# US 12,213,979 B2 · Biomarkers of methotrexate-induced immune tolerance

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- Number: US 12,213,979 B2
- Document ID: US12213979B2
- Status: Granted
- Kind: B2
- Application number: 16/955,391
- Filed: 2018-12-21
- Published: 2021-01-14
- Granted: 2025-02-04
- Earliest claimed: 2017-12-22
- Assignees: Genzyme Corporation
- Applicants: Genzyme Corporation
- Inventors: Alexandra Joseph; Johnson Tran; Susan M. Richards
- Web page: https://patentgrep.com/patent/US12213979B2

## CPC

- A61K 31/519: ortho- or peri-condensed with heterocyclic rings
- A61K 9/0019: {Injectable compositions; Intramuscular, intravenous, arterial, subcutaneous administration; Compositions to be administered through the skin in an invasive manner (non-active ingredients are additionally classified in A61K47/00)}
- A61K 31/365: Lactones
- A61K 31/52: Purines, e.g. adenine
- A61K 31/5377: not condensed and containing further heterocyclic rings, e.g. timolol
- A61K 31/675: having nitrogen as a ring hetero atom, e.g. pyridoxal phosphate
- A61K 31/69: Boron compounds
- A61K 38/13: Cyclosporins
- A61K 38/47: acting on glycosyl compounds (3.2), e.g. cellulases, lactases
- A61K 39/0008: {Antigens related to auto-immune diseases; Preparations to induce self-tolerance}
- A61K 39/395: Antibodies (agglutinins A61K38/36 {; as drug carriers A61K47/50}); Immunoglobulins; Immune serum, e.g. antilymphocytic serum
- A61K 39/3955: {against proteinaceous materials, e.g. enzymes, hormones, lymphokines}
- A61P 3/00: Drugs for disorders of the metabolism (of the blood or the extracellular fluid A61P7/00)
- A61P 21/00: Drugs for disorders of the muscular or neuromuscular system
- C12Q 1/6883: for diseases caused by alterations of genetic material
- C12Y 302/0102: Alpha-glucosidase (3.2.1.20)
- C12Y 302/01022: Alpha-galactosidase (3.2.1.22)
- G01N 33/6893: {related to diseases not provided for elsewhere}
- A61K 2039/54: {characterised by the route of administration}
- A61K 2039/545: {characterised by the dose, timing or administration schedule}
- C12Q 2600/158: Expression markers
- G01N 2800/38: Pediatrics
- G01N 2800/52: Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Y: ENZYMES
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)

## Abstract

The present application provides methods of treating a disease, such as Pompe disease, in a subject, comprising detecting an erythropoiesis biomarker in a sample of the subject after administration of methotrexate and a therapeutic agent to the subject, and administering further treatment with or without concurrently administering additional immune tolerance induction or immunosuppression therapy based on the level of the erythropoiesis biomarker. Further provided by the present application are methods and kits for assessing the level of immune tolerance to a therapeutic agent in a subject based on detection of an erythropoiesis biomarker after administration of methotrexate and the therapeutic agent to the subject.

## Claims

### Claim 1

A method for treating Pompe disease in a subject in need of treatment with human acid α-glucosidase, comprising:
(a) administering to the subject an effective amount of methotrexate;
(b) administering to the subject an effective amount of human acid α-glucosidase;
(c) detecting an erythropoiesis biomarker in a sample obtained from the subject between at least one day and about 30 days after administration of methotrexate, wherein the detecting the erythropoiesis biomarker is detecting the expression of a gene encoding transferrin receptor; and
(d) continuing further treatment with human acid α-glucosidase with or without administering rituximab based on a level of the erythropoiesis biomarker compared to that of a control.

### Claim 2 (depends on 1)

The method of claim 1, wherein a change in the level of the erythropoiesis biomarker is associated with induction of erythropoiesis.

### Claim 3 (depends on 2)

The method of claim 2, wherein if the level of the erythropoiesis biomarker is approximately equal to or less than that of a control, step (d) comprises administering rituximib concurrently with further treatment with human acid α-glucosidase; or wherein if the level of the erythropoiesis biomarker is elevated with respect to that of a control, step (d) comprises continuing further treatment with human acid α-glucosidase without administering rituximib.

### Claim 4 (depends on 1)

The method of claim 1, wherein the sample is a blood sample.

### Claim 5 (depends on 1)

The method of claim 1, wherein the effective amount of methotrexate is administered in a single cycle or in three cycles.

### Claim 6 (depends on 1)

The method of claim 1, wherein the sample is obtained from the subject at least about one day to about 30 days following the last administration of the methotrexate.

### Claim 7 (depends on 1)

The method of claim 1, wherein the Pompe disease is infantile-onset Pompe disease.

### Claim 8 (depends on 1)

The method of claim 1, wherein the subject is cross reactive immunological material (CRIM)-negative.

### Claim 9 (depends on 4)

The method of claim 4, wherein the blood sample is a blood fraction comprising peripheral blood mononuclear cells (PBMC).

### Claim 10 (depends on 9)

The method of claim 9, wherein the blood sample is a serum sample or a plasma sample.

### Claim 11 (depends on 1)

The method of claim 1, wherein the control is a historical control or a placebo control.

### Claim 12 (depends on 5)

The method of claim 5, wherein a cycle of methotrexate consists of 1 day of methotrexate administration or 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11 consecutive days of methotrexate administration.

### Claim 13 (depends on 1)

The method of claim 1, wherein the methotrexate is administered to the subject at a time selected from one or more of before, during, and after administration of human acid α-glucosidase.

### Claim 14 (depends on 13)

The method of claim 13, wherein the methotrexate is administered between 48 hours prior to and 48 hours after administration of human acid α-glucosidase.

### Claim 15 (depends on 1)

The method of claim 1, wherein the methotrexate is administered at about 0.1 mg/kg to about 5 mg/kg.

### Claim 16 (depends on 1)

The method of claim 1, wherein the sample is obtained from the subject at about 7 days to about 14 days following the last administration of the methotrexate.

### Claim 17 (depends on 1)

The method of claim 1, wherein samples are obtained on a plurality of days following the last administration of the methotrexate.

### Claim 18 (depends on 1)

The method of claim 1, wherein a sample is obtained on one or more of day 1, day 2, day 3, day 4, day 5, day 6, day 7, day 14, day 21, or day 28 following the last administration of the methotrexate.