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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 01, 2018 |
| Title |
T helper cells modulate intestinal stem cell renewal and differentiation |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Using single-cell RNA-seq of intestinal epithelial cells we identify surprising expression of MHC class II, which participates in a novel interaction between gut-resident CD4+ T cells and epithelial stem cells, governing the balance between stem cell differentiation and renewal.
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| Overall design |
In the small intestine, a niche of accessory cell types supports the generation of mature epithelial cell types from intestinal stem cells (ISCs). It is unclear, however, if and how immune cells in the niche affect ISC fate or the balance between self-renewal and differentiation. Here, we use single-cell RNA sequencing (scRNA-seq) to identify MHC class II (MHCII) machinery enrichment in two subsets of Lgr5+ ISCs. We show that MHCII+ Lgr5+ ISCs are non-conventional antigen-presenting cells in co-cultures with CD4+ T helper (Th) cells. Stimulation of intestinal organoids with key Th cytokines affects Lgr5+ ISC renewal and differentiation in opposing ways: pro-inflammatory signals promote differentiation, while regulatory cells and cytokines reduce it. In vivo genetic perturbation of Th cells or MHCII expression on Lgr5+ ISCs impacts epithelial cell differentiation and IEC fate during infection. These interactions between Th cells and Lgr5+ ISCs, thus, orchestrate tissue-wide responses to external signals.
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| Contributor(s) |
Biton M, Haber AL, Beyaz S, Rogel N, Smillie C, Shekhar K, Schnell A, Chen Z, Wu C, Ordovas-Montanes J, Alvarez D, Herbst RH, Tirosh I, Burgin G, Dionne D, Xifaras ME, Zhang M, Shalek AK, von Andrian UH, Graham DB, Rozenblatt-Rosen O, Shi HN, Kuchroo V, Yilmaz O, Regev A, Xavier RJ |
| Citation(s) |
30392957 |
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| Submission date |
Nov 03, 2017 |
| Last update date |
Apr 08, 2019 |
| Contact name |
Adam Haber |
| E-mail(s) |
[email protected]
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| Organization name |
Harvard T. H. Chan School of Public Health
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| Street address |
665 Huntington Ave, HSPH Building 1, Room 305
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| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (810)
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| Relations |
| BioProject |
PRJNA417070 |
| SRA |
SRP123595 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE106510_CD45_MHCIIGut--_all_UMIcounts.txt.gz |
50.4 Mb |
(ftp)(http) |
TXT |
| GSE106510_CD45_Salmonella_UMI_counts.txt.gz |
9.0 Mb |
(ftp)(http) |
TXT |
| GSE106510_DivSeq_SS2_All_TPM.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE106510_Foxp3_all_UMIcounts.txt.gz |
8.5 Mb |
(ftp)(http) |
TXT |
| GSE106510_MHCII_FACS_SS2_All_TPM.txt.gz |
8.5 Mb |
(ftp)(http) |
TXT |
| GSE106510_MHCII_antibody_all_UMIcounts.txt.gz |
14.6 Mb |
(ftp)(http) |
TXT |
| GSE106510_MHCII_dGut_all_UMIcounts.txt.gz |
8.7 Mb |
(ftp)(http) |
TXT |
| GSE106510_Nude_UMIcounts.txt.gz |
6.8 Mb |
(ftp)(http) |
TXT |
| GSE106510_Ova_SS2_All_TPM.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSE106510_RAW.tar |
506.5 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
| GSE106510_TCRb_KO_UMIcounts.txt.gz |
16.9 Mb |
(ftp)(http) |
TXT |
| GSE106510_TcellCyto_Orgs_UMIcounts.txt.gz |
119.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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