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Series GSE173652 Query DataSets for GSE173652
Status Public on Jul 06, 2022
Title Asymmetrical forward and reverse developmental trajectories determine molecular programs of B cell antigen receptor editing
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary During B lymphopoiesis, B cell progenitors progress through alternating and mutually exclusive stages of clonal expansion and immunoglobulin (Ig) gene rearrangements. Great diversity is generated through the stochastic recombination of Ig gene segments encoding heavy and light chain variable domains. However, this commonly generates autoreactivity. Receptor editing is the predominant tolerance mechanism for self-reactive B cells in the bone marrow (BM). B cell receptor editing rescues autoreactive B cells from negative selection through renewed light chain recombination first at Igκ then Igλ loci. Receptor editing depends upon BM microenvironment cues and key transcription factors such as Nuclear factor kappa B, Forkhead box protein O and Transcription Factor 3. The specific BM factor required for receptor editing is unknown. Furthermore, how transcription factors coordinate these developmental programs to promote usage of the λ-chain remain poorly defined. Therefore, we utilized two mouse models that recapitulate pathways by which Igλ light chain positive B cells develop. The first possess deleted J kappa (Jκ) genes and, as such, models Igκ expression resulting from failed Igκ recombination (Igκdel). The second models autoreactivity by ubiquitous expression of a single-chain chimeric anti-Igκ antibody (κ-mac). Here, we demonstrated that autoreactive B cells transit asymmetric forward and reverse developmental trajectories. This imparted a unique epigenetic landscape on small pre-B cells, which opened chromatin to transcription factors essential for Igλ recombination. The consequences of this asymmetric developmental path were both amplified and complemented by CXCR4 signaling. These findings reveal how intrinsic molecular programs integrate with extrinsic signals to drive receptor editing.
Overall design 63 samples collectively from Kappa-macroself mice (B6.Cg-Pepcb Ptprca Tg(UBC-scFv)2Nemz/J JAX Stock No: 006259), IgK deleted mice (PMID: 8458340), WT (Littermate control from Kappa-macroself mice), Cxcr4fl/fl Mb1-cre+ Kappa-macroself (+) and Cxcr4fl/fl Mb1-cre+ Kappa-macroself (-) mice. Sorted small pre-B (B220+CD19+CD43-IgM-FSClo) and immature B cells (B220loCD19+CD43-IgM+) were subjected to ATAC-seq (20 samples) and RNA-seq (19 samples). Small pre-B cells (B220+CD19+CD43-IgM-FSClo) were sorted from Cxcr4fl/fl Mb1-cre+ Kappa-macroself (+) and Cxcr4fl/fl Mb1-cre+ Kappa-macroself (-) mice, expanded in culture in the presence or absence of IL-7 and CXCL12 then subjected to RNA-seq (24 samples). Sorted small pre-B (B220+CD19+CD43-IgM-FSClo), large pre-B (B220+CD19+CD43-IgM-FSChi), immature B (B220loCD19+CD43-IgM+) from CD45.1 and CD45.2 mice were subjected to RNA-seq(14 samples).
Contributor(s) Okoreeh MK, Kennedy DE, Emmanuel AO, Veselits M, Moshin A, Ladd RH, Erickson S, McLean K, Nemazee D, Maienschein-Cline M, Mandal M, Clark MR
Citation(s) 35930652
Submission date Apr 30, 2021
Last update date Nov 29, 2022
Contact name Mark Maienschein-Cline
Organization name University of Illinois at Chicago
Department Research Resources Center
Lab Center for Research Informatics
Street address 1819 W Polk Ave, Rm 336 M/C 789
City Chicago
State/province IL
ZIP/Postal code 60612
Country USA
Platforms (4)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL21626 NextSeq 550 (Mus musculus)
Samples (77)
GSM5273016 mm_rna_WP.1
GSM5273017 mm_rna_WP.2
GSM5273018 mm_rna_WP.3
BioProject PRJNA726541
SRA SRP318022

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Supplementary file Size Download File type/resource
GSE173652_RAW.tar 16.6 Gb (http)(custom) TAR (of BED, BW)
GSE173652_gene_counts.txt.gz 481.5 Kb (ftp)(http) TXT
GSE173652_mm9_plus_ig.gtf.gz 4.8 Mb (ftp)(http) GTF
GSE173652_rna_counts.txt.gz 1.3 Mb (ftp)(http) TXT
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Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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