Association of Inherited Copy Number Variation in ADAM3A and ADAM5 Pseudogenes with Oropharynx Cancer Risk and Outcome

Abstract

Inherited copy number variations (CNVs) can provide valuable information for cancer susceptibility and prognosis. However, their association with oropharynx squamous cell carcinoma (OPSCC) is still poorly studied. Using microarrays analysis, we identified three inherited CNVs associated with OPSCC risk, of which one was validated in 152 OPSCC patients and 155 controls and related to pseudogene-microRNA-mRNA interaction. Individuals with three or more copies of ADAM3A and ADAM5 pseudogenes (8p11.22 chromosome region) were under 6.49-fold increased risk of OPSCC. ADAM5 shared a highly homologous sequence with the ADAM9 3'-UTR, predicted to be a binding site for miR-122b-5p. Individuals carrying more than three copies of ADAM3A and ADAM5 presented higher ADAM9 expression levels. Moreover, patients with total deletion or one copy of pseudogenes and with higher expression of miR-122b-5p presented worse prognoses. Our data suggest, for the first time, that ADAM3A and ADAM5 pseudogene-inherited CNV could modulate OPSCC occurrence and prognosis, possibly through the interaction of ADAM5 pseudogene transcript, miR-122b-5p, and ADAM9.

Keywords: ADAM3A; ADAM5; copy number variation; microRNA; oropharynx squamous cell carcinoma; pseudogene.

Figure 1

Potential pseudogene-microRNA(miRNA)-mRNA interaction and head-and-neck squamous cell carcinoma (HNSCC) prognosis. (A) Predicted miRNA miR-122b-5p binding site at ADAM5 pseudogene-derived transcript and at ADAM9 3′-unstranslated region (7mer-m8 site). The miRNA “seed” region is presented in underlined font. The homologous sequence between ADAM5 and ADAM9 is represented in bold letters. (B) ADAM3A and ADAM5 pseudogenes copy number variation and ADAM9 expression in oropharyngeal squamous cell carcinoma (OPSCC) patients. The mean mRNA expression level was higher in OPSCC patients with copy number gain of the ADAM3A and ADAM5 pseudogenes (n = 5) (2.04 arbitrary units (AUs) ± standard deviation (SD): 0.89) than carriers of total deletion, one, or two copies (n = 21) (1.12 AUs ± SD: 0.67, p = 0.02). (C,D) Probability of event-free survival (EFS) of 139 OPSCC patients stratified by ADAM3A and ADAM5 copy number variation. (C) The Kaplan–Meier curve suggests that CNVs status seems to have an association with EFS (p = 0.05). (D) The Kaplan–Meier curve indicates lower EFS in patients with total deletion or one copy of ADAM3A and ADAM5 pseudogenes (19.1% vs. 50.7%, p = 0.04) when compared with carriers of two or more copies. (E,F) Prognostic value of ADAM3A and ADAM5, and miR-122 in 124 and 522 HNSCC patients, respectively, according to the Kaplan–Meier Plotter online database. (E) Lower expression of pseudogenes ADAM3A and ADAM5 indicated lower relapse-free survival (RFS) in HNSCC patients. (F) Although RFS data was not available for miRNAs, higher expression of miR-122b-5p was associated with lower overall survival in HNSCC patients.