Yi, J. M. | Search bioRxiv

bioRxiv2025

Alternative polyadenylation regulates human urothelial differentiation

The urothelium is stratified into progenitor basal cells, intermediate cells, and terminally differentiated umbrella cells. Proper renewal of umbrella cells is necessary for maintaining urinary tract barrier integrity. To investigate whether mRNA alternative cleavage and polyadenylation (APA) regulates urothelial differentiation, we developed a single-cell polyadenylation site usage (scPASU) computational pipeline to map cell state-specific polyadenylation sites in single-cell RNA-seq data from 13,544 urothelial cells. Leveraging single-cell spatial imaging, we directly visualized APA events in situ, revealing their spatial specificity within the adult human ureter. APA shaped urothelial differentiation, independent of gene expression changes. Furthermore, key APA-regulated genes shared conserved motifs in their 3 UTRs, often containing Alu elements, suggesting a potential mechanism regulating poly(A) site selection. Our study establishes APA as a driver of urothelial transcriptome diversity.

systems biology↗

bioRxiv2024

LSD1 inhibition attenuates targeted therapy-induced lineage plasticity in BRAFV600E colorectal cancer

BRAF activating mutations occur in approximately 10% of metastatic colorectal cancer (CRCs) and are associated with worse prognosis due to an inferior response to standard chemotherapy. Standard of care for patients with refractory metastatic BRAFV600E CRC is treatment with BRAF and EGFR inhibitors. However, responses are not durable. Lineage plasticity to neuroendocrine cancer is an emerging mechanism of targeted therapy resistance in several cancer types. Enteroendocrine cells (EECs), the neuroendocrine cell of the intestine, are uniquely present in BRAFV600ECRC as compared to BRAF wildtype CRC. Here, we demonstrated that combined BRAF and EGFR inhibition enriches for EECs in several models of BRAFV600ECRC. Additionally, EECs and other secretory cell types were enriched in a subset of BRAFV600E CRC patient samples following targeted therapy. Importantly, inhibition of the lysine demethylase LSD1 with a clinically relevant inhibitor attenuated targeted therapy-induced EEC enrichment through blocking the interaction of LSD1, CoREST2 and STAT3. Statement of SignificanceOur findings that BRAF plus EGFR inhibition induces lineage plasticity in BRAFV600E CRC represents a new paradigm for how resistance to BRAF plus EGFR inhibition occurs and our finding that LSD1 inhibition blocks lineage plasticity has the potential to improve responses to BRAF plus EGFR inhibitor therapy in patients.

cancer biology↗