Epigenetic analysis of cell therapy and related methods

Patent metadata

Field	Value
Publication number	US-11821027-B2
Application number	US-201816476856-A
Country	US
Kind code	B2
Filing date	Jan 10, 2018
Priority date	Jan 10, 2017
Publication date	Nov 21, 2023
Grant date	Nov 21, 2023

Abstract

Provided herein are methods of identifying genomic region(s) predictive of an outcome of treatment with a cell therapy and/or of a phenotype of function of the cells. In some embodiments, the methods include epigenetic and/or epigenomic analyses of the cells in connection with methods for preparing engineered cells for cell therapy and/or predicting response to a cell therapy, e.g., engineered cells for cell therapy. In some embodiments, the methods include steps to assess, characterize and analyze changes or modifications in an epigenetic property of gene region or regions, such as chromatin accessibility, nucleosome occupancy, histone modification, spatial chromosomal conformation, transcription factor occupancy and/or DNA methylation. In some embodiments, the epigenetic and/or epigenomic analysis includes determining the epigenetic properties of a cell, e.g., an engineered cell for cell therapy.

First claim

The invention claimed is:

1. A method of administering a cell therapy to a subject, the method comprising:
(a) determining an epigenetic property of one or more genomic regions of a composition of genetically engineered cells comprising a recombinant receptor;
(b) identifying the epigenetic property of one or more of the genomic regions of cells of the composition as being correlated with a desired response or safety outcome to a cell therapy, said cell therapy comprising the composition,
wherein the identifying comprises comparing the epigenetic property for each of the one or more genomic regions, individually, to a corresponding epigenetic property from a reference profile, wherein the reference profile correlates with a cell therapy being likely to produce a desired response or safety outcome when administered;

(c) selecting the composition as a cell therapy likely to produce the desired response or safety outcome based on the identifying of (b); and
(d) administering the composition to the subject as a cell therapy.

2. The method of claim 1 , wherein
the desired response is a complete response, a partial response, or durability of response.

3. The method of claim 1 , wherein the composition is enriched for CD4+ primary human T cells or CD8+ primary human T cells.

4. The method of claim 1 , wherein the epigenetic property is chromatin accessibility or nucleosome occupancy.

5. The method of claim 4 , wherein chromatin accessibility is determined by Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq).

6. The method of claim 1 , wherein the determining the epigenetic property comprises:
(1) isolating chromatin from the cells of the composition;
(2) treating the chromatin with an insertional enzyme complex to generate tagged fragments of genomic DNA;
(3) sequencing all or a portion of the tagged fragments to produce a plurality of sequence reads;
(4) aligning, filtering and mapping the sequence reads to genomic regions of a genome; and
(5) determining peaks of sequence reads in a plurality of genomic regions for the cells of the composition.

7. The method of claim 6 , wherein the determining the epigenetic property further comprises:
comparing peaks of sequence reads and identifying peaks of sequence reads that are different between samples from two or more compositions of cells;
determining positions of nucleosomes within genomic regions containing peaks of sequence reads;
generating an epigenetic map showing a profile of sequence reads indicative of the epigenetic property, along each of the one or more genomic regions or a subset thereof; or
generating, for each of a plurality of sites or portions along the length of the genomic region, one or more sequence reads indicative of an epigenetic readout, at said site or portion,
wherein the quantity of said one or more sequence reads indicates a level of said epigenetic property, at said site or portion.

8. The method of claim 7 , wherein the determining comprises:
steps for removal of mitochondrial reads or additional contaminating sequences based on sequence identity, quality, mapping location, or other sequencing properties of said reads;
steps for removal of duplicate reads to improve quantitative accuracy; or
steps for separation of sequence reads into subsets representing a specific epigenetic property, wherein the size of the sequenced fragment is used to determine the level to which it represents said epigenetic property.

9. The method of claim 6 , wherein said determining further comprises performing principle component analysis (PCA), biological pathway analysis, gene ontology (GO) analysis or motif analysis.

10. The method of claim 1 , wherein the determining the epigenetic property is by ATAC-seq of the whole genome of the cells of the composition.

11. The method of claim 1 , wherein:
the recombinant receptor binds to, recognizes or targets an antigen associated with the disease or condition; or the recombinant receptor is a T cell receptor or a functional non-T cell receptor.

12. The method of claim 1 , wherein the administering of the cell therapy is carried out by autologous transfer.

13. The method of claim 1 , wherein the cells of the composition comprise immune cells.

14. The method of claim 1 , wherein the cells of the composition comprise T cells or NK cells.

15. The method of claim 14 , wherein the T cells comprise CD4+ T cells or CD8+ T cells.

16. The method of claim 1 , wherein the desired safety outcome is absence of development of severe cytokine release syndrome (CRS) or severe neurotoxcity (NT).

17. The method of claim 1 , wherein the recombinant receptor is a chimeric antigen receptor (CAR).

18. A method of administering a cell composition to a subject comprising:
(a) comparing an epigenetic property of one or more genomic regions of obtained cells or populations of cells to a corresponding epigenetic property from a reference profile,
wherein the cells or populations of cells are comprised in a composition of cells genetically engineered to comprise a recombinant receptor, and
wherein the reference profile correlates with a cell therapy likely to produce a desired response or safety outcome;

(b) indicating whether the cells or population of cells of the composition is likely to produce the desired response or safety outcome;
(c) selecting the composition as likely to produce the desired response or safety outcome; and
(d) administering the composition selected in (c) to the subject.

19. The method of claim 18 , wherein the desired outcome is a complete response, a partial response, or a durable response.

20. The method of claim 18 , wherein the desired safety outcome is absence of development of severe cytokine release syndrome (CRS) or severe neurotoxicity.

21. The method of claim 18 , wherein the recombinant receptor is a chimeric antigen receptor (CAR).

22. The method of claim 18 , wherein the epigenetic property is chromatin accessibility or nucleosome occupancy.

23. The method of claim 22 , wherein chromatin accessibility is determined by Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq).

24. A method of administering a cell therapy to a subject, the method comprising:
(a) determining an epigenetic property of one or more genomic regions of cells obtained from a subject;
wherein the cells are to be genetically engineered to comprise a recombinant receptor;

(b) identifying the epigenetic property of one or more of the genomic regions of the cells as being correlated with a desired response or safety outcome to a cell therapy, said cell therapy comprising the cells from the subject genetically engineered with the recombinant receptor,
wherein the identifying comprises comparing the epigenetic property for each of the one or more genomic regions, individually, to a corresponding epigenetic property from a reference profile, wherein the reference profile correlates with a cell therapy being likely to produce a desired response or safety outcome when administered;
(c) genetically engineering the cells obtained from the subject with the recombinant receptor based on the identifying of (b) to produce said cell therapy; and
(d) administering the cell therapy to the subject.

25. The method of claim 24 , wherein the cells obtained from the subject comprises enriched CD4+ primary human T cells or CD8+ primary human T cells.

Assignees

• Juno Therapeutics Inc

Inventors

• Bonyhadi Mark L
• Kugler David G
• Johnstone Timothy G
• Hause Jr Ronald James
• Thompson Lucas J
• Larson Ryan P

Classifications

• A61K40/4215

  Receptors for tumor necrosis factors [TNF], e.g. lymphotoxin receptor [LTR], CD30 · CPC title

• A61K40/4211

  CD19 or B4 · CPC title

• A61K40/32

  T-cell receptors [TCR] · CPC title

• A61K40/31

  Chimeric antigen receptors [CAR] · CPC title

• A61K40/11

  T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells · CPC title