Publications

Comer M, Hart A, Lee Yu H, Nazlamova L, Milne-Clark T, Thomas J, Mahalingam V, Dobson L, Robb T, Palma-Reis Goldie F, Hautaviita K, Elwakeel A, Field S, Patikas N, Barber H, Cheung M, Machesky L, Fernandez-Vega I, Metzakopian E, Bradley A, Dev H, de la Rosa J.

Preprint available at SSRN

Therapy-refractory progression in prostate cancer is driven by context-specific combinations of tumour-suppressor loss and lineage plasticity, yet causal interactions in vivo remain poorly defined. We established an orthotopic, transplant-based CRISPR screening platform that initiates tumours from normal primary prostate epithelial cells and permits pooled functional interrogation in immunocompetent mice.

Schlapansky MF, Schröder MS, Santinha AJ, Rothgangl T, Ioannidi EI, Cullot G, Lewkow B, Ortega GC, Nouraiz A, Mailänder D, Selbert L, Lam S, Egea A, Shin JJ, Bordi M, DeWitt M, Gvozdenovic A, Jackson SP, Schroeder T, Gehart H, Schwank G, Platt RJ, Corn JE.

BioRxiv

Genome editing outcomes are governed by DNA repair pathways that vary with cell type and state. We developed scOUT-seq (single-cell Outcomes Using Transcript sequencing), a scalable approach that jointly profiles transcriptomes and matched multi-allelic editing outcomes ranging from homology directed repair (HDR) to inter-chromosomal translocations.

Wilson JCJ, Zhu JY, Vinciauskaite V, Lloyd EG, Lam S, Hart S, Goh CG, Bou-Dagher F, Razumkov H, Kobel L, Kontarakis Z, Fielden J, Schlapansky MF, Loizou JI, Villunger A, Corn JE, Biffi G, Masson GR, Marciniak SJ, Bader AS, Jackson SP.

Nature Communications
16, 8983

Inhibitors of the protein kinase WEE1 have emerged as promising agents for cancer therapy. In this study, we uncover synergistic interactions between WEE1 small-molecule inhibitors and defects in mRNA translation, mediated by activation of the integrated stress response (ISR) through the kinase GCN2. Using a pooled CRISPRi screen, we identify GSPT1 and ALKBH8 as factors whose depletion confer hypersensitivity to the WEE1 inhibitor, AZD1775. We demonstrate that this synergy depends on ISR activation, which is induced by the off-target activity of WEE1 inhibitors.

Zhu JY, Emanuelli G, Masson GR, Vinciauskaite V, Willems H, Lim A, Brown CA, Winperry D, Clarke M, Gilley R, Preston F, Wilson J, Bader AS, Rahman T, Chambers JE, Skidmore J, Morrell NW, Marciniak SJ.

BioRxiv

Mutations of EIF2AK4, which encodes the eIF2α kinase GCN2, cause a severe inherited form of pulmonary hypertension called pulmonary veno-occlusive disease (PVOD). Some pathogenic variants of GCN2 are amenable to pharmacological reactivation by low concentrations of ATP-pocket binding inhibitors. Kinase inhibition at modestly elevated concentrations limits the clinical utility of these drugs against PVOD. We therefore performed an in cellulo chemical screen for GCN2 activators…

Hough SH, Jhujh SS, Awwad SW, Lam S, Thomas JC, Lewis O, Mosler T, Bader AS, Bartik LE, McKee S, Amudhavalli SM, Colin E, Damseh N, Clement E, Cacheiro P, Majumdar A, Smedley D, Thiffault I, Zagnoli Vieira G, Belotserkovskaya R, Smerdon SS, Beli P, Galanty Y, Carnie CJ, Stewart GS, Jackson SJ.

bioRXiv

Ubiquitin E3 ligases play crucial roles in the DNA damage response (DDR) by modulating the turnover, localization, activation, and interactions of DDR and DNA replication proteins. To gain further insight into how the ubiquitin system regulates the DDR, we performed a CRISPR-Cas9 knockout screen focused on E3 ligases and related proteins with the DNA topoisomerase I inhibitor, camptothecin. This uncovered the CTLH ubiquitin E3 ligase complex — and particularly one of its core subunits, MAEA — as a critical regulator of the cellular response to single-ended DNA double-strand breaks (seDSBs) and replication stress.

Jassim A, Nimmervoll BV, Terranova S, Nathan E, Hu L, Taylor JT, Masih KE, Ruff L, Duarte M, Cooper E, Katyal G, Akhbari M, Gilbertson RJ, Coleman JC, Toker JS, Terhune C, Balmus G, Jackson SP, Liu H, Jiang T, Taylor MD, Hua K, Abraham JE, Filbin MG, Hill A, Patrizi A, Dani N, Regev A, Lehtinen MK, Gilbertson RJ.

Cancer Cell. Online ahead of print.

Cancer treatment often fails because combinations of different therapies evoke complex resistance mechanisms that are hard to predict. We introduce REsistance through COntext DRift (RECODR): a computational pipeline that combines co-expression graph networks of single-cell RNA sequencing profiles with a graph-embedding approach to measure changes in gene co-expression context during cancer treatment.

Kochenova OV, D'Alessandro G, Pilger D, Schmid E, Richards SL, Garcia MR, Jhujh SS, Voigt A, Gupta V, Carnie CJ, Alex Wu R, Gueorguieva N, Lam S, Stewart GS, Walter JC, Jackson SP.

Nature Communications 16(1):5333

The eukaryotic replisome, which consists of the CDC45-MCM2-7-GINS (CMG) helicase, replicative polymerases, and several accessory factors, sometimes encounters proteinaceous obstacles that threaten genome integrity. These obstacles are targeted for removal or proteolysis by the E3 ubiquitin ligase TRAIP, which associates with the replisome. However, TRAIP must be carefully regulated to avoid inappropriate ubiquitylation and disassembly of the replisome. Here, we demonstrate that human cells lacking the de-ubiquitylating enzyme USP37 are hypersensitive to topoisomerase poisons and other replication stress-inducing agents.

Muffels IJJ, Waterham HR, D'Alessandro G, Zagnoli-Vieira G, Sacher M, Lefeber DJ, Van der Vinne C, Roifman CM, Gassen KLI, Rehmann H, Van Haaften-Visser DY, Nieuwenhuis ESS, Jackson SP, Fuchs SA, Wijk F, van Hasselt P.

Genome Medicine 17(1):12.

Background: Deciphering variants of uncertain significance (VUS) represents a major diagnostic challenge, partially due to the lack of easy-to-use and versatile cellular readouts that aid the interpretation of pathogenicity and pathophysiology. To address this challenge, we propose a high-throughput screening of cellular functionality through an imaging flow cytometry (IFC)-based platform.