Publications

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…

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. 43(9); 1608-1621.e9

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.

Reilly EL and Aitken SJ

Nature 642(8068):576-577

Instability of the genome is a hallmark of cancer that can arise when damaged DNA is carried across cell divisions, fuelling both small- and large-scale genetic variation in cells. Writing in Nature, Panagopoulos et al. present a multimodal platform that tracks single cells to uncover how DNA damage propagates unevenly through cell lineages. The authors’ approach reveals the origin and extent of differences in the traits and genomic stability of individual cells in each of the daughter and granddaughter generations produced from successive cell divisions.

Fielden J, Siegner SM, Gallagher DN, Schröder MS, Dello Stritto MR, Lam S, Kobel L, Schlapansky MF, Jackson SP, Cejka P, Jost M, Corn JE.

Nature 640(8060):1093-1102

The DNA damage response (DDR) is a multifaceted network of pathways that preserves genome stability. Unravelling the complementary interplay between these pathways remains a challenge. Here we used CRISPR interference (CRISPRi) screening to comprehensively map the genetic interactions required for survival during normal human cell homeostasis across all core DDR genes. We captured known interactions and discovered myriad new connections that are available online.