GEO series

HIF Regulates Multiple Translated Endogenous Retroviruses: Implications for Cancer Immunotherapy [Polysome-Seq]

GSE253323 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/02/20 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 12 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)
Samples: 12 samples: 3 × 786-O, EV, vs 3 × 786-O, VHL, vs 3 × A-498, EV, vs 3 × A-498, VHL,Groups 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: HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapyCell · 2025

Summary (written by the submitters)

Clear cell renal cell carcinoma (ccRCC), despite having a low mutational burden, is considered immunogenic because it occasionally undergoes spontaneous regressions and often responds to immunotherapies. The signature lesion in ccRCC is inactivation of the VHL tumor suppressor gene and consequent upregulation of the HIF transcription factor.

Read the full summary ↓

An earlier case report described a ccRCC patient who was cured by an allogeneic stem cell transplant and later found to have donor-derived T cells that recognized a ccRCC-specific peptide encoded by a HIF-responsive endogenous retrovirus (ERVE-4). We report that ERVE-4 is one of many ERVs that are induced by HIF, translated into HLA-bound peptides in ccRCCs, and capable of generating antigen-specific T cell responses. Moreover, ERV expression can be induced in non-ccRCC tumors with clinical-grade HIF stabilizers. These findings have implications for leveraging ERVs for cancer immunotherapy.

Published in

HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy

Jiang Q, Braun DA, Clauser KR et al. · Cell 2025 · PMID 40023154 · doi:10.1016/j.cell.2025.01.046

This dataset

Open GSE253323 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 GSE253323_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 PRJNA1065293 and SRA study SRP483929. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40023154) ↗

Study design

3 × 786-O, EV, vs 3 × 786-O, VHL, vs 3 × A-498, EV, vs 3 × A-498, VHL,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 of them. 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

GSM8018744 786-O, EV, Rep1 786-O, EV,
GSM8018745 786-O, EV, Rep2 786-O, EV,
GSM8018746 786-O, EV, Rep3 786-O, EV,
GSM8018747 786-O, VHL, Rep1 786-O, VHL,
GSM8018748 786-O, VHL, Rep2 786-O, VHL,
GSM8018749 786-O, VHL, Rep3 786-O, VHL,
GSM8018750 A-498, EV, Rep1 A-498, EV,
GSM8018751 A-498, EV, Rep2 A-498, EV,
GSM8018752 A-498, EV, Rep3 A-498, EV,
GSM8018753 A-498, VHL, Rep1 A-498, VHL,
GSM8018754 A-498, VHL, Rep2 A-498, VHL,
GSM8018755 A-498, VHL, Rep3 A-498, VHL,

Datasets on a similar topic

GSE253327 HIF Regulates Multiple Translated Endogenous Retroviruses: Implications for Cancer Immunotherapy [RNA-Seq_QJ8080] 15 samples shares hif, immunotherapy, retroviruses, implications, translated, endogenous, multiple
GSE336137 mTORC2-HIF-1β signaling creates a targetable sphingolipid vulnerability in lung cancer [Polysome-seq] 24 samples shares hif, polysome-seq
GSE261187 Epigenetic priming induces cancer testis antigens and human endogenous retroviruses in glioma for enhanced T cell responses at single cell resolution (bulk RNA-Seq) 20 samples shares retroviruses, endogenous
GSE301142 Multiple mechanisms lead to differential loss-of-function effects of pathogenic SARS2 variants: implications for genotype-phenotype analyses 18 samples shares implications, multiple
GSE260643 BMAL1–HIF2A heterodimer modulates circadian variations of myocardial injury 155 samples shares hif
GSE256000 Open chromatin, HIF binding and mRNA expression analysis in primary tubule and ccRCC cells [RNA-seq] 32 samples shares hif
GSE302327 HIF-1alpha activity affects stem cell fate in patient-derived ileum organoids 29 samples shares hif
GSE205472 A Single-Cell Atlas of HR+ Breast Cancer Reveals the Shifting of the Tumor Microenvironment in Response to Neoadjuvant Chemotherapy 13 samples shares hif

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