Iso-CUT&MAP (Isolated cell-based Cut Under Target and Mapping Apoptotic Protein-binding sequences): a novel strategy for high-resolution mapping of DNA binding sites

ABSTRACT: DNA and protein interactions are essential for cellular processes and have major implications in cancer biology. DNA binding proteins, particularly transcription factors (TF), are crucial in regulating gene expression and downstream protein functions. Studying the intricate DNA-protein interactions helps unravel specific functions of TFs that are involved in cancer pathogenesis, identify regulatory pathways, and ultimately uncover therapeutic targets. Currently, the lack of high-throughput screening techniques makes research in cancer associated-TFs challenging. Therefore, we have developed an innovative Iso-CUT&MAP (Isolated cell-based Cut Under Target and Mapping Apoptotic Protein-binding sequences). Here, K562 tumor cells were coencapsulated with NK92 and antibody-conjugated (NFkB/RelA) magnetic beads in a microfluidic droplet-based system. After NK92 immune cells killed the K562 target cells, we collected RelA-bound DNA from the dead cells and analyzed DNA-binding sites using ChIP-seq. The results reveal the RelA genome-wide association study (GWAS) of the target K562 tumor cells in response to immune cell killing. The genome-wide mapping matched the expected profile of NFkB, validating the ability of our Iso-CUT&MAP method to accurately identify NFkB binding in response to NK92 killing of K562. This novel technique holds promise for precision medicine in understanding apoptosis biology and the influence of immune cell or chemotherapy-induced tumor cell killings.

ORGANISM(S): Homo sapiens

PROVIDER: GSE237814 | GEO | 2024/07/19

REPOSITORIES: GEO