GEO series

Allogeneic iPSC-derived iNKT cells in recurrent head and neck cancer: a phase 1 trial

GSE290757 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/09/28 Platform GPL28038

At a glance

RNA-seq (gene expression) · human · 18 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Topic: Head and neck cancerThis series is part of our curated briefing on it.
Samples: 18 samples: 18 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: Allogeneic iPSC-derived iNKT cells in recurrent head and neck cancer: a phase 1 trialNature communications · 2025

Summary (written by the submitters)

Invariant Natural killer T (iNKT) cells exhibit cytotoxic activity and immunomodulatory functions and have gained interest in cancer immunotherapy. We conducted a phase 1, first-in human clinical trial to evaluate the safety and efficacy of clinical-grade allogeneic iNKT cells generated from induced pluripotent stem cells (iPSC-iNKT cells) in patients with recurrent head and neck cancer (jRCT2033200116).

Read the full summary ↓

The primary endpoint was the incidence of dose-limiting toxicity (DLT). The secondary endpoints were to assess safety and efficacy, as well as to evaluate immunological dynamics. iPSC-iNKT cells were administered intra-arterially to 10 patients. One subject developed grade 3 skin rash at the second dose, identified as DLT. No other severe adverse events were observed in any patients. Tumor progression was suppressed in two patients, in whom clonal expansion of memory- and effector-phenotype CD8+ T cells was observed, along with activation of the IFN-γ signaling pathway. Here, we show that iPSC-iNKT cells are safe and possess therapeutic potential as an immunotherapy for solid tumors.

Published in

Allogeneic iPSC-derived iNKT cells in recurrent head and neck cancer: a phase 1 trial

Iinuma T, Kurokawa T, Aoki T et al. · Nature communications 2025 · PMID 41298491 · doi:10.1038/s41467-025-66801-w

This dataset

Open GSE290757 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 GSE290757_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1230068 and SRA study SRP567211. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41298491) ↗

Study design

18 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 18 sample titles: 18 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

GSM8821219 Subject ID 12 day21_GEX
GSM8821220 Subject ID 12 day8_GEX
GSM8821221 Subject ID 12 day1_GEX
GSM8821222 Subject ID 08 day21_GEX
GSM8821223 Subject ID 08 day8_GEX
GSM8821224 Subject ID 08 day1_GEX
GSM8821225 Subject ID 09 day21_GEX
GSM8821226 Subject ID 09 day8_GEX
GSM8821227 Subject ID 09 day1_GEX
GSM8821228 Subject ID 12 day21_VDJ
GSM8821229 Subject ID 12 day8_VDJ
GSM8821230 Subject ID 12 day1_VDJ
GSM8821231 Subject ID 08 day21_VDJ
GSM8821232 Subject ID 08 day8_VDJ
GSM8821233 Subject ID 08 day1_VDJ
GSM8821234 Subject ID 09 day21_VDJ
GSM8821235 Subject ID 09 day8_VDJ
GSM8821236 Subject ID 09 day1_VDJ

More Head and neck cancer datasets

GSE103322 Single cell RNA-seq analysis of head and neck cancer 5901 samples same disease briefing · shares head, neck
GSE139324 Immune landscape of viral- and carcinogen-drived head and neck cancer 63 samples same disease briefing · shares head, neck
GSE164690 Investigating Immune and Non-Immune Cell Interactions in Head and Neck Tumors by Single-Cell RNA Sequencing 51 samples same disease briefing · shares head, neck
GSE181919 Single-cell transcriptome profiling of the stepwise progression of head and neck cancer 37 samples same disease briefing · shares head, neck
GSE140042 Single-cell atlas of head and neck squamous cell carcinoma 18 samples same disease briefing · shares head, neck
GSE185965 Single cell RNA sequencing of head and neck squamous carcinoma (HNSCC) patient sample 3 samples same disease briefing · shares head, neck
GSE173647 Single-cell Sequencing Analysis of Head and Neck Squamous Cell Carcinoma 2 samples same disease briefing · shares head, neck
GSE162738 Immune gene signatures in oropharyngeal cancers are associated with inverse prognosis by HPV-status 51 samples same disease briefing

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.