NBDC Research ID: hum0406.v2
SUMMARY
Aims: The ideal way of studying the disease is to use an affected part (tissue) of the patient's body. However, the use of the affected tissue involves many issues; for example, sampling of the affected tissue may impose a severe burden on the patient or is sometimes technically impossible. Therefore, iPS cells are a powerful technology that can differentiate into the various tissues that make up our bodies. The aim of this study is to generate iPS cells from patients’ and/or their family members’ somatic cells and to use them together with clinical information to discover more about the cause of the diseases and to develop new effective treatments.
To elucidate the molecular mechanisms underlying the pathology of Primary Ciliary Dyskinesia (PCD) caused by disease-associated gene variants. To this end, we will establish patient-specific iPSCs and gene-corrected iPSC lines, differentiate them into airway epithelial cells, and perform single-cell RNA sequencing for comparative transcriptomic analysis.
Methods:
[JGAS000617 / E-GEAD-623] Patient iPSC-derived type 2 alveolar epithelial (iAT2) cells (EpCAM+CPM+) and fibroblasts (EpCAM-CPM-) were isolated by fluorescence-activated cell sorting. Total RNA was extracted from the cells and sequenced.
[JGAS000846] Airway epithelial cells derived from human iPSCs (disease-specific: PCD-iPSC; gene-corrected: CCE1-iPSC) were differentiated under air–liquid interface (ALI) conditions and subjected to single-cell RNA sequencing (scRNA-seq).
Participants/Materials:
[JGAS000617 / E-GEAD-623] Familial interstitial pneumonia with SFTPC variant: 1 case
- EpCAM+CPM+ or EpCAM-CPM- cells of alveolar organoids derived from iPSCs established from PBMCs of a familial interstitial pneumonia patient with Y104H variant of SFTPC
- EpCAM+CPM+ or EpCAM-CPM- cells of Y104H-KO iPSC-derived alveolar organoids established from PBMCs of the patient with Y104H variant of SFTPC
[JGAS000846] Primary Ciliary Dyskinesia with a CCNO (Cyclin O) Variant: 1 case
1. Airway epithelial cell sheet derived from iPSCs established from the patient’s peripheral blood
2. Airway epithelial cell sheet derived from gene-corrected iPSCs established from the patient’s peripheral blood
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000617 | NGS (RNA-seq) | Controlled-access (Type I) | 2023/08/29 |
| E-GEAD-623 | NGS (RNA-seq) | Unrestricted-access | 2023/08/29 |
| JGAS000846 | NGS (scRNA-seq) | Controlled-access (Type I) | 2026/03/30 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials |
Familial interstitial pneumonia with SFTPC variant (ICD10: J84.9): 1 case - EpCAM+CPM+ or EpCAM-CPM- cells of alveolar organoids derived from iPSCs established from PBMCs of the patient with Y104H variant of SFTPC: 3 samples each - EpCAM+CPM+ or EpCAM-CPM- cells of Y104H-KO iPSC-derived alveolar organoids established from PBMCs of the patient with Y104H variant of SFTPC: 3 samples each |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 2000] |
| Source | RNAs extracted from EpCAM+CPM+ or EpCAM-CPM- cells derived from iPSCs established from PBMCs of a patient with Y104H variant of SFTPC |
| Cell Lines | - |
| Library Construction (kit name) | Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit |
| Fragmentation Methods | Exposure to divalent cations at elevated temperatures |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 59 bp x 2 |
| Mapping Methods | STAR 2.7.10b |
| Reference Genome Sequence | GRCh38 |
| Detecting method for read count (software) | HTSeq package |
| QC Methods | RSeQC package |
| Gene Number | 36,602 genes |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000746 |
| Genomic Expression Archive ID | E-GEAD-623 |
| Total Data Volume |
JGAD000746: 27.7 GB (fastq) E-GEAD-623: 2.16 MB (csv) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Primary Ciliary Dyskinesia with a CCNO Variant (ICD10: Q348): 1 case 1. Airway epithelial cell sheet derived from iPSCs established from the patient’s peripheral blood 2. Airway epithelial cell sheet derived from gene-corrected iPSCs established from the patient’s peripheral blood |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Source | RNAs extracted from single cells isolated from airway epithelial cell sheet derived from iPSCs established from the patient’s peripheral blood |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Single Cell 3' Reagent Kits v4.0 |
| Fragmentation Methods | included in the above library construction kit (Enzymatic fragmentation) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | Read 1: 28 bp, Read 2: 90 bp |
| Mapping Methods | Cell Ranger (v8.0.1) |
| Reference Genome Sequence | GRCh38 (refdata-gex-GRCh38-2020-A) |
| Detecting method for read count (software) | Cell Ranger (v8.0.1) |
| QC Methods | Cell Ranger (v8.0.1) |
| Gene Number | 38606 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000988 |
| Total Data Volume | 62.9 GB (fastq, h5) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shimpei Gotoh
Affiliation: Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED) | Application of human iPS cells for disclosing the pathogenic mechanisms of intractable respiratory diseases and finding novel therapeutic agents | JP17bm0804007 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Cryptotanshinone is a candidate therapeutic agent for interstitial lung disease associated with a BRICHOS-domain mutation of SFTPC | doi: 10.1016/j.isci.2023.107731 | JGAD000746 E-GEAD-623 |
| 2 | Deuterosomal cells are the responsible lineage for multiciliogenesis in human airway differentiation* | doi: 10.1016/j.stemcr.2026.102860 | JGAD000988 |
*The identifier "J-DS000923" described in the published article corresponds to the dataset deposited in JGA under accession JGAS000846.
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
