Pitts, T. M. | bioRxiv Science

bioRxiv2025

Targeting BRAF kinase fusions with pan-RAF and vertical MAPK inhibition

BRAF kinase fusions are a form of structural variation in the genome and are recurrent events in driver-negative melanomas. While BRAF fusions reproducibly conserve the kinase domain, there is genetic variability with 5 gene partners and specific BRAF breakpoints. We investigated how genetic diversity of BRAF kinase fusions affects dimeric signaling and ERK activation. We overexpressed BRAF fusions with 5 gene partners including AGK, ZKSCAN1, ARMC10, PPFIBP2, and TRIM24 and found fusion dependent signaling and inhibitor sensitivity. Despite the development of next generation RAF inhibitors, there was paradoxical ERK phosphorylation with multiple pan-RAF inhibitors, which was ameliorated in certain BRAF fusions with vertical RAF/MEK inhibition using trametinib and LY3009120. Collectively, we observed some fusion-dependent effects but also tumor growth suppression and resolution of paradoxical activation with vertical pathway inhibition.

cancer biology↗

bioRxiv2023

Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data.

Single-cell technologies enable high-resolution studies of phenotype-defining molecular mechanisms. However, data sparsity and cellular heterogeneity make modeling biological variability across single-cell samples difficult. We present SCORPION, a tool that uses a message-passing algorithm to reconstruct comparable gene regulatory networks from single cell/nuclei RNA-seq data that are suitable for population-level comparisons by leveraging the same baseline priors. Using synthetic data, we found that SCORPION outperforms 12 other gene regulatory network reconstruction techniques. Using supervised experiments, we show that SCORPION can accurately identify differences in regulatory networks between wild-type and transcription factor-perturbed cells. We demonstrate SCORPIONs scalability to population-level analyses using a single-cell RNA-seq atlas containing 200,436 cells from colorectal cancer and adjacent healthy tissues. The differences detected by SCORPION between tumor regions are consistent across population cohorts, as well as with our understanding of disease progression and elucidate phenotypic regulators that may impact patient survival.

bioinformatics↗