Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies

TLDR

Chromosome instability causes aneuploidy, a hallmark of many cancers, yet its persistence in lymphomas may be limited by suppression or selective pressures. The study aims to differentiate suppression versus selection of chromosome instability in lymphoma and to assess karyotype dynamics with single‑cell whole‑genome sequencing, potentially informing cancer treatment stratification. AneuFinder, an automated tool, was created to annotate copy‑number changes and quantify inter‑cell heterogeneity from scWGS data. Single‑cell sequencing revealed extensive copy‑number heterogeneity in murine T‑cell lymphoma and variable heterogeneity in human B‑cell leukemia, indicating ongoing chromosome instability that other methods miss.

Abstract

Chromosome instability leads to aneuploidy, a state in which cells have abnormal numbers of chromosomes, and is found in two out of three cancers. In a chromosomal instable p53 deficient mouse model with accelerated lymphomagenesis, we previously observed whole chromosome copy number changes affecting all lymphoma cells. This suggests that chromosome instability is somehow suppressed in the aneuploid lymphomas or that selection for frequently lost/gained chromosomes out-competes the CIN-imposed mis-segregation. To distinguish between these explanations and to examine karyotype dynamics in chromosome instable lymphoma, we use a newly developed single-cell whole genome sequencing (scWGS) platform that provides a complete and unbiased overview of copy number variations (CNV) in individual cells. To analyse these scWGS data, we develop AneuFinder, which allows annotation of copy number changes in a fully automated fashion and quantification of CNV heterogeneity between cells. Single-cell sequencing and AneuFinder analysis reveals high levels of copy number heterogeneity in chromosome instability-driven murine T-cell lymphoma samples, indicating ongoing chromosome instability. Application of this technology to human B cell leukaemias reveals different levels of karyotype heterogeneity in these cancers. Our data show that even though aneuploid tumours select for particular and recurring chromosome combinations, single-cell analysis using AneuFinder reveals copy number heterogeneity. This suggests ongoing chromosome instability that other platforms fail to detect. As chromosome instability might drive tumour evolution, karyotype analysis using single-cell sequencing technology could become an essential tool for cancer treatment stratification.