Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing

Chang Yu, Jun Yu, Xiaotian Yao, William KK Wu, Youyong Lu, Senwei Tang, Xiangchun Li, Li Bao, Xiaoxing Li, Yong Hou, Renhua Wu, Min Jian, Ruoyan Chen, Fan Zhang, Lixia Xu, Fan Fan, Jun He, Qiaoyi Liang, Hongyi Wang, Xueda Hu, Minghui He, Xiang Zhang, Hancheng Zheng, Qibin Li, Hanjie Wu, Yan Chen, Xu Yang, Shida Zhu, Xun Xu, Huanming Yang, Jian Wang, Xiuqing Zhang, Joseph JY Sung, Yingrui Li, Jun Wang

Single-cell sequencing is a powerful tool for delineating clonal relationship and identifying key driver genes for personalized cancer management. Here we performed single-cell sequencing analysis of a case of colon cancer. Population genetics analyses identified two independent clones in tumor cell population. The major tumor clone harbored APC and TP53 mutations as early oncogenic events, whereas the minor clone contained preponderant CDC27 and PABPC1 mutations. The absence of APC and TP53 mutations in the minor clone supports that these two clones were derived from two cellular origins. Examination of somatic mutation allele frequency spectra of additional 21 whole-tissue exome-sequenced cases revealed the heterogeneity of clonal origins in colon cancer. Next, we identified a mutated gene SLC12A5 that showed a high frequency of mutation at the single-cell level but exhibited low prevalence at the population level. Functional characterization of mutant SLC12A5 revealed its potential oncogenic effect in colon cancer. Our study provides the first exome-wide evidence at single-cell level supporting that colon cancer could be of a biclonal origin, and suggests that low-prevalence mutations in a cohort may also play important protumorigenic roles at the individual level.