BAC clones related to prognosis in patients with esophageal squamous carcinoma: an array comparative genomic hybridization study

Identification of candidate target genes of genomic aberrations in esophageal squamous cell carcinoma

The aim of the present study was to identify the candidate target genes of genomic aberrations in esophageal squamous cell carcinoma (ESCC). Array comparative genomic hybridization (CGH) and quantitative polymerase chain reaction were applied to analyze the copy number changes and expression level of candidate genes, respectively. Integrative analysis revealed that homozygous deletions of cyclin-dependent kinase inhibitor (CDKN) 2A and CDKN2B and gains of fascin actin-bundling protein 1 (FSCN1) and homer scaffolding protein 3 (HOMER3) occurred frequently in ESCC. The results demonstrated that the homozygous deletion of CDKN2A or CDKN2B was significantly associated with lymph node metastasis. Notably, the expression of CDKN2A and CDKN2B was lower in dysplasia than in normal esophageal epithelium. We also observed that the copy number increase of FSCN1 was significantly associated with pT, pN and pStage, and that the gain of HOMER3 was significantly linked with pN and pStage. We further revealed that FSCN1 and HOMER3 were overexpressed in ESCC, and that their overexpression was correlated with copy number increase. In conclusion, CDKN2A, CDKN2B, FSCN1 and HOMER3 are candidate cancer-associated genes and may play a tumorigenic role in ESCC.

Multiple genes identified as targets for 20q13.12-13.33 gain contributing to unfavorable clinical outcomes in patients with hepatocellular carcinoma

BACKGROUND

Recurrent chromosome 20q gain is implicated in progressive cancer behaviors and has been associated with clinical outcomes in multiple types of cancer; however, its prognostic significance in hepatocellular carcinoma (HCC) and the involved genes remain unclear.

METHODS

Array comparative genomic hybridization and expression arrays were used to detect copy number alterations (CNAs) and expression levels, respectively. The associations between CNAs in 20q and outcomes were analyzed on 66 patients, for which the follow-up period was 2.6-73.3 months. One hundred seventeen tumors were further investigated to identify target genes in the potentially outcome-related CNAs.

RESULTS

Regional or whole 20q gain was detected in 24 (36.4%) of the 66 HCC cases. The most recurrent gains were 20q11.21-12, 20q12-13.12, 20q13.12-13.33 and 20q13.33. Of the CNAs, 20q13.12-13.33 gain was significantly associated with reduced extrohepatic metastasis-free and overall survival, as well as with elevated postoperative AFP level, tumor vascular invasion and advanced tumor stage. Multivariate Cox analysis identified 20q13.12-13.33 gain as an independent prognostic marker for metastasis (HR 3.73, 95% CI 1.08-12.87) and death (HR 3.00, 95% CI 1.26-7.13). A panel of 19 genes in 20q13.12-13.33 was significantly overexpressed in HCCs with gain compared to HCCs without. High expression (greater than median) for 5 of the 19 genes, DDX27, B4GALT5, RNF114, ZFP64 and PFDN4, correlated significantly with vascular invasion, and high RNF114 expression also with advanced tumor stage.

CONCLUSIONS

Gain at 20q13.12-13.33 is a prognostic marker of metastasis and death, and DDX27, B4GALT5, RNF114, ZFP64, and PFDN4 are probable target genes which may be involved together in the unfavorable outcomes of HCC patients.

Cell and molecular biology of septins

Septins are a family of GTP-binding proteins that assemble into cytoskeletal filaments. Unlike other cytoskeletal components, septins form ordered arrays of defined stoichiometry that can polymerize into long filaments and bundle laterally. Septins associate directly with membranes and have been implicated in providing membrane stability and serving as diffusion barriers for membrane proteins. In addition, septins bind other proteins and have been shown to function as multimolecular scaffolds by recruiting components of signaling pathways. Remarkably, septins participate in a spectrum of cellular processes including cytokinesis, ciliogenesis, cell migration, polarity, and cell-pathogen interactions. Given their breadth of functions, it is not surprising that septin abnormalities have also been linked to human diseases. In this review, we discuss the current knowledge of septin structure, assembly and function, and discuss these in the context of human disease.

Genomic and molecular characterization of esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is prevalent worldwide and particularly common in certain regions of Asia. Here we report the whole-exome or targeted deep sequencing of 139 paired ESCC cases, and analysis of somatic copy number variations (SCNV) of over 180 ESCCs. We identified previously uncharacterized mutated genes such as FAT1, FAT2, ZNF750 and KMT2D, in addition to those already known (TP53, PIK3CA and NOTCH1). Further SCNV evaluation, immunohistochemistry and biological analysis suggested their functional relevance in ESCC. Notably, RTK-MAPK-PI3K pathways, cell cycle and epigenetic regulation are frequently dysregulated by multiple molecular mechanisms in this cancer. Our approaches also uncovered many druggable candidates, and XPO1 was further explored as a therapeutic target because it showed both gene mutation and protein overexpression. Our integrated study unmasks a number of novel genetic lesions in ESCC and provides an important molecular foundation for understanding esophageal tumors and developing therapeutic targets.

Identification of putative target genes for amplification within 11q13.2 and 3q27.1 in esophageal squamous cell carcinoma

BACKGROUND

Genomic aberration is a common feature of human cancers and also is one of the basic mechanisms that lead to overexpression of oncogenes and underexpression of tumor suppressor genes. Our study aims to identify frequent genomic changes and candidate copy number driving genes in esophageal squamous cell carcinoma (ESCC).

METHODS

We used array comparative genomic hybridization to identify recurrent genomic alterations and screened the candidate targets of selected amplification regions by quantitative and semi-quantitative RT-PCR.

RESULTS

Thirty-four gains and 16 losses occurred in more than 50 % of ESCCs. High-level amplifications at 7p11.2, 8p12, 8q24.21, 11q13.2-q13.3, 12p11.21, 12q12 and homozygous deletions at 2q22.1, 8p23.1-p21.2, 9p21.3 and 14q11.2 were also identified. 11q13.2 was a frequent amplification region, in which five genes including CHKA, GAL, KIAA1394, LRP5 and PTPRCAP were overexpressed in tumor tissues than paracancerous normal tissues. The expression of ALG3 at 3q27.1 was higher in ESCCs, especially in patients with lymph node metastasis.

CONCLUSIONS

Target gene identification of amplifications or homozygous deletions will help to reveal the mechanism of tumor formation and explore new therapy method.

Consistent and differential genetic aberrations between esophageal dysplasia and squamous cell carcinoma detected by array comparative genomic hybridization

PURPOSE

Our aim was to identify frequent genomic aberrations in both esophageal squamous cell carcinoma (ESCC) and esophageal dysplasia and to discover important copy number-driving genes and microRNAs (miRNA) in ESCC.

EXPERIMENTAL DESIGN

We conducted array-based comparative genomic hybridization (array CGH) on 59 ESCC resection samples and 16 dysplasia biopsy samples. Expression of genes at 11q13.3 was analyzed by real-time PCR (RT-PCR) and immunohistochemistry (IHC). Integrated analysis was conducted to identify genes or miRNAs with copy number-expression correlations.

RESULTS

Array CGH identified 11 amplifications and eight homozygous deletions in ESCC. Integrated analysis of array CGH data with matched gene expression microarray data showed that 90 overexpressed genes and 24 underexpressed genes were consistent with DNA copy number changes, including 12 copy number-driving miRNAs. In esophageal dysplasia, six gains, four losses, 12 amplifications, and four homozygous deletions were detected. Amplifications of 7p11.2 and 11q13.2-11q13.3 (CCND1) and homozygous deletion at 9p21.3 (CDKN2A) were consistent genomic changes in both dysplasia and carcinoma. ANO1 at 11q13.3 was overexpressed at the mRNA and protein levels in tumors, and higher mRNA expression was correlated with the copy number increase. In particular, ANO1 expression was elevated in moderate dysplasia compared with normal esophageal epithelium. IHC revealed that ANO1 overexpression was positively correlated with lymph node metastasis and advanced clinical stage. Knockdown of ANO1 significantly inhibited the proliferation of KYSE30 and KYSE510 cells.

CONCLUSION

Copy number aberrations in both esophageal dysplasia and ESCC may be useful as potential biomarkers for early detection. In addition, ANO1 may be a candidate target gene in esophageal tumorigenesis.

Potential role of septins in oral carcinogenesis: An update and avenues for future research

Septins belong to the GTPase superclass of conserved proteins and have been identified to play a role in diverse aspects of cell biology, from cytokinesis to the maintenance of cellular morphology. At least 14 septins have been identified in humans. With their complex patterns in gene expressions and interaction, it has been reported that alterations in septin expression are observed in human diseases. Although much is not known about the role of human septins in oral carcinogenesis, circumstantial evidence does indicate that it may play a major role. This review intends to summarize the basis of septin biology, with the focus being on the evidence for septin involvement in human oral cancer.

Characterization of genetic rearrangements in esophageal squamous carcinoma cell lines by a combination of M-FISH and array-CGH: further confirmation of some split genomic regions in primary tumors

Background

Chromosomal and genomic aberrations are common features of human cancers. However, chromosomal numerical and structural aberrations, breakpoints and disrupted genes have yet to be identified in esophageal squamous cell carcinoma (ESCC).

Methods

Using multiplex-fluorescence in situ hybridization (M-FISH) and oligo array-based comparative hybridization (array-CGH), we identified aberrations and breakpoints in six ESCC cell lines. Furthermore, we detected recurrent breakpoints in primary tumors by dual-color FISH.

Results

M-FISH and array-CGH results revealed complex numerical and structural aberrations. Frequent gains occurred at 3q26.33-qter, 5p14.1-p11, 7pter-p12.3, 8q24.13-q24.21, 9q31.1-qter, 11p13-p11, 11q11-q13.4, 17q23.3-qter, 18pter-p11, 19 and 20q13.32-qter. Losses were frequent at 18q21.1-qter. Breakpoints that clustered within 1 or 2 Mb were identified, including 9p21.3, 11q13.3-q13.4, 15q25.3 and 3q28. By dual-color FISH, we observed that several recurrent breakpoint regions in cell lines were also present in ESCC tumors. In particular, breakpoints clustered at 11q13.3-q13.4 were identified in 43.3% (58/134) of ESCC tumors. Both 11q13.3-q13.4 splitting and amplification were significantly correlated with lymph node metastasis (LNM) (P = 0.004 and 0.022) and advanced stages (P = 0.004 and 0.039). Multivariate logistic regression analysis revealed that only 11q13.3-q13.4 splitting was an independent predictor for LNM (P = 0.026).

Conclusions

The combination of M-FISH and array-CGH helps produce more accurate karyotypes. Our data provide significant, detailed information for appropriate uses of these ESCC cell lines for cytogenetic and molecular biological studies. The aberrations and breakpoints detected in both the cell lines and primary tumors will contribute to identify affected genes involved in the development and progression of ESCC.

[Chromosomal and genomic aberrations in esophageal squamous cell carcinoma]

Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies with poor prognosis in China. Patients with ESCC may present with vague symptoms in early stage and most of the cases are diagnosed at advanced stage, without the chance of optimal therapy. In the development and progression of ESCC, cytogenetic and molecular aberrations are frequently observed. This review is to summarize the advances in the chromosomal and genomic alterations of ESCC reported recently.

DNA copy number profile discriminates between esophageal adenocarcinoma and squamous cell carcinoma and represents an independent prognostic parameter in esophageal adenocarcinoma

We report multiplex ligation-dependent probe amplification analysis (MLPA) of DNA copy number alterations in 59 esophageal cancer samples, stratified by histotype. Results showed that squamous cell carcinoma (SCC) samples present clustered abnormalities with several genes altered at high frequency. Instead, esophageal adenocarcinoma (ADC) samples are characterized by a more widespread genomic instability, and in these patients total DNA copy number alterations resulted to be an independent prognostic factor. The detection of characteristic molecular changes represents a step towards a better understanding of the molecular basis of esophageal tumorigenesis, and might offer the potential for the discovery of tumor-specific biomarkers.

Genomic alterations with impact on survival in esophageal squamous cell carcinoma identified by array comparative genomic hybridization

Risk assessment of esophageal squamous cell carcinoma (ESCC) is currently based on clinicopathological parameters. To identify genomic markers that can predict overall survival in ESCC, we performed array comparative genomic hybridization (array CGH) on a screening set of 35 tumor samples from ESCC patients. Prognosis association of the genes selected on the basis of the array CGH results was further validated by real-time PCR in two independent sample sets (n = 151 and 84). Genomic analysis revealed seven high-level amplifications and two homozygous deletions. Gain of 11q13.2 and loss of 7q34 and 18q21.1-q23 were associated with poor outcome. Gain of 11q13.2 was an independent prognostic factor and was selected for further validation. In both validation sets of samples, copy number increase of CPT1A in 11q13.2 was correlated with short overall survival (P = 0.015, n = 151 and P = 0.044, n = 84). Multivariate analysis confirmed that CPT1A gain provided prognostic information in ESCC (HR, 1.643; 95% CI: 1.076-2.509; P = 0.022; HR, 2.488; 95% CI: 1.235-5.013; P = 0.011). Immunohistochemistry showed significant correlation between strong expression of CPT1A protein and poor outcome of ESCC patients (P = 0.018, n = 73). Our data suggest that gain of CPT1A may be a candidate prognostic factor.

High frequency of common DNA copy number abnormalities detected by bacterial artificial chromosome array comparative genomic hybridization in 24 breast cancer cell lines

Breast cancer is a widespread disease in Japan and across the world. Breast cancer cells, as well as most other types of cancer cells, have diverse chromosomal aberrations. Clarifying the character of these chromosomal aberrations should contribute to the development of more suitable therapies, along with the predictions of metastasis and prognosis. Twenty-four breast cancer cell lines were analyzed by bacterial artificial chromosome (BAC) array comparative genomic hybridization (CGH). The array slide contained duplicate spots of 4030 BAC clone DNAs covering the entire human genome with 1 Mbp resolution. In all 24 breast cancer cell lines, frequent and significant amplifications as well as deletions were detected by BAC array CGH. Common DNA copy number gains, detected in 60% (above 15 cell lines) of the 24 breast cancer cell lines were found in 76 BAC clones, located at 1q, 5p, 8q, 9p, 16p, 17q, and 20q. Moreover, common DNA copy number loss was detected in 136 BAC clones, located at 1q, 2q, 3p, 4p, 6q, 8p, 9p, 11p, 13q, 17p, 18q, 19p, Xp, and Xq. The DNA copy number abnormalities found included abnormality of the well-known oncogene cMYC (8q24.21); however, most of them were not reported to relate to breast cancer. BAC array CGH has great potential to detect DNA copy number abnormalities, and has revealed that breast cancer cell lines have substantial heterogeneity.

Clinicopathological significance of stanniocalcin 2 gene expression in colorectal cancer

Laser microdissection (LMD) and microarray were used to identify genes associated with colorectal cancer. Stanniocalcin 2 (STC2) expression and clinicopathological significance in 139 clinical colorectal cancer samples were specifically investigated using real-time quantitative reverse transcription-polymerase chain reaction. A number of genes upregulated in colorectal cancer cells compared to normal colorectal epithelial cells were identified including STC2. STC2 gene expression in cancer tissue was higher than in corresponding normal colorectal epithelial tissue in 124 of 139 cases (89.2%, p < 0.01). Tumors with high STC2 expression showed higher frequencies of lymph node metastasis, lymphatic invasion, tumor depth, tumor size and AJCC Stage classification (p < 0.01). Patients with high STC2 expression also showed significantly worse overall survival rates than those with low STC2 expression (p < 0.01). Furthermore, STC2 gene appeared to be associated with colorectal cancer progression and may be a useful prognostic indicator for colorectal cancer.

Genomic characterization of esophageal squamous cell carcinoma from a high-risk population in China

Genomic instability plays an important role in most human cancers. To characterize genomic instability in esophageal squamous cell carcinoma (ESCC), we examined loss of heterozygosity (LOH), copy number (CN) loss, CN gain, and gene expression using the Affymetrix GeneChip Human Mapping 500K (n = 30 cases) and Human U133A (n = 17 cases) arrays in ESCC cases from a high-risk region of China. We found that genomic instability measures varied widely among cases and separated them into two groups: a high-frequency instability group (two-thirds of all cases with one or more instability category of > or =10%) and a low-frequency instability group (one-third of cases with instability of <10%). Genomic instability also varied widely across chromosomal arms, with the highest frequency of LOH on 9p (33% of informative single nucleotide polymorphisms), CN loss on 3p (33%), and CN gain on 3q (48%). Twenty-two LOH regions were identified: four on 9p, seven on 9q, four on 13q, two on 17p, and five on 17q. Three CN loss regions-3p12.3, 4p15.1, and 9p21.3-were detected. Twelve CN gain regions were found, including six on 3q, one on 7q, four on 8q, and one on 11q. One of the most gene-rich of these CN gain regions was 11q13.1-13.4, where 26 genes also had RNA expression data available. CN gain was significantly correlated with increased RNA expression in over 80% of these genes. Our findings show the potential utility of combining CN analysis and gene expression data to identify genes involved in esophageal carcinogenesis.

Transglutaminase 3 as a prognostic biomarker in esophageal cancer revealed by proteomics

To develop a prognostic biomarker for esophageal squamous cell carcinoma (ESCC), we examined the proteomic profile of ESCC using two-dimensional difference gel electrophoresis (2D-DIGE), and identified proteins associated with prognosis by mass spectrometry. The prognostic performance of the identified proteins was examined by immunohistochemistry in additional cases. We identified 22 protein spots whose intensity was statistically different between ESCC cases with good (N = 9; survived more than 5 years without evidence of recurrence) and poor (N = 24; died within 2 years postsurgery) prognosis, within the patient group that had two or more lymph node metastases. Mass spectrometric protein identification resulted in 18 distinct gene products from the 22 protein spots. Transglutaminase 3 (TGM3) was inversely correlated with shorter patient survival. The prognostic performance of TGM3 was further examined by immunohistochemistry in 76 ESCC cases. The 5-year disease-specific survival rate was 64.5% and 32.1% for patients with TGM3-positive and TGM3-negative tumors, respectively (p = 0.0033). Univariate and multivariate analyses revealed that TGM3 expression was an independent prognostic factor among the clinicopathologic variables examined. It is noteworthy that the prognostic value of TGM3 was shown to be higher than those of the lymph node metastasis, intramural metastasis and vascular invasion status. These results establish TGM3 as a novel prognostic biomarker for ESCC for the first time. Examination of TGM3 expression may provide novel therapeutic strategies to prevent recurrence of ESCC.

Identification of DNA copy number aberrations associated with metastases of colorectal cancer using array CGH profiles

It is important to estimate the biological characteristics of tumors, including the nodal status at the time of diagnosis for optimal treatment of individual cancer patients. Array-based comparative genomic hybridization (aCGH) was performed on 77 sporadic colorectal adenocarcinomas using a chip spotted with 4030 BAC clones. The nodal status was compared with an aCGH profiles depicted using a combination of decision-tree classifier and a Self-Organizing Map (SOM) analysis. Node metastasis was not detected in any of the 6 poorly differentiated adenocarcinomas with a 3q loss. A SOM analysis following the decision-tree classification of the aCGH data allowed for the differentiation in chromosomal regions between high- and low-level decreases in the DNA copy number. Node metastasis was detected in all 5 tumors with the high-level decrease in DNA copy number at Xp, irrespective of the histological type. Node metastasis was also found exclusively in 6 tumors with increase in DNA copy number at the chromosomal region between 11q13.3 and 11q22.3. Copy number aberrations linked to nodal metastasis were identified more collectively by the combination of the decision-tree classifier and a SOM analysis than by the conventional analysis method in aCGH analysis.

EML4-ALK fusion transcript is not found in gastrointestinal and breast cancers

Fusion genes have been identified as chromosomal rearrangements in certain cancers, such as leukaemia, lymphoma, and sarcoma. The EML4–ALK (EML4: echinoderm microtubule-associated-protein-like 4; ALK: anaplastic lymphoma kinase) fusion gene has been identified as an oncogene in non-small-cell lung cancer (NSCLC). This study examined the presence of this fusion transcript in gastrointestinal and breast cancers. We evaluated the expression of the EML4–ALK transcript in 104 lung cancer cases and in 645 gastrointestinal and breast cancer samples. Only one of the lung cancer samples tested positive for the EML4–ALK fusion transcript, whereas none were detected in 555 gastrointestinal and 90 breast cancer cases. Our data suggest that the EML4–ALK fusion transcript is not present in gastrointestinal or breast cancers and is specific to NSCLC.

Prognostic impact of array-based genomic profiles in esophageal squamous cell cancer

BACKGROUND

Esophageal squamous cell carcinoma (ESCC) is a genetically complex tumor type and a major cause of cancer related mortality. Although distinct genetic alterations have been linked to ESCC development and prognosis, the genetic alterations have not gained clinical applicability. We applied array-based comparative genomic hybridization (aCGH) to obtain a whole genome copy number profile relevant for identifying deranged pathways and clinically applicable markers.

METHODS

A 32 k aCGH platform was used for high resolution mapping of copy number changes in 30 stage I-IV ESCC. Potential interdependent alterations and deranged pathways were identified and copy number changes were correlated to stage, differentiation and survival.

RESULTS

Copy number alterations affected median 19% of the genome and included recurrent gains of chromosome regions 5p, 7p, 7q, 8q, 10q, 11q, 12p, 14q, 16p, 17p, 19p, 19q, and 20q and losses of 3p, 5q, 8p, 9p and 11q. High-level amplifications were observed in 30 regions and recurrently involved 7p11 (EGFR), 11q13 (MYEOV, CCND1, FGF4, FGF3, PPFIA, FAD, TMEM16A, CTTS and SHANK2) and 11q22 (PDFG). Gain of 7p22.3 predicted nodal metastases and gains of 1p36.32 and 19p13.3 independently predicted poor survival in multivariate analysis.

CONCLUSION

aCGH profiling verified genetic complexity in ESCC and herein identified imbalances of multiple central tumorigenic pathways. Distinct gains correlate with clinicopathological variables and independently predict survival, suggesting clinical applicability of genomic profiling in ESCC.

CGH microarrays and cancer

Genetic alterations are a key feature of cancer cells and typically target biological processes and pathways that contribute to cancer pathogenesis. Array-based comparative genomic hybridization (aCGH) has provided a wealth of new information on copy number changes in cancer on a genome-wide level and aCGH data have also been utilized in cancer classification. More importantly, aCGH analyses have allowed highly accurate localization of specific genetic alterations that, for example, are associated with tumor progression, therapy response, or patient outcome. The genes involved in these aberrations are likely to contribute to cancer pathogenesis, and the high-resolution mapping by aCGH greatly facilitates the subsequent identification of these cancer-associated genes.

Establishment and characterization of HEPFT, a cell line derived from hepatoid carcinoma of the fallopian tube, with special reference to alpha-fetoprotein, lectin affinity and histogenesis

A cell line designated "HEPFT" was established from a human fallopian tubal hepatoid carcinoma. This line grew well without interruption for 13 months and was subcultivated over 35 times. The cells were spherical and polygonal in shape and showed neoplastic and pleomorphic features such as a bizarre aggregation of chromatin granules, an irregular thickening membrane and multiple large nucleoli. The cells formed epithelial colonies with a jigsaw puzzle-like arrangement and multilayering without contact inhibition. The cells contained moderate to abundant amounts of eosinophilic cytoplasm and were immunohistochemically positive for alpha-fetoprotein. The cells proliferated rapidly, and the population doubling time was about 45 h. The chromosome number showed a wide distribution of aneuploidy. The modal chromosome number was stable in the hyper triploid range and many marker chromosomes were observed. The culture cells produced bile and a large amount of lentil lectin-reactive alpha-fetoprotein. The recently developed bacterial artificial chromosome array comparative genomic hybridization facilitated detailed analysis with high resolution and sensitivity. Different profiles of genomic copy-number abnormalities were demonstrated in various chromosomal regions in HEPFT cells.