NBDC Research ID: hum0443.v1
SUMMARY
Aims: A fetus expresses paternally derived antigens which is allogenic for a mother, however; fetus is not rejected from maternal immune cells because of feto-maternal immune tolerance during pregnancy. At the same time, maternal immune system still maintains their ability to respond against pathogenic organisms. The adequate balance between tolerogenic regulatory T cells (Treg) and proinflammatory CD4+ T cells and cytotoxic T cells at feto-maternal interface is important for healthy pregnancies. However, diversity of CD4+ T cells and Tregs in healthy pregnancies and its alternation in preeclampsia (PE) have not been fully understood. Therefore, we conducted single-cell mRNA sequencing and T cell receptor repertoire analysis to reveal a landscape of diverse CD4 T cells and Treg in healthy pregnancies and altered gene expression patterns which relate to pathogenesis of PE.
Methods: Lymphocytes were isolated from decidual tissue and peripheral blood. CD4+ T cells were sorted and subjected into BD Rhapsody Single-Cell Analysis System. Targeted RNA-sequence and TCR sequence libraries were constructed. Sequencing was performed using Illumina NovaSeq 6000.
Participants/Materials: Healthy early pregnancy decidual CD4+ T cells (n=4), Healthy late pregnancy decidual CD4+ T cells (n=3), Preeclampsia decidual CD4+ T cells (n=3), Healthy late pregnancy peripheral blood CD4+ T cells (n=1) . One pairs of healthy late decidua and peripheral blood was from the same subject. All samples were subjected to targeted RNA-sequencing with the BD Rhapsody. TCR-sequence was performed in 2 healthy early, 1 healthy late decidua, 1 healthy late peripheral blood, and 1 preeclampsia decidua.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
|
DRA017833 E-GEAD-674 |
NGS (Target RNA-seq, TCR-seq) | Unrestricted-access | 2024/05/10 |
*When the research results including the data which were downloaded from DRA/GEA, 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 |
Healthy pregnancy: 7 subjects (early pregnancy: 4 subjects, late pregnancy: 3 subjects) Preeclampsia (ICD10: O149): 3 cases Healthy early pregnancy decidual CD4+ T cells: 4 samples Healthy late pregnancy decidual CD4+ T cells: 3 samples Preeclampsia decidual CD4+ T cells: 3 samples Healthy late pregnancy peripheral blood CD4+ T cells: 1 sample |
| Targets | Target RNA-seq |
| Target Loci for Capture Methods |
1) BD Rhapsody T Cell Expression Panel Hs (BD Biosciences Cat#633751) 2) Rhapsody Supplemental Gene Primer for IL10 and NRP1. 3) T cell receptor |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from CD4+ T cells isolated from decidual tissue and peripheral blood |
| Cell Lines | - |
| Library Construction (kit name) | BD RhapsodyTM Targeted mRNA and AbSeq Reagent Kit |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 531 bp on average |
| DDBJ Sequence Read Archive ID | DRA017833 |
| Genomic Expression Archive ID | E-GEAD-674 |
| Total Data Volume | 95.1 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Healthy pregnancy: 3 subjects (early pregnancy: 2 subjects, late pregnancy: 1 subject) Preeclampsia (ICD10: O149): 1 case Healthy early pregnancy decidua: 2 samples Healthy late pregnancy decidua: 1 sample Preeclampsia decidua: 1 sample Healthy late pregnancy peripheral blood: 1 sample |
| Targets | TCR-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from CD4+ T cells isolated from decidual tissue and peripheral blood |
| Cell Lines | - |
| Library Construction (kit name) | BD RhapsodyTM Targeted mRNA and AbSeq Reagent Kit |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | TCRα: 659 bp on average, TCRβ: 655 bp on average |
| DDBJ Sequence Read Archive ID | DRA017833 |
| Genomic Expression Archive ID | E-GEAD-674 |
| Total Data Volume | 95.1 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Akitoshi Nakashima
Affiliation: Department of Obstetrics and Gynecology, University of Toyama
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | The crosstalk of paternal antigen specific Treg cells and dendritic cells in feto-maternal tolerance | 17K11221 |
| KAKENHI Grant-in-Aid for Early-Career Scientists | Immunological differece between pregnancy and cancer in terms of T cell receptor repertoire. | 19K18690 |
| KAKENHI Grant-in-Aid for Early-Career Scientists | Single T cell transcriptome analysis for biomarker discovery in the treatment of preeclampsia. | 21K16764 |
| KAKENHI Fund for the Promotion of Joint International Research (Fostering Joint International Research (A)) | Elucidation of pathogenesis mechanisms of preeclampsia focusing on cell-cell interaction between maternal CD4 positive T cells and trophoblasts. | 22KK0287 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | New mechanism of autophagy inhibition from the study of preeclampsia | 19K09750 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Failure of autophagy for the therapeutic target of preeclampsia | 22H03223 |
| Project for Baby and Infant Research of Health and Development to Adolescent and Young adult, Japan Agency for Medical Research and Development (AMED) | Research on elucidation of causes and preventive treatment of recurrent pregnancy loss | JP18gk0110018 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | CD4+ T cell heterogeneity in gestational age and preeclampsia using single-cell RNA sequencing | doi: 10.3389/fimmu.2024.1401738 |
DRA017833 E-GEAD-674 |
| 2 |
