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Wang W, Okajima T, Takeuchi H. Significant Roles of Notch O-Glycosylation in Cancer. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27061783. [PMID: 35335147 PMCID: PMC8950332 DOI: 10.3390/molecules27061783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 12/27/2022]
Abstract
Notch signaling, which was initially identified in Drosophila wing morphogenesis, plays pivotal roles in cell development and differentiation. Optimal Notch pathway activity is essential for normal development and dysregulation of Notch signaling leads to various human diseases, including many types of cancers. In hematopoietic cancers, such as T-cell acute lymphoblastic leukemia, Notch plays an oncogenic role, while in acute myeloid leukemia, it has a tumor-suppressive role. In solid tumors, such as hepatocellular carcinoma and medulloblastoma, Notch may have either an oncogenic or tumor-suppressive role, depending on the context. Aberrant expression of Notch receptors or ligands can alter the ligand-dependent Notch signaling and changes in trafficking can lead to ligand-independent signaling. Defects in any of the two signaling pathways can lead to tumorigenesis and tumor progression. Strikingly, O-glycosylation is one such process that modulates ligand–receptor binding and trafficking. Three types of O-linked modifications on the extracellular epidermal growth factor-like (EGF) repeats of Notch receptors are observed, namely O-glucosylation, O-fucosylation, and O-N-acetylglucosamine (GlcNAc) modifications. In addition, O-GalNAc mucin-type O-glycosylation outside the EGF repeats also appears to occur in Notch receptors. In this review, we first briefly summarize the basics of Notch signaling, describe the latest information on O-glycosylation of Notch receptors classified on a structural basis, and finally describe the regulation of Notch signaling by O-glycosylation in cancer.
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Affiliation(s)
- Weiwei Wang
- Department of Molecular Biochemistry, Nagoya University School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550, Japan; (W.W.); (T.O.)
| | - Tetsuya Okajima
- Department of Molecular Biochemistry, Nagoya University School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550, Japan; (W.W.); (T.O.)
- Institute for Glyco-Core Research (iGCORE), Integrated Glyco-Biomedical Research Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hideyuki Takeuchi
- Department of Molecular Biochemistry, Nagoya University School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550, Japan; (W.W.); (T.O.)
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
- Correspondence:
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Godoy PRDV, Donaires FS, Montaldi APL, Sakamoto-Hojo ET. Anti-Proliferative Effects of E2F1 Suppression in Glioblastoma Cells. Cytogenet Genome Res 2021; 161:372-381. [PMID: 34482308 DOI: 10.1159/000516997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/03/2021] [Indexed: 11/19/2022] Open
Abstract
Glioblastoma (GBM) is an aggressive malignant brain tumor; surgery, radiation, and temozolomide still remain the main treatments. There is evidence that E2F1 is overexpressed in various types of cancer, including GBM. E2F1 is a transcription factor that controls the cell cycle progression and regulates DNA damage responses and the proliferation of pluripotent and neural stem cells. To test the potentiality of E2F1 as molecular target for GBM treatment, we suppressed the E2F1 gene (siRNA) in the U87MG cell line, aiming to inhibit cellular proliferation and modulate the radioresistance of these cells. Following E2F1 suppression, associated or not with gamma-irradiation, several assays (cell proliferation, cell cycle analysis, neurosphere counting, and protein expression) were performed in U87MG cells grown as monolayer or neurospheres. We found that siE2F1-suppressed cells showed reduced cell proliferation and increased cell death (sub-G1 fraction) in monolayer cultures, and also a significant reduction in the number of neurospheres. In addition, in irradiated cells, E2F1 suppression caused similar effects, with reduction of the number of neurospheres and neurosphere cell numbers relative to controls; these results suggest that E2F1 plays a role in the maintenance of GBM stem cells, and our results obtained in neurospheres are relevant within the context of radiation resistance. Furthermore, E2F1 suppression inhibited or delayed GBM cell differentiation by maintaining a reasonable proportion of CD133+ cells when grown at differentiation condition. Therefore, E2F1 proved to be an interesting molecular target for therapeutic intervention in U87MG cells.
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Affiliation(s)
- Paulo R D V Godoy
- Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil,
| | - Flavia S Donaires
- Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Ana Paula L Montaldi
- Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Elza T Sakamoto-Hojo
- Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.,Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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3
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Ramírez-Ramírez R, Gutiérrez-Angulo M, Peregrina-Sandoval J, Moreno-Ortiz JM, Franco-Topete RA, Cerda-Camacho FDJ, Ayala-Madrigal MDLL. Somatic deletion of KDM1A/LSD1 gene is associated to advanced colorectal cancer stages. J Clin Pathol 2019; 73:107-111. [PMID: 31471467 PMCID: PMC7027028 DOI: 10.1136/jclinpath-2019-206128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/20/2019] [Accepted: 08/20/2019] [Indexed: 01/08/2023]
Abstract
Aims KDM1A/LSD1 and ZNF217 are involved in a protein complex that participates in transcriptional regulation. ZNF217 has been analysed in numerous cancers and its amplification has been associated with advanced stages of disease; however, a similar role for KDM1A/LSD1 has not been uncovered. In this study, we estimated the number of KDM1A/LSD1 and ZNF217 gene copies in tissue samples from patients diagnosed with colorectal cancer (CRC), as well as its association with clinicopathological features in patients with CRC. Methods Paraffin-embedded tumour samples from 50 patients with CRC with a histopathological diagnosis of CRC were included. The number of copies of KDM1A/LSD1 and ZNF217 genes was determined by fluorescence in situ hybridisation (FISH). We also analysed the association between copy numbers of selected genes and clinicopathological data based on multivariate analysis. Results Deletion of the KDM1A/LSD1 gene occurred in 19 samples (38%), whereas ZNF217 gene amplification was identified in 11 samples (22%). We found a significant association between lymph node metastasis or advanced tumour stage and KDM1A/LSD1 gene deletion (p value=0.0003 and p value=0.011, respectively). Conclusions KDM1A/LSD1 gene deletion could be considered a novel prognostic biomarker of late-stage CRC.
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Affiliation(s)
- Ruth Ramírez-Ramírez
- Laboratorio de Inmunología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, México
| | - Melva Gutiérrez-Angulo
- Departamento de Clínicas, Centro Universitario de los Altos, Universidad de Guadalajara, Tepatitlán de Morelos, México.,Programa de Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - Jorge Peregrina-Sandoval
- Laboratorio de Inmunología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, México.,Laboratorio de Patología Clínica, Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara, México
| | - José Miguel Moreno-Ortiz
- Programa de Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México.,Instituto de Genética Humana "Dr. Enrique Corona Rivera", Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - Ramon Antonio Franco-Topete
- Servicio de Anatomía Patológica, Hospital Civil de Guadalajara "Dr. Juan I Menchaca", Guadalajara, México.,Departamento de Microbiología y Patología, Universidad de Guadalajara, Guadalajara, México
| | | | - Maria de la Luz Ayala-Madrigal
- Programa de Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México .,Instituto de Genética Humana "Dr. Enrique Corona Rivera", Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
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4
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Chabanais J, Labrousse F, Chaunavel A, Germot A, Maftah A. POFUT1 as a Promising Novel Biomarker of Colorectal Cancer. Cancers (Basel) 2018; 10:cancers10110411. [PMID: 30380753 PMCID: PMC6266312 DOI: 10.3390/cancers10110411] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/26/2018] [Accepted: 10/27/2018] [Indexed: 12/18/2022] Open
Abstract
Background: While protein O-fucosyltransferase 1 (POFUT1) overexpression has been recently proposed as a potential biomarker for different cancer types, no study was carried out on POFUT1 implication in colorectal cancer (CRC). Methods: Data from 626 tumors and 51 non-tumor adjacent tissues available in FireBrowse had been used in this study. Statistical analyses on POFUT1 expression and gene copy number, NOTCH receptors (main targets of POFUT1 enzymatic activity) expression and association of POFUT1 and NOTCH1 expressions with clinical parameters were investigated. Data were completed by POFUT1 histological labeling on six tumor tissues from patients with CRC. Results: We found that POFUT1 is overexpressed from the stage I (p < 0.001) and 76.02% of tumors have a 20q11.21 amplification, associated in 90.13% of cases with a POFUT1 overexpression, compared to non-tumor adjacent tissues. The POFUT1 copy number in tumors is mainly between 2 and 3. POFUT1 is positively correlated with NOTCH1 (rs = 0.34, p < 0.001), NOTCH3 (rs = 0.087, p = 0.0297), and NOTCH4 (rs = 0.097, p = 0.0148) expressions, while negatively correlated with NOTCH2 expression (rs = −0.098, p = 0.0142). POFUT1 overexpression is markedly associated with rectal location, non-mucinous adenocarcinoma and cancer stages IV and M1. NOTCH1 overexpression is only associated with rectal location and non-mucinous adenocarcinoma. Conclusion: We conclude that POFUT1 is overexpressed in CRC from stage I, and its high expression is associated with metastatic process, probably through NOTCH pathway activation. Then, POFUT1 could represent a potential novel biomarker for CRC diagnosis.
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Affiliation(s)
- Julien Chabanais
- Glycosylation and Cell Differentiation, Limoges University, PEIRENE, EA 7500, F-87060 Limoges cedex, France.
| | - François Labrousse
- Department of Pathology, Limoges University Hospital, 87042 Limoges cedex, France.
| | - Alain Chaunavel
- Department of Pathology, Limoges University Hospital, 87042 Limoges cedex, France.
| | - Agnès Germot
- Glycosylation and Cell Differentiation, Limoges University, PEIRENE, EA 7500, F-87060 Limoges cedex, France.
| | - Abderrahman Maftah
- Glycosylation and Cell Differentiation, Limoges University, PEIRENE, EA 7500, F-87060 Limoges cedex, France.
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5
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Saito T, Niida A, Uchi R, Hirata H, Komatsu H, Sakimura S, Hayashi S, Nambara S, Kuroda Y, Ito S, Eguchi H, Masuda T, Sugimachi K, Tobo T, Nishida H, Daa T, Chiba K, Shiraishi Y, Yoshizato T, Kodama M, Okimoto T, Mizukami K, Ogawa R, Okamoto K, Shuto M, Fukuda K, Matsui Y, Shimamura T, Hasegawa T, Doki Y, Nagayama S, Yamada K, Kato M, Shibata T, Mori M, Aburatani H, Murakami K, Suzuki Y, Ogawa S, Miyano S, Mimori K. A temporal shift of the evolutionary principle shaping intratumor heterogeneity in colorectal cancer. Nat Commun 2018; 9:2884. [PMID: 30038269 PMCID: PMC6056524 DOI: 10.1038/s41467-018-05226-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 06/22/2018] [Indexed: 12/17/2022] Open
Abstract
Advanced colorectal cancer harbors extensive intratumor heterogeneity shaped by neutral evolution; however, intratumor heterogeneity in colorectal precancerous lesions has been poorly studied. We perform multiregion whole-exome sequencing on ten early colorectal tumors, which contained adenoma and carcinoma in situ. By comparing with sequencing data from advanced colorectal tumors, we show that the early tumors accumulate a higher proportion of subclonal driver mutations than the advanced tumors, which is highlighted by subclonal mutations in KRAS and APC. We also demonstrate that variant allele frequencies of subclonal mutations tend to be higher in early tumors, suggesting that the subclonal mutations are subject to selective sweep in early tumorigenesis while neutral evolution is dominant in advanced ones. This study establishes that the evolutionary principle underlying intratumor heterogeneity shifts from Darwinian to neutral evolution during colorectal tumor progression.
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Affiliation(s)
- Tomoko Saito
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Atsushi Niida
- Division of Health Medical Computational Science, Health Intelligence Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Ryutaro Uchi
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Hidenari Hirata
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Hisateru Komatsu
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Shotaro Sakimura
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Shuto Hayashi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Sho Nambara
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Yosuke Kuroda
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Shuhei Ito
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Hidetoshi Eguchi
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Keishi Sugimachi
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Taro Tobo
- Department of Pathology, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Haruto Nishida
- Department of Diagnostic Pathology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Tsutomu Daa
- Department of Diagnostic Pathology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Tetsuichi Yoshizato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Kyoto-shi Sakyo-ku, Kyoto, 606-8501, Japan
| | - Masaaki Kodama
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Tadayoshi Okimoto
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Kazuhiro Mizukami
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Ryo Ogawa
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Kazuhisa Okamoto
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Mitsutaka Shuto
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Kensuke Fukuda
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Yusuke Matsui
- Division of Systems Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Takanori Hasegawa
- Division of Health Medical Data Science, Health Intelligence Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Satoshi Nagayama
- Gastroenterological Center, Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto, Tokyo, 135-8550, Japan
| | - Kazutaka Yamada
- Department of Surgery, Takano Hospital, 4-2-88 Obiyama, Chuo-ku, Kumamoto, 862-0924, Japan
| | - Mamoru Kato
- Department of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Kazunari Murakami
- Department of Gastroenterology, Oita University Hospital, 1-1 Idaigaoka, Yufu, 879-5593, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8561, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Kyoto-shi Sakyo-ku, Kyoto, 606-8501, Japan
| | - Satoru Miyano
- Division of Health Medical Computational Science, Health Intelligence Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan.
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Yang CY, Tseng JY, Chen CF, Chou TY, Gao HW, Hua CL, Lin CH, Lin JK, Jiang JK. Genome-wide copy number changes and CD133 expression characterized distinct subset of colon polyps: differentiation between incidental polyps and cancer-associated polyps. Int J Colorectal Dis 2015. [PMID: 26206347 DOI: 10.1007/s00384-015-2319-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
PURPOSE Colorectal polyps are generally believed to be the precursors of colorectal cancers (CRC); however, the proportion and speed of progression differed widely in different subsets of polyps. Using microarray-based comparative genomic hybridization (aCGH) platform and CD133 immunostaining, we characterized colon polyps according to their association with CRC that developed in the same individual. PATIENTS AND METHODS aCGH was performed to unveil genomic changes in 18 cancer-synchronous polyps (CSP), and 9 cancer-preceding polyps (CPP), together with their corresponding cancers and 16 cases of incidental polyps (IP), were examined for comparison. aCGH profiles were analyzed to determine the clonal relationship (CR) between the paired adenoma and carcinoma. CD133 expressions in each subset of polyps were quantified by immunohistochemistry (IHC) staining. RESULTS Progressive genomic changes were observed from IP, CSP/CPP to CRC; they encompass an entire chromosomal region in IP and sub-chromosomal region in CSP/CPP and CRC. CR analyses demonstrated that 50 % of CSP and 67 % of CPP were clonally related to the concurrent or later developed carcinomas, respectively. The CD133 expression levels were significantly higher in CSP/CPP than those in IP (P < 0.0001) and even higher in CSP/CPP that were clonally related to their corresponding carcinomas than CSP/CPP that were unrelated (P < 0.05). CONCLUSIONS There were more genomic changes in CSP/CPP than IP; more than half of the CSP/CPP were clonally related to the corresponding carcinomas. Genomic changes at sub-chromosomal regions and/or high CD133 expression were associated with CSP/CPP and highlighted their carcinogenic potential.
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Affiliation(s)
- Chih-Yung Yang
- Department of Education and Research, Taipei City Hospital, Taipei, Taiwan
| | - Ju-Yu Tseng
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Chian-Feng Chen
- VYM Genome Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Teh-Ying Chou
- Department of Pathology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Hong-Wei Gao
- Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - Chia-Ling Hua
- VYM Genome Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Chi-Hung Lin
- Department of Education and Research, Taipei City Hospital, Taipei, Taiwan.,Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan.,VYM Genome Research Center, National Yang-Ming University, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jen-Kou Lin
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Pei-Tou, Taipei, 11217, Taiwan
| | - Jeng-Kai Jiang
- School of Medicine, National Yang-Ming University, Taipei, Taiwan. .,Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Pei-Tou, Taipei, 11217, Taiwan.
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Tracking the molecular features of nonpolypoid colorectal neoplasms: a systematic review and meta-analysis. Am J Gastroenterol 2013; 108:1042-56. [PMID: 23649184 DOI: 10.1038/ajg.2013.126] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Accepted: 03/16/2013] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Nonpolypoid colorectal neoplasms (NP-CRNs) are proposed as a major contributor to the occurrence of interval cancers, but their underlying biology remains controversial. We conducted a systematic review and meta-analysis to clarify the major biological events in NP-CRNs. METHODS We systematically searched for studies examining molecular characteristics of NP-CRNs. We performed random effect meta-analyses. We measured the heterogeneity among studies using I(2) and possible publication bias using funnel plots. RESULTS Fifty-three studies on KRAS, APC, or BRAF mutations, microsatellite instability (MSI), CpG island methylator phenotype (CIMP), or DNA promoter hypermethylation were included. We observed less KRAS mutations (summary odds ratio (OR) 0.30, confidence interval (CI)=0.19-0.46, I(2)=77.4%, CI=70.1-82.9) and APC mutations (summary OR 0.42, CI=0.24-0.72, I(2)=22.6%, CI=0.0-66.7) in NP-CRNs vs. protruded CRNs, whereas BRAF mutations were more frequent (summary OR 2.20, CI=1.01-4.81, I(2)=0%, CI=0-70.8), albeit all with large heterogeneity. Less KRAS mutations were especially found in NP-CRNs subtypes: depressed CRNs (summary OR 0.12, CI=0.05-0.29, I(2)=0%, CI=0-67.6), non-granular lateral spreading tumors (LSTs-NG) (summary OR 0.61, CI=0.37-1.0, I(2)=0%, CI=0-74.6), and early nonpolypoid carcinomas (summary OR 0.11, CI=0.06-0.19, I(2)=0%, CI=0-58.3). MSI frequency was similar in NP-CRNs and protruded CRNs (summary OR 0.99, CI=0.21-4.71, I(2)=70.3%, CI=38.4-85.7). Data for promoter hypermethylation and CIMP were inconsistent, precluding meaningful conclusions. CONCLUSIONS This meta-analysis provides indications that NP-CRNs are molecularly different from protruded CRNs. In particular, some subtypes of NP-CRNs, the depressed and LST-NG, are featured by less KRAS mutations than polypoid CRNs. Prospective, multicenter studies are needed to clarify the molecular pathways underlying nonpolypoid colorectal carcinogenesis and potential implications for surveillance intervals.
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Höbaus J, Hummel DM, Thiem U, Fetahu IS, Aggarwal A, Müllauer L, Heller G, Egger G, Mesteri I, Baumgartner-Parzer S, Kallay E. Increased copy-number and not DNA hypomethylation causes overexpression of the candidate proto-oncogene CYP24A1 in colorectal cancer. Int J Cancer 2013; 133:1380-8. [PMID: 23463632 PMCID: PMC3807607 DOI: 10.1002/ijc.28143] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 02/14/2013] [Indexed: 12/04/2022]
Abstract
In colorectal cancer (CRC) the vitamin D catabolizing enzyme 1,25-dihydroxyvitamin D 24-hydroxylase (CYP24A1) is overexpressed with a potentially significant, positive impact on the catabolism of 1,25-dihydroxyvitamin D3 (1,25-D3). However, the underlying mechanism of CYP24A1 overexpression is poorly understood. In the present study, we investigated possible causes including hypomethylation of the CYP24A1 promoter, amplification of the CYP24A1 gene locus (20q13.2), and altered expression of CYP24A1-specific transcription factors. We quantified CYP24A1 gene copy-number, performed bisulfite sequencing of the CYP24A1 promoter to assess DNA methylation, and measured mRNA expression of CYP24A1, 25-hydroxyvitamin D 1α-hydroxylase (CYP27B1), vitamin D receptor (VDR) and retinoid X receptor (RXR). We found that 77 (60%) out of 127 colorectal tumors showed increased CYP24A1 gene copy-number and that more than 6 copies of CYP24A1 correlated positively with CYP24A1 mRNA expression suggestive of a causal relationship. No differences in CYP24A1 promoter methylation were found between tumor tissue and adjacent mucosa from the same patient or between tissues with high or low mRNA expression, thus excluding DNA hypomethylation as a possible cause of CYP24A1 overexpression in CRC. Furthermore, mRNA expression of several factors involved in replication licensing positively correlated with CYP24A1 mRNA expression, raising the possibility that CYP24A1 overexpression might favor increased proliferation in tumors by suppressing local 1,25-D3 levels. We conclude that high copy-number gain is a key determinant of CYP24A1 overexpression in CRC. Other postulated causes of CYP24A1 overexpression including promoter hypomethylation and enhanced VDR and/or RXR expression do not appear to be involved. What’s new? Recently, it has been suggested that the association between colorectal cancer and reduced levels of circulating vitamin D may be related to overexpression of the vitamin D-catabolizing enzyme, CYP24A1 in the tumor. In this search for a mechanistic explanation, increased CYP24A1 gene copy number was associated with the enzyme’s overexpression in 60 percent of colorectal tumors, and expression was correlated strongly with proliferation markers. The findings suggest that CYP24A1 overexpression is likely to deplete tumor calcitriol (1,25-dihydroxyvitamin D3) levels, possibly increasing the proliferative potential of the tumors.
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Affiliation(s)
- Julia Höbaus
- Department of Pathophysiology, Medical University of Vienna, Vienna, 1090, Austria
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9
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Simons CCJM, Hughes LAE, Smits KM, Khalid-de Bakker CA, de Bruïne AP, Carvalho B, Meijer GA, Schouten LJ, van den Brandt PA, Weijenberg MP, van Engeland M. A novel classification of colorectal tumors based on microsatellite instability, the CpG island methylator phenotype and chromosomal instability: implications for prognosis. Ann Oncol 2013; 24:2048-56. [PMID: 23532114 DOI: 10.1093/annonc/mdt076] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND We studied the overlap between the major (epi)genomic events microsatellite instability (MSI), the CpG island methylator phenotype (CIMP) and chromosomal instability (CIN) in colorectal cancer (CRC), and whether specific (epi)genotypes were associated with CRC-related deaths. PATIENTS AND METHODS Molecular analyses using tumor DNA were successful in 509 CRC cases identified within the Netherlands Cohort Study in the period 1989-1993. Follow-up for the vital status until May 2005 was 100%. RESULTS MSI (12.6%), CIMP-only (5.3%), CIMP + CIN (13.4%), CIN-only (58.2%) and triple-negative tumors (10.6%) differed significantly regarding tumor localization, differentiation grade, initial adjuvant therapy (AT) use and genetic characteristics (P ≤ 0.03). CIMP-only, CIMP + CIN and triple-negative tumors, compared with CIN-only tumors, were significantly associated with a 3.67, 2.44 and 3.78-fold risk of CRC-related deaths after 2-year follow-up (95% confidence intervals, CIs, 1.70-7.91, 1.35-4.41 and 1.97-7.25, respectively), but not after late follow-up. MSI tumors were borderline significantly associated with a 0.40-fold risk of CRC-related deaths after late follow-up (95% CI 0.15-1.03). CONCLUSION(S) This is the first study to show that specific (epi)genotypes may hold a differential prognostic value that may vary over time. Although no specific treatment data were available, an explanation for the differential findings over time might be that (epi)genotypes modify therapy response.
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Affiliation(s)
- C C J M Simons
- Department of Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
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10
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A correlation of the endoscopic characteristics of colonic laterally spreading tumours with genetic alterations. Eur J Gastroenterol Hepatol 2013; 25:319-26. [PMID: 23354161 DOI: 10.1097/meg.0b013e32835b57e7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
OBJECTIVES Laterally spreading tumours (LSTs) are a heterogeneous group of adenomas that are emerging as important precursors of colorectal cancer and in which the risk for cancer is related to their endoscopically definable morphology. It is currently unclear whether different molecular alterations determine their morphologies. We aimed to assess this relationship in LSTs using strict morphological classifications. METHODS We characterized 135 sessile adenomatous lesions (≥ 20 mm) according to histopathology and the Paris classification. We investigated key molecular changes commonly found in colorectal neoplasms, namely mutation of KRAS, BRAF, APC and CTNNB1 and microsatellite instability, and determined their relationship with morphology. RESULTS The Paris classification revealed a heterogeneous cohort comprising Is/IIa+Is (41.5%), IIa/IIb (53.3%) and IIc/IIa+IIc (5.2%) lesions. Histopathological analysis showed that 19 (14.1%) of these were sessile serrated adenomas. Here, we defined a group of 58 lesions that showed either Paris IIa or IIb morphology with no serrated histopathology. These 'classical LSTs' showed the following molecular characteristics: microsatellite instability 0/56 (0%), APC mutation 29/30 (96.7%), CTNNB1 mutation 2/55 (3.6%), KRAS mutation 24/55 (43.6%) and BRAF mutation 2/55 (3.6%). Separation of lesions according to surface morphology showed that KRAS mutations occurred much more frequently in granular (56.4%, 22/39) than in nongranular LSTs (12.5%, 1/16, P=0.004). CONCLUSION The microsatellite instable pathway is not important in the development of LSTs, which are instead likely to develop along a divergent chromosomal instability pathway. We demonstrate the biological significance of endoscopic findings by showing that the morphological characteristics of LSTs are underpinned by distinctive molecular profiles.
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11
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Chen YL, Uen YH, Li CF, Horng KC, Chen LR, Wu WR, Tseng HY, Huang HY, Wu LC, Shiue YL. The E2F transcription factor 1 transactives stathmin 1 in hepatocellular carcinoma. Ann Surg Oncol 2012; 20:4041-54. [PMID: 22911364 DOI: 10.1245/s10434-012-2519-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Indexed: 12/31/2022]
Abstract
BACKGROUND Through data mining the Stanford Microarray Database, the stathmin 1 (STMN1) transcript was found to be frequently upregulated in the hepatocellular carcinoma (HCC) with low alpha-fetoprotein level. The molecular mechanism of STMN1 upregulation in HCCs remained unclear. METHODS Quantitative RT-PCR, immunoblotting, immunohistochemistry, and transfection of expression or small hairpin RNA interference plasmids, chromatin immunoprecipitation (ChIP), and quantitative ChIP assays were performed in HCC specimens or 2 distinct HCC-derived cell lines. Dual luciferase assay and site-directed mutagenesis were applied to analyze the activities of STMN1 proximal promoter region. RESULTS STMN1 mRNA and proteins were significantly associated with several clinicopathological features. High STMN1 or E2F1 immunoexpression was predictive of poor overall survival (OS) rate (P < .01). In HCC-derived cell lines, E2F1 was elevated before STMN1 mRNA during the cell cycle. Exogenous expression of E2F1 or both transcription factor DP-1 (TFDP1) and E2F1 genes induced E2F1 and STMN1 mRNA (P < .01). Knockdown of the E2F1 gene suppressed E2F1 and STMN1 mRNA and E2F1 and STMN1 protein levels (P < .05). The promoter activity of STMN1 gene increased with overexpression of both E2F1 and TFDP1 genes (P < .05); however, it decreased when mutations were introduced in the E2F1-binding sites (P < .05). CONCLUSIONS Upregulation of E2F1 and STMN1 proteins associate with worse outcomes in patients with HCC. E2F1 significantly correlates with STMN1 protein level in HCC lesions and in vitro transactivation assays, suggesting that STMN1 gene is transactivated by the E2F1 protein.
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Affiliation(s)
- Yi-Ling Chen
- Institute of Biomedical Science, National Sun Yat-sen University, Kaohsiung, Taiwan
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12
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Garcia-Linares C, Mercadé J, Gel B, Biayna J, Terribas E, Lázaro C, Serra E. Applying microsatellite multiplex PCR analysis (MMPA) for determining allele copy-number status and percentage of normal cells within tumors. PLoS One 2012; 7:e42682. [PMID: 22916147 PMCID: PMC3419736 DOI: 10.1371/journal.pone.0042682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 07/11/2012] [Indexed: 11/18/2022] Open
Abstract
The study of somatic genetic alterations in tumors contributes to the understanding and management of cancer. Genetic alterations, such us copy number or copy neutral changes, generate allelic imbalances (AIs) that can be determined using polymorphic markers. Here we report the development of a simple set of calculations for analyzing microsatellite multiplex PCR data from control-tumor pairs that allows us to obtain accurate information not only regarding the AI status of tumors, but also the percentage of tumor-infiltrating normal cells, the locus copy-number status and the mechanism involved in AI. We validated this new approach by re-analyzing a set of Neurofibromatosis type 1-associated dermal neurofibromas and comparing newly generated data with results obtained for the same tumors in a previous study using MLPA, Paralog Ratio Analysis and SNP-array techniques.Microsatellite multiplex PCR analysis (MMPA) should be particularly useful for analyzing specific regions of the genome containing tumor suppressor genes and also for determining the percentage of infiltrating normal cells within tumors allowing them to be sorted before they are analyzed by more expensive techniques.
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Affiliation(s)
- Carles Garcia-Linares
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
| | - Jaume Mercadé
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
| | - Bernat Gel
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
| | - Josep Biayna
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
| | - Ernest Terribas
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
| | - Conxi Lázaro
- Programa de Diagnòstic Molecular de Càncer Hereditari, Laboratori de Recerca Translacional, Institut Català d'Oncologia (ICO) – IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Eduard Serra
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
- * E-mail:
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Voorham QJ, Carvalho B, Spiertz AJ, van Grieken NC, Mongera S, Rondagh EJ, van de Wiel MA, Jordanova ES, Ylstra B, Kliment M, Grabsch H, Rembacken BJ, Arai T, de Bruïne AP, Sanduleanu S, Quirke P, Mulder CJ, van Engeland M, Meijer GA. Chromosome 5q Loss in Colorectal Flat Adenomas. Clin Cancer Res 2012; 18:4560-9. [DOI: 10.1158/1078-0432.ccr-11-2385] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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14
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Ye J, Qi Y, Wang W, Sun F, Wei Q, Su T, Zhou W, Jiang Y, Yuan W, Cai J, Cui B, Ning G. Lower expression of ATM and gene deletion is more frequent in adrenocortical carcinomas than adrenocortical adenomas. Endocrine 2012; 41:479-86. [PMID: 22311173 DOI: 10.1007/s12020-012-9593-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 12/24/2011] [Indexed: 11/24/2022]
Abstract
Adrenocortical carcinoma (ACC) is a rare endocrine malignancy accounting for approximately 0.02-0.2% of all cancer deaths. The molecular pathogenesis of ACC has been the hot topic of recent reviews but it is still poorly understood. It is imperative to have a better understanding on the pathophysiology of ACC so as to establish precise diagnosis and effective treatment. This study aims to identify the molecular markers between ACCs and adrenocortical adenomas (ACAs). With MLPA, we checked on 10 ACA and 9 ACC tissue samples. The MLPA results showed deletion on chromosomes 18q, 11q, 11p, and 13q and duplication on chromosomes 3q, 4q, 6p, and 19p. There was a significant difference in the number of aberration copies of the ataxia telangiectasia-mutated (ATM) gene located on chromosome 11q22-q23 between ACCs and ACAs. Five out of 9 (56%) ACC specimens had deletion of ATM (P = 0.011). RT-PCR result then demonstrated that ATM mRNA level is lower in ACCs than in ACAs (P < 0.001). In addition, immunohistochemistry (IHC) study of the 19 ACA and 18 ACC samples confirmed lower expression of ATM protein in ACCs than in ACAs (P < 0.001). The study demonstrated that ATM expression was diminished in ACC than in ACA, suggesting an important role of ATM in the tumorigenesis of ACC.
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Affiliation(s)
- Junna Ye
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, 197 RuiJin Er Lu, Shanghai, 200025, People's Republic of China
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15
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Sillars-Hardebol AH, Carvalho B, Beliën JAM, de Wit M, Delis-van Diemen PM, Tijssen M, van de Wiel MA, Pontén F, Fijneman RJA, Meijer GA. BCL2L1has a functional role in colorectal cancer and its protein expression is associated with chromosome 20q gain. J Pathol 2012; 226:442-450. [DOI: 10.1002/path.2983] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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16
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Gaiser T, Berroa-Garcia L, Kemmerling R, Dutta A, Ried T, Heselmeyer-Haddad K. Automated analysis of protein expression and gene amplification within the same cells of paraffin-embedded tumour tissue. Cell Oncol (Dordr) 2011; 34:337-42. [PMID: 21656271 DOI: 10.1007/s13402-011-0032-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2010] [Indexed: 10/18/2022] Open
Abstract
BACKGROUND The simultaneous detection of protein expression and gene copy number changes in patient samples, like paraffin-embedded tissue sections, is challenging since the procedures of immunohistochemistry (IHC) and Fluorescence in situ Hybridization (FISH) negatively influence each other which often results in suboptimal staining. Therefore, we developed a novel automated algorithm based on relocation which allows subsequent detection of protein content and gene copy number changes within the same cell. METHODS Paraffin-embedded tissue sections of colorectal cancers were stained for CD133 expression. IHC images were acquired and image coordinates recorded. Slides were subsequently hybridized with fluorescently labeled DNA probes. FISH images were taken at the previously recorded positions allowing for direct comparison of protein expression and gene copy number signals within the same cells/tissue areas. Relocation, acquisition of the IHC and FISH images, and enumeration of FISH signals in the immunophenotyped tumour areas were done in an automated fashion. RESULTS Automated FISH analysis was performed on 13 different colon cancer samples that had been stained for CD133; each sample was scored for MYC, ZNF217 and Chromosome 6 in CD133 positive and negative glands. From the 13 cases four (31%) showed amplification for the MYC oncogene and seven of 13 (54%) cases were amplified for ZNF217. There was no significant difference between CD133 positive tumour and CD133 negative tumour cells. CONCLUSION The technique and algorithm presented here enables an easy and reproducible combination of IHC and FISH based on a novel automated algorithm using relocation and automated spot counting.
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Affiliation(s)
- Timo Gaiser
- Section of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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17
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Andersen CL, Lamy P, Thorsen K, Kjeldsen E, Wikman F, Villesen P, Øster B, Laurberg S, Ørntoft TF. Frequent genomic loss at chr16p13.2 is associated with poor prognosis in colorectal cancer. Int J Cancer 2011; 129:1848-58. [DOI: 10.1002/ijc.25841] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 11/19/2010] [Indexed: 11/09/2022]
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18
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Payne CM, Crowley-Skillicorn C, Bernstein C, Holubec H, Moyer MP, Bernstein H. Hydrophobic bile acid-induced micronuclei formation, mitotic perturbations, and decreases in spindle checkpoint proteins: relevance to genomic instability in colon carcinogenesis. Nutr Cancer 2010; 62:825-40. [PMID: 20661832 DOI: 10.1080/01635581003695756] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We show, for the first time, that hydrophobic bile acids cause aberrations of the mitotic machinery of colon cells that can give rise to aneuploidy, the chromosomal perturbations common in colon tumors. First, we show that DOC induces a statistically significant fourfold increase in the number of micronuclei in NCM-460 cells (a noncancerous colon cell line) and a threefold increase in the number of micronuclei in binucleated HT-29 colon cancer cells using the cytokinesis block micronucleus assay. Second, we observed mitotic aberrations after DOC treatment, including improper alignment of chromosomes at the metaphase plate, lagging chromosomes during anaphase, anaphase/telophase chromatin bridges, multipolar divisions, and formation of polynucleated cells. It was determined that there was a statistically significant threefold increase in the number of aberrant metaphases after short-term and long-term exposure of HT-29 and HCT-116 cells, respectively. Third, we showed with Western blots and immunohistochemistry that a likely basis for these mitosis-related perturbations included decreased expression of the spindle checkpoint proteins, Mad2, BubR1, and securin. Fourth, results of DOC treatment on nocodazole-challenged cells further indicated deficiencies in activation of the spindle assembly checkpoint. This study provides mechanisms by which hydrophobic bile acids can induce genomic instability in colon epithelial cells.
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Affiliation(s)
- Claire M Payne
- Department of Cell Biology and Anatomy, College of Medicine, University of Arizona, Tucson, AZ 85724-5044, USA.
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Stuckenholz C, Lu L, Thakur P, Kaminski N, Bahary N. FACS-assisted microarray profiling implicates novel genes and pathways in zebrafish gastrointestinal tract development. Gastroenterology 2009; 137:1321-32. [PMID: 19563808 PMCID: PMC2785077 DOI: 10.1053/j.gastro.2009.06.050] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 06/02/2009] [Accepted: 06/18/2009] [Indexed: 01/26/2023]
Abstract
BACKGROUND & AIMS The zebrafish Danio rerio is an excellent model system for mammalian gastrointestinal development. To identify differentially regulated genes important in gastrointestinal organogenesis, we profiled the transcriptome of the zebrafish developing gastrointestinal tract. METHODS Embryos from a transgenic zebrafish line expressing green fluorescent protein (GFP) in the developing intestine, liver, and pancreas were dissociated at 4 developmental time points, their cells sorted based on GFP expression with fluorescence-activated cell sorting (FACS), and analyzed with microarrays. To improve our analysis, we annotated the Affymetrix Zebrafish GeneChip with human orthologs. RESULTS Transcriptional profiling showed significant differences between GFP(+) and GFP(-) cells. Up-regulated genes and pathways were consistent with mammalian gastrointestinal development, such as hepatic nuclear factor gene networks and cancer. We implicate the phosphatidylinositol 3 kinase (PI3K) pathway and show that inhibition with LY294002 causes gastrointestinal defects in zebrafish. We identified novel genes, such as the microRNAs miR-217 and miR-122, the tight junction protein claudin c, the gene fam136a, and a zebrafish tetraspanin. Novel pathways include genes containing a putative transcription factor binding sequence, GGAANCGGAANY, and a nucleolar gene network. The zebrafish microarrays also identify a set of 32 genes that may mediate the effects of gain of chromosome arm 8q in human colon, liver, and pancreatic cancers. CONCLUSIONS We successfully combine FACS and microarray profiling to follow organogenesis throughout development. These experiments identify novel genes and pathways that probably play a role in mammalian gastrointestinal development and are potential targets for therapeutic intervention in the management of gastrointestinal disease and cancer.
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Affiliation(s)
- Carsten Stuckenholz
- Department of Medicine, Division of Hematology/Oncology University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Lili Lu
- Department of Medicine, Division of Hematology/Oncology University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Prakash Thakur
- Department of Medicine, Division of Hematology/Oncology University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Naftali Kaminski
- Dorothy P. & Richard P. Simmons Center for Interstitial Lung Disease, Pulmonary, Allergy and Critical Care Medicine University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Nathan Bahary
- Department of Medicine, Division of Hematology/Oncology University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania,Department of Microbiology and Molecular Genetics University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
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High frequency of down-regulation of E-cadherin detected in benign sporadic insulinomas by multiplex ligation-dependent probe amplification. Hum Pathol 2009; 40:1336-41. [DOI: 10.1016/j.humpath.2009.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 03/02/2009] [Accepted: 03/03/2009] [Indexed: 01/30/2023]
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21
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Buffart TE, van Grieken NCT, Tijssen M, Coffa J, Ylstra B, Grabsch HI, van de Velde CJH, Carvalho B, Meijer GA. High resolution analysis of DNA copy-number aberrations of chromosomes 8, 13, and 20 in gastric cancers. Virchows Arch 2009; 455:213-23. [PMID: 19697059 PMCID: PMC2744787 DOI: 10.1007/s00428-009-0814-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2009] [Revised: 07/12/2009] [Accepted: 07/16/2009] [Indexed: 02/06/2023]
Abstract
DNA copy-number gains of chromosomes 8q, 13q, and 20q are frequently observed in gastric cancers. Moreover gain of chromosome 20q has been associated with lymph node metastasis. The aim of this study was to correlate DNA copy-number changes of individual genes on chromosomes 8q, 13q, and 20q in gastric adenocarcinomas to clinicopathological data. DNA isolated from 63 formalin-fixed and paraffin-embedded gastric adenocarcinoma tissue samples was analyzed by whole-genome microarray comparative genomic hybridization and by multiplex ligation-dependent probe amplification (MLPA), targeting 58 individual genes on chromosomes 8, 13, and 20. Using array comparative genomic hybridization, gains on 8q, 13q, and 20q were observed in 49 (77.8%), 25 (39.7%), and 49 (77.8%) gastric adenocarcinomas, respectively. Gain of chromosome 20q was significantly correlated with lymph node metastases (p = 0.05) and histological type (p = 0.02). MLPA revealed several genes to be frequently gained in DNA copy number. The oncogene c-myc on 8q was gained in 73% of the cancers, while FOXO1A and ATP7B on 13q were both gained in 28.6% of the cases. Multiple genes on chromosome 20q showed gains in more than 60% of the cancers. DNA copy-number gains of TNFRSF6B (20q13.3) and ZNF217 (20q13.2) were significantly associated with lymph node metastasis (p = 0.02) and histological type (p = 0.02), respectively. In summary, gains of chromosomes 8q, 13q, and 20q in gastric adenocarcinomas harbor DNA copy-number gains of known and putative oncogenes. ZNF217 and TNFRSF6B are associated with important clinicopathological variables, including lymph node status.
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Affiliation(s)
- Tineke E Buffart
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007, Amsterdam, The Netherlands
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Derks S, Bosch LJW, Niessen HEC, Moerkerk PTM, van den Bosch SM, Carvalho B, Mongera S, Voncken JW, Meijer GA, de Bruïne AP, Herman JG, van Engeland M. Promoter CpG island hypermethylation- and H3K9me3 and H3K27me3-mediated epigenetic silencing targets the deleted in colon cancer (DCC) gene in colorectal carcinogenesis without affecting neighboring genes on chromosomal region 18q21. Carcinogenesis 2009; 30:1041-8. [PMID: 19329758 DOI: 10.1093/carcin/bgp073] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chromosomal loss of 18q21 is a frequent event in colorectal cancer (CRC) development, suggesting that this region harbors tumor suppressor genes (TSGs). Several candidate TSGs, among which methyl-CpG-binding domain protein 1 (MBD1), CpG-binding protein CXXC1, Sma- and Mad-related protein 4 (SMAD4), deleted in colon cancer (DCC) and methyl-CpG-binding domain protein 2 (MBD2) are closely linked on a 4-Mb DNA region on chromosome18q21. As TSGs can be epigenetically silenced, this study investigates whether MBD1, CXXC1, SMAD4, DCC and MBD2 are subject to epigenetic silencing in CRC. Methylation-specific polymerase chain reaction and sodium bisulfite sequencing of these genes show that DCC, but not MBD1, CXXC1, SMAD4 and MBD2, has promoter CpG island methylation in CRC cell lines and tissues {normal mucosa [29.5% (18/61)], adenomas [81.0% (47/58)] and carcinomas [82.7% (62/75)] (P = 8.6 x 10(-9))} that is associated with reduced DCC expression, independent of 18q21 loss analyzed by multiplex ligation-dependent probe amplification. Reduced gene expression of CXXC1, SMAD4 and MBD2 correlates with 18q21 loss in CRC cell lines (P = 0.04, 0.02 and 0.02, respectively). Treatment with the demethylating agent 5-aza-2'-deoxycytidine, but not with the histone deacetylase inhibitor trichostatin A exclusively restored DCC expression in CRC cell lines. Chromatin immunoprecipitation studies reveal that the DCC promoter is marked with repressive histone-tail marks H3K9me3 and H3K27me3, whereas activity related H3K4me3 was absent. Only active epigenetic marks were detected for MBD1, CXXC1, SMAD4 and MBD2. This study demonstrates specific epigenetic silencing of DCC in CRC as a focal process not affecting neighboring genes on chromosomal region 18q21.
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Affiliation(s)
- Sarah Derks
- Department of Pathology, Maastricht University Medical Center, The Netherlands
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Wilting SM, Steenbergen RD, Tijssen M, van Wieringen WN, Helmerhorst TJ, van Kemenade FJ, Bleeker MC, van de Wiel MA, Carvalho B, Meijer GA, Ylstra B, Meijer CJ, Snijders PJ. Chromosomal Signatures of a Subset of High-Grade Premalignant Cervical Lesions Closely Resemble Invasive Carcinomas. Cancer Res 2009; 69:647-55. [DOI: 10.1158/0008-5472.can-08-2478] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Payne CM, Bernstein C, Dvorak K, Bernstein H. Hydrophobic bile acids, genomic instability, Darwinian selection, and colon carcinogenesis. Clin Exp Gastroenterol 2008; 1:19-47. [PMID: 21677822 PMCID: PMC3108627 DOI: 10.2147/ceg.s4343] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Sporadic colon cancer is caused predominantly by dietary factors. We have selected bile acids as a focus of this review since high levels of hydrophobic bile acids accompany a Western-style diet, and play a key role in colon carcinogenesis. We describe how bile acid-induced stresses cause cell death in susceptible cells, contribute to genomic instability in surviving cells, impose Darwinian selection on survivors and enhance initiation and progression to colon cancer. The most likely major mechanisms by which hydrophobic bile acids induce stresses on cells (DNA damage, endoplasmic reticulum stress, mitochondrial damage) are described. Persistent exposure of colon epithelial cells to hydrophobic bile acids can result in the activation of pro-survival stress-response pathways, and the modulation of numerous genes/proteins associated with chromosome maintenance and mitosis. The multiple mechanisms by which hydrophobic bile acids contribute to genomic instability are discussed, and include oxidative DNA damage, p53 and other mutations, micronuclei formation and aneuploidy. Since bile acids and oxidative stress decrease DNA repair proteins, an increase in DNA damage and increased genomic instability through this mechanism is also described. This review provides a mechanistic explanation for the important link between a Western-style diet and associated increased levels of colon cancer.
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Affiliation(s)
- Claire M Payne
- Department of Cell Biology and Anatomy, College of Medicine, University of Arizona, Tucson, Arizona, USA
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25
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Kudo SE, Lambert R, Allen JI, Fujii H, Fujii T, Kashida H, Matsuda T, Mori M, Saito H, Shimoda T, Tanaka S, Watanabe H, Sung JJ, Feld AD, Inadomi JM, O'Brien MJ, Lieberman DA, Ransohoff DF, Soetikno RM, Triadafilopoulos G, Zauber A, Teixeira CR, Rey JF, Jaramillo E, Rubio CA, Van Gossum A, Jung M, Vieth M, Jass JR, Hurlstone PD. Nonpolypoid neoplastic lesions of the colorectal mucosa. Gastrointest Endosc 2008; 68:S3-47. [PMID: 18805238 DOI: 10.1016/j.gie.2008.07.052] [Citation(s) in RCA: 338] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 07/30/2008] [Indexed: 02/08/2023]
Affiliation(s)
- Shin ei Kudo
- Digestive Disease Center, Northern Yokohama Hospital, Showa University, Yokohama, Japan
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26
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Bläker H, Mechtersheimer G, Sutter C, Hertkorn C, Kern MA, Rieker RJ, Penzel R, Schirmacher P, Kloor M. Recurrent deletions at 6q in early age of onset non-HNPCC- and non-FAP-associated intestinal carcinomas. Evidence for a novel cancer susceptibility locus at 6q14-q22. Genes Chromosomes Cancer 2008; 47:159-64. [PMID: 18008368 DOI: 10.1002/gcc.20516] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Hereditary intestinal cancers mainly occur in the framework of the familial adenomatous polyposis (FAP) and hereditary nonpolyposis colorectal cancer (HNPCC) syndromes. However, in about 50% of young patients with intestinal cancer clinically suspicious of an inherited cancer predisposition, no underlying molecular alteration can be identified. To determine the genetic profile of early onset intestinal cancer in the absence of a known cancer predisposition, we have analyzed 12 small and large intestinal tumors from 11 non-FAP, non-HNPCC, and noninflammatory bowel disease patients diagnosed under the age of 35years using a combination of comparative genomic hybridization and loss of heterozygosity (LOH) analysis. The distribution of chromosomal gains and deletions was similar to late onset carcinomas except for 6q alterations which were found in 50% of carcinomas. To define a shared region affected by allelic imbalance, detailed LOH analysis at chromosome 6 was performed on three carcinomas from two patients which showed small interstitial 6q deletions. A minimal area of deletion overlap between markers D6S1652 and D6S1657 (6q14-22) was identified. In a patient with small and large intestinal carcinoma and seven adenomas, loss of identical parental 6q14-22 alleles was seen in both carcinomas and in three of the adenomas. Our data indicate that alterations affecting 6q are frequent in early onset intestinal carcinomas. Moreover, deletions of identical parental alleles in a 35 Mbp area at 6q in multiple independent tumors from one of the patients are compatible with the existence of a novel 6q-associated cancer susceptibility syndrome.
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Affiliation(s)
- Hendrik Bläker
- Department of Pathology, University of Heidelberg, Heidelberg, Germany.
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27
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Braun MS, Richman SD, Quirke P, Daly C, Adlard JW, Elliott F, Barrett JH, Selby P, Meade AM, Stephens RJ, Parmar MKB, Seymour MT. Predictive biomarkers of chemotherapy efficacy in colorectal cancer: results from the UK MRC FOCUS trial. J Clin Oncol 2008; 26:2690-8. [PMID: 18509181 DOI: 10.1200/jco.2007.15.5580] [Citation(s) in RCA: 238] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Candidate predictive biomarkers for irinotecan and oxaliplatin were assessed in 1,628 patients in Fluorouracil, Oxaliplatin, CPT-11: Use and Sequencing (FOCUS), a large randomized trial of fluorouracil alone compared with fluorouracil and irinotecan and compared with fluorouracil and oxaliplatin in advanced colorectal cancer. METHODS The candidate biomarkers were: tumor immunohistochemistry for MLH1/MSH2, p53, topoisomerase-1 (Topo1), excision repair cross-complementing gene 1 (ERCC1), O-6-methylguanine-DNA-methyltranserase (MGMT), and cyclooxygenase 2 (COX2); germline DNA polymorphisms in GSTP1, ABCB1, XRCC1, ERCC2, and UGT1A1. These were screened in more than 750 patients for interaction with benefit from irinotecan or oxaliplatin; two markers (Topo1 and MLH1/MSH2) met criteria to be taken forward for analysis in the full population. Primary end points were progression-free survival (PFS) and overall survival. RESULTS One thousand three hundred thirteen patients (81%) were assessable for Topo1 immunohistochemistry (low, < 10%; moderate, 10% to 50%; or high, > 50% tumor nuclei). In patients with low Topo1, PFS was not improved by the addition of either irinotecan (hazard ratio [HR], 0.98; 95% CI, 0.78 to 1.22) or oxaliplatin (HR, 0.85; 95% CI, 0.68 to 1.07); conversely, patients with moderate/high Topo1 benefited from the addition of either drug (HR, 0.48 to 0.70 in all categories; interaction P = .005; overall, P = .001 for irinotecan; P = .05 for oxaliplatin). High Topo1 was associated with a major overall survival benefit with first-line combination chemotherapy (HR, 0.60; median benefit, 5.3 months); patients with moderate or low Topo1 did not benefit (HR, 0.92 and 1.09, respectively; interaction P = .005). MLH1/MSH2 did not show significant interaction with treatment, although the low rate of loss (4.4%) limits the power of the study for this biomarker. CONCLUSION Topo1 immunohistochemistry identified subpopulations that did or did not benefit from irinotecan, and possibly also from oxaliplatin. If verified independently, this information will contribute to the individualization of treatment for colorectal cancer.
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Affiliation(s)
- Michael S Braun
- Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
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Sabates-Bellver J, Van der Flier LG, de Palo M, Cattaneo E, Maake C, Rehrauer H, Laczko E, Kurowski MA, Bujnicki JM, Menigatti M, Luz J, Ranalli TV, Gomes V, Pastorelli A, Faggiani R, Anti M, Jiricny J, Clevers H, Marra G. Transcriptome profile of human colorectal adenomas. Mol Cancer Res 2008; 5:1263-75. [PMID: 18171984 DOI: 10.1158/1541-7786.mcr-07-0267] [Citation(s) in RCA: 376] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Colorectal cancers are believed to arise predominantly from adenomas. Although these precancerous lesions have been subjected to extensive clinical, pathologic, and molecular analyses, little is currently known about the global gene expression changes accompanying their formation. To characterize the molecular processes underlying the transformation of normal colonic epithelium, we compared the transcriptomes of 32 prospectively collected adenomas with those of normal mucosa from the same individuals. Important differences emerged not only between the expression profiles of normal and adenomatous tissues but also between those of small and large adenomas. A key feature of the transformation process was the remodeling of the Wnt pathway reflected in patent overexpression and underexpression of 78 known components of this signaling cascade. The expression of 19 Wnt targets was closely correlated with clear up-regulation of KIAA1199, whose function is currently unknown. In normal mucosa, KIAA1199 expression was confined to cells in the lower portion of intestinal crypts, where Wnt signaling is physiologically active, but it was markedly increased in all adenomas, where it was expressed in most of the epithelial cells, and in colon cancer cell lines, it was markedly reduced by inactivation of the beta-catenin/T-cell factor(s) transcription complex, the pivotal mediator of Wnt signaling. Our transcriptomic profiles of normal colonic mucosa and colorectal adenomas shed new light on the early stages of colorectal tumorigenesis and identified KIAA1199 as a novel target of the Wnt signaling pathway and a putative marker of colorectal adenomatous transformation.
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Affiliation(s)
- Jacob Sabates-Bellver
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Yuan W, Wang W, Cui B, Su T, Ge Y, Jiang L, Zhou W, Ning G. Overexpression of ERBB-2 was more frequently detected in malignant than benign pheochromocytomas by multiplex ligation-dependent probe amplification and immunohistochemistry. Endocr Relat Cancer 2008; 15:343-50. [PMID: 18310300 PMCID: PMC2254511 DOI: 10.1677/erc-07-0188] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
To analyze the genetic alterations of pheochromocytomas and evaluate the difference among malignant, extra-adrenal, and benign pheochromocytomas. Forty-three tumor samples were tested for genetic changes using multiplex ligation-dependent probe amplification. Among them, 39 samples were available for protein expression analysis by immunohistochemistry (IHC). All 43 patients (24 women and 19 men; mean age 44.6+/-13.6 years; range 18-75 years; 9 with malignant, 7 extra-adrenal, and 27 benign) showed multiple copy number losses or gains. The average copy number change was 13.10 in malignant, 13.93 in benign, and 13.47 in paraganglioma patients. There is no significant difference among the three groups of pheochromocytomas. However, we discovered that in the malignant pheochromocytomas, 6 of the 9 patients (67%) showed erythroblastic leukemia viral oncogene homolog 2 (ERBB-2) oncogene gain, whereas only 12 of the 34 (35%) identified change in the benign and extra-adrenal pheochromocytomas. Further, IHC confirmed that ERBB-2-positive staining was more frequent and stronger in malignant pheochromocytomas than in benign and extra-adrenal pheochromocytomas. Our study illustrates the chromosomal changes of the whole genome of Chinese pheochromocytoma patients. The results suggest that there may be certain progression of genetic events that involves chromosomes 1p, 3p, 6p, 11q, 12q, 17q, and 19q in the development of pheochromocytomas, and the activation of ERBB-2 located on chromosome 17q is an important and early event in the malignancy development of these tumor types. The overexpression of ERBB-2 identified by IHC suggested that this oncogene could be associated with the malignancy of pheochromocytomas and paragangliomas.
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Affiliation(s)
- WenQi Yuan
- Department of Endocrine and Metabolic Diseases, School of Medicine, Shanghai Clinical Center for Endocrine and Metabolic DiseasesRuijin Hospital, Shanghai JiaoTong University197 Ruijin Er Lu, Shanghai, 200025People's Republic of China
- Laboratory of Endocrine and Metabolic Diseases, Shanghai JiaoTong University School of Medicine and Shanghai Institutes for Biological SciencesInstitute of Health Sciences, Chinese Academy of SciencesShanghai, 200025China
| | - WeiQinq Wang
- Department of Endocrine and Metabolic Diseases, School of Medicine, Shanghai Clinical Center for Endocrine and Metabolic DiseasesRuijin Hospital, Shanghai JiaoTong University197 Ruijin Er Lu, Shanghai, 200025People's Republic of China
- Division of Endocrine and Metabolic Diseases, Shanghai JiaoTong University School of MedicineE-Institute of Shanghai Universities, Ruijin HospitalShanghai, 200025China
| | - Bin Cui
- Department of Endocrine and Metabolic Diseases, School of Medicine, Shanghai Clinical Center for Endocrine and Metabolic DiseasesRuijin Hospital, Shanghai JiaoTong University197 Ruijin Er Lu, Shanghai, 200025People's Republic of China
- Laboratory of Endocrine and Metabolic Diseases, Shanghai JiaoTong University School of Medicine and Shanghai Institutes for Biological SciencesInstitute of Health Sciences, Chinese Academy of SciencesShanghai, 200025China
| | - TingWei Su
- Department of Endocrine and Metabolic Diseases, School of Medicine, Shanghai Clinical Center for Endocrine and Metabolic DiseasesRuijin Hospital, Shanghai JiaoTong University197 Ruijin Er Lu, Shanghai, 200025People's Republic of China
| | - Yan Ge
- Department of Endocrine and Metabolic Diseases, School of Medicine, Shanghai Clinical Center for Endocrine and Metabolic DiseasesRuijin Hospital, Shanghai JiaoTong University197 Ruijin Er Lu, Shanghai, 200025People's Republic of China
- Laboratory of Endocrine and Metabolic Diseases, Shanghai JiaoTong University School of Medicine and Shanghai Institutes for Biological SciencesInstitute of Health Sciences, Chinese Academy of SciencesShanghai, 200025China
| | - Lei Jiang
- Department of Endocrine and Metabolic Diseases, School of Medicine, Shanghai Clinical Center for Endocrine and Metabolic DiseasesRuijin Hospital, Shanghai JiaoTong University197 Ruijin Er Lu, Shanghai, 200025People's Republic of China
| | - WeiWei Zhou
- Department of Endocrine and Metabolic Diseases, School of Medicine, Shanghai Clinical Center for Endocrine and Metabolic DiseasesRuijin Hospital, Shanghai JiaoTong University197 Ruijin Er Lu, Shanghai, 200025People's Republic of China
| | - Guang Ning
- Department of Endocrine and Metabolic Diseases, School of Medicine, Shanghai Clinical Center for Endocrine and Metabolic DiseasesRuijin Hospital, Shanghai JiaoTong University197 Ruijin Er Lu, Shanghai, 200025People's Republic of China
- Laboratory of Endocrine and Metabolic Diseases, Shanghai JiaoTong University School of Medicine and Shanghai Institutes for Biological SciencesInstitute of Health Sciences, Chinese Academy of SciencesShanghai, 200025China
- Division of Endocrine and Metabolic Diseases, Shanghai JiaoTong University School of MedicineE-Institute of Shanghai Universities, Ruijin HospitalShanghai, 200025China
- (Correspondence should be addressed to G Ning; )
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Djarmati A, Guzvić M, Grünewald A, Lang AE, Pramstaller PP, Simon DK, Kaindl AM, Vieregge P, Nygren AOH, Beetz C, Hedrich K, Klein C. Rapid and reliable detection of exon rearrangements in various movement disorders genes by multiplex ligation-dependent probe amplification. Mov Disord 2008; 22:1708-14. [PMID: 17674414 DOI: 10.1002/mds.21370] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Because of the occurrence of different types of mutations, comprehensive genetic testing for Parkinson's disease (PD), dopa-responsive dystonia (DRD), and myoclonus-dystonia (M-D) should include screening for small sequence changes and for large exonic rearrangements in disease-associated genes. In diagnostic and research settings, the latter is frequently omitted or performed by laborious and expensive quantitative real-time PCR (qPCR). Our study aimed to evaluate the utility of a novel method, multiplex ligation-dependent probe amplification (MLPA), in molecular diagnostics of movement disorders. We have analyzed, by MLPA, genomic DNA from 21 patients affected with PD, DRD, or M-D, in which the presence of exon rearrangement(s) (n = 20) or of a specific point mutation (detectable by MLPA, n = 1) had been established previously by qPCR or sequencing. In parallel, we have studied, in a blinded fashion, DNA from 49 patients with an unknown mutational status. Exon rearrangements were evident in 20 samples with previously established mutations; in the 21st sample the known specific point mutation was detected. We conclude that MLPA represents a reliable method for large-scale and cost-effective gene dosage screening of various movement disorders genes. This finding reaches far beyond a simple technical advancement and has two major implications: (1) By improving the availability of comprehensive genetic testing, it supports clinicians in the establishment of a genetically defined diagnosis; (2) By enabling gene dosage testing of several genes simultaneously, it significantly facilitates the mutational analysis of large patient and control populations and thereby constitutes the prerequisite for meaningful phenotype-genotype correlations.
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Affiliation(s)
- Ana Djarmati
- Department of Neurology, University of Lübeck, Lübeck, Germany
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31
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Derks S, Postma C, Carvalho B, van den Bosch SM, Moerkerk PTM, Herman JG, Weijenberg MP, de Bruïne AP, Meijer GA, van Engeland M. Integrated analysis of chromosomal, microsatellite and epigenetic instability in colorectal cancer identifies specific associations between promoter methylation of pivotal tumour suppressor and DNA repair genes and specific chromosomal alterations. Carcinogenesis 2007; 29:434-9. [PMID: 18048385 DOI: 10.1093/carcin/bgm270] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Colorectal cancer (CRC) is a complex and heterogeneous disease in which genomic instability and DNA promoter methylation play important roles. The aim of this study was to investigate the relationship between chromosomal instability (CIN), microsatellite instability (MSI) and promoter methylation of CRC-associated genes. Therefore, 71 CRCs were analysed for CIN and MSI by comparative genomic hybridization and the mononucleotide marker BAT-26, respectively. Promoter methylation of the tumour suppressor and DNA repair genes hMLH1, O(6)-MGMT, APC, p14(ARF), p16(INK4A), RASSF1A, GATA-4, GATA-5 and CHFR was analysed using methylation-specific polymerase chain reaction. These integrative analyses showed that in CIN+ CRCs, promoter methylation of GATA-4 and p16(INK4A) was inversely related to chromosomal loss at 15q11-q21 and gain at 20q13, respectively (P values: 3.8 x 10(-2) and 4.5 x 10(-2), respectively). Interestingly, promoter methylation of RASSF1A, GATA-4, GATA-5 and CHFR, as well as a high methylation index (MI), was positively related to chromosomal gain at 8q23-qter (P values: 1.5 x 10(-2), 3.8 x 10(-2), 3.9 x 10(-2), 4.9 x 10(-2) and 8.2 x 10(-3), respectively). MSI was associated with BRAF mutation, promoter methylation of hMLH1, APC and p16(INK4A) and a high MI (total number of methylated genes) (P values: 2.4 x 10(-2), 2.5 x 10(-3), 1.8 x 10(-2), 4.6 x 10(-2) and 1.0 x 10(-2), respectively). Therefore, we conclude that promoter methylation of pivotal tumour suppressor and DNA repair genes is associated with specific patterns of chromosomal changes in CRC, which are different from methylation patterns in MSI tumours.
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Affiliation(s)
- Sarah Derks
- Department of Pathology, GROW - School for Oncology and developmental biology, Maastricht University, Maastricht, 6200 MD, The Netherlands
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Ollikainen M, Gylling A, Puputti M, Nupponen NN, Abdel-Rahman WM, Butzow R, Peltomäki P. Patterns of PIK3CA alterations in familial colorectal and endometrial carcinoma. Int J Cancer 2007; 121:915-20. [PMID: 17471559 DOI: 10.1002/ijc.22768] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
While the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway is known to be activated in multiple sporadic cancers, the role of this pathway in familial tumors is mostly unknown. We searched for alterations in the catalytic domain of PI3K (PIK3CA), PTEN and KRAS, all of which may contribute to PI3K/AKT pathway activation, in a total of 160-familial colorectal (CRC) and endometrial carcinomas (EC), stratified by the presence vs. absence of germline mutations in DNA mismatch repair (MMR) genes. PIK3CA alterations (consisting of point mutations or low-level amplification, which were mutually exclusive with 1 exception) occurred in 10/70 (14%) of CRCs and 19/90 (21%) of ECs. Within ECs, amplification was significantly associated with the subgroup lacking germline mutations in MMR genes (familial site-specific endometrial cancer) (p = 0.015). Decreased or lost PTEN expression was characteristic of endometrial tumourigenesis (51/81, 63%, in EC compared with 24/62, 39%, in CRC, p = 0.004) and KRAS mutations of colorectal tumourigenesis (19/70, 27% in CRC vs. 9/89, 10%, in EC, p = 0.006) regardless of the MMR gene mutation status. PIK3CA alterations frequently coexisted with PTEN or KRAS changes. Combined with published studies on sporadic tumors, our data broaden the understanding of the role for PI3K pathway genes in human tumorigenesis.
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Affiliation(s)
- Miina Ollikainen
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
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Tweedle EM, Chaudhri S, Azadeh B, Rooney PS. Small, flat colorectal cancers in the UK population: an analysis of resected specimens. Colorectal Dis 2007; 9:641-6. [PMID: 17824982 DOI: 10.1111/j.1463-1318.2006.01205.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
OBJECTIVES To establish the prevalence of small, flat carcinomas in surgically resected colon. To determine whether tumour morphology influences stage at presentation. METHOD 1763 surgically resected colorectal cancers from one UK centre excised between 1995 and 2004 were examined. Age 69 years, (42-90), M:F equal. Sixty-one tumours < or =20 mm across were identified. Slides were reviewed by a consultant histopathologist and classified using Japanese Research Society Classification, JRSC and TNM staging. Fisher's exact test was used for analysis. RESULTS In 61 small cancers, 64% (39/61) showed flat morphology and 33% (20/61) polypoid. Two lesions were unclassifiable. Prevalence was 2.2% of all resected colorectal cancers. More T1 tumours at presentation were polypoid, (30% vs. 8%; P = 0.033). T3 tumours were more likely to be flat than polypoid, (49% vs. 20%; P = 0.016). Infiltration into musclaris mucosa occurred in 77% (30/39) flat tumours. Rates of metastases were high in both groups, (30% polypoid vs. 39% flat, not significant). CONCLUSIONS The prevalence of small, flat cancers in resected specimens in the UK concurs with that of Japanese studies. Small, flat cancers should be staged carefully because of high rates of T3/4 disease. The results support the theory of accelerated carcinogenesis in flat cancers.
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Abstract
This article was presented at the conjoint CSSA and RACS (colorectal section) spring meeting Queensland, Australia, September 2004. The adenoma-carcinoma sequence describes a succession of events from polypoid adenoma to colorectal cancer. However, this model only accounts for up to two-thirds of colorectal cancers. There is growing evidence that flat adenomas are precursor lesions to a flat type of colorectal cancer and certain subtypes of these polyps are at greater risk of malignant transformation. If confirmed, the implications for screening, endoscopic recognition and management will become of increasing importance if we are to decrease the incidence of colorectal cancer.
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Affiliation(s)
- Doug Speake
- Colorectal Unit, Department of Surgery, Manchester Royal Infirmary, Manchester, UK
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35
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Staub E, Gröne J, Mennerich D, Röpcke S, Klamann I, Hinzmann B, Castanos-Velez E, Mann B, Pilarsky C, Brümmendorf T, Weber B, Buhr HJ, Rosenthal A. A genome-wide map of aberrantly expressed chromosomal islands in colorectal cancer. Mol Cancer 2006; 5:37. [PMID: 16982006 PMCID: PMC1601966 DOI: 10.1186/1476-4598-5-37] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Accepted: 09/18/2006] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cancer development is accompanied by genetic phenomena like deletion and amplification of chromosome parts or alterations of chromatin structure. It is expected that these mechanisms have a strong effect on regional gene expression. RESULTS We investigated genome-wide gene expression in colorectal carcinoma (CRC) and normal epithelial tissues from 25 patients using oligonucleotide arrays. This allowed us to identify 81 distinct chromosomal islands with aberrant gene expression. Of these, 38 islands show a gain in expression and 43 a loss of expression. In total, 7.892 genes (25.3% of all human genes) are located in aberrantly expressed islands. Many chromosomal regions that are linked to hereditary colorectal cancer show deregulated expression. Also, many known tumor genes localize to chromosomal islands of misregulated expression in CRC. CONCLUSION An extensive comparison with published CGH data suggests that chromosomal regions known for frequent deletions in colon cancer tend to show reduced expression. In contrast, regions that are often amplified in colorectal tumors exhibit heterogeneous expression patterns: even show a decrease of mRNA expression. Because for several islands of deregulated expression chromosomal aberrations have never been observed, we speculate that additional mechanisms (like abnormal states of regional chromatin) also have a substantial impact on the formation of co-expression islands in colorectal carcinoma.
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Affiliation(s)
- Eike Staub
- Max Planck Institute for Molecular Genetics, Dept. of Computational Molecular Biology., Berlin, Germany
- Present address: ALTANA Pharma AG, Preclinical Research Bioinformatics, Konstanz, Germany
| | - Jörn Gröne
- Dept. of General, Vascular and Thoracic Surgery, Charité – Campus Benjamin Franklin, Berlin, Germany
| | - Detlev Mennerich
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
- metaGen Pharmaceuticals i.L., Berlin, Germany
| | - Stefan Röpcke
- Max Planck Institute for Molecular Genetics, Dept. of Computational Molecular Biology., Berlin, Germany
- Present address: ALTANA Pharma AG, Preclinical Research Bioinformatics, Konstanz, Germany
| | - Irina Klamann
- HELIOS Hospital Emil von Behring, Institute of Pathology, Berlin, Germany
| | | | | | - Benno Mann
- Department of Surgery, Augusta-Kranken-Anstalt GmbH, Bochum, Germany
| | - Christian Pilarsky
- Dept. of Visceral, Thoracic, and Vascular Surgery, University Hospital Carl Gustav Carus Dresden, Germany
| | - Thomas Brümmendorf
- metaGen Pharmaceuticals i.L., Berlin, Germany
- Present address: Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Birgit Weber
- metaGen Pharmaceuticals i.L., Berlin, Germany
- Present address: immatics biotechnologies GmbH, Tübingen, Germany
| | - Heinz-Johannes Buhr
- Dept. of General, Vascular and Thoracic Surgery, Charité – Campus Benjamin Franklin, Berlin, Germany
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Jabeen R, Payne D, Wiktorowicz J, Mohammad A, Petersen J. Capillary electrophoresis and the clinical laboratory. Electrophoresis 2006; 27:2413-38. [PMID: 16718719 DOI: 10.1002/elps.200500948] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Over the past 15 years, CE as an analytical tool has shown great promise in replacing many conventional clinical laboratory methods, such as electrophoresis and HPLC. CE's appeal was that it was fast, used very small amounts of sample and reagents, was extremely versatile, and was able to separate large and small analytes, whether neutral or charged. Because of this versatility, numerous methods have been developed for analytes that are of clinical interest. Other than molecular diagnostic and forensic laboratories CE has not been able to make a major impact in the United States. In contrast, in Europe and Japan an increasing number of clinical laboratories are using CE. Now that automated multicapillary instruments are commercially available along with cost-effective test kits, CE may yet be accepted as an instrument that will be routinely used in the clinical laboratories. This review will focus on areas where CE has the potential to have the greatest impact on the clinical laboratory. These include analyses of proteins found in serum and urine, hemoglobin (A1c and variants), carbohydrate-deficient transferrin, forensic and therapeutic drug screening, and molecular diagnostics.
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Affiliation(s)
- Rukhsana Jabeen
- University of Texas Medical Branch--Pathology, Galveston, TX 77555-0551, USA
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Willem P, Brown J, Schouten J. A novel approach to simultaneously scan genes at fragile sites. BMC Cancer 2006; 6:205. [PMID: 16895604 PMCID: PMC1569856 DOI: 10.1186/1471-2407-6-205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Accepted: 08/08/2006] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Fragile sites are regions of the genome sensitive to replication stress and to exposure to environmental carcinogens. The two most commonly expressed fragile sites FRA3B and FRA16D host the histidine triad (FHIT) and WW domain containing oxidoreductase (WWOX) genes respectively. There is growing evidence that both genes contribute to cancer development and they are frequently altered by allelic and homozygous deletions in a variety of tumors. Their status is linked to prognosis in several malignancies and they are thought to be involved in early tumorigenesis. The loci for FHIT and WWOX both span over a megabase but the genes encode for small transcripts. Thus the screening of intragenic deletion can be difficult and has relied on loss of heterozygosity LOH assays, or genomic arrays. METHODS Multiplex ligation dependent probe amplification MLPA, allows for the detection of deletions/duplications and relative quantification of up to 40 specific probes in a single assay. A FHIT/WWOX MLPA assay was designed, applied and validated in five esophageal squamous cell carcinoma ESCC, cell lines established in South Africa where this cancer is of high prevalence. Sixteen probes covered all FHIT exons and 7 probes covered WWOX. RESULTS Both homozygous and hemizygous deletions were detected in FHIT, in four of the cell lines with a preferential deletion of exons 5 and 4. Chromosome 3 short arm was present in normal copy number indicating that deletions were site specific. In contrast WWOX was not altered in any cell lines. RT-PCR expression pattern paralleled the pattern of deletions. Ten primary ESCC tumor specimens were subsequently screened with this assay. FHIT exon deletions were found in four of them. CONCLUSION This method offers an alternative to loss of heterozygosity studies. Simultaneous scanning of FHIT and WWOX exons in the context of early tumorigenesis and tumor progression, may help clarify the mechanistic events related to cancer development which are not revealed by immuno histochemistry assays. The presence of site specific deletions of FHIT in these cell lines and primary tumors support its possible role in South African ESCC and justifies a wider screening.
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Affiliation(s)
- Pascale Willem
- Department of Hematology and Molecular Medicine University of the Witwatersrand and the National Health Laboratory Services, WITS Medical School, 8 York road, 2193 Parktown, South Africa
| | - Jacqueline Brown
- Department of Hematology and Molecular Medicine University of the Witwatersrand and the National Health Laboratory Services, WITS Medical School, 8 York road, 2193 Parktown, South Africa
| | - Jan Schouten
- MRC Holland, Hudsonstraat, Amsterdam, The Netherlands
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Wilting SM, Snijders PJF, Meijer GA, Ylstra B, van den Ijssel PRLA, Snijders AM, Albertson DG, Coffa J, Schouten JP, van de Wiel MA, Meijer CJLM, Steenbergen RDM. Increased gene copy numbers at chromosome 20q are frequent in both squamous cell carcinomas and adenocarcinomas of the cervix. J Pathol 2006; 209:220-30. [PMID: 16538612 DOI: 10.1002/path.1966] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Genome-wide microarray-based comparative genomic hybridization (array CGH) was used to identify common chromosomal alterations involved in cervical carcinogenesis as a first step towards the discovery of novel biomarkers. The genomic profiles of nine squamous cell carcinomas (SCCs) and seven adenocarcinomas (AdCAs), as well as four human papillomavirus (HPV)-immortalized keratinocyte cell lines, were assessed. On a genome-wide scale, SCCs showed significantly more gains than AdCAs. More specifically, there was a striking and highly significant difference between the two histological types for gain at 3q12.1-28, which was predominantly observed in SCC. Other frequent alterations included gains of 1q21.1-31.1 and 20q11.21-13.33, and losses of 11q22.3-25 and 13q14.3-21.33. Subsequent FISH analysis for hTR, located at 3q26, confirmed the presence of 3q gain in SCCs and HPV-immortalized cell lines. Fine mapping of chromosome 20q using multiplex ligation-dependent probe amplification (MLPA) showed copy number increases for a number of genes located at 20q11-q12, including DNMT3B and TOP1. For DNMT3B, this correlated with elevated mRNA expression in 79% of cases. In conclusion, the assessment of frequent genomic alterations resulted in the identification of potential novel biomarkers, which may ultimately enable a better risk stratification of high-risk (hr)-HPV-positive women.
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Affiliation(s)
- S M Wilting
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
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Söreide K, Janssen EAM, Söiland H, Körner H, Baak JPA. Microsatellite instability in colorectal cancer. Br J Surg 2006; 93:395-406. [PMID: 16555243 DOI: 10.1002/bjs.5328] [Citation(s) in RCA: 184] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Microsatellite instability (MSI) causes hereditary non-polyposis colorectal cancer (HNPCC), and occurs in about 15 per cent of sporadic colorectal cancers. Although the basic mechanisms are not clear, there is increased understanding of the clinicopathological consequences of MSI. METHODS Medline was searched for articles with a combination of keywords relating to MSI in colorectal cancer, focusing on molecular mechanisms, clinicopathological implications, and prognostic and predictive value. Emphasis was placed on articles from the past 5 years. RESULTS The genetic mechanisms differ in hereditary (germline mutation) and sporadic (epigenetic silencing) colorectal cancer. The MSI pathway frequently has altered transforming growth factor beta receptor II and BAX genes, often beta-catenin, and occasionally p16INK4A and PTEN. Changes in K-ras, adenomatous polyposis coli and p53 are rare. Polymerase chain reaction testing for MSI is superior to immunohistochemistry, but complicated by the number and types of nucleotide markers. The Bethesda panel guides HNPCC testing, but guidelines are lacking for general screening. The presence and role of low-frequency MSI remains controversial. Tumours with MSI tend to occur in the proximal colon and be large, but they have a good prognosis. Their reduced response to adjuvant chemotherapy requires confirmation. CONCLUSION Research on colorectal cancer needs to be stratified according to microsatellite status in order further to explore the molecular mechanisms and clinicopathological consequences of MSI.
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Affiliation(s)
- K Söreide
- Departments of Pathology, Stavanger University Hospital, Stavanger, Norway.
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Tuhkanen H, Anttila M, Kosma VM, Heinonen S, Juhola M, Helisalmi S, Kataja V, Mannermaa A. Frequent gene dosage alterations in stromal cells of epithelial ovarian carcinomas. Int J Cancer 2006; 119:1345-53. [PMID: 16642473 DOI: 10.1002/ijc.21785] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Stromal cells are an active and integral part of epithelial neoplasms. We have previously observed allelic imbalance on chromosome 3p21 in both stromal and epithelial cells of ovarian tumors. This study was designed to explore gene dosage alterations throughout human chromosomes from stromal and epithelial cells of epithelial ovarian carcinomas. Thirteen stromal and 24 epithelial samples, microdissected from epithelial ovarian carcinomas, were analyzed using multiplex ligation-dependent probe amplification technique. Analysis covered 110 cancer related genes. Frequent genetic alterations were detected both in the stroma and epithelium of ovarian carcinomas. The mean number of altered genes per tumor was 10.8 in stroma and 23.6 in epithelium. In the stroma, the mean number of gains was 6.6 and of losses 4.2 and in the epithelium 13.7 and 9.9. The high number of changes associated with advanced tumor stage (p = 0.035) and death due to ovarian cancer (p = 0.032). The most frequent alteration was the deletion of the deleted in colorectal carcinoma (DCC) on chromosome 18q21.3 in 62% of samples. Loss of DCC was related to endometrioid subtype (p = 0.033). Large chromosomal aberrations were detected on the basis of alterations in adjacent genes. Most importantly, 38 genes showed similar genetic alterations (gain-gain or loss-loss) in stromal and epithelial compartments of 11 tumor pairs. Thus, frequent genetic alterations in stromal cells of epithelial ovarian carcinomas resembled those of malignant epithelial cells and may indicate a common precursor cell type. Epithelial-mesenchymal transition may generate transformed cancer cells and modify the tumor microenvironment with distinct properties.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Endometrioid/genetics
- Carcinoma, Endometrioid/pathology
- Chromosome Aberrations
- Chromosomes, Human, Pair 18/genetics
- Cystadenocarcinoma, Serous/genetics
- Cystadenocarcinoma, Serous/pathology
- DCC Receptor
- Female
- Gene Dosage
- Humans
- Middle Aged
- Neoplasms, Glandular and Epithelial/genetics
- Neoplasms, Glandular and Epithelial/pathology
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/pathology
- Receptors, Cell Surface/genetics
- Stromal Cells/pathology
- Tumor Suppressor Proteins/genetics
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Affiliation(s)
- Hanna Tuhkanen
- Department of Pathology and Forensic Medicine, University of Kuopio and Kuopio University Hospital, Kuopio, Finland
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Natté R, van Eijk R, Eilers P, Cleton-Jansen AM, Oosting J, Kouwenhove M, Kros JM, van Duinen S. Multiplex ligation-dependent probe amplification for the detection of 1p and 19q chromosomal loss in oligodendroglial tumors. Brain Pathol 2005; 15:192-7. [PMID: 16196385 PMCID: PMC8095888 DOI: 10.1111/j.1750-3639.2005.tb00520.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Multiplex ligation-dependent probe amplification (MLPA) is a new assay for the detection of multiple chromosomal deletions in tumor tissue in a single experiment. Since genotyping of gliomas with oligodendroglial features by the detection of 1p/19q chromosomal deletions became essential for treatment decisions, we developed and validated an MLPA-based assay to determine these losses in formalin fixed and paraffin embedded oligodendroglial tumors (OG). Nineteen OGs, and 10 control samples were analyzed by MLPA and the results were correlated with those obtained by fluorescent in situ hybridization (FISH). The MLPA results were reproducible in all samples in which repeated experiments were performed. In 18 of 19 OGs, MLPA and FISH were concordant for presence or absence of 1p deletion. In 3 OGs, MLPA detected a 19q deletion not shown by FISH. For the other 15 OGs, MLPA and FISH were concordant. In one sample with 50% to 75% of tumor, MLPA failed to detect the 1p/19q deletions revealed by FISH (though with borderline values of significance). We conclude that MLPA is a valid and reproducible method for the detection of 1p/19q chromosomal deletions in OGs stored on formalin fixed, paraffin embedded tissue.
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Affiliation(s)
- Remco Natté
- Department of Pathology, Leiden University Medical Center, P.O. box 9600, 2300RC, Leiden, The Netherlands.
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Abstract
The E2F family of transcription factors is a central modulator of important cellular events, including cell cycle progression, apoptosis and DNA damage response. The role of E2F family members in various human malignancies is yet unclear and may provide vital clues to the diagnosis, prognosis and therapy of cancer patients. In this review we provide a brief but concise overview of E2F function and its putative role in the most common human tumour types.
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Affiliation(s)
- P K Tsantoulis
- Department of Histology and Embryology, Molecular Carcinogenesis Group, School of Medicine, University of Athens, Antaiou 53 Str, Lamprini, Ano Patissia, GR-11146, Athens, Greece
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Takata M, Suzuki T, Ansai S, Kimura T, Shirasaki F, Hatta N, Saida T. Genome profiling of melanocytic tumors using multiplex ligation-dependent probe amplification (MLPA): Its usefulness as an adjunctive diagnostic tool for melanocytic tumors. J Dermatol Sci 2005; 40:51-7. [PMID: 16054806 DOI: 10.1016/j.jdermsci.2005.06.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Revised: 06/13/2005] [Accepted: 06/16/2005] [Indexed: 11/25/2022]
Abstract
BACKGROUND The histopathology of melanocytic tumors sometimes presents diagnostic problems. Applicable parameters other than routine pathology are needed. OBJECTIVE We assessed the feasibility of multiplex ligation-dependent probe amplification (MLPA), a novel PCR-based genome profiling method, in the classification of melanocytic tumors. METHOD We extracted DNA from paraffin-embedded tissue sections of 24 primary melanomas, 14 Spitz nevi and 17 common melanocytic nevi. We analyzed the copy number gains or losses of a total of 76 genes spanning almost all chromosome arms using commercially available MLPA kits. RESULTS Although four melanocytic nevi and three Spitz nevi did not yield sufficient DNA for reliable analysis due to small tumor size, the MLPA analysis was feasible and applicable to the remaining 88% of samples. We found multiple genetic aberrations in primary melanomas. The total number of aberrations in each tumor ranged from 1 to 32 (average, 12.04). All but two melanomas showed aberrations at more than three genetic loci. Seventeen (70.8%) of the 24 melanomas showed a copy number loss of either the CDKN2A or CDKN2B gene on chromosome 9p21. All the Spitz nevi and 7 (50%) of 14 common melanocytic nevi had copy number changes at one or two gene loci (average, 1.04). The receiver operator characteristic curve analysis showed that the threshold value of copy number aberrations corresponding to 98% specificity for melanoma was 2.42 and the sensitivity using this threshold value was 92.5%. CONCLUSIONS MLPA could be used as an adjunctive diagnostic tool for melanocytic tumors.
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Affiliation(s)
- Minoru Takata
- Department of Dermatology, Shinshu University School of Medicine, Asahi 3-1-1, Matsumoto 390-8621, Japan.
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