Research ID
hum0214-v9Release info
This page is a past version (v9). The latest version is v10.
Latest version (v10)Research title
Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases
Research overview
- Aims
- To elucidate the regulation of gene expression in each immune cell subset and its contribution to autoimmune diseases.
- Methods
- JGAS000220 (JGAD000309, JGAD000310): Various immune cell subsets from 21 systemic sclerosis patients, 26 ANCA associated vasculitis, and 28 healthy controls were collected (Naive_B, SM_B, USM_B, DN_B, Plasmablast, Th1, Th2, Th17, Tfh, Naive_CD4, Mem_CD4, Fr._II_eTreg, Naive_CD8, Mem_CD8, mDC, pDC, CD16p_Mono, CD16n_Mono, NK, Neu) and total RNAs were extracted from each subset. RNA-seq was performed for each sample.
E-GEAD-397 / E-GEAD-398 / E-GEAD-420: Whole blood and 28 immune cell subsets from study population were collected (Naive_CD4, Mem_CD4, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Th1, Th2, Th17, Tfh, NK, Naive_CD8, Mem_CD8, EM_CD8, CM_CD8, TEMRA_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono (or CD16n_Mono), CD16p_Mono, Int_Mono, NC_Mono, mDC, pDC, LDG, Neu). Whole genome sequencing was performed with whole blood samples. RNA-seq was performed with each immune cell subset samples. After filtering and normalization of the gene expression data, eQTL analysis was performed in each immune cell type.
JGAS000296: 24 peripheral blood immune cell subsets from 50 systemic sclerosis patients and 48 healthy controls were collected (Naive_CD4, Mem_CD4, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Th1, Th2, Th17, Tfh, NK, Naive_CD8, EM_CD8, CM_CD8, TEMRA_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono, Int_Mono, NC_Mono, mDC, pDC). RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered.
JGAS000220 (JGAD000371, JGAD000372, JGAD000373): 19 immune cell subsets from study population were collected (Naive_CD4, Mem_CD4, Fr._II_eTreg, Th1, Th2, Th17, Tfh, NK, Naive_CD8, Mem_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CD16n_Mono, CD16p_Mono, mDC, pDC). RNA-seq was performed with each immune cell subset sample. ATAC-seq of 15 immune cell subsets was also performed.
JGAS000486: Various peripheral blood immune cell subsets from 89 healthy volunteers and 136 systemic lupus erhythematosus (SLE) donors were collected (Naive_CD4, Mem_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Naive_CD8, EM_CD8, CM_CD8, TEMRA_CD8, NK, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono (or CD16n_Mono), CD16p_Mono, Int_Mono, NC_Mono, mDC, pDC, Neu, LDG). 22 SLE patients were analyzed longitudinally. RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered.
JGAS000598: Various peripheral blood immune cell subsets from 39 healthy volunteers and 50 rheumatoid (RA) donors were collected (CD16p_Mono, CL_Mono, DN_B, Fr_II_eTreg, mDC, Mem_CD4, Naive_B, Naive_CD4, Neu, NK, pDC, Plasmablast, SM_B, Tfh, Th1, Th17, Th2, USM_B). 15 RA patients were analyzed longitudinally. RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered.
JGAS000485: Peripheral blood B cell subsets from study population were collected (Naive_B, USM_B, SM_B, DN_B, Plasmablast). RNA-seq was performed with each B cell subset samples. B cell receptor sequences were aligned.
JGAS000626: 9 immune cell subsets from study population were collected (Naive_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, ThA). RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered.
JGAS000627: 27 immune cell subsets from study population were collected (Naive_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, ThA, Naive_CD8, Naive_B, SM_B, USM_B, DN_B, Plasmablast, NK, CD16p_Mono, CL_Mono, Neu, mDC, pDC, TEMRA_CD8, CM_CD8, EM_CD8, NC_Mono, Int_Mono, LDG). RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered.
JGAS000648: Peripheral blood, muscle tissue, and bronchial lavage fluid were collected from each subject. For peripheral blood, CD4T cells were collected and scRNA-seq was performed to quantify gene expression. For muscle tissue and bronchial lavage fluid, CD45-positive cells were collected, scRNA-seq was performed, gene expression was quantified, and CD4T cluster was selected. - Participants/materials
- Systemic Sclerosis, Systemic Lupus Erythematosus, Myositis, Mixed Connective Tissue Disease, Sjögren's Syndrome, Rheumatoid Arthritis, Behçet's Disease, Adult Onset Still's Disease, ANCA-associated Vasculitis, Takayasu's Arteritis, healthy individuals
Datasets
The list is the one this version published; each dataset's content is shown as it is now.
| Cart | Dataset ID | Type of data | Analysis method | Access criteria | Date published |
|---|---|---|---|---|---|
| JGAD000309 | NGS (RNA-seq: Systemic sclerosis) |
| Controlled-access (Type I) | 2021-03-09 | |
| JGAD000310 | NGS (RNA-seq: Systemic sclerosis) |
| Controlled-access (Type I) | 2021-03-09 | |
| JGAD000371 | NGS (RNA-seq: Systemic sclerosis) |
| Controlled-access (Type I) | 2022-03-16 | |
| JGAD000372 | NGS (RNA-seq: Systemic sclerosis) |
| Controlled-access (Type I) | 2022-03-16 | |
| JGAD000373 | NGS (RNA-seq: Systemic sclerosis) |
| Controlled-access (Type I) | 2022-03-16 | |
| E-GEAD-397 | Read count data from RNA-seq |
| Unrestricted-access | 2021-04-30 | |
| E-GEAD-398 | Conditional eQTL summary data (significant associations) |
| Unrestricted-access | 2021-04-30 | |
| E-GEAD-420 | Nominal eQTL data (including non-significant associations) |
| Unrestricted-access | 2021-06-09 | |
| JGAD000406 | NGS (RNA-seq) |
| Controlled-access (Type I) | 2022-01-19 | |
| JGAD000603 | NGS (RNA-seq) |
| Controlled-access (Type I) | 2022-08-24 | |
| JGAD000727 | NGS (RNA-seq) |
| Controlled-access (Type I) | 2023-03-28 | |
| JGAD000602 | B cell receptor repertoire clonotype data from B cell RNA-seq |
| Controlled-access (Type I) | 2023-07-10 | |
| JGAD000755 | NGS (RNA-seq) |
| Controlled-access (Type I) | 2024-02-14 | |
| JGAD000756 | NGS (RNA-seq) |
| Controlled-access (Type I) | 2024-02-14 | |
| JGAD000778 | NGS (scRNA-seq) |
| Controlled-access (Type I) | 2024-02-14 |
Data provider
- Principal investigator
- Keishi Fujio
- Affiliation
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo
Research projects
| Name | URL |
|---|---|
Immune cell multi-omics analysis of immune-mediated diseases |
Grants
| Name | Title | Project number |
|---|---|---|
Practical Research Project for Rare / Intractable Diseases, Japan Agency for Medical Research and Development (AMED) | Identification of therapeutic targets and development of intervention strategy for systemic lupus erythematosus based on the comprehensive analysis of genome and transcriptome. |
|
Platform Program for Promotion of Genome Medicine, Japan Agency for Medical Research and Development (AMED) | Construction of stratification and prognosis prediction models from immune-mediated disease genomic information using immune cell eQTL data |
|
Moonshot Research and Development Program, Japan Agency for Medical Research and Development (AMED) | Quantum and neuron modulation technologies to suppress tissue-specific disease-related microinflammation |
|
Practical Research Project for Allergic Diseases and Immunology, Japan Agency for Medical Research and Development (AMED) | Integrative multi-omics analysis of autoimmune diseases based on single cell RNA-sequencing of inflammatory organs |
|
Advanced Research and Development Programs for Medical Innovation , Japan Agency for Medical Research and Development (AMED-CREST) | Study of T cell subsets associated with immune memory for both cytotoxic and adaptive immune responses in autoimmune diseases |
|
KAKENHI Grant-in-Aid for Scientific Research (B) | Single-cell multiome profiling and functional analysis of human age-associated T cells in autoimmune diseases |
|
Collaborative research fund with Chugai Pharmaceutical Co., Ltd. | N/A | N/A |
Related publications
| Title | DOI | Dataset ID |
|---|---|---|
Integrated bulk and single-cell RNA-sequencing identified disease-relevant monocytes and a gene network module underlying systemic sclerosis | ||
Identifying the most influential gene expression profile in distinguishing ANCA-associated vasculitis from healthy controls | ||
Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases | ||
Dysregulation of the gene signature of effector regulatory T cells in the early phase of systemic sclerosis | ||
Immune cell multiomics analysis reveals contribution of oxidative phosphorylation to B-cell functions and organ damage of lupus | ||
Distinct transcriptome architectures underlying lupus establishment and exacerbation | ||
Immunomics analysis of rheumatoid arthritis identified precursor dendritic cells as a key cell subset of treatment resistance | ||
Multimodal repertoire analysis unveils B cell biology in immune-mediated diseases | ||
Age-associated CD4+ T cells with B cell-promoting functions are regulated by ZEB2 in autoimmunity |
Controlled access users
| Principal investigator | Affiliation | Country/Region | Research title | Period of data use | Dataset ID |
|---|---|---|---|---|---|
| Michiaki Hamada | Hamada Laboratory, Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | 2023-01-05 – 2027-10-31 | |
| Ana Rita Grosso | Computational Multi-Omics Lab, Department of Life Sciences, Universidade Nova de Lisboa - NOVA School of Science and Technology | Portugal | Assessing transcriptional dyregulation of repetitive elements and monoallelic-expressed genes in lupus | 2023-04-25 – 2026-04-10 | |
| jiucun wang | jiu-cunwang lab , jiu-cun wang , department of anthropology and human genetics, department of anthropology and human genetics of fudan university | China | The role and mechanism study of glycosyltransferase-B3GNT2 in regulating macrophages of Ankylosing Spondylitis | 2023-03-08 – 2024-03-01 | |
| Jacob Jaffe | Data Science, Odyssey Therapeutics | Massachusetts, United States | Investigation of immune cell transition states in autoimmune disease | 2023-04-06 – 2023-11-02 | |
| yoshito takeda | Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University | Japan | Pathophysiology and diagnostic development with a focus on extracellular vesicles in respiratory and immunological diseases | 2023-04-12 – 2025-01-17 | |
| Yong-Fei WANG | Warshel Institue for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen | China | Investigating the Molecular Mechanisms of Systemic Lupus Erythematosus Using Functional Genomics Data | 2023-06-21 – 2025-05-28 | |
| Shimpei Kubota | Molecular Psychoneuroimmunology, Hokkaido University | Japan | Gene expression and IL-6 amplifying circuit activators in rheumatoid arthritis and systemic lupus erythematosus | 2024-02-26 – 2026-03-31 | |
| Timothy Vyse | molecular and medical genetics, King's College London | United Kingdom | Sequencing Based Genetic Analysis of Systemic Lupus | 2023-08-25 – 2025-10-16 | |
| Hironao Suzuki | Pharmacology Department, Drug Research Center, Kaken Pharmaceutical,co.,LTD. | Japan | Bioinformatics analysis of immune cells from SLE patients | 2024-05-09 – 2025-04-17 | |
| Hui Li | Department of Pathology, University of Virginia | United States | Gene fusions and RNA Trans-splicing in normal and neoplastic human cells | 2025-06-25 – 2026-12-31 | |
| Tatsuma Ban | Department of Immunology, Graduate School of Medicine, Yokohama City University | Japan | Pathophysiology and therapeutic development of autoimmune diseases focusing on transcription factors of the immune system | 2024-11-12 – 2027-03-31 | |
| Pranidhi Sood | Wield Therapeutics, Inc | California, United States | Identifying Gene Expression Based Biomarkers in Patients with Autoimmune Diseases to Predict Response to New Therapies Developed by Wield Therapeutics | 2025-06-25 – 2027-04-23 | |
| Isao Matsumoto | Department of Rheumatology, Institute of Medicine, University of Tsukuba | Japan | Investigation of aging-related functional alterations in CD4⁺ T cells in rheumatoid arthritis and experimental arthritis models | 2025-12-05 – 2029-03-31 | |
| Eisuke Itakura | Graduate School of Science, Chiba University | Japan | Linking SLE Symptoms to Gene Expression Variation through ImmuNexUT | 2025-10-27 – 2026-04-02 |