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Wahner Hendrickson AE, Visscher DW, Hou X, Goergen KM, Atkinson HJ, Beito TG, Negron V, Lingle WL, Bruzek AK, Hurley RM, Wagner JM, Flatten KS, Peterson KL, Schneider PA, Larson MC, Maurer MJ, Kalli KR, Oberg AL, Weroha SJ, Kaufmann SH. CHFR and Paclitaxel Sensitivity of Ovarian Cancer. Cancers (Basel) 2021; 13:cancers13236043. [PMID: 34885153 PMCID: PMC8657201 DOI: 10.3390/cancers13236043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/17/2021] [Accepted: 11/27/2021] [Indexed: 12/14/2022] Open
Abstract
The poly(ADP-ribose) binding protein CHFR regulates cellular responses to mitotic stress. The deubiquitinase UBC13, which regulates CHFR levels, has been associated with better overall survival in paclitaxel-treated ovarian cancer. Despite the extensive use of taxanes in the treatment of ovarian cancer, little is known about expression of CHFR itself in this disease. In the present study, tissue microarrays containing ovarian carcinoma samples from 417 women who underwent initial surgical debulking were stained with anti-CHFR antibody and scored in a blinded fashion. CHFR levels, expressed as a modified H-score, were examined for association with histology, grade, time to progression (TTP) and overall survival (OS). In addition, patient-derived xenografts from 69 ovarian carcinoma patients were examined for CHFR expression and sensitivity to paclitaxel monotherapy. In clinical ovarian cancer specimens, CHFR expression was positively associated with serous histology (p = 0.0048), higher grade (p = 0.000014) and higher stage (p = 0.016). After correction for stage and debulking, there was no significant association between CHFR staining and overall survival (p = 0.62) or time to progression (p = 0.91) in patients with high grade serous cancers treated with platinum/taxane chemotherapy (N = 249). Likewise, no association between CHFR expression and paclitaxel sensitivity was observed in ovarian cancer PDXs treated with paclitaxel monotherapy. Accordingly, differences in CHFR expression are unlikely to play a major role in paclitaxel sensitivity of high grade serous ovarian cancer.
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Affiliation(s)
- Andrea E. Wahner Hendrickson
- Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA; (X.H.); (J.M.W.); (S.J.W.)
- Correspondence: (A.E.W.H.); (S.H.K.); Tel.: +1-507-284-3731 (A.E.W.H.); +1-507-284-8950 (S.H.K.); Fax: +1-507-293-0107 (A.E.W.H. & S.H.K.)
| | - Daniel W. Visscher
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA;
| | - Xiaonan Hou
- Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA; (X.H.); (J.M.W.); (S.J.W.)
| | - Krista M. Goergen
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; (K.M.G.); (H.J.A.); (M.C.L.); (M.J.M.); (A.L.O.)
| | - Hunter J. Atkinson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; (K.M.G.); (H.J.A.); (M.C.L.); (M.J.M.); (A.L.O.)
| | | | - Vivian Negron
- Pathology Research Core, Mayo Clinic, Rochester, MN 55905, USA; (V.N.); (W.L.L.); (A.K.B.)
| | - Wilma L. Lingle
- Pathology Research Core, Mayo Clinic, Rochester, MN 55905, USA; (V.N.); (W.L.L.); (A.K.B.)
| | - Amy K. Bruzek
- Pathology Research Core, Mayo Clinic, Rochester, MN 55905, USA; (V.N.); (W.L.L.); (A.K.B.)
| | - Rachel M. Hurley
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA;
| | - Jill M. Wagner
- Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA; (X.H.); (J.M.W.); (S.J.W.)
| | - Karen S. Flatten
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA; (K.S.F.); (K.L.P.); (P.A.S.)
| | - Kevin L. Peterson
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA; (K.S.F.); (K.L.P.); (P.A.S.)
| | - Paula A. Schneider
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA; (K.S.F.); (K.L.P.); (P.A.S.)
| | - Melissa C. Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; (K.M.G.); (H.J.A.); (M.C.L.); (M.J.M.); (A.L.O.)
| | - Matthew J. Maurer
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; (K.M.G.); (H.J.A.); (M.C.L.); (M.J.M.); (A.L.O.)
| | | | - Ann L. Oberg
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; (K.M.G.); (H.J.A.); (M.C.L.); (M.J.M.); (A.L.O.)
| | - S. John Weroha
- Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA; (X.H.); (J.M.W.); (S.J.W.)
| | - Scott H. Kaufmann
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA;
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA; (K.S.F.); (K.L.P.); (P.A.S.)
- Correspondence: (A.E.W.H.); (S.H.K.); Tel.: +1-507-284-3731 (A.E.W.H.); +1-507-284-8950 (S.H.K.); Fax: +1-507-293-0107 (A.E.W.H. & S.H.K.)
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Wang H, Lu Y, Wang M, Wu Y, Wang X, Li Y. Roles of E3 ubiquitin ligases in gastric cancer carcinogenesis and their effects on cisplatin resistance. J Mol Med (Berl) 2021; 99:193-212. [PMID: 33392633 DOI: 10.1007/s00109-020-02015-5] [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: 07/08/2020] [Revised: 11/15/2020] [Accepted: 11/20/2020] [Indexed: 12/28/2022]
Abstract
Although gastric cancer (GC) is one of the most common cancers with high incidence and mortality rates, its pathogenesis is still not elucidated. GC carcinogenesis is complicated and involved in the activation of oncoproteins and inactivation of tumor suppressors. The ubiquitin-proteasome system (UPS) is crucial for protein degradation and regulation of physiological and pathological processes. E3 ubiquitin ligases are pivotal enzymes in UPS, containing various subfamily proteins. Previous studies report that some E3 ligases, including SKP2, CUL1, and MDM2, act as oncoproteins in GC carcinogenesis. On the other hand, FBXW7, FBXL5, FBXO31, RNF43, and RNF180 exert as tumor suppressors in GC carcinogenesis. Moreover, E3 ligases modulate cell growth, cell apoptosis, and cell cycle; thus, it is complicated to confer cisplatin resistance/sensitivity in GC cells. The intrinsic and acquired cisplatin resistance limits its clinical application against GC. In this review, we explore oncogenic and tumor suppressive roles of E3 ligases in GC carcinogenesis and focus on the effects of E3 ligases on cisplatin resistance in GC cells, which will provide novel therapeutic targets for GC therapy, especially for cisplatin-resistant patients.
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Affiliation(s)
- Huizhen Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Yida Lu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Mingliang Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Youliang Wu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Xiaodong Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Yongxiang Li
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
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Dai D, Zhou B, Xu W, Jin H, Wang X. CHFR Promoter Hypermethylation Is Associated with Gastric Cancer and Plays a Protective Role in Gastric Cancer Process. J Cancer 2019; 10:949-956. [PMID: 30854101 PMCID: PMC6400794 DOI: 10.7150/jca.27224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022] Open
Abstract
Background: Chromosomally unstable tumors account for 50% of gastric cancer. CHFR plays a role in controlling chromosomal instability and its inactivation will eventually lead to tumorigenesis. In addition to genetic deletion, DNA methylation could silence the expression of many cancer-related genes including CHFR. Its methylation was found to be associated with the initiation and progression of gastric cancer. Methods: We performed a meta-analysis involving methylation analyses of CHFR promoter in gastric cancer. Nineteen studies with 1,249 tumor tissues and 745 normal tissues had been included in current study. Results: We found that CHFR methylation was significantly higher in gastric cancer (studies numbers = 15, cases/controls = 862/745, odds ratio (OR) = 7.46, 95% confidence index (95% CI) = 4.99-11.14). Methylation array data was also obtained from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas network (TCGA). There were 7 out of 13 CHFR methylation probes target to the same CpG island region (hg19, 131973620-131975130) showed the CHFR methylation was higher in gastric cancers than normal controls. Eight probes showed CHFR promoter hypermethylation was associated with longer overall survival of gastric cancer patients (Hazard Ratio < 1). Conclusions: The CHFR promoter hypermethylation was associated with gastric cancer and played a protective role in gastric cancer process. Its methylation could be a potential biomarker for the diagnosis and prognosis of gastric cancer.
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Affiliation(s)
- Dongjun Dai
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Bingluo Zhou
- Laboratory of Cancer Biology, Key Lab of Biotherapy, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Wenxia Xu
- Laboratory of Cancer Biology, Key Lab of Biotherapy, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Key Lab of Biotherapy, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Xian Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
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Ding Y, Lian HF, Du Y. Clinicopathological significance of CHFR promoter methylation in gastric cancer: a meta-analysis. Oncotarget 2017. [PMID: 29515792 PMCID: PMC5839373 DOI: 10.18632/oncotarget.23394] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The mitotic checkpoint gene (CHFR) (Checkpoint with Forkhead-associated and Ring finger domains is a G2 phase/mitosis checkpoint and tumor-suppressor gene. Recent studies have reported the relationship of CHFR promoter methylation with clinicopathological significance of gastric cancer. However, the results remain unclear due to small size of sample. We pooled 15 studies including 827 gastric cancer patients and conducted a meta-analysis to investigate the clinicopathological significance of CHFR promoter methylation in gastric cancer. Our data revealed that the frequency of CHFR promoter methylation was higher in gastric cancer than in normal gastric tissue, Odd Ratio (OR) was 10.12 with 95% CI 5.17–19.79, p < 0.00001. Additionally, the rate of CHFR promoter methylation was significantly increased in high grade of gastric cancer compared to low grade, OR was 1.64 with 95% CI 1.00–2.68, p = 0.05. CHFR methylation was significantly associated with the positive lymph node metastasis, OR was 1.56 with 95% CI 1.05–2.32, p = 0.03. We concluded that CHFR could serve as a biomarker for diagnosis of gastric cancer, and a drug target for development of gene therapy in gastric cancer. CHFR promoter methylation is associated with tumor poor differentiation and lymph node metastasis.
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Affiliation(s)
- Yong Ding
- School of Basic Medical Science, Henan University, Kaifeng, 475004, China
| | - Hai-Feng Lian
- Department of Gastroenterology, Affiliated Hospital of Binzhou Medical College, Binzhou, 256600, China
| | - Yaowu Du
- Laboratory for Nanomedicine, School of Basic Medical Science, Henan University, Kaifeng, 475004, China
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Shi H, Wang X, Wang J, Pan J, Liu J, Ye B. Association between CHFR gene hypermethylation and gastric cancer risk: a meta-analysis. Onco Targets Ther 2016; 9:7409-7414. [PMID: 27994471 PMCID: PMC5153312 DOI: 10.2147/ott.s118070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The association between the hypermethylation of CHFR gene and gastric cancer risk has been investigated by a number of studies. However, the sample size of the majority of these studies was very small. To get a more a convincing conclusion, here we performed a meta-analysis of the previously published studies to assess the association between CHFR methylation and the risk of gastric cancer. METHODS Eligible studies were identified by searching the MEDLINE/PubMed, Embase, and Web of Science databases before May 2016 without any language restriction. The strength of the association was estimated by odds ratio with its 95% confidence interval (CI). RESULTS Totally 1,399 samples, including 758 gastric cancer cases and 641 controls, from 13 studies were included in the present meta-analysis. Compared with non-cancer controls, the pooled OR of CHFR methylation in gastric cancer patients was 9.08 (95% CI: 6.40-12.88, P<0.001), suggesting that the methylation of CHFR was significantly associated with increased risk of gastric cancer. Similar results were observed when subgroup analyses were performed stratified by country, ethnicity, and methylation testing methods. CONCLUSION Our meta-analysis showed a strong positive correlation between CHFR methylation and risk of gastric cancer, suggesting that CHFR methylation might be a promising biomarker for the diagnosis of gastric cancer.
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Affiliation(s)
- Hua Shi
- Department of Gastroenterology, Lishui Central Hospital, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, People's Republic of China
| | - Xiaojing Wang
- Department of Gastroenterology, Lishui Central Hospital, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, People's Republic of China
| | - Jianbo Wang
- Department of Gastroenterology, Lishui Central Hospital, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, People's Republic of China
| | - Jundi Pan
- Department of Gastroenterology, Lishui Central Hospital, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, People's Republic of China
| | - Junwei Liu
- Department of Gastroenterology, Lishui Central Hospital, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, People's Republic of China
| | - Bin Ye
- Department of Gastroenterology, Lishui Central Hospital, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, People's Republic of China
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Liu Z, Zhou J, Gu L, Deng D. Significant impact of amount of PCR input templates on various PCR-based DNA methylation analysis and countermeasure. Oncotarget 2016; 7:56447-56455. [PMID: 27487147 PMCID: PMC5302926 DOI: 10.18632/oncotarget.10906] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/20/2016] [Indexed: 12/21/2022] Open
Abstract
Methylation changes of CpG islands can be determined using PCR-based assays. However, the exact impact of the amount of input templates (TAIT) on DNA methylation analysis has not been previously recognized. Using COL2A1 gene as an input reference, TAIT difference between human tissues with methylation-positive and -negative detection was calculated for two representative genes GFRA1 and P16. Results revealed that TAIT in GFRA1 methylation-positive frozen samples (n = 332) was significantly higher than the methylation-negative ones (n = 44) (P < 0.001). Similar difference was found in P16 methylation analysis. The TAIT-related effect was also observed in methylation-specific PCR (MSP) and denatured high performance liquid chromatography (DHPLC) analysis. Further study showed that the minimum TAIT for a successful MethyLight PCR reaction should be ≥ 9.4 ng (CtCOL2A1 ≤ 29.3), when the cutoff value of the methylated-GFRA1 proportion for methylation-positive detection was set at 1.6%. After TAIT of the methylation non-informative frozen samples (n = 94; CtCOL2A1 > 29.3) was increased above the minimum TAIT, the methylation-positive rate increased from 72.3% to 95.7% for GFRA1 and 26.6% to 54.3% for P16, respectively (Ps < 0.001). Similar results were observed in the FFPE samples. In conclusion, TAIT critically affects results of various PCR-based DNA methylation analyses. Characterization of the minimum TAIT for target CpG islands is essential to avoid false-negative results.
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Affiliation(s)
- Zhaojun Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Haidian District, Beijing, 100142, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Haidian District, Beijing, 100142, China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Haidian District, Beijing, 100142, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Haidian District, Beijing, 100142, China
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Krause L, Nones K, Loffler KA, Nancarrow D, Oey H, Tang YH, Wayte NJ, Patch AM, Patel K, Brosda S, Manning S, Lampe G, Clouston A, Thomas J, Stoye J, Hussey DJ, Watson DI, Lord RV, Phillips WA, Gotley D, Smithers BM, Whiteman DC, Hayward NK, Grimmond SM, Waddell N, Barbour AP. Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma. Carcinogenesis 2016; 37:356-365. [PMID: 26905591 PMCID: PMC4806711 DOI: 10.1093/carcin/bgw018] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/21/2015] [Accepted: 01/13/2016] [Indexed: 12/11/2022] Open
Abstract
The incidence of esophageal adenocarcinoma (EAC) has risen significantly over recent decades. Although survival has improved, cure rates remain poor, with <20% of patients surviving 5 years. This is the first study to explore methylome, transcriptome and ENCODE data to characterize the role of methylation in EAC. We investigate the genome-wide methylation profile of 250 samples including 125 EAC, 19 Barrett's esophagus (BE), 85 squamous esophagus and 21 normal stomach. Transcriptome data of 70 samples (48 EAC, 4 BE and 18 squamous esophagus) were used to identify changes in methylation associated with gene expression. BE and EAC showed similar methylation profiles, which differed from squamous tissue. Hypermethylated sites in EAC and BE were mainly located in CpG-rich promoters. A total of 18575 CpG sites associated with 5538 genes were differentially methylated, 63% of these genes showed significant correlation between methylation and mRNA expression levels. Pathways involved in tumorigenesis including cell adhesion, TGF and WNT signaling showed enrichment for genes aberrantly methylated. Genes involved in chromosomal segregation and spindle formation were aberrantly methylated. Given the recent evidence that chromothripsis may be a driver mechanism in EAC, the role of epigenetic perturbation of these pathways should be further investigated. The methylation profiles revealed two EAC subtypes, one associated with widespread CpG island hypermethylation overlapping H3K27me3 marks and binding sites of the Polycomb proteins. These subtypes were supported by an independent set of 89 esophageal cancer samples. The most hypermethylated tumors showed worse patient survival.
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Affiliation(s)
- Lutz Krause
- Diamantina Institute, Translational Research Institute, The University of Queensland, Woolloongabba, Brisbane, Queensland 4102, Australia, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, Queensland 4006, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, Queensland 4006, Australia, Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia
| | - Kelly A Loffler
- Surgical Oncology Group, School of Medicine, The University of Queensland, Translational Research Institute at the Princess Alexandra Hospital, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Derek Nancarrow
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, Queensland 4006, Australia
| | - Harald Oey
- Diamantina Institute, Translational Research Institute, The University of Queensland, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Yue Hang Tang
- Surgical Oncology Group, School of Medicine, The University of Queensland, Translational Research Institute at the Princess Alexandra Hospital, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Nicola J Wayte
- Surgical Oncology Group, School of Medicine, The University of Queensland, Translational Research Institute at the Princess Alexandra Hospital, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Ann Marie Patch
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, Queensland 4006, Australia, Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia
| | - Kalpana Patel
- Surgical Oncology Group, School of Medicine, The University of Queensland, Translational Research Institute at the Princess Alexandra Hospital, Woolloongabba, Brisbane, Queensland 4102, Australia, Mater Medical Research Institute, Level 3 Aubigny Place, Raymond Terrace, Brisbane, Queensland 4101, Australia
| | - Sandra Brosda
- Diamantina Institute, Translational Research Institute, The University of Queensland, Woolloongabba, Brisbane, Queensland 4102, Australia, Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Suzanne Manning
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia
| | - Guy Lampe
- Department of Anatomical Pathology, Princess Alexandra Hospital, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Andrew Clouston
- School of Medicine, Centre for Liver Disease Research, The University of Queensland, 1/49 Butterfield Street, Herston, Brisbane, Queensland 4006, Australia
| | - Janine Thomas
- Upper GI Research Unit, Division of Surgery, Princess Alexandra Hospital, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Jens Stoye
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Damian J Hussey
- Department of Surgery, Flinders Medical Centre, Flinders University, Bedford Park, South Australia 5042, Australia
| | - David I Watson
- Department of Surgery, Flinders Medical Centre, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Reginald V Lord
- St. Vincent's Centre for Applied Medical Research, Sydney, New South Wales 2011, Australia, University of Notre Dame, Sydney, New South Wales 2011, Australia, University of New South Wales, Sydney, New South Wales 2011, Australia
| | - Wayne A Phillips
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia, Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - David Gotley
- Department of Surgery, School of Medicine, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, Queensland 4102, Australia and
| | - B Mark Smithers
- Department of Surgery, School of Medicine, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, Queensland 4102, Australia and
| | - David C Whiteman
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, Queensland 4006, Australia
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, Queensland 4006, Australia
| | - Sean M Grimmond
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia, Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow Scotland G61 1BD, UK
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, Queensland 4006, Australia, Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia,
| | - Andrew P Barbour
- Surgical Oncology Group, School of Medicine, The University of Queensland, Translational Research Institute at the Princess Alexandra Hospital, Woolloongabba, Brisbane, Queensland 4102, Australia, Department of Surgery, School of Medicine, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, Queensland 4102, Australia and
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High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing. Mod Pathol 2016; 29:182-93. [PMID: 26769141 DOI: 10.1038/modpathol.2015.144] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/01/2015] [Indexed: 12/12/2022]
Abstract
Gastric cancers are the most frequent gastric malignancy and usually arise in the sequence of Helicobacter pylori-associated chronic gastritis. CpG methylation is a central mechanism of epigenetic gene regulation affecting cancer-related genes, and occurs early in gastric carcinogenesis. DNA samples from non-metaplastic gastric mucosa with variable levels of gastritis (non-metaplastic mucosa), intestinal metaplasia, or gastric cancer were screened with methylation arrays for CpG methylation of cancer-related genes and 30 gene targets were further characterized by high-definition bisulfite next-generation sequencing. In addition, data from The Cancer Genome Atlas were analyzed for correlation of methylation with gene expression. Overall, 13 genes had significantly increased CpG methylation in gastric cancer vs non-metaplastic mucosa (BRINP1, CDH11, CHFR, EPHA5, EPHA7, FGF2, FLI1, GALR1, HS3ST2, PDGFRA, SEZ6L, SGCE, and SNRPN). Further, most of these genes had corresponding reduced expression levels in gastric cancer compared with intestinal metaplasia, including novel hypermethylated genes in gastric cancer (FLI1, GALR1, SGCE, and SNRPN), suggesting that they may regulate neoplastic transformation from non-malignant intestinal metaplasia to cancer. Our data suggest a tumor-suppressor role for FLI1 in gastric cancer, consistent with recently reported data in breast cancer. For the genes with strongest methylation/expression correlation, namely FLI1, the expression was lowest in microsatellite-unstable tumors compared with other gastric cancer molecular subtypes. Importantly, reduced expression of hypermethylated BRINP1 and SGCE was significantly associated with favorable survival in gastric cancer. In summary, we report novel methylation gene targets that may have functional roles in discrete stages of gastric carcinogenesis and may serve as biomarkers for diagnosis and prognosis of gastric cancer.
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