Genetic imbalances detected by multiplex ligation-dependent probe amplification in a cohort of patients with oral squamous cell carcinoma—the first step towards clinical personalized medicine

Abstract

Oral tumors are a growing health problem worldwide; thus, it is mandatory to establish genetic markers in order to improve diagnosis and early detection of tumors, control relapses and, ultimately, delineate individualized therapies. This study was the first to evaluate and discuss the clinical applicability of a multiplex ligation-dependent probe amplification (MLPA) probe panel directed to head and neck cancer. Thirty primary oral squamous cell tumors were analyzed using the P428 MLPA probe panel. We detected genetic imbalances in 26 patients and observed a consistent pattern of distribution of genetic alterations in terms of losses and gains for some chromosomes, particularly for chromosomes 3, 8, and 11. Regarding the latter, some specific genes were highlighted due to frequent losses of genetic material--RARB, FHIT, CSMD1, GATA4, and MTUS1--and others due to gains--MCCC1, MYC, WISP1, PTK2, CCND1, FGF4, FADD, and CTTN. We also verified that the gains of MYC and WISP1 genes seem to suggest higher propensity of tumors localized in the floor of the mouth. This study proved the value of this MLPA probe panel for a first-tier analysis of oral tumors. The probemix was developed to include target regions that have been already shown to be of diagnostic/prognostic relevance for oral tumors. Furthermore, this study emphasized several of those specific genetic targets, suggesting its importance to oral tumor development, to predict patients' outcomes, and also to guide the development of novel molecular therapies.

Differences in cancer gene copy number alterations between Epstein‐Barr virus‐positive and Epstein‐Barr virus‐negative nasopharyngeal carcinoma

“…22 The PIK3CA has a function in cell growth, proliferation, survival, and evasion of growth suppressors in tumor cells. Gain/ amplification of PIK3CA and MCCC1 have already been reported in HNSCC.…”

“…Gain/ amplification of PIK3CA and MCCC1 have already been reported in HNSCC. 22 The PIK3CA has a function in cell growth, proliferation, survival, and evasion of growth suppressors in tumor cells. 23 In our cohort, however, no correlation with survival could be demonstrated for PIK3CA, thus gain/ amplification of PIC3CA can be best classified as a passenger event, or an event in the framework of older age.…”

Genetic and epigenetic characterization of the tumors in a patient with a tongue primary tumor, a recurrence and a pharyngoesophageal second primary tumor

“…We analyzed copy number alterations (CNAs) of the three tumor samples through array Comparative Genomic Hybridization (aCGH) using Agilent SurePrint G3 Human Genome microarray 180K, (Agilent technologies, Santa Clara, CA) as previously described [9]. Multiplex Ligation-dependent Probe Amplification (MLPA) and Methylation Specific MLPA (MS-MLPA) using the P248 and ME002 SALSA probemixes (MRC-Holland, Amsterdam, The Netherlands) were performed in tumor and non-tumor tissue samples in order to simultaneously evaluate the CNAs and methylation patterns in a specific set of genes as we previously described [10, 11]. DNA from gender-matched gingival tissue of healthy subjects submitted to wisdom teeth removal was used as controls.…”

Copy number profiling of tumor suppressor genes in head and neck cancer

“…The power of MLPA has not been evaluated for the analysis of gene copy numbers in head and neck cancer. The method has only been used to analyze the methylation profiles in head and neck tumors in very few studies and there is only a single recent publication in the literature investigating genetic imbalances in oral tumors . Recent studies indicate that methylation‐induced silencing of various tumor suppressor genes and involvement of copy number alterations, in addition to the wide distribution of somatic genetic alterations, contribute to the development of head and neck cancer .…”

“…The method has only been used to analyze the methylation profiles in head and neck tumors in very few studies [22][23][24] and there is only a single recent publication in the literature investigating genetic imbalances in oral tumors. 25 Recent studies indicate that methylation-induced silencing of various tumor suppressor genes and involvement of copy number alterations, in addition to the wide distribution of somatic genetic alterations, contribute to the development of head and neck cancer. [26][27][28][29][30] The purpose of this study was to provide a confirmatory study in a specific cohort of head and neck tumors to elucidate the role of the common tumor suppressor genes that are frequently silenced by methylation and have been associated with different types of cancers as well as with head and neck cancer.…”