Biology subjects

Bowlan, J.

Publications and source records attributed to Bowlan, J..

4 recordsLinked to original sources

bioRxiv2026

CRISPR-enabled genetic screens identify synthetic lethal targets across frequently altered cancer drivers

Synthetic lethality (SL) provides a treatment paradigm for targeting cancer with alterations in driver genes that are not conventionally druggable, including loss-of-function (LoF) mutations in tumor suppressor genes and gain-of-function (GoF) alterations in oncogenes. We undertook a series of genome-wide CRISPR screens using functionally validated isogenic cell lines and also conducted a large-scale SL analysis using data from the cancer dependency map (DepMap). We charted SL interactions across 15 genetic alterations characteristic of diseases with high incidence and unmet clinical need: FBXW7, CCNE1, CDK12, ARID1A, KMT2D, DNMT3A, TET2, KEAP1, STK11, IDH1, SF3B1, SRSF2, U2AF1, chromosome 18q loss, and chromosome 13q loss. We show validation of several SL interactions between tractable targets with cancer drivers, including ARID1A and the hexosamine biosynthetic pathway aminotransferase GFPT1, STK11 with CAMK protein kinase family members including MARK2, FBXW7 and the CDK1 regulatory kinase PKMYT1, and CCNE1 amplification and the anaphase promoting complex or cyclosome (APC/C). In summary, this study offers a rich resource of genetic interactions across cancer drivers enabling the discovery of new biological insights and drug targets for future therapeutic development.

cancer biology↗

bioRxiv2026

Anticipating on-target resistance to WRN inhibitors in microsatellite unstable cancers

Leveraging WRN helicase dependency in microsatellite instability (MSI) cancers offers a synthetic lethal (SL) therapeutic opportunity, with several WRN inhibitors in development. However, the hypermutator nature of MSI tumors creates strong evolutionary pressure for rapid resistance. Here, we apply a multimodal functional genomics framework integrating base editing screens and deep mutational scanning to map on-target resistance to two clinical WRN inhibitors, HRO761 and VVD-214. We identify discrete resistance hotspots within WRN and demonstrate that single-allele (heterozygous) mutations at the drug-binding site are sufficient to abrogate WRN inhibitor-induced cytotoxicity. Resistance profiles diverged between HRO761 and VVD-214, revealing mutations that impair one but preserve sensitivity to the other. Genome-wide CRISPR screens further identified non-homologous end joining (NHEJ) factors and the checkpoint phosphatase WIP1 as tractable synthetic vulnerabilities that potentiate WRN inhibition. Together, these findings establish a framework for resistance-aware deployment of WRN inhibitors through rational drug selection, therapeutic switching, and combination strategies. Statement of SignificanceResistance to WRN inhibitors threatens the clinical durability of synthetic lethal therapies in microsatellite-instable cancers. Using multimodal functional genomics, we identify predictable, drug-specific on-target resistance mechanisms and reveal DNA-PK as a tractable combination partner. These findings provide a framework for resistance-aware deployment of WRN inhibitors to improve therapeutic durability.

cancer biology↗

bioRxiv2025

A dual mechanism of sensitivity to PLK4 inhibition by RP-1664 in neuroblastoma

A novel therapeutic strategy was recently proposed for high-risk neuroblastoma carrying copy number gain of the TRIM37 gene: centriole loss upon inhibition of polo-like kinase 4 (PLK4), while tolerated by normal cells, induces aberrant mitotic spindle formation and p53-dependent cell death in TRIM37-overexpressing cells. Interestingly, while full PLK4 inhibition causes centriole loss, partial inhibition is known to elevate centriole numbers. Here we show using a novel selective PLK4 inhibitor RP-1664 that both centriole loss and amplification contribute to hypersensitivity of neuroblastoma cells. Whereas inactivation of TRIM37 and TP53 rescues neuroblastoma cell death at higher concentrations of RP-1664, at lower doses cell death is TRIM37/TP53-independent. With CRISPR screens and live cell imaging we demonstrate that upon centriole amplification, neuroblastoma cells succumb to multipolar mitoses due to inability to cluster or inactivate supernumerary centrosomes. In vivo, RP-1664 shows robust efficacy in neuroblastoma xenografts at doses consistent with centriole amplification. STATEMENT OF SIGNIFICANCEHigh-risk neuroblastoma is associated with poor outcomes in pediatric patients and novel therapies need to be developed. We show that neuroblastoma cells are remarkably sensitive to PLK4 inhibitors due to a combination of two complementary mechanisms, supporting the evaluation of PLK4 inhibitors in clinical trials of high-risk neuroblastoma.

cancer biology↗

bioRxiv2021

CCNE1 amplification is synthetic-lethal with PKMYT1 kinase inhibition

Amplification of the gene encoding cyclin E (CCNE1) is an oncogenic driver in several malignancies and is associated with chemoresistance and poor prognosis. To uncover therapeutic targets for CCNE1-amplified tumors, we undertook genome-scale CRISPR/Cas9-based synthetic lethality screens in cellular models of CCNE1 amplification. Here, we report that increasing CCNE1 dosage engenders a vulnerability to the inhibition of the PKMYT1 kinase, a negative regulator of CDK1. To inhibit PKMYT1, we developed RP-6306, an orally bioavailable and selective inhibitor that shows single-agent activity and durable tumor regressions when combined with gemcitabine in models of CCNE1-amplification. RP-6306 treatment causes unscheduled activation of CDK1 selectively in CCNE1 overexpressing-cells, promoting early mitosis in cells undergoing DNA synthesis. CCNE1 overexpression disrupts CDK1 homeostasis at least in part through an early activation of the FOXM1/MYBL2/MuvB-dependent mitotic transcriptional program. We conclude that PKMYT1 inhibition is a promising therapeutic strategy for CCNE1-amplified cancers.

cancer biology↗