Evaluation Of Molecular Alterations In Esophageal Squamous Cell Carcinoma Using RNA Sequencing (RNA-seq)

NETO P. ¹ , BREWER L. ² , MENEZES A. ³ , BORONI M. ¹ , MOREIRA M. ¹ , SEUANEZ H. ¹ , SIMAO T. ² , PINTO L. ^1,2

Esophageal cancer is the eighth most frequent cancer type and the sixth most lethal worldwide. There are two main histological types of this disease, but the most frequent is esophageal squamous cell carcinoma (ESCC). ESCC represents a challenge regarding its diagnosis and treatment. The 5-year survival for this cancer is less than 10%, mainly due to late diagnosis. Characterizing the molecular alterations present in ESCC can help identifying possible targets for diagnosis and treatment improval. Thus, this study aimed to analyze the gene expression and mutational profiles, and the presence of gene fusions by RNA sequencing in 14 ESCC samples and matched non-malignant mucosa. When comparing ESCC and adjacent mucosa 6,698 genes were classified as differentially expressed. The enrichment analysis using KEGG database revealed pathways mainly related to inflammation and others linked to cancer. The thorough analysis of Pathways in Cancer led to the observation of an enrichment of the WNT signaling pathway in which three members had impact on overall survival (WNT16, WNT7B and FZD6). WNT7B overexpression and impact on prognosis were validated in an independent cohort. The mutational analysis revealed that TP53 is the most frequently mutated gene in ESCC with a frequency of around 80%, both in the training and validation cohorts. The evaluation of gene fusions revealed 21 events in seven tumors with no common alterations among samples. The presence of gene fusions was not associated with any clinic-pathological characteristic , but samples with this profile showed an increased expression of ATR. Our data suggests a role for the WNT-signaling pathway in ESCC progression and proposes new prognostic factors. Also, we show for the first time such a high frequency of TP53 mutations in Brazilian samples. Finally, the gene fusion phenomena seems to be a consequence and not a cause of ESCC development.