DNA Copy Number Gains at Loci of Growth Factors and Their Receptors in Salivary Gland Adenoid Cystic Carcinoma

Abstract

Purpose: Adenoid cystic carcinoma (ACC) is a malignant salivary gland tumor with a high mortality rate due to late, distant metastases. This study aimed at unraveling common genetic abnormalities associated with ACC. Additionally, chromosomal changes were correlated with patient characteristics and survival. Experimental Design: Microarray-based comparative genomic hybridization was done to a series of 18 paraffin-embedded primaryACCs using a genome-wide scanning BAC array. Results: A total of 238 aberrations were detected, representing more gains than losses (205 versus 33, respectively). Most frequent gains (>60%) were observed at 9q33. 3-q34.3, 11q13.3, 11q23.3, 19p13.3-p13.11, 19q12-q13.43, 21q22.3, and 22q13.33. These loci harbor numerous growth factor [fibroblast growth factor (FGF) and platelet-derived growth factor (PDGF)] and growth factors receptor (FGFR3 and PDGFRh) genes. Gains at the FGF(R) regions occurred significantly more frequently in the recurred/metastasized ACCs compared with indolent ACCs. Furthermore, patients with 17 or more chromosomal aberrations had a significantly less favorable outcome than patients with fewer chromosomal aberrations (log-rank = 5.2; P = 0.02). Conclusions: Frequent DNA copy number gains at loci of growth factors and their receptors suggest their involvement in ACC initiation and progression. Additionally, the presence of FGFR3 and PDGFRh in increased chromosomal regions suggests a possible role for autocrine stimulation in ACC tumorigenesis.Adenoid cystic carcinoma (ACC) is one of the most common malignant tumors of the salivary glands. The tumor consists of epithelial and myoepithelial cells and is characterized by slow growth, multiple late recurrences, and distant metastases, mostly to the lungs, bone, and liver (1). The neoplasm rarely metastasizes to lymph nodes, preferring the hematogenous route. Furthermore, ACC shows pronounced infiltration, often with perineural spread.Three different histologic subtypes have been described: the cribriform type (1), exhibiting monomorphic cell islands with punched-out spaces, causing the ''Swiss cheese pattern''; the tubular type (2), composed of ductal structures lined by two or more cell layers within a fibrous stroma; and the solid type (3), which is composed of basaloid tumor cells and can contain foci of necrosis, cellular polymorphism, and mitoses. However, in most ACCs, two or more patterns are recognized.With respect to chromosomal alterations in ACC, fluorescence in situ hybridization and loss of heterozygosity (LOH) analysis studies (2 -7) have shown frequent 6q and 17p deletions and a recurrent t(6;9)(q21-q25;p21-p22) translocation. Immunohistochemistry has implied various proteins as molecular markers of progression in ACC, but results were inconclusive (8 -12). Only p53 proved to be a consistent marker of aggressiveness in ACC, being highly expressed in the solid pattern (13), correlating with unfavorable clinical outcome (14) and having high LOH rates (15). Recent oligonucleotide microarray analyses ...

High-resolution array comparative genomic hybridization analysis of human bronchial and salivary adenoid cystic carcinoma

“…Choosing to use conservative criteria with a deliberate bias against high-copy repetitive or GC-rich sequences, it is likely that we underestimated the number of aberrations. Reviewing our primary data we noticed, albeit at a far lower frequency, abnormalities consistent with 15 of the 21 gains that were reported by Vekony et al 12 . Strikingly, 12 of these 15 gains are localized to telomeres (1p36.33, 4p16.3, 8q24.3, 9q34.3, 11p15.5, 13q34, 16p13.3, 16q24.3, 17p13.…”

“…12 Here, we analyzed 17 samples, but the number of aberrations, particularly gains, in our report is clearly lower than that found by Vékony. Choosing to use conservative criteria with a deliberate bias against high-copy repetitive or GC-rich sequences, it is likely that we underestimated the number of aberrations.…”

“…11 Array CGH has been developed to increase the spatial resolution for the detection of chromosomal copy number alterations (CNAs). Vékony et al 12 , published the results of a study using BAC-based CGH array in a series of 18 paraffinembedded primary ACCs, showing very frequent copy number gains at loci of growth factors and their receptors. Here, we report the results of a study using high-resolution oligonucleotide CGH array in frozen samples with the goal to increase the knowledge of CNAs in ACC and establish a catalog of candidate cancer genes residing in the altered regions.…”

Adenoid Cystic Carcinoma: Clinical and Molecular Features

“…Secondary genetic mechanisms are not well-understood, however. In attempts to identify genomic alterations that occur in ACC, there have been at least 6 studies of ACC cohorts employing the techniques of comparative genomic hybridization (CGH) and array comparative genomic hybridization (aCGH) which globally sample the copy number status of tumor genomes [38][39][40][41][42][43]. The results of these studies have been quite variable but areas of deletion that have been identified in two or more tumors in each of two or more of these studies include 1p (8-44 %), 5q (8-18 %), 6q (14-30 %), 9p (12-33 %), 9q (8-9 %), 12q (9-33 %), 13q (11-35 %), 14q (4-22 %), 17p (11-13 %), and Xp (8-9 %).…”

An efficient protocol for genomic DNA extraction from formalin-fixed paraffin-embedded tissues

“…Therefore diverse nucleic acid extraction methods already described from FFPET, enable the use of DNA extracted for specific approaches: nested PCR-SSCP assay (Wang et al, 1996), RAPD-PCR (Jacobs et al, 2007), real-time quantitative PCR (Gjerdrum et al,2004), Southern blot hybridisation (e.g. Dubeau et al, 1986;Jackson et al, 1990;Rogers et al, 1990), flow cytometry (Leers et al,1999), microarray comparative genomic hybridization (Vékony et al, 2007) and SNP BeadArrays (Oosting et al, 2007).…”