75O - The role of FAT1 and the Hippo pathway in chromosomal instability and whole-genome doubling

Background

Chromosomal instability (CIN) is pervasive during cancer evolution, particularly in non-small cell lung cancer (NSCLC) where it is associated with poor recurrence-free survival and correlates with the frequency of whole genome doubling events (WGD). By duplicating the complete set of chromosomes, WGD is a key event during cancer evolution and correlates with poor prognosis and targeted therapy resistance. Despite the importance of these events, genetic events responsible for the initiation and maintenance of CIN and WGD in NSCLC have not been systematically investigated.

Methods

TRAcking Cancer Evolution through Therapy/Rx (TRACERx) is a multicancer longitudinal study which utilizes multiregional sampling and whole exome sequencing (WES) to elucidate potential causes of tumor heterogeneity and cancer progression. TRACERx enables us to investigate genetic alterations and their relationship with WGD and CIN, and proceed to functionally characterize them.

Results

We identified that genetic alterations in 6 genes, including FAT1, results in homologous recombination (HR) repair deficiencies and CIN. Mutations in FAT1 are further associated with HR deficiency in patient cohorts. Using orthogonal genetic and experimental approaches, we demonstrate that FAT1 alterations are positively selected before WGD in lung cancer evolution. FAT1 ablation causes persistent replication stress, an elevated mitotic failure rate, nuclear deformation, and elevated structural CIN including chromosome translocations and radial chromosomes. Furthermore, FAT1 loss contributes to WGD, which we attribute to the dysregulation of YAP1. Co-depletion of the oncogene YAP1 partially reduces the elevated numerical CIN caused by FAT1 loss but does not relieve HR deficiencies nor structural CIN. Importantly, overexpression of constitutively active YAP1^5SA is sufficient to induce numerical CIN. HR deficiencies and high CIN caused by FAT1 loss synergizes with WGD to fuel tumor evolution, a prominent factor underpinning therapy resistance.

Conclusions

These data suggest that FAT1 loss in lung cancer attenuates HR repair and exacerbates structural and numerical CIN through two distinct downstream mechanisms, leading to increased tumor heterogeneity.

Editorial acknowledgement

Clinical trial identification

Legal entity responsible for the study

The authors.

Funding

CRUK.

Disclosure

M. Jamal-Hanjani: Financial Interests, Personal, Invited Speaker, Invited speaker honorarium: Oslo Cancer Cluster, Astex Pharmaceutical; Financial Interests, Personal, Invited Speaker, Speaker honorarium: Pfizer, Bristol Myers Squibb; Financial Interests, Personal, Advisory Board, Cancer cachexia research advisory board: Pfizer; Non-Financial Interests, Personal, Advisory Role, Scientific Advisory Board and Steering Committee member: Achilles Therapeutics; Other, Personal, Other, I am named as co-inventor on patent PCT/US2017/028013 relating to methods for lung cancer detection: Patent. N. McGranahan: Financial Interests, Institutional, Stocks/Shares: Achilles Therapeutics. C. Swanton: Financial Interests, Personal, Invited Speaker, Activity took place in 2016: Pfizer, Celgene; Financial Interests, Personal, Invited Speaker, October 26th 2020: Novartis; Financial Interests, Personal, Invited Speaker: Roche/Ventana, BMS, AstraZeneca, MSD, Illumina, GSK; Financial Interests, Personal, Advisory Board, Ad Board - November 12th, 2020: Amgen; Financial Interests, Personal, Advisory Board, Current - since 2018: Genentech; Financial Interests, Personal, Advisory Board: Sarah Canon Research Institute; Financial Interests, Personal, Advisory Board, Joined October 2020. Also have stock options: Bicycle Therapeutics; Financial Interests, Personal, Other, Consultancy: Medicxi; Financial Interests, Personal, Advisory Board, Member of the Science Advisory Board. Also had stock options until June 2021: GRAIL; Financial Interests, Personal, Other, Consultancy agreement: Roche Innovation Centre Shanghai; Financial Interests, Personal, Advisory Board, 29 November - 1 December 2022: Novartis; Financial Interests, Personal, Invited Speaker, Oncology Collective - 2nd Nov - 4 Nov 2022 - Atlanta, USA: Roche; Financial Interests, Personal, Advisory Board, ctDNA advisory Board - 24th March 2023: AstraZeneca; Financial Interests, Personal, Invited Speaker, Pfizer Oncology 'Leading the revolution for the future: Pfizer; Financial Interests, Personal, Advisory Board, Scientific Advisory Board and Stock options from September 2023: Relay Therapeutics; Financial Interests, Personal, Advisory Board, Member of the Scientific Advisory Board: SAGA Diagnostics; Financial Interests, Personal, Full or part-time Employment, Chief Clinician since October 2017: Cancer Research UK; Financial Interests, Personal, Ownership Interest, Co-Founder of Achilles Therapeutics. Also, have stock options in this company: Achilles Therapeutics; Financial Interests, Personal, Stocks/Shares, Stocks owned until June 2021: GRAIL, Apogen Biotechnologies; Financial Interests, Personal, Stocks/Shares: Epic Biosciences, Bicycle Therapeutics; Financial Interests, Personal, Stocks/Shares, Stock options: Relay Therapeutics; Financial Interests, Institutional, Research Grant, Funded RUBICON grant - October 2018 - April 2021: Bristol Myers Squibb; Financial Interests, Institutional, Research Grant, Collaboration in minimal residual disease sequencing technologies: Archer Dx Inc; Financial Interests, Institutional, Research Grant: Pfizer, Boehringer Ingelheim; Financial Interests, Institutional, Invited Speaker, Chief Investigator for the MeRmaiD 1and 2 clinical trials and chair of the steering committee: AstraZeneca; Financial Interests, Institutional, Research Grant, Research grant from Oct 2019 - July 2023 - Genetics of CIN and SCNAs for Targeted Discovery (SCEPTRE): Ono Pharmaceutical; Financial Interests, Institutional, Research Grant, Research Grants from 2015: Roche; Financial Interests, Personal, Other, Co-chief investigator: NHS-Galleri Clinical Trial; Financial Interests, Institutional, Research Grant, from October 2022: Personalis; Non-Financial Interests, Personal, Principal Investigator, Chief Investigator for MeRmaiD 1 and 2 clinical trials: AstraZeneca; Non-Financial Interests, Personal, Member of Board of Directors, From 2019-2022: AACR; Non-Financial Interests, Personal, Other, Board of Directors: AACR; Non-Financial Interests, Personal, Advisory Role, EACR Advisory Council member: EACR. All other authors have declared no conflicts of interest.