Comprehensive Analysis Transcriptome And Epigenetics Of Circulating Tumor Cells Based On Single Cell Sequencing Technology

Circulating tumor cells(CTCs)are malignant cells that depart from cancerous lesions and shed into the bloodstream.Studies have reported the significance of CTC transcriptomes,but these efforts only focus on gene expression or genetic mutations in a single cancer type.Although CTCs from different tumor types have their unique characters,there are also some features that are common to different tumor types.Therefore,identification of both tumor-specific and common features through pancancer analysis may have significant implications for the tumor diagnosis and detection.In addition,high-throughput technologies have become a powerful tool to provide a genomewide view of transcriptomic changes associated with CTCs.Unfortunately,these data have been deposited into various repositories,and a uniform resource for the cancer metastasis is still unavailable.To address these issues,we integrated CTC transcriptomes of six cancer types and systematically compared the concordant and discordant expression profiles of CTCs with primary tumors.Our study revealed the shared and distinct transcript signatures of CTCs and found 72 genes that are specifically activated in CTCs.We summarized a general gene expression profile for CTCs in pan-cancer.Moreover,our findings demonstrated the effectiveness of CTC genes expression as biomarkers for tracing the tissue of origin of cancers.Then,we integrated previously published transcriptome datasets of CTCs and constructed a web-accessible database(ctc Rbase).ctc Rbase also collected the expression data of primary tumors and metastases,which allows user to discover a unique ‘circulating tumor cell gene signature’ that is distinct from primary tumor and metastases.An easy-to-use search engine was constructed to query and browse CTC genes.Moreover,DNA methylation plays a pivotal role in regulating cellular processes,and altered DNA methylation pattern is a general hallmark of cancer.However,DNA methylome in circulating tumor cells(CTCs)is still a mystery due to the lack of proper analytical techniques.We introduced an efficient workflow,LCM–sc WGBS,which can efficiently profile the DNA methylation of microdissected CTC samples.LCM–sc WGBS combines the laser capture microdissection(LCM)-based CTC capture method and whole-genome bisulfite sequencing in very small CTC population(sc WGBS)to gain insight into the DNA methylation landscape of CTCs.We herein profiled the DNA methylome of CTCs from lung cancer patients.Deriving from a comprehensive analysis of CTC methylome,a unique ‘CTC DNA methylation signature’ that is distinct from primary lung cancer tissues was identified.This work constitutes a unique DNA methylation analysis of CTCs at single base-pair resolution,which might facilitate to propose noninvasive CTC DNA methylation biomarkers contributing to clinical diagnosis.All in all,we progressed comprehensive analysis of CTCs in whole transcriptomes and whole genome methylation levels.We believe our work in CTC analysis will provide a roadmap for further analysis in exploring and verifying molecular signatures of CTCs for monitoring early cancer detection.