Analysis of the TCGA Dataset Reveals that Subsites of Laryngeal Squamous Cell Carcinoma are Molecularly Distinct.
Alana SorginiHugh Andrew Jinwook KimPeter Y F ZengMushfiq Hassan ShaikhNeil MundiFarhad GhasemiEric Di GravioHalema KhanDanielle MacNeilMohammed Imran KhanAdrian MendezJohn YooKevin FungPencilla LangDavid A PalmaJoe S MymrykJohn W BarrettKrupal B PatelPaul C BoutrosAnthony Charles NicholsPublished in: Cancers (2020)
Laryngeal squamous cell carcinoma (LSCC) from different subsites have distinct presentations and prognosis. In this study, we carried out a multiomic comparison of LSCC subsites. The Cancer Genome Atlas (TCGA) LSCC cohort was analyzed in the R statistical environment for differences between supraglottic and glottic cancers in single nucleotide variations (SNVs), copy number alterations (CNAs), mRNA abundance, protein abundance, pathway overrepresentation, tumor microenvironment (TME), hypoxia status, and patient outcome. Supraglottic cancers had significantly higher overall and smoking-associated SNV mutational load. Pathway analysis revealed upregulation of muscle related pathways in glottic cancer and neural pathways in supraglottic cancer. Proteins involved in cancer relevant signaling pathways including PI3K/Akt/mTOR, the cell cycle, and PDL1 were differentially abundant between subsites. Glottic and supraglottic tumors have different molecular profiles, which may partially account for differences in presentation and response to therapy.
Keyphrases
- papillary thyroid
- squamous cell carcinoma
- cell cycle
- copy number
- squamous cell
- lymph node metastasis
- cell proliferation
- signaling pathway
- genome wide
- case report
- single cell
- stem cells
- dna methylation
- small molecule
- oxidative stress
- rectal cancer
- poor prognosis
- mesenchymal stem cells
- locally advanced
- protein protein
- amino acid
- data analysis