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| Status |
Public on Sep 30, 2020 |
| Title |
Shared transcriptional profiles at the single cell level of atypical memory B cells suggest common drivers of expansion and function in malaria, HIV and autoimmune diseases [HIV scRNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Human chronic infectious diseases, including malaria and HIV and autoimmune diseases, notably SLE, are accompanied by a striking expansion of a subpopulation of B cells termed atypical memory B cells (MBCs). We compared the single cell transcriptional profiles of B cells in malaria and HIV, characterizing and uncovering heterogeneity within each B cell subset. Remarkably, atypical MBC clusters in these two diseases showed significant similarities to each other as well as to atypical MBCs in autoimmune diseases, suggesting a common driver of their expansion and shared functions. Focusing on atypical MBCs in malaria we identified an IgD+IgMlo subpopulation that expanded in children upon the onset of febrile malaria, showed a distinct V gene usage characteristic of antigen-driven B cell populations and unexpectedly, had acquired high antigen-affinity thresholds for activation. We speculate that in malaria IgD+IgMlo atypical MBCs expand to limit responses to low-affinity self-antigens, a function that may be shared by atypical MBCs in other chronic infections and autoimmune diseases.
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| Overall design |
scRNA seq of peripheral blood B cells isolated by negative selection from three HIV-infected adults and three healthy adults, all from the US
The raw data is to be made available through dbGaP (controlled access; phsnnnnnn)
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| Contributor(s) |
Holla P, Dizon B, Ambegaonkar AA, Rogel N, Goldschmidt E, Boddapati AK, Sohn H, Sturdevant D, Austin JW, Kardava L, Yuesheng L, Liu P, Moir S, Pierce SK, Madi A |
| Citation(s) |
34039612 |
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| Submission date |
Sep 15, 2020 |
| Last update date |
Jun 15, 2021 |
| Contact name |
Arun Boddapati |
| E-mail(s) |
[email protected]
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| Organization name |
Yerkes National Primate research center
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| Department |
Genomics Core
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| Street address |
954 Gatewood Road, NE
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE149729 |
Chronic Malaria drives functional heterogenity in B cell subpopilations and expansion of unswitched atypical memory B cells |
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| Relations |
| BioProject |
PRJNA663562 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE157966_RAW.tar |
4.0 Mb |
(http)(custom) |
TAR (of CSV) |
| GSE157966_scRNA_Seq_Integrated_Matrix_Supplementary.tsv.gz |
41.5 Mb |
(ftp)(http) |
TSV |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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