EXPERIMENT_TITLE: GSM8745167: MCF7 cell, treated by DMSO, 8h; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C was performed following Dovetails TopoLink V2 kit and protocol. Library preparation was performed following Dovetails TopoLink V2 kit and protocol
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Gene-gene chromatin interactions (GGIs) bring distal genes into close spatial proximity to permit strong co-expression, which could potentially contribute to cancer progression. High-throughput methods like Hi-C are impractical for very large cohort analyses, thus we developed AI4Loop, an Artificial Intelligence (AI) Deep Learning -based tool to predict GGIs using RNA-Seq data. Applying AI4Loop to 12,000 patient samples from The Cancer Genome Atlas (TCGA) database across 32 cancer types revealed that GGIs show increased cancer sub-type predictivity compared to RNA-Seq data and demonstrated oncogenic gains of GGIs in almost all cancers examined. To target the therapeutic vulnerability of gain of GGIs in cancers, using low-information RNA expression datasets from the CLUE database, we also constructed a drug-perturbation GGI atlas from 50,000 drug-treated samples to identify and repurposed compounds that disrupt oncogenic GGIs. Notably, we found that the antibiotics eperezolid and radezolid reduced cancer-acquired GGIs, which we confirmed with Hi-C experiment. This work showcases AI-directed research in epigenetics, enhances cancer biology predictivity and can promote wide-range drug repurposing in the future. This GEO submission contains the Hi-C data used to test the accuracy of AI4Loop when applied to compounds leading to loss of gene-gene interactions from the CLUE datasets. Overall design: Hi-C, performed with the TOPO-Link Hi-C Kit from Dovetail in DMSO, Eperezolid, Radezolid, JQ1 and Trihexyphenidyl treated MCF7 cells for 8h
SAMPLE_TITLE: MCF7 cell, treated by DMSO, 8h
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Breast"}, {"TAG": "tissue", "VALUE": "Breast"}, {"TAG": "cell line", "VALUE": "MCF7"}, {"TAG": "cell type", "VALUE": "Epithelial"}, {"TAG": "genotype", "VALUE": "Wild type for BRCA1/BRCA2"}, {"TAG": "treatment", "VALUE": "DMSO"}, {"TAG": "batch", "VALUE": "Batch 1, Batch 2"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: MCF7 cell, treated by DMSO, 8h
RUN_SET_RUN_Pool_Member_@attributes_sample_title: MCF7 cell, treated by DMSO, 8h
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