NBDC Research ID: hum0266.v1

 

SUMMARY

Aims: Pemphigus, an autoimmune skin disease, is caused by the production of autoantibodies against desmoglein, an autoantigen. Clinically, treatment targeting B cells has been shown to be effective, and desmoglein-specific B cells may play an important role in the pathogenesis. The purpose of this research is to isolate desmoglein-specific B cells in the peripheral blood of patients using labeled desmoglein protein, and to analyze their characteristics and changes in gene expression due to treatment by comprehensive genetic analysis, and to link them to disease markers and treatments.

Methods: Antigen-specific B cells from PBMCs were single-cell sorted with FACS ARIA3 using labeled desmoglein protein or influenza HA antigen, libraries were prepared with SMART-seq, and sequenced with Novaseq.

Participants/Materials: Desmoglein-specific B cells and non-desmoglein-specific B cells from 3 patients with pemphigus

One of the patients, desmoglein-specific B cells and non-desmoglein-specific B cells after PSL treatment are also included.

Influenza HA specific B cells and non-influenza HA specific B cells from 3 healthy subjects as controls

 

Dataset IDType of DataCriteriaRelease Date
JGAS000281 NGS (scRNA-seq) Controlled-access (Type I) 2022/12/27

*Release Note

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MOLECULAR DATA

JGAS000281

Participants/Materials

Pemphigus (ICD10: L10.0/L10.2): 3 cases (number of single cells)

    Desmoglein-specific B cell (37 , 30 , 36)

    non-desmoglein-specific B cell (44 , 40 , 44)

    One of the patients, desmoglein-specific B cells and non-desmoglein-specific B cells (31 , 96) after PSL treatment are also included.

3 healthy controls (number of single cells)

    Influenza HA specific B cell (48 , 36 , 36)

    non-influenza HA specific B cell (48 , 48 , 48)

Targets scRNA-seq
Target Loci for Capture Methods -
Platform Illumina [NovaSeq 6000]
Library Source RNAs extracted from antigen-specific B cells
Cell Lines -
Library Construction (kit name) SMART-Seq HT Kit
Fragmentation Methods Nextera XT DNA Library Prep Kit
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000387
Total Data Volume 200 GB (fastq)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Shohei Egami

Affiliation: Department of Dermatology, Keio University School of Medicine

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for Scientific Research (B) Elucidating pathophysiology of pemphigus by single cell analysis of auto-reactive B cells 19H03683
Health and Labor Sciences Research Grants for Research on Rare and Intractable Diseases Research on rare intractable skin diseases 20FC1052

 

PUBLICATIONS

TitleDOIDataset ID
1
2

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use