GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Series GSE137818

Query DataSets for GSE137818

Status

Public on Aug 27, 2020

Title

Mutations in homologous recombination genes BRCA1 and BRCA2 differentially affect the tumor microenvironment and response to checkpoint blockade immunotherapy

Organism

Experiment type

Expression profiling by high throughput sequencing

Summary

We report differential effects of mutations in genes of the homologous recombination (HR) pathway on response after ICB administration in mouse and human tumors, and show that truncating mutations in BRCA2 are associated with superior response to ICB compared to BRCA1-deficient tumors. Immunogenomic analyses demonstrated that mutations in BRCA1 and BRCA2 differentially modulate the tumor-immune microenvironment, with gene expression programs related to both adaptive and innate immune pathways enriched in BRCA2-deficient tumors. Single-cell RNA sequencing further revealed distinct T cell, NK, macrophage, and dendritic cell populations enriched in BRCA2 mutant tumors relative to BRCA1-deficient tumors.

Overall design

Bulk RNA-sequencing from immunotherapy-naïve and immunotherapy-treated mouse 4T1 parental, Brca1 mutant, and Brca2 mutant tumors. Single cell RNA-sequencing from immunotherapy-naïve 4T1 parental, Brca1 mutant, and Brca2 mutant tumors

Contributor(s)

Riaz N, Chan TA, Samstein R, Krishna C

Citation(s)

Submission date

Sep 22, 2019

Last update date

Jul 31, 2023

Contact name

Vladimir Makarov

E-mail(s)

makarov@ccf.org

Organization name

Cleveland Clinic

Department

LRI

Lab

CITI

Street address

9500 Euclid Ave

City

Cleveland

State/province

OH

ZIP/Postal code

44195

Country

USA

Platforms (2)

GPL21103	Illumina HiSeq 4000 (Mus musculus)
GPL24247	Illumina NovaSeq 6000 (Mus musculus)

Samples (40)

More...

GSM4088892	Mouse 4T1 Brca2 KO Untreated bulk RNA-seq Rep 1
GSM4088893	Mouse 4T1 Brca2 KO Untreated bulk RNA-seq Rep 2
GSM4088894	Mouse 4T1 Brca2 KO Untreated bulk RNA-seq Rep 3

GSM4088895	Mouse 4T1 Brca2 KO Untreated bulk RNA-seq Rep 4
GSM4088896	Mouse 4T1 Brca2 KO Untreated bulk RNA-seq Rep 5
GSM4088897	Mouse 4T1 Brca1 KO Untreated bulk RNA-seq Rep 1
GSM4088898	Mouse 4T1 Brca1 KO Untreated bulk RNA-seq Rep 2
GSM4088899	Mouse 4T1 Brca1 KO Untreated bulk RNA-seq Rep 3
GSM4088900	Mouse 4T1 Brca1 KO Untreated bulk RNA-seq Rep 4
GSM4088901	Mouse 4T1 Brca1 KO Untreated bulk RNA-seq Rep 5
GSM4088902	Mouse 4T1 Parental (BRCA WT) Untreated bulk RNA-seq Rep 1
GSM4088903	Mouse 4T1 Parental (BRCA WT) Untreated bulk RNA-seq Rep 2
GSM4088904	Mouse 4T1 Parental (BRCA WT) Untreated bulk RNA-seq Rep 3
GSM4088905	Mouse 4T1 Parental (BRCA WT) Untreated bulk RNA-seq Rep 4
GSM4088906	Mouse 4T1 Parental (BRCA WT) Untreated bulk RNA-seq Rep 5
GSM4088907	4T1 Cell Line Brca2 KO bulk RNA-seq Rep 1
GSM4088908	4T1 Cell Line Brca2 KO bulk RNA-seq Rep 2
GSM4088909	4T1 Cell Line Brca2 KO bulk RNA-seq Rep 3
GSM4088910	4T1 aCell Line Brca1 KO bulk RNA-seq Rep 1
GSM4088911	4T1 Cell Line Brca1 KO bulk RNA-seq Rep 2
GSM4088912	4T1 Cell Line Brca1 KO bulk RNA-seq Rep 3
GSM4088913	4T1 Cell Line Brca1 KO bulk RNA-seq Rep 4
GSM4088914	4T1 Cell Line Brca1 KO bulk RNA-seq Rep 5
GSM4088915	4T1 Cell Line Brca1 KO bulk RNA-seq Rep 6
GSM4088916	Mouse 4T1 Brca2 KO Immunotherapy-treated bulk RNA-seq Rep 1
GSM4088917	Mouse 4T1 Brca2 KO Immunotherapy-treated bulk RNA-seq Rep 2
GSM4088918	Mouse 4T1 Brca2 KO Immunotherapy-treated bulk RNA-seq Rep 3
GSM4088919	Mouse 4T1 Brca1 KO Immunotherapy-treated bulk RNA-seq Rep 1
GSM4088920	Mouse 4T1 Brca1 KO Immunotherapy-treated bulk RNA-seq Rep 2
GSM4088921	Mouse 4T1 Brca1 KO Immunotherapy-treated bulk RNA-seq Rep 3
GSM4088922	Mouse 4T1 Brca1 KO Immunotherapy-treated bulk RNA-seq Rep 4
GSM4088923	Mouse 4T1 Brca1 KO Immunotherapy-treated bulk RNA-seq Rep 5
GSM4088924	Mouse 4T1 Brca2 KO Untreated single cell RNA-seq Rep 1
GSM4088925	Mouse 4T1 Brca2 KO Untreated single cell RNA-seq Rep 2
GSM4088926	Mouse 4T1 Brca2 KO Untreated single cell RNA-seq Rep 3
GSM4088927	Mouse 4T1 Brca1 KO Untreated single cell RNA-seq Rep 1
GSM4088928	Mouse 4T1 Brca1 KO Untreated single cell RNA-seq Rep 2
GSM4088929	Mouse 4T1 Parental (BRCA WT) Untreated single cell RNA-seq Rep 1
GSM4088930	Mouse 4T1 Parental (BRCA WT) Untreated single cell RNA-seq Rep 2
GSM4088931	Mouse 4T1 Parental (BRCA WT) Untreated single cell RNA-seq Rep 3

Relations

BioProject

SRA

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE137818_Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv.gz	994.2 Kb	(ftp)(http)	CSV
GSE137818_Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv.gz	291.1 Kb	(ftp)(http)	CSV
GSE137818_Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv.gz	908.3 Kb	(ftp)(http)	CSV
GSE137818_Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv.gz	262.1 Kb	(ftp)(http)	CSV
GSE137818_Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv.gz	1.2 Mb	(ftp)(http)	CSV
GSE137818_Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv.gz	346.1 Kb	(ftp)(http)	CSV
GSE137818_Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_normcounts.csv.gz	1.2 Mb	(ftp)(http)	CSV
GSE137818_Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_rawcounts.csv.gz	358.6 Kb	(ftp)(http)	CSV
GSE137818_scRNA_logcounts.csv.gz	608.0 Mb	(ftp)(http)	CSV
SRA Run Selector
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |