GEO series
Critical role for a high-plasticity cell state in lung cancer
GSE277777
Mus musculus (mouse)
RNA-seq (gene expression)
32 samples
Submitted 2025/11/25
Platform GPL34328Platform GPL24247
At a glance
RNA-seq (gene expression) · mouse · 32 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
- Mus musculus (mouse)
- Samples
- 32 samples: 31 distinct titles, 1 of them repeatedGroups 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
- Critical role for a high-plasticity cell state in lung cancerNature · 2026
Summary (written by the submitters)
Plasticity—the ability of cells to undergo phenotypic transitions—drives cancer progression and therapy resistance. Recent studies have suggested that plasticity in solid tumors is concentrated in a minority subset of cancer cells, yet functional studies interrogating this high plasticity cell state (HPCS) in situ are lacking. Here, we develop mouse models enabling detection, longitudinal lineage tracing, and ablation of the HPCS in autochthonous lung tumors in vivo.
Read the full summary ↓
Lineage tracing reveals that the HPCS cells possess high capacity for cell state transitions, giving rise to both early neoplastic (differentiated) and progressed lung cancer cell states in situ. Longitudinal lineage tracing using secreted luciferases reveals HPCS-derived cells harbor high capacity for growth when compared to bulk cancer cells or another cancer cell state with features of differentiated lung epithelium. HPCS ablation in early neoplasias abrogates benign-to-malignant transition, whereas ablation in established tumors by suicide gene or CAR T cells robustly reduces tumor burden. We further demonstrate that the HPCS gives rise to therapy-resistant cell states, whereas HPCS ablation suppresses resistance to chemotherapy and oncoprotein-targeted therapy. Interestingly, an HPCS-like state is ubiquitous in regenerating epithelia and in carcinomas of multiple other tissues, revealing a convergence of plasticity programs. Our work establishes the HPCS as a critical hub enabling reciprocal transitions between cancer cell states. Targeting the HPCS in lung cancer and in other carcinomas may suppress cancer progression and eradicate treatment resistance.
Published in
Chan JE, Pan CH, Rub J et al.
· Nature 2026
· PMID 41565826
· doi:10.1038/s41586-025-09985-x
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 GSE277777_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 PRJNA1164164 and SRA study SRP534187. Searching any of these in the dataset finder brings you back here.
Study design
31 distinct titles, 1 of them repeated
KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumors trea… ×2
How we read this: Read from 32 sample titles: 31 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
- GSM8529524 KPfrt Slc4a11-MCD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI after 2 weeks of tracing, GEX
- GSM8529525 KPfrt Slc4a11-MCD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI after 2 weeks of tracing, HTO
- GSM8529526 KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumor cells harvested 14 weeks PTI after 2 weeks of tracing, GEX
- GSM8529527 KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumor cells harvested 14 weeks PTI after 2 weeks of tracing, HTO
- GSM8529528 KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumor cells harvested 8 weeks PTI after 2 weeks of tracing, GEX
- GSM8529529 KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumor cells harvested 8 weeks PTI after 2 weeks of tracing, HTO
- GSM8529530 KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumor cells harvested 14 weeks PTI after 2 weeks of tracing, replicates, GEX
- GSM8529531 KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumor cells harvested 14 weeks PTI after 2 weeks of tracing, replicates, HTO
- GSM8529532 KPfrt Slc4a11-MCD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI after 1 week of ablation, GEX
- GSM8529533 KPfrt Slc4a11-MCD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI after 1 week of ablation, HTO
- GSM8529534 KPfrt Slc4a11-MCD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI after 1 week of ablation, replicate, GEX
- GSM8529535 KPfrt Slc4a11-MCD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI after 1 week of ablation, replicate, HTO
- GSM8529536 KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumors treated and harvested at 17 weeks PTI after 3 weeks of tracing, GEX, rep1
- GSM8529537 KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumors treated and harvested at 17 weeks PTI after 3 weeks of tracing, HTO, rep1
- GSM8529538 KPfrt Hopx-MACD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI, GEX
- GSM8529539 KPfrt Hopx-MACD/+ Hipp11-GGCB/+ tumor cells harvested 16 weeks PTI, HTO
- GSM8529540 KP Rosa26-tdTomato/+ tumors harvested at 14 weeks post tumor initiation, GEX
- GSM8529541 KP Rosa26-tdTomato/+ tumors harvested at 14 weeks post tumor initiation, HTO
- GSM8529542 KP Rosa26-tdTomato/+ tumors harvested at 14 weeks post tumor initiation, replicate, GEX
- GSM8529543 KP Rosa26-tdTomato/+ tumors harvested at 14 weeks post tumor initiation, repilcate, HTO
- GSM9193561 KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumors treated and harvested at 17 weeks PTI after 3 weeks of tracing, GEX rep2
- GSM9193562 KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumors treated and harvested at 17 weeks PTI after 3 weeks of tracing, HTO, rep2
- GSM9193563 KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumors treated with Tamoxifen and harvested at 12 weeks PTI after 3d tracing, GEX
- GSM9193564 KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumors treated with Tamoxifen and harvested at 12 weeks PTI after 3d tracing, HTO
- GSM9193565 KPfrt (Slc4a11-MCD/+ or Hopx-MACD/+) Rosa26-mTmG/+ tumors harvested at (6 or 12) weeks PTI, 3d tracing, GEX
- GSM9193566 KPfrt (Slc4a11-MCD/+ or Hopx-MACD/+) Rosa26-mTmG/+ tumors harvested at (6 or 12) weeks PTI, 3d tracing, HTO
- GSM9193567 KPfrt Hopx-MACD/+ Rosa26-mTmG/+ tumors; harvested at 14 weeks PTI after 14 days of tracing, GEX
- GSM9193568 KPfrt Hopx-MACD/+ Rosa26-mTmG/+ tumors; harvested at 14 weeks PTI after 14 days of tracing, HTO
- GSM9193569 KPfrt Slc4a11-MCD/+ iRFP670-Gluc cell line; tail vein injected, harvested 5 weeks post transplant (1 week DT), GEX
- GSM9193570 KPfrt Slc4a11-MCD/+ iRFP670-Gluc cell line; tail vein injected, harvested 5 weeks post transplant (1 week Saline), GEX
- GSM9315338 KPfrt Hopx-MACD/+ BG/+ cell line; tail vein injected, harvested 5 weeks post transplant (1 week DT), GEX
- GSM9315339 KPfrt Hopx-MACD/+ BG/+ cell line; tail vein injected, harvested 5 weeks post transplant (1 week Saline), GEX
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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.