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Series GSE161529 Query DataSets for GSE161529
Status Public on Mar 19, 2021
Title scRNA-seq profiling of breast cancer tumors, BRCA1 mutant pre-neoplastic mammary gland cells and normal mammary gland cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary This study presents a single cell transcriptome map of nearly 430,000 cells encompassing normal breast at different hormonal stages, preneoplastic BRCA1+/- tissue, the major clinical subtypes of breast cancer, and matching pairs of tumors and involved axillary lymph nodes. Comparison of normal tissue specimens according to menopausal status primarily revealed changes in the stroma. Although there were modest changes in the microenvironment of preneoplastic BRCA1+/- versus normal tissue, a profound increase in infiltrating immune cells and a concomitant decrease in fibroblasts accompanied the transition to neoplasia. Single cell profiling of 32 tumors representing treatment-naive ER+, HER2+, triple negative (TN) breast cancers revealed equivalent diversity between tumor cells across the subtypes, each comprising a broad cluster and a prominent subset of cycling cells. In the immune landscape of tumors, highly proliferative T cells characterize TN and HER2+ tumors, whereas cycling tumor-associated macrophages featured in ER+ tumors. Copy number variant and scRNA-seq analysis of paired ER+ tumors and lymph node (LN) samples revealed either collective migration of primary tumor cells into LNs or seeding by genetically distinct clones. This large-scale integration of patient samples provides a high resolution map of cell diversity for normal and cancerous human breast.
Overall design The data provides 69 scRNA-seq profiles using the 10X Genomics Chromium platform, comprising a total of 421,761 cells from 52 patients. This includes profiles of 4 TNBCs, 4 BRCA1 TNBCs, 6 HER+ tumors, 19 ER+ tumors and 6 lymph-node metastases of ER+ tumors. It also includes profiles of total mammary gland cells from 13 normal patients without breast cancer, of epithelial mammary gland cells from 11 normal patients, and of total mammary gland cells from 4 preneoplastic patients with BRCA1 mutations.

Detailed cell annotation and downstream Seurat analysis objects are available from Chen et al (Scientific Data, 2022, ).

Note from submitter: we are unable to upload the raw data files because of privacy issues with human samples.
Contributor(s) Smyth GK, Chen Y, Pal B, Visvader JE
Citation(s) 33950524, 35322042
Submission date Nov 16, 2020
Last update date Jan 16, 2023
Contact name Gordon K Smyth
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (69)
GSM4909253 Normal Total cells from Patient 0092
GSM4909254 Normal Total cells from Patient 0019
GSM4909255 Normal Epithelial cells from Patient 0280
BioProject PRJNA678650

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE161529_RAW.tar 2.2 Gb (http)(custom) TAR (of MTX, TSV)
GSE161529_features.tsv.gz 264.0 Kb (ftp)(http) TSV
Processed data provided as supplementary file
Raw data not provided for this record

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