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Series GSE134809 Query DataSets for GSE134809
Status Public on Aug 29, 2019
Title Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Clinical benefits of cytokine blockade in ileal Crohn’s disease (iCD) are limited to a subset of patients. Here we applied single cell technologies to iCD lesions to address whether cellular heterogeneity contributes to treatment resistance. We found that a subset of patients expressed a unique cellular module in inflamed tissues that consisted of IgG plasma cells, inflammatory mononuclear phagocytes, activated T cells and stromal cells, which we named the GIMATS module. Analysis of ligand-receptor interaction pairs identified a distinct connectivity network that likely drives the GIMATS module. Strikingly, the GIMATS module was also present in a subset of patients in 4 independent iCD cohorts (n=441), and its presence at diagnosis correlated with failure to achieve corticosteroid-free durable remission upon anti-TNF therapy. These results emphasize the limitations of current diagnostic assays and the potential for single cell mapping tools to identify novel biomarkers of treatment response and tailored therapeutic opportunities
Overall design Single cell seq analysis of paired resection ileal samples from inflamed and uninflamed area
Contributor(s) Cho J, Martin J, Merad M, Kenigsberg E, Giri M
Citation(s) 31474370, 37080976
NIH grant(s)
Grant ID Grant title Affiliation Name
U24 DK062429 Inflammatory Bowel Disease Genetics Consortium Data Coordinating Center MOUNT SINAI SCHOOL OF MEDICINE JUDY H. CHO
U01 DK062422 Mount Sinai School of Medicine Inflammatory Bowel Disease Genetics Research Cente MOUNT SINAI SCHOOL OF MEDICINE JUDY H. CHO
R01 DK106593 Integrative Genomic Analyses of Macrophages in Crohns Disease MOUNT SINAI SCHOOL OF MEDICINE JUDY H. CHO
Submission date Jul 24, 2019
Last update date May 12, 2023
Contact name Mamta Giri
Organization name Mount Sinai hospital
Department Institute of Personalized medicine
Lab Cho lab
Street address 1470 madison ave
City new york
State/province new york
ZIP/Postal code 10029
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (31)
GSM3972009 Ileal Involved 69
GSM3972010 Ileal Uninvolved 68
GSM3972011 Ileal Involved 122
BioProject PRJNA556461
SRA SRP216273

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Supplementary file Size Download File type/resource
GSE134809_RAW.tar 579.3 Mb (http)(custom) TAR (of MTX, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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