WO2022006277A1

WO2022006277A1 - Methods for treatment of fibrotic kidney diseases

Info

Publication number: WO2022006277A1
Application number: PCT/US2021/039898
Authority: WO
Inventors: Prakash Narayan
Original assignee: Angion Biomedica Corp.
Priority date: 2020-07-01
Filing date: 2021-06-30
Publication date: 2022-01-06

Abstract

The present disclosure provides biomarkers and methods that are useful in treating, screening, and/or evaluating treatment of fibrotic diseases of the kidney, with methyl (Z)-3-(((4- (N-methyl-2-(4-methylpiperazin1l-yl)acetamido)phenyl)amino)(phenyl)methylene)-2-oxo-2,3- dihydro-1H-pyrrolo[2,3-b]pyridine-6-carboxylate.

Description

METHODS FOR TREATMENT OF FIBROTIC KIDNEY DISEASES

GOVERNMENT SUPPORT

[0001] This invention was made with U. S. government support under Grant No. PR180780/W81X1H1910448 awarded by the United States Department of Defense. The U.S. government has certain rights in the invention.

RELATED APPLICATIONS

[0002] This application claims priority to U.S. Provisional Patent Application No. 63/046,930, filed July 1, 2020, the entire contents of which are hereby incorporated by reference.

BACKGROUND

[0003] Fibrosis of the kidney can result in progressive loss of renal function, which can lead to end-stage renal failure. Renal failure is fatal without regular dialysis or a kidney transplant. There exists a continuing need for improved treatments for fibrotic diseases of the kidney.

SUMMARY

[0004] The present disclosure provides methods related to treatment of fibrotic disease(s) of the kidney and related diseases, disorders, and conditions and selecting, identifying, and/or characterizing patients likely to benefit from a treatment with Compound 1 :

1

[0005] The present disclosure is based in part on the discovery that certain biomarkers can distinguish patients who are likely to respond to therapy, for example because the drivers of their kidney disease correspond with the mechanism of action of Compound 1. For example, in some embodiments, a patient to be treated with a method of the present disclosure has an altered level of one or more gene products or one or more proteins (or fragments thereof) that are part of the mechanism of action of Compound 1 (e.g., down regulated by Compound 1). In some embodiments, a patient to be treated with a method of the present disclosure has an elevated level of gene expression (e.g., COL3A1 expression and/or COL1A1 expression). In some embodiments, a patient to be treated with a method of the present disclosure has an elevated level of protein expression (e.g., COL3A1 protein and/or COL1A1 protein) or elevated level of a fragment thereof. As used herein, an elevated level of expression, e.g., of COL3A1 and/or COL1 Al, may refer to either to an elevated level of a gene product (e.g., mRNA expressed from a COL3A1 gene and/or COL1A1 gene) and/or protein (e.g., COL3A1 protein and/or COL1 Al protein), or a fragment thereof. For simplicity, a non-italicized name will be used to refer to both the gene and protein product.

[0006] In some embodiments, a level of COL3A1 and/or COL1A1 corresponds to a level of gene expression (e.g., RNA expression, e.g., mRNA expression). In some embodiments, a level of COL3A1 and/or COL1 Al corresponds to a level of collagen protein expression. As used herein, collagen protein expression includes expression of a protein in any form, including, a procollagen polypeptide (e.g., type III procollagen or type I procollagen), a collagen protein (e.g., type III collagen or type I collagen), a preprocollagen polypeptide, an amino-terminal procollagen polypeptide (e.g., pN-type III collagen (“PIIINP”) or pN-type I collagen (“PINP”)), collagen fibril, collagen fiber, and/or any fragment or degradation product thereof. It will be appreciated that “type III collagen” may also be referred to as “collagen type III” or “collagen III”, and “type I collagen” may also be referred to as “collagen type I” or “collagen I”.

[0007] In one aspect, the present disclosure provides a method for treating a patient diagnosed with, suspected of having, or at risk for a fibrotic disease of the kidney, the method comprising (i) obtaining or determining a level of COL3A1 expression and/or COL1 Al expression in a biological sample from the patient; and (ii) comparing the level of COL3 Al expression and/or COL1 Al expression with that of a threshold level (e.g., those of a healthy subject control or a mean or median of a population of healthy subject controls), wherein if the expression level of COL3A1 and/or COL1 Al is different from the threshold level (e.g., above the threshold level or below the threshold level), administering to the patient an effective amount of Compound 1, or a pharmaceutical composition thereof. It will be appreciated that obtaining a level of expression of a biomarker may comprise obtaining knowledge of a level that has been determined previously (e.g., obtaining said level from a report, database, etc. containing the value of a previously determined level).

[0008] In one aspect, the present disclosure provides a method for treating a patient diagnosed with, suspected of having, or at risk for a fibrotic disease of the kidney, the method comprising (i) obtaining or determining a level of COL3A1 expression and/or COL1 A1 expression in a biological sample from the patient; and (ii) comparing the level of COL3 A1 expression and/or COL1 A1 expression with that of a threshold level (e.g., those of a healthy subject control or a mean or median of a population of healthy subject controls), wherein if the expression level of COL3A1 and/or COL1 A1 is above the threshold level, administering to the patient an effective amount of Compound 1, or a pharmaceutical composition thereof.

[0009] In one aspect, the present disclosure provides a method for treating a patient diagnosed with, suspected of having, or at risk for a fibrotic disease of the kidney, the method comprising administering an effective amount of Compound 1, or a pharmaceutical composition thereof, to a patient who has been determined to have an altered (e.g., elevated or reduced) level of COL3A1 and/or COL1A1. In some embodiments, the present disclosure provides a method for treating a patient diagnosed with, suspected of having, or at risk for a fibrotic disease of the kidney, the method comprising administering an effective amount of Compound 1, or a pharmaceutical composition thereof, to a patient who has been determined to have an elevated level of COL3A1 and/or COL1A1. In some embodiments, an elevated level of COL3A1 and/or COL1A1 comprises a level that is above a corresponding threshold level. In some embodiments, a reduced level of COL3A1 and/or COL1 A1 comprises a level that is below a corresponding threshold level. In some embodiments, the level of COL3A1 and/or COL1 A1 was obtained from or previously determined from a biological sample from the patient. In some embodiments, the method further comprises obtaining or determining a level of COL3A1 and/or COL1 A1 in a biological sample from the patient.

[0010] In one aspect, a method for treating a patient diagnosed with, suspected of having, or at risk for a fibrotic disease of the kidney in a patient characterized by an elevated level of COL3A1 and/or COL1 A1 is provided, the method comprising administering an effective amount of Compound 1, or a pharmaceutical composition thereof, to the patient. In some embodiments, an elevated level of COL3A1 and/or COL1 A1 comprises a level that is above a corresponding threshold level. In some embodiments, the level of COL3A1 and/or COL1 A1 was obtained from or previously determined from a biological sample from the patient. In some embodiments, the method further comprises obtaining or determining a level of COL3A1 and/or COL1 A1 in a biological sample from the patient.

[0011] In some embodiments, a threshold expression level corresponds to a predetermined mean or median level of COL3A1 and/or COL1A1 of a population of healthy subjects (e.g., healthy human subjects). In some embodiments, a threshold expression level corresponds to a predetermined normal range of COL3A1 and/or COL1A1 of a population of healthy subjects (e.g., healthy human subjects).

[0012] In some embodiments, the expression level of COL3 A1 is at least 20% higher than the corresponding threshold expression level. In some embodiments, the expression level of COL1 A1 is at least 20% higher than the corresponding threshold expression level. In some embodiments, the expression levels of both COL3A1 and COL1 A1 are at least 20% higher than the respective corresponding threshold expression levels.

[0013] In some embodiments, the expression level of COL3 A1 is at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% higher than the corresponding threshold expression level. In some embodiments, the expression level of COL1 A1 is at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% higher than the corresponding threshold expression level. In some embodiments, the expression levels of both COL3A1 and COL1 A1 are at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% higher than the respective corresponding threshold expression levels.

[0014] In some embodiments, the biological sample (e.g., from which an expression level of a biomarker is obtained or has been determined) is a renal biopsy sample, a urine sample, or a blood sample. In some embodiments, an expression level of a protein biomarker (e.g., a propeptide, protein, prepropeptide, amino-terminal propeptide, fibril or fiber, e.g., of COL3A1 and/or of COL1 Al) is obtained from or has been determined in a renal biopsy sample, a urine sample or a blood sample. In some embodiments, an expression level of a genetic biomarker (e.g., a gene product, e.g., RNA, e.g., mRNA, e.g., mRNA encoding COL3A1 and/or COL1A1) is obtained from or has been determined in a renal biopsy sample, a urine sample, and/or a blood sample. [0015] In some embodiments, an expression level of a biomarker is obtained from or determined in a renal biopsy sample from a patient. In some embodiments, an expression level of a biomarker (e.g., COL3A1 and/or COL1 Al) in a renal biopsy sample is a gene biomarker (e.g., RNA, e.g., mRNA) and/or a protein biomarker. In some certain embodiments, the biological sample is a renal biopsy sample and the expression level of COL3 Al is an mRNA level and/or the expression level of COL1 Al is an mRNA level.

[0016] In some embodiments, an expression level of a biomarker is obtained from or determined in a urine sample from a patient. In some embodiments, the biological sample is a urine sample and the expression level of COL3 Al is a level of COL3 Al protein or fragments thereof and/or the expression level of COL1 Al is a level of COL1 Al protein or fragments thereof.

[0017] In some embodiments, an expression level of a biomarker is obtained from or determined in a blood sample from a patient. In some embodiments, the biological sample is a blood sample and the expression level of COL3 Al is a level of COL3 Al protein or fragments thereof and/or the expression level of COL1 Al is a level of COL1 Al protein or fragments thereof.

[0018] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises: focal segmental glomerulosclerosis (FSGS), steroid resistant nephrotic syndrome (SRNS), proteinuria, lupus nephritis, minimal change disease, an anti-neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis, anti-globular basement membrane (anti-GBM) nephropathy, IgA nephropathy, membranous glomerulonephritis (MG), autosomal dominant polycystic kidney disease (ADPKD), or chronic kidney disease.

[0019] In some certain embodiments, provided methods are useful in treating a kidney disease that is or comprises an anti-neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis. In some embodiments, ANCA-associated glomerulonephritis is selected from Wegener’s granulomatosis, microscopic polyangiitis (MPA), or renal limited vasculitis. [0020] In some certain embodiments, provided methods are useful in treating a kidney disease that is or comprises focal and segmental glomerulosclerosis (FSGS).

[0021] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises primary proteinuric kidney disease. In some embodiments, provided methods are useful in treating a kidney disease that is or comprises primary glomerular disease. [0022] In some embodiments, a patient with a fibrotic disease of the kidney exhibits increased renal COL3 A1 expression that is correlated with urine protein to creatinine ratio. In some embodiments, a patient with a fibrotic disease of the kidney exhibits COL3 A1 expression that is inversely correlated with eGFR.

[0023] In some embodiments, a patient has FSGS and also exhibits (i) increased renal COL3 A1 expression that is correlated with urine protein to creatinine ratio and/or (ii) COL3 A1 expression that is inversely correlated with eGFR.

[0024] In some embodiments, the kidney fibrotic disease is stabilized (i.e., does not worsen) and/or is ameliorated (i.e., one or more symptoms improve) in a patient treated with Compound 1. In some embodiments, treatment of a patient with Compound 1 reduces a level of one or more biomarkers (e.g., COL1 A1 and/or COL3A1).

[0025] In some embodiments, administration of Compound 1 to the patient: (i) reduces the expression of renal COL3A1 , (ii) reduces the expression of renal COL1A1 , (iii) reduces renal COL3A1 accumulation, (iv) reduces renal COL1A1 accumulation, or (v) any combination thereof.

[0026] In some embodiments, a patient to be treated with a method of the present disclosure exhibits proteinuria.

[0027] In another aspect, the present disclosure provides a method comprising: (i) receiving a report listing the expression level of one or more biomarkers (e.g., COL3A1 and/or COL1 Al) for a patient with a fibrotic kidney disease; (ii) receiving a request for reimbursement for the biomarker screening and/or a particular therapeutic regimen; (iii) approving payment and/or reimbursement for Compound 1 therapy if the report indicates the level of biomarker is above a threshold level, wherein Compound 1 is described by the formula:

[0028] In some embodiments, a threshold expression level corresponds to a predetermined mean or median level of COL3A1 and/or COL1A1 of a population of healthy subjects. In some embodiments, a threshold expression level corresponds to a predetermined normal range of COL3A1 and/or COL1A1 of a population of healthy subjects.

[0029] In some embodiments, the expression level of COL3 A1 is at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% higher than the corresponding threshold expression level. In some embodiments, the expression level of COL1 A1 is at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% higher than the corresponding threshold expression level. In some embodiments, the expression levels of both COL3A1 and COL1 A1 are at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% higher than the respective corresponding threshold expression levels.

[0030] In some embodiments, the biological sample (e.g., from which an expression level of a biomarker is or has been determined) is a renal biopsy sample, a urine sample or a blood sample. In some embodiments, the biological sample is a renal biopsy sample and the expression level of COL3 A1 is an mRNA level and/or the expression level of COL1 A1 is an mRNA level. In some embodiments, the biological sample is a urine sample and the expression level of COL3 A1 is a level of COL3 A1 protein or fragments thereof and/or the expression level of COL1 A1 is a level of COL1 A1 protein or fragments thereof.

[0031] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises: focal segmental glomerulosclerosis (FSGS), steroid resistant nephrotic syndrome (SRNS), proteinuria, lupus nephritis, minimal change disease, an anti-neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis, anti-globular basement membrane (anti-GBM) nephropathy, IgA nephropathy, membranous glomerulonephritis (MG), autosomal dominant polycystic kidney disease (ADPKD), collagen type III glomerulopathy, nail-patella syndrome, or chronic kidney disease.

[0032] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises focal and segmental glomerulosclerosis (FSGS). In some embodiments, a patient has FSGS and an elevated level of COL3A1 and/or COL1 A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.). In some embodiments, a patient has FSGS and also exhibits (i) increased renal COL3 A1 expression that is correlated with urine protein to creatinine ratio and/or (ii) COL3 A1 expression that is inversely correlated with eGFR. [0033] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises primary proteinuric kidney disease (PPKD). In some embodiments, a patient has PPKD and an elevated level of COL3A1 and/or COL1 A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.).

[0034] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises primary glomerular disease (PGD). In some embodiments, a patient has PGD and an elevated level of COL3A1 and/or COL1 A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.).

[0035] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises steroid resistant nephrotic syndrome (SRNS). In some embodiments, a patient has SRNS and an elevated level of COL3A1 and/or COL1 A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.).

[0036] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises proteinuria. In some embodiments, a patient has proteinuria and an elevated level of COL3A1 and/or COL1 A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.).

[0037] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises lupus nephritis. In some embodiments, a patient has lupus nephritis and an elevated level of COL3A1 and/or COL1A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.).

[0038] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises minimal change disease. In some embodiments, a patient has minimal change disease and an elevated level of COL3A1 and/or COL1 A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.). [0039] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises ANCA-associated glomerulonephritis. In some embodiments, a patient has ANCA-associated glomerulonephritis and an elevated level of COL3A1 and/or COL1A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.).

[0040] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises anti-GBM nephropathy. In some embodiments, a patient has anti-GBM nephropathy and an elevated level of COL3A1 and/or COL1 A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.).

[0041] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises IgA nephropathy. In some embodiments, a patient has IgA nephropathy and an elevated level of COL3A1 and/or COL1A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.).

[0042] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises membranous glomerulonephritis (MG). In some embodiments, a patient has MG and an elevated level of COL3A1 and/or COL1 A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.).

[0043] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises autosomal dominant polycystic kidney disease (ADPKD). In some embodiments, a patient has ADPKD and an elevated level of COL3A1 and/or COL1 A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.).

[0044] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises chronic kidney disease. In some embodiments, a patient has chronic kidney disease and an elevated level of COL3A1 and/or COL1 A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.). [0045] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises collagen type III glomerulopathy. In some embodiments, a patient has collagen type III glomerulopathy and an elevated level of COL3A1 and/or COL1 A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.).

[0046] In some embodiments, provided methods are useful in treating a kidney disease that is or comprises nail-patella syndrome. In some embodiments, a patient has nail-patella syndrome and an elevated level of COL3A1 and/or COL1 A1 (e.g., mRNA and/or protein), for example, as determined in or obtained from a biological sample from the patient (e.g., renal biopsy sample, urine sample, blood sample, etc.).

[0047] In some embodiments, provided methods recognize when to adjust or discontinue treatment of a patient with Compound 1. For example, in some embodiments, the present disclosure provides a method for treating a patient diagnosed with, suspected of having, or at risk for a fibrotic disease of the kidney, the method comprising: (i) obtaining or determining a level of expression of one or more gene products or proteins in a biological sample from the patient, wherein the one or more gene products or proteins are selected from: COL3A1 and COL1A1; (ii) comparing the expression level of the one or more gene products or proteins with that of a corresponding threshold level; and (iii) if the expression level of COL3 A1 and/or the expression level of COL1 A1 is above the threshold expression level, then administering to the patient an effective amount of Compound 1 or a pharmaceutical composition thereof, and if the expression level of COL3A1 and/or the expression level of COL1 A1 is not above the threshold expression level, then the patient is not administered Compound 1.

[0048] In some embodiments, the present disclosure provides a method for treating a patient diagnosed with, suspected of having, or at risk for a fibrotic disease of the kidney, which patient is characterized by an elevated level of a biomarker (e.g., COL3A1 and/or COL1 Al), the method comprising: (i) administering an effective amount of Compound 1 or a pharmaceutical composition thereof, and (ii) monitoring a level of biomarker (e.g., COL3A1 and/or COL1A1) subsequent to administration (e.g., after a duration of a day, a week, two weeks, a month, two months, 3 months, etc.). In some embodiments, if the level of biomarker (e.g., COL3A1 and/or COL1 Al) increases in a patient administered Compound 1, then further treatment with Compound 1 is discontinued. In some embodiments, if the level of biomarker (e.g., COL3A1 and/or COL1A1) increases in a patient administered Compound 1, then the dose of Compound 1 administered to the patient is increased. In some embodiments, if the level of biomarker (e.g., COL3A1 and/or COL1 Al) decreases in a patient administered Compound 1, then treatment with Compound 1 is continued (e.g., subsequent doses are administered).

[0049] Throughout the description, where methods are described as having, including, or comprising specific steps, it is contemplated that, additionally, there are methods according to the present invention that consist essentially of, or consist of, the recited processing steps. It should be understood that the order of steps or order for performing certain action is immaterial so long as the invention remains operable. Moreover, two or more steps or actions may be conducted simultaneously.

[0050] The mention herein of any publication is not an admission that the publication serves as prior art with respect to any of the claims presented herein. References cited herein are hereby incorporated by reference in their entirety.

[0051] The following description is for illustration and exemplification of the disclosure only and is not intended to limit the invention to the specific embodiments described.

BRIEF DESCRIPTION OF THE DRAWINGS [0052] FIG. 1 provides levels of various inflammation and fibrosis related markers with exposure to escalating levels of Compound 1.

[0053] FIG. 2 provides a cartoon schematic of varying relationships between genomic responses and kidney disease outcomes.

[0054] FIG. 3 provides proteinuria of PAN treated model rats treated with Compound 1.

[0055] FIG. 4 provides fold change in expression for COL1 Al and COL3A1 mRNA in a rat

PAN model with treatment of Compound 1.

[0056] FIG. 5 depicts correlation between COL3 Al expression and renal dysfunction in both murine model and human patients.

[0057] FIG. 6 depicts a Compound 1 interactome built using in vitro activity data.

[0058] FIG. 7 provides urine protein levels in PAN treated model rats.

[0059] FIG. 8A provides COL3 Al mRNA levels in PAN-treated model rats.

[0060] FIG. 8B provides an association of COL3 Al mRNA levels and urine protein values.

[0061] FIG. 9A depicts a glomerular COL3 Al interactome. [0062] FIG. 9B depicts a tubular COL3 A1 interactome.

CERTAIN DEFINITIONS

[0063] The term “about”, when used herein in reference to a value, refers to a value that is similar, in context to the referenced value. In general, those skilled in the art, familiar with the context, will appreciate the relevant degree of variance encompassed by “about” in that context. For example, in some embodiments, the term “about” may encompass a range of values that is within 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less of the referred value.

[0064] As used herein, the term “administering” or “administration” typically refers to administration of a composition to a subject to achieve delivery of an active agent to a site of interest (e.g., a target site which may, in some embodiments, be a site of disease or damage, and/or a site of responsive processes, cells, tissues, etc.) As will be understood by those skilled in the art, reading the present disclosure, in some embodiments, one or more particular routes of administration may be feasible and/or useful in the practice of the present invention. For example, in some embodiments, administration may be parenteral. In some embodiments, administration may be oral. In some embodiments, administration may involve only a single dose. In some embodiments, administration may involve application of a fixed number of doses. In some embodiments, administration may involve dosing that is intermittent (e.g., a plurality of doses separated in time) and/or periodic (e.g, individual doses separated by a common period of time) dosing.

[0065] As used herein, the term “comparable” refers to two or more agents, entities, situations, sets of conditions, circumstances, individuals, or populations, etc. that may not be identical to one another but that are sufficiently similar to permit comparison there between so that one skilled in the art will appreciate that conclusions may reasonably be drawn based on differences or similarities observed. In some embodiments, comparable agents, entities, situations, sets of conditions, circumstances, individuals, or populations are characterized by a plurality of substantially identical features and one or a small number of varied features. Those of ordinary skill in the art will understand, in context, what degree of identity is required in any given circumstance for two or more such agents, entities, situations, sets of conditions, circumstances, individuals, or populations, etc. to be considered comparable. For example, those of ordinary skill in the art will appreciate that sets of circumstances, agents, entities, situations, individuals, or populations are comparable to one another when characterized by a sufficient number and type of substantially identical features to warrant a reasonable conclusion that differences in results obtained or phenomena observed under or with different agents, entities, situations, sets of circumstances, individuals, or populations are caused by or indicative of the variation in those features that are varied.

[0066] Those skilled in the art will appreciate that the term “dosage form” may be used to refer to a physically discrete unit of an active agent (e.g., a therapeutic agent) for administration to a subject. Typically, each such unit contains a predetermined quantity of active agent. In some embodiments, such quantity is a unit dosage amount (or a whole fraction thereof) appropriate for administration in accordance with a dosing regimen that has been determined to correlate with a desired or beneficial outcome when administered to a relevant population (i.e., with a therapeutic dosing regimen). Those of ordinary skill in the art appreciate that the total amount of a therapeutic composition or agent administered to a particular subject is determined by one or more attending physicians and may involve administration of multiple dosage forms. [0067] The term “pharmaceutically acceptable salt form,” as used herein, refers to a form of a relevant compound as a salt appropriate for use in pharmaceutical contexts, i.e., salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and/or lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, S. M. Berge, et al. describes pharmaceutically acceptable salts in detail in ./. Pharmaceutical Sciences , 66: 1-19 (1977).

[0068] As used herein, the term “reference” describes a standard or control relative to which a comparison is performed. For example, in some embodiments, an agent, individual, population, sample, sequence or value of interest is compared with a reference or control agent, individual, population, sample, sequence or value. In some embodiments, a reference or control is tested and/or determined substantially simultaneously with the testing or determination of interest. In some embodiments, a reference or control is a historical reference or control, optionally embodied in a tangible medium. Typically, as would be understood by those skilled in the art, a reference or control is determined or characterized under comparable conditions or circumstances to those under assessment. Those skilled in the art will appreciate when sufficient similarities are present to justify reliance on and/or comparison to a particular possible reference or control.

[0069] As will be understood from context, “risk” of a disease, disorder, and/or condition refers to a likelihood that a particular individual will develop the disease, disorder, and/or condition. In some embodiments, risk is expressed as a percentage. In some embodiments, risk is from 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90 up to 100%. In some embodiments risk is expressed as a risk relative to a risk associated with a reference sample or group of reference samples. In some embodiments, a reference sample or group of reference samples have a known risk of a disease, disorder, condition and/or event. In some embodiments a reference sample or group of reference samples are from individuals comparable to a particular individual. In some embodiments, relative risk is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more.

[0070] As used herein, the term “subject” refers an organism, typically a mammal (e.g., a human). In some embodiments, a subject is suffering from a relevant disease, disorder or condition. In some embodiments, a human subject is an adult, adolescent, or pediatric subject.

In some embodiments, a subject is at risk of (e.g., susceptible to), e.g., at elevated risk of relative to an appropriate control individual or population thereof, a disease, disorder, or condition. In some embodiments, a subject displays one or more symptoms or characteristics of a disease, disorder or condition. In some embodiments, a subject does not display any symptom or characteristic of a disease, disorder, or condition. In some embodiments, a subject is someone with one or more features characteristic of susceptibility to or risk of a disease, disorder, or condition. In some embodiments, a subject is an individual to whom diagnosis and/or therapy and/or prophylaxis is and/or has been administered. The terms “subject” and “patient” are used interchangeably herein.

[0071] As used herein, the term “treat” (also “treatment” or “treating”) refers to any administration of a therapy that partially or completely alleviates, ameliorates, relieves, inhibits, delays onset of, reduces severity of, and/or reduces incidence of one or more symptoms, features, and/or causes of a particular disease, disorder, and/or condition. In some embodiments, such treatment may be of a subject who does not exhibit signs of the relevant disease, disorder and/or condition and/or of a subject who exhibits only early signs of the disease, disorder, and/or condition. Alternatively or additionally, such treatment may be of a subject who exhibits one or more established signs of the relevant disease, disorder and/or condition. In some embodiments, treatment may be of a subject who has been diagnosed as suffering from the relevant disease, disorder, and/or condition.

DETAILED DESCRIPTION

[0072] The present disclosure recognizes a problem with current treatments for fibrotic diseases of the kidney and related diseases, disorders, and conditions, namely that there is a lack of specific therapies to treat these diseases. For example, it is estimated that -20,000 patients are living with FSGS in the United States, which affects African-Americans more than other demographics. Current treatments for FSGS include corticosteroids, calcineurin inhibitors, mycophenolate mofetil, adrenocorticotropic hormone (ACTH) and rituximab, which are applied in a trial and error manner, and are effective in at most 25-40% of patients. Each of these therapies, developed decades ago, have been merely repurposed for FSGS. The present disclosure provides specific treatments for patients with fibrotic kidney diseases and related diseases, disorders, and conditions, such as FSGS, based on the genomic mechanism of the disease in those patients. For example, the present disclosure encompasses the recognition that one or more biomarkers can distinguish patients with fibrotic kidney diseases and related diseases, disorders, and conditions that are likely to benefit from therapy with Compound 1.

Compound 1

[0073] PCT Application No. PCT/US2013/023324, filed January 26, 2013 and published as WO 2013/112959 on August 1, 2013, the entirety of which is hereby incorporated by reference, describes certain anti-fibrotic compounds. Such compounds include Compound 1 :

1

Compound 1, i.e., methyl (Z)-3-(((4-(N-methyl-2-(4-methylpiperazin-l-yl)acetamido)phenyl) amino)(phenyl)methylene)-2-oxo-2,3-dihydro-lH-pyrrolo[2,3-b]pyridine-6-carboxylate, is in a pharmacological class of tyrosine kinase inhibitors (TKI). Compound 1 is an orally bioavailable small molecule dual kinase inhibitor of platelet-derived growth factor receptors (PDGFR) and vascular endothelial growth factor receptors (VEGFR2). Compound 1 is useful in methods provided herein.

[0074] Synthesis of Compound 1, i.e., methyl (Z)-3-(((4-(N-methyl-2-(4-methylpiperazin-l- yl)acetamido)phenyl)amino)(phenyl)methylene)-2-oxo-2,3-dihydro-lH-pyrrolo[2,3-b]pyridine- 6-carboxylate, is described in detail in Example 1 of WO 2013/112959.

[0075] In some embodiments, Compound 1 is provided and/or utilized (e.g., for inclusion in a composition and/or for delivery to a subject) in accordance with the present disclosure in a form such as a salt form (e.g., a pharmaceutically acceptable salt form). As already noted herein, pharmaceutically acceptable salt forms are well known in the art. In some embodiments, Compound 1 is provided and/or utilized in a hydrochloride salt form, a maleate salt form, a mesylate salt form, or a tosylate salt form.

[0076] In some embodiments, Compound 1 is provided and/or utilized (e.g., for inclusion in, e.g., during one or more steps of manufacturing of, a composition and/or for delivery to a subject) in accordance with the present disclosure in a form such as a solid form. In some embodiments, Compound 1 is provided and/or utilized in accordance with the present disclosure in an amorphous solid form, in a crystalline solid form, or in a mixture thereof. In some embodiments, a crystalline solid form may be or comprise a solvate, hydrate, or an unsolvated form. The use of any and all such forms are contemplated by the present disclosure.

[0077] Unless otherwise indicated, as used herein “Compound 1” refers to Compound 1 (i.e., methyl (Z)-3-(((4-(N-methyl-2-(4-methylpiperazin-l-yl)acetamido)phenyl)amino)(phenyl) methylene)-2-oxo-2,3-dihydro-lH-pyrrolo[2,3-b]pyridine-6-carboxylate) in any available form, such as, e.g., a salt form and/or solid form. It will be understood, therefore, that reference to an amount (e.g., in mg) of Compound 1 means the amount of Compound 1 in free base form. Accordingly, Compound 1 may be provided and/or utilized as, e.g., a salt form of Compound 1 such that the amount of the salt (or other form) is an amount that corresponds to the “free base equivalent” of Compound 1. For example, “50 mg Compound 1” means, e.g., approx. 53.4 mg of Compound 1 Hydrochloride anhydrate, approx. 58.4 mg of Compound 1 Hydrochloride trihydrate, and approx. 58.9 mg of Compound 1 Mesylate anhydrate, etc. Methods

[0078] Provided herein are methods of treating a subject or a population of subjects comprising administering Compound 1 (e.g., by administering a composition that comprises and/or delivers Compound 1 as described herein) to the subject(s) in need thereof.

[0079] In some embodiments, such administering is achieved by administering a composition that delivers Compound 1 (e.g., in some embodiments, a composition that is or comprises Compound 1, or a composition that otherwise delivers Compound 1 - e.g., that is or comprises a prodrug of Compound 1, a complex or other entity that releases Compound 1 upon administration, etc.).

[0080] In some embodiments, provided are methods related to treatment of fibrotic disease(s) of the kidney and selecting, identifying, and/or characterizing patients likely to benefit from a treatment with Compound 1 :

1

[0081] The present disclosure is based in part on the discovery that certain biomarkers can distinguish patients who are likely to respond to therapy, for example because the drivers of their kidney disease correspond with the mechanism of action of Compound 1. In some embodiments, a patient to be treated with a method of the present disclosure has an altered level of one or more gene products or proteins that are part of the mechanism of action of Compound 1 (e.g., down regulated by Compound 1).

[0082] In some embodiments, a patient to be treated with a method of the present disclosure has an elevated level of COL3A1 expression and/or COL1A1 expression. In some embodiments provided herein, a level of COL3A1 refers to a gene product (e.g., RNA, e.g., mRNA) or a protein product (e.g., a prepropolypeptide, propolypeptide, amino-terminal propolypeptide, protein, fibril, fiber, or any fragment or degradation product thereof). In some embodiments provided herein, a level of COL1A1 refers to a gene product (e.g., RNA, e.g., mRNA) or a protein product (e.g., a prepropolypeptide, propolypeptide, amino-terminal propolypeptide, protein, fibril, fiber, or any fragment or degradation product thereof).

[0083] In one aspect, the present disclosure provides a method for treating a patient diagnosed with, suspected of having, or at risk for a fibrotic disease of the kidney, the method comprising: (i) obtaining or determining a level of expression of a biomarker (e.g., COL3 A1 and/or COL1 Al) in a biological sample from the patient; (ii) comparing the level of biomarker expression with that of a threshold level (e.g., a predetermined mean or median level of a population of healthy subjects), wherein if the expression level of the biomarker is above the threshold level, administering to the patient an effective amount of Compound 1, or a pharmaceutical composition thereof.

[0084] In one aspect, the present disclosure provides a method for treating a patient diagnosed with, suspected of having, or at risk for a fibrotic disease of the kidney, the method comprising administering an effective amount of Compound 1, or a pharmaceutical composition thereof, to a patient who has been determined to have an elevated level of a biomarker (e.g., COL3A1 and/or COL1 Al). In some embodiments, an elevated level of a biomarker comprises a level that is above that of a corresponding threshold level. In some embodiments, the level of biomarker (e.g., COL3A1 and/or COL1 Al) was obtained from or previously determined from a biological sample from the patient. In some embodiments, the method further comprises obtaining or determining a level of a biomarker (e.g., COL3A1 and/or COL1 Al) in a biological sample from the patient.

[0085] In one aspect, a method for treating a patient diagnosed with, suspected of having, or at risk for a fibrotic disease of the kidney in a patient characterized by an elevated level of a biomarker (e.g., COL3A1 and/or COL1A1) is provided, the method comprising administering an effective amount of Compound 1, or a pharmaceutical composition thereof, to the patient. In some embodiments, an elevated level of a biomarker comprises a level that is above a corresponding threshold level. In some embodiments, the level of biomarker (e.g., COL3A1 and/or COL1 Al) was obtained from or previously determined from a biological sample from the patient. In some embodiments, the method further comprises obtaining or determining a level of a biomarker (e.g., COL3A1 and/or COL1 Al) in a biological sample from the patient. [0086] In some embodiments, the biological sample (e.g., from which an expression level of a biomarker is or has been determined) is a renal biopsy sample, a urine sample or a blood sample.

[0087] In some embodiments, the biological sample is a renal biopsy sample and the expression level of COL3 A1 is an mRNA level and/or the expression level of COL1 A1 is an mRNA level. Methods for measuring and/or determining levels of a biomarker (e.g., mRNA level) in renal biopsy samples are known in the art, for example, Genovese et ah, Biomark Insights. 2016 May 22; 11 :77-84.

[0088] In some embodiments, the biological sample is a urine sample and the expression level of COL3 A1 is a level of COL3 A1 protein or fragments thereof and/or the expression level of COL1 A1 is a level of COL1 A1 protein or fragments thereof. In some embodiments, the biological sample is a blood sample and the expression level of COL3 A1 is a level of COL3 A1 protein or fragments thereof and/or the expression level of COL1A1 is a level of COL1 A1 protein or fragments thereof. Methods for measuring and/or determining levels of a biomarker (e.g., a level of collagen protein and/or fragment thereof) in urine and/or blood samples are known in the art, for example, Soylemezoglu et al., Nephrol Dial Transplant. 1997 Sep;12(9):1883-9.

[0089] In some embodiments, the present disclosure provides methods of administering Compound 1 to a subject or population of subjects described herein, according to a regimen established to achieve one or more desirable outcomes. In some embodiments, the kidney fibrotic disease is stabilized (i.e., does not worsen) and/or is ameliorated (i.e., one or more symptoms improve) in a patient treated with Compound 1. In some embodiments, treatment of a patient with Compound 1 reduces a level of one or more biomarkers (e.g., COL1 Al and/or COL3A1). In some embodiments, treatment of a patient with Compound 1 reduces proteinuria. [0090] In some embodiments, a regimen has been established to achieve one or more desirable outcomes, relative to that observed for a comparable reference population that has not received Compound 1 (e.g., that has received a placebo). A placebo as used herein is a dosage form that matches that of an active study compound, but does not deliver the active study compound (e.g., Compound 1). For example, a placebo can be a capsule that visually matches an active study drug and is composed of the same capsule shell but is filled with a pharmaceutical excipient (and lacking the active study drug), e.g., silicified microcrystalline cellulose. In some embodiments, in methods provided herein, a reference composition may be or may have been administered at the same intervals and/or in the same amounts as a composition providing Compound 1.

[0091] In some embodiments, a regimen has been established to achieve one or more desirable outcomes, relative to that observed for a comparable reference population that does not have an altered level of a biomarker (e.g., an elevated level of COL3A1 and/or COL1 Al). In some embodiments, a patient who expresses a biomarker treated with Compound 1 has an improved outcome (e.g., improved stability and/or amelioration of the fibrotic kidney disease) relative to a patient with the same disease that does not express an elevated level of the biomarker. In some embodiments, treatment of a patient with Compound 1 reduces a level of one or more biomarkers (e.g., COL1 Al and/or COL3A1). In some embodiments, treatment of a patient with Compound 1 reduces proteinuria.

[0092] In some embodiments, a composition providing Compound 1 is administered according to a regimen established to achieve a particular effect, e.g., at a particular time point.

In some embodiments, a composition providing Compound 1 is administered according to a regimen established to achieve a particular effect.

[0093] In some embodiments, a provided method includes: (i) receiving a report listing the expression level of one or more biomarkers (e.g., COL3 Al and/or COL1 Al) for a patient with a fibrotic kidney disease; (ii) receiving a request for reimbursement of the screening and/or of a particular therapeutic regimen; and (iii) approving payment and/or reimbursement for Compound 1 therapy if the report indicates the level of biomarker is above a threshold level.

Renal Diseases, Disorders, and Conditions

[0094] In some embodiments, provided methods are useful for treating renal diseases, disorders, and conditions. In some embodiments, provided methods are useful for reducing fibrosis of the kidney in a subject in need thereof. In some embodiments, provided methods are useful for treating a kidney disease, disorder, or condition characterized by or otherwise associated with fibrosis. The present disclosure encompasses the recognition that treating fibrosis (e.g., using provided methods) instead of the underlying etiology may allow for broadly applicable antifibrotic kidney therapies. It will be appreciated that provided methods may be suitable for treating kidney diseases, disorders, and conditions in which fibrosis is the sole or a predominant component, as well as those in which fibrosis is a secondary component (e.g., a symptom and/or result of an underlying disease, disorder, or condition).

[0095] In some embodiments, provided methods are useful for treating acute injuries (e.g., acute organ injuries, such as acute kidney injury), as well as for treating chronic injuries (e.g., chronic kidney injury). In some embodiments, provided methods are useful for treating fibrosis associated with an acute injury, such as that incurred from trauma and/or surgery. In some embodiments, provided methods are useful for treating damaged and/or ischemic organs, transplants, or grafts, as well as ischemia/reperfusion injury or post-surgical scarring.

[0096] In some embodiments, provided methods are useful for treating renal fibrosis. In some embodiments, provided methods are useful for treating renal fibrosis secondary to, or otherwise associated with, an underlying indication. In some embodiments, provided methods are useful for treating renal fibrosis associated with renal failure, renal obstruction, renal trauma, renal transplantation, chronic kidney disease, diabetes, hypertension, radiocontrast nephropathy, immune-mediated glomerulonephritides (e.g., lupus nephritis, ANCA-associated glomerulonephritides (e.g., Wegener’s granulomatosis, microscopic polyangiitis, or renal limited vasculitis), anti-GBM nephropathy, IgA nephropathy, membranous glomerulonephritis, or focal and segmental glomerulosclerosis), non-immune-mediated glomerulonephritides (e.g., autosomal dominant polycystic kidney disease, collagen type III glomerulopathy, or nail-patella syndrome), minimal change disease, or nephrotic syndrome (e.g., steroid-resistant nephrotic syndrome). In some embodiments, provided methods are useful for treating nephrotic syndrome and/or diseases, disorders, or conditions associated with nephrotic syndrome (e.g., focal and segmental glomerulosclerosis, minimal change disease, and membranous nephropathy). In some embodiments, provided methods are useful for treating a fibrotic disease of the kidney that is or comprises: focal segmental glomerulosclerosis (FSGS), steroid resistant nephrotic syndrome (SRNS), proteinuria, lupus nephritis, minimal change disease, an anti-neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis, anti-globular basement membrane (anti-GBM) nephropathy, IgA nephropathy, membranous glomerulonephritis (MG), autosomal dominant polycystic kidney disease (ADPKD), or chronic kidney disease. In some embodiments, provided methods are useful for treating a fibrotic disease of the kidney that is or comprises an anti neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis. In some embodiments, ANCA-associated glomerulonephritis is selected from Wegener’s granulomatosis, microscopic polyangiitis (MPA), or renal limited vasculitis. In some embodiments, provided methods are useful for treating focal and segmental glomerulosclerosis. In some embodiments, provided methods are useful for treating polycystic kidney disease (e.g., autosomal dominant polycystic kidney disease or autosomal recessive polycystic kidney disease).

[0097] In some embodiments, provided methods are useful for treating primary proteinuric kidney disease (PPKD). In some embodiments, provided methods are useful for treating primary glomerular diseases (PGDs). PGDs are among the leading causes of chronic kidney disease and end-stage kidney disease in the world. PGDs predominantly affect younger patients, significantly reducing their quality of life, productivity, and longevity. FSGS, membranous nephropathy (MN), and IgA nephropathy are among the three most common primary glomerular diseases in adults. Accordingly, in some embodiments, provided methods are useful for treating FSGS. In some embodiments, provided methods are useful for treating MN. In some embodiments, provided methods are useful for treating IgA nephropathy.

[0098] Currently, there are no therapies approved specifically for PPKDs and/or PGDs. Various immunosuppressive and/or cytotoxic agents primarily approved for other indications are first-line therapy for patients considered to be at a high risk of progression. Such therapies aim to induce remission, defined as a normalization of the urinary protein excretion. The patients who undergo a complete or a partial remission have significantly improved renal prognosis. Unfortunately, remission rates with immunosuppressive agents and cytotoxic therapy range only between 30-60% depending on the underlying disease, and up to 50% of these patients subsequently experience a relapse. Relapses in proteinuria are frequently treated with repeat administration of immunosuppressive and/or cytotoxic therapy; however, long-term treatment with these agents is limited by their significant dose-limiting toxicities. Some of the drugs, such as calcineurin inhibitors (CNIs), have a narrow therapeutic index necessitating close monitoring of the drug levels. Long-term use of CNIs is associated with hypertension, nephrotoxicity, and metabolic abnormalities such as diabetes and dyslipidemia. In most patients, cessation of calcineurin inhibitors results in the relapse of proteinuria (Meyrier, A. et ak, Kidney International. 1994;45(5): 1446-56). A significant number of patients eventually become either resistant or dependent on these toxic agents. Some of these glomerular diseases also recur after renal transplantation posing unique management problems (Choy, B.Y., et ak, Am. J. Transplant. 2006;6(11):2535-42). [0099] In some embodiments, provided methods are useful for treating patients with proteinuria (e.g., persistent proteinuria). It is well established that higher rates of urinary protein excretion are associated with worse prognosis, and therapies that reduce proteinuria are desirable for improving renal outcomes. Patients with persistent proteinuria (e.g., who continue to have >

1 gram of proteinuria per day) are at high risk of progressing to end-stage kidney disease (ESKD). Risk of progression is significantly increased in the presence of a reduced estimated glomerular filtration rate (eGFR) at the time of diagnosis or during the course of the disease. Patients with persistent proteinuria also develop further complications of chronic kidney disease (CKD) such as dyslipidemia, cardiovascular disease, abnormalities in mineral-bone metabolism, and hypertension, resulting in significant increases in morbidity and mortality and utilization of health care resources.

[0100] In addition to immunosuppressive agents, standard of care for patients with persistent proteinuria includes treatment with the renin-angiotensin-aldosterone system (RAAS) blockers, most commonly ACE inhibitors or angiotensin-receptor blockers (ARBs). The RAAS blockers reduce proteinuria and improve clinical outcomes in proteinuric renal diseases regardless of the etiology. Other standard of care recommendations include aggressive blood pressure control (< 130/80), and HMG-CoA reductase inhibitors (e.g., statins) in patients with hyperlipidemia. The inhibitors of the mineralocorticoid receptor and sodium glucose co-transporter-2 (SGLT-2) are increasingly being used in these patients as well.

[0101] In some embodiments, provided methods are useful for treating primary glomerular diseases (e.g., FSGS, membranous nephropathy, or IgA nephropathy) and persistent proteinuria. [0102] Several growth factor receptors have been implicated in the development of fibrosis of the kidney (Liu, F., et al. Int. J. Mol. Sci. 2016 Jun 20; 17(5), PMCID:PMC4926504). Platelet- derived growth factor receptor beta (PDGFRP) is postulated to play a particularly important role in the development of renal fibrosis (Floege, J., et al. J. Am. Soc. Nephrol. 2008 Jan; 19(1): 12-23; Ostendorf, T., et al. Pediartr. Nephrol. 2012 Jul;27(7): 1041-50; Ostendorf. T., et al. Kidney Int. Suppl. (2011) 2014 Nov;4(l):65-9, PMCID:PMC4536969; Abbound, H E. Annu. Rev. Physiol. 1995;57:297-309).

[0103] In some embodiments, a kidney disease to be treated by methods of the present disclosure is nephrotic syndrome (NS). NS is a group of rare renal diseases, including focal and segmental glomerulosclerosis (FSGS), minimal change disease (MCD), and membranous nephropathy. FSGS is a rare disease that attacks the kidney’s filtering units (glomeruli) causing serious scarring which leads to permanent kidney damage and even failure (Fogo, A.B. Nat. Rev. Nephrol. 2015 Feb;l l(2):76-87, PMCID:PMC4772430). It will be appreciated that there are at least three types of FSGS. Primary FSGS is FSGS that has no known cause (also referred to as idiopathic FSGS). Secondary FSGS is caused by one or more factors such as infection, drug toxicity, diseases such as diabetes or sickle cell disease, obesity, or other kidney diseases. Genetic FSGS (also called familial FSGS) is caused by one or more genetic mutations. Primary FSGS is idiopathic in nature. Manifestations of this disease include hypoalbuminemia and edema, lipid abnormalities and nephrotic range proteinuria. More than 5400 patients are diagnosed with FSGS every year (O’Shaughnessy, M.M., et al. Nephrol. Dial. Transplant 2018 Apr l;33(4):661-9). However, this is considered an underestimate because a limited number of biopsies are performed, and the number of FSGS cases is rising more than any other cause of NS. Standard of care for this patient population is steroid therapy. Current treatments for FSGS include corticosteroids, calcineurin inhibitors, mycophenolate mofetil, adrenocorticotropic hormone (ATCH), and rituximab; these are effective in at most 25-40% of patients. A subset of this population is resistant to steroids (steroid-resistant, or SR), and proteinuria, which is toxic to renal tubules, remains uncorrected. Consequently, this subset proceeds relatively rapidly to end- stage renal disease (ESRD). There is therefore an urgent need to develop therapies that reduce proteinuria in primary SR-FSGS (Nourbakhsh, N. and Mak, R.H. Pediatric Health Med. Ther. 2017;8:29-37, PMCID:PMC5774596).

[0104] In some embodiments, a kidney disease to be treated by methods of the present disclosure is minimal change disease (MCD). MCD is a kidney disease in which large amounts of protein are lost in the urine. It is one of the most common causes of the nephrotic syndrome worldwide. In children, MCD is usually primary (or idiopathic), but in adults, the disease is usually secondary. Secondary causes for MCD include allergic reactions, use of certain painkillers such as non-steroidal anti-inflammatory drugs (NSAIDs), tumors, or viral infections. [0105] In some embodiments, a kidney disease to be treated by methods of the present disclosure is membranous glomerulonephritis (MG or MGN), also known as membranous nephropathy (MN). MG is a slowly progressive renal disease caused by immune complex formation in the glomerulus. Immune complexes are formed by binding of antibodies to antigens in the glomerular basement membrane. The antigens may be part of the basement membrane, or deposited from elsewhere by the systemic circulation.

[0106] In some embodiments, a kidney disease to be treated by methods of the present disclosure is anti -neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis. ANCA-associated glomerulonephritis is a rapidly progressive renal disease and includes, e.g., Wegener's granulomatosis, microscopic polyangiitis, and renal limited vasculitis. Wegener's granulomatosis is an organ- and/or life-threatening autoimmune disease of unknown etiology.

The classical clinical triad consists of necrotizing granulomatous inflammation of the upper and/or lower respiratory tract, necrotizing glomerulonephritis, and an autoimmune necrotizing systemic vasculitis affecting predominantly small vessels. The detection of anti-neutrophil cytoplasmic antibodies directed against proteinase 3 (PR3-ANCA) is a highly specific indicator for Wegener's granulomatosis. Microscopic polyangiitis is a disorder that causes blood vessel inflammation (vasculitis), which can lead to organ damage. The kidneys, lungs, nerves, skin, and joints are the most commonly affected areas of the body. MPA is diagnosed in people of all ages, all ethnicities, and both genders. The cause of this disorder is unknown. Renal limited vasculitis is a type of anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis that presents with only a renal manifestation; no other organs, including lungs, are involved.

[0107] In some embodiments, a kidney disease to be treated by methods of the present disclosure is lupus nephritis. Lupus nephritis is inflammation of the kidney that is caused by the autoimmune disease systemic lupus erythematous (SLE). With lupus, the body's immune system targets its own body tissues; lupus nephritis occurs when lupus involves the kidneys.

[0108] In some embodiments, a kidney disease to be treated by methods of the present disclosure is anti-globular basement membrane (anti-GBM) nephropathy. Anti-GBM nephropathy is a disease that occurs as a result of injury to small blood vessels (capillaries) in the kidneys and/or lungs. In anti-GBM disease, autoantibodies are targeted to the basement membrane in capillary blood vessels of the kidneys and lung, where they target and damage GBM.

[0109] In some embodiments, a kidney disease to be treated by methods of the present disclosure is IgA nephropathy, also known as Berger’s disease. IgA nephropathy is a kidney disease that occurs when IgA deposits build up in the kidneys, causing inflammation that damages kidney tissues. IgA nephropathy affects the kidneys by attacking the glomeruli. The buildup of IgA deposits inflames and damages the glomeruli, causing the kidneys to leak blood and protein into the urine. The damage may lead to scarring of the nephrons that progresses slowly over many years. Eventually, IgA nephropathy can lead to end-stage kidney disease. [0110] In some embodiments, a kidney disease to be treated by methods of the present disclosure is polycystic kidney disease (e.g., autosomal recessive polycystic kidney disease (ARPKD) - congenital hepatic fibrosis (CHF)). ARPKD-CHF is a highly aggressive fibropolycystic disease that is characterized by the formation and expansion of fluid-filled cysts in the kidneys, enlargement of the kidneys and progressive fibrosis of both the kidney and the liver (Hartung, E.A., and Guay -Woodford, L.M. Pediatrics 2014 Sep;134(3):e833-e845; Gunay- Aygun, M., et al. J. Pediatr. 2006 Aug; 149(2): 159-64). Caroli’s disease manifests as cystic dilatation of the intrahepatic ducts, often accompanies ARPKD-CHF (Sung, J.M., et al. Clin. Nephrol. 1992 Dec;38(6):324-8). In some embodiments, a subject is suffering from, susceptible to, or at risk of Caroli’s disease. Afflicted children that survive past two years of age more often than not require renal and/or hepatic transplantation by age ten. The need for transplantation is often driven by both progressive organ dysfunction and by significant enlargement of the diseased organ(s), and is accompanied by severe pain (www.arpkdchf.org).

[0111] In some embodiments, a kidney disease to be treated by methods of the present disclosure is or includes renal cysts. Aberrant signaling by tyrosine kinases, including platelet- derived growth factor (PDGF) and vascular endothelial growth factor (VEGF) and their receptors (R), PDGFR and VEGFR/KDR, respectively, has been implicated in the formation and expansion of renal cysts. A PDGF-driven ciliopathy and/or overexpression of PDGF in the cyst lining and adjacent tubules are thought to, in part, drive renal cystic disease (Torres, V.E., et al. Lancet 2007 Apr 14;369(9569): 1287-301; Park. J.H. et al. Polycystic Kidney Disease Brisbane; 2015:375-96; Nakamura, T., et al. J. Am. Soc. Nephrol. 1993 Jan;3(7): 1378-86). Cowley et al. posited that elevated and abnormal c-myc proto-oncogene expression drives ARPKD (Proc. Natl. Acad. Sci. U.S.A. 1987 Dec:84(23):8394-8); c-myc expression is controlled by PDGF (Frick, K.K., et al. C. J. Biol. Chem. 1988 Feb 25;263(6):2948-52).

[0112] In some embodiments, a kidney disease to be treated by methods of the present disclosure is collagen type III glomerulopathy. Collagen type III glomerulopathy, also known as collagenic or collagenofibrotic glomerulopathy, is characterized by pathological accumulation of collagen type III in glomeruli. Collagen type III glomerulopathy presents either in childhood, often with a family history suggesting autosomal recessive inheritance, or in adults as a sporadic occurrence. Proteinuria is a typical manifestation, with progression to end stage renal disease (ESRD) in approximately 10 years. Although there is markedly elevated serum precursor collagen type III protein in the circulation, the usual manner of diagnosis is with kidney biopsy, which discloses type III collagen in subendothelial aspects of capillary walls and often in the mesangial matrix.

[0113] In some embodiments, a kidney disease to be treated by methods of the present disclosure is nail-patella syndrome. Nail-patella syndrome is a multi-organ disorder caused by mutations in the LMX1B gene. Nail-patella syndrome manifests with orthopedic and cutaneous deformities, as well as kidney complications due to development of structural lesions of collagen type III within glomerular basement membranes. Although the structural lesions may be asymptomatic, they are usually accompanied by proteinuria.

[0114] VEGF-driven angiogenesis is also thought to contribute to the growth of renal cysts, and inhibition of VEGFR/KDR signaling is associated with decreased tubule cell proliferation, decreased cystogenesis, and blunted renal enlargement (Bello-Ruess, E., et al. Kidney Int. 2001 Jul;60(l):37-45; Schrijvers, B.F., et al. Kidney Int. 2004 Jun;65(6):2003-17). Nevertheless, the role of VEGF in fibropoly cystic disease is more controversial, with at least some reports suggesting that this growth factor might be associated with disease mitigation (Spirli, C., et al. Gastroenterology 2010 Jan;138(l):360-71). Aside from their roles in renal cyst formation and expansion, it is being recognized in ARPKD-CHF that aberrant PDGF and VEGF signaling are also associated with extracellular matrix deposition in the liver and kidney (Rajekar, FL, et al. J. Clin. Exp. Hepatol. 2011 Sep;l(2):94-108; Jiang, L., et al. Biomed. Res. Int.

2016;2016:4918798; Tao, Y., et al. Kidney Int. 2007 Dec;72(l l);1358-66.

Subjects to Be Treated

[0115] In some embodiments, one or more subjects or populations are selected to received Compound 1 as described herein based on one or more markers and/or characteristics such as, for example, one or more risk factors of fibrosis or an associated disease, disorder or condition and/or one or more biomarkers, etc.

[0116] In some embodiments, a subject or population thereof is selected to receive Compound 1 using technologies provided herein (e.g., based on assessment of one or more markers and/or characteristics, such as one or more biomarkers, e.g., COL3A1 and/or COL1 Al). In some embodiments, such technologies are used to inform or determine one or more features of a therapeutic regimen (e.g., selection of subject(s) to receive a particular therapy (e.g.,

Compound 1 therapy) and/or dose thereof and/or timing of administration of such therapy).

[0117] In some embodiments, assessment of one or more markers and/or characteristics is performed with respect to the same subject at a plurality of different time points. In some embodiments, assessment of one or more markers and/or characteristics is performed with respect to a particular patient prior to initiation of a particular therapeutic regimen (e.g., a Compound 1 therapeutic regimen) and/or prior to administration of a particular dose of therapy (e.g., Compound 1 therapy) in accordance with such therapeutic regimen.

[0118] In some embodiments, a subject or population thereof is suffering from or is susceptible to a kidney disease as described herein. In some embodiments, a subject or population thereof is suffering from or is susceptible to fibrotic disease of the kidney as described herein. In some embodiments, a subject or population thereof is suffering from or is susceptible to a disease, disorder, or condition characterized by or otherwise associated with fibrosis of the kidney as described herein.

[0119] In some embodiments, a subject or population thereof is suffering from or is susceptible to an acute kidney injury. In some embodiments, a subject or population thereof is suffering from or is susceptible to a chronic kidney injury. In some embodiments, a subject or population thereof is suffering from a traumatic injury. In some embodiments, a subject or population thereof has undergone, is undergoing, or will undergo an organ transplantation. In some embodiments, a subject or population thereof is suffering from or susceptible to a damaged and/or ischemic organ, transplant, or graft. In some embodiments, a subject or population thereof is suffering from or susceptible to ischemia/reperfusion injury. In some embodiments, a subject or population thereof is suffering from or susceptible to post-surgical scarring.

[0120] In some embodiments, a subject or population thereof is suffering from or is susceptible to renal fibrosis. In some embodiments, a subject or population thereof is suffering from or is susceptible to renal fibrosis secondary to, or otherwise associated with, an underlying indication. In some embodiments, a subject or population thereof is suffering from or is susceptible to renal failure, renal obstruction, renal trauma, renal transplantation, chronic kidney disease, diabetes, hypertension, radiocontrast nephropathy, immune-mediated glomerulonephritides (e.g., lupus nephritis, ANCA-associated glomerulonephritides (e.g., Wegener’s granulomatosis, microscopic polyangiitis, or renal limited vasculitis), anti-GBM nephropathy, IgA nephropathy, membranous glomerulonephritis, or focal and segmental glomerulosclerosis), non-immune-mediated glomerulonephritides (e.g., autosomal dominant polycystic kidney disease), minimal change disease, or nephrotic syndrome (e.g., steroid- resistant nephrotic syndrome). In some embodiments, a subject or population thereof is suffering from or is susceptible to a fibrotic disease of the kidney that is or comprises: focal segmental glomerulosclerosis (FSGS), steroid resistant nephrotic syndrome (SRNS), proteinuria, lupus nephritis, minimal change disease, an anti-neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis, anti-globular basement membrane (anti-GBM) nephropathy, IgA nephropathy, membranous glomerulonephritis (MG), autosomal dominant polycystic kidney disease (ADPKD), or chronic kidney disease. In some embodiments, a subject or population thereof is suffering from or is susceptible to a fibrotic disease of the kidney that is or comprises an anti-neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis. In some embodiments, ANCA-associated glomerulonephritis is selected from Wegener’s granulomatosis, microscopic polyangiitis (MPA), or renal limited vasculitis. In some embodiments, a subject or population thereof is suffering from or is susceptible to collagen type III glomerulopathy or nail- patella syndrome. In some embodiments, a subject or population thereof is suffering from or is susceptible to nephrotic syndrome and/or diseases, disorders, or conditions associated with nephrotic syndrome (e.g., focal and segmental glomerulosclerosis, minimal change disease, and membranous nephropathy). In some embodiments, a subject or population thereof is suffering from or is susceptible to focal and segmental glomerulosclerosis (FSGS). In some embodiments, a subject or population thereof is suffering from or is susceptible to collagen type III glomerulopathy. In some embodiments, a subject or population thereof is suffering from or is susceptible to nail-patella syndrome. In some embodiments, a subject or population thereof is suffering from or is susceptible to polycystic kidney disease (e.g., autosomal dominant polycystic kidney disease or autosomal recessive polycystic kidney disease).

[0121] In some embodiments, a subject or population thereof is suffering from or is susceptible to primary proteinuric kidney disease (e.g., as confirmed from a renal biopsy). In some embodiments, a subject or population thereof is suffering from or is susceptible to primary glomerular diseases (e.g., as confirmed from a renal biopsy). In some embodiments, a subject or population thereof is suffering from or susceptible to persistent proteinuria. In some embodiments, a subject or population thereof is suffering from or susceptible to primary glomerular disease (e.g., as confirmed from a renal biopsy) and persistent proteinuria. In some embodiments, a subject or population thereof is suffering from or susceptible to proteinuric chronic kidney disease. In some embodiments, a subject or population thereof is suffering from or is susceptible to focal and segmental glomerulosclerosis. In some embodiments, a subject or population thereof is suffering from or is susceptible to membranous nephropathy. In some embodiments, a subject or population thereof is suffering from or susceptible to IgA nephropathy.

[0122] In some embodiments, a subject or population thereof is suffering from or is susceptible to renal fibrosis and has an altered level of one or more biomarkers (e.g., an elevated level of COL3A1 and/or COL1A1).

Biomarkers

[0123] In some embodiments, the present disclosure provides certain biomarkers that can distinguish subjects (e.g., subjects suffering from or at risk of renal fibrosis or associated diseases, disorders, and conditions) who are more likely than others to respond to therapy with Compound 1. The present disclosure provides the insight that certain biomarkers can distinguish patients who are likely to respond to therapy, for example because the drivers of their kidney disease correspond with the mechanism of action of Compound 1. For example, in some embodiments, an altered level of one or more gene products or proteins that are part of the mechanism of action of Compound 1 (e.g., down- or up-regulated by Compound 1). In some embodiments, one or more biomarkers comprise an elevated level of COL3 A1 expression and/or COL1A1 expression.

[0124] In some embodiments, a patient with an altered level of one or more biomarkers may have an improved response to treatment with Compound 1 relative to a patient who does not have a level of the biomarker that meets the threshold criteria.

[0125] In some embodiments, one biomarker is used to characterize subjects; in some embodiments, more than one biomarker (e.g., two, three, etc.) is used to characterize subjects. [0126] Generally, a biomarker is a component of a biological sample that may be detected and/or quantified when present in the biological sample. [0127] In some embodiments, a level of a biomarker corresponds to a level of gene expression (e.g., RNA expression, e.g., mRNA expression). In some embodiments, a level of a biomarker corresponds to a level of collagen protein expression. For example, in some embodiments, a biomarker is or includes collagen protein expression in any form, e.g., procollagen polypeptide, collagen protein, preprocollagen polypeptide, amino-terminal procollagen polypeptide, collagen fibril, collagen fiber, and/or any fragment or degradation product of any thereof.

[0128] In some embodiments, a biomarker is differentially present in a sample taken from a subject of one status as compared with another status (e.g., more responsive to Compound 1 therapy vs. less responsive to Compound 1 therapy). In some embodiments, a biomarker is differentially present in a sample taken from the same subject at two or more different time points, i.e., when the status of the subject has changed from one time point to another.

[0129] In some embodiments, a biomarker is detected and/or quantified in a tissue sample (e.g., from a biopsy, such as a kidney biopsy) and/or in a biological fluid (e.g., blood, urine, etc.). In some embodiments, a biomarker is a level of mRNA that is detected and/or quantified in a kidney tissue sample, e.g., obtained from a kidney biopsy. In some embodiments, a biomarker is detected and/or quantified in a urine sample (e.g., a level of a protein or protein fragment). In some embodiments, a biomarker is detected and/or quantified in a blood sample (e.g., a level of a protein or protein fragment).

[0130] A biomarker may include one or more of a peptide, protein, nucleic acid (e.g., polynucleotide, DNA, RNA, etc.), polysaccharide (e.g., lectins or sugars), lipid, enzyme, small molecule, ligand, receptor, antigen, or antibody. In some embodiments, a biomarker comprises a protein. In some embodiments, a biomarker comprises a nucleic acid (e.g., mRNA).

[0131] In some embodiments, detection of a threshold level of one or more biomarkers is used to select and/or characterize patients who may be responsive to Compound 1 therapy. In some embodiments, levels of one or more biomarkers in a sample from a subject are compared to a threshold level. In some embodiments, a biomarker is considered increased if the level is increased relative to a threshold level (e.g., increased by at least about 5%, about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or about 100%, or more). In some embodiments, a threshold level is determined from a population of healthy volunteers (e.g., a mean or median level from a population of healthy volunteers). [0132] Any suitable means can be used to determine levels or one or more biomarkers in accordance with the present disclosure. In some embodiments, a method includes an in vitro method for determining a level of a biomarker. For example, in vitro methods for determining a level of a biomarker include, but are not limited to, a chemiluminescence assay, enzymatic assay, enzyme immunoassay, multiplex immunoassay, ELISA, chromatographic immunoassay, electrophoresis assay, radioimmunoassay, colorimetric assay, chromatography/mass spectrometry (e.g., GC/MS, LC/MS, LC/MS/MS, etc.), High Performance Liquid Chromatography (“HPLC”), and/or PCR (e.g., real-time PCR).

[0133] In some embodiments, a method for detecting a level of a biomarker includes chromatographic and/or MS methods. Exemplary methods include, but are not limited to, gas chromatography (GC), liquid chromatography/mass spectroscopy (LC-MS), gas chromatography/mass spectroscopy (GC-MS), nuclear magnetic resonance (NMR), magnetic resonance imaging (MRI), Fourier Transform InfraRed (FT-IR), and inductively coupled plasma mass spectrometry (ICP-MS).

[0134] In some embodiments, the present disclosure encompasses the recognition that COL1 A1 and/or COL3A1 are useful biomarkers in the methods provided herein. In some embodiments, the present disclosure provides insight that increased levels of COL1 A1 and/or COL3 A1 expression may be useful in selecting and/or characterizing patients for Compound 1 therapy. In some embodiments, COL1 A1 is a biomarker useful in the methods provided herein. In some embodiments, COL3 A1 is a biomarker useful in the methods provided herein.

[0135] In some embodiments, an elevated level of COL1A1 and/or COL3A1 corresponds to a level of gene expression (e.g., RNA, e.g., mRNA). In some embodiments, an elevated level of COL1A1 and/or COL3A1 corresponds to a level of collagen protein expression. For example, in some embodiments, an elevated level of COL1A1 and/or COL3A1 protein is or includes e.g., a corresponding procollagen polypeptide, collagen protein, preprocollagen polypeptide, amino- terminal procollagen polypeptide, collagen fibril, collagen fiber, and/or any fragment or degradation product of any thereof.

[0136] In some embodiments, an increased level of COL1 A1 and/or COL3A1 is above a threshold level (e.g., a predetermined median or mean level). In some embodiments, an increased level of COL1 A1 and/or COL3A1 is more than about 5%, about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or about 100%, or more of a threshold level. In some embodiments, an increased level of COL1 A1 and/or COL3A1 is more than about 0.5, about 1.0, about 1.5, or about 2.0, or more standard deviations above a threshold level.

[0137] In some embodiments, subjects who are selected for Compound 1 therapy based on increased levels of COL1 A1 and/or COL3A1 achieve improved outcomes (e.g., compared to subjects who do not meet one or more selection criteria for Compound 1 therapy).

In some embodiments, the present disclosure provides methods of treating a disease, disorder, or condition characterized by increased expression of COL1 A1 and/or COL3A1, comprising administering Compound 1 to a subject or population of subjects in need thereof. In some such embodiments, a disease, disorder, or condition is a renal disease, disorder, or condition (e.g., a renal disease, disorder, or condition associated with fibrosis) as described herein. For example, in some embodiments, a renal disease, disorder, or condition is characterized by increased expression of COL1A1 and/or COL3A1.

[0138] In some embodiments, the present disclosure provides methods comprising administering Compound 1 to a subject in need thereof, wherein the subject has been determined to have increased level(s) of COL1A1 and/or COL3A1. In some embodiments, a subject has been determined to have increased level(s) of COL1 A1 and/or COL3A1 in a renal biopsy sample and/or a urine sample.

[0139] In some embodiments, the present disclosure provides methods comprising determining level(s) of COL1A1 and/or COL3A1 by: obtaining a biological sample from a subject; performing an assay on the sample to determine level(s) of COL1 A1 and/or COL3A1 in the sample; and comparing the determined level(s) to a threshold level. In some embodiments, if a sample has increased level(s) of COL1 A1 and/or COL3A1 compared to a threshold level, then Compound 1 is administered to the subject. In some embodiments, if a sample does not have increased level(s) of COL1 A1 and/or COL3A1 compared to a threshold level, then Compound 1 is not administered to the subject.

[0140] In some embodiments, the present disclosure provides methods comprising determining level(s) of COL1 A1 and/or COL3A1 in a biological sample from a subject; comparing the determined level(s) to a threshold level; and identifying the subject as in need of therapeutic intervention when the sample is determined to have increased level(s) of COL1 A1 and/or COL3A1 compared to the threshold level. For example, in some embodiments, a subject is identified as in need of therapeutic intervention with Compound 1 therapy.

[0141] In some embodiments, a provided method further comprises administering Compound 1 to a subject (e.g., a subject identified as in need of therapeutic intervention).

[0142] In some embodiments, provided technologies are useful for monitoring subjects (e.g., monitoring status of subjects over time and/or monitoring therapy). In some embodiments, the present disclosure provides methods comprising determining level(s) of COL1A1 and/or COL3A1 in each of a plurality of biological samples obtained at different time points from a single patient; and comparing the determined level(s) from a first time point with that from at least one later time point. In some embodiments, the present disclosure provides methods comprising determining level(s) of COL1 A1 and/or COL3A1 from a biological sample obtained from a subject for whom level(s) of COL1 A1 and/or COL3A1 have previously been obtained at least once; and comparing the determined level(s) with the previously obtained level(s). In some embodiments, a first time point and one or more later time points are separated from one another by a reasonably consistent interval.

[0143] In some embodiments, a significant change in the determined level over time indicates a change in the subject’s status. In some embodiments, a significant change in a determined level over time is a change (e.g., an increase or a decrease) of at least about 5%, about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or about 100%, or more compared to a threshold level. In some embodiments, a significant change in a determined level over time is a change of more than about 0.5, about 1.0, about 1.5, or about 2.0, or more standard deviations away a threshold level.

[0144] In some embodiments, such methods further comprise administering Compound 1 therapy to a subject (e.g., a subject who has been determined to have moved from a non- responsive to a responsive state).

[0145] In some embodiments, provided methods are useful for monitoring therapy (e.g., efficacy and/or other indicators of response). In some embodiments, a sample from a first time point was obtained from a subject prior to administration of Compound 1, and a sample from a second time point was obtained from a subject after administration of Compound 1. In some such embodiments, if a decrease in COL1 A1 and/or COL3A1 level(s) is observed in a later sample compared to a first sample, then Compound 1 therapy is continued. In some such embodiments, if no change or an increase in COL1A1 and/or COL3A1 level(s) is observed in a later sample compared to a first sample, then Compound 1 therapy is discontinued, or dosage amount and/or frequency of Compound 1 therapy is increased.

[0146] In some embodiments, a method includes an in vitro method for determining a level of a biomarker. In some embodiments, a method for determining a level of a biomarker can be or include a chemiluminescence assay, enzymatic assay, enzyme immunoassay, multiplex immunoassay, ELISA, chromatographic immunoassay, electrophoresis assay, radioimmunoassay, colorimetric assay, UV spectroscopy, chromatography/mass spectrometry (e.g., GC/MS, LC/MS, LC/MS/MS, etc.), High Performance Liquid Chromatography (“HPLC”), and/or PCR (e.g., quantitative PCR and/or real-time PCR).

[0147] In some embodiments, a level of a biomarker (e.g., COL1A1 and/or COL3A1 ) corresponds to a level of gene expression (e.g., RNA, e.g., mRNA) and is quantified using methods known in the art. In some embodiments, a method of determining a level of expression of a biomarker gene (e.g., RNA, e.g., mRNA) can be or include a chemiluminescence assay, UV spectroscopy, hybridization assay (e.g., Fluorescent in Situ Hybridization (FISH), e.g., RNA- FISH), enzymatic assay, enzyme immunoassay (e.g., ELISA), multiplex assay, electrophoresis assay, radioassay, colorimetric assay, chromatography/mass spectrometry (e.g., GC/MS, LC/MS, LC/MS/MS, etc.), High Performance Liquid Chromatography (“HPLC”), and/or PCR (e.g., quantitative PCR and/or real-time PCR).

[0148] In some embodiments, a level of a biomarker (e.g., COL1 A1 and/or COL3A1) corresponds to a level of protein (e.g., procollagen polypeptide, collagen protein, preprocollagen polypeptide, amino-terminal procollagen polypeptide, collagen fibril, collagen fiber, and/or any fragment or degradation product of any thereof) and is quantified using methods known in the art. In some embodiments, a method of determining a level of expression of a biomarker protein (e.g., COL1 A1 and/or COL3A1) can be or include a chemiluminescence assay, enzymatic assay, enzyme immunoassay, multiplex immunoassay, ELISA, chromatographic immunoassay, electrophoresis assay, radioimmunoassay, colorimetric assay, UV spectroscopy, chromatography/mass spectrometry (e.g., GC/MS, LC/MS, LC/MS/MS, etc.), or High Performance Liquid Chromatography (“HPLC”). Administration

[0149] A composition providing Compound 1, as described herein, can be administered to subjects in accordance with methods provided herein.

[0150] In some embodiments, a composition providing Compound 1 is a composition comprising Compound 1 (in a pharmaceutically acceptable form as described herein), formulated together with one or more pharmaceutically acceptable carriers. In some embodiments, a composition providing Compound 1 is or comprises Compound 1 present in unit dose amount appropriate for administration in a therapeutic regimen that shows a statistically significant probability of achieving a predetermined therapeutic effect when administered to a relevant population. In some embodiments, compositions providing Compound 1 may be specially formulated for administration in solid or liquid form, including those adapted for the following: oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), capsules, tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue; parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained-release formulation; topical application, for example, as a cream, ointment, or a controlled-release patch or spray applied to the skin, lungs, or oral cavity; intravaginally or intrarectally, for example, as a pessary, cream, or foam; sublingually; ocularly; transdermally; or nasally, pulmonary, and to other mucosal surfaces.

[0151] In some embodiments, as described herein, a composition providing Compound 1 is formulated for oral administration (e.g., in a capsule form). In some embodiments, a composition providing Compound 1 is administered orally.

[0152] In some embodiments, a composition providing Compound 1 is administered as one or more unit dosage forms. In some embodiments, a composition providing Compound 1 is administered as one or more solid unit dosage forms (e.g., one or more capsules or tablets). In some embodiments, Compound 1 is administered as one or more oral unit dosage forms. In some embodiments, a composition providing Compound 1 is an immediate release solid unit dosage forms.

[0153] In some embodiments, a composition providing Compound 1 is a capsule. In some embodiments, a composition providing Compound l is a tablet. [0154] In some embodiments, a composition providing Compound 1 is administered as a single dose. In some embodiments, a composition providing Compound 1 is administered at regular intervals. Administration at an “interval,” as used herein, indicates that the therapeutically effective amount is administered periodically (as distinguished from a one-time dose). In some embodiments, a composition providing Compound 1 is administered bimonthly, monthly, twice monthly, triweekly, biweekly, weekly, twice weekly, thrice weekly, daily, twice daily, or every six hours in accordance with methods provided herein.

[0155] In some embodiments, a composition providing Compound 1 is administered at regular intervals indefinitely. In some embodiments, a composition providing Compound 1 is administered at regular intervals for a defined period of time.

EXAMPLES

[0156] The following examples are provided to illustrate, but not limit, the claimed invention.

Example 1. Compound 1 Decreases Expression of Certain Fibrosis and Inflammation Related Markers

[0157] The present example probed the effects of Compound 1 on expression of various anti inflammatory and anti-fibrotic marker proteins in a cell culture-based model of fibrosis. Compound 1 is in a pharmacological class of tyrosine kinase inhibitors (TKI) and has a chemical name of: (Z)-methyl 3-(((4-(N-methyl-2-(4-methylpiperazin-l-yl)acetamido)phenyl)amino) (phenyl)methylene)-2-oxo-2,3-dihydro-lH-pyrrolo[2,3-b]pyridine-6-carboxylate. Compound 1 is an orally bioavailable small molecule dual kinase inhibitor of platelet-derived growth factor receptors (PDGFR) and vascular endothelial growth factor receptors (VEGFR2).

[0158] Specifically, the present example describes Bio-Map studies of Compound 1 in cell culture systems using DiscoverX technology platform and that were profiled in a KINOMEscan (Ambit/Di scoveRx/Eurofms, CA) biochemical assay. Exemplary culture systems analyzed were: (1) Lung fibroblasts only (MyF) and (2) Renal proximal tubular epithelial cells + lung fibroblasts (REMyF). When activated, these cell systems mimic pathological conditions such as chronic inflammation, fibrosis, and matrix remodeling. [0159] Co-cultures of epithelial cells and fibroblasts or fibroblasts alone were activated with TGFp i (10 ng/mL) + TNF alpha (lOng/mL) and treated with Compound 1 at 100 nM, 500 nM, 2.5mM and 13mM concentrations and incubated for 48 hours. Expression of numerous critical anti-inflammatory and anti-fibrotic marker proteins were evaluated. This revealed that Compound 1 treatment decreased levels of several inflammation-related markers including monocyte chemotactic protein (MCP-1), macrophage colony stimulating factor (M-CSF), soluble interleukin (sIL-8), Interferon induced T cell alpha chemoattractant (I-TAC), IL-8, Interferon gamma induced Protein- 10 (IP- 10). Compound 1 treatment also decreased levels of fibrosis- related markers including N-cadherin, a-SMA, Collagen I and III, TIMP-1, plasminogen activator inhibitor (PAI-1), matrix metalloprotease, MMP-1, MMP-9, tissue and urokinase plasminogen activator (tPA and uPA), soluble VEGF and epidermal growth factor (EGFR) as shown in FIG. 1.

[0160] Accordingly, the present example demonstrates that Compound 1 induced dose- dependent decrease in expression of a number of different inflammation and fibrosis-related markers. In particular, the present example demonstrates that a mixed cell culture comprising renal epithelial cells and activated myofibroblasts treated with Compound 1 (13 mM) reduced expression of COL1 and COL3.

Example 2. Identification of Biomarkers for Treatment of Kidney Fibrotic Diseases with Compound 1

[0161] The present disclosure encompasses a recognition that in different patients, disease driving pathways may have divergent outcomes or converge on a common disease related outcome. For example, as depicted in FIG. 2, in some instances, different individuals may have distinct genomic responses that all result in a common kidney disease endpoint, while in other instances, different individuals may have a shared genomic response that leads to different kidney disease endpoints. For example, distinct disease-driving pathways in different individuals may lead to a common outcome of a fibrotic kidney disease, such as, e.g., FSGS. As such, different patients may respond to different therapies and interventions for the same disease. The present disclosure provides the insight that identifying and neutralizing the particular disease drivers of a given patient may provide an early and effective way to manage kidney disease endpoints. Specifically, the present example determined the signalosome in various models of Focal and Segmental Glomerulosclerosis (FSGS) to identify biomarkers for treatment with Compound 1.

[0162] Exemplary and etiologically distinct murine models of FSGS were used to characterize the kidney transcriptome and proteome that are associated with therapeutic activity of Compound 1. At the end of the in-life component of each of the studies, kidneys were harvested. For the rat models, kidney tissue was preserved in RNAlater (Sigma-Aldrich) for glomerular isolation by manual microdissection. For the mouse model, glomeruli were isolated by magnetic bead extraction. RNA was extracted from glomerular preparations. RNA extraction, RNA sequencing, data normalization and filtering were then performed. Differential expression analysis was performed using DESeq2 and EdgeR (M. F Love, et ak, (December 5, 2014) Genome Biol. 15: 550; M. D. Robinson, et ak, (January 1, 2010) Bioinformatics, 26(1): 139-140). Significantly regulated genes were analyzed by creating biological literature-based networks with Genomatix Pathway System software (GePS) (www.genomatix.de). Canonical pathways were analyzed using Ingenuity Pathway Analysis software (IP A)

(www.ingenuity.com). Hierarchical cluster dendrograms were generated to determine the ability of overall transcriptional profiles to recapitulate treatment groups. Rat and murine genes were converted to the corresponding human orthologs using the NCBI homolog (Build 64) and Genomatix annotated ortholog databases. Signalosome of rodent models treated with Compound 1 was analyzed and compared with transcriptome of renal dysfunction in human patients to thereby identify biomarkers of patients to be treated with Compound 1.

Exemplary Rodent Model of Kidney Disease

[0163] Administration of puromycin aminonucleoside (PAN) to Wistar rats (a sensitive strain) produces overt proteinuria (Moreno-Manzano, V., et al. Br. J. Pharmacol. 2003 Jun; 139(4): 823 -31). Adult Wistar rats were administered PAN (-100 mg/kg, IP). On Day 4 after PAN administration and after confirming increased urine protein (24 hr), animals were randomized to vehicle (n=14) or Compound 1 (45 mg/kg Compound 1 Hydrochloride trihydrate, PO, BID, n=14). Urine protein was determined again on Days 8, 12, and 21 (FIG. 3).

[0164] These data show that rat puromycin aminonucleoside nephropathy (PAN) model of proteinuric kidney disease exhibit proteinuria that is mitigated by treatment with Compound 1, but not with sham. Animals were sacrificed on Day 21 after PAN administration. Mean arterial pressure (MAP) was evaluated prior to sacrifice and was not substantially different between vehicle treated and Compound 1 treated animals (data not shown). Thus, therapeutic intervention with Compound 1 in this rodent model was associated with a decrease in urine protein with no change in MAP.

[0165] Kidneys were harvested and one of the two kidneys were used for analysis of the glomerular transcriptome. The other kidneys were homogenized for determination of COL1 A1 and COL3 A1 expression. Therapeutic intervention with Compound 1 was associated with decreased renal COL1 A1 and COL3A1 expression, shown in FIG. 4.

[0166] Similar results are observed using a uninephrectomy (UNX) + DOCA + Salt rat model of renal dysfunction. In this model, renal dysfunction is introduced by removing one kidney and administering subcutaneous injections of the aldosterone precursor deoxycorticosterone acetate (DOCA), while providing 1% NaCl in the drinking water. Characteristics of this model include the development of severe proteinuria and glomerulosclerosis, which reflects several aspects of the pathogenesis of focal and segmental glomerulosclerosis (FSGS). The use of this model has been described extensively in the literature (See Arai, K., et al. J. Pharm. Exp. Ther. 2016 Sep;358(3):548-57; Kretzler, M., et al. Virchows Arch. 1994;425(2): 181-93).

[0167] The present disclosure provides the insight that disease-driving networks in animal (e.g., murine) models of kidney disease may prove beneficial in those human patients that share the same transcriptional elements. Using network level human-rodent transcriptome mapping strategies for diabetic kidney disease (Hodgin, J. B., et al. Diabetes 2013 Jan;62(l):299-308) and lupus nephritis (Berthier, C. C., et al. J. Immunol. 2012 Jul 15; 189(2):988-1001), human-model network intersects were generated using available transcriptional profiling in human subjects with minimal change disease (MCD) and/or FSGS (from the European Renal cDNA Bank, n = 48, and from NEPTUNE, n =123). These network models were used to identify disease marker genes and signatures that respond Compound 1 therapeutic intervention.

[0168] Compound 1 responsive disease marker genes were also evaluated in samples from patients with established steroid-resistant FSGS and frequently relapsing FSGS (n = 45) in the NEPTUNE cohort; specifically those with available baseline transcriptional profiling (n = 19) or urine Luminex proteomic profiling (n = 11) of 54 proteins (e.g., cytokines, TIMP, and metalloproteases) to determine the ability of the Compound 1 responsive disease marker genes and signatures to stratify patients with steroid resistant FSGS.

[0169] COL1A1 and COL3A1 have been identified as disease-associated nodes in human FSGS. See , e.g., Canadas-Garre, M., et al. J. Transl. Med. (2018) 16:292; Grgic, F, et al. Kidney Int. 2014 Dec; 86(6): 1116-1129; Schwab, K., et al. Am. J. Nephrol. 2004;24:438-447; and Grgic, F, et al. Kidney International. Furthermore, increased renal COL3A1 expression is associated with increased renal dysfunction in human FSGS. Additionally, expression of renal COL3A1 was shown to correlate with renal dysfunction in a rat PAN model of FSGS, similarly to the correlation observed in human kidney disease (FIG. 5).

[0170] These data confirm the therapeutic relevance of the Compound 1 interactome in clinical kidney disease, as COL1A1 and COL3A1 are components of this network and play a role in kidney disease (FIG. 6).

[0171] Other components of the Compound 1 interactome network include MAP2K5, MAP3K3, MAPK7, PRKAR1A, PIK3R1, SMPD1, AXL, FYN, PLXND1, CDC42PB, VAT1, RPS6KA2, RBPMS, CAV1, BGN, NPRl, FGFR1, EFEMP2, COL6A1, HEG1, PCGF2, COL6A2, MYH11, PDGFRA, PDGFRB, and KIT.

[0172] Thus, the present disclosure identified biomarkers in rodent models of kidney disease and in human patients that correspond with the Compound 1 mechanism of action. The present disclosure encompasses a recognition that patients with fibrotic kidney diseases who have an altered level of one or more of these biomarkers may benefit from treatment with Compound 1.

Example 3. Therapeutic Treatment of Patients Expressing Biomarkers for Compound 1 [0173] The present example describes treatment of fibrotic disease of the kidney in a patient. Specifically, a nephropathy patient with suspected or confirmed glomerular disease (i.e., suspected of having FSGS or MCD) is subjected to a renal biopsy. For example, mRNA is extracted from single glomeruli (see Menon et al., JCI Insight. 2020, 5(6):el33267), and sequenced to quantify levels of certain biomarkers associated with Compound l’s mechanism of action. In particular, COL1A1 and COL3A1 expression are quantified. If the subject has a level of COL3A1 and/or COL1 Al that is above a threshold level, then the subject is to be treated with Compound 1. An exemplary threshold level is a level that is about 20% or more above a predetermined normal range or mean or median level in a healthy patient. If a subject does not have a level of biomarker above the threshold level, then alternate treatment is determined. In some embodiments, in a patient to be treated with Compound 1, the kidney disease is stabilized and/or ameliorated.

Example 4. Puromycin Aminonucleoside Administration in Rat is Associated with Collagen Type III Glomerulopathy

[0174] Adult male Wistar rats (~75 g) were administered PAN (100 mg/kg, intaperitoneally, n=8) and followed out to 21 days when they were sacrificed. A sham cohort (n=4) was injected with an equivalent volume of water. Twenty-four hour urine samples were obtained on Days 4,

8, 14 and 21 after PAN administration and from the sham cohort. Urine protein was determine using the Bradford assay.

[0175] Administration of PAN was associated with a steep increase in urine protein that peaked at ~ day 14 (FIG. 7). By Day 21 urine protein level had decreased although it was still elevated compared to the sham cohort. Histopathological analysis of the kidney showed an increased hypertrophy of the glomerulus in the PAN cohort accompanied by expansion of both the Bowman’s capsule and Bowman’s space.

[0176] At sacrifice the left kidney was retrieved. Renal homogenates were subjected to analysis for COL3A1 and peptidylprolyl isomerase A (housekeeping gene) mRNA. qPCR was performed on a Thermofisher Quant-Studio 3 Real-Time PCR system, each sample was diluted three-fold, and qPCR reaction was performed in triplicate for all tissue samples. Renal slices were stained with periodic acid Schiff for morphometric analysis or with Collagen Type III (Col3al) Antibody (BioCompare) for immunohistochemical analysis.

[0177] HumanBase was used to build glomerular (G) and tubular (T) COL3 A1 transcriptomic networks. Network analysis was restricted to 51 elements each, inclusive of COL3A1, with a minimum interaction confidence of 0.01. The Jaccard-Tanimoto similarity index was used to calculate common elements within the two compartments. j (G,T) =j n T ÷j u T

[0178] Data are expressed as average ± standard error of mean. Between group differences were calculated using Student’s T-test and a p value < 0.05 assumed significant.

[0179] COL3 A1 mRNA level was elevated ~4-fold in the PAN cohort (FIG. 8A). There was a significant and direct association between the fold-increase in renal COL3 A1 mRNA level and the corresponding urine protein value (FIG. 8B). Immunohistochemical analysis indicated deposition of collagen type III restricted to the glomerular mesangium.

[0180] Network analysis revealed a relative strong glomerular COL3 A1 interactome with an average strength of 0.8±0.08 (FIG. 9A) and a relatively weaker tubular COL3A1 interactome with an average strength of 0.56±0.01 (FIG. 9B). The Jaccard-Tannimoto similarity index between the glomerular (G) and tubular (T) COL3A1 signaling elements was 5.1%.

[0181] The present example demonstrates that an increase in COL3A1 mRNA is directly associated with an increase in urine protein in a rat model of kidney disease. In particular, collagen type III deposition is restricted to the glomerulus, which may be indicative of a robust COL3A1 transcriptomic network in that compartment, compared to, e.g., the tubulointerstitium.

[0182] The embodiments of the disclosure described above are intended to be merely exemplary; numerous variations and modifications will be apparent to those skilled in the art.

All such variations and modifications are intended to be within the scope of the present invention as defined in any appended claims.

Claims

1. A method for treating a fibrotic disease of the kidney, the method comprising: administering an effective amount of a Compound 1:

1 or a pharmaceutical composition thereof, to a patient who has been determined to have an elevated level of COL3A1 and/or COL1A1.

2. A method for treating a fibrotic disease of the kidney in a patient characterized by an elevated level of COL3A1 and/or COL1A1, the method comprising: administering to the patient an effective amount of a Compound 1 :

1 or a pharmaceutical composition thereof.

3. The method of claim 1 or 2, wherein the elevated level of COL3A1 and/or COL1A1 comprises a level that is above that of a corresponding threshold expression level.

4. The method of any one of claims 1 to 3, wherein the elevated level of COL3A1 and/or COL1 A1 was obtained from or determined in a biological sample from the patient.

5. The method of any one of claims 1 to 3, wherein the method further comprises obtaining or determining a level of COL3A1 and/or COL1 A1 in a biological sample from the patient.

6. A method for treating a patient diagnosed with, suspected of having, or at risk for a fibrotic disease of the kidney, the method comprising:

(i) obtaining or determining a level of expression of one or more gene products or proteins in a biological sample from the patient, wherein the one or more gene products or proteins are selected from: COL3A1 and COL1A1;

(ii) comparing the expression level of the one or more gene products or proteins with that of a corresponding threshold level, wherein if the expression level of COL3A1 and/or the expression level of COL1 A1 is above the threshold expression level: administering to the patient an effective amount of Compound 1 :

1 or a pharmaceutical composition thereof.

7. The method of claim 3 or 6, wherein the threshold expression level corresponds to a predetermined mean or median level of COL3A1 and/or COL1A1 of a population of healthy subjects.

8. The method of claim 7, wherein the expression level of COL3A1 is at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% higher than the corresponding threshold expression level and/or the expression level of COL1 A1 is at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% higher than the corresponding threshold expression level.

9. The method of any one of claims 1 to 8, wherein the biological sample is a renal biopsy sample, a urine sample or a blood sample.

10. The method of claim 9, wherein the biological sample is a renal biopsy sample and the expression level of COL3A1 is an mRNA level and/or the expression level of COL1 A1 is an mRNA level.

11. The method of claim 9, wherein the biological sample is a urine sample and the expression level of COL3 A1 is a level of COL3 A1 protein or fragments thereof and/or the expression level of COL1 A1 is a level of COL1 A1 protein or fragments thereof.

12. The method of any one of claims 1 to 11, wherein the fibrotic disease of the kidney is or comprises: focal segmental glomerulosclerosis (FSGS), steroid resistant nephrotic syndrome (SRNS), proteinuria, lupus nephritis, minimal change disease, an anti-neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis, anti-globular basement membrane (anti-GBM) nephropathy, IgA nephropathy, membranous glomerulonephritis (MG), autosomal dominant polycystic kidney disease (ADPKD), collagen type III glomerulopathy, nail-patella syndrome, or chronic kidney disease.

13. The method of claim 12, wherein the anti -neutrophil cytoplasmic antibody (ANCA)- associated glomerulonephritis is Wegener’s granulomatosis, microscopic polyangiitis (MPA), or renal limited vasculitis.

14. The method of claim 12, wherein the fibrotic disease of the kidney is or comprises focal and segmental glomerulosclerosis (FSGS).

15. The method of claim 14, wherein:

(i) increased renal COL3 A1 expression is correlated with urine protein to creatinine ratio; and/or (ii) COL3 A1 expression is inversely correlated with eGFR.

16. The method of any one of claims 1 to 11, wherein the fibrotic disease of the kidney is or comprises primary proteinuric kidney disease.

17. The method of any one of claims 1 to 11, wherein the fibrotic disease of the kidney is or comprises primary glomerular disease.

18. The method of any one of claims 1 to 17, wherein administration of Compound 1 to the patient: (i) reduces the expression of renal COL3A1 , (ii) reduces the expression of renal COL1A1 , (iii) reduces renal COL3A1 accumulation, (iv) reduces renal COL1 A1 accumulation, or (v) any combination thereof.

19. The method of any one of claims 1 to 18, wherein the patient has proteinuria.

20. The method of any one of claims 1 to 19, wherein Compound 1 is administered in a pharmaceutically acceptable salt form.

21. A method compri sing :

(a) receiving a report listing the expression level of COL3A1 and COL1 A1 for a patient with a focal segmental glomerulosclerosis (FSGS);

(b) receiving a request for reimbursement of the screening and/or of a particular therapeutic regimen;

(c) approving payment and/or reimbursement for treatment with Compound 1 therapy if the report indicates the level of COL3A1 and/or COL1 A1 is above a threshold level, wherein Compound 1 is:

1

22 A method for treating a patient diagnosed with, suspected of having, or at risk for a fibrotic disease of the kidney, the method comprising:

(ii) comparing the expression level of the one or more gene products or proteins with that of a corresponding threshold level, and

(iii) if the expression level of COL3A1 and/or the expression level of COL1 A1 is above the threshold expression level, then administering to the patient an effective amount of Compound 1:

1, and if the expression level of COL3 A1 and/or the expression level of COL1 A1 is not above the threshold expression level, then the patient is not administered Compound 1.

23. A method for treating a patient diagnosed with, suspected of having, or at risk for a fibrotic disease of the kidney, which patient is characterized by an elevated level of COL3 A1 and/or COL1A1, the method comprising:

(i) administering an effective amount of Compound 1:

1 or a pharmaceutical composition thereof, and

(ii) monitoring a level of COL3A1 and/or COL1A1.

24. The method of claim 23, wherein if the level of COL3A1 and/or COL1 A1 increases in a patient administered Compound 1, discontinuing further treatment with Compound 1.

25. The method of claim 23, wherein if the level of COL3A1 and/or COL1A1 increases in a patient administered Compound 1, increasing the dose of Compound 1 administered to the patient.

26. The method of any one of claims 22 to 25, wherein the fibrotic disease of the kidney is or comprises: focal segmental glomerulosclerosis (FSGS), steroid resistant nephrotic syndrome (SRNS), proteinuria, lupus nephritis, minimal change disease, an anti-neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis, anti-globular basement membrane (anti-GBM) nephropathy, IgA nephropathy, membranous glomerulonephritis (MG), autosomal dominant polycystic kidney disease (ADPKD), collagen type III glomerulopathy, nail-patella syndrome, or chronic kidney disease.

27. The method of any one of claims 22 to 25, wherein the fibrotic disease of the kidney is or comprises primary proteinuric kidney disease.

28. The method of any one of claims 22 to 25, wherein the fibrotic disease of the kidney is or comprises primary glomerular disease.

29. The method of any one of claims 22 to 28, wherein Compound 1 is administered in a pharmaceutically acceptable salt form.