and log 10 adjusted p value of differentially expressed genes in Vcan + monocytes or Vegfa + macrophages from Irg1 +/+ and Irg1 -/- mice, according to scRNA-seq results.
  • E Gene expression heatmap in BMDMs co-cultured with B16-F10 for indicated time points.
  • F T cell migration in a transwell system. BMDMs were co-cultured with B16-F10 or stimulated with B16-F10-TCM in the lower chambers of a 5 ⁇ m Transwell plate. CD8 + T cells were placed in the upper chambers with or without CXCR3 antagonists SCH546738. After incubation at 37°C for 4 hours, CD8 + T cells that migrated into the lower chambers were collected and counted. Data shown are from 4 independent experiments. The p values were calculated by two-way ANOVA.
  • the percentages of Cd8 + T cells (Cd3 + Cd8 + ) were determined by flow cytometry (G) .
  • B16-F10 tumor growth was determined by the measurement of tumor volume (mm 3 ) .
  • Data are mean ⁇ s.d. (G) or s.e.m. (H) , the p values were calculated one-way ANOVA (G) and two-way ANOVA (H) .
  • *p ⁇ 0.05; **p ⁇ 0.01; ***p ⁇ 0.001; ****p ⁇ 0.0001 and n.s. denotes not significant.
  • FIG. 4 shows that Irg1 deletion in mice enhances the efficacy of anti-PD- (L) 1 immunotherapy.
  • B, D Overall survival of mice as described in A-C. The p values were calculated using Log-rank (Mantel-Cox) test.
  • E Experimental schematics of macrophage adoptive transfer into tumor-bearing wild-type mice (E, upper panel) .
  • mice were injected intratumorally (i. t. ) with Irg1 +/+ or Irg1 -/- BMDMs and intraperitoneally (i.p. ) with aPD-L1 antibody at the same time.
  • Data shown are mean ⁇ s.e.m.
  • the p values were calculated using two-way ANOVA.
  • F Overall survival of mice as described in E. The p values were calculated using Log-rank (Mantel-Cox) test. *p ⁇ 0.05, **p ⁇ 0.01, ***p ⁇ 0.001, ****p ⁇ 0.0001 and n.s. denotes not significant.
  • FIG. 5 show that Irg1-deficient macrophages inhibit pancreatic cancer growth.
  • C Experimental schematics of macrophage adoptive transfer into wild-type recipients bearing KPC tumor (left panel) .
  • Tumors were harvested and weighted at day 15 post inoculation (middle and right panels) .
  • the p values were calculated using one-way ANOVA.
  • D Macrophage adoptive transfer into wild-type recipients was conducted as described in C.
  • the percentages of immune cells (Cd45 + ) , MDSC (Cd45 + Cd11b + Gr1 + ) , M1-like macrophages (Cd45 + Cd11b + F4/80 + iNos + ) , and Cd8 + T cells (Cd45 + Cd3 + Cd8 + ) were measured and calculated. The p values were calculated by one-way ANOVA.
  • E Representative images of IF staining of CD8 and Tunel in KPC tumors as described in C. Scale bars of a low and a high magnification represent 200 ⁇ m and 50 ⁇ m, respectively.
  • F The quantification of average cell number with s.d. from 6 random high-power fields (HPFs) is shown. *p ⁇ 0.05, **p ⁇ 0.01, ***p ⁇ 0.001, ****p ⁇ 0.0001 and n.s. denotes not significant.
  • FIG. 6 shows the positive correlation between IRG1 mRNA expression and TAM fractions in multiple types of human tumors.
  • EPIC Estimatimating the Proportions of Immune and Cancer cells
  • Spearman rank correlation test was used to determine the significance of correlation between TAM fraction and IRG1 expression.
  • FIG. 7 shows that tumor cells induce Irg1 mRNA expression in macrophages by NF- ⁇ B activation.
  • A Irg1 induction and ITA accumulation in BMDMs co-cultured with tumor cells. Wild-type BMDMs were co-cultured with different types of syngeneic tumor cells (B16-F10, MC38, E0771, KPC) for 6 or 12 hours. The p values were calculated by unpaired, two-tailed Student’s t test.
  • B Irg1 induction and ITA accumulation in BMDMs stimulated with TCM. Wild-type BMDMs were treated with conditioned medium from different types of syngeneic tumor cells for 6 or 12 hours.
  • the mRNA expression of Irg1 and intracellular levels of ITA were determined by qRT-PCR and LC-MS, respectively. The p values were calculated by unpaired, two-tailed Student’s t test. C, B16-F10-TCM with indicated inhibitors (ruxolitinib, PDTC) were used to stimulate BMDMs for 6 hours. The mRNA expression of Il-1 ⁇ and Il-6 were determined by qRT-PCR. Data shown are mean ⁇ s.d. of four independent experiments. The p values were calculated by one-way ANOVA. *p ⁇ 0.05; ** ⁇ 0.01; ***p ⁇ 0.001; ****p ⁇ 0.0001.
  • FIG. 8 shows that scRNA-seq unveils major immune populations in the TME of B16-F10 tumor.
  • A Sequenced cells were divided into 19 clusters, and representative genes in each cluster is shown.
  • B 19 clusters were assigned to 8 types of cells, whose marker genes are shown in the table.
  • C Dot-plot was used to show the identity of 8 types of cells.
  • FIG. 9 shows the developmental trajectory of monocytes and macrophage subsets in the TME of B16-F10 tumor.
  • A t-SNE plot was used to show 6 monocytes/macrophages subsets with the expression of selected genes.
  • B KEGG analysis of curated set of transcriptomic signatures in 6 monocyte/macrophage subsets.
  • C Pseudotime trajectory analysis of 6 monocytes/macrophages subsets (left panel) .
  • Model of the developmental trajectory of monocyte/macrophage subsets in B16-F10 tumor (right panel) .
  • FIG. 10 shows that Irg1-deficient macrophages acquire more M1-like features but reduce pro-angiogenic potential.
  • A Single sample gene set enrichment analysis (ssGSEA) was conducted to calculate gene signature-based scores in intratumoral monocytes/macrophages in B16-F10 tumors. The enrichment score of indicated pathways between tumor-bearing Irg1 +/+ and Irg1 -/- mice were compared, and the p values were calculated by an unpaired, two-tailed Student’s t test.
  • B-C BMDMs were challenged with B16-F10-TCM for 12 hours, followed by qRT-PCR to detect the mRNA expression (B) and protein expression (C) of indicated cytokines.
  • BMDMs were co-cultured with B16-F10 (D) or stimulated with B16-F10-TCM for 12 hours, followed by flow cytometry to determine the markers of M1/M2 polarization as indicated.
  • F BMDMs were challenged with B16-F10-TCM for 12 hours, followed by qRT-PCR to detect the mRNA expression of genes which were highly expressed in Vegfa + macrophages. Data shown were the mean ⁇ s.d. of four (B, D, E, F) or eight (C) independent experiments. The p values were calculated by an unpaired, two-tailed Student’s t test. **p ⁇ 0.01, ****p ⁇ 0.0001 and n.s. denotes not significant.
  • FIG. 11 shows that Irg1 promotes immune suppressive function of macrophages partially through Tet2 inhibition.
  • A Representative images of 5hmC or F4/80 staining in serial sections of E0771 breast tumors as described in Figure 1C. Scale bars of low to high magnification represent 50 ⁇ m and 20 ⁇ m, respectively.
  • B-C 5hmC enrichment at the promoter regions of indicated genes were determined by hMeDIP-qPCR using TAMs isolated from B16-F10 melanoma (C) or BMDMs treated with or without B16-F10-TCM (C) .
  • D Gene expression heatmap in BMDMs from Tet2 +/+ and Tet2 HxD mice, as determined by qRT-PCR.
  • the cells were pre-treated with 0.5 mM ITA for 12 hours, followed by treatment with B16-F10-TCM for another 12 hours.
  • Data are the mean ⁇ s.d. of four (B) or three (C) independent experiments.
  • the p values were calculated by two-way ANOVA (B) and unpaired, two-tailed Student’s t test (C) .
  • FIG. 12 shows that Irg1 does not affect the cytotoxicity of CD8 + T cells in the TME.
  • Percentages of cytotoxic Cd8 T cells (Ifn ⁇ + Cd8 + ) , T cell cytoxicity (Cd8 + Ifn ⁇ + Tnf ⁇ + ) , exhausted T cells (Cd8 + Pd1 + ) were measured as described in Method.
  • the p values were calculated by an unpaired, two-tailed Student’s t test. **p ⁇ 0.01, and n.s. denotes not significant.
  • FIG. 13 shows that targeting IRG1 in human macrophages facilitates T cell chemotaxis.
  • A Tumor cells induce IRG1 in human macrophages. IRG1 was depleted in THP-1 cells by using sgRNA and these cells were differentiated to macrophages by treatment with Phorbol 12-myristate 13-acetate (PMA, 100 ng/ml) for 24 hours, and then were stimulated with MDA-MB-231-TCM for another 12 hours, following western-blot to detect IRG1 protein.
  • PMA Phorbol 12-myristate 13-acetate
  • FIG. 14 shows that Irg1 cannot affect the macrophage infiltration into engrafted KPC tumors.
  • FIG. 15 shows that targeting Irg1 in TAMs may reduce angiogenesis in KPC tumors.
  • A Representative images of CD31 immunohistochemistry staining in KPC tumors receiving macrophage therapy as described in FIG. 5C. Scale bar represents 50 ⁇ m.
  • B-C IF staining of indicated markers in KPC tumors receiving macrophage therapy. Scale bar represents 50 ⁇ m. The quantification of average cell number from 5 random high-power fields (HPFs) is shown. *p ⁇ 0.05, **p ⁇ 0.01, ***p ⁇ 0.001 and n.s. denotes not significant.
  • FIG. 16 shows that IRG1 acts as a master controller of macrophage anti-tumor activity.
  • Tumor cells induce Irg1 expression in macrophages through NF- ⁇ B activation and subsequently lead to the accumulation of the immunomodulatory metabolite ITA, which dampens the inflammatory response in TAM subsets.
  • Irg1/ITA alter the functional diversity of TAMs, such as restricted M1-like polarization and reduced pro-angiogenic potential in Vegfa + macrophages, and thereby creates and/or maintains the immunosuppressive TME favorable for tumor growth.
  • Irg1-deficent macrophages were discovered to acquire M1-like proinflammatory features, enhance immunogenic antigen presentation, and confer an anti-tumor microenvironment highly infiltrated by cytotoxic T cells. Consequently, Irg1 deficiency suppressed the growth of mouse syngeneic tumors, including melanoma, colorectal cancer, breast cancer, and pancreatic cancer. Finally, Irg1-deficient macrophages not only dictated the tumoricidal effect but also enhanced the efficacy of anti-PD (L) 1 immunotherapy.
  • a macrophage may mean a plurality of macrophages, or a population of macrophages.
  • administer refers to delivery of the agent or agents to a subject, regardless of the route or mode of delivery.
  • Two or more agents may be administered sequentially, concurrently, or simultaneously, in any order and on any dosing schedule unless otherwise specified, especially within time intervals that allow the combination to show a synergistic effect.
  • Sequential administration may be particularly useful when the co-agents in the combination therapy are administered according to different dosing schedules, for example, one agent is administered daily, and the second agent is administered less frequently, such as weekly or biweekly.
  • Concurrent or sequential administration may be particularly useful where the co-agents are administered in different dosage forms, for example, one agent is in an oral dosage form and the other agent is in an intravenous dosage form.
  • Simultaneous administration may be particularly useful where the co-agents are administered in the same dosage form, e.g., both as intravenous solutions, and/or are administered on the same dosing schedule.
  • cancer includes locally advanced (non-metastatic) disease or metastatic disease.
  • agent may be used interchangeably to refer to agents such as ACOD1 inhibitors (e.g., small molecule inhibitors) , PD-1 axis binding antagonists (e.g., anti-PD-1 or anti-PD-L1 antibodies) , or to cell-based therapeutic agents (e.g., modified macrophages, monocytes, stem cell-derived macrophages/monocytes, or stem cells as described herein) .
  • ACOD1 inhibitors e.g., small molecule inhibitors
  • PD-1 axis binding antagonists e.g., anti-PD-1 or anti-PD-L1 antibodies
  • cell-based therapeutic agents e.g., modified macrophages, monocytes, stem cell-derived macrophages/monocytes, or stem cells as described herein
  • antibody refers to an immunoglobulin molecule capable of specific binding to a target, such as a carbohydrate, polynucleotide, lipid, polypeptide, etc., through at least one antigen recognition site, located in the variable region of the immunoglobulin molecule.
  • a target such as a carbohydrate, polynucleotide, lipid, polypeptide, etc.
  • the term encompasses a polyclonal antibody, a monoclonal antibody, a chimeric antibody, a bispecific antibody, a dual-specific antibody, bifunctional antibody, a trispecific antibody, a multispecific antibody, a bispecific heterodimeric diabody, a bispecific heterodimeric IgG, a labeled antibody, a humanized antibody, a human antibody.
  • antibody fragment refers to at least one portion of an intact antibody, or a recombinant variant thereof, and the antigen binding domain, e.g., an antigenic determining variable region of an intact antibody, that is sufficient to confer recognition and specific binding of the antibody to the fragment to a target, such as an antigen.
  • antibody fragments include, but are not limited to, Fab, Fab’ , F (ab’ ) 2, Fv, single chain (ScFv) and domain antibodies (including, for example, shark and camelid antibodies) , fusion proteins comprising an antibody, any other modified configuration of the immunoglobulin molecule that comprises an antigen recognition site, and antibody like binding peptidomimetics (ABiPs) .
  • anti-cancer effect refers to a biological effect which can be manifested by various means, including but not limited to, e.g., decreasing the number of cancer cells; reducing tumor size; reducing tumor volume; decreasing the incidence of metastases; decreasing cancer cell proliferation; decreasing cancer cell survival; ameliorating one or more physiological symptoms associated with the cancerous condition; increasing the quality of life of a subject having cancer; decreasing the dose of other medications used to treat the cancer; enhancing the effect of another anti-cancer medication; delaying the progression of the cancer; curing the cancer; overcoming one or more resistance mechanisms of the cancer; increasing life expectancy; and/or prolonging progression free survival.
  • allogeneic refers to any material derived from a different animal of the same species as the subject to whom the material is to be introduced. Two or more individuals are said to be allogeneic to one another when the genes at one or more loci are not identical. In some embodiments, allogeneic material from individuals of the same species may be sufficiently unlike genetically to interact antigenically.
  • autologous refers to any material derived from the same subject to whom the material is to be re-introduced.
  • modified macrophages, monocytes, stem cell-derived macrophages/monocytes, or stem cells described herein can be from a single individual, i.e., autologous, or pooled from multiple individuals (non-autologous/allogeneic) .
  • Biotherapeutic agent refers to a biological molecule, such as an antibody or fusion protein, that blocks ligand/receptor signaling in any biological pathway that supports tumor maintenance and/or growth or suppresses the anti-tumor immune response.
  • PD-1 axis binding antagonists such as anti-PD-1 antibodies or anti-PD-L1 antibodies may be referred to as “biotherapeutic agents” .
  • cancer refers to or describes the physiological condition in a subject that is typically characterized by unregulated cell growth.
  • cancer refers to any malignant and/or invasive growth or tumor caused by abnormal cell growth, and includes solid tumors named for the type of cells that form them, as well as cancers of blood, bone marrow, or the lymphatic system. Solid tumors include but are not limited to sarcomas and carcinomas. Cancers of the blood include but are not limited to leukemias, lymphomas and myeloma.
  • cancer includes a primary cancer that originates at a specific site in the body, a metastatic cancer that has spread from the place in which it started to other parts of the body, a recurrence from the original primary cancer after remission, or a second primary cancer in a subject with a history of prior cancer of a different type.
  • a subject may be identified as having de novo metastatic disease or after progression from an earlier-identified cancer.
  • a “cell-based therapy” or “cell-based therapeutic agent” includes but is not limited to the modified macrophages, monocytes, stem cell-derived macrophages/monocytes, or stem cells described herein, or chimeric antigen receptor (CAR) therapies, such as CAR T-cell (CAR-T) therapies, CAR natural killer (CAR-NK) therapies, CAR macrophage (CAR-M) therapies, and the like.
  • CAR CAR T-cell
  • CAR-NK CAR natural killer
  • CAR-M CAR macrophage
  • the genetically modified macrophages, monocytes, stem cell-derived macrophages/monocytes, or stem cells described herein may be referred to as “cell-based therapeutics” .
  • the genetically modified macrophages, monocytes, stem cell-derived macrophages/monocytes, or stem cells described herein may be incorporated into other cell-based therapies, e.g., CAR-based therapies.
  • chemotherapeutic agent is a chemical compound useful in the treatment of cancer.
  • chemotherapeutic agents include, but are not limited to, alkylating agents, platinum coordination complexes, cytotoxic antibiotics, antimetabolites, biologic response modifiers, histone deacetylase inhibitors, hormonal agents, monoclonal antibodies, growth factor inhibitors, taxanes, topoisomerase inhibitors, Vinca alkaloids and the like.
  • combination refers to a combination of two or more agents, which may be either a fixed combination in one dosage unit form, or a combined administration of the two or more co-agents, alone or in the form of pharmaceutical compositions or medicaments.
  • the combination therapy may be administered independently at the same time, or separately within time intervals especially where these time intervals allow the combination to show a cooperative effect (e.g., preferably a synergistic effect) .
  • in combination with refers to the administration of a first agent before, during, or after administration of at least one other agent to the individual
  • the administration of two or more agents is intended to include treatment regimens in which the agents are not necessarily administered by the same route of administration or at the same time.
  • composition may be used interchangeably to refer to a preparation of a therapeutic agents (or co-agents) in a form suitable to permit the biological activity of the active ingredient (s) to be effective when administered to a subject, and which contains no additional components which are unacceptably toxic to a subject to whom the formulation would be administered.
  • the co-agents may be packaged in a kit or separately. One or both co-agents may be reconstituted or diluted to a desired dose prior to administration.
  • an effective amount refers to the amount of an agent (including, e.g., a population of modified macrophages, monocytes, or stem cells, an ACOD1 inhibitor, or a PD-1 binding axis antagonist) , or combination of two or more such agents, that is sufficient to affect one or more beneficial or desired biological results, including for example biochemical, histological and/or behavioral symptoms of the disease, its complications and intermediate pathological phenotypes presenting during development of the disease.
  • an effective amount refers to that amount of an agent or combination that provides an anti-cancer effect.
  • An effective dosage can be administered in one or more administrations.
  • the amount of each co-agent in a combination will be an amount that would provide a therapeutic effect if the individual agent was administered alone.
  • the amounts of one or both co-agents in a combination will be sub-therapeutic relative to the amount of each agent required for single agent efficacy, provided the amounts of the co-agents in combination is sufficient to show a therapeutic effect.
  • endogenous refers to any material from or produced inside an organism, cell, tissue or system.
  • exogenous refers to any material introduced from or produced outside an organism, cell, tissue or system.
  • expression refers to the transcription and/or translation of a particular nucleotide sequence. In some embodiments, expression comprises translation of an mRNA introduced into a cell.
  • subject or “patient” refers to any single subject for which therapy is desired, or that is participating in a clinical trial, epidemiological study or used as a control, including humans and mammalian veterinary patients such as cattle, horses, dogs and cats. In preferred embodiments, the subject is a human.
  • treat refers to administering to a subject having cancer, or diagnosed with cancer, a combination therapy according to the invention that is effective to achieve at least one anti-cancer effect.
  • treating also includes adjuvant and neo-adjuvant treatment of a subject.
  • treatment refers to the act of treating as defined above.
  • the methods, combinations and uses herein may be usefully administered to a subject during different stages of their treatment.
  • the combination therapy is administered to a subject who is previously untreated (i.e. is treatment ) .
  • the combination therapy is administered to a subject who has failed to achieve a sustained response after a prior therapy with a biotherapeutic or chemotherapeutic agent (i.e. is treatment experienced) .
  • the combination therapy is administered: (a) prior to, or after, surgery to remove a tumor, (b) prior to, during, or after radiation therapy, and/or (c) prior to, during, or after chemotherapy.
  • the invention relates to neoadjuvant therapy, adjuvant therapy, first-line therapy, second-line therapy, or third-line or later line therapy.
  • the cancer may be localized, advanced or metastatic, and the intervention may occur at point along the disease continuum (i.e., at any stage of the cancer) .
  • the efficacy of combinations described herein in certain tumors may be enhanced by combination with one or more additional anti-cancer agents, e.g., with other approved or experimental cancer therapies, such as radiation, surgery, chemotherapeutic agents, targeted therapies, agents that inhibit other signaling pathways that are dysregulated in tumors, and other immune enhancing agents.
  • additional anti-cancer agents e.g., with other approved or experimental cancer therapies, such as radiation, surgery, chemotherapeutic agents, targeted therapies, agents that inhibit other signaling pathways that are dysregulated in tumors, and other immune enhancing agents.
  • the methods, combinations and uses of the current invention may further comprise one or more additional anti-cancer agents.
  • Administration of the combination therapies described herein may be affected by any method that enables delivery of the agent or agents to the site of action. These methods include oral routes, intraduodenal routes, parenteral injection (including intravenous, subcutaneous, intramuscular, intravascular or infusion) , topical, intrathecal, and rectal administration.
  • parenteral injection including intravenous, subcutaneous, intramuscular, intravascular or infusion
  • topical intrathecal
  • rectal administration including intravenous, subcutaneous, intramuscular, intravascular or infusion
  • modified macrophages, monocytes or stem cells are administered by intravenous injection or infusion.
  • T/C tumor growth inhibition
  • NCI National Cancer Institute
  • the treatment achieved by a combination of the invention is defined by reference to any of the following: partial response (PR) , complete response (CR) , overall response (OR) , progression free survival (PFS) , disease free survival (DFS) and overall survival (OS) .
  • PFS also referred to as “Time to Tumor Progression” indicates the length of time during and after treatment that the cancer does not grow and includes the amount of time patients have experienced a CR or PR, as well as the amount of time patients have experienced stable disease (SD) .
  • DFS refers to the length of time during and after treatment that the patient remains free of disease.
  • OS refers to a prolongation in life expectancy as compared to or untreated subjects or patients.
  • response to a combination of the invention is any of PR, CR, PFS, DFS, OR or OS that is assessed using Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 response criteria.
  • the treatment regimen for a combination of the invention that is effective to treat a cancer patient may vary according to factors such as the disease state, age, and weight of the patient, and the ability of the therapy to elicit an anti-cancer response in the subject. While an embodiment of any of the aspects of the invention may not be effective in achieving a positive therapeutic effect in every subject, it should do so in a statistically significant number of subjects as determined by any statistical test known in the art such as the Student's t-test, the chi2-test the U-test according to Mann and Whitney, the Kruskal-Wallis test (H-test) , Jonckheere-Terpstrat-testy and the Wilcon on-test.
  • any statistical test known in the art such as the Student's t-test, the chi2-test the U-test according to Mann and Whitney, the Kruskal-Wallis test (H-test) , Jonckheere-Terpstrat-testy and the Wilcon on-test.
  • treatment regimen “dosage regimen” or “dosing regimen” are used interchangeably to refer to the dose, timing, and mode of administration of each therapeutic agent in a combination of the invention. Dosage regimens may be adjusted to provide the optimum therapeutic response. For example, an agent of the combination therapy may be administered as a single bolus, as several divided doses administered over time, or the dose may be proportionally reduced or increased as indicated by the specific therapeutic situation.
  • additive is used to mean that the result of the combination of two compounds, agents or compositions is no greater than the sum of each compound, agent or composition individually.
  • the term “synergy” or “synergistic” are used to mean that the result of the combination of two compounds, agents or compositions is greater than the sum of each compound, agent or compositions individually. This improvement in the disease, condition or disorder being treated is a “synergistic” effect.
  • a “synergistic amount” is an amount of the combination of the two compounds, agents or compositions that results in a synergistic effect.
  • the optimum range for the effect and absolute dose ranges of each component for the effect may be definitively measured by administration of the components over different dose ranges, and/or dose ratios to patients in need of treatment.
  • the observation of synergy in in vitro models or in vivo models can be predictive of the effect in humans and other species and such models may be useful to measure a synergistic effect.
  • the agents of the present invention can be administered completely separately or in the form of one or more separate compositions.
  • the agents may be given separately at different times during the course of therapy (in a chronologically staggered manner, especially a sequence-specific manner) in such time intervals that the combination therapy is effective in treating cancer.
  • the combination comprises genetically modified macrophages monocytes, or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown (as described herein) in combination with an anti-PD-1 axis binding antagonist.
  • Irg1 immune responsive gene 1
  • the combination comprises an ACOD1 inhibitor in combination with an anti-PD-1 axis binding antagonist.
  • the ACOD1 inhibitor is a small molecule inhibitor and the anti-PD-1 axis binding antagonist is an anti-PD-1 or anti-PD-L1 antibody or antibody fragment thereof.
  • a combination as described herein e.g., an ACOD1 inhibitor in combination with a PD-1 axis binding antagonist
  • a combination as described herein is administered in a single dose.
  • a combination as described herein, e.g., an ACOD1 inhibitor in combination with a PD-1 axis binding antagonist is administered in multiple doses.
  • an amount of a combination as described herein may be administered periodically at regular intervals (e.g., 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10 or more times every 1, 2, 3, 4, 5, or 6 days, or every 1 , 2, 3, 4, 5, 6, 7, 8, or 9 weeks, or every 1 , 2, 3, 4, 5, 6, 7, 8, 9 months or longer) .
  • a combination as described herein e.g., an ACOD1 inhibitor in combination with a PD-1 axis binding antagonist, is administered at a predetermined interval (e.g., 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10 or more times every 1 , 2, 3, 4, 5, or 6 days, or every 1 , 2, 3, 4, 5, 6, 7, 8, or 9 weeks, or every 1 , 2, 3, 4, 5, 6, 7, 8, 9 months or longer) .
  • a predetermined interval e.g., 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10 or more times every 1 , 2, 3, 4, 5, or 6 days, or every 1 , 2, 3, 4, 5, 6, 7, 8, or 9 weeks, or every 1 , 2, 3, 4, 5, 6, 7, 8, 9 months or longer
  • each agent will be administered at a dose and/or on a time schedule determined for that agent.
  • the two or more agents may (but do not necessarily) belong to different classes of agents (e.g., cell-based therapeutic agents, biotherapeutic agents, or small molecule therapeutic agents) .
  • packaged pharmaceutical products may contain one or more dosage forms that contain the combination of agents, and one or more dosage forms that contain one of the combination of agents, but not the other agent (s) of the combination.
  • a unit dosage form refers to physically discrete units (e.g., capsules or tablets) suited as unitary dosages for the subjects to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.
  • the specification for the dosage unit forms of the invention may be dictated by and directly dependent on (a) the physicochemical characteristics of the agent and the therapeutic or prophylactic effect to be achieved, and (b) the limitations inherent in the art of compounding such an active compound for use in treatment.
  • each therapeutic agent in a combination may be administered in further combination with one or more additional anti-cancer therapies or anti-cancer agents.
  • the combinations may be administered concurrently with, prior to, or subsequent to, such additional anti-cancer agents.
  • the additional anti-cancer agent utilized in this combination may be administered together in a single composition or administered separately in different compositions.
  • additional anti-cancer agents utilized in connection with a particular combination will be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually.
  • the invention relates to methods, combinations and compositions comprising genetically modified macrophages, monocytes, or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown.
  • Such genetically modified macrophages, monocytes, or stem cell-derived macrophages/monocytes may be useful in methods and combinations for treating cancer and/or for inducing or potentiating an immune response in a subject in need thereof.
  • genetically modified macrophages, monocytes or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown may be useful in combination with a PD-1 axis binding antagonist.
  • the Irg1 gene knockout, mutation, or knockdown is introduced by gene editing or an RNA interference (RNAi) agent in a population of macrophages, monocytes or stem cell-derived macrophages/monocytes.
  • RNAi RNA interference
  • the population of macrophages, monocytes or stem cell-derived macrophages/monocytes is autologous to the subject.
  • the population of macrophages, monocytes or stem cell-derived macrophages/monocytes is allogeneic to the subject.
  • the Irg1 gene knockout, mutation, or knockdown is introduced by gene editing.
  • the gene editing system comprises an endonuclease selected from a clustered regularly interspaced short palindromic repeats (CRISPR) /Cas nuclease system, a zinc finger nuclease (ZFN) , a Transcription Activator Like Effector nuclease (TALEN) , or a meganuclease.
  • CRISPR clustered regularly interspaced short palindromic repeats
  • ZFN zinc finger nuclease
  • TALEN Transcription Activator Like Effector nuclease
  • CRISPR/Cas systems are found in approximately 40%of sequenced eubacteria genomes and 90%of sequenced archaea.
  • This system is a type of prokaryotic immune system that confers resistance to foreign genetic elements such as plasmids and phages and provides a form of acquired immunity.
  • CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA, Science 322: 1843-1845 (2008) ) .
  • the CRISPR/Cas system has been modified for use in gene editing (silencing, enhancing or changing specific genes) in eukaryotes such as mice or primates. (B. Wiedenheft, et al., RNA-guided genetic silencing systems in bacteria and archaea, Nature 482: 331-8 (2012) ) . This is accomplished by, for example, introducing into the eukaryotic cell a plasmid containing a specifically designed CRISPR and one or more appropriate Cas.
  • the CRISPR sequence sometimes called a CRISPR locus, comprises alternating repeats and spacers.
  • the spacers usually comprise sequences foreign to the bacterium such as a plasmid or phage sequence; in an exemplary CRISPR/Cas system targeting the IRG1 gene, the spacers are derived from the IRG1 gene sequence, or a sequence of its regulatory elements.
  • the CRISPR/Cas system can thus be used to modify, e.g., delete one or more nucleic acids, the IRG1 gene, or a gene regulatory element of the IRG1 gene, or introduce a premature stop which thus decreases expression of a functional of the IRG1 gene.
  • the CRISPR/Cas system can alternatively be used like RNA interference, turning off the IRG1 gene in a reversible fashion.
  • the RNA can guide the Cas protein to a promoter of the IRG1 gene, sterically blocking RNA polymerases.
  • CRISPR/Cas systems for gene editing in eukaryotic cells typically involve (1) a guide RNA molecule (gRNA) comprising a targeting sequence (which is capable of hybridizing to the genomic DNA target sequence) , and sequence which is capable of binding to a Cas, e.g., Cas9 enzyme, and (2) a Cas, e.g., Cas9, protein.
  • gRNA guide RNA molecule
  • the targeting sequence and the sequence that is capable of binding to a Cas, e.g., Cas9 enzyme may be disposed on the same or different molecules. If disposed on different molecules, each includes a hybridization domain which allows the molecules to associate, e.g., through hybridization.
  • RNA from the CRISPR locus is constitutively expressed and processed into small RNAs. These comprise a spacer flanked by a repeat sequence. The RNAs guide other Cas proteins to silence exogenous genetic elements at the RNA or DNA level.
  • the spacers thus serve as templates for RNA molecules, analogously to small interfering RNAs (siRNAs) . (E. Pennisi, The CRISPR craze, Science (2013) 341: 833-836) .
  • a simpler CRISPR system relies on the protein Cas9, which is a nuclease with two active cutting sites, one for each strand of the double helix. Combining Cas9 and modified CRISPR locus RNA can be used in a system for gene editing. (E. Pennisi (2013) ) .
  • ZFN Zinc Finger Nuclease
  • Zinc Finger Nuclease refers to a zinc finger nuclease, an artificial nuclease which can be used to modify, e.g., delete one or more nucleic acids of, a desired nucleic acid sequence, e.g., the IRG1 gene.
  • TALEN gene editing systems are produced artificially by fusing a TAL effector DNA binding domain to a DNA cleavage domain.
  • Transcription activator-like effects can be engineered to bind any desired DNA sequence.
  • a restriction enzyme can be produced which is specific to any desired DNA sequence. These can then be introduced into a cell, wherein they can be used for genome editing.
  • TALENs specific to sequences in the IRG1 gene can be constructed using any method known in the art, including various schemes using modular components. (F. Zhang, et al., Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription, Nature Biotech. 29: 149-53 (2011) ; US 8,420,782; US 8,470,973) .
  • gene editing system binds to a target sequence in the IRG1 gene. In an embodiment, the gene editing system binds to a target sequence that comprises an exon or intron of the IRG1 gene. In an embodiment, the gene editing system binds to a target sequence that comprises a splice junction of the IRG1 gene. In an embodiment, the gene editing system binds to a target sequence in a coding region of the IRG1 gene. In an embodiment, the gene editing system binds to a target sequence in a non-coding region of the IRG1 gene. In an embodiment, the gene editing system binds to a target sequence in a regulatory element of the IRG1 gene. In an embodiment, the gene editing system is a CRISPR/Cas system comprising a guide RNA (gRNA) molecule comprising a targeting sequence which hybridizes to a target sequence of the IRG1 gene.
  • gRNA guide RNA
  • the Irg1 gene knockout, mutation, or knockdown is introduced by an RNA interference (RNAi) agent.
  • RNAi agent is microRNA (miRNA) , small interfering RNA (siRNA) , or short hairpin RNA (shRNA) .
  • the genetically modified macrophages and monocytes exhibit an anti-tumor phenotype.
  • the genetically modified macrophages or monocytes are genetically modified bone marrow-derived macrophages or bone marrow-derived monocytes.
  • the genetically modified macrophages and monocytes are stem cell-derived macrophages/monocytes.
  • the cell-based therapeutic agents described herein may be provided or administered in the form of a pharmaceutical composition, comprising at least one cell-based therapeutic agent and one or more pharmaceutically acceptable vehicles, carriers or excipients.
  • the pharmaceutical composition comprises about 0.01 %to 99.9%of the cell-based therapeutic agent and about 0.1 to 99.99%of a pharmaceutically acceptable carrier or excipient.
  • the pharmaceutical composition comprises about 0.01 %to 99.9%of the cell-based therapeutic agent and about 0.1 to 99.99%of a pharmaceutically acceptable carrier or excipient.
  • the pharmaceutical composition comprises about 1%to 90%of the cell-based therapeutic agent and about 10 to 99%of a pharmaceutically acceptable carrier or excipient. In some embodiments, the pharmaceutical composition comprises about 5%to 90%of the cell-based therapeutic agent and about 10 to 95%of a pharmaceutically acceptable carrier or excipient.
  • Suitable vehicles include, but are not limited to, water, saline, dextrose, glycerol, ethanol, or the like, and combinations thereof.
  • Pharmaceutically acceptable carriers include, but are not limited to, physiologically acceptable compounds that act to stabilize, increase, or decrease the absorption or clearance rates of the pharmaceutical compositions of the invention.
  • Suitable excipients include, but are not limited to, wetting agents, emulsifying agents, dispersing agents, pH buffering agents, anti-oxidants, or preservatives.
  • Such compounds can include, e.g., carbohydrates, antioxidants, chelating agents, low molecular weight proteins, detergents, liposomal carriers, or other stabilizers and/or buffers.
  • Excipients include, but are not limited to, nonionic surfactants, polyvinylpyrollidone, human serum albumin, aluminum hydroxide, anesthetic agents, unmodified or derivatized cyclodextrins, and the like.
  • the invention relates to methods, combinations and compositions comprising an ACOD1 inhibitor.
  • the ACOD1 inhibitor is selected from the group consisting of a small molecule inhibitor, a small molecule degrader, a peptide inhibitor, a peptidomimetic inhibitor, a nucleic acid, and an anti-ACOD1 antibody, or a combination thereof.
  • Such ACOD1 inhibitors may be useful in methods and combinations for treating cancer and/or for inducing or potentiating an immune response in a subject in need thereof.
  • ACOD1 inhibitors may be useful in combination with a PD-1 axis binding antagonist.
  • the ACOD1 inhibitor is a small molecule inhibitor.
  • the small molecule inhibitor is a C 4 -C 6 dicarboxylic acid, or a derivative, bioisostere, salt, ester, or prodrug thereof.
  • the C 4 -C 6 dicarboxylic acid is itaconic acid, mesaconic acid, or citraconic acid, or a derivative, bioisostere, salt, ester, or prodrug thereof.
  • Examples of small molecule inhibitors may include derivatives of ITA. Such derivatives have been suggested for treatment of diseases characterized by activation or suppression of the immune system, including inflammation, fibrosis, viral or bacterial infections, ischemia, sepsis, bone disease, and cancer (International Publication Nos. WO 2020/006557, WO 2020/222010, WO 2020/222011 and WO 2019/036509) . Inhibitors of SDH have been reported for the treatment of fibrosis (International Publication No. WO 2022/058700) .
  • the ACOD1 inhibitor is a nucleic acid.
  • the nucleic acid is an antisense oligonucleotide, an aptamer, a CRISPR guide RNA (gRNA) , or an RNAi agent.
  • the nucleic acid is an RNAi agent.
  • the RNAi agent is microRNA (miRNA) , small interfering RNA (siRNA) , or short hairpin RNA (shRNA) .
  • Double stranded RNA ( "dsRNA” ) , e.g., siRNA or shRNA, can be used as an ACOD1 inhibitor.
  • nucleic acids encoding such dsRNA inhibitors.
  • the ACOD1 inhibitor is a dsRNA specific for a nucleic acid encoding a IRG1 gene product.
  • the nucleic acid may include genomic DNA or mRNA encoding an IRG1 gene product, i.e., ACOD1.
  • compositions comprising a dsRNA comprising at least 15 contiguous nucleotides, e.g., 15 to 25 contiguous nucleotides, which are complementary (e.g., 100%complementary) to a sequence of the IRG1 gene.
  • Antibody molecules can be used as ACOD1 inhibitors. Also contemplated are the uses of nucleic acid sequences encoding the antibody molecules targeting ACOD1.
  • the ACOD1 inhibitor is a single-domain antibody (sdAb) , i.e., a nanobody.
  • the ACOD1 inhibitor is a nucleic acid encoding the single domain antibody.
  • the ACOD1 inhibitor may be provided or administered in the form of a pharmaceutical composition, comprising at least one ACOD1 inhibitor and one or more pharmaceutically acceptable vehicles, carriers or excipients.
  • the pharmaceutical acceptable vehicles, carriers or excipients may comprise any conventional pharmaceutical vehicle, carrier or excipient. The choice of vehicle, carrier and/or excipient will to a large extent depend on factors such as the mode of administration, the effect of the vehicle, carrier or excipient on solubility and stability, and the nature of the dosage form.
  • Suitable pharmaceutical carriers include inert diluents or fillers, water and various organic solvents.
  • the pharmaceutical compositions may, if desired, contain additional ingredients such as binders, diluents, disintegrants, surface active agents, pH modifying agents, glidants, lubricants, anti-oxidants, colorants, flavorants, preservatives and the like.
  • the pharmaceutical composition may be in a form suitable for oral administration, such as a tablet, capsule, pill, powder, sustained release formulations, solution suspension; in a form suitable for parenteral injection as a sterile solution, suspension or emulsion; in a form for topical administration as an ointment or cream; or in a form for rectal administration as a suppository.
  • exemplary parenteral administration forms include solutions or suspensions of active compounds in sterile aqueous solutions, for example, aqueous propylene glycol or dextrose solutions, which may be suitably buffered if desired.
  • Irg1 deficiency inhibited tumor growth in immune competent mice.
  • IRG1 The expression of the IRG1 gene in patients from The Cancer Genome Atlas (TCGA) Pan-Cancer Dataset cohorts was analyzed. The mRNA expression of IRG1 was compared across 19 distinct solid tumors. IRG1 mRNA expression was found to be up-regulated in multiple types of tumors as compared to the corresponding para-carcinoma normal tissues, including BLCA (bladder cancer) , BRCA (breast cancer) , COAD (colon adenocarcinoma) , ESCA (esophageal carcinoma) , HNSC (head and neck squamous cell carcinoma) , KICH (kidney chromophobe) , KIRP (kidney renal papillary cell carcinoma) , LUSC (lung squamous cell carcinoma) , PAAD (Pancreatic adenocarcinoma) , STAD (stomach adenocarcinoma) , and UCEC (uterine corpus endometrial carcinoma
  • IRG1 mRNA expression was up-regulated in patients with SKCM (skin cutaneous melanoma) compared with healthy skin tissues (FIG. 1A) .
  • EPIC Estimating the Proportions of Immune and Cancer cells
  • IRG1 mRNA expression was found to be positively correlated with the TAM fraction in many cancer types (FIG. 6) , suggesting that IRG1 is expressed in TAMs in a broad spectrum of human cancers.
  • Irg1 mRNA expression was readily detected in TAMs (F4/80 + Cd45 + ) sorted from B16-F10 tumors grown in Irg1 +/+ mice, but not in non-TAMs (F4/80 - Cd45 + or F4/80 - Cd45 - ) (FIG. 1B) .
  • ITA accumulation was observed in TAMs (F4/80 + Cd45 + ) from B10-F10 tumors in Irg1 +/+ mice, but not those in Irg1 -/- animals (FIG. 1B) .
  • the mRNA expression of Irg1 and intracellular levels of ITA were determined by qRT-PCR and LC-MS, respectively. Data are the mean ⁇ s.d., and the p values were calculated by an unpaired, two-tailed Student’s t test (FIG. 1B) .
  • BMDMs mouse bone marrow-derived macrophages
  • TAM tumor-cell-conditioned medium
  • Data are mean ⁇ s.e.m., and the p values were calculated by two-way ANOVA.
  • the survival probability was significantly prolonged in these tumor-bearing Irg1 -/- mice inoculated with B16-F10, MC38, and E0771 tumor cells (FIG. 1F) .
  • the p values were calculated using Log-rank (Mantel-Cox) test. *p ⁇ 0.05; **p ⁇ 0.01; ***p ⁇ 0.001; ****p ⁇ 0.0001 and n.s. denotes non-significant.
  • Irg1 deficiency reversed the immunosuppressive tumor microenvironment.
  • immune cells Cd45 +
  • scRNA-seq scRNA-seq schematics, left panel
  • FIG. 8A 19 clusters of major immune populations were distinguished (FIG. 8A) , and these clusters were assigned to 8 different types of immune cells, including macrophages (M ⁇ ) &monocytes, T cells, B cells, natural killer (NK) cells, plasmacytoid dendritic cells, dendritic cells, neutrophils, and limited leaked melanocytes (FIG. 8B-C) .
  • M ⁇ macrophages
  • NK natural killer cells
  • plasmacytoid dendritic cells dendritic cells
  • neutrophils neutrophils
  • limited leaked melanocytes FIG. 8B-C
  • Irg1 mRNA expression was readily detected in myeloid cells (characterized with high expression of Cd11b) and particularly in macrophages (characterized with high expression of F4/80) in the TME of B16-F10 tumors (FIG. 2B) . Expression of Irg1 and macrophage marker genes is illustrated in the UMAP plots.
  • TAMs were divided into 6 distinguishable clusters by using UMAP clustering (FIG. 2C) .
  • Annotated clusters of intratumoral monocytes/macrophages in Irg1 +/+ or Irg1 -/- mice are shown by t-SNE plots (left panel) . Cell numbers of each cluster are listed (right panel) .
  • Vcan + monocytes exhibited high expression of Ly6c2, Cxcl10 and Vcan (FIG. 9A) , which is similar with hemopoietic system-derived classical inflammatory monocytes as previously termed (L. Zhang, et al., Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer.
  • Vegfa + macrophages exhibited high expression of Spp1, Vegfa and Mmp12, sharing the similarity with the previously termed SPP1 + macrophages which possess an enrichment of tumor angiogenesis and pro-tumorigenic role (L. Zhang, et al., (2020) ) .
  • the two clusters of Vcan + monocytes and Vegfa + macrophages displayed distinct enrichment of inflammatory pathways, such as Type I and II interferon response in the former cluster, while M2-like macrophage polarization and anti-inflammatory pathway in the latter cluster (FIG. 9B) .
  • Vegfa + macrophages together with M1 and M2-like macrophages, were differentiated from Vcan + monocytes and Itgal + monocytes (FIG. 9C) , supporting the notion that TAMs can sequentially develop from monocytes into functional macrophages.
  • Irg1 expression was restricted to three TAM subsets, including Vcan + monocytes, M1-like macrophages, and Vegfa + macrophages (FIG. 2D) .
  • Irg1 deficiency seemed to alter the functional diversity of the TAM subsets, as evidenced by more Vcan + monocytes and M1-like macrophages, but less Vegfa + macrophages in the TME of B16-F10 tumors from Irg1 -/- mice compared with Irg1 +/+ controls (FIG. 2C) .
  • Percentages of myeloid cells (Cd45 + Cd11b + ) , Monocytes (Cd45 + Cd11b + Ly6c + ) , MDSC (Cd45 + Cd11b + Gr1 + ) , macrophages (Cd11b + F4/80 + ) , M1-like macrophages (Cd45 + Cd11b + F4/80 + iNos + ) , M2-like macrophages (Cd45 + Cd11b + F4/80 + iNos + ) , lymphocytes (Cd45 + Cd11b - ) , T cells (Cd45 + Cd3 + ) , Cd8 + T cells (Cd3 + Cd8 + ) , CD4 + T cells (Cd3 + Cd4 + ) and NK cells (Cd45 + Cd11b + Nk1.1 + ) are shown by violin plot.
  • Immunofluorescent (IF) staining confirmed more iNOS + or Cd8 + cells in B16-F10 tumors growing in Irg1 -/- mice than Irg1 +/+ controls (FIG. 2F) .
  • the tumors were collected as described in FIG. 1F.
  • Scale bar 20 ⁇ m.
  • HPFs high-power fields
  • the p values were calculated by unpaired, two-tailed Student’s t test. *p ⁇ 0.05; ** ⁇ 0.01; ****p ⁇ 0.0001; n.s. denotes non-significant.
  • Irg1-deficient macrophages acquired more M1-like features and promote antigen presentation and T cell chemotaxis
  • Irg1 was enriched in the tumor macrophage compartment in both human tumors and mouse models of cancer
  • GSEA gene set enrichment analysis
  • ssGSEA single sample gene set enrichment analysis
  • intratumoral monocytes/macrophages in melanoma from Irg1 -/- mice were found to exhibit higher gene signature scores of cytokine production, antigen processing and presentation, chemokine signaling pathway, and positive regulation of T cell migration as compared with those cells from Irg1 +/+ controls (FIG. 10A; FIG. 3A) .
  • Vcan + monocytes exhibited upregulation of interferon-stimulated genes (e.g. Irf7, Isg15, Ifi44, Ifi27l2a) in the TME of B16-F10 tumors from Irg1 - /- mice compared with Irg1 +/+ controls, and genes associated with antigen presentation and T cell migration (e.g. Aif1, Timd4, Tap1) were also up-regulated in M1-like TAMs from tumor-bearing Irg1 - /- mice (FIG. 3B) . Shown in FIG.
  • interferon-stimulated genes e.g. Irf7, Isg15, Ifi44, Ifi27l2a
  • genes associated with antigen presentation and T cell migration e.g. Aif1, Timd4, Tap1 were also up-regulated in M1-like TAMs from tumor-bearing Irg1 - /- mice (FIG. 3B) . Shown in FIG.
  • 3B are volcano plots of log 2 fold change and log 10 adjusted p value of differentially expressed genes in Vcan + monocytes or Vegfa + macrophages from Irg1 +/+ and Irg1 -/- mice, according to scRNA-seq results. Red dots, genes up-regulated in Irg1 -/- mice; blue dots, genes down-regulated in Irg1 -/- mice.
  • flow cytometry analysis illustrated that TAMs from tumor-bearing Irg1 -/- mice manifested enhanced immunogenic antigen presentation, as evidenced by higher expression of cell surface markers, such as MHC-I, MHC-II, or Cd40 (FIG. 3C) .
  • the p values were calculated by an unpaired, two-tailed Student’s t test.
  • pro-inflammatory cytokines e.g. Tnf ⁇ and Il-6
  • Tnf ⁇ and Il-6 pro-inflammatory cytokines
  • FIG. 10B The mRNA expression of pro-inflammatory cytokines was also upregulated in Irg1 -/- BMDMs compared to Irg1 +/+ controls after B16-F10-TCM treatment.
  • the protein secretion of Tnf ⁇ or Il-6 was increased in Irg1 -/- BMDMs compared to Irg1 +/+ controls after B16-F10-TCM treatment (FIG. 10C) .
  • Irg1 -/- BMDMs exhibited higher levels of iNOS than Irg1 +/+ cells after either co-culture with B16-F10 tumor cells or treatment with B16-F10-TCM (FIG. 10D-E) .
  • the M2-like macrophage marker Cd206 did not differ between Irg1 +/+ and Irg1 -/- BMDMs after either co-culture with B16-F10 tumor cells or treatment with B16-F10-TCM (FIG. 10D-E) .
  • Vegfa + macrophage enriched genes as distinguished by scRNA-seq (FIG.
  • Irg1-deficient macrophages exhibit altered diversity, including more proinflammatory M1-like features but reduced pro-angiogenic potential.
  • Irg1 mRNA expression in wild-type BMDMs was found to be induced at 6 hours after co-culture with B16-F10 tumor cells, and that higher mRNA expression of pro-inflammatory genes and those involved in antigen presentation and chemotaxis was observed in Irg1 -/- BMDMs at 12 hours post B16-F10 co-culture (FIG. 3E) .
  • a gene expression heatmap in BMDMs co-cultured with B16-F10 for indicated time points is shown in FIG. 3E.
  • the difference in inflammatory genes occurred after Irg1 induction in BMDMs upon stimulation by tumor cells, re-affirming the immunomodulatory role of IRG1/ITA during macrophage activation.
  • ITA is structurally similar with ⁇ -ketoglutaric acid ( ⁇ -KG) and binds to and inhibits ⁇ KG-dependent TET DNA demethylases, thereby downregulating NF- ⁇ B and STAT target genes to dampen the inflammatory response in classically activated macrophages (L. L.Chen, et al., (2022) ) .
  • 5hmC staining intensity was increased in tumors from Irg1 -/- than Irg1 +/+ mice (FIG. 11A) .
  • 5hmC mapping showed that its enrichment at the promoter regions of chemokine and cytokine genes (e.g. Ccl2, Ccl3, Ccl4, Cxcl9, Cxcl10, Il-1 ⁇ ) was higher in TAMs from Irg1 -/- tumor-bearing mice than Irg1 +/+ cells (FIG. 11B) . Higher 5hmC at the promoter regions of these selected genes was also observed in Irg1 -/- BMDMs treated with B16-F10-TCM (FIG. 11C) .
  • chemokine and cytokine genes e.g. Ccl2, Ccl3, Ccl4, Cxcl9, Cxcl10, Il-1 ⁇
  • BMDMs were also isolated from catalytically inactive Tet2 HxD knock-in (KI) mutant or wild-type mice, and then treated these macrophages with B16-F10-TCM either alone or together with ITA.
  • the Tet2 HxD KI mutant contains H1295Y and D1297A double substitution mutations in mouse Tet2, which are equivalent to human TET2 H1382 and H1384, respectively (Z. Zhao, et al., The catalytic activity of TET2 is essential for its myeloid malignancy-suppressive function in hematopoietic stem/progenitor cells. Leukemia 30, 1784-1788 (2016) ) , and disrupt the binding with the essential cofactor Fe 2+ .
  • Exogenous ITA inhibited the expression of inflammatory genes induced by B16-F10-TCM in Tet2+/+ BMDMs.
  • a transwell system was developed in which BMDMs were co-cultured with B16-F10 or treated with B16-F10-TCM in the lower chambers of a 5 ⁇ m Transwell plate and were separated from direct contact with Cd8 + T cells (FIG. 3F) .
  • CD8 + T cells were placed in the upper chambers with or without CXCR3 antagonists SCH546738. After incubation at 37°C for 4 hours, CD8 + T cells that migrated into the lower chambers were collected and counted. Data shown are from 4 independent experiments. The p values were calculated by two-way ANOVA.
  • Irg1 -/- BMDMs promoted the migration of Cd8 + T cells more efficiently than Irg1 +/+ cells, and this effect was abrogated by the CXCR3 specific antagonist SCH546738, which is known to block the CXCL9, 10, 11/CXCR3 axis and thus T cell migration (C. Yue, et al., STAT3 in CD8+ T Cells Inhibits Their Tumor Accumulation by Downregulating CXCR3/CXCL10 Axis. Cancer Immunol Res 3, 864-870 (2015) ) .
  • the percentages of Cd8 + T cells (Cd3 + Cd8 + ) were determined by flow cytometry (FIG. 3G) .
  • B16-F10 tumor growth was determined by the measurement of tumor volume (mm 3 ) . Data are mean ⁇ s.d. (FIG. 3G) or s.e.m. (FIG.
  • Irg1 deletion in mice enhances the efficacy of anti-PD- (L) 1 immunotherapy
  • Irg1 deficiency enhances the chemotaxis of cytotoxic Cd8 + T cells
  • the functional consequences of Irg1 loss on cancer responses to immunotherapy was investigated.
  • Data shown are mean ⁇ s.e.m., and the p values were calculated using two-way ANOVA (FIG. 4A and 4C) .
  • the p values were calculated using Log-rank (Mantel-Cox) test (FIG. 4B and 4D) .
  • B16-F10 was inoculated subcutaneously into Irg1 +/+ and Irg1 -/- mice which were then subjected to PD-L1 blockade. Strikingly, the growth of B16-F10 tumor in Irg1 -/- mice (without PD-L1 blockade) was found to be comparable to that in anti-PD-L1-treated Irg1 +/+ mice (FIG. 4A, B) .
  • Anti-PD-L1-treated Irg1 -/- mice showed the most effective tumor inhibition and prolonged survival, with the mean lifespan being extended to 27 days compared with 18 days in either Irg1 -/- mice (without PD-L1 blockade) or anti-PD-L1-treated Irg1 +/+ mice (FIG. 4A, B) .
  • FIG. 4E Experimental schematics of macrophage adoptive transfer into tumor-bearing wild-type mice are shown in FIG. 4E (upper panel) .
  • Mice were injected intratumorally (i. t. ) with Irg1 +/+ or Irg1 -/- BMDMs and intraperitoneally (i.p. ) with anti-PD-L1 antibody at the same time.
  • Data shown are mean ⁇ s.e.m.
  • the p values were calculated using two-way ANOVA.
  • FIG. 4F shows overall survival of mice as described in FIG. 4E. The p values were calculated using Log-rank (Mantel-Cox) test.
  • Anti-PD-L1-treated Irg1 -/- mice showed the most effective tumor inhibition and prolonged survival, with the mean lifespan being extended to 26 days compared with 23 and 21 days in Irg1 -/- mice (without PD-L1 blockade) and anti-PD-L1-treated Irg1 +/+ mice, respectively (FIG. 4F) .
  • IRG1 is a novel myeloid immune check-point gene, and that Irg1-deficient macrophages dictate the tumoricidal effect in vivo and can enhance the efficacy of cancer immunotherapy.
  • Irg1-deficient macrophages inhibited pancreatic cancer growth
  • Pancreatic cancer evades immunologic elimination by a variety of mechanisms, including induction of an immunosuppressive TME.
  • pancreatic cancer cells derived from the genetically engineered mouse tumor model (LSL-KrasG12D; LSL-Trp53R172H; Pdx1-Cre mice; KPC) , were implanted into the pancreas of Irg1 -/- and Irg1 +/+ mice.
  • KPC pancreatic cancer cells were inoculated orthotopically in the pancreas of Irg1 +/+ and Irg1 -/- mice followed by i.p.
  • KPC tumor growth was inhibited in myeloid cell-specific Irg1-deficient mice (Irg1 f/f Lyz-Cre) (FIG. 5B) , further supporting that targeting Irg1 in macrophages dictates the tumoricidal effect in vivo.
  • the macrophage adoptive transfer was conducted by intravenous injection of Irg1 -/- or Irg1 +/+ BMDMs into KPC-tumor bearing wild-type mice.
  • Irg1 -/- or Irg1 +/+ BMDMs were labelled with FITC-conjugated beads and then intravenously injected (1 x 10 7 per mouse) (FIG. 14A) .
  • the transferred macrophages comprised ⁇ 40%of total intratumoral macrophages in the TME of KPC tumors receiving either Irg1 -/- or Irg1 +/+ macrophages (FIG.
  • FIG. 5C Experimental schematics of macrophage adoptive transfer into wild-type recipients bearing KPC tumor (left panel) .
  • Tumors were harvested and weighted at day 15 post inoculation (middle and right panels) .
  • the p values were calculated using one-way ANOVA.
  • Flow cytometry analysis revealed that the populations of M1-like TAMs (iNOS + F4/80 + Cd11b + ) and CD8 + T cells (Cd8 + Cd3 + ) were significantly increased in KPC tumors receiving Irg1 -/- macrophages compared to Irg1 +/+ controls (FIG. 5D) .
  • Macrophage adoptive transfer into wild-type recipients was conducted as described for FIG. 5C.
  • the percentages of immune cells (Cd45 + ) , MDSC (Cd45 + Cd11b + Gr1 + ) , M1-like macrophages (Cd45 + Cd11b + F4/80 + iNos + ) , and Cd8 + T cells (Cd45 + Cd3 + Cd8 + ) were measured and calculated. The p values were calculated by one-way ANOVA. Immunofluorescent staining in KPC tumors receiving the therapy with Irg1 -/- macrophages confirmed more iNOS + or Cd8 + cells (FIG. 5E; FIG. 14C) and TUNEL-positive apoptotic cells (FIG. 5E, F) .
  • FIG. 5C Representative images of IF staining of CD8 and Tunel in KPC tumors as described in FIG. 5C. Scale bars of a low and a high magnification represent 200 ⁇ m and 50 ⁇ m, respectively. The quantification of average cell number with s.d. from 6 random high-power fields (HPFs) is shown. *p ⁇ 0.05, **p ⁇ 0.01, ***p ⁇ 0.001, ****p ⁇ 0.0001 and n.s. denotes not significant.
  • a method of treating cancer in a subject in need thereof comprising administering to the subject an amount of genetically modified macrophages, monocytes or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown, in combination with an amount of a PD-1 axis binding antagonist, wherein the amounts together are effective in treating cancer.
  • Irg1 immune responsive gene 1
  • a method of treating cancer in a subject in need thereof comprising: (a) providing genetically modified macrophages, monocytes or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown; and (b) administering to the subject an amount of a composition comprising the genetically modified macrophages, monocytes or stem cell-derived macrophages/monocytes in combination with an amount of a PD-1 axis binding antagonist, wherein the amounts together are effective in treating cancer.
  • Irg1 immune responsive gene 1
  • a method of inducing or potentiating an immune response in a subject in need thereof comprising administering to the subject an amount of a composition comprising genetically modified macrophages, monocytes or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown, in combination with an amount of a PD-1 axis binding antagonist, wherein the amounts together are effective in inducing or potentiating an immune response.
  • a composition comprising genetically modified macrophages, monocytes or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown
  • a method of inducing or potentiating an immune response in a subject in need thereof comprising: (a) providing genetically modified macrophages, monocytes or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown; and (b) administering to the subject an amount of a composition comprising the genetically modified macrophages, monocytes or stem cell-derived macrophages/monocytes, in combination with an amount of a PD-1 axis binding antagonist, wherein the amounts together are effective in inducing or potentiating an immune response.
  • Irg1 immune responsive gene 1
  • RNA interference RNA interference
  • the gene editing comprises an endonuclease selected from a clustered regularly interspaced short palindromic repeats (CRISPR) /Cas nuclease system, a zinc finger nuclease (ZFN) , a Transcription Activator Like Effector nuclease (TALEN) , or a meganuclease.
  • CRISPR clustered regularly interspaced short palindromic repeats
  • ZFN zinc finger nuclease
  • TALEN Transcription Activator Like Effector nuclease
  • RNAi RNA interference
  • RNAi agent is microRNA (miRNA) , small interfering RNA (siRNA) , or short hairpin RNA (shRNA) .
  • miRNA microRNA
  • siRNA small interfering RNA
  • shRNA short hairpin RNA
  • PD-1 axis binding antagonist comprises a PD-1 binding antagonist, a PD-L1 binding antagonist, or a PD-L2 binding antagonist.
  • E18 The method of embodiment E17, wherein the anti-PD-1 antibody is nivolumab, pembrolizumab, pidilizumab, cemiplimab, dostarlimab, tislelizumab, spartalizumab, sasanlimab, camrelizumab, sintilimab, toripalimab, AMP-514 (MEDI-0680) , AMP-224, JTX-4014, INCMGA00012 (MGA012) , BGB-108, or AGEN-2034, or a combination thereof.
  • the anti-PD-1 antibody is nivolumab, pembrolizumab, pidilizumab, cemiplimab, dostarlimab, tislelizumab, spartalizumab, sasanlimab, camrelizumab, sintilimab, toripalimab, AMP-514 (MEDI-
  • E22 The method of any one of embodiments E1, E2 and E5 to E21, wherein the cancer is selected from the group consisting of melanoma, colorectal cancer, breast cancer, and pancreatic cancer.
  • a combination comprising: (a) genetically modified macrophages, monocytes or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown; and (b) a PD-1 axis binding antagonist.
  • Irg1 immune responsive gene 1
  • a combination for use in inducing or potentiating an immune response comprising: (a) genetically modified macrophages, monocytes or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown; and (b) a PD-1 axis binding antagonist.
  • Irg1 immune responsive gene 1
  • a combination for use in the treatment of cancer comprising: (a) genetically modified macrophages, monocytes or stem cell-derived macrophages/monocytes comprising an immune responsive gene 1 (Irg1) gene knockout, mutation, or knockdown; and (b) a PD-1 axis binding antagonist.
  • Irg1 immune responsive gene 1
  • RNA interference RNA interference
  • E29 The combination of embodiment E28, wherein the gene editing comprises an endonuclease selected from a clustered regularly interspaced short palindromic repeats (CRISPR) /Cas nuclease system, a zinc finger nuclease (ZFN) , a Transcription Activator Like Effector nuclease (TALEN) , or a meganuclease.
  • CRISPR clustered regularly interspaced short palindromic repeats
  • ZFN zinc finger nuclease
  • TALEN Transcription Activator Like Effector nuclease
  • RNA interference RNA interference
  • RNAi agent is microRNA (miRNA) , small interfering RNA (siRNA) , or short hairpin RNA (shRNA) .
  • miRNA microRNA
  • siRNA small interfering RNA
  • shRNA short hairpin RNA
  • E32 The combination of any one of embodiments E27 to E31, wherein the population of macrophages, monocytes or stem cell-derived macrophages/monocytes is autologous to the subject.
  • E33 The combination of any one of embodiments E27 to E31, wherein the population of macrophages, monocytes or stem cell-derived macrophages/monocytes is allogeneic to the subject.
  • E35 The combination of any one of embodiments E24 to E34, wherein the genetically modified macrophages or monocytes are genetically modified bone marrow-derived macrophages or bone marrow-derived monocytes.
  • E36 The combination of any one of embodiments E24 to E35, wherein the PD-1 axis binding antagonist comprises a PD-1 binding antagonist, a PD-L1 binding antagonist, or a PD-L2 binding antagonist.
  • E43 The combination of any one of embodiments E26 to E42, wherein the cancer is selected from the group consisting of melanoma, colorectal cancer, breast cancer, and pancreatic cancer.
  • a method of treating cancer in a subject in need thereof comprising administering to the subject an amount of an aconitate decarboxylase 1 (ACOD1) inhibitor, in combination with an amount of a PD-1 axis binding antagonist, wherein the amounts together are effective in treating cancer.
  • ACOD1 aconitate decarboxylase 1
  • a method of inducing or potentiating an immune response in a subject in need thereof comprising administering to the subject an amount of an aconitate decarboxylase 1 (ACOD1) inhibitor, in combination with an amount of a PD-1 axis binding antagonist, wherein the amounts together are effective in inducing or potentiating an immune response.
  • ACOD1 aconitate decarboxylase 1
  • PD-1 axis binding antagonist comprises a PD-1 binding antagonist, a PD-L1 binding antagonist, or a PD-L2 binding antagonist.
  • E50 The method of embodiment E49, wherein the anti-PD-1 antibody is nivolumab, pembrolizumab, pidilizumab, cemiplimab, dostarlimab, tislelizumab, spartalizumab, sasanlimab, camrelizumab, sintilimab, toripalimab, AMP-514 (MEDI-0680) , AMP-224, JTX-4014, INCMGA00012 (MGA012) , BGB-108, or AGEN-2034, or a combination thereof.
  • the anti-PD-1 antibody is nivolumab, pembrolizumab, pidilizumab, cemiplimab, dostarlimab, tislelizumab, spartalizumab, sasanlimab, camrelizumab, sintilimab, toripalimab, AMP-514 (MEDI-
  • E54 The method of any one of embodiments E44 to E53, wherein the ACOD1 inhibitor is selected from the group consisting of a small molecule inhibitor, a small molecule degrader, a peptide inhibitor, a peptidomimetic inhibitor, a nucleic acid, and an anti-ACOD1 antibody, or a combination thereof.
  • the ACOD1 inhibitor is selected from the group consisting of a small molecule inhibitor, a small molecule degrader, a peptide inhibitor, a peptidomimetic inhibitor, a nucleic acid, and an anti-ACOD1 antibody, or a combination thereof.
  • nucleic acid is an antisense oligonucleotide, an aptamer, a CRISPR guide RNA (gRNA) , or an RNAi agent.
  • gRNA CRISPR guide RNA
  • RNAi agent is microRNA (miRNA) , small interfering RNA (siRNA) , or short hairpin RNA (shRNA) .
  • miRNA microRNA
  • siRNA small interfering RNA
  • shRNA short hairpin RNA
  • E61 The method of any one of embodiments E44 and E46 to E60, wherein the cancer is selected from the group consisting of melanoma, colorectal cancer, breast cancer, and pancreatic cancer.
  • E63 A combination comprising an ACOD1 inhibitor and a PD-1 axis binding antagonist.
  • a combination for use in inducing or potentiating an immune response comprising an ACOD1 inhibitor and a PD-1 axis binding antagonist.
  • a combination for use in the treatment of cancer comprising an ACOD1 inhibitor and a PD-1 axis binding antagonist.
  • E66 The combination of any one of embodiments E63 to E65, wherein the PD-1 axis binding antagonist comprises a PD-1 binding antagonist, a PD-L1 binding antagonist, or a PD-L2 binding antagonist.
  • E69 The combination of embodiment E68, wherein the anti-PD-1 antibody is nivolumab, pembrolizumab, pidilizumab, cemiplimab, dostarlimab, tislelizumab, spartalizumab, sasanlimab, camrelizumab, sintilimab, toripalimab, AMP-514 (MEDI-0680) , AMP-224, JTX-4014, INCMGA00012 (MGA012) , BGB-108, or AGEN-2034, or a combination thereof.
  • the anti-PD-1 antibody is nivolumab, pembrolizumab, pidilizumab, cemiplimab, dostarlimab, tislelizumab, spartalizumab, sasanlimab, camrelizumab, sintilimab, toripalimab, AMP-514 (MEDI-
  • E73 The combination of any one of embodiments E63 to E72, wherein the ACOD1 inhibitor is selected from the group consisting of a small molecule inhibitor, a small molecule degrader, a peptide inhibitor, a peptidomimetic inhibitor, a nucleic acid, and an anti-ACOD1 antibody, or a combination thereof.
  • the ACOD1 inhibitor is selected from the group consisting of a small molecule inhibitor, a small molecule degrader, a peptide inhibitor, a peptidomimetic inhibitor, a nucleic acid, and an anti-ACOD1 antibody, or a combination thereof.
  • nucleic acid is an antisense oligonucleotide, an aptamer, a CRISPR guide RNA (gRNA) , or an RNAi agent.
  • gRNA CRISPR guide RNA
  • RNAi agent is microRNA (miRNA) , small interfering RNA (siRNA) , or short hairpin RNA (shRNA) .
  • miRNA microRNA
  • siRNA small interfering RNA
  • shRNA short hairpin RNA
  • E80 The combination of any one of embodiments E65 to E79, wherein the cancer is selected from the group consisting of melanoma, colorectal cancer, breast cancer, and pancreatic cancer.
  • Irg1 promotes tumor growth in immune competent mice
  • the genome-wide transcriptome data quantified as FPKM Frragments Per Kilobase per Million
  • TCGA Cancer Genome Atlas
  • the analysis used the data from 18 cancer types, all of which had profiled sufficient numbers of samples for both cancer and normal tissues.
  • Data include bladder urothelial carcinoma (BLCA) , breast invasive carcinoma (BRCA) , cholangiocarcinoma (CHOL) , colon adenocarcinoma (COAD) , esophageal carcinoma (ESCA) , head and neck squamous cell carcinoma (HNSC) , kidney chromophobe (KICH) , kidney clear cell carcinoma (KIRC) , kidney renal papillary cell carcinoma (KIRP) , liver hepatocellular carcinoma (LIHC) , lung adenocarcinoma (LUAD) , lung squamous cell carcinoma (LUSC) , pancreatic adenocarcinoma (PAAD) , prostate adenocarcinoma (PRAD) , rectum adenocarcinoma (READ) , stomach adenocarcinoma (STAD) , thyroid carcinoma (THCA) , and uterine corpus endometrial carcinoma (UCEC) .
  • SKCM skin cutaneous melanoma
  • GTEx Genotype-Tissue Expression
  • GTEx Genotype-Tissue Expression
  • FIG. 1 (A) EPIC (Estimating the Proportions of Immune and Cancer cells) (J. Racle &D. Gfeller, (2020) ) was used to calculate the immune cell fractions for all the samples. The cell fraction of TAMs was identified, and spearman rank correlation test was used to determine the significance of correlation between immune cell fractions and IRG1 expression level.
  • Irg1 -/- mice (JAX stock #029340) were purchased from the Jackson Laboratory. Animals were backcrossed for more than 7 generations onto the C57BL/6J background and were maintained at Shanghai Research Center for Model Organisms. Myeloid cell-specific Irg1-deficient mice (Irg1 f/f , Lyz-Cre) on C57BL/6J background was generated by Shanghai Model Organisms Center, Inc. and were maintained at the Center for New Drug Evaluation and Research, China Pharmaceutical University (Nanjing, China) . Tet2 HxD KI mutant mice on C57BL/6J background were constructed by using CRISPR/Cas9 system. Analysis was performed on 6–10-week-old female mice obtained from the above-mentioned breeding.
  • HEK293T cells ATCC, CRL-3216 TM
  • B16-F10 cells ATCC, CRL-6475 TM
  • MC38 cells Kerfast, Cat#: ENH204
  • E0771 cells ATCC, CRL-3461 TM
  • FC1242 cells were kindly gifted from Dr. Li Fei (Fudan University) .
  • Tumor cells were maintained in DMEM medium containing 10%FBS (ExCell Bio, FSD500) , 1%Penicillin/Streptomycin antibiotics.
  • mice were euthanized in a 5%CO 2 chamber and death was confirmed by cervical dislocation. Bone marrow was harvested from the femur and the tibia and differentiated in DMEM (containing 10%fetal calf serum, 1%penicillin/streptomycin, and 100 ng/mL M-CSF) for 7 days. Then, 1 ⁇ 10 6 BMDMs per milliliter were co-cultured with tumor cells or treated with tumor-derived conditioned medium for different time points.
  • DMEM containing 10%fetal calf serum, 1%penicillin/streptomycin, and 100 ng/mL M-CSF
  • TCM Tumor-derived conditioned medium
  • B16-F10, E0771, MC38, or FC1242 tumor cells were seeded with 10 mL medium in 10 cm dish, and the culture medium were collected after 24 hours followed by filtration using 0.45 ⁇ m filter (Corning) and were then stored at -20°C.
  • Data are mean ⁇ s.e.m., and the p values were calculated by unpaired, two-tailed Student’s t test.
  • FIG. 1 (F) Overall survival of mice inoculated with B16-F10, MC38, and E0771 tumor cells.
  • the p values were calculated using Log-rank (Mantel-Cox) test. *p ⁇ 0.05; **p ⁇ 0.01; ***p ⁇ 0.001 and n.s. denotes non-significant.
  • FC1242 cells were kept in 25 mL DMEM and were mixed with 25 ⁇ l Matrigel (BD Biosciences) . The cell suspension was then injected orthotopically into the pancreas of Irg1 +/+ or Irg1 -/- mice (female, 8-10 weeks) . At day 15 after FC1242 tumor inoculation, the pancreatic tumors were dissected, weighted, and subjected to further analysis.
  • anti-PD-L1 200 ⁇ g/mouse, BioXcell, BP0101
  • anti-PD-1 200 ⁇ g/mouse, BioXcell, BE0146; or Biointron, B176401
  • tumor size was determined.
  • mice were intratumorally injected with the CXCR3 antagonist SCH546738 (600 mg per mouse; MedChem Express, HY-10017) , starting at day 6 after tumor inoculation and then maintained by daily injection for one week.
  • the CXCR3 antagonist SCH546738 600 mg per mouse; MedChem Express, HY-10017
  • 1 ⁇ 10 4 BMDMs/mm 3 tumor volume were injected intratumorally at day 11, 13, 15 and 17 after B16-F10 inoculation with or without i.p. injection of anti-PD-L1 (200 ⁇ g per mouse) (injection at the same time with macrophage) .
  • 1 x 10 7 /50 ⁇ L BMDMs were intravenously (i. v. ) injected at day 10 and 13 after FC1242 inoculation. Mice were euthanized at day 15 after tumor inoculation, and the pancreatic tumors were dissected, weighted, and subjected to further analysis.
  • Cell number and cell diameter were measured using and automated cell counter (Countstar) .
  • C 13 -labelled ITA was added as internal standard.
  • Cells were fixed by immediate addition of 1 mL 80%(v/v) chilled (-80°C) methanol.
  • Cell extracts were analyzed by ultrahigh performance liquid chromatograph (Acquity UPLC I-Class, Waters) coupled to a Triple Quadrupole Mass Spectrometer (Xevo TQ-XS, Waters) .
  • Tumors were harvested at indicated time. Briefly, 100 mm 3 of each tumor was chopped and filtered through a 70- ⁇ m cell strainer to generate a single-cell suspension. After red blood cell lysis (Beyotime, C3702) , cells were counted and plated in PBS. Cell surface molecule staining was performed at 4°C for 15-30 minutes in PBS in the dark.
  • cells were fixed/permeabilized in 50 ⁇ L of a saponin-containing buffer (BD Biosciences, 554722) and incubate at 4°C for 30 minutes in the dark. Cells were then washed 2 times with saponin-containing buffer (BD Biosciences, 554722) and resuspend in staining buffer followed by antibody staining. Stained samples were acquired on a LSRFortessa TM flow cytometer (BD Biosciences) . Collected data were analyzed using FlowJo software (Tree Star, Inc) .
  • the antibodies used in this study are: PE Anti-Cd45 (BD bioscience, 553081) ; FITC Anti-CD45 (BD bioscience, 553079) ; FITC Anti-Cd11b (BD bioscience, 561688) ; APC Anti-Cd11b (BD bioscience, 553312) ; PE Anti-F4/80 (BD bioscience, 565410) ; APC Anti-F4/80 Antibody (Invitrogen, 17-4801-82) ; APC Anti-Mouse Ly-6G (BD bioscience, 553129) ; APC-Cy7 Anti-Ly-6C (BD bioscience, 560596) ; PE-Cy7 Anti-Cd3e (BD bioscience, 552774) ; APC Anti-Cd3e (BD bioscience, 561826) ; FITC Anti-Cd8a (BD bioscience, 553030) ; APC Anti-Cd8a (BD bioscience, 553035) ; PerCP/Cyanine5.5 Anti
  • Irg1 -/- and Irg1 +/+ mice were injected subcutaneously with 2 ⁇ 10 5 B16-F10 cells (in 50 ⁇ L of PBS) .
  • Tumor tissues from three mice of the same group were randomly combined into one mixed sample, and then tissues were digested and went through 70 ⁇ m filters (BD Biosciences, 352350) to achieve single-cell suspensions.
  • red blood cell lysis buffer Beyotime Biotechnology, C3702
  • flow cytometry buffer PBS/0.5%albumin/2 Mm EDTA
  • BD Rhapsody system was used to capture the transcriptomic information of the single cells.
  • Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion (NEB, M0293S) .
  • each cDNA molecule was tagged on the 5’ end (that is, the 3’ end of mRNA transcript) with a uniquE MOlecular identifier (UMI) and cell barcode indicating its cell of origin.
  • UMI uniquE MOlecular identifier
  • Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE) , RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) . Sequencing was performed by sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.
  • scRNA-seq data analysis was performed by using NovelBrain Cloud Analysis Platform. The analysis applied fastp with default parameter filtering the adaptor sequence and removed the low-quality reads to achieve the clean data.
  • UMI-tools were applied to identify the cell barcode whitelist. The UMI-based clean data was mapped to mouse genome (Ensemble version 100) utilizing STAR mapping with customized parameter from UMI-tools standard pipeline to obtain the UMIs counts of each sample. Cells contained over 200 expressed genes and mitochondria UMI rate below 10%passed the cell quality filtering and mitochondria genes were removed in the expression table. Seurat package (version: 3.1.4, https: //satijalab.
  • PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals were used for Tsne construction and UMAP construction.
  • the unsupervised cell cluster result was acquired based the PCA top 10 principal and the marker genes were calculated by FindAllMarkers function with wilcox rank sum test algorithm under following criteria: 1. LnFC > 0.25; 2. p value ⁇ 0.05; 3. Min. pct>0.1.
  • the clusters of same cell type were selected for re-Tsne analysis, graph-based clustering and marker analysis.
  • Chromatin-immunoprecipitation with quantitative PCR (ChIP-qPCR)
  • ChIP assay was performed as described previously (L. L. Chen, et al., SNIP1 recruits TET2 to Regulate c-MYC Target Genes and Cellular DNA Damage Response, Cell Rep. 25 (6) : 1485-1500. e4 (2018) ) . Briefly, cells were cross-linked with 1%paraformaldehyde and sonicated at 4°C for 20 minutes (Bioruptor, low mode) . Chromatin was immunoprecipitated at 4°C for 3 hours with indicated antibodies. Antibody-chromatin complexes were pulled-down using protein A-Sepharose (Millipore, 16-125) , washed and eluted.
  • T cell migration assay was performed by using 24-well 6.5 mm with 5.0 ⁇ m Pore Polycarbonate Membrane Insert.
  • BMDMs (5 ⁇ 10 5 ) were co-cultured with B16-F10 tumor cells (5 ⁇ 10 5 ) or challenged with B16-F10-TCM for 12 hours at the bottom chamber.
  • Cd8 + T cells (1 ⁇ 10 6 ) were isolated from the spleen of wild-type mice and suspended in 200 ⁇ l of 1%FBS RPMI 1640, and were then placed at the top chamber with or without 100 nM SCH546738 (MCE, HY-10017) .
  • MCE nM SCH546738
  • PMA-differentiated THP1-derived macrophages (1 ⁇ 10 6 ) were challenged with MDA-MB-231-TCM for 12 hours at the bottom chamber.
  • Jurkat T cells (1 ⁇ 10 6 ) were suspended in 200 ⁇ l of 1%FBS RPMI 1640 and were placed at the top chamber. The migration of Jurkat T cells from the top to the bottom chamber was evaluated after 4-hour incubation at 37°C in a 5%CO 2 atmosphere.

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Abstract

L'invention concerne des combinaisons et des procédés thérapeutiques faisant appel à des macrophages, à des monocytes ou à des macrophages/monocytes dérivés de cellules souches génétiquement modifiés comprenant une inactivation génique de gène de réponse immunitaire 1 (Irg1), une mutation, ou un knockdown, en combinaison avec un antagoniste de liaison à l'axe PD-1. L'invention concerne des combinaisons et des procédés thérapeutiques comprenant un inhibiteur d'aconitate décarboxylase 1 (ACOD1), en combinaison avec un antagoniste de liaison à l'axe PD-1.
PCT/CN2022/132360 2022-11-16 2022-11-16 Thérapie anticancéreuse basée sur le ciblage d'irg1 WO2024103313A1 (fr)

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Citations (2)

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CN110734493A (zh) * 2018-07-20 2020-01-31 厦门大学 抗pd-1抗体及其用途
CN114657212A (zh) * 2022-03-29 2022-06-24 浙江大学 一种基于基因编辑代谢来增强功能的巨噬细胞，及其制备方法和应用

Patent Citations (2)

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Publication number Priority date Publication date Assignee Title
CN110734493A (zh) * 2018-07-20 2020-01-31 厦门大学 抗pd-1抗体及其用途
CN114657212A (zh) * 2022-03-29 2022-06-24 浙江大学 一种基于基因编辑代谢来增强功能的巨噬细胞，及其制备方法和应用

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PAPATHANASSIU ADONIA E, LODI FRANCESCA; VU HONG A.; LAMBRECHTS DIETHER: "Abstract 1202: ERG344: A novel IRG1 inhibitor for the treatment of colon cancer", CANCER RESEARCH, AMERICAN ASSOCIATION FOR CANCER RESEARCH, vol. 81, no. 13_Supplement, 1 July 2021 (2021-07-01), pages 1202 - 1202, XP093170673, ISSN: 0008-5472, DOI: 10.1158/1538-7445.AM2021-1202 *
WEISS JONATHAN M, WINK DAVID A; MCVICAR DANIEL W: "Itaconic acid mediates crosstalk between macrophage metabolism and peritoneal tumors", JOURNAL OF CLINICAL INVESTIGATION, AMERICAN SOCIETY FOR CLINICAL INVESTIGATION, vol. 128, no. 9, 31 August 2018 (2018-08-31), pages 3794 - 3805, XP093170670, ISSN: 0021-9738, DOI: 10.1172/JCI99169 *
WU QI, YU XIN; LI JUANJUAN; SUN SHENGRONG; TU YI: "Metabolic regulation in the immune response to cancer", CANCER COMMUNICATIONS, vol. 41, no. 8, 1 August 2021 (2021-08-01), pages 661 - 694, XP093170667, ISSN: 2523-3548, DOI: 10.1002/cac2.12182 *
ZHAO HONGYUN, TENG DA; YANG LIFENG; XU XINCHENG; CHEN JIAJIA; JIANG TENGJIA; FENG AUSTIN Y.; ZHANG YAQING; FREDERICK DENNIE T.; GU: "Myeloid-derived itaconate suppresses cytotoxic CD8+ T cells and promotes tumour growth", NATURE METABOLISM, vol. 4, no. 12, 14 November 2022 (2022-11-14), pages 1660 - 1673, XP093170666, ISSN: 2522-5812, DOI: 10.1038/s42255-022-00676-9 *

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