Identification of mutations in the PYRIN-containing NLR genes (NLRP) in Head and Neck Squamous Cell Carcinoma

Abstract

Head and Neck Squamous Cell Carcinoma (HNSCC) encompasses malignancies that arise in the mucosa of the upper aerodigestive tract. Recent high throughput DNA sequencing revealed HNSCC genes mutations that contribute to several cancer cell characteristics, including dysregulation of cell proliferation and death, intracellular proinflammatory signaling, and autophagy. The PYRIN-domain containing NLR (Nucleotide-binding domain, Leucine rich Repeats - containing) proteins have recently emerged as pivotal modulators of cell death, autophagy, inflammation, and metabolism. Their close physiologic association with cancer development prompted us to determine whether mutations within the NLRP (PYRIN-containing NLR) gene family were associated with HNSCC genome instability and their clinicopathologic correlations. Catastrophic mutational events underlie cancer cell genome instability and mark a point-of-no-return in cancer cell development and generation of heterogeneity. The mutation profiles of 62 patients with primary conventional type HNSCC excluding other histologic variants were analyzed. Associations were tested using Fisher's Exact test or Mann-Whitney U test. Mutations in NLRP were associated with elevated genome instability as characterized by higher mutation rates. Clinically, NLRP mutations were more frequently found in HNSCC arising in the floor of mouth (50.0%) in comparison with HNSCC at other head and neck locations (14.8%). These mutations were clustered at the leucine rich repeats region of NLRP proteins, and affected NLRP genes were mostly localized at chromosomes 11p15.4 and 19q13.42-19q13.43. Twenty novel NLRP mutations were identified in HNSCC, and mutations in this group of genes were correlated with increased cancer cell genome mutation rates, and such features could be a potential molecular biomarker of HNSCC genome instability.

Figure 1. Identification of NLRP mutations in FOM HNSCC.

Mutations in four NLRP genes were identified in FOM HNSCC patients. Black triangles indicate novel mutations identified in this study. Gray triangles represent reported mutations in the Catalogue of Somatic Mutations in Cancer (COSMIC) database.

Figure 2. Mutation rates comparisons.

(A) Numbers of missense and nonsense mutations were compared between tumors with or without NLRP mutations. (B) Numbers of missense and nonsense mutations were compared between tumors with or without TP53 mutations. (C) Numbers of missense and nonsense mutations were compared between tumors with or without TLR genes mutations. (D) Mutation rates [shown as mutations per million base (MB) pairs] were compared between tumors with or without NLRP mutations. (E) Mutation rates [shown as mutations per million base (MB) pairs] were compared between tumors with or without TP53 mutations. (F) Mutation rates [shown as mutations per million base (MB) pairs] were compared between tumors with or without TLR genes mutations. P value less than 0.05 was considered significant.

Figure 3. Mutation rates of FOM HNSCC.

(A) Numbers of missense and nonsense mutations were compared between patients with FOM or non-FOM HNSCC. (B) Mutation rates were compared between patients with FOM or non-FOM HNSCC.

Figure 4. Determination of factors affecting overall survival.

Patients overall survival analyses were made between two groups: (A) patients with or without mutations in NLRP genes; (B) patients with or without mutations in TP53 genes; (C) patients with tumors that harbored TLR mutations and those without TLR mutations; (D) patients with or without HPV infections; (E) patients with low stage (stage II) or advanced stage (stage III and beyond) tumors; (F) patients of less or more than 56 years old; (G) patients who received no adjuvant therapy, radiotherapy alone or both chemotherapy and radiotherapy.