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Series GSE229426 Query DataSets for GSE229426
Status Public on Aug 15, 2023
Title Combination therapies to improve the efficacy of immunotherapy in triple-negative breast cancer [ATAC-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Immune checkpoint inhibitors combined with chemotherapy represent a promising treatment option in triple-negative breast cancer (TNBC). However, response rates are still relatively low necessitating the design of novel therapeutic strategies to improve clinical outcomes. Here, we describe a triple combination of anti-PDL-1 immune checkpoint blockade, epigenetic modulation thorough BET bromodomain inhibition, and chemotherapy with paclitaxel that effectively inhibits both primary and metastatic tumor growth in two different syngeneic murine breast cancer models. Detailed cellular and molecular profiling of tumors from single and combination treatment arms revealed increased T and B cell infiltration and macrophage reprogramming from M1 to a M2 phenotype in mice treated with triple combination.
 
Overall design 5- to 6-week-old BALBc mice were injected with 200,000 EMT-6 mammary tumors cells (ATTC, CRL-2755). Both inguinal mammary fat pads were injected in each mouse. Tumor development was monitored by palpation and once tumors were palpable, usually about 5-7 days after cancer cell inoculation, treatment was initiate. JQ1 was administered as single agents or in combination at the following doses: JQ1 at 50mg/kg by daily gavage,, anti-PD-L1 antibody (clone 10F.9G2, BioXCell) and paclitaxel each at 10mg/kg by i.p. injection twice per week. Tumor volumes were measured by caliper every three days until the end of the experiment. Once control tumors reached the study endpoint, all mice were euthanized, and primary tumors and various organs were collected. Tumors were then dissociated into single cells and separated into CD45+ and CD45- cell fractions using anti-CD45 antibody coupled to Dynabeads to enrich for leukocytes and tumor cells, respectively. Cells were counted and about 50,000 cells for each fraction were frozen for bulk ATAC-seq. The remaining cells were used for RNA extraction and bulk RNA-seq.
 
Contributor(s) Alečković M, Li Z, Polyak K
Citation(s) 37676980
NIH grant(s)
Grant ID Grant title Affiliation Name
P01 CA250959 New therapeutic vulnerabilities in breast cancer DANA-FARBER CANCER INSTITUTE Kornelia Polyak
P50 CA168504 Dana-Farber/Harvard Cancer Center SPORE in Breast Cancer DANA-FARBER CANCER INSTITUTE Kornelia Polyak
R35 CA197623 Targeting intratumor heterogeneity in breast cancer DANA-FARBER CANCER INSTITUTE Kornelia Polyak
Submission date Apr 11, 2023
Last update date Nov 14, 2023
Contact name Kornelia Polyak
E-mail(s) kornelia_polyak@dfci.harvard.edu
Phone 617-632-2106
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Lab Polyak
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (12)
GSM7163182 Control_3_C9_4L
GSM7163183 Control_3_C9_4R
GSM7163184 JQ_1_C1_4R
This SubSeries is part of SuperSeries:
GSE229428 Combination therapies to improve the efficacy of immunotherapy in triple-negative breast cancer
Relations
BioProject PRJNA954409

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
GSE229426_RAW.tar 1.3 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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