Genomic Variants And Single-Cell Transcriptomic Alterations In Esophageal Squamous-Cell Carcinoma

Esophageal squamous-cell carcinoma(ESCC)is one of the most common malignancies in the world and has higher mortality rate in Asian countries,particularly in China.Genome and transcriptome abnormalities play important roles in cancer development and progression.Systematically analyzing the genomic variants and transcriptomic alterations in ESCC is extremely important for elucidating the molecular pathogenesis of ESCC and improving patient outcomes in ESCC.Genomic variants including germline mutations and somatic mutations are changes in the base sequence of DNA.While genome-wide association studies(GWAS)have identified multiple germline mutations(i.e.,single nucleotide polymorphisms(SNPs))associated with ESCC risk or patients' survival and whole-genome/exome sequencing studies have discovered multiple somatic mutations associated with ESCC progression,there is no comprehensive association study for this cancer.To comprehensively analyze the associations of germline mutations and somatic mutations with ESCC development and progression,we have performed association analyses between germline mutations or somatic mutations and ESCC risk or patients' overall survival at the genome-wide level.Moreover,we have developed the Chinese Cancer Genomic Database-Esophageal Squamous Cell Carcinoma(CCGD-ESCC)database to share association results,which is freely accessible at http://db.cbi.pku.du.cn/ccgd/ESCCdb/index.html.CCGD-ESCC has integrated the association results of 16,544 SNPs with cancer risk in 2,022 ESCC cases and 2,039 controls and association results of 1,652 SNPs with disease outcome in 1,006 ESCC patients as well as association results between 8,833 somatic mutations and survival time in 675 ESCC patients.Based on bulk whole genome sequencing data and bulk RNA-seq data of 94 ESCC patients,we have also integrated association results of cis expression quantitative trait loci(eQTL)analysis for 15,742 SNPs in ESCC tumors and 46,361 SNPs in adjacent normal tissues.ESCC has a complex but unknown tumor ecosystem.Elucidating the transcriptome characteristics of cancer cells and the microenvironment components and their interactions is basic and fundamental in further understanding the cancer and developing effective early diagnosis and treatment strategies.In this study,we have performed single-cell RNA sequencing(scRNA-seq)in 208,659 cells from ESCC tumor and their adjacent normal samples collected from 60 patients and deciphered for the first time the phenotypes and compositions of the ESCC ecosystem.We have also performed bulk whole-exome/genome sequencing for the same ESCC tumors and paired peripheral blood samples and incorporated genomic data for analysis.We identify 8 essential expression programs from malignant epithelial cells and discover 43 stromal cell types including 26 immune cell subtypes and 17 nonimmune cell subtypes in the tumor microenvironment(TME).We also explicate the interactions between cancer cells and other stromal cells and the interactions among different cell types in the TME.Moreover,we have dissected the relationships between ESCC ecosystem components and genomic alterations and identified several markers significantly associated with survival time in patients,which may be relevant to precision cares of ESCC patients.In conclusion,this study has systematically deciphered the ESCC-associated germline mutations and somatic mutations in Chinese populations and constructed the CCGD-ESCC database to share association results,which will be beneficial for many areas,including basic research as well as clinical application.These results of scRNA-seq analysis deepen and extend our understanding of the complexity of ESCC tumors and provide a valuable example and resource for investigating other types of solid tumor.