Single cell RNA-seq in small intestine

Dataset overview

Participants 4

Samples 2

Reuse readiness 7.1/10 evidence-backed score

Single-cell transcriptomics of human gut T cells identifies cytotoxic CD4+CD8A+ T cells related to mouse CD4 cytotoxic T cells.

Tanemoto S, Sujino T, Miyamoto K, Moody J, Yoshimatsu Y, Ando Y, Koya I, Harada Y, et al. · Frontiers in immunology · 2022

Abstract

Cytotoxic CD4+ T cells (CD4-CTLs) show the presence of cytolytic granules, which include the enzymes granzyme and perforin. The cells have a pathogenic and protective role in various diseases, including cancer, viral infection, and autoimmune disease. In mice, cytotoxic CD4+ T cells express CD8αα+ and reside in the intestine (mouse CD4+CTLs; mCD4-CTLs). The population of cytotoxic CD4+ T cells in the human intestine is currently unknown. Moreover, it is unclear how cytotoxic CD4 T cells change in patients with inflammatory bowel disease (IBD). Here, we aimed to identify cytotoxic CD4+ T cells in the human intestine and analyze the characteristics of the population in patients with IBD using single-cell RNA-seq (scRNA-seq). In CD4+ T cells, granzyme and perforin expression was high in humanMAIT (hMAIT) cells and hCD4+CD8A+ T cell cluster. Both CD4 and CD8A were expressed in hTreg, hMAIT, and hCD4+CD8A+ T cell clusters. Next we performed fast gene set enrichment analysis to identify cell populations that showed homology to mCD4CTLs. The analysis identified the hCD4+CD8A+ T cell cluster (hCTL-like population; hCD4-CTL) similar to mouse CTLs. The percentage of CD4+CD8A+ T cells among the total CD4+ T cells in the inflamed intestine of the patients with Crohn's disease was significantly reduced compared with that in the noninflamed intestine of the patients. In summary, we identified cytotoxic CD4+CD8+ T cells in the small intestine of humans. The integration of the mouse and human sc-RNA-seq data analysis highlight an approach to identify human cell populations related to mouse cell populations, which may help determine the functional properties of several human cell populations in mice.

doi:10.3389/fimmu.2022.977117 ↗ PMID 36353619 ↗ PMC9639511 ↗

Study facts

Organism: Homo sapiens
Platform: MGISEQ-2000RS
Age group: —
Disease groups: —
Anatomical sites: small intestine

Data availability

Raw counts
Processed matrix

File types CSVMTXTSVTXT

CD4+CD8A+ T cells2

Accession	Sample	Tissue	Molecule
`GSM6443304`	Control (nonlesion from cancer patient) and Ulcerative colitis TFHS000025	CD4+CD8A+ T cells	total RNA
`GSM6443305`	Control (nonlesion from cancer patient) and Crohn disease TFHS000053	CD4+CD8A+ T cells	total RNA

Strengths & limitations for reuse

Strengths

Raw reads are advertised
Raw counts are advertised
Processed matrices are advertised
Cell metadata are advertised
Participant counts are documented

Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

Field	Value	Evidence
`assay.assay_type`	10x Genomics Chromium single-cell 5′ gene expression	RNA-seq libraries were prepared using Chromium single-cell 5’ gene expression library preparation (human) according to the manufacturer’s instructions (10X Genomics). Section `Methods — Human Sc-RNA seq`, offset —
`assay.library_chemistry`	Chromium single-cell 5′ v1.1	Library was performed according to the manufacter’s instructions (single cell 5’ v1.1 protocol, 10x Genomics). Section `extract_protocol`, offset —
`assay.platform`	MGISEQ-2000RS	MGISEQ-2000RS Section `instrument_model`, offset —
`assay.reference_genome`	GRCh38 / hg38	Assembly: hg38 Section `data_processing`, offset —
`assay.sequencing_type`	scrna_seq	using single cell RNA-seq Section `series_summary`, offset —

Cohort

Field	Value	Evidence
`cohort.crohns_disease_participants`	1	Small intestinal tissue samples were obtained from nine patients with colon cancer (controls), one with UC, and eight with CD who underwent surgical resection. Section `Methods — Human samples`, offset —
`cohort.disease_activity_metadata_available`	True	one patient with UC, and one with CD (both noninflamed lesions) were obtained Section `Results — Single-cell analysis of samples from control tissues and patients with ibd identified 10 cell populations`, offset —
`cohort.non_ibd_controls`	2	TCRB + T cells from two controls (small intestine apart from the colon cancer lesion), one patient with UC, and one with CD (both noninflamed lesions) were obtained Section `Results — Single-cell analysis of samples from control tissues and patients with ibd identified 10 cell populations`, offset —
`cohort.total_participants`	4	Small intestinal tissue samples were obtained from nine patients with colon cancer (controls), one with UC, and eight with CD Section `Methods — Human samples`, offset —
`cohort.ulcerative_colitis_participants`	1	TCRB + T cells from two controls (small intestine apart from the colon cancer lesion), one patient with UC, and one with CD (both noninflamed lesions) were obtained Section `Results — Single-cell analysis of samples from control tissues and patients with ibd identified 10 cell populations`, offset —

Data_Assets

Field	Value	Evidence
`data_assets.cell_metadata`	True	annotation.csv.gz Section `supplementary_files`, offset —
`data_assets.participant_metadata`	True	freemuxlet.txt.gz Section `supplementary_files`, offset —
`data_assets.processed_matrix`	True	features.tsv.gz Section `supplementary_files`, offset —
`data_assets.raw_counts`	True	matrix.mtx.gz Section `supplementary_files`, offset —
`data_assets.raw_reads`	True	GSE210955_RAW.tar Section `filelist.txt`, offset —

Processing

Field Value Evidence

Field	Value	Evidence
`processing.batch_correction_reported`	True	and integrated with Harmony. Section `data_processing`, offset —
`processing.quality_control_reported`	True	Cells were processed with Seurat to filter cells >6 median absolute deviations in UMI or gene count from the mean, or mitochondrial UMI > 25% Section `data_processing`, offset —

processing.batch_correction_reported

True

and integrated with Harmony.

Section data_processing, offset —

processing.quality_control_reported