Genomic characterization of tobacco/nut chewing HPV-negative early stage tongue tumors identify MMP10 as a candidate to predict metastases

Abstract Objectives Nodal metastases status among early stage tongue squamous cell cancer patients plays a decisive role in the choice of treatment, wherein about 70% patients can be spared from surgery with an accurate prediction of negative pathological lymph node status. This underscores an unmet need for prognostic biomarkers to stratify the patients who are likely to develop metastases. Materials and methods We performed high throughput sequencing of fifty four samples derived from HPV negative early stage tongue cancer patients habitual of chewing betel nuts, areca nuts, lime or tobacco using whole exome (n = 47) and transcriptome (n = 17) sequencing that were analyzed using in-house computational tools. Additionally, gene expression meta-analyses were carried out for 253 tongue cancer samples. The candidate genes were validated using qPCR and immuno-histochemical analysis in an extended set of 50 early primary tongue cancer samples. Results and conclusion Somatic analysis revealed a classical tobacco mutational signature C:G > A:T transversion in 53% patients that were mutated in TP53 , NOTCH1 , CDKN2A , HRAS , USP6 , PIK3CA , CASP8 , FAT1 , APC , and JAK1 . Similarly, significant gains at genomic locus 11q13.3 ( CCND1 , FGF19 , ORAOV1 , FADD ), 5p15.33 ( SHANK2 , MMP16 , TERT ), and 8q24.3 ( BOP1 ); and, losses at 5q22.2 ( APC ), 6q25.3 ( GTF2H2 ) and 5q13.2 ( SMN1 ) were observed in these samples. Furthermore, an integrated gene-expression analysis of 253 tongue tumors suggested an upregulation of metastases-related pathways and over-expression of MMP10 in 48% tumors that may be crucial to predict nodal metastases in early tongue cancer patients. In overall, we present the first descriptive portrait of somatic alterations underlying the genome of tobacco/nut chewing HPV-negative early tongue cancer, and identify MMP10 as a potential prognostic biomarker to stratify those likely to develop metastases.