	US 12,105,089 B2
	Cell atlas of the healthy and ulcerative colitis human colon
Alexander K. Shalek, Cambridge, MA (US); Christopher Smillie, Cambridge, MA (US); Rebecca H. Herbst, Cambridge, MA (US); Moshe Biton, Cambridge, MA (US); Aviv Regev, Cambridge, MA (US); Jose Ordovas-Montanes, Cambridge, MA (US); and Ramnik Xavier, Cambridge, MA (US)
Assigned to The Broad Institute, Inc., Cambridge, MA (US); Massachusetts Institution of Technology, Cambridge, MA (US); and The General Hospital Corporation, Boston, MA (US)
Appl. No. 16/632,018
Filed by The Broad Institute, Inc., Cambridge, MA (US); Massachusetts Institute of Technology, Cambridge, MA (US); and The General Hospital Corporation, Boston, MA (US)
PCT Filed Jul. 17, 2018, PCT No. PCT/US2018/042554 § 371(c)(1), (2) Date Jan. 17, 2020, PCT Pub. No. WO2019/018844, PCT Pub. Date Jan. 24, 2019.
Claims priority of provisional application 62/533,638, filed on Jul. 17, 2017.
Claims priority of provisional application 62/581,424, filed on Nov. 3, 2017.
Claims priority of provisional application 62/692,541, filed on Jun. 29, 2018.
Prior Publication US 2021/0325387 A1, Oct. 21, 2021
Int. Cl. G01N 33/569 (2006.01); C12Q 1/6883 (2018.01); G01N 33/68 (2006.01)

CPC G01N 33/56966 (2013.01) [C12Q 1/6883 (2013.01); G01N 33/6893 (2013.01); C12Q 2600/106 (2013.01); C12Q 2600/158 (2013.01); G01N 2800/065 (2013.01); G01N 2800/52 (2013.01)]

20 Claims

1. A method for treating a subject suffering from inflammatory bowel disease (IBD) comprising the steps of:

determining the presence of colitis-associated inflammatory fibroblasts (CAIFs) by:

a. obtaining a biological sample from the subject,

b. detecting MMP3, MMP10, PLAU, IL11, IL1R1, IL13RA2, CXCL6, CCL11, TNFSF11, TNFRSF11B, CHI3L1, WNT2 gene expression, or any combination thereof in the biological sample, and

c. administering to the subject determined to have CAIFs, a treatment comprising modulating the activity of one or more gastrointestinal tract cell types,

wherein the one or more gastrointestinal tract cell types is chosen from the group consisting of: plasma B cells, class switching B cells, follicular B cells, microvascular cells, post-capillary venules, vitamin metabolizing, endothelial pericytes, enterocytes, tuft cells, goblet 2, absorptive TA 1, secretory TA, absorptive TA 2, cycling TA, goblet 1, stem cells, enteroendocrine, glial cells, inflammatory fibroblasts, fibroblast pericytes, myofibroblasts, villus fibroblasts, crypt fibroblasts (hiFos), crypt fibroblasts (loFos), T cells, macrophages, dendritic cells, mast cells, cycling monocytes, tolerogenic DCs, neutrophils, activated CD4 cells loFos, activated CD4 cells hiFos, CD8 IELs, CD8 LP cells, T regs, memory T cells, NK cells and cycling CD8 cells.