GEO series

CD161 expression of TRM cells counteracts the HPV-associated clinical benefit in oropharyngeal cancer immunotherapy

GSE226620 Homo sapiens (human) Single-cell RNA-seq 30 samples Submitted 2024/06/01 Platform GPL20795

At a glance

Single-cell RNA-seq · human · 30 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)
Topic: Head and neck cancerThis series is part of our curated briefing on it.
Samples: 30 samples: 30 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: Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomesJournal for immunotherapy of cancer · 2024

Summary (written by the submitters)

Oropharyngeal squamous cell carcinoma (OPSCC), a distinct head and neck cancer subtype that develops in the oropharynx, is well known to be categorized into human papillomavirus induced (HPV+) and non-HPV induced (HPV-). While HPV+ OPSCC is reported to be clinically advantageous compared to HPV- OPSCC, the heterogeneous responses in HPV+ OPSCC during immunotherapy treatment have not been well characterized at the molecular level.

Read the full summary ↓

In this study, we assess both tumor and immune cells of the OPSCC tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) and single-cell TCR sequencing (scTCR-seq). By dissecting the transcriptome of OPSCC tumor cells, we find that cancer cell transcriptional diversity may be a strong factor in negating HPV associated clinical benefits. By assessing immune cells, we observed molecular antiviral and anti-tumor characteristics of T cells that is associated with HPV infection, and key cell-cell interaction differences among resident memory T cells (Trm), follicular helper T cells, and B cells. Importantly, we identify a novel molecular state within the HPV+ OPSCC that is distinguished by the expression KLRB1 (CD161) in the Trm that inhibits anti-tumor activity, which may further explain the heterogeneous clinical benefits of HPV+OPSCC. Association of KLRB1 expression of Trm and immunotherapy outcome was confirmed via immunofluorescence analysis, suggesting CD161 as a novel therapeutic target to improve cancer treatment of HPV+ OPSCC.

Published in

Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes

Cha J, Kim DH, Kim G et al. · Journal for immunotherapy of cancer 2024 · PMID 38857913 · doi:10.1136/jitc-2023-008667

This dataset

Open GSE226620 in finder → Find more human RNA-seq datasets → Head and neck cancer landscape →

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 GSE226620_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 PRJNA940826 and SRA study SRP426637. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38857913) ↗

Study design

30 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 30 sample titles: 30 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

GSM7080427 HPV01, positive
GSM7080428 HPV02, positive
GSM7080429 HPV03, positive
GSM7080430 HPV04, positive
GSM7080431 HPV05, positive
GSM7080432 HPV06, negative
GSM7080433 HPV07, negative
GSM7080434 HPV08, positive
GSM7080435 HPV09, negative
GSM7080436 HPV10, negative
GSM7080437 P18, positive
GSM7080438 P29, positive
GSM7080439 P20, positive
GSM7080440 P23, positive
GSM7080441 P25, positive
GSM7080442 P27, positive
GSM7080443 P28, positive
GSM7080444 P31, positive
GSM7080445 P30, negative
GSM7080446 P32, negative
GSM7157425 P18, positive, TCR
GSM7157426 P29, positive, TCR
GSM7157427 P20, positive, TCR
GSM7157428 P23, positive, TCR
GSM7157429 P25, positive, TCR
GSM7157430 P27, negative, TCR
GSM7157431 P28, negative, TCR
GSM7157432 P31, positive, TCR
GSM7157433 P30, negative, TCR
GSM7157434 P32, negative, TCR

More Head and neck cancer datasets

GSE162738 Immune gene signatures in oropharyngeal cancers are associated with inverse prognosis by HPV-status 51 samples same disease briefing · shares oropharyngeal
GSE182227 Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma 24 samples same disease briefing · shares oropharyngeal
GSE103322 Single cell RNA-seq analysis of head and neck cancer 5901 samples same disease briefing
GSE139324 Immune landscape of viral- and carcinogen-drived head and neck cancer 63 samples same disease briefing
GSE164690 Investigating Immune and Non-Immune Cell Interactions in Head and Neck Tumors by Single-Cell RNA Sequencing 51 samples same disease briefing
GSE181919 Single-cell transcriptome profiling of the stepwise progression of head and neck cancer 37 samples same disease briefing
GSE114446 Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines 33 samples same disease briefing
GSE172146 Aberrant translation regulation by METTL1/WDR4-mediated tRNA N7-methylguanosine modification drives HNSCC progression 28 samples same disease briefing

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