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| Status |
Public on Nov 24, 2018 |
| Title |
Single cell profiling of CD4+ T cells from human fetal intestine |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The fetus is thought to be protected from exposure to foreign antigens, yet CD45RO+ T-cells reside in the fetal intestine. We combined functional assays with mass cytometry, single-cell RNA-sequencing, and high-throughput TCR-sequencing to characterize the fetal intestinal CD4+ T-cell compartment. We identified 22 CD4+ T-cell clusters, including naive-like, regulatory-like, and memory-like subpopulations, which were confirmed and further characterized at the transcriptional level. Memory-like cells expressed high levels of Ki-67, indicating cell division, and CD5, a surrogate marker of TCR-avidity, and produced IFN-γ and IL-2. Pathway analysis revealed a differentiation trajectory associated with cellular activation and proinflammatory effector functions, and TCR-repertoire analysis demonstrated clonal expansions, distinct repertoire characteristics, and interconnections between subpopulations of memory-like CD4+ T-cells. Imaging-mass cytometry further showed that memory-like CD4+ T-cells colocalized with antigen-presenting cells. Collectively, these results provided evidence for the generation of memory-like CD4+ T-cells in the human fetal intestine, consistent with exposure to foreign antigens.
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| Overall design |
Single, live, CD3+CD8a–TCRγδ–CD4+/– T-cells from one human fetal intestines were processed on the Chromium 3' single cell platform (10x Genomics) and sequenced on an Illumina HiSeq 4000.
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| Contributor(s) |
Li N, Koning F, Kloet SL |
| Citation(s) |
30664737, 36899020 |
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| Submission date |
Nov 23, 2018 |
| Last update date |
Jul 14, 2023 |
| Contact name |
Na Li |
| E-mail(s) |
l.li@lumc.nl
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| Phone |
+31715261820
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| Organization name |
LUMC
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| Street address |
Albinusdreef 2
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| City |
Leiden |
| ZIP/Postal code |
2333 ZA |
| Country |
Netherlands |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (1) |
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| Relations |
| BioProject |
PRJNA506660 |
| SRA |
SRP170417 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE122846_RAW.tar |
13.1 Mb |
(http)(custom) |
TAR (of H5, MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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