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Series GSE144378 Query DataSets for GSE144378
Status Public on Dec 01, 2020
Title The 3D Genomic Landscape of Differential Response to EGFR/HER2 Inhibition in Endocrine-Resistant Breast Cancer [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Recent studies suggested that crosstalk between ERα and EGFR/HER2 pathways plays a critical role in mediating endocrine therapy resistance. Several targeting EGFR/HER2 signaling inhibitors including FDA-approved lapatinib and gefitinib as well as a novel dual tyrosine kinase inhibitor (TKI) sapitnib showed greater inhibitory efficacies. However, how a 3D chromatin landscape of the response to the inhibition to EGFR/HER2 pathway remains to be elucidated. In this study, we conducted in situ Hi-C and RNA-seq in two ERα+ breast cancer cell systems, tamoxifen-sensitive MCF7 and T47D and tamoxifen-resistant MCF7TR and T47DTR before and after the treatment of sapitnib. We identified differential response of topologically associated domains (TADs), looping genes and expressed genes. Interestingly, we found that many differential TADs and looping genes are reversible, indicating that EGFR/HER2 signaling may play a role in reshaping and rewiring the high order genome organization. We further examined and recapitulated the reversible looping genes in 3D spheroids of breast cancer cells. Our data provides a rich resource for further evaluating chromatin structural response to anti-EGFR/HER2 targeted therapies in endocrine-resistant breast cancer.
Overall design RNA-seq experiment of 6 cell types with or without drugs, 3 biological replicates for each condition;
Contributor(s) Yang Y, Choppavarapu L
Citation(s) 32956836
Submission date Jan 28, 2020
Last update date Dec 01, 2020
Contact name Victor Jin
Phone +1 210 562 9209
Organization name Medical college of Wisconsin
Department IHE
Street address 8701 Watertown Plank Rd
City Milwaukee
State/province WI
ZIP/Postal code 53226
Country USA
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (18)
GSM4287008 RNAseq_MCF7L_parental_rep1
GSM4287009 RNAseq_MCF7L_parental_rep2
GSM4287010 RNAseq_MCF7L_parental_rep3
This SubSeries is part of SuperSeries:
GSE144380 The 3D Genomic Landscape of Differential Response to EGFR/HER2 Inhibition in Endocrine-Resistant Breast Cancer
BioProject PRJNA603525
SRA SRP245604

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

Supplementary file Size Download File type/resource
GSE144378_diffExprGenes_MCF7TamR_vs_MCF7TamR+sa.xlsx 303.4 Kb (ftp)(http) XLSX
GSE144378_diffExprGenes_MCF7_vs_MCF7TamR.xlsx 604.1 Kb (ftp)(http) XLSX
GSE144378_diffExprGenes_T47D-TamR_vs_T47D-TamR+sa.xlsx 377.4 Kb (ftp)(http) XLSX
GSE144378_diffExprGenes_T47D_vs_T47D-TamR.xlsx 972.8 Kb (ftp)(http) XLSX
GSE144378_yini_data_raw_read_counts_for_GEO.txt.gz 572.8 Kb (ftp)(http) TXT
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Processed data are available on Series record

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