Nucleotide variants and protein expression of TP53 in a Sri Lankan cohort of patients with head and neck cancer

Abstract

Head and neck cancer (HNC) is the leading cancer in Sri Lankan males and second most common cancer among Sri Lankan females. This is the first study, to the best of our knowledge, that has focused on investigating the association between TP53 somatic DNA variants, with p53 protein expression and risk factors in a cohort of Sri Lankan patients with HNC. A total of 44 patients with cancer and 20 healthy controls were studied. In total, 36 genomic DNA sequence variants were found, including several novel variants (two deletions in exons 4 and 6, two in the 3' untranslated region and several intronic variants). A total of 14 tumour samples carried pathogenic TP53 mutations. A random selection of 24 samples was analysed immunohistochemically for p53 protein expression. All the samples with point missense variants were strongly immuno‑positive, whereas, samples with nonsense and frameshift TP53 variants were immuno‑negative for p53 immunohistochemical staining. Although, the human papilloma virus is a known risk factor for HNC, results from the present study identified an absence or lower level of infection in the Sri Lankan cohort.

Figure 1.

Novel frameshift variant c.298delC/p.Gln100Argfs*23 detected in Exon 4. (A) Mutation Surveyor^®V4.0.9 image indicating the one base pair heterozygous deletion point; R indicates the reference TP53 sequence and S indicates the study sample TP53 sequence. (B) p53 immunohistochemical staining of the tumour sample with the above mutation. Magnification, ×20. (C) Protein prediction using Mutalyzer 2.0.26.

Figure 2.

Novel in-frame deletion c.626_637delGAAACACTTTTC/p.Asn210_Arg213del detected in exon 6. (A) Mutation Surveyor^®V4.0.9 image indicating the 12-base pair heterozygous deletion; R indicates the reference TP53 sequence and S indicates the study sample TP53 sequence. (B) Protein prediction using Mutalyzer 2.0.26.

Figure 3.

IHC characterization of p53 detected by DO7 antibody. (A) Pattern A with wide spread IHC positive nuclei-IHC score >20. (B) Pattern B with rare positive single tumour nuclei-IHC score from ≥1 to ≤20; arrows indicate the rare positive cells. (C) Pattern C with no IHC positive nuclei-IHC score from 0 to <1. Magnification, ×20. IHC, immunohistochemistry.

Figure 4.

Detection of p16 expression using Ventana Benchmark XT Automated immunohistochemistry/in situ hybridization slide staining system. (A) Positive control showing positive staining of nuclei and cytoplasm. (B) A study sample with negative staining. Magnification, ×20.