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 IDType of DataCriteriaRelease Date

DRA017833

E-GEAD-674

NGS (Target RNA-seq, TCR-seq) Unrestricted-access 2024/05/10

*Release Note

*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

Target RNA-seq

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

 

TCR-seq

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):  

NameTitleProject 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

TitleDOIDataset 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