# US 2023/0053540 A1 · Treatment of liver injury > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2023/0053540 A1 - Document ID: US20230053540A1 - Status: Published application - Kind: A1 - Application number: 17/431,835 - Filed: 2020-02-19 - Published: 2023-02-23 - Earliest claimed: 2019-02-19 - Assignees: Massachusetts Institute of Technology; The Brigham and Women's Hospital, Inc.; Dana-Farber Cancer Institute, Inc. - Applicants: Massachusetts Institute of Technology; The Brigham and Women's Hospital, Inc.; Dana-Farber Cancer Institute, Inc. - Inventors: Alexander K. Shalek; Kellie Elizabeth Kolb; Chad Walesky; Wolfram Goessling - Web page: https://patentgrep.com/patent/US20230053540A1 ## CPC - A61K 38/005: {Enzyme inhibitors (protease inhibitors A61K38/55)} - A61K 38/465: {acting on ester bonds (3.1), e.g. lipases, ribonucleases} - A61K 39/39: characterised by the immunostimulating additives, e.g. chemical adjuvants - A61K 45/06: Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca - A61P 1/16: for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics - C12N 15/111: {General methods applicable to biologically active non-coding nucleic acids} - C12N 15/63: Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression - A01K 2207/25: Animals on a special diet - A01K 2227/105: Murine - A01K 2267/03: Animal model, e.g. for test or diseases - A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D) - A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS - C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00) - A01K: ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS ## Abstract A method of treating an injury in an organ or tissue includes administering to a subject in need thereof an agent that modulates expression and/or activity of one or more genes involved in the regeneration and functional compensation of the tissue or organ in response to the injury. ## Claims ### Claim 1 A method of treating liver injury comprising stimulating functional compensation in liver cells by administering an agent that stimulates macrophage Wnt signaling. ### Claim 2 (depends on 1) The method of claim 1, wherein administering an agent comprises delivering a vector that targets liver macrophages. ### Claim 3 (depends on 1) The method of claim 1, wherein administering an agent comprises delivery of an agent targeting hepatocytes thereby stimulating macrophage Wnt signaling at the site of livery injury. ### Claim 3 (depends on 1) The method of claim 1, further comprising administering to the subject in need thereof another agent that modulates expression and/or activity of one or more genes or gene products that have functions in HDAC3 targets, photodynamic therapy stress, CEBP targets, tolerant macrophage, response to salirasib, adult tissue stem module, klfl targets, anatomical structure formation involved in morphogenesis, circulatory system process, cellular response to external stimulus, response to wounding, cellular response to extracellular stimulus, cell activation, cellular response to oxygen containing compound, vesicle mediated transport, enzyme linked receptor protein signaling pathway, response to bacterium, regulation of catabolic process, response to ketone, regulation of cell adhesion, response to hormone, blood vessel morphogenesis, response to estrogen, response to radiation, response to extracellular stimulus, cellular response to nitrogen compound, regulation of catalytic activity, vasculature development, response to abiotic stimulus, response to drug, response to growth factor, regulation of protein metabolic process, transmembrane receptor protein tyrosine kinase signaling pathway, cellular response to peptide, hexose metabolic process, cellular response to stress, endocytosis, circulatory system development, response to starvation, hemostasis, response to molecule of bacterial origin, cell surface, peptidase regulator activity, molecular function regulator, peptidase inhibitor activity, phospholipid binding, TNF-a signaling via NFkB, or a combination thereof. ### Claim 4 A method of decreasing cancer susceptibility and/or inflammation comprising administering a subject in need thereof an inhibitor of peroxisome proliferator-activated receptors (PPARs). ### Claim 4 (depends on 1) The method of claim 1, wherein the agent modulates expression and/or activity of one or more genes or gene products in Wnt pathway. ### Claim 5 (depends on 2) The method of claim 2, wherein the PPAR is alpha, beta/delta or gamma. ### Claim 5 (depends on 1) The method of claim 1, wherein the agent modulates expression and/or activity of one or more genes or gene products that are markers of hepatic stem cells. ### Claim 6 (depends on 2) The method of claim 2, wherein administration of the inhibitor is localized to the gut or localized to the liver. ### Claim 6 (depends on 1) The method of claim 1, wherein the expression and/or activity of the one or more genes or gene products is altered both in response to a zone-dependent injury and a zone-independent injury. ### Claim 7 (depends on 2) The method of claim 2, wherein the subject is obese or on a high fat diet. ### Claim 7 (depends on 1) The method of claim 1, wherein the one or more genes or gene products comprises Gclc, Txnrd1, Lars2, Cyp4a14, Apoc2, Apoc1, Cyp2c29, Mt1, Mt2, Saa1, Saa2, Fgl1, Mup17, Mup18, Mup11, Gm23935, mmu-mir-6236, Ly6e, Rnase4, Saa4, Fgl1, Hp, Hpx, Lcn2, Orm1, Apcs, Orm2, Saa1, Saa2, Saa3, Sds, Tacc2, Igfbp1, Cxc11, Thrsp, Serpina3n, Lpin1, Steap4, Mt1, Mt2, Aldh3a2, Cyp2c37, Cyp2c29, Cyp8b1, Ces1d, Apoc1, Hsd17b13, Atp5h, Apoc2, Retsat, Mat1a, Angptl3, Chchd10, Hmgcs2, Cyp4a10, Cyp4a14, Gm26917, Lars2, Hyou1, Arrdc3, Mup12, Gm15564, Pdia3, Gm26924, Sephs2, Grip2, Krt8, Krt18, Plin2, Chka, Gclc, Srxn1, Hmox1, S100a8, S100a9, Mup15, Mup4, Ankrd55, Mup11, Mup5, Mup18, Mup9, Mup6, Mup17, Mup19, Alb, Pck1, Slc2a2, F2, Cyp2e1, Glu1, Arg1, Cdh1, Gls2, Ppargc1a, Sox9, Tbx3, Lgr5, Axin2, or a combination thereof. ### Claim 8 A method of reducing risk of proliferation disorders or cancer in the liver comprising administering to a subject in need thereof an agent that increases expression of Sox9 or decreases expression of Lrg5 and Axin 2. ### Claim 8 (depends on 1) The method of claim 1, wherein the one or more genes or gene products are selected from the genes or gene products in any one of Tables 1a-8c or in all of Tables 1a-8c. ### Claim 9 A method of treating an injury in an organ or tissue, comprising: administering to a subject in need thereof an agent that modulates expression and/or activity of one or more genes or gene products that have functions in: regulation of proteolysis, chemical homeostasis, secretion by cells, regulation of hydrolase activity, regulation of body fluid levels, homeostatic process, wound healing, glycerolipid metabolic process, response to external stimuli, response to oxygen containing compounds, response to lipid, neutral lipid metabolic process, negative regulation of hydrolase activity, ion homeostasis, response to biotic stimulus, exocytosis, platelet degranulation, response to alcohol, regulated exocytosis, negative regulation of peptidase activity, extracellular matrix, secretory granule, platelet alpha granule, secretory granule lumen, secretory vesicle, vesicle lumen, blood microparticle, intracellular vesicle, extracellular space, cytoplasmic vesicle part, protein lipid complex, enzyme inhibitor activity, enzyme regulator activity, response to hypoxia, apoptosis, complement components functions and activities, or a combination thereof. ### Claim 9 (depends on 1) The method of claim 1, wherein the agent induces regeneration and/or functional compensation of the organ or tissue. ### Claim 10 (depends on 1) The method of claim 1, further comprising: administering to the subject in need thereof another agent that modulates expression and/or activity of one or more genes or gene products that have functions in PPAR signaling pathway, complement and/or coagulation cascades, PPARa activated gene expression, biological oxidations, metabolism of lipids and lipoproteins, nasopharyngeal carcinoma, intestine probiotics, plasma cell vs plasmablast, liver cancer, liver specific genes, multiple myeloma, response to UVb radiation, heart atrium vs ventricle, aging kidney no blood, endocrine therapy resistance, liver cancer, breast cancer basal, foxa2 targets, stem cell, lung cancer kras, tlx targets, liver cancer subclass g123, liver cancer subclass proliferation, liver cancer stem cell, liver cancer recurrence, liver cancer subclass s3, hepatoblastoma, liver development, liver hnf1a targets, matrisome, liver cancer krt19, fatty acid catabolic process, ammonium ion metabolic process, protein activation cascade, regulation of wound healing, response to estradiol, response to acid chemical, sterol homeostasis, lipoprotein metabolic process, fatty acid beta oxidation, protein maturation, regulation of locomotion, organic hydroxy compound metabolic process, organic acid biosynthetic process, monocarboxylic acid metabolic process, response to inorganic substance, regulation of vesicle mediated transport, regulation of fatty acid metabolic process, organic hydroxy compound transport, defense response, organophosphate ester transport, lipid homeostasis, secretion, anion transport, regulation of lipid biosynthetic process, response to xenobiotic stimulus, regulation of response to external stimulus, small molecule biosynthetic process, regulation of response to external stimulus, regulation of lipid metabolic process, amine metabolic process, autophagy, regulation of secretion, apoptotic signaling pathway, acute inflammatory response, regulation of catabolic process, maintenance of location, regulation of protein secretion, organic acid metabolic process, response to oxygen levels, regulation of cellular ketone metabolic process, organic acid catabolic process, regulation of response to wounding, regulation of extrinsic apoptotic signaling pathway, cellular lipid catabolic process, regulation of reactive oxygen species metabolic process, detoxification, regulation of peptidase activity, organic anion transport, inflammatory response, negative regulation of cell death, fatty acid metabolic process, lipid metabolic process, divalent inorganic cation homeostasis, regulation of endocytosis, alcohol metabolic process, immune response, cellular lipid metabolic process, monocarboxylic acid transport, negative regulation of apoptotic signaling pathway, multicellular organismal homeostasis, organic hydroxy compound biosynthetic process, regulation of cell death, lipid catabolic process, regulation of lipid metabolic process, regulation of steroid metabolic process, regulation of inflammatory response, response to toxic substance, cellular chemical homeostasis, regulation of transport, regulation of lipid catabolic process, regulation of immune effector process, lipid localization, regulation of proteolysis, regulation of secretion, regulation of response to wounding, regulation of multicellular organismal process, cellular homeostasis, single organism catabolic process, response to oxidative stress, behavior, acute phase response, regulation of response to external stimulus, regulation of apoptotic signaling pathway, regulation of cell proliferation, response to reactive oxygen species, endocytic vesicle, endoplasmic reticulum part, endoplasmic reticulum lumen, endoplasmic reticulum, lipid transporter activity, sulfur compound binding, steroid binding, glycosaminoglycan binding, alcohol binding, carboxylic ester hydrolase activity, lipid binding, receptor binding, coenzyme binding, adipogenesis, xenobiotic metabolism, fatty acid metabolism, coagulation, bile acid metabolism, peroxisome, or a combination thereof. ### Claim 10 (depends on 1) The method of claim 1, wherein the agent induces generation of cells that compensate for function loss caused by the injury in the organ or tissue. ### Claim 11 (depends on 1) The method of claim 1, wherein the agent induces cell proliferation in the organ or tissue. ### Claim 12 (depends on 1) The method of claim 1, wherein the organ or tissue is liver, spleen, intestine, colon, bone marrow, an immune tissue or organ, or a tissue or organ of the gastrointestinal tract. ### Claim 13 (depends on 1) The method of claim 1, wherein the injury is an acute injury. ### Claim 14 (depends on 1) The method of claim 1, wherein the injury is a chronic injury. ### Claim 15 (depends on 1) The method of claim 1, wherein the injury is caused by a metabolic or toxic insult. ### Claim 16 (depends on 1) The method of claim 1, wherein the injury is caused by high fat diet. ### Claim 17 (depends on 1) The method of claim 1, wherein the injury is caused by a disease. ### Claim 18 (depends on 1) The method of claim 1, wherein the injury is caused by a chronic disease. ### Claim 19 (depends on 1) The method of claim 1, wherein the disease is a liver disease. ### Claim 20 (depends on 19) The method of claim 19, wherein the liver disease is non-alcoholic fatty liver disease, non-alcoholic steatohepatitis, or cirrhosis. ### Claim 21 (depends on 1) The method of claim 1, wherein the injury is a zone-independent injury. ### Claim 22 (depends on 1) The method of claim 1, wherein the injury is a zone-dependent injury. ### Claim 23 (depends on 1) The method of claim 1, wherein the agent is a CRISPR-Cas agent. ### Claim 24 A method of treating an injury in an organ or tissue, comprising: a. determining expression of one or more genes from single cells in the organ or tissue at a first time point and a second time point; b. selecting a first subset of genes from the one or more genes, wherein expression of the first subset of genes at the first and the second time points are different; c. determining spatial locations of cells expressing the first subset of genes in the organ or tissue at the first and the second time points by an in situ hybridization assay; d. selecting a second subset of genes based on the spatial locations of the cells expressing the second subset of genes; and e. administering an agent that modulates expression and/or activity of one or more of the second subset of genes to a subject in need thereof.