Smith, P. S. | Search bioRxiv

bioRxiv2026

scUnique: Measuring Ongoing Chromosomal Instability

Chromosomal instability is a hallmark of cancer that can drive tumour heterogeneity and treatment resistance. However, scalable methods to measure the dynamics of chromosomal instability are lacking and thus historic genomic scars can be hard to distinguish from markers of currently active mutational processes. Here, we introduce scUnique, a novel approach to measure ongoing chromosomal instability from single-cell whole genome sequencing (scWGS) data. scUnique performs phylogeny-aware joint segmentation to refine single-cell copy number profiles and identifies recent copy number aberrations as statistically supported changes on the leaves of the inferred phylogenetic tree. This yields a per-cell measure of ongoing chromosomal instability at genome-wide resolution. We validate scUnique in (i) a comprehensive benchmarking study, (ii) in CRISPR-Cas-based experimental systems, and (iii) single-cell derived clones of a well-characterised ovarian model. We show that scUnique distinguishes ongoing HRD and FBI mutational processes. These results show that scUnique provides quantitative, scalable, genome-level information about ongoing chromosomal instability, not available in previous studies relying on bulk DNA-sequencing or single-cell imaging. In the future, these improved measurements could refine the understanding of mechanisms of chromosomal instability and lead to dynamic biomarkers for improved treatment decisions.

cancer biology↗

bioRxiv2019

The genomic landscape of intrinsic and acquired resistance to cyclin-dependent kinase 4/6 inhibitors in patients with hormone receptor positive metastatic breast cancer

Clinical resistance mechanisms to CDK4/6 inhibitors in HR+ breast cancer have not been clearly defined. Whole exome sequencing of 59 tumors with CDK4/6i exposure revealed multiple candidate resistance mechanisms including RB1 loss, activating alterations in AKT1, RAS, AURKA, CCNE2, ERBB2, and FGFR2, and loss of ER expression. In vitro experiments confirmed that these alterations conferred CDK4/6i resistance. Cancer cells cultured to resistance with CDK4/6i also acquired RB1, KRAS, AURKA, or CCNE2 alterations, which conferred sensitivity to AURKA, ERK, or CHEK1 inhibition. Besides inactivation of RB1, which accounts for [~]5% of resistance, seven of these mechanisms have not been previously identified as clinical mediators of resistance to CDK4/6 inhibitors in patients. Three of these--RAS activation, AKT activation, and AURKA activation--have not to our knowledge been previously demonstrated preclinically. Together, these eight mechanisms were present in 80% of resistant tumors profiled and may define therapeutic opportunities in patients. SignificanceWe identified eight distinct mechanisms of resistance to CDK4/6 inhibitors present in 80% of resistant tumors profiled. Most of these have a therapeutic strategy to overcome or prevent resistance in these tumors. Taken together, these findings have critical implications related to the potential utility of precision-based approaches to overcome resistance in many patients with HR+ MBC.

cancer biology↗