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Series GSE140795 Query DataSets for GSE140795
Status Public on Feb 21, 2020
Title Peyer’s Patch Germinal Centers Select Innate-like BCRs
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Other
Summary Primary B cell receptor (BCR)/antibody variable region exons are generated by V(D)J recombination with junctional diversification creating immensely diverse antigen contact-encoding CDR3s. While most antigen-driven germinal centers (GCs) are transient, gut microbiota-dependent intestinal Peyer’s patch (PP) GCs are chronic. The nature of chronic PP GC BCR repertoires and somatic hyper-mutation (SHM) patterns has remained enigmatic. To elucidate the physiological repertoire of PP GC BCRs, we developed a high throughput antibody repertoire and SHM assay. Remarkably, PP GCs from different mice expanded public clonotypes, each often with identical IgH CDR3. These CDR3s represent innate-like BCRs that appear much more frequently than expected in naïve B cell repertoire by IGoR modeling, but not frequently enough to enter PP GCs at the observed recurrence without cellular selection. Consistently, some public clonotypes are gut microbiota-dependent and encode antibodies reactive to bacteria glycans, while others are not. SPF fecal transfer to germ-free (GF) mice restored two germ-dependent clonotypes, providing direct evidence for BCR selection. In support of this, we identified recurrently selected SHMs in four of the public clonotypes, demonstrating affinity maturation in chronic PP GCs. Our findings suggest that persistent gut antigens select for innate-like BCR clonotypes to seed chronic PP GCs.
 
Overall design We validated our primer design for LAM-HTGTS-Rep-SHM-Seq with mixed JH or JL bait compared with VH or VL bait, with 3 replicates each. We included NP-CGG and SRBCs IP immunized splenic GC and naïve samples as controls for our LAM-HTGTS-Rep-SHM-Seq method to follow BCR selection. We did LAM-HTGTS-Rep-SHM-Seq on PP GC and naïve samples from 18 SPF mice, 10x3 GF mice, 5 GF+SFB mice, 10 GF+SPF mice, 15 AID-deficient SPF mice. We also included single cell RNA sequencing data from 4 of the PP GC samples from SPF mice.
 
Contributor(s) Chen H, Zhang Y, Ye AY, Du Z, Xu M, Lee C, Hwang JK, Kyritsis N, Ba Z, Littman DR, Alt FW
Citation(s) 32499646
Submission date Nov 21, 2019
Last update date Jun 10, 2020
Contact name Frederick W Alt
Organization name Boston Children's Hospital / Harvard Medical School
Department Program in Cellular and Molecular Medicine (PCMM)
Lab Frederick Alt
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL21626 NextSeq 550 (Mus musculus)
Samples (225)
GSM4185194 NP10d-1_SP_IgH_nonGC
GSM4185195 NP10d-1_SP_IgH_GC
GSM4185196 NP10d-2_SP_IgH_nonGC
Relations
BioProject PRJNA591005
SRA SRP231174

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE140795_RAW.tar 1.3 Gb (http)(custom) TAR (of VLOUPE, XLS)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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