Single-cell genomic variation induced by mutational processes in cancer

Abstract

How cell-to-cell copy number alterations that underpin genomic instability1 in human cancers drive genomic and phenotypic variation, and consequently the evolution of cancer2, remains understudied. Here, by applying scaled single-cell whole-genome sequencing3 to wild-type, TP53-deficient and TP53-deficient;BRCA1-deficient or TP53-deficient;BRCA2-deficient mammary epithelial cells (13,818 genomes), and to primary triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSC) cells (22,057 genomes), we identify three distinct ‘foreground’ mutational patterns that are defined by cell-to-cell structural variation. Cell- and clone-specific high-level amplifications, parallel haplotype-specific copy number alterations and copy number segment length variation (serrate structural variations) had measurable phenotypic and evolutionary consequences. In TNBC and HGSC, clone-specific high-level amplifications in known oncogenes were highly prevalent in tumours bearing fold-back inversions, relative to tumours with homologous recombination deficiency, and were associated with increased clone-to-clone phenotypic variation. Parallel haplotype-specific alterations were also commonly observed, leading to phylogenetic evolutionary diversity and clone-specific mono-allelic expression. Serrate variants were increased in tumours with fold-back inversions and were highly correlated with increased genomic diversity of cellular populations. Together, our findings show that cell-to-cell structural variation contributes to the origins of phenotypic and evolutionary diversity in TNBC and HGSC, and provide insight into the genomic and mutational states of individual cancer cells.

Ovarian cancer mutational processes drive site-specific immune evasion

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amplification-associated foldback inversion (FBI)-bearing tumours and CDK12-associated tandem duplicator (TD)-bearing tumours 5,6 .HGSOC presents a distinctive clinical challenge resulting from the widespread intraperitoneal disease at diagnosis. Long latency allows for broad periods of clonal diversification and tumour-immune interactions to unfold in the heterogeneous microenvironments of the peritoneal cavity 7,10,17 .

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“…amplification-associated foldback inversion (FBI)-bearing tumours and CDK12-associated tandem duplicator (TD)-bearing tumours 5,6 .…”

“…High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability [1][2][3][4] patterned by distinct mutational processes 5,6 , tumour heterogeneity [7][8][9] and intraperitoneal spread 7,8,10 . Immunotherapies have had limited efficacy in HGSOC [11][12][13] , highlighting an unmet need to assess how mutational processes and the anatomical sites of tumour foci determine the immunological states of the tumour microenvironment.…”

scAbsolute: measuring single-cell ploidy and replication status

“…The approach is fundamentally different from other approaches originally developed in bulk sequencing settings and recently extended to the single-cell domain 53 that use B-allele frequency (BAF) in order to help identify ploidy solutions. However, by using cell specific haplotype counts, and the high quality total copy number predictions provided by scAbsolute , it is possible to estimate allele and haplotype specific copy number states, as recently demonstrated 48,53 . In particular, it is straightforward to estimate the allele specific copy numbers using the BAF as estimator, once the total copy number is known.…”

“…Existing computational methods are unable to distinguish these cases. In practice, tools such as HMMCopy 46 are commonly used 39,41,47,48 and serve as the basis for some novel copy number callers 49,50 . Gingko 51 shows improved performance for calling of accurate ploidy on a single cell level 52 .…”