Allelic loss on chromosome bands 13q11-q13 in esophageal squamous cell carcinoma.

Allelic loss on chromosome 13 occurs frequently in esophageal squamous cell carcinoma. However, studies of the two known tumor suppressor genes located on 13q, RB1 and BRCA2, have shown few mutations, suggesting that other genes are likely to be involved in the development of this tumor type. To identify a minimal deletion interval, we first analyzed 42 microsatellite markers spanning chromosome bands 13q11-q13 in 56 esophageal squamous cell carcinoma patients, including 34 with a family history of upper gastrointestinal cancer and 22 without a family history of cancer. Lifestyle risk factors and clinical/pathologic characteristics were also collected. Two commonly deleted regions were identified: one was located on band 13q12.11, between markers D13S787 and D13S221; the other was located on bands 13q12.3-q13.1 from markers D13S267 to D13S219. We observed higher allelic loss frequencies for eight of the microsatellite markers in those patients with a family history of upper gastrointestinal cancer compared to patients without such a history. This study suggests that one or more unidentified tumor suppressor genes are located on chromosome arm 13q that play a role in the development of esophageal squamous cell carcinoma.     

CDK4 is a probable target gene in a novel amplicon at 12q13.3-q14.1 in lung cancer

Several chromosomal regions are recurrently amplified or deleted in lung tumors, but little is known about the underlying genes, which could be important mediators in tumor formation or progression. In lung cancer, the RB1-CCND1-CDKN2A pathway, involved in the G1-S transition, is damaged in nearly all tumors. In the present study, we localized a novel amplicon in lung tumors to a fragment of less than 0.5 Mb at 12q13.3-q14.1 by using comparative genomic hybridization (CGH) on cDNA microarrays. This approach enabled us to identify 10-15 genes with the most consistent amplifications. Semiquantitative RT-PCR analyses of 13 genes in this region showed that four of them (CDK4, CYP27B1, METTL1, and TSFM) were also highly up-regulated. Immunohistochemical (IHC) analysis of 141 tumor samples on a tissue microarray showed that CDK4 was expressed at a high level in 23% of lung tumors. Six (21.4%) of the tumors with high CDK4 expression (n = 28) were shown by fluorescence in situ hybridization (FISH) to contain the 12q13.3-q14.1 amplification. For CDK4, a positive correlation was found between gene copy number (FISH and CGH array), mRNA expression (RT-PCR), and level of protein expression (IHC). CDK4 expression did not correlate with CDKN2A methylation status. Amplification of CDK4 has been described in other tumor types, but its role in lung cancer remains to be elucidated. Although CDK4 amplification seems to be a relatively rare event (4.3%) in lung tumors, it indicates the significance of the RB1-CCND1 pathway in lung tumorigenesis.     

Identification of methylated-differentially expressed genes and pathways in esophageal squamous cell carcinoma

Methylation, as an epigenetic modification, can affect gene expression and play a role in the occurrence and development of cancer. This research is devoted to discover methylated-differentially expressed genes (MDEGs) in esophageal squamous cell carcinoma (ESCC) and explore special associated pathways. We downloaded GSE51287 methylation profiles and GSE26886 expression profiles from GEO DataSets, and performed a comprehensive bioinformatics analysis. Totally, 19 hypermethylated, lowly expressed genes (Hyper-LGs) were identified, and involved in regulation of cell proliferation, phosphorus metabolic process and protein kinase activity. Meanwhile, 17 hypomethylated, highly expressed genes (Hypo-HGs) were participated in collagen catabolic process, metallopeptidase and cytokine activity. Pathway analysis determined that Hyper-LGs were enriched in arachidonic acid metabolism pathway, while Hypo-HGs were primarily associated with the cytokine-cytokine receptor interaction pathway. IL 6, MMP3, MMP9, SPP1 were identified as hub genes based on the PPI network that combined 7 ranked methods included in cytoHubba, and verification was performed in human tissues. Our integrated analysis identified many novel genetic lesions in ESCC and provides a crucial molecular foundation to improve our understanding of ESCC. Hub genes, including IL 6, MMP3, MMP9 and SPP1, could be considered for use as aberrant methylation-based biomarkers to facilitate the accurate diagnosis and therapy of ESCC.     

The 11q13 amplicon of a mammary carcinoma cell line

Fifteen to 20% of breast carcinomas show amplification of genes located at 11q13. The HST/FGFK and INT2 fibroblast growth factor (FGF)-related genes and the BCL1 locus are usually present in the amplification units. We have investigated the structure and chromosomal location of the 11q13 amplicon of the MDA-MB-134 mammary carcinoma cell line by using in situ chromosomal and pulsed field gel hybridizations. The results indicate that a limited number of amplification units are involved in the constitution of an extended chromosomal region located on 11q. These units do not show any important rearrangement over rather large distances around the HST/INT2 and BCL1 loci.     

Breakpoints in benign lipoma may be at 12q13 or 12q14

Chromosomal investigations in two unrelated lipoma samples are reported. The breakpoint involving 12q in chromosomal rearrangements could be assigned to band 12q13 in one case and 12q14 in the other case. Evidence is provided that cytogenetically distinct breakpoints on 12q may be found in lipoma cells, resolving previous disagreements based on interpretational difficulties.     

Identification of a novel amplicon at 1q31 in pancreatic cancer cell lines.

Pancreatic adenocarcinoma is a highly lethal malignant tumor that is increasing in frequency, now ranking fifth in the United States as a cause of death attributed to cancer. Patients with pancreatic carcinoma have one of the poorest prognoses of all cancer patients, with the number of deaths being approximately 75% of the total number of cases. The use of comparative genomic hybridization (CGH) has gained widespread use in the study of some types of solid tumors, and it seems to be a very good approach in pancreatic adenocarcinomas, in which just a few cases have been studied cytogenetically, mostly owing to the fact that these tumors are very difficult to grow in culture. Fourteen pancreatic cancer lines were examined with CGH. In 11 of these lines, we found an amplicon at 1q31, not previously reported in pancreatic cancer. More studies need to be done in primary tumors to determine the involvement of 1q31 in this type of tumor.     

Allelic imbalance of 14q32 in esophageal carcinoma

It has been demonstrated that the accumulation of alterations in several oncogenes and tumor suppressor genes plays a role in the initiation and progression of esophageal carcinoma. However, to our knowledge, very few studies have described the molecular genetic changes of chromosome arm 14q in esophageal carcinoma. In this study, we examined 35 primary esophageal carcinomas for allelic imbalance on 14q32. Analysis of four polymorphic microsatellite markers identified 13 (37%) tumors exhibiting allelic imbalance on 14q32 in at least one locus. In particular, the allelic imbalance of the D14S267 marker that has been reported in various tumors as having a high frequency of deletion was observed in 10 of 26 informative cases (38.5%). The commonly deleted regions were delineated by markers D14S65 and D14S250 on 14q32. In regard to the macroscopic features of tumor, the 14q allelic imbalance rate of protruding type tumors was higher than that of the ulcerative type. These data suggest that potential suppressor loci on 14q32 are related to the development and progression of esophageal carcinoma.     

Normal blood lymphocytes from patients with adipose tissue tumors with rearrangements at 12q13-q14 do not express the fragile site fra(12)(q13.1)

An association between chromosomal fragile sites and cancer-specific breakpoints has been found to be statistically significant. Cancer patients have been shown to be carriers of fragile sites in chromosome regions involved in rearrangements in malignant cells. Based on these observations it has been hypothesized that fragile sites may be involved in the pathogenesis of human tumors. We have recently described a new recurrent cancer breakpoint at chromosomal region 12q13-q14 in adipose tissue tumors. The possible involvement in these tumors of the rare folate-sensitive fragile site 12q13.1 has been investigated in PHA-stimulated peripheral blood cells from three patients carrying the t(12;16)(q13;p11) in their liposarcoma cells and one patient with the t(3;12)(q28;q14) in his lipoma cells. No expression of the fragile site 12q13.1 could be detected in the blood lymphocytes of any of the patients. The involvement of the fragile site 12q13.1 in the pathogenesis of adipose tissue tumors with a 12q13-q14 breakpoint remains to be established.     

Identification of a novel 12p13.3 amplicon in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is a distinct type of head and neck cancer commonly occurring in southern China. To decipher the molecular basis of this cancer, we performed high‐resolution array CGH analysis on eight tumour lines and 10 primary tumours to identify the genes involved in NPC tumorigenesis. In this study, multiple regions of gain were consistently found at 1q21‐q24, 7q11‐12, 7q21‐22., 11q13, 12p13, 12q13, 19p13 and 19q13. Importantly, a 2.1 Mb region at 12p13.31 was highly amplified in a NPC xenograft, xeno‐2117. By FISH mapping, we have further delineated the amplicon to a 1.24 region flanked by RP11‐319E16 and RP11‐433J6. Copy number gains of this amplicon were confirmed in 21/41 (51%) primary tumours, while three cases (7.3%) showed high copy number amplification. Among the 13 genes within this amplicon, three candidate genes, lymphotoxin beta receptor (LTβR), tumour necrosis factor receptor superfamily memeber 1A (TNFRSF1R) and FLJ10665, were specifically over‐expressed in the NPC xenograft with 12p13.3 amplification. However, only LTβR was frequently over‐expressed in primary tumours. LTβR is a member of the TNF family of receptors, which can modulate NF‐κB signalling pathways. Over‐expression of LTβR in nasopharyngeal epithelial cells resulted in an increase of NF‐κB activity and cell proliferation. In vivo study showed that suppression of LTβR by siRNA led to growth inhibition in the NPC tumour with 12p13.3 amplification. These findings implied that LTβR is a potential NPC‐associated oncogene within the 12p13.3 amplicon and that its alteration is important in NPC tumorigenesis. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.     

Clear cell sarcoma with t(12;22) (q13-14;q12).

Karyotypic analysis of a clear cell sarcoma revealed a translocation t(12;22) (q13-14;q12) as a primary chromosomal change. This case is the third clear cell sarcoma cytogenetically analyzed; the two previously reported cases had t(12;22)(p11;p11), and a complex karyotype with trisomy 22, respectively.     

Identification of individual genes altered in squamous cell carcinoma of the vulva

Chromosome rearrangements in squamous cell carcinoma of the vulva (SCV) have indicated common consistent regions of loss and gain. The overall aim of our research was to define and characterize individual genes that underlie the pathogenesis of SCV. Thirteen cell lines from 12 SCV patients were evaluated for loss and gain of 122 genes distributed throughout the genome. Individual genes were analyzed for genetic alterations using a novel genomewide strategy, the multiplex ligation-dependent probe amplification assay. Our candidate gene approach identified several altered loci. Most frequent was the loss of 1 copy of TMSB10, observed in 11 of 12 SCV patients, followed by loss of CTNNB1 and BCL2, which occurred in 7 of 12 patients. Frequent gains/amplifications included CCND1, observed in 8 of 12 patients, and IL12A, in 7 of the 12 patients. Loss and gain of specific genes observed in our study were generally concordant with the results of previous studies of cytogenetics and CGH utilizing the same SCV cell lines. Genetic alterations are hallmarks of tumorigenesis, and there is wide agreement that recurrent altered genomic loci contain genes important for tumor development and progression. Understanding the interplay of cancer genes and the pathways they utilize can lead to the detection of novel molecular targets in the diagnosis, prognosis, and treatment of SCV.     

Amplification and expression of genes from the 17q11 approximately q12 amplicon in breast cancer cells

Amplification of a portion of 17q11 approximately q12 involving the human epidermal growth factor receptor-2 (HER-2/neu) gene is common in solid tumors. HER-2/neu amplification in breast cancer is associated with a poor prognosis and may predict response to therapeutic interventions. The molecular complexity and informative content of the 17q11 approximately q12 amplified DNA remain largely unknown. Study of available sequence information in public database allowed us to construct a contig in bacterial artificial chromosome that covers this region. We have identified a several hundred kilobase core segment from this region that is amplified in three out of three breast cancer cell lines with HER-2/neu amplification. There is striking correlation between amplification and overexpression of genes from this region. Amplified and overexpressed genes, in addition to HER-2/neu, may play functional roles in the pathogenesis of breast cancer and may serve as additional targets for therapy. Published by Elsevier Science Inc.     

食管鳞状细胞癌中SFRP基因家族启动子区甲基化状态的检测

目的: 检测食管鳞状细胞癌(ESCC)中Wnt通路拮抗基因家族分泌型卷曲相关蛋白(SFRP)基因的甲基化状态,探讨其与食管鳞癌发生的关系。方法: 应用甲基化特异性PCR(MS-PCR)及RT-PCR的方法检测78例食管鳞癌及相应癌旁非肿瘤组织中 SFRP1 、 SFRP2 、 SFRP4 和 SFRP5 基因的甲基化状态及mRNA表达情况,并分析其与Wnt通路中心因子β-catenin蛋白表达的关系。结果: 在食管鳞癌组织中, SFRP1 、 SFRP2 、 SFRP4 和 SFRP5 基因的甲基化率分别为65.4%(51/78)、69.2%(54/78)、62.8%(49/78)和52.6%(41/78),均明显高于癌旁非肿瘤组织(P<0.01)。这4个基因的甲基化率与肿瘤患者的组织学分级及临床分期均无关,但它们共同发生甲基化的频率则与临床分期显著相关(P<0.05)。这4个基因mRNA的阳性表达率分别为42.3%(33/78)、46.2%(36/78)、50.0%(39/78)和39.7%(31/78),均明显低于癌旁非肿瘤组织(P<0.01)。在发生甲基化的食管癌组织中这4个基因的mRNA表达阳性率及β-catenin蛋白的异质表达率均明显低于未发生甲基化的癌组织,且差异显著(P<0.05)。结论: 食管鳞癌组织中 SFRP1 、 SFRP2 、 SFRP4 和 SFRP5 基因均呈高甲基化状态,并有可能通过Wnt/β-catenin信号转导通路参与了食管癌的发生。联合检测SFRP基因家族甲基化状态对于食管癌的预后判断有一定指导意义。