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Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Research ID

hum0512-v1Release info

Latest

Research title

Identification and functional analysis of risk polymorphisms in autoimmune diseases

Research overview

Aims
Autoimmune diseases occur when the immune system damages the body's tissues, affecting over 1% of the population. Genomic polymorphisms strongly influence autoimmune disease risk, with many identified through large-scale genomic analyses. Since these risk polymorphisms often cluster in gene expression regulatory regions of immune cells, evaluating their relationship with gene regulation in these cells is essential for understanding their functions. This research aims to elucidate risk polymorphism functions using both natural polymorphisms and artificial ones introduced through genome editing. We will analyze multi-omics data from various cells and employ comprehensive genomic analysis to precisely identify risk polymorphism locations and understand their functions.
Methods
bulk RNA-seq, bulk ATAC-seq, single cell CITE-seq (RNA-seq)
Participants/materials
3 healthy donors
URL

Datasets

CartDataset IDType of dataAnalysis methodAccess criteriaDate published
JGAD000960bulk RNA-seq / bulk ATAC-seq / scCITE-seq of CD4+ / CD3+ T cells from 3 healthy donors following LEF1 siRNA knockdown.
  • bulk RNA-seq
  • bulk ATAC-seq
  • scCITE-seq
Controlled-access (Type I)2025-07-31

Data provider

Principal investigator
Kazuyoshi Ishigaki
Affiliation
Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences

Research projects

No research projects.

Grants

NameTitleProject number
KAKENHI Grant-in-Aid for Scientific Research (B)
Establishment of personalized anti-cytokine therapy through functional analysis of autoimmune disease risk polymorphisms
  • 22H03114
KAKENHI Grant-in-Aid for Research Activity Start-up
Identification of transcription factor controlling autoimmunity risk allele's pathogenic function
  • 21K20647
KAKENHI Grant-in-Aid for Early-Career Scientists
Functional analysis of rheumatoid arthritis risk polymorphisms using genome editing technology and targeted analysis
  • 25K19621
Biobank - Construction and Utilization biobank for genomic medicine REalization (B-Cure), Japan Agency for Medical Research and Development (AMED)
Development of technology for evaluating the impact of polygenic risk scores on biological systems
  • JP22tm0424223
Practical Research Project for Allergic Diseases and Immunology, Japan Agency for Medical Research and Development (AMED)
Elucidation of rheumatoid arthritis pathogenesis through functional analysis of risk polymorphisms combined with genome editing technology
  • JP22ek0410099
Research and Development Program for Translating Genomic Research into Drug Discovery and Other Applications, Japan Agency for Medical Research and Development (AMED)
Identification of novel diagnostic markers for rheumatoid arthritis based on T cell receptor sequence information using biobanks
  • JP23tm0524005
Practical Research Project for Allergic Diseases and Immunology, Japan Agency for Medical Research and Development (AMED)
Comprehensive elucidation of T cell-level immune tolerance breakdown through interaction between HLA gene polymorphisms and smoking in rheumatoid arthritis
  • JP25ek0410139
Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS), Japan Agency for Medical Research and Development (AMED)
Support for large-scale functional genomics analysis using biological samples and advancement of human immune function evaluation platform
  • JP22ama121015
Japan Initiative for World-leading Vaccine Research and Development Centers, Japan Agency for Medical Research and Development (AMED)
Support organization for establishment and implementation of human immune evaluation methods centered on multi-omics of genetic diversity and function
  • JP223fa627010

Related publications

TitleDOIDataset ID
Accurate, sensitive, and efficient chromatin accessibility quantification at target loci using UNIChro-seq
https://doi.org/10.1038/s41467-026-75767-2 (opens in a new tab)

Controlled access users

Principal investigatorAffiliationCountry/RegionResearch titlePeriod of data useDataset ID
Michiaki HamadaHamada Laboratory, Faculty of Science and Engineering, Waseda UniversityJapanConstruction of RNA-targeted Drug Discovery Database2023-01-05 – 2027-10-31