GEO series

A single-cell map of intratumoral heterogeneity during combination treatment of anti-PD1 and chemotherapy in triple-negative breast cancer

GSE302453 Homo sapiens (human) Single-cell RNA-seq 2 samples Submitted 2025/12/31 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 2 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Topic: Breast cancerThis series is part of our curated briefing on it.
Samples: 2 samples
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.

Summary (written by the submitters)

Triple-negative breast cancer (TNBC) is the most malignant subtype of breast cancer (BC), which exhibited a poor prognosis due to the highly tumor microenvironmental heterogeneity and specific mutations. Recent studies have investigated the different celltypes in TNBC microenvironment, however, the effects of immunotherapy and chemotherapy combination therapy on TNBC are largely unknown.

Read the full summary ↓

Here we explored the changes of TNBC microenvironment upon immunotherapy and chemotherapy combination therapy by scRNA-seq. We found that the insensitive (PCPAi) patient exhibited high CNV score in tumor cells, lower cytotoxicity in CD8+ T cells, higher quiescence and exhaustion characteristics CD4+ T cells, compared to sensitive (PCPAs) patient. Meanwhile, the PCPAi patient showed more complex fibroblasts and tumor-associated macrophages heterogeneity. We also found the key ligand-receptor based cellular interactions, such as SPP1 and TGFβ. These results provide a research basis for us to understand the microenvironment changes and therapeutic efficacy of triple negative breast cancer after chemotherapy combined with immunotherapy.

This dataset

Open GSE302453 in finder → Find more human RNA-seq datasets → Breast 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 GSE302453_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 PRJNA1290950 and SRA study SRP601150. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 2 more — browse all 2 samples with per-sample file links →

More Breast cancer datasets

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GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing
GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing
GSE243013 A single-cell atlas of immune heterogeneity in anti-PD1-treated non-small cell lung cancer 243 samples shares anti-pd1, heterogeneity, single-cell
GSE328275 Single-cell RNA sequencing of CD45+ immune cells across primary tumor, sentinel tumor-draining lymph node, and axillary lymph node in treatment-naive triple-negative breast cancer 28 samples shares triple-negative, single-cell, treatment
GSE243375 HER2 heterogeneity and treatment response-associated profiles in HER2-positive breast cancer in the NCT02326974 clinical trial 287 samples shares heterogeneity, treatment

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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.