Identification of novel candidate target genes, including EPHB3, MASP1 and SSTat 3q26.2–q29 in squamous cell carcinoma of the lung

Abstract

BackgroundThe underlying genetic alterations for squamous cell carcinoma (SCC) and adenocarcinoma (AC) carcinogenesis are largely unknown.MethodsHigh-resolution array- CGH was performed to identify the differences in the patterns of genomic imbalances between SCC and AC of non-small cell lung cancer (NSCLC).ResultsOn a genome-wide profile, SCCs showed higher frequency of gains than ACs (p = 0.067). More specifically, statistically significant differences were observed across the histologic subtypes for gains at 2q14.2, 3q26.2–q29, 12p13.2–p13.33, and 19p13.3, as well as losses at 3p26.2–p26.3, 16p13.11, and 17p11.2 in SCC, and gains at 7q22.1 and losses at 15q22.2–q25.2 occurred in AC (P < 0.05). The most striking difference between SCC and AC was gains at the 3q26.2–q29, occurring in 86% (19/22) of SCCs, but in only 21% (3/14) of ACs. Many significant genes at the 3q26.2–q29 regions previously linked to a specific histology, such as EVI1,MDS1, PIK3CA and TP73L, were observed in SCC (P < 0.05). In addition, we identified the following possible target genes (> 30% of patients) at 3q26.2–q29: LOC389174 (3q26.2),KCNMB3 (3q26.32),EPHB3 (3q27.1), MASP1 and SST (3q27.3), LPP and FGF12 (3q28), and OPA1,KIAA022,LOC220729, LOC440996,LOC440997, and LOC440998 (3q29), all of which were significantly targeted in SCC (P < 0.05). Among these same genes, high-level amplifications were detected for the gene, EPHB3, at 3q27.1, and MASP1 and SST, at 3q27.3 (18, 18, and 14%, respectively). Quantitative real time PCR demonstrated array CGH detected potential candidate genes that were over expressed in SCCs.ConclusionUsing whole-genome array CGH, we have successfully identified significant differences and unique information of chromosomal signatures prevalent between the SCC and AC subtypes of NSCLC. The newly identified candidate target genes may prove to be highly attractive candidate molecular markers for the classification of NSCLC histologic subtypes, and could potentially contribute to the pathogenesis of the squamous cell carcinoma of the lung.

Genomics of Squamous Cell Lung Cancer

“…The majority of patients with high-grade lesions and 3q amplification developed invasive cancer in this study. Genes of interest in the 3q region include SOX2, TP63, PIK3CA, and EPHB3 [15,17].…”

Characterization of amplification patterns and target genes on the short arm of chromosome 7 in early-stage lung adenocarcinoma

“…Array-CGH is a successful and valuable tool for the analysis of chromosome copy-number alterations in human cancer and may be suitable for individualized diagnostic, prognostic and therapeutic decision-making (12). In this study, genome wide array-CGH was conducted to comprehensively characterize genome copy number aberrations associated with early-stage ADC.…”

“…No patients had received pre-operative chemotherapy or radiation. This study was reviewed and approved by the Institutional Characterization of amplification patterns and target genes on the short arm of chromosome 7 in early-stage lung adenocarcinoma Preparation of DNA targets, labeling, hybridization, washing, staining and scanning was conducted according to the manufacturer's instructions (Macrogen, Seoul, Korea) (8)(9)(10)(11)(12)(13). Briefly, arrays were pre-hybridized with salmon sperm DNA to block repetitive sequences in the BACs.…”

ORAOV1 is a probable target within the 11q13.3 amplicon in lymph node metastases from gastric adenocarcinoma

“…DNA isolation was performed following the manufacturer's instructions (Promega, Madison, WI, USA), with some modifications as previously described (9,10). Array-CGH was performed using the MacArray™ Karyo 1.4 K BAC-chip (Macrogen, Seoul, Korea) (11)(12)(13) according to the manufacturer's instructions and as described in ORAOV1 is a probable target within the 11q13.3 amplicon in lymph node metastases from gastric adenocarcinoma our previous studies (14,15). Briefly, all clones were two-end sequenced using an ABI PRISM 3700 DNA Analyzer (Applied Biosystems, Foster City, CA, USA), and their sequences were blasted (using BLAST; http://blast.ncbi.nlm.nih.gov/Blast.cgi).…”

“…Hybridizations were carried out using a standard direct method as previously described (14,15). Briefly, 500 ng of normal male DNA (reference) and digested tumor DNA (test) were labeled with Cy5-dCTP and Cy3-dCTP, respectively, by random primed labeling (Array-CGH Genomic Labeling System; Invitrogen, Carlsbad, CA, USA).…”