title: Genomic analyses reveal mutational signatures and frequently altered genes in esophageal squamous cell carcinoma.
abstract: Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers worldwide and the fourth most lethal cancer in China. However, although genomic studies have identified some mutations associated with ESCC, we know little of the mutational processes responsible. To identify genome-wide mutational signatures, we performed either whole-genome sequencing (WGS) or whole-exome sequencing (WES) on 104 ESCC individuals and combined our data with those of 88 previously reported samples. An APOBEC-mediated mutational signature in 47% of 192 tumors suggests that APOBEC-catalyzed deamination provides a source of DNA damage in ESCC. Moreover, PIK3CA hotspot mutations (c.1624G>A [p.Glu542Lys] and c.1633G>A [p.Glu545Lys]) were enriched in APOBEC-signature tumors, and no smoking-associated signature was observed in ESCC. In the samples analyzed by WGS, we identified focal (<100 kb) amplifications of CBX4 and CBX8. In our combined cohort, we identified frequent inactivating mutations in AJUBA, ZNF750, and PTCH1 and the chromatin-remodeling genes CREBBP and BAP1, in addition to known mutations. Functional analyses suggest roles for several genes (CBX4, CBX8, AJUBA, and ZNF750) in ESCC. Notably, high activity of hedgehog signaling and the PI3K pathway in approximately 60% of 104 ESCC tumors indicates that therapies targeting these pathways might be particularly promising strategies for ESCC. Collectively, our data provide comprehensive insights into the mutational signatures of ESCC and identify markers for early diagnosis and potential therapeutic targets.
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mesh_terms: D000071479:APOBEC-1 Deaminase; D000704:Analysis of Variance; D001483:Base Sequence; D050882:CREB-Binding Protein / Q000235:genetics; D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D045744:Cell Line, Tumor; D002681:China; D058534:Class I Phosphatidylinositol 3-Kinases; D003564:Cytidine Deaminase / Q000235:genetics*; D056915:DNA Copy Number Variations / Q000235:genetics; D004938:Esophageal Neoplasms / Q000235:genetics*; D000077277:Esophageal Squamous Cell Carcinoma; D055785:Gene Knockdown Techniques; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D015151:Immunoblotting; D007150:Immunohistochemistry; D017404:In Situ Hybridization, Fluorescence; D060588:LIM Domain Proteins / Q000235:genetics; D008025:Ligases; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics*; D000072079:Patched Receptors; D000072081:Patched-1 Receptor; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics*; D063150:Polycomb Repressive Complex 1 / Q000235:genetics; D063146:Polycomb-Group Proteins / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D011956:Receptors, Cell Surface / Q000235:genetics; D017422:Sequence Analysis, DNA; D015398:Signal Transduction / Q000235:genetics*; D013778:Tetrazolium Salts; D013844:Thiazoles; D014157:Transcription Factors / Q000235:genetics; D025521:Tumor Suppressor Proteins / Q000235:genetics; D043222:Ubiquitin Thiolesterase / Q000235:genetics; D044767:Ubiquitin-Protein Ligases / Q000235:genetics
chemical_list: D000071479:APOBEC-1 Deaminase; D050882:CREB-Binding Protein; D058534:Class I Phosphatidylinositol 3-Kinases; D003564:Cytidine Deaminase; D060588:LIM Domain Proteins; D008025:Ligases; D000072079:Patched Receptors; D000072081:Patched-1 Receptor; D019869:Phosphatidylinositol 3-Kinases; D063150:Polycomb Repressive Complex 1; D063146:Polycomb-Group Proteins; D011956:Receptors, Cell Surface; D013778:Tetrazolium Salts; D013844:Thiazoles; D014157:Transcription Factors; D025521:Tumor Suppressor Proteins; D043222:Ubiquitin Thiolesterase; D044767:Ubiquitin-Protein Ligases; C485608:AJUBA protein, human; C400134:BAP1 protein, human; C570428:CBX8 protein, human; C000606236:PTCH1 protein, human; C570799:ZNF750 protein, human; C494363:CREBBP protein, human; C484760:PIK3CA protein, human; C000605089:APOBEC1 protein, human; C570427:CBX4 protein, human; C022616:thiazolyl blue
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