GEO series
A macrophage-predominant, immunosuppressive immune microenvironment and subtype-specific therapeutic vulnerabilities in advanced salivary gland cancer [bulk RNA-seq]
GSE294016
Homo sapiens (human)
RNA-seq (gene expression)
95 samples
Submitted 2025/04/14
Platform GPL24676Platform GPL20301Platform GPL33758
At a glance
RNA-seq (gene expression) · human · 95 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
- 95 samples: 93 × bulkrna seq of tumor biopsy, patient PGroups 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
- A macrophage-predominant immunosuppressive microenvironment and therapeutic vulnerabilities in advanced salivary gland cancerNature communications · 2025
Summary (written by the submitters)
Salivary gland cancers are rare, diverse malignancies characterized by poor response to immunotherapy. The tumor immune environment in these cancers remains poorly understood. To address this, we perform an integrative analysis of the tumor immune microenvironment in a large cohort of advanced salivary gland cancer samples. Most tumors exhibit low immune activity with limited immune cell infiltration.
Read the full summary ↓
Inflammation is linked to higher tumor mutational burden in non-adenoid cystic carcinoma histologies. Subtype specific expression of immune checkpoints is identified with prominent expression of VTCN1 in luminal-like cells within adenoid cystic carcinoma. Macrophages with immunosuppressive properties dominate the immune microenvironment across subtypes. Responses to immunotherapy are limited and associated with a higher ratio of T-cells relative to macrophages in individual cases, warranting further investigation. Here, we show an immunosuppressive environment in salivary gland cancers and identify subtype-specific immune vulnerabilities that could inform tailored therapeutic strategies.
Published in
Zuljan E, von der Emde B, Piwonski I et al.
· Nature communications 2025
· PMID 40506428
· doi:10.1038/s41467-025-60421-0
This dataset
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.
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 GSE294016_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1247796. Searching any of these in the dataset finder brings you back here.
Study design
93 × bulkrna seq of tumor biopsy, patient P
Supports a between-group comparison across 93 samples.
How we read this: 1 replicated groups read from 95 sample titles; they account for 93 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
- GSM8896543 bulkrna seq of tumor biopsy, patient P-1 bulkrna seq of tumor bi…
- GSM8896544 bulkrna seq of tumor biopsy, patient P-3 bulkrna seq of tumor bi…
- GSM8896545 bulkrna seq of tumor biopsy, patient P-4 bulkrna seq of tumor bi…
- GSM8896546 bulkrna seq of tumor biopsy, patient P-5 bulkrna seq of tumor bi…
- GSM8896547 bulkrna seq of tumor biopsy, patient P-6 bulkrna seq of tumor bi…
- GSM8896548 bulkrna seq of tumor biopsy, patient P-7 bulkrna seq of tumor bi…
- GSM8896549 bulkrna seq of tumor biopsy, patient P-8 bulkrna seq of tumor bi…
- GSM8896550 bulkrna seq of tumor biopsy, patient P-9 bulkrna seq of tumor bi…
- GSM8896551 bulkrna seq of tumor biopsy, patient P-10 bulkrna seq of tumor bi…
- GSM8896552 bulkrna seq of tumor biopsy, patient P-11 bulkrna seq of tumor bi…
- GSM8896553 bulkrna seq of tumor biopsy, patient P-12 bulkrna seq of tumor bi…
- GSM8896554 bulkrna seq of tumor biopsy, patient P-13 bulkrna seq of tumor bi…
- GSM8896555 bulkrna seq of tumor biopsy, patient P-14 bulkrna seq of tumor bi…
- GSM8896556 bulkrna seq of tumor biopsy, patient P-15 bulkrna seq of tumor bi…
- GSM8896557 bulkrna seq of tumor biopsy, patient P-16 bulkrna seq of tumor bi…
- GSM8896558 bulkrna seq of tumor biopsy, patient P-18 bulkrna seq of tumor bi…
- GSM8896559 bulkrna seq of tumor biopsy, patient P-19 bulkrna seq of tumor bi…
- GSM8896560 bulkrna seq of tumor biopsy, patient P-20 bulkrna seq of tumor bi…
- GSM8896561 bulkrna seq of tumor biopsy, patient P-22 bulkrna seq of tumor bi…
- GSM8896562 bulkrna seq of tumor biopsy, patient P-23 bulkrna seq of tumor bi…
- GSM8896563 bulkrna seq of tumor biopsy, patient P-24 bulkrna seq of tumor bi…
- GSM8896564 bulkrna seq of tumor biopsy, patient P-26 bulkrna seq of tumor bi…
- GSM8896565 bulkrna seq of tumor biopsy, patient P-27 bulkrna seq of tumor bi…
- GSM8896566 bulkrna seq of tumor biopsy, patient P-28 bulkrna seq of tumor bi…
- GSM8896567 bulkrna seq of tumor biopsy, patient P-29 bulkrna seq of tumor bi…
- GSM8896568 bulkrna seq of tumor biopsy, patient P-30 bulkrna seq of tumor bi…
- GSM8896569 bulkrna seq of tumor biopsy, patient P-32 bulkrna seq of tumor bi…
- GSM8896570 bulkrna seq of tumor biopsy, patient P-33 bulkrna seq of tumor bi…
- GSM8896571 bulkrna seq of tumor biopsy, patient P-34 bulkrna seq of tumor bi…
- GSM8896572 bulkrna seq of tumor biopsy, patient P-35 bulkrna seq of tumor bi…
- GSM8896573 bulkrna seq of tumor biopsy, patient P-36 bulkrna seq of tumor bi…
- GSM8896574 bulkrna seq of tumor biopsy, patient P-37 bulkrna seq of tumor bi…
- GSM8896575 bulkrna seq of tumor biopsy, patient P-38 bulkrna seq of tumor bi…
- GSM8896576 bulkrna seq of tumor biopsy, patient P-40 bulkrna seq of tumor bi…
- GSM8896577 bulkrna seq of tumor biopsy, patient P-41 bulkrna seq of tumor bi…
- GSM8896578 bulkrna seq of tumor biopsy, patient P-42 bulkrna seq of tumor bi…
- GSM8896579 bulkrna seq of tumor biopsy, patient P-43 bulkrna seq of tumor bi…
- GSM8896580 bulkrna seq of tumor biopsy, patient P-44 bulkrna seq of tumor bi…
- GSM8896581 bulkrna seq of tumor biopsy, patient P-45 bulkrna seq of tumor bi…
- GSM8896582 bulkrna seq of tumor biopsy, patient P-46 bulkrna seq of tumor bi…
+ 55 more — browse all 95 samples with per-sample file links →
Datasets on a similar topic
- GSE294017 A macrophage-predominant, immunosuppressive immune microenvironment and subtype-specific therapeutic vulnerabilities in advanced salivary gland cancer [Single nuclei RNAseq] 16 samples shares macrophage-predominant, immunosuppressive, microenvironment, subtype-specific, vulnerabilities, therapeutic, advanced, salivary
- GSE309595 Longitudinal Analysis of Multiple Myeloma: Therapeutic Response and Immune Microenvironment Dynamics in the Context of Tumor Heterogeneity [scRNA-seq] 270 samples shares microenvironment, therapeutic
- GSE263733 Single-cell transcriptome analysis reveals subtype-specific clonal evolution and microenvironmental changes in liver metastasis of pancreatic adenocarcinoma and their clinical implications 218 samples shares microenvironment, subtype-specific
- GSE269629 Metabolic programs drive function of therapeutic natural killer (NK) cells in low oxygen tumor microenvironments 63 samples shares microenvironment, therapeutic
- GSE290805 Meningioma microenvironment harbors a rich immune landscape with therapeutic implications (Bulk RNA-seq part) 47 samples shares microenvironment, therapeutic
- GSE148071 Comprehensive Profiling of Cancer Cells and Their Microenvironment in Advanced NSCLC 42 samples shares microenvironment, advanced
- GSE311200 Comprehensive analysis of the correlation between circulating biomarkers and tumor-immune microenvironment in advanced or recurrence non-small cell lung cancer in various treatment options, i.e., immunotherapy, EGFR TKI, and chemotherapy 41 samples shares microenvironment, advanced
- GSE198315 Multiregional single-cell profiling reveals extensive field cancerization and an immunosuppressive microenvironment in oral squamous cell carcinoma 36 samples shares immunosuppressive, microenvironment
Share this dataset
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.