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| Status |
Public on Sep 04, 2020 |
| Title |
Epigenomic and transcriptomic analysis of Systemic Sclerosis CD4+ T cells [Affymetrix] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Epigenomic and transcriptomic analysis of Systemic Sclerosis CD4+ T cells reveals long range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci range dysregulation of key inflammatory pathways mediated by disease-associated
System sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the principle drivers of pathogenesis. In this study, we obtained DNA methylation and RNA expression profiles of CD4+ T cells from 48 SSc patients and 16 healthy controls. Consequently, we identified 9112 and 3929 differentially methylated CpGs positions (DMPs) and differentially expressed genes (DEGs) respectively. These DMPs and DEGs are enriched in functional categories related to inflammation and T cell biology. Furthermore, correlation analysis identified 17,500 possible DMP-DEG interaction pairs within a window of 5 Mb, and utilizing promoter capture Hi-C data, we confirmed 168 pairs of DMP-DEG physical interactions. Finally, utilizing SSc GWAS data, we identified three important SSc-associated susceptibility loci, CSK (rs1378942), IL12RB1 (rs2305743) and IKZF3-GSDMB (rs9303277), that physically interact with cg11062629-ULK3, cg10808810-JUND and cg19458020-CCR7 respectively. Overall, our study reveals a solid link between genetic, epigenetic and transcriptional deregulation in CD4+ T cells of SSc patients, providing further understanding to SSc pathogenesis.
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| Overall design |
CD4+ T cells were isolated from peripheral blood of 48 SSc patients and 16 healthy donors by positive cell sorting.
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| Contributor(s) |
Li T, Ortiz L, Andrés-León E, Ciudad L, Javierre BM, López-Isac E, Guillén-Del-Castillo A, Simeón-Aznar CP, Ballestar E, Martin J |
| Citation(s) |
32977850 |
| Submission date |
Feb 28, 2020 |
| Last update date |
Oct 06, 2020 |
| Contact name |
Esteban Ballestar |
| Organization name |
Josep Carreras Research Institute (IJC)
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| Lab |
Epigenetics and Immune Disease
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| Street address |
Ctra de Can Ruti, Camí de les Escoles s/n
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| City |
Badalona, Barcelona |
| State/province |
N/A = Not Applicable |
| ZIP/Postal code |
08916 |
| Country |
Spain |
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| Platforms (1) |
| GPL23159 |
[Clariom_S_Human] Affymetrix Clariom S Assay, Human (Includes Pico Assay) |
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| Samples (64)
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| GSM4364456 |
CD4+ T cells, healthy donor 7 |
| GSM4364457 |
CD4+ T cells, healthy donor 8 |
| GSM4364458 |
CD4+ T cells, healthy donor 9 |
| GSM4364459 |
CD4+ T cells, healthy donor 10 |
| GSM4364460 |
CD4+ T cells, healthy donor 11 |
| GSM4364461 |
CD4+ T cells, healthy donor 12 |
| GSM4364462 |
CD4+ T cells, healthy donor 13 |
| GSM4364463 |
CD4+ T cells, SSc patient 1 |
| GSM4364464 |
CD4+ T cells, SSc patient 2 |
| GSM4364465 |
CD4+ T cells, SSc patient 3 |
| GSM4364466 |
CD4+ T cells, SSc patient 4 |
| GSM4364467 |
CD4+ T cells, SSc patient 5 |
| GSM4364468 |
CD4+ T cells, SSc patient 6 |
| GSM4364469 |
CD4+ T cells, SSc patient 7 |
| GSM4364470 |
CD4+ T cells, SSc patient 8 |
| GSM4364471 |
CD4+ T cells, SSc patient 9 |
| GSM4364472 |
CD4+ T cells, SSc patient 10 |
| GSM4364473 |
CD4+ T cells, SSc patient 11 |
| GSM4364474 |
CD4+ T cells, SSc patient 12 |
| GSM4364475 |
CD4+ T cells, SSc patient 13 |
| GSM4364476 |
CD4+ T cells, SSc patient 14 |
| GSM4364477 |
CD4+ T cells, SSc patient 15 |
| GSM4364478 |
CD4+ T cells, SSc patient 16 |
| GSM4364479 |
CD4+ T cells, SSc patient 17 |
| GSM4364480 |
CD4+ T cells, SSc patient 18 |
| GSM4364481 |
CD4+ T cells, SSc patient 19 |
| GSM4364482 |
CD4+ T cells, SSc patient 20 |
| GSM4364483 |
CD4+ T cells, SSc patient 21 |
| GSM4364484 |
CD4+ T cells, SSc patient 22 |
| GSM4364485 |
CD4+ T cells, SSc patient 23 |
| GSM4364486 |
CD4+ T cells, SSc patient 24 |
| GSM4364487 |
CD4+ T cells, SSc patient 25 |
| GSM4364488 |
CD4+ T cells, SSc patient 26 |
| GSM4364489 |
CD4+ T cells, SSc patient 27 |
| GSM4364490 |
CD4+ T cells, SSc patient 28 |
| GSM4364491 |
CD4+ T cells, SSc patient 29 |
| GSM4364492 |
CD4+ T cells, SSc patient 30 |
| GSM4364493 |
CD4+ T cells, SSc patient 31 |
| GSM4364494 |
CD4+ T cells, SSc patient 32 |
| GSM4364495 |
CD4+ T cells, SSc patient 33 |
| GSM4364496 |
CD4+ T cells, SSc patient 34 |
| GSM4364497 |
CD4+ T cells, SSc patient 35 |
| GSM4364498 |
CD4+ T cells, SSc patient 36 |
| GSM4364499 |
CD4+ T cells, SSc patient 37 |
| GSM4364500 |
CD4+ T cells, SSc patient 38 |
| GSM4364501 |
CD4+ T cells, SSc patient 39 |
| GSM4364502 |
CD4+ T cells, SSc patient 40 |
| GSM4364503 |
CD4+ T cells, SSc patient 41 |
| GSM4364504 |
CD4+ T cells, SSc patient 42 |
| GSM4364505 |
CD4+ T cells, SSc patient 43 |
| GSM4364506 |
CD4+ T cells, SSc patient 44 |
| GSM4364507 |
CD4+ T cells, SSc patient 45 |
| GSM4364508 |
CD4+ T cells, SSc patient 46 |
| GSM4364509 |
CD4+ T cells, SSc patient 47 |
| GSM4364510 |
CD4+ T cells, SSc patient 48 |
| GSM4364511 |
CD4+ T cells, healthy donor 17 |
| GSM4364512 |
CD4+ T cells, healthy donor 18 |
| GSM4364513 |
CD4+ T cells, healthy donor 19 |
| GSM4364514 |
CD4+ T cells, healthy donor 20 |
| GSM4364515 |
CD4+ T cells, healthy donor 25 |
| GSM4364516 |
CD4+ T cells, healthy donor 26 |
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| This SubSeries is part of SuperSeries: |
| GSE146093 |
Epigenomic and transcriptomic analysis of Systemic Sclerosis CD4+ T cells |
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| Relations |
| BioProject |
PRJNA609271 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE146088_RAW.tar |
78.8 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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