Abstract PR012: Evolutionary dynamics of whole-genome doubling in ovarian cancer
Authors: Ignacio Vázquez-García, Matthew Myers, Marc J. Williams, Samuel S. Freeman, Jun Li, Hongyu Shi, Gryte Satas, Nicholas Ceglia, Florian Uhlitz, Britta Weigelt, Dmitriy Zamarin, Andrew McPherson, Samuel F. Bakhoum, Sohrab P. Shah
Journal: Cancer Research (2024)

Abstract Chromosomal instability (CIN) is a major driver of tumor progression and treatment resistance in many cancers. CIN is characterized by ongoing chromosome missegregation, segmental aneuploidy and whole-genome doubling (WGD), generating copy number heterogeneity that provides a substrate for natural selection. Although well characterized in model systems, the evolutionary dynamics and genomic impact of WGD is underexplored in primary tumors and metastases. Newly developed single-cell genomics assays now allow for the measurement of the whole genomes of single cells obtained from patient tissues, thus providing a direct view into the evolution of tumor genomes undergoing WGD. We performed multi-region single-cell whole genome sequencing (scWGS) in a cohort of patients with high-grade serous ovarian cancer (HGSOC), an archetype of high CIN cancers. We profiled a total of 70,644 single cells from 63 pre-treatment samples obtained for 36 HGSOC patients. For each patient, we computed total and allele-specific copy number per cell, and inferred the evolutionary history of each patient’s tumor, including clonal and subclonal WGD events and cell-specific whole-chromosome or arm-level copy number changes indicative of missegregations. To determine the role of CIN-associated micronuclei (MN) formation, we used high-resolution cGAS immunofluorescence (IF) microscopy to profile FFPE tissues site-matched to scWGS, and quantify spatially-resolved rates of MN formation and rupture across 120 samples. A majority of tumors were characterized by early clonal WGD (61%, 22/36 cases). The remaining patients exhibited subclonal WGD subpopulations averaging 10% of cancer cells in total. To understand the interplay between recent WGD and CIN across the cohort, we subset all patients cells into non-WGD, subclonal WGD, and clonal WGD and computed mis-segregation rates for these subsets. Non-WGD cells showed the lowest levels of mis-segregation. Subclonal WGD exhibited the highest CIN rates, including mis-segregation and multipolar cells indicative of CIN following a recent WGD event. Clonal WGD exhibited intermediate levels of mis-segregation indicative of stabilization following a historical WGD event. CIN following WGD often resulted in a reduction in ploidy relative to the ancestral WGD cell. Micronucleus rupture was ubiquitously detected in IF across HGSOC tumors, and MN rates varied widely between patients and across primary and metastatic sites. Micronucleus rupture commonly resulted from the impact of WGD, which increased sequestration of missegregated chromosomes into MN. Through multimodal single cell measurements of HGSOC tumors, we were able to characterize genomic complexity from individual cell division errors in HGSOC, and shed light into how the transient processes governing ovarian cancer cell evolution impact the genomes of cell populations. Citation Format: Ignacio Vázquez-García, Matthew Myers, Marc J. Williams, Samuel S. Freeman, Jun Li, Hongyu Shi, Gryte Satas, Nicholas Ceglia, Florian Uhlitz, MSK SPECTRUM Consortium, Britta Weigelt, Dmitriy Zamarin, Andrew McPherson, Samuel F. Bakhoum, Sohrab P. Shah. Evolutionary dynamics of whole-genome doubling in ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr PR012.