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

Abstract

BackgroundChromosome 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.ResultsTo 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.ConclusionOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-0971-7) contains supplementary material, which is available to authorized users.

Chromosomal Instability as a Driver of Tumor Heterogeneity and Evolution

“…Second, because CIN is defined by a rate of chromosome missegregation, methods interrogating this process in cancer should be refined to not only measure the extent of chromosome-level copy number alterations in cancer but also the rate at which chromosome number changes throughout consecutive cell divisions. Widely used methods such as comparative genomic hybridization and DNA sequencing of bulk tumor samples significantly mask the extent of karyotypic cell-to-cell variation, which may now be extensively probed through single-cell analyses Bakker et al 2016). Third, our efforts to understand chromosome copy number changes would need to be coupled with quantitative models that aim to predict the behavior of tumor cell populations derived from our knowledge of chromosome segregation at the single-cell level.…”

CIN and Aneuploidy: Different Concepts, Different Consequences

“…[36] In this case, the heterogeneity resulting from the mis-segregation events is used as a measure to estimate CIN. However, single-cell aneuploidy assessments are still end-point measurements, which are likely skewed by strong selection pressures for or against certain karyotypes, as well as by the length of time a cell population has been chromosomal instable.…”

“…This indicates that aneuploid cells, while not cancerous initially, are prone to adopt a malignant fate when combined with other predisposing mutations. [16,36,72] Interestingly, a recent study suggests that aneuploid cells might be cleared by the immune system. In this study CIN is induced to create senescent, aneuploid cells that were then cocultured with natural killer cells (NK92) in vitro.…”

“…[80][81][82][83][84][85][86][87][88][89] The karyotypes observed in cancer are not random, as different cancer types display specific karyotypes. [36,72,90] While certain forms of aneuploidy can be beneficial to tumor growth, the relationship between cancer and CIN remains paradoxical. On the one hand CIN itself can lead to tumorigenesis in some models, [91,92] but on the other hand, CIN has been found to act as a tumor suppressor in other models.…”

“…[101] However, to better understand which CIN rates in cancer drive further evolution toward therapy resistance and which CIN rates are toxic for tumor progression, we need better tools to quantify CIN rates in vivo. While measuring karyotype heterogeneity to estimate CIN rates might provide part of the answer, [36] new models in which chromosome mis-segregation can be monitored live in vivo [3] will be an important step forward toward linking chromosome mis-segregation frequency to tumor outcome.…”