Array Comparative Genomic Hybridization Analysis Reveals Significantly Enriched Pathways in Canine Oral Melanoma

Abstract

Human Mucosal Melanoma (hMM) is an aggressive neoplasm of neuroectodermal origin with distinctive features from the more common cutaneous form of malignant melanoma (cMM). At the molecular level, hMMs are characterized by large chromosomal aberrations rather than single-nucleotide mutations, typically observed in cMM. Given the scarcity of available cases, there have been many attempts to establish a reliable animal model. In pet dogs, Canine Oral Melanoma (COM) is the most common malignant tumor of the oral cavity, sharing clinical and histological aspects with hMM.To improve the knowledge about COM's genomic DNA alterations, in the present work, formalin-fixed, paraffin-embedded (FFPE) samples of COM from different European archives were collected to set up an array Comparative Genomic Hybridization (aCGH) analysis to estimate recurrent Copy Number Aberrations (CNAs). DNA was extracted in parallel from tumor and healthy fractions and 19 specimens were successfully submitted to labeling and competitive hybridization. Data were statistically analyzed through GISTIC2.0 and a pathway-enrichment analysis was performed with ClueGO. Recurrent gained regions were detected, affecting chromosomes CFA 10, 13 and 30, while lost regions involved chromosomes CFA 10, 11, 22, and 30. In particular, CFA 13 showed a whole-chromosome gain in 37% of the samples, while CFA 22 showed a whole-chromosome loss in 25%. A distinctive sigmoidal trend was observed in CFA 10 and 30 in 25 and 30% of the samples, respectively. Comparative analysis revealed that COM and hMM share common chromosomal changes in 32 regions. MAPK-and PI3K-related genes were the most frequently involved, while pathway analysis revealed statistically significant perturbation of cancer-related biological processes such as immune response, drug metabolism, melanocytes homeostasis, and neo-angiogenesis. The latter is a new evidence of a significant involvement of neovascularization-related pathways in COMs and can provide the rationale for future application in anti-cancer targeted therapies.

KIT Somatic Mutations and Immunohistochemical Expression in Canine Oral Melanoma

“…Data related to the aCGH analysis are published and extensively discussed in the paper from Brocca and colleagues [ 25 ]. Twenty samples were submitted for aCGH analysis, and a total number of 14 samples were selected for this study: seven harboring a KIT amplification, and seven without KIT amplification, which were randomly chosen among the remaining 13 samples to maintain a balanced number of samples between the two groups.…”

“…Twenty of the 40 samples showed an adequate DNA yield and were submitted to an aCGH analysis as described in the work from Brocca and colleagues [ 25 ]. The aCGH allowed us to learn the aberrational status of CFA 13, and in particular of the portion containing the KIT gene.…”

“…Several studies noted some similarities in can profiles between hMMs [ 10 , 18 , 19 , 20 , 21 ] and COMs [ 10 , 22 , 23 , 24 ]. In a recent comparative investigation, we were able to detect common chromosomal changes in 32 regions affecting human chromosomes (HSA) and the canine orthologous regions (CFA), with amplification in 35% of cases of the KIT-coding region located on CFA 13 [ 25 ].…”

“…In this study, we investigated the role of KIT in COMs at both the gene and protein level. Taking advantage of the cohort of COMs assembled for the array Comparative Genomic Hybridization (aCGH) study published in 2019 [ 25 ], we decided to deepen our knowledge of the possible role of the gene KIT and the protein KIT in our cohort of samples. We performed an accurate evaluation of the possible SNPs by sequencing Ex-13, Ex-17, and Ex-18, and by evaluating KIT expression in COMs.…”

Exploring protective effect of Glycine tabacina aqueous extract against nephrotic syndrome by network pharmacology and experimental verification

“…To explore the role of predicted targets connected with GATE against NS, ClueGO and CluePedia, two plugins of Cytoscape, were used to perform Gene Ontology (GO) enrichment analysis of overlapping targets [ 30 – 32 ]. In ClueGo, Two-side hypergeometric test was used to evaluate the significance of each term.…”