Enhancing transcription-replication conflict targets ecDNA-positive cancers

Jun Tang; Natasha E Weiser; Guiping Wang; Sudhir Chowdhry; Ellis J Curtis; Yanding Zhao; Ivy Tsz-Lo Wong; Georgi K Marinov; Rui Li; Philip Hanoian; Edison Tse; Salvador Garcia Mojica; Ryan Hansen; Joshua Plum; Auzon Steffy; Snezana Milutinovic; S Todd Meyer; Jens Luebeck; Yanbo Wang; Shu Zhang; Nicolas Altemose; Christina Curtis; William J Greenleaf; Vineet Bafna; Stephen J Benkovic; Anthony B Pinkerton; Shailaja Kasibhatla; Christian A Hassig; Paul S Mischel; Howard Y Chang

doi:10.1038/s41586-024-07802-5

Enhancing transcription-replication conflict targets ecDNA-positive cancers

Nature. 2024 Nov;635(8037):210-218. doi: 10.1038/s41586-024-07802-5. Epub 2024 Nov 6.

Authors

Jun Tang^#^{1

2}, Natasha E Weiser^#^{1

3}, Guiping Wang^#^{3

4}, Sudhir Chowdhry⁵, Ellis J Curtis^{1

2

6}, Yanding Zhao^{3

4

7}, Ivy Tsz-Lo Wong^{1

2}, Georgi K Marinov⁴, Rui Li³, Philip Hanoian⁸, Edison Tse⁵, Salvador Garcia Mojica⁵, Ryan Hansen⁵, Joshua Plum⁵, Auzon Steffy⁵, Snezana Milutinovic⁵, S Todd Meyer⁵, Jens Luebeck⁹, Yanbo Wang^{1

2

3}, Shu Zhang^{1

2

3}, Nicolas Altemose⁴, Christina Curtis^{4

10

11}, William J Greenleaf⁴, Vineet Bafna⁹, Stephen J Benkovic⁸, Anthony B Pinkerton⁵, Shailaja Kasibhatla⁵, Christian A Hassig¹², Paul S Mischel^{13

14}, Howard Y Chang^{15

16

17

18}

Affiliations

¹ Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
² Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
³ Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
⁴ Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
⁵ Boundless Bio, San Diego, CA, USA.
⁶ Medical Scientist Training Program, University of California, San Diego, La Jolla, CA, USA.
⁷ Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA.
⁸ Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
⁹ Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
¹⁰ Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
¹¹ Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
¹² Boundless Bio, San Diego, CA, USA. chassig@boundlessbio.com.
¹³ Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. pmischel@stanford.edu.
¹⁴ Sarafan ChEM-H, Stanford University, Stanford, CA, USA. pmischel@stanford.edu.
¹⁵ Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. howchang@stanford.edu.
¹⁶ Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. howchang@stanford.edu.
¹⁷ Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA. howchang@stanford.edu.
¹⁸ Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. howchang@stanford.edu.

^# Contributed equally.

Abstract

Extrachromosomal DNA (ecDNA) presents a major challenge for cancer patients. ecDNA renders tumours treatment resistant by facilitating massive oncogene transcription and rapid genome evolution, contributing to poor patient survival^1-7. At present, there are no ecDNA-specific treatments. Here we show that enhancing transcription-replication conflict enables targeted elimination of ecDNA-containing cancers. Stepwise analyses of ecDNA transcription reveal pervasive RNA transcription and associated single-stranded DNA, leading to excessive transcription-replication conflicts and replication stress compared with chromosomal loci. Nucleotide incorporation on ecDNA is markedly slower, and replication stress is significantly higher in ecDNA-containing tumours regardless of cancer type or oncogene cargo. pRPA2-S33, a mediator of DNA damage repair that binds single-stranded DNA, shows elevated localization on ecDNA in a transcription-dependent manner, along with increased DNA double strand breaks, and activation of the S-phase checkpoint kinase, CHK1. Genetic or pharmacological CHK1 inhibition causes extensive and preferential tumour cell death in ecDNA-containing tumours. We advance a highly selective, potent and bioavailable oral CHK1 inhibitor, BBI-2779, that preferentially kills ecDNA-containing tumour cells. In a gastric cancer model containing FGFR2 amplified on ecDNA, BBI-2779 suppresses tumour growth and prevents ecDNA-mediated acquired resistance to the pan-FGFR inhibitor infigratinib, resulting in potent and sustained tumour regression in mice. Transcription-replication conflict emerges as a target for ecDNA-directed therapy, exploiting a synthetic lethality of excess to treat cancer.

MeSH terms

Animals
Antineoplastic Agents / pharmacology
Antineoplastic Agents / therapeutic use
Cell Death / drug effects
Cell Line, Tumor
Checkpoint Kinase 1 / antagonists & inhibitors
Checkpoint Kinase 1 / genetics
Checkpoint Kinase 1 / metabolism
DNA Breaks, Double-Stranded / drug effects
DNA Repair / drug effects
DNA Replication* / drug effects
DNA, Single-Stranded / genetics
DNA, Single-Stranded / metabolism
Female
Humans
Male
Mice
Protein Kinase Inhibitors / pharmacology
Protein Kinase Inhibitors / therapeutic use
Replication Protein A / chemistry
Replication Protein A / metabolism
Stomach Neoplasms* / drug therapy
Stomach Neoplasms* / genetics
Stomach Neoplasms* / pathology
Synthetic Lethal Mutations / drug effects
Transcription, Genetic* / drug effects

Substances

Checkpoint Kinase 1
CHEK1 protein, human
DNA, Single-Stranded
FGFR2 protein, human
infigratinib
Protein Kinase Inhibitors
RPA2 protein, human
Replication Protein A
Antineoplastic Agents