|
1
|
Batista S, Madar VS, Freda PJ, Bhandary P, Ghosh A, Matsumoto N, Chitre AS, Palmer AA, Moore JH. Interaction models matter: an efficient, flexible computational framework for model-specific investigation of epistasis. BioData Min 2024; 17:7. [PMID: 38419006 PMCID: PMC10900690 DOI: 10.1186/s13040-024-00358-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/20/2024] [Indexed: 03/02/2024] Open
Abstract
PURPOSE Epistasis, the interaction between two or more genes, is integral to the study of genetics and is present throughout nature. Yet, it is seldom fully explored as most approaches primarily focus on single-locus effects, partly because analyzing all pairwise and higher-order interactions requires significant computational resources. Furthermore, existing methods for epistasis detection only consider a Cartesian (multiplicative) model for interaction terms. This is likely limiting as epistatic interactions can evolve to produce varied relationships between genetic loci, some complex and not linearly separable. METHODS We present new algorithms for the interaction coefficients for standard regression models for epistasis that permit many varied models for the interaction terms for loci and efficient memory usage. The algorithms are given for two-way and three-way epistasis and may be generalized to higher order epistasis. Statistical tests for the interaction coefficients are also provided. We also present an efficient matrix based algorithm for permutation testing for two-way epistasis. We offer a proof and experimental evidence that methods that look for epistasis only at loci that have main effects may not be justified. Given the computational efficiency of the algorithm, we applied the method to a rat data set and mouse data set, with at least 10,000 loci and 1,000 samples each, using the standard Cartesian model and the XOR model to explore body mass index. RESULTS This study reveals that although many of the loci found to exhibit significant statistical epistasis overlap between models in rats, the pairs are mostly distinct. Further, the XOR model found greater evidence for statistical epistasis in many more pairs of loci in both data sets with almost all significant epistasis in mice identified using XOR. In the rat data set, loci involved in epistasis under the XOR model are enriched for biologically relevant pathways. CONCLUSION Our results in both species show that many biologically relevant epistatic relationships would have been undetected if only one interaction model was applied, providing evidence that varied interaction models should be implemented to explore epistatic interactions that occur in living systems.
Collapse
Affiliation(s)
- Sandra Batista
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA.
| | | | - Philip J Freda
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA
| | - Priyanka Bhandary
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA
| | - Attri Ghosh
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA
| | - Nicholas Matsumoto
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California, San Diego, 9500 Gilman Dr., Mailcode: 0667, La Jolla, CA, 92093-0667, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California, San Diego, 9500 Gilman Dr., Mailcode: 0667, La Jolla, CA, 92093-0667, USA
- Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Dr., Mailcode: 0667, La Jolla, CA, 92093-0667, USA
| | - Jason H Moore
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA.
| |
Collapse
|
|
2
|
Genetic association between TRAIL-R1 Thr209Arg and cancer susceptibility. Sci Rep 2015; 5:10382. [PMID: 26315998 PMCID: PMC4551968 DOI: 10.1038/srep10382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 04/10/2015] [Indexed: 12/21/2022] Open
Abstract
We aimed to determine the indecisive association between tumor necrosis factor-related apoptosis-inducing ligand receptor 1 (TRAIL-R1) Thr209Arg polymorphism and inherited susceptibility to cancer. A meta-analysis combining data on 9,517 individuals was performed to assess the association between TRAIL-R1 Thr209Arg and cancer incidence. The summary ORs with 95% CI calculated with the fixed effects model suggested that Thr209Arg was not significantly associated with cancer susceptibility (homozygous model: OR 0.98, 95% CI 0.88–1.09; heterozygous model: OR 0.95, 95% CI 0.87–1.04; allele frequency model: OR 0.99, 95% CI 0.94–1.05; dominant model: OR 0.98, 95% CI 0.91–1.05; recessive model: OR 1.01, 95% CI 0.92–1.10). Stratified analysis by ethnicity and cancer type yielded similar null associations. These statistical data suggest that Thr209Arg in exon 4 of the TRAIL-R1 gene may not represent a modifier of susceptibility to cancer.
Collapse
|
|
3
|
Chavda B, Arnott JA, Planey SL. Targeting protein palmitoylation: selective inhibitors and implications in disease. Expert Opin Drug Discov 2014; 9:1005-19. [DOI: 10.1517/17460441.2014.933802] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Burzin Chavda
- The Commonwealth Medical College, Department of Basic Sciences, Scranton, PA 18509, USA
| | - John A Arnott
- The Commonwealth Medical College, Department of Basic Sciences, Scranton, PA 18509, USA
| | - Sonia Lobo Planey
- The Commonwealth Medical College, Department of Basic Sciences, Scranton, PA 18509, USA
| |
Collapse
|
|
4
|
A critical role for ZDHHC2 in metastasis and recurrence in human hepatocellular carcinoma. BIOMED RESEARCH INTERNATIONAL 2014; 2014:832712. [PMID: 24995331 PMCID: PMC4068081 DOI: 10.1155/2014/832712] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/22/2014] [Indexed: 12/18/2022]
Abstract
It has been demonstrated that loss of heterozygosity (LOH) was frequently observed on chromosomes 8p22-p23 in hepatocellular carcinoma (HCC) and was associated with metastasis and prognosis of HCC. However, putative genes functioning on this chromosomal region remain unknown. In this study, we evaluated LOH status of four genes on 8p22-p23 (MCPH1, TUSC3, KIAA1456, and ZDHHC2). LOH on ZDHHC2 was associated with early metastatic recurrence of HCC following liver transplantation and was correlated with tumor size and portal vein tumor thrombi. Furthermore, our results indicate that ZDHHC2 expression was frequently decreased in HCC. Overexpression of ZDHHC2 could inhibit proliferation, migration, and invasion of HCC cell line Bel-7402 in vitro. These results suggest an important role for ZDHHC2 as a tumor suppressor in metastasis and recurrence of HCC.
Collapse
|
|
5
|
Li SX, Tang GS, Zhou DX, Pan YF, Tan YX, Zhang J, Zhang B, Ding ZW, Liu LJ, Jiang TY, Hu HP, Dong LW, Wang HY. Prognostic significance of cytoskeleton-associated membrane protein 4 and its palmitoyl acyltransferase DHHC2 in hepatocellular carcinoma. Cancer 2014; 120:1520-31. [DOI: 10.1002/cncr.28593] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/04/2013] [Accepted: 12/12/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Shuang-Xi Li
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute; the Second Military Medical University; Shanghai China
- National Center for Liver Cancer; Shanghai China
- Department of Liver Medicine, Eastern Hepatobiliary Surgery Hospital; Second Military Medical University; Shanghai China
| | - Gu-Sheng Tang
- Department of Laboratory Medicine, Changhai Hospital; Second Military Medical University; Shanghai China
| | - Dong-Xun Zhou
- Department of Liver Medicine, Eastern Hepatobiliary Surgery Hospital; Second Military Medical University; Shanghai China
| | - Yu-Fei Pan
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute; the Second Military Medical University; Shanghai China
- National Center for Liver Cancer; Shanghai China
| | - Ye-Xiong Tan
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute; the Second Military Medical University; Shanghai China
- National Center for Liver Cancer; Shanghai China
| | - Jian Zhang
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute; the Second Military Medical University; Shanghai China
- National Center for Liver Cancer; Shanghai China
| | - Bo Zhang
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute; the Second Military Medical University; Shanghai China
- National Center for Liver Cancer; Shanghai China
| | - Zhi-Wen Ding
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute; the Second Military Medical University; Shanghai China
- National Center for Liver Cancer; Shanghai China
| | - Li-Juan Liu
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute; the Second Military Medical University; Shanghai China
- National Center for Liver Cancer; Shanghai China
| | - Tian-Yi Jiang
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute; the Second Military Medical University; Shanghai China
- National Center for Liver Cancer; Shanghai China
| | - He-Ping Hu
- Department of Liver Medicine, Eastern Hepatobiliary Surgery Hospital; Second Military Medical University; Shanghai China
| | - Li-Wei Dong
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute; the Second Military Medical University; Shanghai China
- National Center for Liver Cancer; Shanghai China
| | - Hong-Yang Wang
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute; the Second Military Medical University; Shanghai China
- National Center for Liver Cancer; Shanghai China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital; Shanghai Jiaotong University School of Medicine; China
| |
Collapse
|
|
6
|
Yan SM, Tang JJ, Huang CY, Xi SY, Huang MY, Liang JZ, Jiang YX, Li YH, Zhou ZW, Ernberg I, Wu QL, Du ZM. Reduced expression of ZDHHC2 is associated with lymph node metastasis and poor prognosis in gastric adenocarcinoma. PLoS One 2013; 8:e56366. [PMID: 23457560 PMCID: PMC3574152 DOI: 10.1371/journal.pone.0056366] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 01/08/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Zinc finger, DHHC-type containing 2 (ZDHHC2), originally named as reduced expression associated with metastasis protein (REAM), has been proposed as a putative tumor/metastasis suppressor gene and is often aberrantly decreased in human cancers. However ZDHHC2 expression pattern and its clinical significance have not yet been investigated in gastric adenocarcinoma. METHODOLOGY/PRINCIPAL FINDINGS Quantitative Real-Time PCR (qRT-PCR) and immunostaining were performed to detect ZDHHC2 expression in gastric adenocarcinoma, and then the correlation between ZDHHC2 expression and clinicpathologic parameters, and patient survival was analyzed. Compared to the adjacent normal tissues, ZDHHC2 expression was significantly reduced in gastric tumor tissues as shown by qRT-PCR and immunostaining. Low expression of ZDHHC2 was observed in 44.7% (211/472) of gastric adenocarcinoma patients, and was associated significantly with lymph node metastasis (p<0.001) and histological grade (p<0.001). Multivariate Cox regression analysis indicated that ZDHHC2 expression had a significant, independent predictive value for survival of gastric cancer patients (HR = 0.627, p = 0.001). CONCLUSIONS/SIGNIFICANCE Our data suggest that reduced ZDHHC2 expression is associated with lymph node metastasis and independently predicts an unfavorable prognosis in gastric adenocarcinoma patients.
Collapse
Affiliation(s)
- Shu-Mei Yan
- State Key Laboratory of Oncology in South China and Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, P. R. China
| | - Jian-Jun Tang
- Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, P. R. China
| | - Chun-Yu Huang
- Department of Gastric and Pancreatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, P. R. China
| | - Shao-Yan Xi
- State Key Laboratory of Oncology in South China and Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, P. R. China
| | - Ma-Yan Huang
- State Key Laboratory of Oncology in South China and Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, P. R. China
| | - Jian-Zhong Liang
- State Key Laboratory of Oncology in South China and Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, P. R. China
| | - Yuan-Xue Jiang
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P. R. China
| | - Yu-Hong Li
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P. R. China
| | - Zhi-Wei Zhou
- Department of Gastric and Pancreatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, P. R. China
| | - Ingemar Ernberg
- Department of Microbiolgy, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Qiu-Liang Wu
- State Key Laboratory of Oncology in South China and Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, P. R. China
- * E-mail: (Z-MD); (Q-LW)
| | - Zi-Ming Du
- State Key Laboratory of Oncology in South China and Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, P. R. China
- * E-mail: (Z-MD); (Q-LW)
| |
Collapse
|
|
7
|
Korycka J, Łach A, Heger E, Bogusławska DM, Wolny M, Toporkiewicz M, Augoff K, Korzeniewski J, Sikorski AF. Human DHHC proteins: a spotlight on the hidden player of palmitoylation. Eur J Cell Biol 2011; 91:107-17. [PMID: 22178113 DOI: 10.1016/j.ejcb.2011.09.013] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 09/14/2011] [Accepted: 09/19/2011] [Indexed: 11/24/2022] Open
Abstract
Palmitoylation is one of the most common posttranslational lipid modifications of proteins and we now know quite a lot about it. However, the state of knowledge about the enzymes that catalyze this process is clearly insufficient. This review is focused on 23 human DHHC genes and their products - protein palmitoyltransferases. Here we describe mainly the structure and function of these proteins, but also, to a lesser degree, what the substrates of the enzymes are and whether they are related to various diseases. The main aim of this review was to catalogue existing information concerning the human DHHC family of genes/proteins, making them and their functions easier to understand.
Collapse
Affiliation(s)
- Justyna Korycka
- University of Wrocław, Laboratory of Cytobiochemistry, Biotechnology Faculty, Przybyszewskiego 63-77, 51-148 Wrocław, Poland
| | | | | | | | | | | | | | | | | |
Collapse
|
|
8
|
Li W, Li TT, Liu H, Zhao YY. [Screening and identification of interactive proteins of SH2D4A]. YI CHUAN = HEREDITAS 2010; 32:712-8. [PMID: 20650852 DOI: 10.3724/sp.j.1005.2010.00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
SH2D4A is a member of SH2 signaling protein family, which is involved in the signal transduction mediated by protein tyrosine kinase-related receptor, cell growth, proliferation, differentiation, and thereby affects the development of human disorders. To determine the role of SH2D4A in the cell signal transduction pathway, SH2D4A interactive proteins were screened using yeast two-hybrid system, and yeast mating and GST pull-down assays were carried out to further confirm the interaction. We successfully generated a bait protein expression construct-pGBKT7-SH2D4A, screened the human kidney cDNA library, and obtained 46 positive yeast clones. After isolation of positive colonies, DNA sequencing, and sequence alignment analysis with BLAST software, we obtained 5 potential SH2D4A interactive proteins, AZGP1, DAD1, HSD17B10, KAT5, and PKM2, which were predicted by NetPhos 2.0 Server software and were all shown to be phosphorylated tyrosine (pY)-containing proteins except for HSD17B10. KAT5 and HSD17B10 were selected to perform yeast mating and GST pull-down experiments, indicating their direct binding to SH2D4A.
Collapse
Affiliation(s)
- Wei Li
- Department of Medical genetics, China Medical University, Shenyang 110001, China.
| | | | | | | |
Collapse
|
|
9
|
Planey SL, Keay SK, Zhang CO, Zacharias DA. Palmitoylation of cytoskeleton associated protein 4 by DHHC2 regulates antiproliferative factor-mediated signaling. Mol Biol Cell 2009; 20:1454-63. [PMID: 19144824 PMCID: PMC2649263 DOI: 10.1091/mbc.e08-08-0849] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Revised: 12/22/2008] [Accepted: 01/05/2009] [Indexed: 12/27/2022] Open
Abstract
Previously, we identified cytoskeleton-associated protein 4 (CKAP4) as a major substrate of the palmitoyl acyltransferase, DHHC2, using a novel proteomic method called palmitoyl-cysteine identification, capture and analysis (PICA). CKAP4 is a reversibly palmitoylated and phosphorylated protein that links the ER to the cytoskeleton. It is also a high-affinity receptor for antiproliferative factor (APF), a small sialoglycopeptide secreted from bladder epithelial cells of patients with interstitial cystitis (IC). The role of DHHC2-mediated palmitoylation of CKAP4 in the antiproliferative response of HeLa and normal bladder epithelial cells to APF was investigated. Our data show that siRNA-mediated knockdown of DHHC2 and consequent suppression of CKAP4 palmitoylation inhibited the ability of APF to regulate cellular proliferation and blocked APF-induced changes in the expression of E-cadherin, vimentin, and ZO-1 (genes known to play a role in cellular proliferation and tumorigenesis). Immunocytochemistry revealed that CKAP4 palmitoylation by DHHC2 is required for its trafficking from the ER to the plasma membrane and for its nuclear localization. These data suggest an important role for DHHC2-mediated palmitoylation of CKAP4 in IC and in opposing cancer-related cellular behaviors and support the idea that DHHC2 is a tumor suppressor.
Collapse
Affiliation(s)
- Sonia L Planey
- Whitney Laboratory, Department of Neuroscience, University of Florida, St. Augustine, FL 32080, USA.
| | | | | | | |
Collapse
|
|
10
|
Zhang J, Planey SL, Ceballos C, Stevens SM, Keay SK, Zacharias DA. Identification of CKAP4/p63 as a major substrate of the palmitoyl acyltransferase DHHC2, a putative tumor suppressor, using a novel proteomics method. Mol Cell Proteomics 2008; 7:1378-88. [PMID: 18296695 DOI: 10.1074/mcp.m800069-mcp200] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Protein palmitoylation is the post-translational addition of the 16-carbon fatty acid palmitate to specific cysteine residues by a labile thioester linkage. Palmitoylation is mediated by a family of at least 23 palmitoyl acyltransferases (PATs) characterized by an Asp-His-His-Cys (DHHC) motif. Many palmitoylated proteins have been identified, but PAT-substrate relationships are mostly unknown. Here we present a method called palmitoyl-cysteine isolation capture and analysis (or PICA) to identify PAT-substrate relationships in a living vertebrate system and demonstrate its effectiveness by identifying CKAP4/p63 as a substrate of DHHC2, a putative tumor suppressor.
Collapse
Affiliation(s)
- Jun Zhang
- The Whitney Laboratory, Department of Neuroscience, University of Florida, St. Augustine, Florida 32080, USA
| | | | | | | | | | | |
Collapse
|
|
11
|
Katzenellenbogen M, Mizrahi L, Pappo O, Klopstock N, Olam D, Jacob-Hirsch J, Amariglio N, Rechavi G, Domany E, Galun E, Goldenberg D. Molecular mechanisms of liver carcinogenesis in the mdr2-knockout mice. Mol Cancer Res 2007; 5:1159-70. [PMID: 18025261 DOI: 10.1158/1541-7786.mcr-07-0172] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mouse models of hepatocellular carcinoma (HCC) simulate specific subgroups of human HCC. We investigated hepatocarcinogenesis in Mdr2-knockout (Mdr2-KO) mice, a model of inflammation-associated HCC, using gene expression profiling and immunohistochemical analyses. Gene expression profiling showed that although Mdr2-KO mice differ from other published murine HCC models, they share several important deregulated pathways and many coordinately differentially expressed genes with human HCC data sets. Analysis of genome positions of differentially expressed genes in liver tumors revealed a prolonged region of down-regulated genes on murine chromosome 8 in three of the six analyzed tumor samples. This region is syntenic to human chromosomal regions that are frequently deleted in human HCC and harbor multiple tumor suppressor genes. Real-time reverse transcription-PCR analysis of 16 tumor samples confirmed down-regulation of several tumor suppressors in most tumors. We show that in the aged Mdr2-KO mice, cyclin D1 nuclear level is increased in dysplastic hepatocytes that do not form nodules; however, it is decreased in most dysplastic nodules and in liver tumors. We found that this decrease is mostly at the protein, rather than the mRNA, level. These findings raise the question on the role of cyclin D1 at early stages of hepatocarcinogenesis in the Mdr2-KO HCC model. Furthermore, we show that most liver tumors in Mdr2-KO mice were characterized by the absence of beta-catenin activation. In conclusion, the Mdr2-KO mouse may serve as a model for beta-catenin-negative subgroup of human HCCs characterized by low nuclear cyclin D1 levels in tumor cells and by down-regulation of multiple tumor suppressor genes.
Collapse
Affiliation(s)
- Mark Katzenellenbogen
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Kiryat Hadassah, P.O. Box 12000, Jerusalem 91120, Israel
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
|
12
|
Peng D, Ren CP, Yi HM, Zhou L, Yang XY, Li H, Yao KT. Genetic and epigenetic alterations of DLC-1, a candidate tumor suppressor gene, in nasopharyngeal carcinoma. Acta Biochim Biophys Sin (Shanghai) 2006; 38:349-55. [PMID: 16680376 DOI: 10.1111/j.1745-7270.2006.00164.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The DLC-1 gene, located at the human chromosome region 8p22, behaves like a tumor suppressor gene and is frequently deleted in diverse tumors. The deletion of 8p22 is not an uncommon event in nasopharyngeal carcinoma (NPC), therefore we explored the expression levels of the DLC-1 gene in NPCs and NPC cell lines by reverse transcription-polymerase chain reaction. The results showed the mRNA level of DLC-1 was downregulated. To identify the mechanism of DLC-1 downregulation in NPC, we investigated the methylation status of the DLC-1 gene using methylation-specific PCR, and found that 79% (31 of 39) of the NPC tissues and two DLC-1 nonexpressing NPC cell lines, 6-10B and 5-8F, were methylated in the DLC-1 CpG island. Microsatellite PCR was also carried out, and loss of heterozygosity was found at four microsatellite sites (D8S552, D8S1754, D8S1790 and D8S549) covering the whole DLC-1 gene with ratios of 33% (4 of 12 informative cases), 18% (2 of 11), 5% (1 of 18), and 25% (3 of 12), respectively. Taken together, our results suggest that DLC-1 might be an NPC-related tumor suppressor gene affected by aberrant promoter methylation and gene deletion.
Collapse
Affiliation(s)
- Dan Peng
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha 410078, China
| | | | | | | | | | | | | |
Collapse
|
|
13
|
Abstract
Hepatocellular carcinoma (HCC) is associated with multiple risk factors and is believed to arise from pre-neoplastic lesions, usually in the background of cirrhosis. However, the genetic and epigenetic events of hepatocarcinogenesis are relatively poorly understood. HCC display gross genomic alterations, including chromosomal instability (CIN), CpG island methylation, DNA rearrangements associated with hepatitis B virus (HBV) DNA integration, DNA hypomethylation and, to a lesser degree, microsatellite instability. Various studies have reported CIN at chromosomal regions, 1p, 4q, 5q, 6q, 8p, 10q, 11p, 16p, 16q, 17p and 22q. Frequent promoter hypermethylation and subsequent loss of protein expression has also been demonstrated in HCC at tumor suppressor gene (TSG), p16, p14, p15, SOCS1, RIZ1, E-cadherin and 14-3-3 sigma. An interesting observation emerging from these studies is the presence of a methylator phenotype in hepatocarcinogenesis, although it does not seem advantageous to have high levels of microsatellite instability. Methylation also appears to be an early event, suggesting that this may precede cirrhosis. However, these genes have been studied in isolation and global studies of methylator phenotype are required to assess the significance of epigenetic silencing in hepatocarcinogenesis. Based on previous data there are obvious fundamental differences in the mechanisms of hepatic carcinogenesis, with at least two distinct mechanisms of malignant transformation in the liver, related to CIN and CpG island methylation. The reason for these differences and the relative importance of these mechanisms are not clear but likely relate to the etiopathogenesis of HCC. Defining these broad mechanisms is a necessary prelude to determine the timing of events in malignant transformation of the liver and to investigate the role of known risk factors for HCC.
Collapse
Affiliation(s)
- Nirmitha I Herath
- Leukaemia Foundation Laboratory, Queensland Institute of Medical Research, Clinical Research Center, Royal Brisbane Hospital Research Foundation, Brisbane, Queensland, Australia.
| | | | | |
Collapse
|
|
14
|
Wong CM, Yam JWP, Ching YP, Yau TO, Leung THY, Jin DY, Ng IOL. Rho GTPase-activating protein deleted in liver cancer suppresses cell proliferation and invasion in hepatocellular carcinoma. Cancer Res 2005; 65:8861-8. [PMID: 16204057 DOI: 10.1158/0008-5472.can-05-1318] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Deleted in liver cancer (DLC1) is a candidate tumor suppressor gene recently isolated from human hepatocellular carcinoma. Structurally, DLC1 protein contains a conserved GTPase-activating protein for Rho family protein (RhoGAP) domain, which has been thought to regulate the activity of Rho family proteins. Previous studies indicated that DLC1 was frequently inactivated in cancer cells. In the present study, we aimed to characterize the tumor suppressor roles of DLC1 in hepatocellular carcinoma. We showed that DLC1 significantly inhibited cell proliferation, anchorage-independent growth, and in vivo tumorigenicity when stably expressed in hepatocellular carcinoma cells. Moreover, DLC1 expression greatly reduced the motility and invasiveness of hepatocellular carcinoma cells. With RhoGAP-deficient DLC1 mutant (DLC1-K714E), we showed that the RhoGAP activity was essential for DLC1-mediated tumor suppressor function. Furthermore, the 292- to 648-amino acid region and the steroidogenic acute regulatory related lipid transfer domain played an auxiliary role to RhoGAP and tumor suppressor function of DLC1. Taken together, our findings showed that DLC1 functions as a tumor suppressor in hepatocellular carcinoma and provide the first evidence to support the hypothesis that DLC1 suppresses cancer cell growth by negatively regulating the activity of Rho proteins.
Collapse
Affiliation(s)
- Chun-Ming Wong
- Department of Pathology, S.H. Ho Foundation Research Laboratories and Jockey Club Clinical Research Centre, Pokfulam, Hong Kong
| | | | | | | | | | | | | |
Collapse
|
|
15
|
Sundararajan R, Chen G, Mukherjee C, White E. Caspase-dependent processing activates the proapoptotic activity of deleted in breast cancer-1 during tumor necrosis factor-alpha-mediated death signaling. Oncogene 2005; 24:4908-20. [PMID: 15824730 DOI: 10.1038/sj.onc.1208681] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Deleted in breast cancer-1 (DBC-1) was initially cloned from a homozygously deleted region in breast and other cancers on human chromosome 8p21, although no function is known for the protein product it encodes. We identified the generation of amino-terminally truncated versions of DBC-1 during tumor necrosis factor (TNF)-alpha-mediated apoptosis. Full-length 150 kDa DBC-1 underwent caspase-dependent processing during TNF-alpha-mediated death signaling, to produce p120 DBC-1 and p66 DBC-1 carboxy-terminal fragments. Endogenous DBC-1 localized to the nucleus in healthy cells, but localized to the cytoplasm during TNF-alpha-mediated apoptosis, consistent with the loss of the amino-terminus containing the nuclear localization signal. Overexpression of an amino-terminal truncated DBC-1, resembling p120 DBC-1, caused mitochondrial clustering, mitochondrial matrix condensation, and sensitized cells to TNF-alpha-mediated apoptosis. The carboxy-terminal coiled-coil domain of DBC-1 was responsible for the cytoplasmic and mitochondrial localization, and for the death-promoting activity of DBC-1. Thus, caspase-dependent processing of DBC-1 may act as a feed-forward mechanism to promote apoptosis and possibly also tumor suppression. DBC-1, like its homolog cell cycle and apoptosis regulatory protein-1 (CARP-1), may function in the regulation of apoptosis.
Collapse
|
|
16
|
Adams J, Cuthbert-Heavens D, Bass S, Knowles MA. Infrequent mutation of TRAIL receptor 2 (TRAIL-R2/DR5) in transitional cell carcinoma of the bladder with 8p21 loss of heterozygosity. Cancer Lett 2005; 220:137-44. [PMID: 15766588 DOI: 10.1016/j.canlet.2004.06.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2004] [Revised: 06/28/2004] [Accepted: 06/30/2004] [Indexed: 10/26/2022]
Abstract
Loss of heterozygosity (LOH) on 8p is a frequent event in many cancers and is often associated with more aggressive disease. Tumour necrosis factor-related apoptosis inducing ligand (TRAIL) receptor 2 (TRAIL-R2) also known as TNFRSF10B (tumour necrosis factor receptor (TNFR) super family 10b) or KILLER/DR5, a member of the TNFR family, is a promising candidate tumour suppressor gene at 8p21-22. Mutations in this gene have been identified in non-small cell lung cancer, head and neck cancer, breast cancer and non-Hodgkin's lymphoma. We carried out mutation analysis of TRAIL-R2 in bladder cancer cell lines and in primary bladder tumours. One novel protein truncating mutation was identified in a bladder cancer cell line. Our results suggest that if TRAIL-R2 is the target of LOH events in these cancers, inactivation of the remaining allele is by a mechanism other than mutation.
Collapse
Affiliation(s)
- Jacqui Adams
- Cancer Research UK Clinical Centre, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | | | | | | |
Collapse
|
|
17
|
Chang SC, Lin JK, Lin TC, Liang WY. Loss of heterozygosity: An independent prognostic factor of colorectal cancer. World J Gastroenterol 2005; 11:778-84. [PMID: 15682467 PMCID: PMC4250583 DOI: 10.3748/wjg.v11.i6.778] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: Colorectal cancers result from the accumulation of several distinct genetic alterations. This study was to investigate the frequency and prognostic value of loss of heterozygosity (LOH) and microsatellite instability (MSI) at 14 genetic loci located near or within regions containing important genes implicated in colorectal tumorigenesis.
METHODS: We studied colorectal cancers with corresponding normal mucosae in 207 patients (139 males and 68 females, mean age at the time of tumor resection 66.2±12.4 years, range 22-88 years). There were 37 right-sided colonic tumors, 85 left-sided colonic tumors and 85 rectal tumors. The distribution of tumor staging was stage I in 25, stage II in 73, stage III in 68, and stage IV in 41. We analyzed the LOH and MSI of HPC1, hMSH2, hMLH1, APC, MET, P53, NH23-H1, DCC, BAT25, BAT26, D17S250, MYCL1 and D8S254 with fluorescent polymerase chain reaction and denatured gel electrophoresis. High-frequency LOH was determined to be greater than three, or more than 50% of the informative marker with LOH. High-frequency MSI (MSI-H) was determined as more than four markers with instability (>30%). Correlations of LOH and MSI with clinical outcomes and pathological features were analyzed and compared.
RESULTS: The occurrence of MSI-H was 7.25%, located predominantly in the right colons (7/15) and had a higher frequency of poor differentiation (6/15) and mucin production (7/15). LOH in at least one genetic locus occurred in 78.7% of the tumors and was significantly associated with disease progression. Of the 166 potentially cured patients, 45 developed tumor recurrence within 36 mo of follow-up. Clinicopathological factors affecting 3-year disease-free survival (DFS) were TNM staging, grade of differentiation, preoperative CEA level, and high LOH status. Patients with high LOH tumors had a significantly lower DFS (50%) compared with patients with low LOH tumors (84%). Of the patients developing subsequent tumor recurrence, the number and percentage of LOH were 2.97 and 46.8% respectively, similar to the stage IV disease patients. TNM staging had the most significant impact on DFS, followed by high LOH status.
CONCLUSION: Clinical manifestations of LOH and MSI are different in colorectal cancer patients. High-frequency LOH is associated with high metastatic potential of colorectal cancers.
Collapse
Affiliation(s)
- Shih-Ching Chang
- Division of Colon and Rectal Surgery, Department of Surgery, Veterans General Hospital-Taipei, National Yang-Ming University, Taiwan, China
| | | | | | | |
Collapse
|
|
18
|
French AJ, Petroni G, Thibideau SN, Smolkin M, Bissonette E, Roviello F, Harper JC, Koch BR, Anderson SA, Hebbring SJ, Powell SM. Allelic imbalance of 8p indicates poor survival in gastric cancer. J Mol Diagn 2005; 6:243-52. [PMID: 15269302 PMCID: PMC1867637 DOI: 10.1016/s1525-1578(10)60517-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Gastric cancer is a common tumor worldwide and a tremendous health burden. However, the underlying mechanisms of tumorigenesis in this cancer's development are primarily undefined. Allelic imbalance (AI) of 8p has been reported in many cancers, yet, the target(s) of alteration and the importance of allelic imbalance on this chromosomal arm in gastric carcinoma development remained to be characterized. Our findings confirmed a high rate of AI on 8p in gastric cancers. Moreover, we demonstrated that AI on 8p, either overall or at marker D8S560, was associated with poorer survival in patients with gastric cancer. Finally, gastric cancers with a high rate of microsatellite instability were significantly associated with noncardia tumors and with female gender.
Collapse
Affiliation(s)
- Amy J French
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
|
19
|
Van Geelen CMM, de Vries EGE, de Jong S. Lessons from TRAIL-resistance mechanisms in colorectal cancer cells: paving the road to patient-tailored therapy. Drug Resist Updat 2005; 7:345-58. [PMID: 15790545 DOI: 10.1016/j.drup.2004.11.002] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2004] [Revised: 11/02/2004] [Accepted: 11/03/2004] [Indexed: 02/06/2023]
Abstract
Colorectal cancer is one of the leading causes of cancer-related deaths worldwide. Intrinsic, as well as acquired, resistance to chemotherapy remains a major problem in the treatment of this disease. It is, therefore, of great importance to develop new, patient-tailored, treatment strategies for colorectal cancer patients. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) acts through the pro-apoptotic DR4 and DR5 receptors in tumor cells without harming normal cells and will soon be tested in clinical trials as a novel anti-cancer agent. However, not all human colon cancer cell lines are sensitive to TRAIL due to intrinsic or acquired TRAIL-resistance. This review discusses the mechanisms and modulation of TRAIL-resistance in colon cancer cells. Cell sensitivity to TRAIL can be affected by TRAIL-receptor expression at the cell membrane, DR4/DR5 ratio and functionality of TRAIL-receptors. Additional intracellular factors leading to TRAIL-resistance affect the caspase 8/c-FLIP ratio, such as loss of caspase 8 and caspase 10 due to mutations or gene methylation, CARP-dependent degradation of active caspase 8 and changes in caspase 8 or c-FLIP expression levels. Further downstream in the TRAIL apoptotic pathway, Bax mutations, or increased expression of IAP family members, in particularly XIAP and survivin, also cause resistance. Chemotherapeutic drugs, NSAIDs, interferon-gamma and proteasome inhibitors can overcome TRAIL-resistance by acting on TRAIL-receptor expression or changing the expression of pro- or anti-apoptotic proteins.
Collapse
Affiliation(s)
- Caroline M M Van Geelen
- Department of Medical Oncology, University Hospital of Groningen, PO Box 30.001, 9700 RB Groningen, Groningen, The Netherlands
| | | | | |
Collapse
|
|
20
|
Adams J, Williams SV, Aveyard JS, Knowles MA. Loss of Heterozygosity Analysis and DNA Copy Number Measurement on 8p in Bladder Cancer Reveals Two Mechanisms of Allelic Loss. Cancer Res 2005. [DOI: 10.1158/0008-5472.66.65.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Many epithelial tumors show deletion of the short arm of chromosome 8 that is related to aggressive disease or adverse prognosis. In undissected samples of urothelial cell carcinoma of the bladder, at least two regions of loss of heterozygosity (LOH) were identified previously within a small region of 8p11-p12. LOH analysis on a panel of pure tumor DNA samples confirmed this and identified tumors with allelic imbalance, some with clear breakpoints in 8p12. This suggests either that these samples contained genetically distinct subclones or that breakpoints in 8p12 may confer a selective advantage without LOH. To assess the mechanism of LOH and to map breakpoints precisely, a panel of bladder cancer cell lines was examined. Microsatellite analysis of 8p markers identified regions of contiguous homozygosity that coincided with regions of LOH in tumors. Fluorescence in situ hybridization analysis was carried out on seven cell lines predicted to have 8p LOH using a chromosome 8 paint, a chromosome 8 centromeric probe, and a series of single-copy genomic probes. This revealed overall underrepresentation of 8p and overrepresentation of 8q. Several breakpoints and one interstitial deletion were identified in 8p12. Two cell lines with extensive interstitial regions of homozygosity showed no reduction in DNA copy number by fluorescence in situ hybridization analysis, indicating that, in addition to large deletions and rearrangements of 8p, small regions of interstitial LOH on 8p12 may be generated by mitotic recombination. This implicates both major DNA double-strand break repair mechanisms in the generation of 8p alterations.
Collapse
Affiliation(s)
- Jacqui Adams
- Cancer Research UK Clinical Centre, St. James' University Hospital, Leeds, United Kingdom
| | - Sarah V. Williams
- Cancer Research UK Clinical Centre, St. James' University Hospital, Leeds, United Kingdom
| | - Joanne S. Aveyard
- Cancer Research UK Clinical Centre, St. James' University Hospital, Leeds, United Kingdom
| | - Margaret A. Knowles
- Cancer Research UK Clinical Centre, St. James' University Hospital, Leeds, United Kingdom
| |
Collapse
|
|
21
|
Lin JK, Chang SC, Yang YC, Li AFY. Loss of heterozygosity and DNA aneuploidy in colorectal adenocarcinoma. Ann Surg Oncol 2004; 10:1086-94. [PMID: 14597448 DOI: 10.1245/aso.2003.12.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND This study evaluated the relationship between DNA aneuploidy and loss of heterozygosity (LOH) at different genetic loci in colorectal adenocarcinoma. METHODS A total of 112 patients with surgically removed colorectal adenocarcinoma in Taipei Veterans General Hospital from January 1999 to July 2001 were included in this study. The pattern of DNA ploidy was determined with DNA flow cytometry, and the LOH of various genetic loci was determined with fluorescence polymerase chain reaction and denaturing gradient gel electrophoresis. The relationship between DNA ploidy, LOH of various genetic loci, and clinicopathologic variables was analyzed with the chi(2) test with Yates' correction as well as by multivariate binary logistic regression analysis. RESULTS Seventy-one (63.4%) of the 112 carcinomas had DNA aneuploidy. The DNA aneuploidy was not associated with any clinicopathologic variable. Ninety-one tumors (81.3%) exhibited LOH in at least one genetic locus. In the univariate analysis, the DNA aneuploidy was associated with LOH of Tp53-penta, D8S254, D5S346, and high-frequency LOH (P =.001, P =.016, P =.041, and P <.001, respectively). In the multivariate analysis, the most significant factor influencing DNA aneuploidy was D8S254, followed by Tp53-penta, high-frequency LOH, and D5S346. CONCLUSIONS DNA aneuploidy is strongly associated with LOH at specific genetic loci.
Collapse
Affiliation(s)
- Jen-Kou Lin
- Department of Surgery, Veterans General Hospital, Taipei, Taiwan.
| | | | | | | |
Collapse
|
|
22
|
Kim TY, Jong HS, Song SH, Dimtchev A, Jeong SJ, Lee JW, Kim TY, Kim NK, Jung M, Bang YJ. Transcriptional silencing of the DLC-1 tumor suppressor gene by epigenetic mechanism in gastric cancer cells. Oncogene 2003; 22:3943-3951. [PMID: 12813468 DOI: 10.1038/sj.onc.1206573] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2002] [Revised: 03/05/2003] [Accepted: 03/07/2003] [Indexed: 12/22/2022]
Abstract
DLC-1 (deleted in liver cancer) gene is frequently deleted in hepatocellular carcinoma. However, little is known about the genetic status and the expression of this gene in gastric cancer. In this study, Northern and Southern analysis showed that seven of nine human gastric cancer cell lines did not express DLC-1 mRNA, but contained the DLC-1 gene. To identify the mechanism of the loss of DLC-1 mRNA expression in these cell lines, we investigated the methylation status of DLC-1 gene by using methylation-specific PCR (MSP) and Southern blot, and found that five of seven DLC-1 nonexpressing gastric cancer cell lines were methylated in the DLC-1 CpG island. Treatment with 5-aza-2'-deoxycytidine (5-Aza-dC) induced DLC-1 mRNA expression in the gastric cancer cell lines that have the methylated alleles. Studies using SNU-601 cell line with methylated DLC-1 alleles revealed that nearly all CpG sites within DLC-1 CpG island were methylated, and that the in vitro methylation of the DLC-1 promoter region is enough to repress DLC-1 mRNA expression, regardless of the presence of transcription factors capable of inducing this gene. In all, 29 of 97 (30%) primary gastric cancers were also shown to be methylated, demonstrating that methylation of the DLC-1 CpG island is not uncommon in gastric cancer. In addition, we demonstrated that DLC-1 mRNA expression was induced, and an increase in the level of acetylated H3 and H4 was detected by the treatment with trichostatin A (TSA) in two DLC-1 nonexpressing cell lines that have the unmethylated alleles. Taken together, the results of our study suggest that the transcriptional silencing of DLC-1, by epigenetic mechanism, may be involved in gastric carcinogenesis.
Collapse
MESH Headings
- Acetylation/drug effects
- Acetyltransferases/antagonists & inhibitors
- Alleles
- Azacitidine/analogs & derivatives
- Azacitidine/pharmacology
- Blotting, Northern
- Blotting, Southern
- CpG Islands
- DNA Methylation/drug effects
- Decitabine
- Enzyme Inhibitors/pharmacology
- GTPase-Activating Proteins
- Gene Expression Regulation, Neoplastic/physiology
- Gene Silencing/physiology
- Genes, Tumor Suppressor
- Histone Acetyltransferases
- Histones/metabolism
- Humans
- Hydroxamic Acids/pharmacology
- Neoplasm Proteins/genetics
- Protein Processing, Post-Translational/drug effects
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Neoplasm/biosynthesis
- RNA, Neoplasm/genetics
- Saccharomyces cerevisiae Proteins/antagonists & inhibitors
- Stomach Neoplasms/genetics
- Stomach Neoplasms/metabolism
- Tumor Cells, Cultured/metabolism
- Tumor Suppressor Proteins/genetics
Collapse
Affiliation(s)
- Tai Young Kim
- National Research Laboratory for Cancer Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul 110-744, Korea
| | | | | | | | | | | | | | | | | | | |
Collapse
|
|
23
|
Seitz S, Wassmuth P, Fischer J, Nothnagel A, Jandrig B, Schlag PM, Scherneck S. Mutation analysis and mRNA expression of trail-receptors in human breast cancer. Int J Cancer 2002; 102:117-28. [PMID: 12385006 DOI: 10.1002/ijc.10694] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The chromosome region 8p12-p22 shows frequent allelic loss in a variety of human malignancies, including breast cancer (BC). The tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-receptors TRAIL-R1, -R2, -R3 and -R4 are located on 8p21-p22 and might be candidate tumor suppressor genes in this region. To evaluate the involvement of TRAIL receptors in breast carcinogenesis, we have analyzed the entire coding region of TRAIL-R2 and the death domain (DD) regions of TRAIL-R1 and -R4 for the detection of somatic mutations in a series of breast tumors, lymph node metastases and BC cell lines. Overall, we detected 1, 11 and 3 alterations in the TRAIL-R1, -R2 and -R4 genes, respectively. Although functional studies have not yet been performed, we assume that most of these alterations do not alter the function of TRAIL-receptors. Additionally, we analyzed individuals from BC families for the detection of TRAIL-R2 germline mutations. One alteration has been found in the Kozak consensus motif at position -4 with respect to the translation initiation AUG [1-4 (C-->A)]. We further studied the mRNA expression of TRAIL and the 4 TRAIL receptors. In BC cell lines, a strongly decreased mRNA expression of TRAIL, TRAIL-R1, -R3 and -R4 was found, whereas the expression of TRAIL-R2 was only slightly reduced. In breast tumors, a 1.2-3.6-fold reduction of mRNA signals of the 5 genes was observed. No correlation was found between the expression level of TRAIL and the receptor mRNAs and clinicopathologic variables and between the expression of TRAIL-R2 and TP53 mutation status and loss of heterozygosity (LOH) at 8p21-p22. Taken together, we cannot exclude the involvement of TRAIL-receptors in BC. Our mutation studies indicate that DD receptor mutations occur at low frequency and are not the primary cause for the altered mRNA expression of TRAIL and TRAIL-receptors in BC.
Collapse
Affiliation(s)
- Susanne Seitz
- Abteilung Tumorgenetik, Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13092 Berlin, Germany.
| | | | | | | | | | | | | |
Collapse
|
|
24
|
Wong N, Lai P, Pang E, Leung TW, Lau JW, Johnson PJ. A comprehensive karyotypic study on human hepatocellular carcinoma by spectral karyotyping. Hepatology 2000; 32:1060-8. [PMID: 11050057 DOI: 10.1053/jhep.2000.19349] [Citation(s) in RCA: 218] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
The current paucity of cytogenetic information on hepatocellular carcinoma (HCC) reflects the difficulties in culturing hepatocytes in vitro. Here, we report on the successful culture of 15 HCC cases. Chromosome aneuploidy ranging from a near-diploid to hyperhexaploid karyotype was found, but their complete karyotypic interpretations were hampered by the presence of many unidentifiable rearrangements. Spectral karyotyping (SKY) was used to elucidate structural changes in these HCC samples and 3 liver cancer cell lines (PLC/PRF/5, Hep3B, and HepG2). Frequent structural abnormalities were found on chromosomes 1 (13 of 15 cases; 3 of 3 cell lines), 8 (10 of 15 cases; 2 of 3 cell lines), 17 (9 of 15 cases; 3 of 3 cell lines), and 19 (9 of 15 cases; 1 of 3 cell lines). In particular, the chromosome regions 1p13-q21, 8p12-q21, 17p11-q12, 17q22, and 19p10-q13.1 were involved in multiple rearrangements. SKY analysis also suggested several previously undescribed breakpoints in HCC. These breakpoints, predominantly pericentromeric, clustered around the chromosome bands 2q33-q34, 3p13-q12, 4p14-q12, 5p10-q11, 7p12-q11, 10q10-q11, 11q10, 11q13-q21, 12q10-q13, 12q22-q23, 13q10-q14, 15q10, 16q10-q13, 18p11-q11, 20p11-q13.1, 21q10, and 22q10. When tumor sizes were compared, a significantly higher number of structural abnormalities was found in tumors larger than 4 cm (P =.007). Rearrangements such as t(1;8), t(1;11), t(1;19), and t(17;21) that were identified in both primary tumors and cell lines might represent markers that reflect proliferative advantages. Although SKY analysis did not indicate consistent translocations, it suggested nonrandom breakpoints, predominantly in the pericentromeric region, on a number of chromosomes. These breakpoint clusters may thus prove to be more important in the liver carcinogenesis and targets for further molecular investigations.
Collapse
Affiliation(s)
- N Wong
- Departments of Clinical Oncology at the Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, SAR Hong Kong, China.
| | | | | | | | | | | |
Collapse
|
|
25
|
Affiliation(s)
- C Abate-Shen
- Center for Advanced Biotechnology and Medicine, Cancer Institute of New Jersey, UMDNJ-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854,
| | | |
Collapse
|
|
26
|
Oyama T, Miyoshi Y, Koyama K, Nakagawa H, Yamori T, Ito T, Matsuda H, Arakawa H, Nakamura Y. Isolation of a novel gene on 8p21.3-22 whose expression is reduced significantly in human colorectal cancers with liver metastasis. Genes Chromosomes Cancer 2000; 29:9-15. [PMID: 10918388 DOI: 10.1002/1098-2264(2000)9999:9999<::aid-gcc1001>3.0.co;2-#] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Metastasis, a major factor contributing to poor prognosis of cancer patients, is caused by a complex series of events that involve many genes. To investigate this process, we analyzed by differential display three cell lines that had been established from a murine colon adenocarcinoma (colon 26), NL4, NL17, and NL22, each of which possessed a different potential for metastasis in mice. We report here the identification of a novel gene, ream (reduced expression associated with metastasis), which showed significantly lower expression in NL17 and NL22 with a high potential for metastasis than in NL4 without a metastatic potential. The human counterpart of murine ream expressed two sizes of transcript, 4.4 kb and 1.8 kb, both encoding the same 367-amino acid peptide, which appeared to contain four membrane-spanning regions. The cDNA showed no significant homology to any known genes in the public database. Human REAM was found to lie within an 800-kb segment of 8p21.3-22, where we had previously identified a commonly deleted region in colorectal and hepatocellular carcinomas. Its expression was reduced in more than half of the human colorectal cancers we examined, particularly in advanced stages with liver metastasis. Furthermore, we identified somatic mutations of this gene in a colorectal cancer, a hepatocellular carcinoma, and a nonsmall lung cancer among 111 human tumors of various stages examined.
Collapse
Affiliation(s)
- T Oyama
- Division of Clinical Genetics, Biomedical Research Center, Osaka University School of Medicine, Osaka, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
|
27
|
Wilson PJ, McGlinn E, Marsh A, Evans T, Arnold J, Wright K, Biden K, Young J, Wainwright B, Wicking C, Chenevix-Trench G. Sequence variants of DLC1 in colorectal and ovarian tumours. Hum Mutat 2000; 15:156-65. [PMID: 10649492 DOI: 10.1002/(sici)1098-1004(200002)15:2<156::aid-humu4>3.0.co;2-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Loss of heterozygosity occurs frequently on the short arm of chromosome 8 in many neoplasms, including colorectal and ovarian cancer. Monochromosome transfer experiments into colorectal tumour cell lines have provided functional evidence for a tumour suppressor gene located at 8p22-23. One of the genes from this region that is expressed by our suppressed hybrids is a candidate tumour suppressor gene, DLC1 (deleted in liver cancer), which has homology to rat RhoGAP. We have delineated the structure of the DLC1 gene and used single-stranded conformation polymorphism analysis (SSCP) to look for sequence variants in 126 colorectal and 33 ovarian primary tumours and cell lines. One exonic missense mutation and three intronic insertions/deletions were identified in primary colorectal tumours, as well as many polymorphisms present in germline DNAs. The rarity of exonic missense mutations, and the absence of protein-truncating mutations, indicates that DLC1 is not the target of 8p LOH in colorectal or ovarian tumours. The delineation of the gene structure allows mutation analysis of DLC1 in other tumour types for which it remains a candidate tumour suppressor gene based on its location and homology to rhoGAP.
Collapse
Affiliation(s)
- P J Wilson
- Joint Experimental Oncology Programme, The Queensland Institute of Medical Research and the University of Queensland, Brisbane, Australia.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
|
28
|
Arbieva ZH, Banerjee K, Kim SY, Edassery SL, Maniatis VS, Horrigan SK, Westbrook CA. High-resolution physical map and transcript identification of a prostate cancer deletion interval on 8p22. Genome Res 2000; 10:244-57. [PMID: 10673282 PMCID: PMC310830 DOI: 10.1101/gr.10.2.244] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A genomic interval of approximately 1-1.5 Mb centered at the MSR marker on 8p22 has emerged as a possible site for a tumor suppressor gene, based on high rates of allele loss and the presence of a homozygous deletion found in metastatic prostate cancer. The objective of this study was to prepare a bacterial contig of this interval, integrate the contig with radiation hybrid (RH) databases, and use these resources to identify transcription units that might represent the candidate tumor suppressor genes. Here we present a complete bacterial contig across the interval, which was assembled using 22 published and 17 newly originated STSs. The physical map provides twofold or greater coverage over much of the interval, including 17 BACs, 15 P1s, 2 cosmids, and 1 PAC clone. The position of the selected markers across the interval in relation to the other markers on the larger chromosomal scale was confirmed by RH mapping using the Stanford G3 RH panel. Transcribed units within the deletion region were identified by exon amplification, searching of the Human Transcript Map, placement of unmapped expressed sequence tags (ESTs) from the Radiation Hybrid Database (RHdb), and from other published sources, resulting in the isolation of six unique expressed sequences. The transcript map of the deletion interval now includes two known genes (MSR and N33) and six novel ESTs.
Collapse
Affiliation(s)
- Z H Arbieva
- Section of Hematology-Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois 60607-7170 USA
| | | | | | | | | | | | | |
Collapse
|
|
29
|
Halling KC, French AJ, McDonnell SK, Burgart LJ, Schaid DJ, Peterson BJ, Moon-Tasson L, Mahoney MR, Sargent DJ, O'Connell MJ, Witzig TE, Farr GH, Goldberg RM, Thibodeau SN. Microsatellite instability and 8p allelic imbalance in stage B2 and C colorectal cancers. J Natl Cancer Inst 1999; 91:1295-303. [PMID: 10433618 DOI: 10.1093/jnci/91.15.1295] [Citation(s) in RCA: 310] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Microsatellite instability (MSI) and allelic imbalance involving chromosome arms 5q, 8p, 17p, and 18q are genetic alterations commonly found in colorectal cancer. We investigated whether the presence or absence of these genetic alterations would allow stratification of patients with Astler-Coller stage B2 or C colorectal cancer into favorable and unfavorable prognostic groups. METHODS Tumors from 508 patients were evaluated for MSI and allelic imbalance by use of 11 microsatellite markers located on chromosome arms 5q, 8p, 15q, 17p, and 18q. Genetic alterations involving each of these markers were examined for associations with survival and disease recurrence. All P values are two-sided. RESULTS In univariate analyses, high MSI (MSI-H), i.e., MSI at 30% or more of the loci examined, was associated with improved survival (P =.02) and time to recurrence (P =.01). The group of patients whose tumors exhibited allelic imbalance at chromosome 8p had decreased survival (P =.02) and time to recurrence (P =.004). No statistically significant associations with survival or time to recurrence were observed for markers on chromosome arms 5q, 15q, 17p, or 18q. In multivariate analyses, MSI-H was an independent predictor of improved survival (hazard ratio [HR] = 0.51; 95% confidence interval [CI] = 0.31-0.82; P =.006) and time to recurrence (HR = 0.42; 95% CI = 0.24-0.74; P =.003), and 8p allelic imbalance was an independent predictor of decreased survival (HR = 1.89; 95% CI = 1.25-2.83; P =. 002) and time to recurrence (HR = 2.07; 95% CI = 1.32-3.25; P =.002). CONCLUSIONS Patients whose tumors exhibited MSI-H had a favorable prognosis, whereas those with 8p allelic imbalance had a poor prognosis; both alterations served as independent prognostic factors. To our knowledge, this is the first report of an association between 8p allelic imbalance and survival in patients with colorectal cancer.
Collapse
Affiliation(s)
- K C Halling
- Departments of Laboratory Medicine and Pathology, Mayo Foundation, Rochester, MN 55905, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
|
30
|
Sakakura C, Hagiwara A, Taniguchi H, Yamaguchi T, Yamagishi H, Takahashi T, Koyama K, Nakamura Y, Abe T, Inazawa J. Chromosomal aberrations in human hepatocellular carcinomas associated with hepatitis C virus infection detected by comparative genomic hybridization. Br J Cancer 1999; 80:2034-9. [PMID: 10471057 PMCID: PMC2363156 DOI: 10.1038/sj.bjc.6690638] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Thirty-five hepatocellular carcinomas (HCCs) associated with hepatitis C virus (HCV) were analysed by comparative genomic hybridization (CGH), to screen for changes in copy-number of DNA sequences. Chromosomal losses were noted in 1p34-36 (37%), 4q12-21 (48%), 5q13-21 (35%), 6q13-16 (23%), 8p21-23 (28%), 13q (20%), 16q (33%) and 17p13 (37%). Gains were noted in 1q (46%), 6p (20%), 8q21-24 (31%) and 17q (43%). High level gains indicative of gene amplifications were found in 7q31 (3%), 11q13 (3%), 14q12 (6%) and 17q12 (3%); amplification at 14q12 may be characteristic for HCCs. No significant difference in chromosomal aberrations was noted between carcinomas associated with HCV-infection in our study and those reported earlier in HCCs infected with hepatitis B virus (HBV), indicating that both HBV- and HCV-related carcinomas may progress through a similar cascade of molecular events.
Collapse
Affiliation(s)
- C Sakakura
- First Department of Surgery, Kyoto Prefectural University of Medicine, Kawaramachi-dori, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
|
31
|
Bläker H, Graf M, Rieker RJ, Otto HF. Comparison of losses of heterozygosity and replication errors in primary colorectal carcinomas and corresponding liver metastases. J Pathol 1999; 188:258-62. [PMID: 10419592 DOI: 10.1002/(sici)1096-9896(199907)188:3<258::aid-path350>3.0.co;2-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In order to investigate genetic alterations specific to liver metastases of colorectal carcinomas, losses of heterozygosity and replication errors have been compared in 15 cases of primary colorectal carcinoma and in the corresponding metastatic liver tumours. Fifteen microsatellite markers located on 13 different chromosomal arms were used in the study. The LOH patterns of the primary and the metastatic tumours were identical in eight cases and showed differences in seven cases. Areas of deletion predominantly or completely common to the colorectal and the metastatic tumour were detected on chromosomes 5q, 8p, 17p, 18q, and 22q. Preferential loss in metastatic tumours was observed on chromosomal arm 3p. Replication errors were found in four primary tumours and in three of the corresponding secondaries. A replication error phenotype specific to a metastasis was not observed.
Collapse
Affiliation(s)
- H Bläker
- Department of Pathology, University of Heidelberg, Im Neuenheimer Feld 220/221, 69120 Heidelberg, Germany.
| | | | | | | |
Collapse
|
|
32
|
Lerebours F, Olschwang S, Thuille B, Schmitz A, Fouchet P, Buecher B, Martinet N, Galateau F, Thomas G. Fine deletion mapping of chromosome 8p in non-small-cell lung carcinoma. Int J Cancer 1999; 81:854-8. [PMID: 10362129 DOI: 10.1002/(sici)1097-0215(19990611)81:6<854::aid-ijc3>3.0.co;2-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Several somatic genetic alterations have been described in non-small-cell lung carcinomas (NSCLC). Recurrent chromosomal deletions have suggested the presence of tumor-suppressor genes specifically involved in lung carcinogenesis. For one of these, 2 non-overlapping regions have been proposed on the short arm of chromosome 8, encompassing the LPL and NEFL genes. The LPL region has been extensively studied in NSCLC and other cancer types. Two genes, N33 and PRLTS, have been identified, but the small number of mutations excludes their involvement in the vast majority of tumors. In order to delineate a reliable region of deletional overlap on chromosome 8p in NSCLC, a series of 77 NSCLC was studied for 34 microsatellite polymorphisms distributed on chromosome 8p, using multiplex-PCR amplification. After purification of tumor nuclei by flow cytometry based on either the abnormal DNA index or the presence of a high expression of cytokeratin, allelic losses on chromosome 8p were observed in 39% of cases. Measurement of DNA index showed that 62% of tumors were hyperploid; allelic losses were more frequent in hyperploid than in diploid tumors (54% vs. 14%; p < 10(-4)). Deletions of part of the short arm were observed in 7 instances. Our data allow definition of an interval of common deletion, flanked by the loci D8S511 and D8S1992, where the putative tumor-suppressor gene might be localized.
Collapse
|
|
33
|
Lerebours F, Olschwang S, Thuille B, Schmitz A, Fouchet P, Laurent-Puig P, Boman F, Fléjou JF, Monges G, Paraf F, Bedossa P, Sabourin JC, Salmon RJ, Parc R, Thomas G. Deletion mapping of the tumor suppressor locus involved in colorectal cancer on chromosome band 8p21. Genes Chromosomes Cancer 1999; 25:147-53. [PMID: 10337998 DOI: 10.1002/(sici)1098-2264(199906)25:2<147::aid-gcc10>3.0.co;2-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Several somatic genetic alterations have been described in colorectal carcinoma (CRC). Recurrent chromosomal deletions have suggested the presence of tumor suppressor genes (TSG) specifically involved in colorectal carcinogenesis. For one of them, two non-overlapping regions have been proposed on the short arm of chromosome 8, encompassing the LPL and NEFL genes. The short arm of chromosome 8 has been extensively studied in colorectal cancer and in other cancer types. Both regions have been reported as candidate loci for a TSG. In order to delineate a reliable region of deletional overlap on chromosome arm 8p in CRC, a series of 365 CRC samples was selected for the absence of microsatellite instability (RER, replication error); tumor and normal matched DNAs were studied for 54 microsatellite polymorphisms distributed on 8p using multiplex-PCR amplification. After purification of tumor nuclei by flow cytometry based on either the abnormal DNA index or the presence of a high expression of cytokeratin, complete allelic losses on 8p were observed in 48% of cases. Measurement of the DNA index showed that 88% of RER tumors were hyperploid. Complete allelic losses of only part of the short arm were observed on 26 occasions. These data allowed us to define a 1 cM interval of common deletion, flanked by the loci D8S1771 and NEFL, where a putative TSG may be localized.
Collapse
|
|
34
|
Pineau P, Nagai H, Prigent S, Wei Y, Gyapay G, Weissenbach J, Tiollais P, Buendia MA, Dejean A. Identification of three distinct regions of allelic deletions on the short arm of chromosome 8 in hepatocellular carcinoma. Oncogene 1999; 18:3127-34. [PMID: 10340384 DOI: 10.1038/sj.onc.1202648] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The chromosome 8p is associated with a large number of allelic imbalances in epithelial tumors including hepatocellular carcinoma (HCC). However, no tumor suppressor gene has been identified so far in this particular region of the genome. To further clarify the pattern of allelic deletions on chromosome 8p in HCC, we have undertaken high-density polymorphic marker analysis of 109 paired normal and primary tumor samples using 40 microsatellites positioned every 2 cm in average throughout 8p. We found that 60% of the tumors exhibited loss of heterozygosity (LOH) at one or more loci at 8p with three distinct minimal deleted areas: a 13 cm region in the distal part of 8p21, a 9 cm area in the more proximal portion of 8p22 and a 5 cm area in 8p23. These data strongly suggest the presence of at least three novel tumor suppressor loci on 8p in hepatocellular carcinoma.
Collapse
Affiliation(s)
- P Pineau
- Unité de Recombinaison & Expression Génétique, INSERM U163, Institut Pasteur, Paris, France
| | | | | | | | | | | | | | | | | |
Collapse
|
|
35
|
Ohgaki K, Iida A, Ogawa O, Kubota Y, Akimoto M, Emi M. Localization of tumor suppressor gene associated with distant metastasis of urinary bladder cancer to a 1-Mb interval on 8p22. Genes Chromosomes Cancer 1999; 25:1-5. [PMID: 10221333 DOI: 10.1002/(sici)1098-2264(199905)25:1<1::aid-gcc1>3.0.co;2-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
To identify the location of one or more putative tumor suppressor genes that may be involved in urinary bladder cancer, we examined 82 such tumors for allelic losses at 19 microsatellite loci on 8p. Loss of heterozygosity was observed in 31 of the cases. Deletion mapping identified a commonly deleted region at 8p22, within the 1-Mb interval flanked by D8S1135 and AFM177XB10. Allelic loss at 8p22 was associated with higher tumor grade (17/31, 55%, vs. 12/51, 23%; P = 0.0013). Furthermore, no tumor that retained heterozygosity for markers at 8p22 had metastasized to distant organs, whereas a substantial portion of tumors that lost alleles in that region had done so (0/51, 0%, vs. 6/31, 20%; P = 0.001). These data imply that loss or inactivation of tumor-suppressing activity encoded on 8p contributes to malignancy and to the metastatic potential of bladder cancers.
Collapse
Affiliation(s)
- K Ohgaki
- Department of Molecular Biology, Institute of Gerontology, Nippon Medical School, Tokyo, Japan
| | | | | | | | | | | |
Collapse
|
|
36
|
Sheu JC, Lin YW, Chou HC, Huang GT, Lee HS, Lin YH, Huang SY, Chen CH, Wang JT, Lee PH, Lin JT, Lu FJ, Chen DS. Loss of heterozygosity and microsatellite instability in hepatocellular carcinoma in Taiwan. Br J Cancer 1999; 80:468-76. [PMID: 10408855 PMCID: PMC2362334 DOI: 10.1038/sj.bjc.6690380] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Elucidation of the basic genetic changes of human hepatocellular carcinoma is important for the understanding and treatment of this cancer. We used microsatellite polymorphism markers to study 30 cases of hepatocellular carcinoma (34 tumours) on all human chromosomes. DNA from 34 pairs of hepatocellular carcinomas and corresponding non-tumour parts was prepared. Loss of heterozygosity (LOH) and microsatellite instability on 23 chromosomes were investigated by 231 sets of microsatellite markers. More than 20% LOH was shown for loci on 16q (47.1%), 13q (32.4%), 17p (32.4%), 5q (26.5%), 11p (23.5%) and 9p (20.6%). The commonly affected regions were mapped to 16q12.1, 16q12.2, 16q24, 13q12.1-32, 17p13, 5q32, 5q34, 5q3, 11p15, 11q23-24 and 9p21. Hepatitis B virus carriers had a significantly higher frequency of LOH on chromosomes 5q, 11p and 16q. Furthermore, larger tumour size tended to have higher frequency of LOH at D16S409 locus (16q12.1). Microsatellte instability was only found in 12 of 231 markers and the frequency is very low. These data suggest that the chromosomes 16q, 13q, 17p, 5q, 11p and 9p might participate in hepatocarcinogenesis. However, microsatellite instability might play little role in the development of this cancer in Taiwan.
Collapse
Affiliation(s)
- J C Sheu
- Department of Internal Medicine, College of Medicine, National Taiwan University Hospital, Taipei
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
|
37
|
Yokota T, Yoshimoto M, Akiyama F, Sakamoto G, Kasumi F, Nakamura Y, Emi M. Localization of a tumor suppressor gene associated with the progression of human breast carcinoma within a 1-cm interval of 8p22-p23.1. Cancer 1999. [DOI: 10.1002/(sici)1097-0142(19990115)85:2<447::aid-cncr24>3.0.co;2-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
|
38
|
Schullerus D, von Knobloch R, Chudek J, Herbers J, Kovacs G. Microsatellite analysis reveals deletion of a large region at chromosome 8p in conventional renal cell carcinoma. Int J Cancer 1999; 80:22-24. [PMID: 9935224 DOI: 10.1002/(sici)1097-0215(19990105)80:1<22::aid-ijc5>3.0.co;2-s] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Loss of heterozygosity (LOH) at chromosome 8p is associated with the progression of conventional (non-papillary) renal cell carcinomas (RCC). To determine the tumor suppressor gene locus, we carried out a deletion mapping of chromosome 8p at 10 microsatellite loci in 96 RCCs. LOH occurred in 32% of the tumors. The smallest overlapping region of deletion at chromosome 8p11.2-p23.1 corresponds to approximately 34-cM genetic distance. No small interstitial deletion was seen.
Collapse
Affiliation(s)
- D Schullerus
- Department of Urology, Ruprecht-Karls-University, Heidelberg, Germany
| | | | | | | | | |
Collapse
|
|
39
|
Hermsen MA, Baak JP, Meijer GA, Weiss JM, Walboomers JW, Snijders PJ, van Diest PJ. Genetic analysis of 53 lymph node-negative breast carcinomas by CGH and relation to clinical, pathological, morphometric, and DNA cytometric prognostic factors. J Pathol 1998; 186:356-62. [PMID: 10209483 DOI: 10.1002/(sici)1096-9896(199812)186:4<356::aid-path196>3.0.co;2-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Within the subgroup of lymph node-negative breast cancers, there is a need for accurate prognostic indicators to select high-risk patients. Comparative genomic hybridization (CGH) provides an opportunity to screen the whole genome for chromosomal aberrations which may be associated with poor clinical outcome. The results of CGH analysis of 53 lymph node-negative breast carcinomas are presented and correlated with a set of clinico-pathological and cytometric features with strong prognostic value. The most frequent chromosomal gains were, in descending order of frequency, 8q, 1q, Xq, 5q, 4q, and 3q. Recurring losses were observed at chromosomal arms 19p, 1p, 17p, 22q, 4q, and 8p. There was not a single, unique combination of chromosomal aberrations, but gains of 1q and 8q were frequently observed simultaneously (15/53 cases). DNA aneuploid tumours harboured more gains than DNA diploid tumours, but there was no correlation between the total number of events per tumour detected by CGH and any of the prognostic features. Of the many chromosomal aberrations found, only gains of chromosome 8q were strongly correlated with high values of mean nuclear area. A clearer picture was obtained when comparing only those cases which, according to their cytometric and morphometric features, had either the worst or the best prognosis. Gains occurred mainly in the 'poor prognostic features' group, in particular at 8q, 11q13, 17q, and 20q. It is hypothesized that these gains could be late, progression-related events and may be associated with aggressive clinical behaviour. These four chromosomal regions may therefore be of potential prognostic value. Correlation with real follow-up data will enable us better to identify those patients who have a high risk of recurrence within the subgroup of lymph node-negative breast cancer patients.
Collapse
Affiliation(s)
- M A Hermsen
- Department of Pathology, University Hospital Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
|
40
|
Antonio Parada L, Hallén M, Tranberg KG, Hägerstrand I, Bondeson L, Mitelman F, Johansson B. Frequent rearrangements of chromosomes 1, 7, and 8 in primary liver cancer. Genes Chromosomes Cancer 1998. [DOI: 10.1002/(sici)1098-2264(199809)23:1<26::aid-gcc5>3.0.co;2-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
|
|
41
|
Macdonald GA, Greenson JK, Saito K, Cherian SP, Appelman HD, Boland CR. Microsatellite instability and loss of heterozygosity at DNA mismatch repair gene loci occurs during hepatic carcinogenesis. Hepatology 1998; 28:90-7. [PMID: 9657101 DOI: 10.1002/hep.510280114] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
DNA mismatch repair is an important mechanism involved in maintaining the fidelity of genomic DNA. Defective DNA mismatch repair is implicated in a variety of gastrointestinal and other tumors; however, its role in hepatocellular carcinoma (HCC) has not been assessed. Formalin-fixed, paraffin-embedded archival pathology tissues from 46 primary liver tumors were studied by microdissection and microsatellite analysis of extracted DNA to assess the degree of microsatellite instability, a marker of defective mismatch repair, and to determine the extent and timing of allelic loss of two DNA mismatch repair genes, human Mut S homologue-2 (hMSH2) and human Mut L homologue-1 (hMLH1), and the tumor suppressor genes adenomatous polyposis coli gene (APC), p53, and DPC4. Microsatellite instability was detected in 16 of the tumors (34.8%). Loss of heterozygosity at microsatellites linked to the DNA mismatch repair genes, hMSH2 and/or hMLH1, was found in 9 cases (19.6%), usually in association with microsatellite instability. Importantly, the pattern of allelic loss was uniform in 8 of these 9 tumors, suggesting that clonal loss had occurred. Moreover, loss at these loci also occurred in nonmalignant tissue adjacent to 4 of these tumors, where it was associated with marked allelic heterogeneity. There was relatively infrequent loss of APC, p53, or DPC4 loci that appeared unrelated to loss of hMSH2 or hMLH1 gene loci. Loss of heterozygosity at hMSH2 and/or hMLH1 gene loci, and the associated microsatellite instability in premalignant hepatic tissues suggests a possible causal role in hepatic carcinogenesis in a subset of hepatomas.
Collapse
Affiliation(s)
- G A Macdonald
- Department of Internal Medicine, University of Michigan, Ann Arbor, USA
| | | | | | | | | | | |
Collapse
|
|
42
|
De Gregorio L, Manenti G, Incarbone M, Pilotti S, Pastorino U, Pierotti MA, Dragani TA. Prognostic value of loss of heterozygosity and KRAS2 mutations in lung adenocarcinoma. Int J Cancer 1998; 79:269-72. [PMID: 9645349 DOI: 10.1002/(sici)1097-0215(19980619)79:3<269::aid-ijc10>3.0.co;2-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The prognostic values of loss of heterozygosity (LOH) at loci frequently involved in non-small cell lung cancer and of KRAS2 gene mutations were studied in lung adenocarcinoma patients. LOHs were relatively common, ranging from 24% at chromosome 10p to 55% at chromosome 17p13. KRAS2 mutations at codon 12 were present in 26% of cases, were more common in male than in female patients and were associated with a smoking habit. No association between LOH at any site and clinical stage or survival rate was found. On the other hand, we observed a trend between the presence of any type of KRAS2 mutations and poor survival. Analysis of specific KRAS2 mutations showed a strong effect of Asp (GAT) and Val (GTT) mutations, resulting in a very poor survival compared with wild type group, whereas the most common mutation (Cys, TGT) was not associated with prognosis. Our results indicate the importance of specific activating mutations of the KRAS2 gene as genetic markers of clinical outcome for patients with lung adenocarcinoma.
Collapse
Affiliation(s)
- L De Gregorio
- Division of Experimental Oncology A, Istituto Nazionale Tumori, Milan, Italy
| | | | | | | | | | | | | |
Collapse
|
|
43
|
Sato M, Mori Y, Sakurada A, Fukushige S, Ishikawa Y, Tsuchiya E, Saito Y, Nukiwa T, Fujimura S, Horii A. Identification of a 910-Kb region of common allelic loss in chromosome bands 16q24.1–q24.2 in human lung cancer. Genes Chromosomes Cancer 1998. [DOI: 10.1002/(sici)1098-2264(199805)22:1<1::aid-gcc1>3.0.co;2-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
|
44
|
Matsushima M, Fujiwara T, Takahashi EI, Minaguchi T, Eguchi Y, Tsujimoto Y, Suzumori K, Nakamura Y. Isolation, mapping, and functional analysis of a novel human cDNA (BNIP3L) encoding a protein homologous to human NIP3. Genes Chromosomes Cancer 1998. [DOI: 10.1002/(sici)1098-2264(199803)21:3<230::aid-gcc7>3.0.co;2-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
|
45
|
|
|
46
|
Wu CL, Roz L, Sloan P, Read AP, Holland S, Porter S, Scully C, Speight PM, Thakker N. Deletion mapping defines three discrete areas of allelic imbalance on chromosome arm 8p in oral and oropharyngeal squamous cell carcinomas. Genes Chromosomes Cancer 1997; 20:347-53. [PMID: 9408750 DOI: 10.1002/(sici)1098-2264(199712)20:4<347::aid-gcc5>3.0.co;2-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Deletions on chromosome arm 8p, as defined by allelic imbalance, are a frequent event in many different types of malignant tumors, including those of the head and neck. These regions are thought to harbor tumor suppressor genes. In order to define a high-density deletion map of this chromosomal arm in oral and oropharyngeal squamous cell carcinomas, we have tested for allelic imbalance in 35 such tumors with 22 short tandem-repeat polymorphisms. Overall, 21 (60%) of the 35 tumors showed allelic imbalance at one or more loci on chromosome arm 8p. Interstitial deletions defined three discrete areas of deletion: at 8p23, 8p22, and 8p12-p21. Tumors of TNM stages II-IV showed a significantly higher frequency of allelic imbalance on 8p than did TNM stage I tumors. Our data suggest that there are least three tumor suppressor loci on chromosome arm 8p that may be implicated in oral carcinogenesis. Furthermore, inactivation of such genes may be associated with high-grade tumors.
Collapse
Affiliation(s)
- C L Wu
- Department of Medical Genetics, University of Manchester, United Kingdom
| | | | | | | | | | | | | | | | | |
Collapse
|
|
47
|
Parada LA, Bardi G, Hallén M, Hägerstrand I, Tranberg KG, Mitelman F, Johansson B. Cytogenetic abnormalities and clonal evolution in an adult hepatoblastoma. Am J Surg Pathol 1997; 21:1381-6. [PMID: 9351578 DOI: 10.1097/00000478-199711000-00015] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Hepatoblastomas usually occur in children < 3 years of age, and only occasional adult cases have been described. To date, 20 cytogenetically abnormal childhood hepatoblastomas have been reported. Karyotypic investigations have shown that most hepatoblastomas are diploid or hyperdiploid, often displaying trisomies for chromosomes 2 and 20. We have cytogenetically investigated an adult hepatoblastoma for which no previous karyotypic data exist. A hypertriploid stemline with multiple numerical and structural chromosomal aberrations, including +2 and +20, was found. In addition, the tumor displayed extensive clonal evolution with 11 subclones. Although the tumor thus displayed some chromosomal abnormalities commonly observed in childhood tumors, providing further support for the importance of these abnormalities in the development of hepatoblastoma, the level of genomic complexity seen in the present case has never been described in childhood hepatoblastomas and may suggest a different etiology or pathogenesis.
Collapse
Affiliation(s)
- L A Parada
- Department of Clinical Genetics, University Hospital, Lund, Sweden
| | | | | | | | | | | | | |
Collapse
|
|
48
|
He WW, Sciavolino PJ, Wing J, Augustus M, Hudson P, Meissner PS, Curtis RT, Shell BK, Bostwick DG, Tindall DJ, Gelmann EP, Abate-Shen C, Carter KC. A novel human prostate-specific, androgen-regulated homeobox gene (NKX3.1) that maps to 8p21, a region frequently deleted in prostate cancer. Genomics 1997; 43:69-77. [PMID: 9226374 DOI: 10.1006/geno.1997.4715] [Citation(s) in RCA: 267] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have isolated a prostate-specific gene (NKX3.1) in humans that is homologous to the Drosophila NK homeobox gene family. Northern blot analyses indicate that this gene is expressed at high levels in adult prostate and at a much lower level in testis, but is expressed little or not at all in several other tissues. In an androgen-dependent prostate carcinoma line, LNCaP, NKX3.1 mRNA is expressed at a basal level that was increased markedly upon androgen stimulation; the NKX3.1 mRNA was undetectable in several other human tumor cell lines including two androgen-independent prostate carcinoma lines. The NKX3.1 gene maps to chromosome band 8p21, a region frequently reported to undergo a loss of heterozygosity associated with tissue dedifferentiation and loss of androgen responsiveness during the progression of prostate cancer. Based on these data we propose that NKX3.1 is a candidate gene for playing a role in the opposing processes of androgen-driven differentiation of prostatic tissue and loss of that differentiation during the progression of prostate cancer.
Collapse
MESH Headings
- Adult
- Amino Acid Sequence
- Androgens/metabolism
- Androgens/pharmacology
- Animals
- Base Sequence
- Chromosome Deletion
- Chromosome Mapping
- Chromosomes, Human, Pair 8/genetics
- Cloning, Molecular
- DNA/genetics
- Drosophila/genetics
- Gene Expression Regulation/drug effects
- Genes, Homeobox
- Genes, Insect
- Homeodomain Proteins/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Male
- Mice
- Molecular Sequence Data
- Neoplasms, Hormone-Dependent/genetics
- Neoplasms, Hormone-Dependent/metabolism
- Prostate/growth & development
- Prostate/metabolism
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Tissue Distribution
- Transcription Factors/genetics
- Tumor Cells, Cultured
Collapse
Affiliation(s)
- W W He
- Department of Molecular Biology, Human Genome Sciences Inc., Rockville, Maryland 20850, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
|
49
|
Komiya A, Suzuki H, Ueda T, Aida S, Ito N, Shiraishi T, Yatani R, Emi M, Yasuda K, Shimazaki J, Ito H. PRLTS gene alterations in human prostate cancer. Jpn J Cancer Res 1997; 88:389-93. [PMID: 9197531 PMCID: PMC5921422 DOI: 10.1111/j.1349-7006.1997.tb00394.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Since loss of heterozygosity on 8p22-p21.3 has been found frequently in prostate cancer, the status of a candidate tumor suppressor gene named PRLTS gene, recently cloned from the same region in some human malignancies, was examined in the present study. DNAs were isolated from 69 Japanese prostate cancer patients (37 localized and 32 cancer-death cases). Loss of heterozygosity at this gene locus was observed in 15 of 36 (42%) localized prostate cancer patients and 22 of 32 (69%) cancer-death patients. One cancer-death patient had a missense mutation, ACG-->ATG (Thr-->Met) at codon 64 in metastatic tumor tissues of pelvic lymph node and liver, and these tissues showed loss of the homologous allele, indicating that "two-hit" mutation of the PRLTS gene had occurred in this case. The others did not show any mutation, regardless of the presence or absence of loss of heterozygosity. Although loss of heterozygosity at the PRLTS gene locus is a relatively common abnormality, mutation of this gene is rare in prostate cancer.
Collapse
Affiliation(s)
- A Komiya
- Department of Urology, School of Medicine, Chiba University, Chuo-ku
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
|
50
|
Bookstein R, Bova GS, MacGrogan D, Levy A, Isaacs WB. Tumour-suppressor genes in prostatic oncogenesis: a positional approach. BRITISH JOURNAL OF UROLOGY 1997; 79 Suppl 1:28-36. [PMID: 9088270 DOI: 10.1111/j.1464-410x.1997.tb00798.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Genetic alterations, such as mutation, methylation and aneuploidy, are thought to underlie the multistep genesis and progression of many human cancers. However, the genetic events occurring in prostatic oncogenesis are still relatively poorly understood. This is especially so in early-stage tumours, in which mutations of known oncogenes or tumour-suppressor genes appear to be quite infrequent. Allelic losses of chromosome arms 7q, 8p, 10, 16q and 18q suggest the involvement of novel suppressor loci on these chromosomes; allelic losses of chromosome arm 8p are especially frequent and may be detected even in early-stage tumours. We have used a positional approach to seek novel genetic targets in prostate cancer, including allelic-loss mapping of chromosome 8p and physical mapping of chromosome band 8p22 around the MSR gene. A homozygous somatic deletion in one prostatic nodal metastasis was mapped in this region and spanned 730-970 kb. This region was then examined in detail for expressed sequences. One novel gene, called N33, was found to be silenced by a methylation mechanism in most colon cancer cell lines and some primary colorectal tumours. Characterization of additional chromosome 8p22 candidates is in progress.
Collapse
|