GEO series
Archetype analysis of lung adenocarcinoma premalignancy links heterogeneity in premalignant lesions to diverging features of invasive disease
GSE319666
Homo sapiens (human)
RNA-seq (gene expression)
177 samples
Submitted 2026/04/24
Platform GPL30173Platform GPL18573
At a glance
RNA-seq (gene expression) · human · 177 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
- Lung cancerThis series is part of our curated briefing on it.
- Samples
- 177 samples: 177 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
- Archetype Analysis of Lung Adenocarcinoma Premalignancy Links Heterogeneity in Premalignant Lesions to Diverging Features of Invasive DiseaseMolecular cancer research : MCR · 2026
Summary (written by the submitters)
Lung adenocarcinoma (LUAD), the most common form of lung cancer, is a heterogeneous disease with highly variable histopathologic features and clinical outcomes. LUAD premalignant lesions (PMLs) are localized proliferative lesions of atypical pneumocytes that proliferate along the alveolar walls. In this study, we characterized the molecular heterogeneity across PMLs, regardless of histologic designation, and identified four unique groups or “archetypes” of PMLs using bulk RNA and exome sequencing data from laser captured microdissected PMLs, normal, and tumor tissue from LUAD resection cases.
Read the full summary ↓
The archetypes were defined based on expression of recurrent gene co-expression modules discovered using the LUAD PMLs we profiled and three publicly available datasets. One PML archetype, termed “proliferation”, was associated with increased expression of genes involved in cell proliferation, a pro-tumor immune environment, and enrichment for EGFR driver mutations. Another archetype, termed “normal-like”, was associated with similar features to normal tissue, an anti-tumor immune response, and lacked enrichment for driver mutations compared to other archetypes. We projected the PML archetypes into independent gene expression datasets profiling LUAD and found that tumors closest to the proliferation archetype were enriched for multiple features of aggressive LUAD, including high tumor grade and lymph node invasion, and had significantly lower disease-free survival. Proliferation archetype PMLs may represent a subset of lesions with more aggressive features that could improve patient stratification and suggest novel targets for lung cancer interception.
Published in
Anderson KE, Tran LM, Krysan K et al.
· Molecular cancer research : MCR 2026
· PMID 42089783
· doi:10.1158/1541-7786.MCR-25-1093
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 GSE319666_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 PRJNA1424925. Searching any of these in the dataset finder brings you back here.
Study design
177 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 177 sample titles: 177 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
- GSM9523179 RNA from patient HTA2_20457, derived from Normal #2 [HTA2_20457_6000103]
- GSM9523180 RNA from patient HTA2_20457, derived from AAH #2 [HTA2_20457_6000106]
- GSM9523181 RNA from patient HTA2_20457, derived from Normal #3 [HTA2_20457_6000107]
- GSM9523182 RNA from patient HTA2_21522, derived from LUAD (Stage 1B) [HTA2_21522_6000101]
- GSM9523183 RNA from patient HTA2_21522, derived from Normal [HTA2_21522_6000103]
- GSM9523184 RNA from patient HTA2_21522, derived from AAH [HTA2_21522_6000104]
- GSM9523185 RNA from patient HTA2_21522, derived from Normal [HTA2_21522_6000105]
- GSM9523186 RNA from patient HTA2_23998, derived from Normal [HTA2_23998_6000104]
- GSM9523187 RNA from patient HTA2_23998, derived from Normal [HTA2_23998_6000106]
- GSM9523188 RNA from patient HTA2_24568, derived from AAH [HTA2_24568_6000104]
- GSM9523189 RNA from patient HTA2_24568, derived from Normal #2 [HTA2_24568_6000105]
- GSM9523190 RNA from patient HTA2_24648, derived from Normal #2 [HTA2_24648_6000103]
- GSM9523191 RNA from patient HTA2_24648, derived from AAH [HTA2_24648_6000104]
- GSM9523192 RNA from patient HTA2_24648, derived from Normal #3 [HTA2_24648_6000105]
- GSM9523193 RNA from patient HTA2_24958, derived from Normal #1 [HTA2_24958_6000103]
- GSM9523194 RNA from patient HTA2_24958, derived from AAH [HTA2_24958_6000104]
- GSM9523195 RNA from patient HTA2_24958, derived from Normal #2 [HTA2_24958_6000105]
- GSM9523196 RNA from patient HTA2_26866, derived from LUAD Region 1 (Stage 1B) [HTA2_26866_6000101]
- GSM9523197 RNA from patient HTA2_26866, derived from LUAD Region 2 (Stage 1B) [HTA2_26866_6000103]
- GSM9523198 RNA from patient HTA2_26866, derived from AAH #1 [HTA2_26866_6000106]
- GSM9523199 RNA from patient HTA2_26866, derived from AAH #2 [HTA2_26866_6000108]
- GSM9523200 RNA from patient HTA2_26866, derived from Normal #2 [HTA2_26866_6000109]
- GSM9523201 RNA from patient HTA2_26866, derived from AAH #3 [HTA2_26866_6000110]
- GSM9523202 RNA from patient HTA2_27097, derived from LUAD (Stage 1A) [HTA2_27097_6000101]
- GSM9523203 RNA from patient HTA2_27097, derived from Normal #2 [HTA2_27097_6000103]
- GSM9523204 RNA from patient HTA2_27097, derived from Normal #3 [HTA2_27097_6000105]
- GSM9523205 RNA from patient HTA2_27117, derived from LUAD (Stage 1A) [HTA2_27117_6000101]
- GSM9523206 RNA from patient HTA2_27117, derived from Normal #2 [HTA2_27117_6000103]
- GSM9523207 RNA from patient HTA2_27117, derived from AAH [HTA2_27117_6000104]
- GSM9523208 RNA from patient HTA2_27117, derived from Normal #3 [HTA2_27117_6000105]
- GSM9523209 RNA from patient HTA2_90008, derived from LUAD Region 1 (Stage 1A) [HTA2_90008_6000101]
- GSM9523210 RNA from patient HTA2_90008, derived from LUAD Region 2 (Stage 1A) [HTA2_90008_6000102]
- GSM9523211 RNA from patient HTA2_90008, derived from Normal [HTA2_90008_6000103]
- GSM9523212 RNA from patient HTA2_90008, derived from LUAD Region 3 (Stage 1A) [HTA2_90008_6000104]
- GSM9523213 RNA from patient HTA2_90009, derived from LUAD Region 1 (Stage Unknown) [HTA2_90009_6000101]
- GSM9523214 RNA from patient HTA2_90009, derived from Normal [HTA2_90009_6000102]
- GSM9523215 RNA from patient HTA2_90009, derived from LUAD Region 2 (Stage Unknown) [HTA2_90009_6000103]
- GSM9523216 RNA from patient HTA2_90009, derived from LUAD Region 3 (Stage Unknown) [HTA2_90009_6000107]
- GSM9523217 RNA from patient HTA2_90009, derived from Normal [HTA2_90009_6000108]
- GSM9523218 RNA from patient HTA2_90010, derived from LUAD Region 1 (Stage 1B) [HTA2_90010_6000104]
+ 137 more — browse all 177 samples with per-sample file links →
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