Yong Hou:
Understanding Cancer Genome and Its Evolution by Next Generation Sequencing

Date: 15-12-2016    Supervisor: Jun Wang & Karsten Kristiansen

Cancer will cause 13 million deaths by the year of 2030, ranking the second leading cause of death worldwide. Previous studies indicate that most of the cancers originate from cells that acquired somatic mutations and evolved as Darwin Theory. Ten biological insights of cancer have been summarized recently. Cutting-age technologies like next generation sequencing (NGS) enable exploring cancer genome and evolution much more efficiently. However, integrated cancer genome sequencing studies showed great inter-/intra-tumoral heterogeneity (ITH) and complex evolution patterns beyond the cancer biological knowledge we previously know.

There is very limited knowledge of East Asia lung cancer genome except enrichment of EGFR mutations and lack of KRAS mutations. We carried out integrated genomic, transcriptomic and methylomic analysis of 335 primary Chinese lung adenocarcinomas (LUAD) and 35 corresponding lymph node metastases. We discovered novel recurrent mutated genes such as RHPN2, GLI3 and MRC2 and significant copy number variations (CNVs) in IQGAP3 that have never been reported previously in The Cancer Genome Atlas (TCGA) study. To improve the variation calling accuracy in the lymph node metastatic tumor, we also developed tumor purity estimating tool-MethylPurify. With the help of this tool, we found quite different mutation pattern in the lymph node metastatic tumor compared with the primary tumor, such as lack of KRAS mutations and enrichment of TP53 mutations.

To investigate the ITH and cancer evolution by NGS, we first developed high throughput single cell sequencing (SCS) pipeline on whole exome and trascriptome and updated the pipeline after systematically reviewed the existed single cell whole genome amplification (WGA) and whole transcriptome amplification methods. Using SCS pipeline we developed, we demonstrated that cells in a primary colon tumor showed genetic mosaic during the evolution. More importantly, we also showed that subclonally mutated gene-SLC12A5 might play potential oncogenic role by in vitro study. In combining with SNP array, WGS and SCS, we provided a comprehensive dynamic molecular landscape of the indolent disease, acute disease, response to therapy and remission, and finally relapsed disease of a 29-year following up chronic lymphocytic leukaemia (CLL) patient. What’s more, we also demonstrated the feasibility of combining liquid biopsy and SCS to analyse circulating tumor cells (CTCs) and infer the heterogeneity and evolution of solid tumors after relapsed. Taken together, we showed that NGS on cancers could provide novel biological insights of cancer genetics and SCS may serve as powerful tool to investigate the ITH and evolution of both primary tumor and metastatic/relapse tumor.