1
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Krivec N, Ghosh MS, Spits C. Gains of 20q11.21 in human pluripotent stem cells: Insights from cancer research. Stem Cell Reports 2024; 19:11-27. [PMID: 38157850 PMCID: PMC10828824 DOI: 10.1016/j.stemcr.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
The genetic abnormalities observed in hPSC cultures worldwide have been suggested to pose an important hurdle in their safe use in regenerative medicine due to the possibility of oncogenic transformation by mutant cells in the patient posttransplantation. One of the best-characterized genetic lesions in hPSCs is the gain of 20q11.21, found in 20% of hPSC lines worldwide, and strikingly, also amplified in 20% of human cancers. In this review, we have curated the existing knowledge on the incidence of this mutation in hPSCs and cancer, explored the significance of chromosome 20q11.21 amplification in cancer progression, and reviewed the oncogenic role of the genes in the smallest common region of gain, to shed light on the significance of this mutation in hPSC-based cell therapy. Lastly, we discuss the state-of-the-art strategies devised to detect aneuploidies in hPSC cultures, avoid genetic changes in vitro cultures of hPSCs, and strategies to eliminate genetically abnormal cells from culture.
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Affiliation(s)
- Nuša Krivec
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Manjusha S Ghosh
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium.
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2
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Chen H, Zhai C, Xu X, Wang H, Han W, Shen J. Multilevel Heterogeneity of Colorectal Cancer Liver Metastasis. Cancers (Basel) 2023; 16:59. [PMID: 38201487 PMCID: PMC10778489 DOI: 10.3390/cancers16010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Colorectal cancer liver metastasis (CRLM) is a highly heterogeneous disease. Therapies that target both primary foci and liver metastasis are severely lacking. Therefore, understanding the features of metastatic tumor cells in the liver is valuable for the overall control of CRLM patients. In this review, we summarize the heterogeneity exhibited in CRLM from five aspects (gene, transcriptome, protein, metabolism, and immunity). In addition to genetic heterogeneity, the other four aspects exhibit significant heterogeneity. Compared to primary CRC, the dysregulation of epithelial-mesenchymal transition (EMT)-related proteins, the enhanced metabolic activity, and the increased infiltration of immunosuppressive cells are detected in CRLM. Preclinical evidence shows that targeting the EMT process or enhancing cellular metabolism may represent a novel approach to increasing the therapeutic efficacy of CRLM.
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Affiliation(s)
| | | | | | | | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China; (H.C.); (C.Z.); (X.X.); (H.W.)
| | - Jiaying Shen
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China; (H.C.); (C.Z.); (X.X.); (H.W.)
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3
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Astaras C, De Vito C, Chaskar P, Bornand A, Khanfir K, Sciarra A, Letovanec I, Corro C, Dietrich PY, Tsantoulis P, Koessler T. The first comprehensive genomic characterization of rectal squamous cell carcinoma. J Gastroenterol 2023; 58:125-134. [PMID: 36357817 PMCID: PMC9876866 DOI: 10.1007/s00535-022-01937-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/31/2022] [Indexed: 11/12/2022]
Abstract
BACKGROUND Rectal cancers represent 35% of colorectal cancers; 90% are adenocarcinomas, while squamous cell carcinoma accounts for 0.3% of them. Given its rarity, little is known concerning its pathogenesis, molecular profile and therapeutic management. The current treatment trend is to treat rectal squamous cell carcinoma by analogy to anal squamous cell carcinoma with definitive chemo-radiotherapy, setting aside surgery in case of local recurrence. METHODS We performed an in-depth genomic analysis (next-generation sequencing, copy number variation, and human papilloma virus characterization) on 10 rectal squamous cell carcinoma samples and compared them in silico to those of anal squamous cell carcinoma and rectal adenocarcinoma. RESULTS Rectal squamous cell carcinoma shows 100% HPV positivity. It has a mutational (PIK3CA, PTEN, TP53, ATM, BCL6, SOX2) and copy number variation profile (3p, 10p, 10q, 16q deletion and 1q, 3q, 5p, 8q, 20p gain) similar to anal squamous cell carcinoma. PI3K/Akt/mTOR is the most commonly affected signaling pathway similarly to anal squamous cell carcinoma. Most commonly gained or lost genes seen in rectal adenocarcinoma (FLT3, CDX2, GNAS, BCL2, SMAD4, MALT1) are not found in rectal squamous cell carcinoma. CONCLUSION This study presents the first comprehensive genomic characterization of rectal squamous cell carcinoma. We confirm the existence of this rare histology and its molecular similarity with anal squamous cell carcinoma. This molecular proximity confirms the adequacy of therapeutic management based on histology and not localization, suggesting that rectal squamous cell carcinoma should be treated like anal squamous cell carcinoma and not as a rectal adenocarcinoma.
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Affiliation(s)
- Christoforos Astaras
- grid.150338.c0000 0001 0721 9812Medical Oncology Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland
| | - Claudio De Vito
- grid.150338.c0000 0001 0721 9812Pathology Department, Geneva University Hospitals, Geneva, Switzerland
| | - Prasad Chaskar
- grid.150338.c0000 0001 0721 9812Pathology Department, Geneva University Hospitals, Geneva, Switzerland
| | - Aurelie Bornand
- grid.150338.c0000 0001 0721 9812Pathology Department, Geneva University Hospitals, Geneva, Switzerland
| | - Kaouthar Khanfir
- grid.418149.10000 0000 8631 6364Radiation Oncology Department, Valais Hospital, Sion, Switzerland
| | - Amedeo Sciarra
- grid.418149.10000 0000 8631 6364Histopathology, Central Institute, Valais Hospital, Sion, Switzerland
| | - Igor Letovanec
- grid.418149.10000 0000 8631 6364Histopathology, Central Institute, Valais Hospital, Sion, Switzerland
| | - Claudia Corro
- grid.150338.c0000 0001 0721 9812Medical Oncology Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland ,grid.511014.0Swiss Cancer Center Léman, Lausanne, Geneva Switzerland ,grid.8591.50000 0001 2322 4988Translational Research Center in Onco-Hematology, Department of Medicine, Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Pierre-Yves Dietrich
- grid.150338.c0000 0001 0721 9812Medical Oncology Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland ,grid.511014.0Swiss Cancer Center Léman, Lausanne, Geneva Switzerland ,grid.8591.50000 0001 2322 4988Translational Research Center in Onco-Hematology, Department of Medicine, Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Petros Tsantoulis
- grid.150338.c0000 0001 0721 9812Medical Oncology Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Translational Research Center in Onco-Hematology, Department of Medicine, Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Thibaud Koessler
- Medical Oncology Department, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland. .,Swiss Cancer Center Léman, Lausanne, Geneva, Switzerland.
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4
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Yamamoto S, Midorikawa Y, Nagae G, Tatsuno K, Ueda H, Moriyama M, Takayama T, Aburatani H. Spatial and temporal expansion of intrahepatic metastasis by molecularly-defined clonality in multiple liver cancers. Cancer Sci 2020; 111:601-609. [PMID: 31845427 PMCID: PMC7004543 DOI: 10.1111/cas.14282] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022] Open
Abstract
Multiple hepatocellular carcinoma (HCC) is divided into two categories: intrahepatic metastasis (IM), which is a true relapse of HCC, and multicentric origin (MO), which is a second primary tumor. Clinical diagnosis of multiple HCC is usually made based on tumor location and/or time to recurrence; however, it is often difficult to distinguish the two types of multiple HCC. Using 41 matched pairs of multiple HCC specimens, we confirmed the accuracy of clinical diagnoses using exome sequence data and investigated the importance of discriminating the type of multiple HCC. Genomic analysis revealed that 18 (43.9%) patients diagnosed as having genomic IM had common mutations in a pair of HCC tumors with the main tumor of these patients being more progressive compared to those with genomic MO. The accuracy of clinical diagnosis based on lobe (Definition 1) and segment (Definition 2) were 68.3% and 78.0%, respectively. Intriguingly, recurrence ≥2 years after initial surgery for 3 patients was IM. The survival of patients with clinical IM was significantly shorter than for those with clinical MO based on both Definition 1 (P = 0.045) and Definition 2 (P = 0.043). However, mean survival was not different between the patients with genomic IM and those with MO (P = 0.364). Taken together, genomic analysis elucidated that liver cancer may spread more extensively and more slowly than previously thought. In addition, distinguishing multiple HCC as IM or MC may have provided biological information but was not of clinical importance with respect to patient prognosis.
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Affiliation(s)
- Shogo Yamamoto
- Genome Science Division, RCAST, University of Tokyo, Tokyo, Japan
| | - Yutaka Midorikawa
- Genome Science Division, RCAST, University of Tokyo, Tokyo, Japan.,Department of Digestive Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Genta Nagae
- Genome Science Division, RCAST, University of Tokyo, Tokyo, Japan
| | - Kenji Tatsuno
- Genome Science Division, RCAST, University of Tokyo, Tokyo, Japan
| | - Hiroki Ueda
- Genome Science Division, RCAST, University of Tokyo, Tokyo, Japan
| | - Mitsuhiko Moriyama
- Gastroenterology and Hepatology, Nihon University School of Medicine, Tokyo, Japan
| | - Tadatoshi Takayama
- Department of Digestive Surgery, Nihon University School of Medicine, Tokyo, Japan
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5
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Blank A, Roberts DE, Dawson H, Zlobec I, Lugli A. Tumor Heterogeneity in Primary Colorectal Cancer and Corresponding Metastases. Does the Apple Fall Far From the Tree? Front Med (Lausanne) 2018; 5:234. [PMID: 30234115 PMCID: PMC6128217 DOI: 10.3389/fmed.2018.00234] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/01/2018] [Indexed: 01/05/2023] Open
Abstract
Colorectal cancer harbors tremendous heterogeneity, with temporal and spatial differences in genetic mutations, epigenetic regulation, and tumor microenvironment. Analyzing the distribution and frequency of genetic, epigenetic, and microenvironment differences within a given tumor and between different sites of a metastatic tumor has been used as a powerful tool to investigate tumorigenesis, tumor progression, and to yield insight into various models of tumor development. A better understanding of tumor heterogeneity would have tremendous clinical relevance, which may manifest most clearly when genetic analyses to inform treatment decisions are performed on a very limited sample of a large tumor. This review summarizes the current concepts of tumor heterogeneity, with a focus on primary colorectal cancers and their corresponding metastases as well as potential clinical implications.
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Affiliation(s)
- Annika Blank
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States.,Clinical Pathology Division, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Daniel Edward Roberts
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Heather Dawson
- Clinical Pathology Division, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Inti Zlobec
- Translational Research Unit, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Alessandro Lugli
- Clinical Pathology Division, Institute of Pathology, University of Bern, Bern, Switzerland
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6
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A functional variant at the miRNA binding site in HMGB1 gene is associated with risk of oral squamous cell carcinoma. Oncotarget 2018; 8:34630-34642. [PMID: 28423715 PMCID: PMC5470997 DOI: 10.18632/oncotarget.16120] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/15/2017] [Indexed: 12/12/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a common malignancy that has been causally associated with both hereditary and acquired factors. The high mobility group box 1 (HMGB1) gene plays an important role as a DNA chaperone to help maintain nuclear homeostasis. Altered expression of HMGB1 has been implicated in a wide range of pathological processes, including inflammation and cancer. The present study explores the impact of HMGB1 gene polymorphisms, combined with environmental risks regarding susceptibility to oral tumorigenesis. Four single-nucleotide polymorphisms (SNPs) of the HMGB1 gene, rs1412125, rs2249825, rs1045411, and rs1360485, were evaluated in 1,200 normal controls and 772 patients with OSCC. We found an association between the wild-type allele of rs1045411 and genotypes CT and CT/TT (AOR=0.754, 95% CI=0.582-0.978 and AOR=0.778, 95% CI=0.609-0.995, respectively). Additionally, bioinformatics analysis was used to characterize the functional relevance of these variants for the miRNA-505-5p binding site and transcriptional regulation by the HMGB1 3’-UTR and promoter regions. Moreover, in considering behavioral exposure to environmental carcinogens, the presence of the four HMGB1 SNPs, combined with/without betel quid chewing and smoking showed, profoundly synergistic effects on the risk of OSCC. In conclusion, we present a potential clinical relevance for HMGB1 variants in OSCC, as well as associations between HMGB1 polymorphisms, haplotypes and environmental risk factors. The finding may help in development of optimal therapeutic approaches for OSCC patients.
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7
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Chang C, Liu J, He W, Qu M, Huang X, Deng Y, Shen L, Zhao X, Guo H, Jiang J, Fu XY, Huang R, Zhang D, Yan J. A regulatory circuit HP1γ/miR-451a/c-Myc promotes prostate cancer progression. Oncogene 2017; 37:415-426. [PMID: 28967902 DOI: 10.1038/onc.2017.332] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 06/08/2017] [Accepted: 07/13/2017] [Indexed: 02/06/2023]
Abstract
Heterochromatin protein 1γ (HP1γ) has been implicated in carcinogenesis of various cancer types. However, the role of HP1γ in prostate cancer (PCa) progression and the underlying molecular mechanisms remain largely unknown. We found that HP1γ is upregulated in PCa and elevated levels of HP1γ in PCa predict poor outcome. In addition, depletion of HP1γ in PCa cells not only repressed proliferation and induced apoptosis but also impaired tumorigenicity. We also found that c-Myc was capable of upregulating HP1γ by directly binding to the E-box element in the first intron of HP1γ gene, and the upregulated HP1γ, in turn, repressed the expression of miR-451a by enhancing H3K9 methylation at the promoter region of miR-451a. Furthermore, reduction of miR-451a significantly reversed HP1γ loss-induced PCa cell apoptosis, whereas miR-451a overexpression repressed cell survival by targeting and downregulating c-Myc. The association among c-Myc, HP1γ and miR-451a was further confirmed in human clinical samples. Therefore, we propose that an HP1γ/miR-451a/c-Myc regulatory circuitry exists in PCa cells and this circuit has a crucial role in PCa progression.
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Affiliation(s)
- C Chang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - J Liu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - W He
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - M Qu
- Department of Bioscience and Bioengineering, School of Chemistry and Life Science, Jinling College of Nanjing University, Nanjing, China
| | - X Huang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Y Deng
- Department of Urology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing, China
| | - L Shen
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - X Zhao
- Department of Urology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing, China
| | - H Guo
- Department of Urology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing, China
| | - J Jiang
- Department of Urology, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China
| | - X Y Fu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - R Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - D Zhang
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA, USA
| | - J Yan
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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8
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Lai CH, Huang YC, Lee JC, Tseng JTC, Chang KC, Chen YJ, Ding NJ, Huang PH, Chang WC, Lin BW, Chen RY, Wang YC, Lai YC, Hung LY. Translational upregulation of Aurora-A by hnRNP Q1 contributes to cell proliferation and tumorigenesis in colorectal cancer. Cell Death Dis 2017; 8:e2555. [PMID: 28079881 PMCID: PMC5386382 DOI: 10.1038/cddis.2016.479] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 12/18/2022]
Abstract
By using RNA-immunoprecipitation assay following next-generation sequencing, a group of cell cycle-related genes targeted by hnRNP Q1 were identified, including Aurora-A kinase. Overexpressed hnRNP Q1 can upregulate Aurora-A protein, but not alter the mRNA level, through enhancing the translational efficiency of Aurora-A mRNA, either in a cap-dependent or -independent manner, by interacting with the 5′-UTR of Aurora-A mRNA through its RNA-binding domains (RBDs) 2 and 3. By ribosomal profiling assay further confirmed the translational regulation of Aurora-A mRNA by hnRNP Q1. Overexpression of hnRNP Q1 promotes cell proliferation and tumor growth. HnRNP Q1/ΔRBD23-truncated mutant, which loses the binding ability and translational regulation of Aurora-A mRNA, has no effect on promoting tumor growth. The expression level of hnRNP Q1 is positively correlated with Aurora-A in colorectal cancer. Taken together, our data indicate that hnRNP Q1 is a novel trans-acting factor that binds to Aurora-A mRNA 5′-UTRs and regulates its translation, which increases cell proliferation and contributes to tumorigenesis in colorectal cancer.
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Affiliation(s)
- Chien-Hsien Lai
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yu-Chuan Huang
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Jenq-Chang Lee
- Department of Surgery, College of Medicine, National Cheng Kung University Hospital, Tainan 70403, Taiwan
| | - Joseph Ta-Chien Tseng
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Kung-Chao Chang
- Department of Pathology, College of Medicine, National Cheng Kung University Hospital, Tainan 70403, Taiwan
| | - Yen-Ju Chen
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Nai-Jhu Ding
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Pao-Hsuan Huang
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Wen-Chang Chang
- Graduate Institute of Medical Science, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Bo-Wen Lin
- Department of Surgery, College of Medicine, National Cheng Kung University Hospital, Tainan 70403, Taiwan
| | - Ruo-Yu Chen
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yu-Chu Wang
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yi-Chien Lai
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Liang-Yi Hung
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.,Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.,Institute for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
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9
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Sveen A, Løes IM, Alagaratnam S, Nilsen G, Høland M, Lingjærde OC, Sorbye H, Berg KCG, Horn A, Angelsen JH, Knappskog S, Lønning PE, Lothe RA. Intra-patient Inter-metastatic Genetic Heterogeneity in Colorectal Cancer as a Key Determinant of Survival after Curative Liver Resection. PLoS Genet 2016; 12:e1006225. [PMID: 27472274 PMCID: PMC4966938 DOI: 10.1371/journal.pgen.1006225] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 07/07/2016] [Indexed: 12/11/2022] Open
Abstract
Chromosomal instability is a well-defined hallmark of tumor aggressiveness and metastatic progression in colorectal cancer. The magnitude of genetic heterogeneity among distinct liver metastases from the same patient at the copy number level, as well as its relationship with chemotherapy exposure and patient outcome, remains unknown. We performed high-resolution DNA copy number analyses of 134 liver metastatic deposits from 45 colorectal cancer patients to assess: (i) intra-patient inter-metastatic genetic heterogeneity using a heterogeneity score based on pair-wise genetic distances among tumor deposits; and (ii) genomic complexity, defined as the proportion of the genome harboring aberrant DNA copy numbers. Results were analyzed in relation to the patients' clinical course; previous chemotherapy exposure and outcome after surgical resection of liver metastases. We observed substantial variation in the level of intra-patient inter-metastatic heterogeneity. Heterogeneity was not associated with the number of metastatic lesions or their genomic complexity. In metachronous disease, heterogeneity was higher in patients previously exposed to chemotherapy. Importantly, intra-patient inter-metastatic heterogeneity was a strong prognostic determinant, stronger than known clinicopathological prognostic parameters. Patients with a low level of heterogeneity (below the median level) had a three-year progression-free and overall survival rate of 23% and 66% respectively, versus 5% and 18% for patients with a high level (hazard ratio0.4, 95% confidence interval 0.2-0.8, P = 0.01; and hazard ratio0.3,95% confidence interval 0.1-0.7, P = 0.007). A low patient-wise level of genomic complexity (below 25%) was also a favorable prognostic factor; however, the prognostic association of intra-patient heterogeneity was independent of genomic complexity in multivariable analyses. In conclusion, intra-patient inter-metastatic genetic heterogeneity is a pronounced feature of metastatic colorectal cancer, and the strong prognostic association reinforces its clinical relevance and places it as a key feature to be explored in future patient cohorts.
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Affiliation(s)
- Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Inger Marie Løes
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Sharmini Alagaratnam
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Gro Nilsen
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Computer Science, University of Oslo, Oslo, Norway
| | - Maren Høland
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ole Christian Lingjærde
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Computer Science, University of Oslo, Oslo, Norway
| | - Halfdan Sorbye
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Kaja Christine Graue Berg
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Arild Horn
- Department of Digestive Surgery, Haukeland University Hospital, Bergen, Norway
| | - Jon-Helge Angelsen
- Department of Digestive Surgery, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Stian Knappskog
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Per Eystein Lønning
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Ragnhild A. Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- * E-mail:
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10
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Hugen N, Simmer F, Mekenkamp LJM, Koopman M, van den Broek E, de Wilt JHW, Punt CJA, Ylstra B, Meijer GA, Nagtegaal ID. Reduced rate of copy number aberrations in mucinous colorectal carcinoma. Oncotarget 2016; 6:25715-25. [PMID: 26329972 PMCID: PMC4694861 DOI: 10.18632/oncotarget.4706] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/13/2015] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Mucinous carcinoma (MC) is found in 10%-15% of colorectal cancer (CRC) patients. It differs from the common adenocarcinoma (AC) in histopathological appearance and clinical behavior. METHODS Genome-wide DNA copy number and survival data from MC and AC primary CRC samples from patients from two phase III trials (CAIRO and CAIRO2) was compared. Chromosomal copy number data from The Cancer Genome Atlas (TCGA) was used for validation. Altogether, 470 ACs were compared to 57 MCs. RESULTS MC showed a reduced amount of copy number aberrations (CNAs) compared with AC for the CAIRO/CAIRO2 cohort, with a median amount of CNAs that was 1.5-fold lower (P = 0.002). Data from TCGA also showed a reduced amount of CNAs for MC. MC samples in both cohorts displayed less gain at chromosome 20q and less loss of chromosome 18p. A high rate of chromosomal instability was a strong negative prognostic marker for survival in MC patients from the CAIRO cohorts (hazard ratio 15.60, 95% CI 3.24-75.05). CONCLUSIONS Results from this study indicate that the distinct MC phenotype is accompanied by a different genetic basis when compared with AC and show a strong association between the rate of chromosomal instability and survival in MC patients.
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Affiliation(s)
- Niek Hugen
- Department of Surgery, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Femke Simmer
- Department of Pathology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Leonie J M Mekenkamp
- Department of Internal Medicine, Medical Spectrum Twente Enschede, 7500 KA Enschede, The Netherlands
| | - Miriam Koopman
- Department of Medical Oncology, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
| | - Evert van den Broek
- Department of Pathology, VU University Medical Centre, 1007 MB Amsterdam, The Netherlands
| | - Johannes H W de Wilt
- Department of Surgery, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Cornelis J A Punt
- Department of Medical Oncology, Academic Medical Center University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Centre, 1007 MB Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, VU University Medical Centre, 1007 MB Amsterdam, The Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
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11
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Masuda T, Ishikawa T, Mogushi K, Okazaki S, Ishiguro M, Iida S, Mizushima H, Tanaka H, Uetake H, Sugihara K. Overexpression of the S100A2 protein as a prognostic marker for patients with stage II and III colorectal cancer. Int J Oncol 2016; 48:975-82. [PMID: 26783118 PMCID: PMC4750537 DOI: 10.3892/ijo.2016.3329] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 12/17/2015] [Indexed: 11/25/2022] Open
Abstract
We aimed to identify a novel prognostic biomarker related to recurrence in stage II and III colorectal cancer (CRC) patients. Stage II and III CRC tissue mRNA expression was profiled using an Affymetrix Gene Chip, and copy number profiles of 125 patients were generated using an Affymetrix 250K Sty array. Genes showing both upregulated expression and copy number gains in cases involving recurrence were extracted as candidate biomarkers. The protein expression of the candidate gene was assessed using immunohistochemical staining of tissue from 161 patients. The relationship between protein expression and clinicopathological features was also examined. We identified 9 candidate genes related to recurrence of stage II and III CRC, whose mRNA expression was significantly higher in CRC than in normal tissue. Of these proteins, the S100 calcium-binding protein A2 (S100A2) has been observed in several human cancers. S100A2 protein overexpression in CRC cells was associated with significantly worse overall survival and relapse-free survival, indicating that S100A2 is an independent risk factor for stage II and III CRC recurrence. S100A2 overexpression in cancer cells could be a biomarker of poor prognosis in stage II and III CRC recurrence and a target for treatment of this disease.
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Affiliation(s)
- Taiki Masuda
- Department of Surgical Oncology, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo 113-8510, Japan
| | - Toshiaki Ishikawa
- Department of Surgical Oncology, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo 113-8510, Japan
| | - Kaoru Mogushi
- Department of Systems Biology, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo 113-8510, Japan
| | - Satoshi Okazaki
- Department of Surgical Oncology, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo 113-8510, Japan
| | - Megumi Ishiguro
- Department of Translational Oncology, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo 113-8510, Japan
| | - Satoru Iida
- Department of Surgical Oncology, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo 113-8510, Japan
| | - Hiroshi Mizushima
- Department of Medical Omics Informatics, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo 113-8510, Japan
| | - Hiroshi Tanaka
- Department of Systems Biology, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo 113-8510, Japan
| | - Hiroyuki Uetake
- Department of Surgical Oncology, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo 113-8510, Japan
| | - Kenichi Sugihara
- Department of Surgical Oncology, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo 113-8510, Japan
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Wang D, Zhu ZZ, Jiang H, Zhu J, Cong WM, Wen BJ, He SQ, Liu SF. Multiple genes identified as targets for 20q13.12-13.33 gain contributing to unfavorable clinical outcomes in patients with hepatocellular carcinoma. Hepatol Int 2015; 9:438-46. [PMID: 26067772 DOI: 10.1007/s12072-015-9642-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 05/19/2015] [Indexed: 01/26/2023]
Abstract
BACKGROUND Recurrent chromosome 20q gain is implicated in progressive cancer behaviors and has been associated with clinical outcomes in multiple types of cancer; however, its prognostic significance in hepatocellular carcinoma (HCC) and the involved genes remain unclear. METHODS Array comparative genomic hybridization and expression arrays were used to detect copy number alterations (CNAs) and expression levels, respectively. The associations between CNAs in 20q and outcomes were analyzed on 66 patients, for which the follow-up period was 2.6-73.3 months. One hundred seventeen tumors were further investigated to identify target genes in the potentially outcome-related CNAs. RESULTS Regional or whole 20q gain was detected in 24 (36.4%) of the 66 HCC cases. The most recurrent gains were 20q11.21-12, 20q12-13.12, 20q13.12-13.33 and 20q13.33. Of the CNAs, 20q13.12-13.33 gain was significantly associated with reduced extrohepatic metastasis-free and overall survival, as well as with elevated postoperative AFP level, tumor vascular invasion and advanced tumor stage. Multivariate Cox analysis identified 20q13.12-13.33 gain as an independent prognostic marker for metastasis (HR 3.73, 95% CI 1.08-12.87) and death (HR 3.00, 95% CI 1.26-7.13). A panel of 19 genes in 20q13.12-13.33 was significantly overexpressed in HCCs with gain compared to HCCs without. High expression (greater than median) for 5 of the 19 genes, DDX27, B4GALT5, RNF114, ZFP64 and PFDN4, correlated significantly with vascular invasion, and high RNF114 expression also with advanced tumor stage. CONCLUSIONS Gain at 20q13.12-13.33 is a prognostic marker of metastasis and death, and DDX27, B4GALT5, RNF114, ZFP64, and PFDN4 are probable target genes which may be involved together in the unfavorable outcomes of HCC patients.
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Affiliation(s)
- Dong Wang
- Department of General Surgery, The Fourth Hospital of Harbin Medical University, 37 Yiyuan Street, Harbin, 150001, China,
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13
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Basen-Engquist K, Carmack C, Brown J, Jhingran A, Baum G, Song J, Scruggs S, Swartz MC, Cox MG, Lu KH. Response to an exercise intervention after endometrial cancer: differences between obese and non-obese survivors. Gynecol Oncol 2014; 133:48-55. [PMID: 24680591 PMCID: PMC3979927 DOI: 10.1016/j.ygyno.2014.01.025] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 01/15/2014] [Accepted: 01/16/2014] [Indexed: 01/10/2023]
Abstract
OBJECTIVE The objective of this paper is to describe baseline differences between obese and non-obese endometrial cancer survivor in anthropometrics, exercise behavior, fitness, heart rate and blood pressure, and quality of life, and to analyze whether the effect of a home-based exercise intervention on these outcomes differed for obese and non-obese participants. METHODS One hundred post-treatment Stage I-IIIa endometrial cancer survivors participated in a single arm 6month study in which they received a home-based exercise intervention. Cardiorespiratory fitness, anthropometrics, and exercise behavior were measured every two months, and quality of life (QOL) and psychological distress were measured at baseline and 6months. RESULTS Adjusting for potential confounders, at baseline obese survivors had poorer cardiorespiratory fitness (p=.002), higher systolic blood pressure (p=.018), and lower physical functioning (p<.001) and ratings of general health (p=.002), and more pain (p=.037) and somatization (.002). Significant improvements were seen in exercise behavior, resting heart rate, systolic blood pressure, and multiple QOL domains over the course of the intervention. Obese survivors had less improvement in exercise behavior and cardiorespiratory fitness than non-obese survivors, but there were no differences with regard to improvements in QOL and stress. CONCLUSIONS Home based exercise interventions are beneficial to endometrial cancer survivors, including those whose BMI is in the obese range. While obese survivors have lower levels of physical activity and fitness, they experienced similar activity, fitness, quality of life and mental health benefits. Exercise should be encouraged in endometrial cancer survivors, including those who are obese.
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Affiliation(s)
- K Basen-Engquist
- Department of Behavioral Science, University of Texas MD Anderson Cancer Center, USA.
| | - C Carmack
- Department of Behavioral Science, University of Texas MD Anderson Cancer Center, USA
| | - J Brown
- Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, USA
| | - A Jhingran
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, USA
| | - G Baum
- Department of Behavioral Science, University of Texas MD Anderson Cancer Center, USA
| | - J Song
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, USA
| | - S Scruggs
- Department of Behavioral Science, University of Texas MD Anderson Cancer Center, USA
| | - M C Swartz
- Department of Behavioral Science, University of Texas MD Anderson Cancer Center, USA
| | - M G Cox
- Department of Behavioral Science, University of Texas MD Anderson Cancer Center, USA
| | - K H Lu
- Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, USA
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Significant evidence of linkage for a gene predisposing to colorectal cancer and multiple primary cancers on 22q11. Clin Transl Gastroenterol 2014; 5:e50. [PMID: 24572700 PMCID: PMC3940837 DOI: 10.1038/ctg.2014.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 11/15/2013] [Accepted: 12/23/2013] [Indexed: 01/28/2023] Open
Abstract
Objectives: The genetic basis of colorectal cancer (CRC) is not completely specified. Part of the difficulty in mapping predisposition genes for CRC may be because of phenotypic heterogeneity. Using data from a population genealogy of Utah record linked to a statewide cancer registry, we identified a subset of CRC cases that exhibited familial clustering in excess of that expected for all CRC cases in general, which may represent a genetically homogeneous subset of CRC. Methods: Using a new familial aggregation method referred to as the subset genealogic index of familiality (subsetGIF), combined with detailed information from a statewide tumor registry, we identified a subset of CRC cases that exhibited excess familial clustering above that expected for CRC: CRC cases who had at least one other primary tumor at a different site. A genome-wide linkage analysis was performed on a set of high-risk CRC pedigrees that included multiple CRC cases with additional primaries to identify evidence for predisposition loci. Results: A total of 13 high-risk CRC pedigrees with multiple CRC cases with other primary cancers were identified. Linkage analysis identified one pedigree with a significant linkage signal at 22q11 (LOD (logarithm (base 10) of odds)=3.39). Conclusions: A predisposition gene or variant for CRC that also predisposes to other primary cancers likely resides on chromosome 22q11. The ability to use statewide population genealogy and tumor registry data was critical to identify an informative subset of CRC cases that is possibly more genetically homogeneous than CRC in general, and may have improved statistical power for predisposition locus identification in this study.
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15
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Zhang C, Xiong Y, Li J, Yang Y, Liu L, Wang W, Wang L, Li M, Fang Z. Deletion and down-regulation of HRH4 gene in gastric carcinomas: a potential correlation with tumor progression. PLoS One 2012; 7:e31207. [PMID: 22363581 PMCID: PMC3282702 DOI: 10.1371/journal.pone.0031207] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Accepted: 01/04/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Histamine is an established growth factor for gastrointestinal malignancies. The effect of histamine is largely determined locally by the histamine receptor expression pattern. Histamine receptor H4 (HRH4), the newest member of the histamine receptor family, is positively expressed on the epithelium of the gastrointestinal tract, and its function remains to be elucidated. Previously, we reported the decreased expression of HRH4 in colorectal cancers and revealed its correlation with tumor proliferation. In the current study, we aimed to investigate the abnormalities of HRH4 gene in gastric carcinomas (GCs). METHODOLOGY/PRINCIPAL FINDINGS We analyzed H4R expression in collected GC samples by quantitative PCR, Western blot analysis, and immunostaining. Our results showed that the protein and mRNA levels of HRH4 were reduced in some GC samples, especially in advanced GC samples. Copy number decrease of HRH4 gene was observed (17.6%, 23 out of 131), which was closely correlated with the attenuated expression of H4R. In vitro studies, using gastric cancer cell lines, showed that the alteration of HRH4 expression on gastric cancer cells influences tumor growth upon exposure to histamine. CONCLUSIONS/SIGNIFICANCE We show for the first time that deletion of HRH4 gene is present in GC cases and is closely correlated with attenuated gene expression. Down-regulation of HRH4 in gastric carcinomas plays a role in histamine-mediated growth control of GC cells.
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Affiliation(s)
- Chao Zhang
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, Guangdong Province, Shenzhen, People's Republic of China
| | - Yi Xiong
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, Guangdong Province, Shenzhen, People's Republic of China
| | - Jiana Li
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, Guangdong Province, Shenzhen, People's Republic of China
| | - Yang Yang
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, Guangdong Province, Shenzhen, People's Republic of China
| | - Li Liu
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, Guangdong Province, Shenzhen, People's Republic of China
| | - Wen Wang
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, Guangdong Province, Shenzhen, People's Republic of China
| | - Luo Wang
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, Guangdong Province, Shenzhen, People's Republic of China
| | - Manhui Li
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, Guangdong Province, Shenzhen, People's Republic of China
| | - Zhengyu Fang
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, Guangdong Province, Shenzhen, People's Republic of China
- * E-mail:
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Abstract
Background: Molecular characterisation using gene-expression profiling will undoubtedly improve the prediction of treatment responses, and ultimately, the clinical outcome of cancer patients. Methods: To establish the procedures to identify responders to FOLFOX therapy, 83 colorectal cancer (CRC) patients including 42 responders and 41 non-responders were divided into training (54 patients) and test (29 patients) sets. Using Random Forests (RF) algorithm in the training set, predictor genes for FOLFOX therapy were identified, which were applied to test samples and sensitivity, specificity, and out-of-bag classification accuracy were calculated. Results: In the training set, 22 of 27 responders (81.4% sensitivity) and 23 of 27 non-responders (85.1% specificity) were correctly classified. To improve the prediction model, we removed the outliers determined by RF, and the model could correctly classify 21 of 23 responders (91.3%) and 22 of 23 non-responders (95.6%) in the training set, and 80.0% sensitivity and 92.8% specificity, with an accuracy of 69.2% in 29 independent test samples. Conclusion: Random Forests on gene-expression data for CRC patients was effectively able to stratify responders to FOLFOX therapy with high accuracy, and use of pharmacogenomics in anticancer therapy is the first step in planning personalised therapy.
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Chen G, Kim SH, King AN, Zhao L, Simpson RU, Christensen PJ, Wang Z, Thomas DG, Giordano TJ, Lin L, Brenner DE, Beer DG, Ramnath N. CYP24A1 is an independent prognostic marker of survival in patients with lung adenocarcinoma. Clin Cancer Res 2010; 17:817-26. [PMID: 21169243 DOI: 10.1158/1078-0432.ccr-10-1789] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The active form of vitamin D, 1α,25-dihydroxyvitamin D(3) (1,25-D(3)), exerts antiproliferative effects in cancers, including lung adenocarcinoma (AC). CYP24A1 is overexpressed in many cancers and encodes the enzyme that catabolizes 1,25-D(3). The purpose of our study was to assess CYP24A1 as a prognostic marker and to study its relevance to antiproliferative activity of 1,25-D(3) in lung AC cells. EXPERIMENTAL DESIGN Tumors and corresponding normal specimens from 86 patients with lung AC (stages I-III) were available. Affymetrix array data and subsequent confirmation by quantitative real time-PCR were used to determine CYP24A1 mRNA expression. A subsequent validation set of 101 lung AC was used to confirm CYP24A1 mRNA expression and its associations with clinical variables. The antiproliferative effects of 1,25-D(3) were examined using lung cancer cell lines with high as well as low expression of CYP24A1 mRNA. RESULTS CYP24A1 mRNA was elevated 8- to 50-fold in lung AC (compared to normal nonneoplastic lung) and significantly higher in poorly differentiated cancers. At 5 years of follow-up, the probability of survival was 42% (high CYP24A1, n = 29) versus 81% (low CYP24A1, n = 57) (P = 0.007). The validation set of 101 tumors showed that CYP24A1 was independently prognostic of survival (multivariate Cox model adjusted for age, gender, and stage, P = 0.001). A549 cells (high CYP24A1) were more resistant to antiproliferative effects of 1,25-D(3) compared with SKLU-1 cells (low CYP24A1). CONCLUSIONS CYP24A1 overexpression is associated with poorer survival in lung AC. This may relate to abrogation of antiproliferative effects of 1,25-D(3) in high CYP24A1 expressing lung AC.
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Affiliation(s)
- Guoan Chen
- Section of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA
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