GEO series

Oligoclonal CD4+CXCR5+ T cells with a cytotoxic phenotype in tonsils and blood

GSE218131 Homo sapiens (human) Single-cell RNA-seq 33 samples Submitted 2024/06/24 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 33 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 33 samples: 33 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: Oligoclonal CD4(+)CXCR5(+) T cells with a cytotoxic phenotype appear in tonsils and bloodCommunications biology · 2024

Summary (written by the submitters)

In human studies, mononuclear cells from peripheral blood (PBMC) often serve as a source of clinical study markers. Therefore, it is essential to understand to what extent phenotypes of PBMCs reflect their tissue-resident equivalents. In order to determine the heterogeneity of T-follicular helper (TFH) cells in peripheral blood versus tonsils, CD3+CD4+CD45RA–CXCR5+ cells of both origins were sorted and transcriptomes, TCR repertoires and cell-surface protein expression were analysed by single-cell RNA sequencing, flow cytometry and immunohistochemistry.

Read the full summary ↓

Four subsets of TFH cells with classical T-follicular gene expression patterns were mostly found in tonsils. Interestingly, however, all circulating CD3+CD4+CXCR5+ T-cell subpopulations also appeared in tonsils. Still, when circulating, cells of the same cluster rather displayed markers of proliferation and migration, whereas their tonsillar counterparts exhibited known TFH characteristics resembling bona fide germinal center-typical TFH cell subtypes. Surprisingly, one distinct and oligoclonal CD4+CXCR5+ subpopulation displayed pronounced cytotoxic properties. Those ‘killer TFH (TFK) cells’ were found among PBMCs as well as tonsillar cells but were located outside of germinal centers. Accordingly, they were the only CD4+CXCR5+ T-cell subtype in tonsils featuring transcripts for CXCR3 and PSLG1. They appeared terminally differentiated and could be distinguished from all other TFH subsets by expression of NKG7 (TIA-1), granzymes, perforin, CCL5, CCR5, EOMES, CRTAM and CX3CR1. This hitherto undescribed subpopulation is indicative for chronic infection and inflammation and therefore is a valuable candidate to be included in any CD4+CXCR5+ TFH cell assessment.

Published in

Oligoclonal CD4(+)CXCR5(+) T cells with a cytotoxic phenotype appear in tonsils and blood

Liang C, Spoerl S, Xiao Y et al. · Communications biology 2024 · PMID 39025930 · doi:10.1038/s42003-024-06563-1

This dataset

Open GSE218131 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE218131_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA902388. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39025930) ↗

Study design

33 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 33 sample titles: 33 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM6735150 Donor 1, During CsA treatment, Gene expression
GSM6735151 Donor 1, After CsA treatment, Gene expression
GSM6735152 Donor 2, During CsA treatment, Gene expression
GSM6735153 Donor 2, After CsA treatment, Gene expression
GSM6735154 Tonsil1, Gene expression
GSM6735155 Tonsil2, Gene expression
GSM6735156 Tonsil3, Gene expression
GSM6735157 Donor 3, Before booster vaccination, Gene expression
GSM6735158 Donor 3, after booster vaccination, Gene expression
GSM6735159 Donor 4, Before booster vaccination, Gene expression
GSM6735160 Donor 4, after booster vaccination, Gene expression
GSM6735161 Donor 1, During CsA treatment, ADT
GSM6735162 Donor 1, After CsA treatment, ADT
GSM6735163 Donor 2, During CsA treatment, ADT
GSM6735164 Donor 2, After CsA treatment, ADT
GSM6735165 Tonsil1, ADT
GSM6735166 Tonsil2, ADT
GSM6735167 Tonsil3, ADT
GSM6735168 Donor 3, Before booster vaccination, ADT
GSM6735169 Donor 3, after booster vaccination, ADT
GSM6735170 Donor 4, Before booster vaccination, ADT
GSM6735171 Donor 4, after booster vaccination, ADT
GSM6735172 Donor 1, During CsA treatment, TCR-seq
GSM6735173 Donor 1, After CsA treatment, TCR-seq
GSM6735174 Donor 2, During CsA treatment, TCR-seq
GSM6735175 Donor 2, After CsA treatment, TCR-seq
GSM6735176 Tonsil1, TCR-seq
GSM6735177 Tonsil2, TCR-seq
GSM6735178 Tonsil3, TCR-seq
GSM6735179 Donor 3, Before booster vaccination, TCR-seq
GSM6735180 Donor 3, after booster vaccination, TCR-seq
GSM6735181 Donor 4, Before booster vaccination, TCR-seq
GSM6735182 Donor 4, after booster vaccination, TCR-seq

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