Single cell genomic variation induced by mutational processes in cancer

How cell-to-cell copy number alterations that underpin genomic instability in human cancers drive genomic and phenotypic variation, and consequently cancer evolution, remains understudied. Here, applying scaled single cell whole genome sequencing to wildtype, TP53-deficient and TP53/BRCA1/2-deficient mammary epithelial cells (n=13,818 genomes) and primary triple negative breast (TNBC) and high grade serous ovarian cancers (HGSC) (n=22,057 genomes), we identified three distinct ‘foreground’ mutational patterns defined by cell-to-cell copy number and structural variation properties occurring in the ‘background’ of cancer-associated genomic instability. Cell and clone-specific high level amplifications (HLAMPs), parallel allele-specific copy number alterations and copy number segment length variation (serrate structural variations) exhibited measurable phenotypic and evolutionary consequences. Clone-specific HLAMPs in known oncogenes were highly prevalent in fold back inversion (FBI)-bearing tumors and associated with increased clone-to-clone phenotypic variation in gene expression inferred from matched single cell RNASeq. Parallel allele-specific alterations were linked with phylogenetically determined evolutionary diversity and clone-specific mono-allelic expression. Serrate patterns present across all clones were increased in FBI tumors, most prominently on a tetraploid background and were highly correlated with increased genomic diversity of cellular populations. Taken together, we show that cell-to-cell structural-copy number variation significantly impacts the phenotypes and evolutionary diversity of TNBC and HGSC, revealing previously hidden genomic states of cancer cells.EGA study EGAS00001006343

人类癌症中驱动基因组不稳定性的细胞间拷贝数变异，如何推动基因组与表型变异、进而促进癌症演化，这一问题迄今仍未得到充分探究。本研究对野生型、TP53缺陷型以及TP53/BRCA1/2三缺陷型乳腺上皮细胞（共13818个基因组）与原发性三阴性乳腺癌（triple negative breast cancer, TNBC）、高级别浆液性卵巢癌（high grade serous ovarian cancer, HGSC）样本（共22057个基因组）应用规模化单细胞全基因组测序技术，在癌症相关基因组不稳定性的“背景”特征中，鉴定出三种由细胞间拷贝数与结构变异属性定义的独特“前景”突变模式。细胞与克隆特异性高水平扩增（high level amplifications, HLAMPs）、平行等位基因特异性拷贝数变异，以及拷贝数片段长度变异（锯齿状结构变异，serrate structural variations）均表现出可被检测的表型与演化效应。已知癌基因中的克隆特异性HLAMPs在携带反向折叠倒位（fold back inversion, FBI）的肿瘤中高度常见，且与通过匹配单细胞RNA测序（single cell RNASeq）推断的基因表达中克隆间表型变异程度升高相关。平行等位基因特异性变异与系统发育定义的演化多样性，以及克隆特异性单等位基因表达存在关联。在所有克隆中均存在的锯齿状变异模式，在携带FBI的肿瘤中更为显著，尤以四倍体背景下最为突出，且与细胞群体基因组多样性升高呈高度相关。综上，本研究证实细胞间结构-拷贝数变异可显著影响TNBC与HGSC的表型及演化多样性，揭示了此前未被发现的癌细胞基因组状态。[EGA研究编号：EGAS00001006343]