# US 10,870,885 B2 · Dendritic cell response gene expression, compositions of matters and methods of use thereof

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- Number: US 10,870,885 B2
- Document ID: US10870885B2
- Status: Granted
- Kind: B2
- Application number: 14/846,219
- Filed: 2015-09-04
- Published: 2015-12-24
- Granted: 2020-12-22
- Earliest claimed: 2013-03-15
- Assignees: The Broad Institute, Inc.; Massachusetts Institute of Technology; President and Fellows of Harvard College
- Applicants: The Broad Institute, Inc.; Massachusetts Institute of Technology; President and Fellows of Harvard College
- Inventors: Aviv Regev; Alexander K. Shalek; Rahul Satija; Hongkun Park
- Web page: https://patentgrep.com/patent/US10870885B2

## CPC

- C12Q 1/6883: for diseases caused by alterations of genetic material
- G01N 33/5047: {Cells of the immune system}
- G01N 33/6893: {related to diseases not provided for elsewhere}
- C12Q 2600/158: Expression markers
- G01N 2800/24: Immunology or allergic disorders
- 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
- 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

This invention relates generally to compositions and methods for identifying the regulatory network that modulates, controls or otherwise influences dendritic cell (DC) response(s), for example, dendritic cell maturation, dendritic cell antiviral response(s) and/or dendritic cell inflammatory response(s), as well compositions and methods for exploiting the regulatory network that modulates, controls or otherwise influences dendritic cell response(s) in a variety of therapeutic and/or diagnostic indications.

## Claims

### Claim 1

A method of detecting single dendritic cells expressing a maturation gene signature in a subject, comprising:
detecting increased expression of TMEM39A, or TMEM39A and one or more signature genes or one or more products of one or more signature genes selected from the group consisting of AKNA, APOL7C, APPL1, ARL5C, BATF, BC035044, BCL2L1, BIRC3, BLNK, CCL22, CCR7, CD72, CD80, CD83, CD86, CDKN1A, CHAC2, CRLF3, CSF1, DENND5A, EBI3, EIF2C3, ETS2, ETV3, EXOC3L4, FAM129A, FAM177A1, GPR85, H2-Q7, HSD17B11, IL12B, IL23A, IL4I1, IRF8, ITGA4, KTELC1, LACC1, MKIAA0769, MMP25, NFKBIB, NUDT17, OSGIN2, PALM2, PDZK1IP1, PGAP2, PLAT, PPP1CB, PVR, PVRL2, RAB8B, REL, RHOB, RND3, SAMSN1, SEMA6D, SERPINB9, SRGN, ST3GAL1, STAT3, STAT5A, SWAP70, TBC1D1, TIMP1, TNIP3 and VCAM1 in single dendritic cells of a population of dendritic cells obtained from the subject using single-cell RNA-seq, RNA-fluorescence in situ hybridization (FISH), single-cell quantitative reverse-transcription polymerase chain reaction, fluorescence-activated cell-sorting (FACS), Immunofluorescence (IF), or a combination thereof, wherein the expression is compared to the average expression of the single cells of the population of dendritic cells.

### Claim 2 (depends on 1)

The method of claim 1, wherein TMEM39A and one or more signature genes or one or more products of one or more signature genes selected from the group consisting of IRF8, SERPINB9, CCR7, CD83, CD86, and CCL22 are detected.

### Claim 3 (depends on 1)

The method of claim 1, wherein TMEM39A and IRF8 are detected.

### Claim 4 (depends on 1)

The method of claim 1, wherein TMEM39A and SERPINB9 are detected.

### Claim 5 (depends on 1)

The method of claim 1, wherein the subject is suffering from or is at risk for an autoimmune response.

### Claim 6 (depends on 1)

A method for identifying an agent capable of modulating a maturation gene signature in a population of dendritic cells comprising:
a) applying a candidate agent to the population of dendritic cells; and
b) detecting single dendritic cells expressing a maturation gene signature according to claim 1, thereby identifying the agent.