GEO series

MiT Fusions, TSC1–TSC2 Divergence, and Stem-like Programs Reveal Distinct Origins and Vulnerabilities in PEComa [RNA-seq]

GSE328026 Homo sapiens (human) Single-nucleus RNA-seq 69 samples Submitted 2026/04/18 Platform GPL30173Platform GPL20301

At a glance

Single-nucleus RNA-seq · human · 69 samples

What it is: Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). 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: 69 samples: 69 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: MiT fusions, TSC1-TSC2 divergence, and stem-like programs reveal distinct origins and vulnerabilities in PEComaNature communications · 2026

Summary (written by the submitters)

Perivascular epithelioid cell neoplasms (PEComas) are ultra-rare mesenchymal tumors lacking a molecular classification to guide therapy. Here we perform comprehensive multi-omic profiling of an unselected PEComa cohort. We identify frequent MITF rearrangements involving actin gene partners (ACTA2, ACTG1 and ACTB). Anatomical stratification reveals cyclin-dependent kinase module mutations in gynecologic tumors, whereas soft tissue, gastrointestinal, and pelvic tumors lacked mTOR pathway alterations but are enriched for TFE3/MITF rearrangements.

Read the full summary ↓

Transcriptomic analysis defines four subtypes with distinct lineage programs—melanocytic, mesenchymal, or adipogenic—as well as unique mutational patterns and clinical behaviors. Notably, an aggressive stem-like subtype enriched for TP53/RB1 mutations exhibits high proliferation, activation of embryonic and Hedgehog signaling, immune infiltration, and resistance to mTOR inhibitors, but potential responsiveness to immunotherapy. Single-nucleus RNA sequencing reveals intra-tumoral heterogeneity within this subtype, including divergent inflammatory states. Together, these findings establish a molecular classification framework and identify actionable vulnerabilities in PEComa.

Published in

MiT fusions, TSC1-TSC2 divergence, and stem-like programs reveal distinct origins and vulnerabilities in PEComa

Gantzer J, Lu X, Charon-Barra C et al. · Nature communications 2026 · PMID 42331846 · doi:10.1038/s41467-026-74545-4

This dataset

Open GSE328026 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 GSE328026_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 PRJNA1453532. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42331846) ↗

Study design

69 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 69 sample titles: 69 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

GSM9670487 JNGR15, PEComa tumor, bulk RNA-seq, pair-end
GSM9670488 JNGR16, PEComa tumor, bulk RNA-seq, pair-end
GSM9670489 JNGR17, PEComa tumor, bulk RNA-seq, pair-end
GSM9670490 JNGR19, PEComa tumor, bulk RNA-seq, pair-end
GSM9670491 JNGR20, PEComa tumor, bulk RNA-seq, pair-end
GSM9670492 JNGR21, PEComa tumor, bulk RNA-seq, pair-end
GSM9670493 JNGR22, PEComa tumor, bulk RNA-seq, pair-end
GSM9670494 JNGR23, PEComa tumor, bulk RNA-seq, pair-end
GSM9670495 JNGR24, PEComa tumor, bulk RNA-seq, pair-end
GSM9670496 JNGR95, PEComa tumor, bulk RNA-seq, pair-end
GSM9670497 JNGR96, PEComa tumor, bulk RNA-seq, pair-end
GSM9670498 JNGR97, PEComa tumor, bulk RNA-seq, pair-end
GSM9670499 JNGR100, PEComa tumor, bulk RNA-seq, pair-end
GSM9670500 JNGR99, PEComa tumor, bulk RNA-seq, pair-end
GSM9670501 JNGR101, PEComa tumor, bulk RNA-seq, pair-end
GSM9670502 JNGR102, PEComa tumor, bulk RNA-seq, pair-end
GSM9670503 JNGR103, PEComa tumor, bulk RNA-seq, pair-end
GSM9670504 JNGR107, PEComa tumor, bulk RNA-seq, pair-end
GSM9670505 JNGR108, PEComa tumor, bulk RNA-seq, pair-end
GSM9670506 JNGR109, PEComa tumor, bulk RNA-seq, pair-end
GSM9670507 JNGR113, PEComa tumor, bulk RNA-seq, pair-end
GSM9670508 JNGR115, PEComa tumor, bulk RNA-seq, pair-end
GSM9670509 JNGR116, PEComa tumor, bulk RNA-seq, pair-end
GSM9670510 JNGR117, PEComa tumor, bulk RNA-seq, pair-end
GSM9670511 JNGR118, PEComa tumor, bulk RNA-seq, pair-end
GSM9670512 JNGR119, PEComa tumor, bulk RNA-seq, pair-end
GSM9670513 JNGR120, PEComa tumor, bulk RNA-seq, pair-end
GSM9670514 JNGR122, PEComa tumor, bulk RNA-seq, pair-end
GSM9670515 JNGR123, PEComa tumor, bulk RNA-seq, pair-end
GSM9670516 JNGR124, PEComa tumor, bulk RNA-seq, pair-end
GSM9670517 JNGR125, PEComa tumor, bulk RNA-seq, pair-end
GSM9670518 JNGR126, PEComa tumor, bulk RNA-seq, pair-end
GSM9670519 JNGR127, PEComa tumor, bulk RNA-seq, pair-end
GSM9670520 JNGR128, PEComa tumor, bulk RNA-seq, pair-end
GSM9670521 JNGR129, PEComa tumor, bulk RNA-seq, pair-end
GSM9670522 JNGR131, PEComa tumor, bulk RNA-seq, pair-end
GSM9670523 JNGR132, PEComa tumor, bulk RNA-seq, pair-end
GSM9670524 JNGR133, PEComa tumor, bulk RNA-seq, pair-end
GSM9670525 JNGR135, PEComa tumor, bulk RNA-seq, pair-end
GSM9670526 JNGR136, PEComa tumor, bulk RNA-seq, pair-end

+ 29 more — browse all 69 samples with per-sample file links →

Datasets on a similar topic

GSE327937 MiT Fusions, TSC1–TSC2 Divergence, and Stem-like Programs Reveal Distinct Origins and Vulnerabilities in PEComa [scRNA-seq] 5 samples shares tsc1, tsc2, vulnerabilities, divergence, stem-like, programs, distinct, fusions
GSE266517 Metabolic reprogramming driven by TFE3 fusions unveils novel vulnerabilities in translocation renal cell carcinoma [RNA-Seq] 24 samples shares vulnerabilities, fusions
GSE248855 Integrative multi-omics analyses identify molecular subtypes of head and neck squamous cell carcinoma with distinct therapeutic vulnerabilities 13 samples shares vulnerabilities, distinct
GSE269942 YAP1 status defines two intrinsic subtypes of LCNEC with distinct molecular features and therapeutic vulnerabilities 12 samples shares vulnerabilities, distinct
GSE294002 Transcriptomic analyses of ovarian clear cell carcinoma sphe-roids reveal distinct proliferative phenotypes and therapeutic vulnerabilities 8 samples shares vulnerabilities, distinct
GSE212977 EWS-WT1 fusion isoforms establish oncogenic programs and therapeutic vulnerabilities in Desmoplastic Small Round Cell Tumors [ChIP-seq] 87 samples shares vulnerabilities, programs
GSE266530 Metabolic reprogramming driven by TFE3 fusions unveils novel vulnerabilities in translocation renal cell carcinoma [ChIP-Seq] 32 samples shares vulnerabilities, fusions
GSE248842 EWS-WT1 fusion isoforms establish oncogenic programs and therapeutic vulnerabilities in Desmoplastic Small Round Cell Tumors. 12 samples shares vulnerabilities, programs

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