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From subcutaneous to orthotopic: Bridging the gap to human disease in lung cancer research [mouse]

GSE301349 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/12/17 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 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
Mus musculus (mouse)
Samples
12 samples: 3 × LLC cells, parental, vs 3 × LLC cells, circulating tumor cells, vs 3 × LLC cells, bone metastasis, vs 3 × LLC cells, brain metastasis,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
Establishment and characterization of an orthotopic implanted lung cancer model to mimic human tumor structure, microenvironment, and metastatic spreadTranslational lung cancer research · 2025
Summary (written by the submitters)
Preclinical lung cancer models frequently fail to predict clinical outcomes due to their limited ability to replicate the complex tumor microenvironment and metastatic processes seen in patients. In this study, we establish and characterize a clinically relevant orthotopic lung cancer model in mice, offering a substantial advancement over conventional subcutaneous models.
Read the full summary ↓
Using thoracotomy-based injection of luciferase-expressing lung adenocarcinoma cells, we consistently generate single, well-defined nodules within the lung parenchyma that closely mimic human primary tumors. Longitudinal monitoring with bioluminescence imaging and computed tomography enables accurate spatial and volumetric assessment of tumor progression, with tumor size correlating with the initial cell dose. Comparative analyses demonstrate that orthotopic tumors exhibit enhanced vascularization, proliferation, and reduced hypoxic and stress markers (HIF-1α, γH2AX, p16, p21), alongside elevated Cyclin D1 expression-features reflecting a more physiologically relevant tumor environment. Importantly, orthotopic tumors display an enriched and organized immune infiltration, including enriched CD4⁺ and CD8⁺ T cells and dendritic cells, forming immune niches not present in subcutaneous models. To model metastasis, we isolate and culture circulating tumor cells (CTCs) from orthotopic tumor-bearing mice. Intracardiac injection of these CTCs leads to organ-specific metastases (e.g., liver, brain, bone), recapitulating clinical dissemination patterns. Transcriptomic and proteomic profiling of metastatic sublines reveals both conserved pro-metastatic programs-including chemokine signaling, EMT, and immune evasion-and niche-specific adaptations, particularly in bone metastases. This orthotopic model offers enhanced translational relevance for evaluating therapies and dissecting metastatic progression in lung cancer.
Published in
Establishment and characterization of an orthotopic implanted lung cancer model to mimic human tumor structure, microenvironment, and metastatic spread
Picabea B, Orive D, Rodríguez C et al. · Translational lung cancer research 2025 · PMID 41367565 · doi:10.21037/tlcr-2025-871
This dataset
Open GSE301349 in finder → Find more mouse 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 GSE301349_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 PRJNA1284837 and SRA study SRP596438. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41367565) ↗
Study design
3 × LLC cells, parental, vs 3 × LLC cells, circulating tumor cells, vs 3 × LLC cells, bone metastasis, vs 3 × LLC cells, brain metastasis,

Supports a case/control comparison: 9 samples read as cases, 3 as controls.

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
Datasets on a similar topic

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