Publications

Reilly EL and Aitken SJ

Nature 2025 May 21. Online ahead of print.

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 Online ahead of print

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.

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

Biorxiv

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.

Awwad SW, Doyle C, Coulthard J, Bader AS, Gueorguieva N, Lam S, Gupta V, Belotserkovskaya R, Tran TA, Balasubramanian S, Jackson SP.

Nature Communications 16(1):480

ATR plays key roles in cellular responses to DNA damage and replication stress, a pervasive feature of cancer cells. ATR inhibitors (ATRi) are in clinical development for treating various cancers, including those with high replication stress, such as is elicited by ARID1A deficiency, but the cellular mechanisms that determine ATRi efficacy in such backgrounds are unclear. Here, we have conducted unbiased genome-scale CRISPR screens in ARID1A-deficient and proficient cells treated with ATRi.

Gang Goh C, Bader AS, Tran T-A, Belotserkovskaya R, D’Alessandro G and Jackson SP.

Nucleic Acids Research, gkae1163

HAP1 is a near-haploid human cell line commonly used for mutagenesis and genome editing studies due to its hemizygous nature. We noticed an unusual hypersensitivity of HAP1 to camptothecin, an antineoplastic drug that stabilizes topoisomerase I cleavage complexes (TOP1ccs). We have attributed this hypersensitivity to a deficiency of TDP1, a key phosphodiesterase involved in resolving abortive TOP1ccs.

Carnie CJ, Jackson SP and Stingele J.

Trends in Cell Biology 35(4), 316-329

DNA–protein crosslinks (DPCs) are highly toxic DNA lesions that are relevant to multiple human diseases. They are caused by various endogenous and environmental agents, and from the actions of enzymes such as topoisomerases. DPCs impede DNA polymerases, triggering replication-coupled DPC repair. Until recently the consequences of DPC blockade of RNA polymerases remained unclear. New methodologies for studying DPC repair have enabled the discovery of a transcription-coupled (TC) DPC repair pathway.

Lam S, Thomas JC and Jackson SP.

Genome Medicine 16:139 (2024)

Background CRISPR-Cas9 technology has revolutionised genetic screens and can inform on gene essentiality and chemo-genetic interactions. It is easily deployed and widely supported with many pooled CRISPR libraries available commercially. However, discrepancies between the reference genomes used in the design of those CRISPR libraries and the cell line under investigation can lead to loss of signal or introduction of bias. The problem is particularly acute when dealing with variant cell lines such as cancer cell lines.

Results Here, we present an algorithm, EXOme-guided Re-annotation of nuCleotIde SEquences (Exorcise), which uses sequence search to detect and correct mis-annotations in CRISPR libraries.

Kochenova OV, D’Alessandro G, Pilger D, Schmid E, Richards SL, Rios Garcia M, Jhujh SS, Voigt A, Gupta V, Carnie CJ, Wu RA, Gueorguieva N, Stewart GS, Walter JC, Jackson SP.

BioRXiv

The E3 ubiquitin ligase TRAIP associates with the replisome and helps this molecular machine deal with replication stress. Thus, TRAIP promotes DNA inter-strand crosslink repair by triggering the disassembly of CDC45-MCM2-7-GINS (CMG) helicases that have converged on these lesions. However, disassembly of single CMGs that have stalled temporarily would be deleterious, suggesting that TRAIP must be carefully regulated. Here, we demonstrate that human cells lacking the de-ubiquitylating enzyme USP37 are hypersensitive to topoisomerase poisons and other replication stress-inducing agents.