1
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Yang J, Liu Y, Geng Q, Wang B. Death associated protein kinase 1 predicts the prognosis and the immunotherapy response of various cancers. Mol Biol Rep 2024; 51:670. [PMID: 38787485 DOI: 10.1007/s11033-024-09240-y] [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: 07/23/2023] [Accepted: 01/09/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Death Associated Protein Kinase 1 (DAPK1) is a calcium/calmodulin-dependent serine/threonine kinase, which has been reported to be a tumor suppressor with unbalanced expression in various tissues. However, its function in tumor immunotherapy is still unclear. METHODS The online GEPIA2 database was used to support TCGA results. We explored the DAPK1 pan-cancer genomic alteration analysis using the cBioPortal web tool. The Human Protein Atlas (HPA) was employed to mine DAPK1 protein information. We verified the expression of DAPK1 in lung adenocarcinoma samples using RT-qPCR. Subsequently, the relationship between the expression of DAPK1 and the clinical stage was analyzed. We used TIMER2.0 as the primary platform for studying DAPK1-related immune cell infiltration. Associations between DAPK1 and immunotherapy biomarkers were analyzed using Spearman correlation analysis. TMB and MSI expression was also examined. Finally, we used Kaplan-Meier Plots to evaluate the relationship between DAPK1 expression and the efficacy of immunotherapy. RESULTS DAPK1 is aberrantly expressed in most cancer types and has prognostic power in various cancers. Gene mutation was the most common DAPK1 alteration across pan-cancers. The DAPK1 protein was mainly localized to tumor cell centrosomes. DAPK1 was also significantly associated with immune-activated hallmarks, immune cell infiltration, and the expression of immunomodulators. Notably, DAPK1 can also significantly predict responses to anti-PD1 and anti-CTLA-4 therapy in cancer patients. CONCLUSIONS Our findings suggest that DAPK1 may not only be an effective prognostic factor in cancer patients but may also function as a promising predictive immunotherapy biomarker for cancer patients treated with immune checkpoint inhibitors.
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Affiliation(s)
- Jianjian Yang
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, China
| | - Ying Liu
- Department of Anesthesia, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, Hubei Province, China
| | - Qing Geng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, China.
| | - Bo Wang
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, China.
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2
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Identification and validation of DNA methylation markers to predict axillary lymph node metastasis of breast cancer. PLoS One 2022; 17:e0278270. [PMID: 36454866 PMCID: PMC9714834 DOI: 10.1371/journal.pone.0278270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/12/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Axillary lymph node metastasis (ALNM) is one of the most important prognostic factors for breast cancer patients, and DNA methylation is involved in ALNM of breast cancer. However, the methylation profile of breast cancer ALNM remains unknown. METHODS Breast cancer tissues were collected from patients with and without ALNM. We investigated the genome-wide DNA methylation profile in breast cancer with and without ALNM using reduced representation bisulfite sequencing (RRBS). Then, differentially methylated regions (DMRs) were verified by targeted bisulfite sequencing. RESULTS A total of 21491 DMRs were identified between the lymph node positive group and negative group. Compared to the LN-negative breast cancer, LN-positive breast cancer had 10,920 hypermethylated DMRs and 10,571 hypomethylated DMRs. Then, 10 DMRs in the gene promoter region were detected by targeted bisulfite sequencing, these gene included HOXA5, PTOV1-AS1, RHOF, PAX6, GSTP1, RASGRF2, AKR1B1, BNIP3, CRMP1, ING5. Compared with negative lymph node, the promoter methylation levels of RASGRF2, AKR1B1 and CRMP1 increased in positive lymph node, while the promoter methylation level of RHOF decreased in positive lymph node. In addition, Cancer Genome Atlas (TCGA) data showed that RASGRF2, AKR1B1 and CRMP1 were low expressed in breast Cancer tissues, while RHOF was high expressed in breast Cancer tissues. Furthermore, in addition to highly methylated AKR1B1, RASGRF2 and CRMP1 gene promoters, BNIP3, GSTP1, HOXA5 and PAX6 gene promoters were also methylated in ER-positive and HER2-negative breast cancer with ALNM. CONCLUSIONS When compared to negative lymph node breast cancer, the positive lymph node breast cancer has a differential methylation status. Promoter methylation of RASGRF2, AKR1B1, CRMP1 and RHOF in lymph node positive breast cancer tissues was significantly different from that in lymph node negative breast cancer tissues. AKR1B1, RASGRF2, CRMP1, BNIP3, GSTP1, HOXA5 and PAX6 genes were methylated in ER-positive and HER2-negative breast cancer with ALNM. The study provides an important biological base for understanding breast cancer with ALNM and developing therapeutic targets for breast cancer with ALNM.
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3
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Identification and Validation of Immune Cells and Hub Genes in Gastric Cancer Microenvironment. DISEASE MARKERS 2022; 2022:8639323. [PMID: 35422890 PMCID: PMC9005323 DOI: 10.1155/2022/8639323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/24/2022] [Indexed: 12/30/2022]
Abstract
Gastric cancer (GC) is the most common malignant tumor in the digestive system, traditional radiotherapy and chemotherapy are not effective for some patients. The research progress of immunotherapy seems to provide a new way for treatment. However, it is still urgent to predict immunotherapy biomarkers and determine novel therapeutic targets. In this study, the gene expression profiles and clinical data of 407 stomach adenocarcinoma (STAD) patients were downloaded from The Cancer Genome Atlas (TCGA) portal, and the abundance ratio of immune cells in each sample was obtained via the “Cell Type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT)” algorithm. Five immune cells were obtained as a result of abundance comparison, and 295 immune-related genes were obtained through differential gene analysis. Enrichment, protein interaction, and module analysis were performed on these genes. We identified five immune cells associated with infiltration and 20 hub genes, of which five genes were correlated with overall survival. Finally, we used Real-time PCR (RT-PCR) to detect the expression differences of the five hub genes in 18 pairs of GC and adjacent tissues. This research not only provides cellular and gene targets for immunotherapy of GC but also provides new ideas for researchers to explore immunotherapy for various tumors.
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Karamitrousis EI, Balgkouranidou I, Xenidis N, Amarantidis K, Biziota E, Koukaki T, Trypsianis G, Karayiannakis A, Bolanaki H, Kolios G, Lianidou E, Kakolyris S. Prognostic Role of RASSF1A, SOX17 and Wif-1 Promoter Methylation Status in Cell-Free DNA of Advanced Gastric Cancer Patients. Technol Cancer Res Treat 2021; 20:1533033820973279. [PMID: 33928818 PMCID: PMC8113658 DOI: 10.1177/1533033820973279] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Epigenetic modification of several genes is a key component in the development of gastric cancer. The methylation status of RASSF1A, SOX17 and Wif-1 genes was evaluated in the cell free circulating DNA of 70 patients with advanced gastric cancer, using methylation-specific PCR. Patients with higher cell-free DNA concentration seem to have lower PFS, than patients with lower cell-free DNA concentration (p = 0.001). RASSF1A was the tumor suppressor gene, most frequently methylated in metastatic gastric cancer patients, followed by SOX17 and Wif-1 (74.3%, 60.0% and 47.1%, respectively). Patients having the SOX17 promoter methylated, had lower progression free survival and overall survival, than unmethylated ones (p < 0.001). Patients having the Wif-1 promoter methylated, had lower progression free survival and overall survival, than unmethylated ones (p = 0.001). Patients having the RASSF1A promoter methylated, had lower progression free survival and overall survival, than unmethylated ones (p = 0.004). Promoter methylation of the examined genes was significantly associated with a decrease in progression free survival and overall survival, comparing to that of patients without methylation. Simultaneous methylation of the above genes was associated with even worse progression free survival and overall survival. The methylation of RASSF1A, SOX-17 and Wif-1 and genes, is a frequent epigenetic event in patients with advanced gastric cancer.
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Affiliation(s)
| | - Ioanna Balgkouranidou
- Department of Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Nikolaos Xenidis
- Department of Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Kyriakos Amarantidis
- Department of Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eirini Biziota
- Department of Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Triantafyllia Koukaki
- Department of Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Grigorios Trypsianis
- Department of Medical Statistics, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Anastasios Karayiannakis
- Second Department of Surgery, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Helen Bolanaki
- Second Department of Surgery, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - George Kolios
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Evi Lianidou
- Department of Chemistry, Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, University of Athens, Athens, Greece
| | - Stylianos Kakolyris
- Department of Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
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5
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de Jesus LM, Dos Reis MB, Carvalho RS, Scapulatempo Neto C, de Almeida GC, Laus AC, Marczynski GT, Leal LF, Melendez ME, de Marchi P, Manuel Reis R, Carvalho AL, de Carvalho AC. Feasibility of methylated ctDNA detection in plasma samples of oropharyngeal squamous cell carcinoma patients. Head Neck 2020; 42:3307-3315. [PMID: 32687251 DOI: 10.1002/hed.26385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/18/2020] [Accepted: 06/26/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Oropharyngeal squamous cell carcinomas (OpSCCs) are commonly associated with high rates of treatment failure. OBJECTIVES To evaluate methylation-based markers in plasma from OpSCC patients as emerging tools for accurate/noninvasive follow-up. METHODS Pretreatment formalin-fixed paraffin-embedded (FFPE) biopsies (n = 52) and paired plasma (n = 15) were tested for the methylation of CCNA1, DAPK, CDH8, and TIMP3 by droplet digital PCR (ddPCR). RESULTS Seventy-one percent (37/52) of the biopsies showed methylation of at least one of the evaluated genes and tumor CCNA1 methylation was associated with recurrence-free survival. Methylated circulating tumor DNA (meth-ctDNA) was detected in 11/15 (73.3%) plasma samples; conversely, plasma samples from healthy controls were all negative for DNA methylation (area under the curve = 0.867; 95% confidence interval = 0.720-1.000). Additionally, preliminary results on the detection of meth-ctDNA in plasma collected during follow-up closely matched patient outcome. CONCLUSIONS The results suggest the feasibility of detecting meth-ctDNA in plasma using ddPCR and a possible application on routine setting after further validation.
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Affiliation(s)
| | | | | | | | | | - Ana Carolina Laus
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Leticia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Matias Eliseo Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Pelé Little Prince Research Institute, Curitiba, Brazil.,Little Prince Complex, Curitiba, Brazil
| | - Pedro de Marchi
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
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6
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George S, Lucero Y, Torres JP, Lagomarcino AJ, O'Ryan M. Gastric Damage and Cancer-Associated Biomarkers in Helicobacter pylori-Infected Children. Front Microbiol 2020; 11:90. [PMID: 32117120 PMCID: PMC7029740 DOI: 10.3389/fmicb.2020.00090] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
Helicobacter pylori (H. pylori) is well-known to be involved in gastric carcinogenesis, associated with deregulation of cell proliferation and epigenetic changes in cancer-related genes. H. pylori infection is largely acquired during childhood, persisting long-term in about half of infected individuals, a subset of whom will go on to develop peptic ulcer disease and eventually gastric cancer, however, the sequence of events leading to disease is not completely understood. Knowledge on carcinogenesis and gastric damage-related biomarkers is abundant in adult populations, but scarce in children. We performed an extensive literature review focusing on gastric cancer related biomarkers identified in adult populations, which have been detected in children infected with H. pylori. Biomarkers were related to expression levels (RNA or protein) and/or methylation levels (DNA) in gastric tissue or blood of infected children as compared to non-infected controls. In this review, we identified 37 biomarkers of which 24 are over expressed, three are under expressed, and ten genes are significantly hypermethylated in H. pylori-infected children compared to healthy controls in at least 1 study. Only four of these biomarkers (pepsinogen I, pepsinogen II, gastrin, and SLC5A8) have been studied in asymptomatically infected children. Importantly, 13 of these biomarkers (β-catenin, C-MYC, GATA-4, DAPK1, CXCL13, DC-SIGN, TIMP3, EGFR, GRIN2B, PIM2, SLC5A8, CDH1, and VCAM-1.) are consistently deregulated in infected children and in adults with gastric cancer. Future studies should be designed to determine the clinical significance of these changes in infection-associated biomarkers in children and their persistence over time. The effect of eradication therapy over these biomarkers in children if proven significant, could lead to modifications in treatment guidelines for younger populations, and eventually promote the development of preventive strategies, such as vaccination, in the near future.
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Affiliation(s)
- Sergio George
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Yalda Lucero
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Department of Pediatrics and Pediatric Surgery, Dr. Roberto del Río Hospital, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Juan Pablo Torres
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Department of Pediatrics and Pediatric Surgery, Dr. Luis Calvo Mackenna Hospital, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Anne J Lagomarcino
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Miguel O'Ryan
- Host-Pathogen Interaction Laboratory, Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy (IMII), Faculty of Medicine, Universidad de Chile, Santiago, Chile
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7
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Bin Y, Ding Y, Xiao W, Liao A. RASSF1A: A promising target for the diagnosis and treatment of cancer. Clin Chim Acta 2020; 504:98-108. [PMID: 31981586 DOI: 10.1016/j.cca.2020.01.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
Abstract
The Ras association domain family 1 isoform A (RASSF1A), a tumor suppressor, regulates several tumor-related signaling pathways and interferes with diverse cellular processes. RASSF1A is frequently demonstrated to be inactivated by hypermethylation in numerous types of solid cancers. It is also associated with lymph node metastasis, vascular invasion, and chemo-resistance. Therefore, reactivation of RASSF1A may be a viable strategy to block tumor progress and reverse drug resistance. In this review, we have summarized the clinical value of RASSF1A for screening, staging, and therapeutic management of human malignancies. We also highlighted the potential mechanism of RASSF1A in chemo-resistance, which may help identify novel drugs in the future.
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Affiliation(s)
- Yuling Bin
- Digestive System Department, the First Affiliated Hospital of University of South China, Hengyang, Hunan 421001, China
| | - Yong Ding
- Department of Vascular Surgery, Zhongshan Hospital, Institue of Vascular Surgery, Fudan University, Shanghai 200032, China
| | - Weisheng Xiao
- Digestive System Department, the First Affiliated Hospital of University of South China, Hengyang, Hunan 421001, China
| | - Aijun Liao
- Digestive System Department, the First Affiliated Hospital of University of South China, Hengyang, Hunan 421001, China.
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8
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Vedeld HM, Goel A, Lind GE. Epigenetic biomarkers in gastrointestinal cancers: The current state and clinical perspectives. Semin Cancer Biol 2018; 51:36-49. [PMID: 29253542 PMCID: PMC7286571 DOI: 10.1016/j.semcancer.2017.12.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/17/2017] [Accepted: 12/12/2017] [Indexed: 02/07/2023]
Abstract
Each year, almost 4.1 million people are diagnosed with gastrointestinal (GI) cancers. Due to late detection of this disease, the mortality is high, causing approximately 3 million cancer-related deaths annually, worldwide. Although the incidence and survival differs according to organ site, earlier detection and improved prognostication have the potential to reduce overall mortality burden from these cancers. Epigenetic changes, including aberrant promoter DNA methylation, are common events in both cancer initiation and progression. Furthermore, such changes may be identified non-invasively with the use of PCR based methods, in bodily fluids of cancer patients. These features make aberrant DNA methylation a promising substrate for the development of disease biomarkers for early detection, prognosis and for predicting response to therapy. In this article, we will provide an update and current clinical perspectives for DNA methylation alterations in patients with colorectal, gastric, pancreatic, liver and esophageal cancers, and discuss their potential role as cancer biomarkers.
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Affiliation(s)
- Hege Marie Vedeld
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Norwegian Radium 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.
| | - Ajay Goel
- Center for Gastrointestinal Research, and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA.
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Norwegian Radium 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.
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9
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Mohsenzadeh M, Sadeghi RN, Vahedi M, Kamani F, Hashemi M, Asadzadeh H, Zali MR. Promoter hypermethylation of RAR-β tumor suppressor gene in gastric carcinoma: Association with histological type and clinical outcomes. Cancer Biomark 2018; 20:7-15. [PMID: 28759951 DOI: 10.3233/cbm-160331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND While gastric cancer is a common cancer in the world and Iran, its molecular mechanisms are not fully understood as yet. Epigenetic modifications can lead to alteration of gene expression and development of tumorigenesis mechanisms. METHODS To clarify the difference in DNA methylation pattern of histological types in gastric carcinoma, CpG islands in the promoters of retinoic acid receptor β gene (RAR-β) was studied using methylation-specific PCR. RESULTS In gastric cancer tissues, hypermethylation frequency of RAR-β gene was respectively 61 and 33% for diffuse and intestinal type. In diffuse type, hypermethylation of RAR-β has been significantly associated with invasion (P= 0.007), differentiation (P= 0.033) and location (P= 0.012) of the tumor. However, hypermethylation of RAR-β correlated only with tumor size (P= 0.029) in intestinal type. For adjacent non-tumor samples, hypermethylation of RAR-β was not detected and there was no significant association between age of diagnosis and hypermethylation of RAR-β in both types of gastric cancer. CONCLUSIONS These results support previous findings denoting a distinct profile of promoter hypermethylation status in the development of the intestinal and diffuse type of gastric carcinoma and the process of the tumorigenesis in these subtypes of gastric cancer is different from each other.
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Affiliation(s)
- Maedeh Mohsenzadeh
- Department of Cellular and Molecular Sciences, Faculty of Advanced Sciences and Technology, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Rouhallah Najjar Sadeghi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Faculty of Medicine, Department of Clinical Biochemistry, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohsen Vahedi
- Department of Biostatistics, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fereshteh Kamani
- Department of Surgery, Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Hamid Asadzadeh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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10
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Wong CC, Li W, Chan B, Yu J. Epigenomic biomarkers for prognostication and diagnosis of gastrointestinal cancers. Semin Cancer Biol 2018; 55:90-105. [PMID: 29665409 DOI: 10.1016/j.semcancer.2018.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/04/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022]
Abstract
Altered epigenetic regulation is central to many human diseases, including cancer. Over the past two decade, major advances have been made in our understanding of the role of epigenetic alterations in carcinogenesis, particularly for DNA methylation, histone modifications and non-coding RNAs. Aberrant hypermethylation of DNA at CpG islands is a well-established phenomenon that mediates transcriptional silencing of tumor suppressor genes, and it is an early event integral to gastrointestinal cancer development. As such, detection of aberrant DNA methylation is being developed as biomarkers for prognostic and diagnostic purposes in gastrointestinal cancers. Diverse tissue types are suitable for the analyses of methylated DNA, such as tumor tissues, blood, plasma, and stool, and some of these markers are already utilized in the clinical setting. Recent advances in the genome-wide epigenomic approaches are enabling the comprehensive mapping of the cancer methylome, thus providing new avenues for mining novel biomarkers for disease prognosis and diagnosis. Here, we review the current knowledge on DNA methylation biomarkers for the prognostication and non-invasive diagnosis of gastrointestinal cancers and highlight their clinical application.
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Affiliation(s)
- Chi Chun Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong.
| | - Weilin Li
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong; Department of Surgery, The Chinese University of Hong Kong, Hong Kong
| | - Bertina Chan
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong.
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11
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Rivas-Ortiz CI, Lopez-Vidal Y, Arredondo-Hernandez LJR, Castillo-Rojas G. Genetic Alterations in Gastric Cancer Associated with Helicobacter pylori Infection. Front Med (Lausanne) 2017; 4:47. [PMID: 28512631 PMCID: PMC5411440 DOI: 10.3389/fmed.2017.00047] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/07/2017] [Indexed: 12/11/2022] Open
Abstract
Gastric cancer is a world health problem and depicts the fourth leading mortality cause from malignancy in Mexico. Causation of gastric cancer is not only due to the combined effects of environmental factors and genetic variants. Recent molecular studies have transgressed a number of genes involved in gastric carcinogenesis. The aim of this review is to understand the recent basics of gene expression in the development of the process of gastric carcinogenesis. Genetic variants, polymorphisms, desoxyribonucleic acid methylation, and genes involved in mediating inflammation have been associated with the development of gastric carcinogenesis. Recently, these genes (interleukin 10, Il-17, mucin 1, β-catenin, CDX1, SMAD4, SERPINE1, hypoxia-inducible factor 1 subunit alpha, GSK3β, CDH17, matrix metalloproteinase 7, RUNX3, RASSF1A, TFF1, HAI-2, and COX-2) have been studied in association with oncogenic activation or inactivation of tumor suppressor genes. All these mechanisms have been investigated to elucidate the process of gastric carcinogenesis, as well as their potential use as biomarkers and/or molecular targets to treatment of disease.
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Affiliation(s)
- Claudia I. Rivas-Ortiz
- Programa de Inmunología Molecular Microbiana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Yolanda Lopez-Vidal
- Programa de Inmunología Molecular Microbiana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | | | - Gonzalo Castillo-Rojas
- Programa de Inmunología Molecular Microbiana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
- *Correspondence: Gonzalo Castillo-Rojas,
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12
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Llorca-Cardeñosa MJ, Fleitas T, Ibarrola-Villava M, Peña-Chilet M, Mongort C, Martinez-Ciarpaglini C, Navarro L, Gambardella V, Castillo J, Roselló S, Navarro S, Ribas G, Cervantes A. Epigenetic changes in localized gastric cancer: the role of RUNX3 in tumor progression and the immune microenvironment. Oncotarget 2016; 7:63424-63436. [PMID: 27566570 PMCID: PMC5325374 DOI: 10.18632/oncotarget.11520] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/15/2016] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer (GC) pathogenesis involves genetic, epigenetic and environmental factors. Epigenetic alterations, such as DNA methylation are considered pivotal in the inactivation of tumor-related genes. We assessed a methylation panel of 5 genes to study their association to GC progression and microsatellite instability (MSI), and studied the role of RUNX3 in GC pathogenesis and the tumor immune microenvironment.The methylation status of 47 promoter-CpG islands was studied through MALDI-TOF mass spectrometry analysis in 35 Microsatellite stable (MSS) GC, 26 MSI, and 18 cancer-free samples (CFS), and 6 MSS GC and 4 MSI GC cell lines. We also studied RUNX3 expression by immunohistochemistry (IHC) in 40 samples, and validated differences in methylation levels between tumor, normal, and immune tissue in 14 additional samples.Unsupervised hierarchical clustering of methylation levels revealed no distinct subgroups between MSI and MSS samples or cell lines. CFSs clustered together showing higher levels of RUNX3 methylation compared to GC samples. RUNX3 showed protein silencing in cancer and normal mucosa, compared to inflammatory peritumoural infiltrate in almost all cases, showing a non-lymphocytic predominant pattern and being correlated with epigenetic silencing.Our results show aberrant promoter's methylation in APC, CDH1, CDKN2A, MLH1 and RUNX3 associated with GC, as well as a non-lymphocytic predominant infiltrate with high expression of RUNX3. Deep study of RUNX3 inflammation signaling could help in understanding inflammation and immune activation in the tumor microenvironment.
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Affiliation(s)
| | - Tania Fleitas
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Maider Ibarrola-Villava
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - María Peña-Chilet
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Cristina Mongort
- Department of Pathology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | | | - Lara Navarro
- Department of Pathology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Valentina Gambardella
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Josefa Castillo
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Susana Roselló
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Samuel Navarro
- Department of Pathology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Gloria Ribas
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Andrés Cervantes
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
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13
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Cao J, Li Z, Yang L, Liu C, Luan X. Association Between Tissue Inhibitor of Metalloproteinase-3 Gene Methylation and Gastric Cancer Risk: A Meta-Analysis. Genet Test Mol Biomarkers 2016; 20:427-31. [PMID: 27314831 DOI: 10.1089/gtmb.2015.0332] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The tumor suppressor gene tissue inhibitor of metalloproteinase-3 (TIMP-3) has been reported to be frequently and significantly downregulated in gastric cancer, and its downregulation is correlated with hypermethylation in its promoter region. However, the association between TIMP-3 methylation and gastric cancer risk remains unclear. AIM In this study, we assessed the relationship between TIMP-3 promoter methylation and gastric cancer risk by performance of a meta-analysis. METHODS Relevant studies were identified in a comprehensive literature search using PubMed, Embase, and Web of Science databases. The strength of the association between TIMP-3 methylation and the risk of gastric cancer was assessed by odds ratio (OR) with the corresponding 95% confidence interval (CI). The heterogeneity among studies was tested using the Q-statistics and I(2) metric. The publication bias was examined by Begg's funnel plots and Egger's linear regression test. RESULTS A total of 1096 subjects from eight studies were included in the present meta-analysis. Overall, a significant association between TIMP-3 methylation and gastric cancer risk was observed (OR = 8.65; 95% CI 4.31-17.37; p < 0.001). Stratified analyses by ethnicity, sample materials, and detection methods also revealed increased gastric cancer risk in individuals harboring methylated TIMP-3. Moreover, no publication bias was detected in the present meta-analysis. CONCLUSIONS Our results show a positive correlation between TIMP-3 promoter methylation and gastric cancer risk and indicated that TIMP-3 promoter methylation may be used as a molecular marker for gastric cancer.
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Affiliation(s)
- Jinghua Cao
- 1 Department of Internal Medicine, Binzhou Medical University , Yantai, People's Republic of China
| | - Zhenfeng Li
- 2 State-Owned Asset Management Department, Binzhou Medical University , Yantai, People's Republic of China
| | - Lijuan Yang
- 3 Laboratory of Oncology, the Affiliated Hospital of Binzhou Medical University , Binzhou, People's Republic of China
| | - Chengxia Liu
- 4 Department of Digestive Medicine, the Affiliated Hospital of Binzhou Medical University , Binzhou, People's Republic of China
| | - Xiying Luan
- 5 Department of Immunology, Binzhou Medical University , Yantai, People's Republic of China
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14
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Balgkouranidou I, Matthaios D, Karayiannakis A, Bolanaki H, Michailidis P, Xenidis N, Amarantidis K, Chelis L, Trypsianis G, Chatzaki E, Lianidou ES, Kakolyris S. Prognostic role of APC and RASSF1A promoter methylation status in cell free circulating DNA of operable gastric cancer patients. Mutat Res 2015; 778:46-51. [PMID: 26073472 DOI: 10.1016/j.mrfmmm.2015.05.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 04/18/2015] [Accepted: 05/09/2015] [Indexed: 12/12/2022]
Abstract
Gastric carcinogenesis is a multistep process including not only genetic mutations but also epigenetic alterations. The best known and more frequent epigenetic alteration is DNA methylation affecting tumor suppressor genes that may be involved in various carcinogenetic pathways. The aim of the present study was to investigate the methylation status of APC promoter 1A and RASSF1A promoter in cell free DNA of operable gastric cancer patients. Using methylation specific PCR, we examined the methylation status of APC promoter 1A and RASSF1A promoter in 73 blood samples obtained from patients with gastric cancer. APC and RASSF1A promoters were found to be methylated in 61 (83.6%) and 50 (68.5%) of the 73 gastric cancer samples examined, but in none of the healthy control samples (p < 0.001). A significant association between methylated RASSF1A promoter status and lymph node positivity was observed (p = 0.005). Additionally, a significant correlation between a methylated APC promoter and elevated CEA (p = 0.033) as well as CA-19.9 (p = 0.032) levels, was noticed. The Kaplan-Meier estimates of survival, significantly favored patients with a non-methylated APC promoter status (p = 0.008). No other significant correlations between APC and RASSF1A methylation status and different tumor variables examined was observed. Serum RASSF1A and APC promoter hypermethylation is a frequent epigenetic event in patients with early operable gastric cancer. The observed correlations between APC promoter methylation status and survival as well as between a hypermethylated RASSF1A promoter and nodal positivity may be indicative of a prognostic role for those genes in early operable gastric cancer. Additional studies, in a larger cohort of patients are required to further explore whether these findings could serve as potential molecular biomarkers of survival and/or response to specific treatments.
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Affiliation(s)
- I Balgkouranidou
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Greece.
| | - D Matthaios
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Greece
| | - A Karayiannakis
- Second Department of Surgery, Medical School, Democritus University of Thrace, Greece
| | - H Bolanaki
- Second Department of Surgery, Medical School, Democritus University of Thrace, Greece
| | - P Michailidis
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Greece
| | - N Xenidis
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Greece
| | - K Amarantidis
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Greece
| | - L Chelis
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Greece
| | - G Trypsianis
- Laboratory of Statistics, Medical School, Democritus University of Thrace, Greece
| | - E Chatzaki
- Department of Pharmacology, Medical School, Democritus University of Thrace, Greece
| | - E S Lianidou
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Greece
| | - S Kakolyris
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Greece
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15
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Grawenda AM, O'Neill E. Clinical utility of RASSF1A methylation in human malignancies. Br J Cancer 2015; 113:372-81. [PMID: 26158424 PMCID: PMC4522630 DOI: 10.1038/bjc.2015.221] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/11/2015] [Accepted: 05/13/2015] [Indexed: 02/06/2023] Open
Abstract
The high frequency of RASSF1A methylation has been noted in a vast number of patients in a broad spectrum of malignancies, suggesting that RASSF1A inactivation is associated with cancer pathogenesis. However, whether this recurrent incidence of RASSF1A hypermethylation in human malignancies and its association with more aggressive tumour phenotype is a frequent event across different cancer types has not yet been discussed. In this review, we interrogated existing evidence for association of RASSF1A hypermethylation with clinicopathological characteristics that can indicate more invasive lesions.
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Affiliation(s)
- A M Grawenda
- CRUK/MRC Oxford Institute, Department of Oncology, University of Oxford, Oxford, UK
| | - E O'Neill
- CRUK/MRC Oxford Institute, Department of Oncology, University of Oxford, Oxford, UK
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16
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Li Y, Liang J, Hou P. Hypermethylation in gastric cancer. Clin Chim Acta 2015; 448:124-32. [PMID: 26148722 DOI: 10.1016/j.cca.2015.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 07/02/2015] [Accepted: 07/02/2015] [Indexed: 02/07/2023]
Abstract
Although gastric cancer (GC) is highly prevalent in China and is a leading cause of cancer-related death, major advances in early diagnostic and effective therapeutic strategies have not been made. GC patients are usually diagnosed at an advanced stage and the prognosis is still poor. Over the years, many efforts have been done on exploring the pathology of GC. In particular, genome-wide analysis tools have been widely used in the detection of genetic and epigenetic alterations in GC. For example, many tumor suppressor genes have been found to be aberrantly hypermethylated in GCs, and some even in gastric precancerous lesions, suggesting a role of this molecular event in early gastric tumorigenesis. In addition, accumulating evidences have demonstrated that some hypermethylated genes can be used as potential biomarkers for detection and diagnosis of GC in biopsy specimens and non-invasive body fluids. These exciting advances provide unprecedented opportunities for the development of molecular-based novel diagnostic, prognostic, and therapeutic strategies for GC. Here, we reviewed recent findings on the promoter hypermethylation of tumor suppressor genes in GC and aimed to provide better understanding of the contribution of this epigenetic event to gastric tumorigenesis.
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Affiliation(s)
- Yujun Li
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, People's Republic of China
| | - Junrong Liang
- Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, People's Republic of China
| | - Peng Hou
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, People's Republic of China.
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17
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Xia X, Yin W, Zhang X, Yu X, Wang C, Xu S, Feng W, Yang H. PAX6 overexpression is associated with the poor prognosis of invasive ductal breast cancer. Oncol Lett 2015; 10:1501-1506. [PMID: 26622698 DOI: 10.3892/ol.2015.3434] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 04/28/2015] [Indexed: 12/21/2022] Open
Abstract
Paired box 6 (PAX6) plays a significant role in the development of human neuroectodermal epithelial tissues. Previous studies have suggested that the PAX6 promoter is hypermethylated in breast cancer and that it is involved in breast cancer cell proliferation. The present study aimed to investigate the expression of PAX6 in invasive breast cancer tissues, and to evaluate its prognostic significance. Immunohistochemistry (IHC) was used to detect PAX6 expression on a breast cancer tissue microarray containing tissues from 111 patients. Associations of PAX6 expression with staging and prognosis were analyzed. PAX6 was mainly expressed in the nucleus. The PAX6 staining intensity was not associated with age, histological grade, lymph node status, tumor size, or progesterone receptor and human epidermal growth factor receptor 2 expression (all P>0.05). A high level of PAX6 staining was more frequent in estrogen receptor (ER)-negative cases compared with ER-positive cases (43.9 vs. 25.7%; P=0.049). After a median follow-up time of 110 months, the patients with low PAX6 expression exhibited an improved survival rate compared with the patients with high PAX6 expression (P<0.001). Cox analysis showed a worse survival rate in the patients with high PAX6 staining (hazard ratio, 3.458; 95% confidence interval, 1.575-7.593; P=0.002). In conclusion, high tumor PAX6 staining intensity by IHC was associated with a poor prognosis in breast cancer patients.
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Affiliation(s)
- Xianghou Xia
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, P.R. China
| | - Wenjuan Yin
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, P.R. China
| | - Xiping Zhang
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, P.R. China
| | - Xingfei Yu
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, P.R. China
| | - Chen Wang
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, P.R. China
| | - Shenhua Xu
- Zhejiang Cancer Research Institute, Hangzhou, Zhejiang, P.R. China
| | - Weiliang Feng
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, P.R. China
| | - Hongjian Yang
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, P.R. China ; Department of Surgical Oncology, School of the First Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
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18
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Thompson MJ, Rubbi L, Dawson DW, Donahue TR, Pellegrini M. Pancreatic cancer patient survival correlates with DNA methylation of pancreas development genes. PLoS One 2015; 10:e0128814. [PMID: 26039411 PMCID: PMC4454596 DOI: 10.1371/journal.pone.0128814] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/30/2015] [Indexed: 02/07/2023] Open
Abstract
DNA methylation is an epigenetic mark associated with regulation of transcription and genome structure. These markers have been investigated in a variety of cancer settings for their utility in differentiating normal tissue from tumor tissue. Here, we examine the direct correlation between DNA methylation and patient survival. We find that changes in the DNA methylation of key pancreatic developmental genes are strongly associated with patient survival.
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Affiliation(s)
- Michael J. Thompson
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, 90095, United States of America
| | - Liudmilla Rubbi
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, 90095, United States of America
| | - David W. Dawson
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, 90095, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, 90095, United States of America
| | - Timothy R. Donahue
- Department of Surgery, University of California Los Angeles, Los Angeles, California, 90095, United States of America
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, 90095, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, 90095, United States of America
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, 90095, United States of America
- * E-mail:
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19
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Calcagno DQ, de Arruda Cardoso Smith M, Burbano RR. Cancer type-specific epigenetic changes: gastric cancer. Methods Mol Biol 2015; 1238:79-101. [PMID: 25421656 DOI: 10.1007/978-1-4939-1804-1_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gastric cancer (GC) remains a major cause of mortality despite declining rate in the world. Epigenetic alterations contribute significantly to the development and progression of gastric tumors. Epigenetic refers to the number of modifications of the chromatin structure that affect gene expression without altering the primary sequence of DNA, and these changes lead to transcriptional activation or silencing of the gene. Over the years, the study of epigenetic processes has increased, and novel therapeutic approaches have emerged. This chapter summarizes the main epigenomic mechanisms described recently involved in gastric carcinogenesis, focusing on the roles that aberrant DNA methylation, histone modifications (histone acetylation and methylation), and miRNAs (oncogenic and tumor suppressor function of miRNA) play in the onset and progression of gastric tumors. Clinical implications of these epigenetic alterations in GC are also discussed.
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Affiliation(s)
- Danielle Queiroz Calcagno
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Rua dos Mundurucus, 4487, Guamá, CEP 66073-000 Belém, PA, Brazil,
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20
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Abstract
Epigenetic changes frequently occur in human gastric cancer. Gene promoter region hypermethylation, genomic global hypomethylation, histone modifications, and alterations of noncoding RNAs are major epigenetic changes in gastric cancer. As a key risk factor of gastric cancer, H. pylori infection is an independent predictive indicator of gene methylation. A growing number of epigenetic studies in gastric cancer have provided lots of potential diagnostic and prognostic markers and therapeutic targets.
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Affiliation(s)
- Mingzhou Guo
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853, China,
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21
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Liu C, Li N, Lu H, Wang Z, Chen C, Wu L, Liu J, Lu Y, Wang F. Circulating SFRP1 promoter methylation status in gastric adenocarcinoma and esophageal square cell carcinoma. Biomed Rep 2014; 3:123-127. [PMID: 25469261 DOI: 10.3892/br.2014.388] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 11/11/2014] [Indexed: 02/07/2023] Open
Abstract
The secreted frizzled-related protein 1 (SFRP1) gene plays an important role in carcinogenesis of digestive system cancer. Previous studies proved that circulating DNA promoter methylation may be a suitable biomarker for cancer patients. The aim of the present study was to investigate whether the promoter methylation status of serum SFRP1 is a potential biomarker for gastric adenocarcinoma (GAC) and esophageal square cell carcinoma (ESCC). The blood samples obtained from 42 GAC and 36 ESCC patients were detected for the promoter methylation status of SFRP1 by methylation-specific polymerase chain reaction. The control group included 42 benign gastrointestinal disease volunteers (24 benign gastric disease and 18 benign esophageal disease) and 20 healthy volunteers. Serum SFRP1 methylation was evident in 30.95% (13/42) GAC patients and 38.89% (14/36) ESCC patients, which is clearly higher compared to 8.33% (2/24) in benign gastric disease, 11.11% (2/18) in benign esophageal disease and 5% (1/20) in healthy volunteers (P<0.05). The association between the serum SFRP1 promoter methylation status and the clinical pathological features were further analyzed and methylation of the SFRP1 gene was significantly associated with age >60 years in GAC patients (P=0.027). However, no correlations between the SFRP1 methylation status and other clinicopathological parameters were found. In conclusion, the SFRP1 promoter was detected frequently in the serum of GAC and ESCC patients. The detection of circulating methylated SFRP1 in the serum may be a useful biomarker for upper gastrointestinal cancer patients.
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Affiliation(s)
- Chang Liu
- Department of Gastroenterology and Hepatology, Jinling Hospital, School of Medicine, Southern Medical University, Nanjing, Jiangsu 210002, P.R. China
| | - Nan Li
- Department of Gastroenterology and Hepatology, Jinling Hospital, School of Medicine, Southern Medical University, Nanjing, Jiangsu 210002, P.R. China
| | - Heng Lu
- Department of Gastroenterology and Hepatology, Jinling Hospital, School of Medicine, Southern Medical University, Nanjing, Jiangsu 210002, P.R. China
| | - Zhengkai Wang
- Department of Gastroenterology and Hepatology, Jinling Hospital, School of Medicine, Southern Medical University, Nanjing, Jiangsu 210002, P.R. China
| | - Chunyan Chen
- Department of Gastroenterology and Hepatology, Jinling Hospital, School of Medicine, Southern Medical University, Nanjing, Jiangsu 210002, P.R. China
| | - Lin Wu
- Department of Gastroenterology and Hepatology, Jinling Hospital, School of Medicine, Southern Medical University, Nanjing, Jiangsu 210002, P.R. China
| | - Jiong Liu
- Department of Gastroenterology and Hepatology, Jinling Hospital, School of Medicine, Southern Medical University, Nanjing, Jiangsu 210002, P.R. China
| | - Youke Lu
- Department of Gastroenterology and Hepatology, Jinling Hospital, School of Medicine, Southern Medical University, Nanjing, Jiangsu 210002, P.R. China
| | - Fangyu Wang
- Department of Gastroenterology and Hepatology, Jinling Hospital, School of Medicine, Southern Medical University, Nanjing, Jiangsu 210002, P.R. China
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22
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Shi J, Qu YP, Hou P. Pathogenetic mechanisms in gastric cancer. World J Gastroenterol 2014; 20:13804-13819. [PMID: 25320518 PMCID: PMC4194564 DOI: 10.3748/wjg.v20.i38.13804] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/15/2014] [Accepted: 05/29/2014] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) is a major public health issue as the fourth most common cancer and the second leading cause of cancer-related death. Recent advances have improved our understanding of its molecular pathogenesis, as best exemplified by elucidating the fundamental role of several major signaling pathways and related molecular derangements. Central to these mechanisms are the genetic and epigenetic alterations in these signaling pathways, such as gene mutations, copy number variants, aberrant gene methylation and histone modification, nucleosome positioning, and microRNAs. Some of these genetic/epigenetic alterations represent effective diagnostic and prognostic biomarkers and therapeutic targets for GC. This information has now opened unprecedented opportunities for better understanding of the molecular mechanisms of gastric carcinogenesis and the development of novel therapeutic strategies for this cancer. The pathogenetic mechanisms of GC are the focus of this review.
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23
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Nakamura J, Tanaka T, Kitajima Y, Noshiro H, Miyazaki K. Methylation-mediated gene silencing as biomarkers of gastric cancer: A review. World J Gastroenterol 2014; 20:11991-12006. [PMID: 25232236 PMCID: PMC4161787 DOI: 10.3748/wjg.v20.i34.11991] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 01/29/2014] [Accepted: 04/09/2014] [Indexed: 02/06/2023] Open
Abstract
Despite a decline in the overall incidence of gastric cancer (GC), the disease remains the second most common cause of cancer-related death worldwide and is thus a significant global health problem. The best means of improving the survival of GC patients is to screen for and treat early lesions. However, GC is often diagnosed at an advanced stage and is associated with a poor prognosis. Current diagnostic and therapeutic strategies have not been successful in decreasing the global burden of the disease; therefore, the identification of reliable biomarkers for an early diagnosis, predictive markers of recurrence and survival and markers of drug sensitivity and/or resistance is urgently needed. The initiation and progression of GC depends not only on genetic alterations but also epigenetic changes, such as DNA methylation and histone modification. Aberrant DNA methylation is the most well-defined epigenetic change in human cancers and is associated with inappropriate gene silencing. Therefore, an increasing number of genes methylated at the promoter region have been targeted as possible biomarkers for different purposes, including early detection, classification, the assessment of the tumor prognosis, the development of therapeutic strategies and patient follow-up. This review article summarizes the current understanding and recent evidence regarding DNA methylation markers in GC with a focus on the clinical potential of these markers.
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24
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Wang D, Yang PN, Chen J, Zhou XY, Liu QJ, Li HJ, Li CL. Promoter hypermethylation may be an important mechanism of the transcriptional inactivation of ARRDC3, GATA5, and ELP3 in invasive ductal breast carcinoma. Mol Cell Biochem 2014; 396:67-77. [PMID: 25148870 DOI: 10.1007/s11010-014-2143-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 07/11/2014] [Indexed: 12/24/2022]
Abstract
Hypermethylation of promoter CpG islands represents an alternative mechanism to inactivate tumor suppressor genes. This study was to detect promoter methylation status and mRNA expression levels of ARRDC3, ELP3, GATA5, and PAX6, and to explore the association between methylation and expression in invasive ductal carcinomas (IDCs) and matched normal tissues (MNTs) from breast cancer patients. Aberrant gene methylation was observed as follows: ARRDC3 in 38.5 %, ELP3 in 73.1 %, GATA5 in 48.1 %, and PAX6 in 50.0 % of IDCs. mRNA expression of ARRDC3, ELP3, and GATA5 in IDCs showed a lower level than that in MNTs (P < 0.001, P = 0.001 and P < 0.001, respectively). For ARRDC3, both methylated and unmethylated IDCs showed significantly lower expression values compared to MNTs (P = 0.001 and P = 0.007, respectively). For ELP3 and GATA5, methylated tumors only showed significantly lower expression values compared to MNTs (P = 0.001 and P < 0.001, respectively). For ARRDC3 and GATA5, methylation was associated with their less fold change in IDCs (P = 0.049 and P = 0.020, respectively). Methylation of ARRDC3 was significantly associated with grades and lymph node status of IDCs (P = 0.036 and P = 0.002, respectively). Methylation frequency of ELP3 was higher in lymph node positive versus lymph node negative tumors (P = 0.020); whereas methylation frequency of PAX6 was lower in tumors with the ER negative samples (P = 0.025). Our data suggested that promoter hypermethylation may be an important mechanism of the transcriptional inactivation of ARRDC3, GATA5, and ELP3 in IDCs.
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Affiliation(s)
- Da Wang
- Department of Biochemistry and Molecular Biology, School of Preclinical and Forensic Medicine, Sichuan University, 3-17 Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
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25
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Bai Y, Fang N, Gu T, Kang Y, Wu J, Yang D, Zhang H, Suo Z, Ji S. HOXA11 gene is hypermethylation and aberrant expression in gastric cancer. Cancer Cell Int 2014; 14:79. [PMID: 25788862 PMCID: PMC4364045 DOI: 10.1186/s12935-014-0079-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/29/2014] [Indexed: 12/11/2022] Open
Abstract
Background Aberrant DNA methylation is an acquired epigenetic alteration that serves as an alternative to genetic defects in the inactivation of tumor suppressor genes and other genes in diverse human cancers. Gastric carcinoma is one of the tumors with a high frequency of aberrant methylation in promoter region. Hence we investigated the promoter methylation status and expression level of HOXA11 gene which may involve in GC development. Methods Thirty-two surgical excised gastric cancer specimens, twelve paired adjacent non-cancerous specimens and seven normal gastric mucosas were examined. The methylation status and expression level of HOXA11 gene were determined by bisulfite sequencing polymerase chain reaction (BSP), real-time polymerase chain reaction (RT-PCR) and immunohistochemistry (IHC) respectively. HOXA11 expression was knocked-down with siRNA to mimic HOXA11 gene hypermethylation and ability of cell proliferation and migration was determinate. In addition, we analyzed and correlated the findings with clinicopathological features. Results The methylation level of HOXA11 gene in gastric cancer tissues and adjacent non-cancerous tissues were higher than those in normal gastric mucosa (P < 0.05). The methylation level was higher in TNM III and IV patients of GC than those in TNM I and II patients (P < 0.05). The expression of HOXA11 mRNA and protein decreased in normal gastric mucosa, peri-cancer tissue and GC (P < 0.05). HOXA11 expression was inversely correlated with DNA methylation (P < 0.05). Knocked-down of HOXA11 expression with siRNA in BGC-823 cells enhanced cell proliferation compared with control, but no significant different was observed in migration ability. Conclusion Hypermethylation and decreased expression of HOXA11 gene may be involved in the carcinogenesis and development of GC and may provide useful information for the prediction of the malignant behaviors of GC. And the expression of HOXA11 is impaired by DNA methylation. However, repression of HOXA11 expression promoted BGC-823 cell proliferation.
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Affiliation(s)
- Yinguo Bai
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China ; Department of Biochemistry and Molecular Biology, Medical School of Henan University, Kaifeng 475004, Henan Province, China
| | - Na Fang
- Department of Biochemistry and Molecular Biology, Medical School of Henan University, Kaifeng 475004, Henan Province, China
| | - Tingxun Gu
- Department of Biochemistry and Molecular Biology, Medical School of Henan University, Kaifeng 475004, Henan Province, China
| | - Yuhua Kang
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Jiang Wu
- Department of pathology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Desheng Yang
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Hui Zhang
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Zhimin Suo
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Shaoping Ji
- Department of Biochemistry and Molecular Biology, Medical School of Henan University, Kaifeng 475004, Henan Province, China
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Concomitant PIK3CA amplification and RASSF1A or PAX6 hypermethylation predict worse survival in gastric cancer. Clin Biochem 2014. [PMID: 24505629 DOI: 10.1016/j.clinbiochem.2013.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVES A large number of genetic and epigenetic alterations have been found in gastric cancer, but there is remarkably little consensus on the value of individual biomarker in diagnosis and prognosis of this cancer. This study was designed to illustrate the value of PIK3CA amplification in combination with promoter methylation of RASSF1A and PAX6 genes in early diagnosis and prognosis of gastric cancer. DESIGN AND METHODS Using real-time quantitative PCR, quantitative methylation-specific PCR (Q-MSP), and methylation-specific PCR (MSP) assays, we examined PIK3CA amplification and promoter methylation of RASSF1A and PAX6 genes in a cohort of gastric cancers, and explored the association of various (epi)genotypes with clinical outcomes of gastric cancer patients. RESULTS We demonstrated that PIK3CA gene was specifically amplified in gastric cancers, but not in normal gastric tissues. Moreover, frequent methylation of RASSF1A and PAX6 was also found in gastric cancers. Given the patients harboring diverse (epi)genotypes, we thus investigated the effect of various (epi)genotypes on poor prognosis in gastric cancer. The data showed that concomitant PIK3CA amplification and RASSF1A or PAX6 methylation were closely associated with poor clinical outcomes, particularly survival, as compared to other (epi)genotypes in gastric cancer. CONCLUSIONS We found frequent PIK3CA amplification and promoter methylation of RASSF1A and PAX6 genes in gastric cancers, and demonstrated that concomitant PIK3CA amplification and promoter methylation in any one of these two genes were significantly associated with worse survival in gastric cancer. Collectively, such (epi)genotypes may be strong and independent poor prognostic factors for gastric cancer patients.
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Zhang X, Zhang X, Sun B, Lu H, Wang D, Yuan X, Huang Z. Detection of aberrant promoter methylation of RNF180, DAPK1 and SFRP2 in plasma DNA of patients with gastric cancer. Oncol Lett 2014; 8:1745-1750. [PMID: 25202403 PMCID: PMC4156173 DOI: 10.3892/ol.2014.2410] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 07/11/2014] [Indexed: 12/18/2022] Open
Abstract
Gastric cancer (GC) is one of the most frequently diagnosed malignancies in East Asia, particularly in China, and remains the second leading cause of cancer-associated mortality worldwide. However, no effective plasma biomarkers have been identified for the diagnosis of patients with GC. The aim of this study was to investigate the DNA methylation status of the ring finger protein 180 (RNF180), secreted frizzled-related protein 2 (SFRP2) and death-associated protein kinase 1 (DAPK1) genes in the plasma samples of 57 GC patients and 42 control individuals with no malignant disease, and to evaluate the clinical utility of these makers. A significantly higher level of methylation was observed in the plasma DNA of GC patients when compared with that of controls for the three genes investigated (RNF180, 57.89% vs. 23.81%; DAPK1, 49.12% vs. 28.57%; and SFRP2, 71.93% vs. 42.86%). No association was identified between the DAPK1 or SFRP2 methylation level in the plasma DNA and the clinicopathological parameters of patients. Notably, RNF180 methylation was found to positively correlate with tumor size (P=0.018), histological type (P=0.025), TNM stage (P=0.002), lymph node metastasis (P=0.008) and distant metastasis (P=0.018). Overall, 50 cancer patients (87.72%) exhibited methylation of at least one of the three markers, while 26 normal subjects presented methylation in plasma DNA [specificity, 38.1%; odds ratio (OR), 4.4]. The combined use of RNF180 and SFRP2 as methylation markers appeared to be the most preferable predictor with regard to predictive power and cost-performance (OR, 5.57; P=0.0002). The results of the present study indicate that aberrant promoter methylation of genes in the plasma may be detected in a substantial proportion of GC patients and thus, these genes must be evaluated in the screening and surveillance of GC.
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Affiliation(s)
- Xie Zhang
- Department of Gastroenterology, Ningbo Medical Treatment Center, Li Huili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Xuesong Zhang
- Department of Gastroenterology, Ningbo Medical Treatment Center, Li Huili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Beilei Sun
- Department of Gastroenterology, Ningbo Medical Treatment Center, Li Huili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Hongna Lu
- Department of Gastroenterology, Ningbo Medical Treatment Center, Li Huili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Danping Wang
- School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Xiaogang Yuan
- Department of Gastroenterology, Ningbo Medical Treatment Center, Li Huili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Zhigang Huang
- Department of Gastroenterology, Ningbo Medical Treatment Center, Li Huili Hospital, Ningbo, Zhejiang 315040, P.R. China
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Quantification of DAPK1 promoter methylation in bone marrow and peripheral blood as a follicular lymphoma biomarker. J Mol Diagn 2014; 16:467-76. [PMID: 24814955 DOI: 10.1016/j.jmoldx.2014.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/30/2014] [Accepted: 03/19/2014] [Indexed: 12/31/2022] Open
Abstract
Hypermethylation of DAPK1 promoter gene was found to be a frequent epigenetic alteration in follicular lymphoma (FL). We evaluated whether the quantification of DAPK1 methylation in the bone marrow (BM) and peripheral blood of FL patients at diagnosis and during follow-up provides important prognostic information. DAPK1 methylation was quantitated by real-time MethyLight PCR in 107 patients at diagnosis, at end of therapy, and during follow-up. Information on BCL2-IGH rearrangement and clinical characteristics were available for all patients. Aberrant DAPK1 methylation was found in 22 of 26 (85%) lymph node biopsy samples, 62 of 107 (58%) BM specimens, and 25 of 63 (40%) peripheral blood samples at diagnosis. DAPK1 methylation was greater in patients with BM infiltration and a higher Follicular Lymphoma International Prognostic Index score. The presence of aberrant DAPK1 methylation in BM significantly reduced progression-free survival following immunochemotherapy, independent of Follicular Lymphoma International Prognostic Index score. Residual or increased methylation after treatment was associated with an increased risk for relapse. With watchful waiting, greater DAPK1 methylation at diagnosis was associated with a shorter time to antilymphoma treatment. Our study indicates that quantification of DAPK1 methylation represents a prognostically relevant FL biomarker, with promising implications for risk assessment.
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Selvarajah S, Pyne S, Chen E, Sompallae R, Ligon AH, Nielsen GP, Dranoff G, Stack E, Loda M, Flavin R. High-resolution array CGH and gene expression profiling of alveolar soft part sarcoma. Clin Cancer Res 2014; 20:1521-30. [PMID: 24493828 DOI: 10.1158/1078-0432.ccr-13-2090] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
PURPOSE Alveolar soft part sarcoma (ASPS) is a soft tissue sarcoma with poor prognosis, and little molecular evidence exists for its origin, initiation, and progression. The aim of this study was to elucidate candidate molecular pathways involved in tumor pathogenesis. EXPERIMENTAL DESIGN We employed high-throughput array comparative genomic hybridization (aCGH) and cDNA-Mediated Annealing, Selection, Ligation, and Extension Assay to profile the genomic and expression signatures of primary and metastatic ASPS from 17 tumors derived from 11 patients. We used an integrative bioinformatics approach to elucidate the molecular pathways associated with ASPS progression. FISH was performed to validate the presence of the t(X;17)(p11.2;q25) ASPL-TFE3 fusion and, hence, confirm the aCGH observations. RESULTS FISH analysis identified the ASPL-TFE3 fusion in all cases. aCGH revealed a higher number of numerical aberrations in metastatic tumors relative to primaries, but failed to identify consistent alterations in either group. Gene expression analysis highlighted 1,063 genes that were differentially expressed between the two groups. Gene set enrichment analysis identified 16 enriched gene sets (P < 0.1) associated with differentially expressed genes. Notable among these were several stem cell gene expression signatures and pathways related to differentiation. In particular, the paired box transcription factor PAX6 was upregulated in the primary tumors, along with several genes whose mouse orthologs have previously been implicated in Pax6 DNA binding during neural stem cell differentiation. CONCLUSION In addition to suggesting a tentative neural line of differentiation for ASPS, these results implicate transcriptional deregulation from fusion genes in the pathogenesis of ASPS.
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Affiliation(s)
- Shamini Selvarajah
- Authors' Affiliations: Department of Pathology, Brigham and Women's Hospital, Harvard Medical School; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute; Massachusetts General Hospital, Boston, Massachusetts; Carver College of Medicine, University of Iowa, Iowa City, Iowa; and Department of Pathology, St. James's Hospital, Dublin, Ireland
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Zhang G, Qu Y, Dang S, Yang Q, Shi B, Hou P. Variable copy number of mitochondrial DNA (mtDNA) predicts worse prognosis in advanced gastric cancer patients. Diagn Pathol 2013; 8:173. [PMID: 24144008 PMCID: PMC4015835 DOI: 10.1186/1746-1596-8-173] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/11/2013] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Change of mitochondrial DNA (mtDNA) copy number is widely reported in various human cancers, including gastric cancer, and is considered to be an important hallmark of cancers. However, there is remarkably little consensus on the value of variable mtDNA content in the prognostic evaluation of this cancer. METHODS Using real-time quantitative PCR approach, we examined mtDNA copy number in a cohort of gastric cancers and normal gastric tissues, and explored the association of variable mtDNA content with clinical outcomes of gastric cancer patients. RESULTS Our data showed that the majority of gastric cancer patients had low mtDNA content as compared to control subjects although the relative mean mtDNA content was higher in the former than the latter. Moreover, we found that variable mtDNA content was strongly associated with lymph node metastasis and cancer-related death of the patients with late-stage tumors. Notably, variable mtDNA content did not affect overall survival of gastric cancer patients, however, we found that increased mtDNA content was associated with poor survival in the patients with late-stage tumors. CONCLUSION In this study, we demonstrated that variable mtDNA content markedly increased the risk of lymph node metastasis and high mortality of the patients with late-stage tumors. Additionally, we found a strong link between increased mtDNA content and worse survival of the patients with late-stage tumors. Taken together, variable mtDNA content may be a valuable poor prognostic factor for advanced gastric cancer patients. VIRTUAL SLIDES The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1344721463103353.
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Affiliation(s)
| | | | | | | | | | - Peng Hou
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an 710061, the People's Republic of China.
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Association of RASSF1A promoter methylation with gastric cancer risk: a meta-analysis. Tumour Biol 2013; 35:943-8. [PMID: 23982879 DOI: 10.1007/s13277-013-1123-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Accepted: 08/16/2013] [Indexed: 12/22/2022] Open
Abstract
Ras-association domain family 1A (RASSF1A), a candidate tumor suppressor gene, is frequently silenced and inactivated by hypermethylation of its promoter region in several human tumors. However, the association between RASSF1A promoter methylation and gastric cancer risk remains conflicting. The aim of this study was to assess the association of RASSF1A promoter methylation with gastric cancer risk by a comprehensive meta-analysis. Relevant studies were identified by searches of PubMed and Web of Science databases with no restrictions. Combined odds ratio (OR) and 95 % confidence interval (CI) were used to assess the strength of the association between RASSF1A promoter methylation and gastric cancer risk. A chi-square-based Q test and sensitivity analyses were performed to test the between-study heterogeneity and the contributions of single studies to the final results, respectively. Funnel plots were carried out to evaluate publication bias. Overall, a significant association was observed between RASSF1A promoter methylation and gastric cancer risk (OR, 12.67; 95 % CI, 8.12-19.78; p < 0.001) with no between-study heterogeneity. Subgroup analyses further revealed that gastric cancer risk was increased for individuals carrying the methylated RASSF1A compared with those with unmethylated RASSF1A. In addition, no publication bias was detected in the overall and subgroup analyses. This study identified a strong association between RASSF1A promoter methylation and risk of gastric cancer and highlighted a promising potential for RASSF1A promoter methylation in gastric cancer risk prediction.
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Tänzer M, Liebl M, Quante M. Molecular biomarkers in esophageal, gastric, and colorectal adenocarcinoma. Pharmacol Ther 2013; 140:133-47. [PMID: 23791941 DOI: 10.1016/j.pharmthera.2013.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 06/06/2013] [Indexed: 02/06/2023]
Abstract
Cancers of the esophagus, stomach and colon contribute to a major health burden worldwide and over 20% of all cancer deaths. Biomarkers that should indicate pathogenic process and are measureable in an objective manner for these tumors are rare and not established in the clinical setting. In general biomarkers can be very useful for cancer management as they can improve clinical decision-making regarding diagnosis, surveillance, and therapy. Biomarkers can be different types of molecular entities (such as DNA, RNA or proteins), which can be detected, in different tissues or body fluids. However, more important is the type of biomarker itself, which allows diagnostic, prognostic or predictive analyses for different clinical problems. This review aims to systematically summarize the recent findings of genetic and epigenetic markers for gastrointestinal tumors within the last decade. While many biomarkers seem to be very promising, especially if used as panels, further development is urgently needed to address practical considerations of biomarkers in cancer treatment.
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Affiliation(s)
- Marc Tänzer
- II. Medizinische Klinik, Klinikum rechts der Isar, Technische Universität München, Ismaninger Str. 22, 81675 München, Germany
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Qu Y, Dang S, Hou P. Gene methylation in gastric cancer. Clin Chim Acta 2013; 424:53-65. [PMID: 23669186 DOI: 10.1016/j.cca.2013.05.002] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 05/03/2013] [Accepted: 05/03/2013] [Indexed: 02/07/2023]
Abstract
Gastric cancer is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide. Over 70% of new cases and deaths occur in developing countries. In the early years of the molecular biology revolution, cancer research mainly focuses on genetic alterations, including gastric cancer. Epigenetic mechanisms are essential for normal development and maintenance of tissue-specific gene expression patterns in mammals. Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Recent advancements in the rapidly evolving field of cancer epigenetics have shown extensive reprogramming of every component of the epigenetic machinery in cancer, including DNA methylation, histone modifications, nucleosome positioning, noncoding RNAs, and microRNAs. Aberrant DNA methylation in the promoter regions of gene, which leads to inactivation of tumor suppressor and other cancer-related genes in cancer cells, is the most well-defined epigenetic hallmark in gastric cancer. The advantages of gene methylation as a target for detection and diagnosis of cancer in biopsy specimens and non-invasive body fluids such as serum and gastric washes have led to many studies of application in gastric cancer. This review focuses on the most common and important phenomenon of epigenetics, DNA methylation, in gastric cancer and illustrates the impact epigenetics has had on this field.
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Key Words
- 5-hmC
- 5-hydroxymethylcytosine
- 5-mC
- 5-methylcytosine
- ADAM metallopeptidase domain 23
- ADAM metallopeptidase with thrombospondin type 1 motif, 9
- ADAM23
- ADAMTS9
- AML
- APC
- ARID1A
- AT motif-binding factor 1
- AT rich interactive domain 1A (SWI-like)
- ATBF1
- Acute myelocytic leukemia
- Adenomatosis polyposis coli
- B-cell translocation gene 4
- BCL2/adenovirus E1B 19kDa interacting protein 3
- BMP-2
- BNIP3
- BS
- BTG4
- Biomarkers
- Bisulfite sequencing
- Bone morphogenetic protein 2
- C-MET
- CACNA1G
- CACNA2D3
- CD44
- CD44 molecule (Indian blood group)
- CDH1
- CDK4
- CDK6
- CDKN1C
- CDKN2A
- CDX2
- CGI
- CHD5
- CHFR
- CKLF-like MARVEL transmembrane domain containing 3
- CMTM3
- CNS
- CRBP1
- Cadherin 1 or E-cadherin
- Calcium channel, voltage-dependent, T type, alpha 1G subunit
- Calcium channel, voltage-dependent, alpha 2/delta subunit 3
- Caudal type homeobox 2
- Central nervous system
- Checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase
- Chromodomain helicase DNA binding protein 5
- Chromosome 2 open reading frame 40
- Clinical outcomes
- CpG islands
- Cyclin-dependent kinase 4
- Cyclin-dependent kinase 6
- Cyclin-dependent kinase inhibitor 1A
- Cyclin-dependent kinase inhibitor 1B
- Cyclin-dependent kinase inhibitor 1C
- Cyclin-dependent kinase inhibitor 2A
- Cyclin-dependent kinase inhibitor 2B
- DAB2 interacting protein
- DACT1
- DAPK
- DNA
- DNA methylatransferases
- DNA mismatch repair
- DNMT
- Dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)
- Death-associated protein kinase
- Deoxyribose Nucleic Acid
- Dickkopf 3 homolog (Xenopus laevis)
- Dkk-3
- EBV
- ECRG4
- EDNRB
- EGCG
- ERBB4
- Endothelin receptor type B
- Epigallocatechin gallate
- Epigenetics
- Epstein–Barr Virus
- FDA
- FLNc
- Filamin C
- Food and Drug Administration
- GC
- GDNF
- GI endoscopy
- GPX3
- GRIK2
- GSTP1
- Gastric cancer
- Gene methylation
- Glutamate receptor, ionotropic, kainate 2
- Glutathione S-transferase pi 1
- Glutathione peroxidase 3 (plasma)
- H. pylori
- HACE1
- HAI-2/SPINT2
- HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1
- HGFA
- HLTF
- HOXA1
- HOXA10
- HRAS-like suppressor
- HRASLS
- Helicase-like transcription factor
- Helicobacter pylori
- Homeobox A1
- Homeobox A10
- Homeobox D10
- HoxD10
- IGF-1
- IGF-1R
- IGFBP3
- IL-1β
- ITGA4
- Insulin-like growth factor 1 (somatomedin C)
- Insulin-like growth factor I receptor
- Insulin-like growth factor binding protein 3
- Integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)
- Interleukin 1, beta
- KL
- KRAS
- Klotho
- LL3
- LMP2A
- LOX
- LRP1B
- Low density lipoprotein receptor-related protein 1B
- Lysyl oxidase
- MAPK
- MBPs
- MDS
- MGMT
- MINT25
- MLF1
- MLL
- MMR
- MSI
- MSP
- Matrix metallopeptidase 24 (membrane-inserted)
- Met proto-oncogene (hepatocyte growth factor receptor)
- Methyl-CpG binding proteins
- Methylation-specific PCR
- Microsatellite instability
- Myeloid leukemia factor 1
- Myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)
- Myeloid/lymphoid or mixed-lineage leukemia 3
- NDRG family member 2
- NDRG2
- NPR1
- NR3C1
- Natriuretic peptide receptor A/guanylate cyclase A
- Notch 1
- Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)
- O-6-methylguanine-DNA methyltransferase
- PCDH10
- PCDH17
- PI3K/Akt
- PIK3CA
- PR domain containing 5
- PRDM5
- PTCH1
- Patched 1
- Phosphatidylethanolamine binding protein 1
- Protein tyrosine phosphatase, non-receptor type 6
- Protocadherin 10
- Protocadherin 17
- Q-MSP
- Quantitative methylation-specific PCR
- RAR-related orphan receptor A
- RARRES1
- RARß
- RAS/RAF/MEK/ERK
- RASSF1A
- RASSF2
- RBP1
- RKIP
- RORA
- ROS
- RUNX3
- Ras association (RalGDS/AF-6) domain family member 1
- Ras association (RalGDS/AF-6) domain family member 2
- Rb
- Retinoic acid receptor responder (tazarotene induced) 1
- Retinoic acid receptor, beta
- Retinol binding protein 1, cellular
- Runt-related transcription factor 3
- S-adenosylmethionine
- SAM
- SFRP2
- SFRP5
- SHP1
- SOCS-1
- STAT3
- SYK
- Secreted frizzled-related protein 2
- Secreted frizzled-related protein 5
- Serine peptidase inhibitor, Kunitz type, 2
- Spleen tyrosine kinase
- Suppressor of cytokine signaling 1
- TCF4
- TET
- TFPI2
- TGF-β
- TIMP metallopeptidase inhibitor 3
- TIMP3
- TNM
- TP73
- TSP1
- Thrombospondin 1
- Tissue factor pathway inhibitor 2
- Transcription factor 4
- Tumor Node Metastasis
- Tumor protein p73
- V-erb-a erythroblastic leukemia viral oncogene homolog 4
- ZFP82 zinc finger protein
- ZIC1
- ZNF545
- Zinc finger protein of the cerebellum 1
- gastrointestinal endoscopy
- glial cell derived neurotrophic factor
- hDAB2IP
- hMLH1
- hepatocyte growth factor activator
- latent membrane protein
- mutL homolog 1
- myelodysplastic syndromes
- p15
- p16
- p21
- p27
- p53
- p73
- phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha
- phosphoinositide 3-kinase (PI3K)/Akt
- reactive oxygen species
- retinoblastoma
- signal transducer and activator of transcription-3
- ten-eleven translocation
- transforming growth factor-β
- tumor protein p53
- tumor protein p73
- v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
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Affiliation(s)
- Yiping Qu
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an 710061, People's Republic of China
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Watters KM, Bryan K, Foley NH, Meehan M, Stallings RL. Expressional alterations in functional ultra-conserved non-coding RNAs in response to all-trans retinoic acid--induced differentiation in neuroblastoma cells. BMC Cancer 2013; 13:184. [PMID: 23565812 PMCID: PMC3626850 DOI: 10.1186/1471-2407-13-184] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 03/20/2013] [Indexed: 12/02/2022] Open
Abstract
Background Ultra-conserved regions (UCRs) are segments of the genome (≥ 200 bp) that exhibit 100% DNA sequence conservation between human, mouse and rat. Transcribed UCRs (T-UCRs) have been shown to be differentially expressed in cancers versus normal tissue, indicating a possible role in carcinogenesis. All-trans-retinoic acid (ATRA) causes some neuroblastoma (NB) cell lines to undergo differentiation and leads to a significant decrease in the oncogenic transcription factor MYCN. Here, we examine the impact of ATRA treatment on T-UCR expression and investigate the biological significance of these changes. Methods We designed a custom tiling microarray to profile the expression of 481 T-UCRs in sense and anti-sense orientation (962 potential transcripts) in untreated and ATRA-treated neuroblastoma cell lines (SH-SY5Y, SK-N-BE, LAN-5). Following identification of significantly differentially expressed T-UCRs, we carried out siRNA knockdown and gene expression microarray analysis to investigate putative functional roles for selected T-UCRs. Results Following ATRA-induced differentiation, 32 T-UCRs were differentially expressed (16 up-regulated, 16 down-regulated) across all three cell lines. Further insight into the possible role of T-UC.300A, an independent transcript whose expression is down-regulated following ATRA was achieved by siRNA knockdown, resulting in the decreased viability and invasiveness of ATRA-responsive cell lines. Gene expression microarray analysis following knockdown of T-UC.300A revealed a number of genes whose expression was altered by changing T-UC.300A levels and that might play a role in the increased proliferation and invasion of NB cells prior to ATRA-treatment. Conclusions Our results indicate that significant numbers of T-UCRs have altered expression levels in response to ATRA. While the precise roles that T-UCRs might play in cancer or in normal development are largely unknown and an important area for future study, our findings strongly indicate that the function of non-coding RNA T-UC.300A is connected with proliferation, invasion and the inhibition of differentiation of neuroblastoma cell lines prior to ATRA treatment.
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Affiliation(s)
- Karen M Watters
- Cancer Genetics, Department of Molecular & Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland.
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Jiang XJ, Chu LL, Cui YX, Song MQ, Xie XJ, Tian ZB. Relationship between promoter methylation of the Runx3 and Rassf1a genes and Dnmt1 expression in gastric cancer. Shijie Huaren Xiaohua Zazhi 2012; 20:3457-3463. [DOI: 10.11569/wcjd.v20.i35.3457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To analyze the promoter methylation of the human runt-related transcription factor 3 (Runx3) and ras-association domain family 1a (Rassf1a) genes and Dnmt1 protein expression in gastric cancer and to analyze their relationship with gastric carcinogenesis.
METHODS: Methylation status of the Runx3 and Rassf1a genes in 68 gastric carcinoma tissues and 68 paired surgical marginal normal gastric tissues was detected using methylation-specific PCR. Real-time RT-PCR was used to detect the expression of Runx3, Rassf1a, and Dnmt1 mRNAs, and immunohistochemistry was used to detect the expression of RUNX3, RASSF1a, and DNMT1 proteins in the above samples.
RESULTS: The positive rates of promoter methylation of the Runx3 and Rassf1a genes were significantly higher in gastric cancer than in normal tissue (45.59% vs 10.29%; 64.70% vs 7.35%; both P < 0.0001). The positive rates of Runx3 and Rassf1a mRNA expression in gastric cancer were significantly lower than those in normal tissue (36.76% vs 100%; 27.94% vs 97.06%; both P < 0.0001), while that of Dnmt1 mRNA expression was higher compared to normal tissue (80.88% vs 17.65%, P < 0.0001). The expression patterns of RUNX3, RASSF1a, and DNMT1 proteins were consistent with those of Runx3, Rassf1a, and Dnmt1 mRNAs. The negative rates of Runx3 and Rassf1a mRNA expression in gastric cancer were significantly higher in the methylation group than in the non-methylation group (72.09% vs 0%; 85.71% vs 2.94%; both P < 0.0001). There was a negative correlation between the expression of RUNX3 and RASSF1a proteins and that of DNMT1 protein in gastric cancer tissue (r = -0.627, P < 0.0001; r = - 0.477, P < 0.0001).
CONCLUSION: The promoter methylation of the Runx3 and Rassf1a genes and high expression of Dnmt1 may be associated with the occurrence of gastric cancer.
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