GEO series

Distinct Characteristics of Brain Metastasis in Lung Adenocarcinoma: Development of High-Confidence Cell Lines

GSE297016 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/05/30 Platform GPL29480

At a glance

RNA-seq (gene expression) · human · 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: Homo sapiens (human)
Topic: Lung cancerThis series is part of our curated briefing on it.
Samples: 12 samples: 3 × Primary, repeat vs 3 × BM1, repeat vs 3 × BM2, repeat vs 3 × BM3, repeatGroups 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: Distinct characteristics of brain metastasis in lung adenocarcinoma: development of high-confidence cell linesActa neuropathologica communications · 2025

Summary (written by the submitters)

Lung cancer is a leading cause of cancer-related deaths worldwide, with brain metastasis occurring in approximately 30-55% of patients, particularly in lung adenocarcinoma. Due to the challenges in obtaining genuine brain metastasis tumor cells, researchers commonly use nude mouse models to establish brain metastasis cell lines, though traditional methods have limitations such as high costs, lengthy timeframes, and the need for specialized imaging equipment.

Read the full summary ↓

To address these issues, we developed an improved approach by performing low cell number circulating intracranial injections (500-4000 cells) in nude mice, successfully establishing the H1975-BM1, BM2, and BM3 cell lines. Through RNA sequencing and bioinformatics analyses, we identified transcriptomic differences among these cell lines, revealing that H1975-BM1 cells primarily exhibit stem cell function and migration characteristics, while H1975-BM3 cells display enhanced chemotaxis, cell adhesion, and cytokine secretion associated with interactions. Experimental validation, including Transwell assays, CCK8, cell adhesion assays, and subcutaneous tumor implantation in nude mice, further confirmed these findings, with H1975-BM3 forming larger tumors and a more pronounced secretion cystic cavity. In conclusion, our improved methodology successfully established high-confidence brain metastasis lung adenocarcinoma cell lines, elucidating distinct transcriptomic and functional characteristics at different stages of brain metastasis progression.

Published in

Distinct characteristics of brain metastasis in lung adenocarcinoma: development of high-confidence cell lines

He J, Tanei ZI, Wu DS et al. · Acta neuropathologica communications 2025 · PMID 40399969 · doi:10.1186/s40478-025-02038-4

This dataset

Open GSE297016 in finder → Find more human RNA-seq datasets → Lung cancer landscape →

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 GSE297016_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 PRJNA1262403 and SRA study SRP585100. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40399969) ↗

Study design

3 × Primary, repeat vs 3 × BM1, repeat vs 3 × BM2, repeat vs 3 × BM3, repeat

Supports a between-group comparison across 12 samples.

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

GSM8981641 Primary, repeat 1 Primary, repeat
GSM8981642 Primary, repeat 2 Primary, repeat
GSM8981643 Primary, repeat 3 Primary, repeat
GSM8981644 BM1, repeat 1 BM1, repeat
GSM8981645 BM1, repeat 2 BM1, repeat
GSM8981646 BM1, repeat 3 BM1, repeat
GSM8981647 BM2, repeat 1 BM2, repeat
GSM8981648 BM2, repeat 2 BM2, repeat
GSM8981649 BM2, repeat 3 BM2, repeat
GSM8981650 BM3, repeat 1 BM3, repeat
GSM8981651 BM3, repeat 2 BM3, repeat
GSM8981652 BM3, repeat 3 BM3, repeat

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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.