Biology subjects

Karim, B. A.

Publications and source records attributed to Karim, B. A..

2 recordsLinked to original sources

bioRxiv2025

Rewiring the fusion oncoprotein EWS/FLI1 in Ewing sarcoma with bivalent small molecules

Deregulated transcription is a defining hallmark of cancer, especially pediatric malignancies, which are frequently driven by fusion transcription factors. Targeting transcription factors directly has been challenging as they lack druggable pockets. Recently, chemically induced proximity has enabled the rewiring of transcriptional activators to drive expression of pro-apoptotic genes using bivalent small molecules. Targeting fusion transcription factors, such as EWS/FLI1 in Ewing sarcoma, with these compounds, may open new therapeutic avenues. Here, we develop a small molecule, EB-TCIP, that recruits FKBP12F36V-tagged EWS/FLI1 to DNA sites bound by the transcriptional regulator BCL6, leading to rapid expression of BCL6 target genes. EB-TCIP activity is dependent on ternary complex formation and specific to cells that express FKBP-EWS/FLI1. This proof-of-concept study demonstrates that EWS/FLI1 can be relocalized on chromatin to induce genes that are ordinarily regulated by a transcriptional repressor. Insights herein will guide the development of bivalent molecules that rewire fusion transcription factors.

cancer biology↗

bioRxiv2023

Borrowing Transcriptional Kinases to Activate Apoptosis

Protein kinases are disease drivers whose therapeutic targeting traditionally centers on inhibition of enzymatic activity. Here chemically induced proximity is leveraged to convert kinase inhibitors into context-specific activators of therapeutic genes. Bivalent molecules that link ligands of the transcription factor B-cell lymphoma 6 (BCL6) to ATP-competitive inhibitors of cyclin-dependent kinases (CDKs) were developed to re-localize CDK to BCL6-bound loci on chromatin and direct phosphorylation of RNA Pol II. The resulting BCL6-target proapoptotic gene expression translated into killing of diffuse large B-cell lymphoma (DLBCL) cells at 72 h with EC50s of 0.9 - 10 nM and highly specific ablation of the BCL6-regulated germinal center response in mice. The molecules exhibited 10,000-fold lower cytotoxicity in normal lymphocytes and are well tolerated in mice. Genomic and proteomic evidence corroborated a gain-of-function mechanism where, instead of global enzyme inhibition, a fraction of total kinase activity is borrowed and re-localized to BCL6-bound loci. The strategy demonstrates how kinase inhibitors can be used to context-specifically activate transcription, accessing new therapeutic space.

cancer biology↗