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Dagar G, Kumar R, Yadav KK, Singh M, Pandita TK. Ubiquitination and deubiquitination: Implications on cancer therapy. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194979. [PMID: 37633647 DOI: 10.1016/j.bbagrm.2023.194979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/28/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023]
Abstract
The ubiquitin proteasomal system (UPS) represents a highly regulated protein degradation pathway essential for maintaining cellular homeostasis. This system plays a critical role in several cellular processes, which include DNA damage repair, cell cycle checkpoint control, and immune response regulation. Recently, the UPS has emerged as a promising target for cancer therapeutics due to its involvement in oncogenesis and tumor progression. Here we aim to summarize the key aspects of the UPS and its significance in cancer therapeutics. We begin by elucidating the fundamental components of the UPS, highlighting the role of ubiquitin, E1-E3 ligases, and the proteasome in protein degradation. Furthermore, we discuss the intricate process of ubiquitination and proteasomal degradation, emphasizing the specificity and selectivity achieved through various signaling pathways. The dysregulation of the UPS has been implicated in cancer development and progression. Aberrant ubiquitin-mediated degradation of key regulatory proteins, such as tumor suppressors and oncoproteins, can lead to uncontrolled cell proliferation, evasion of apoptosis, and metastasis. We outline the pivotal role of the UPS in modulating crucial oncogenic pathways, including the regulation of cyclins, transcription factors, Replication stress components and DNA damage response. The increasing recognition of the UPS as a target for cancer therapeutics has spurred the development of small molecules, peptides, and proteasome inhibitors with the potential to restore cellular balance and disrupt tumor growth. We provide an overview of current therapeutic strategies aimed at exploiting the UPS, including the use of proteasome inhibitors, deubiquitinating enzyme inhibitors, and novel E3 ligase modulators. We further discuss novel emerging strategies for the development of next-generation drugs that target proteasome inhibitors. Exploiting the UPS for cancer therapeutics offers promising avenues for developing innovative and effective treatment strategies, providing hope for improved patient outcomes in the fight against cancer.
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Affiliation(s)
- Gunjan Dagar
- Department of Medical Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir 182320, India.
| | - Kamlesh K Yadav
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA; School of Engineering Medicine, Texas A&M University, School of Medicine, Houston, TX 77030, USA.
| | - Mayank Singh
- Department of Medical Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Tej K Pandita
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA.
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Yano N, Fedulov AV. Targeted DNA Demethylation: Vectors, Effectors and Perspectives. Biomedicines 2023; 11:biomedicines11051334. [PMID: 37239005 DOI: 10.3390/biomedicines11051334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Aberrant DNA hypermethylation at regulatory cis-elements of particular genes is seen in a plethora of pathological conditions including cardiovascular, neurological, immunological, gastrointestinal and renal diseases, as well as in cancer, diabetes and others. Thus, approaches for experimental and therapeutic DNA demethylation have a great potential to demonstrate mechanistic importance, and even causality of epigenetic alterations, and may open novel avenues to epigenetic cures. However, existing methods based on DNA methyltransferase inhibitors that elicit genome-wide demethylation are not suitable for treatment of diseases with specific epimutations and provide a limited experimental value. Therefore, gene-specific epigenetic editing is a critical approach for epigenetic re-activation of silenced genes. Site-specific demethylation can be achieved by utilizing sequence-dependent DNA-binding molecules such as zinc finger protein array (ZFA), transcription activator-like effector (TALE) and clustered regularly interspaced short palindromic repeat-associated dead Cas9 (CRISPR/dCas9). Synthetic proteins, where these DNA-binding domains are fused with the DNA demethylases such as ten-eleven translocation (Tet) and thymine DNA glycosylase (TDG) enzymes, successfully induced or enhanced transcriptional responsiveness at targeted loci. However, a number of challenges, including the dependence on transgenesis for delivery of the fusion constructs, remain issues to be solved. In this review, we detail current and potential approaches to gene-specific DNA demethylation as a novel epigenetic editing-based therapeutic strategy.
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Affiliation(s)
- Naohiro Yano
- Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, 593 Eddy Street, Providence, RI 02903, USA
| | - Alexey V Fedulov
- Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, 593 Eddy Street, Providence, RI 02903, USA
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Kitazawa S, Ohno T, Haraguchi R, Kitazawa R. Histochemistry, Cytochemistry and Epigenetics. Acta Histochem Cytochem 2022; 55:1-7. [PMID: 35444348 PMCID: PMC8913277 DOI: 10.1267/ahc.21-00095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/27/2021] [Indexed: 12/23/2022] Open
Abstract
Over the past few decades, many researchers have individually identified tumor-related genes, and have accumulated information on their basic research in a database. With the development of technology that can comprehensively test the expression status within a short time, oncogene panel testing has become attainable. On the other hand, changes in gene expression that do not depend on changes in base sequences, that is, epigenetics, or more comprehensively, epigenomes, are also highly involved in the development and progression of disease. Oncogene panel tests tend to focus on DNA base mutations such as point mutations, deletions, duplications, and chimera formation. Elucidation leads to correct interpretation of diseases and treatment choices, and we are in an era where integrated understanding of the genome and epigenome is indispensable. In this review, we make every effort to cover a wide range of knowledge, including data on histone protein modification, non-coding (nc)RNA and DNA methylation, and recent application trials for demonstrating epigenetic alterations in histologic and cytologic specimens. We hope this review will help marshal the knowledge accumulated by researchers involved in genomic and epigenomic studies.
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Affiliation(s)
- Sohei Kitazawa
- Department of Molecular Pathology, Ehime University Graduate School of Medicine
| | - Teruyuki Ohno
- Division of Diagnostic Pathology, Ehime University Hospital
| | - Ryuma Haraguchi
- Department of Molecular Pathology, Ehime University Graduate School of Medicine
| | - Riko Kitazawa
- Division of Diagnostic Pathology, Ehime University Hospital
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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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CHFR regulates chemoresistance in triple-negative breast cancer through destabilizing ZEB1. Cell Death Dis 2021; 12:820. [PMID: 34462429 PMCID: PMC8405615 DOI: 10.1038/s41419-021-04114-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/30/2021] [Accepted: 08/20/2021] [Indexed: 12/31/2022]
Abstract
Failures to treat triple-negative breast cancer (TNBC) are mainly due to chemoresistance or radioresistance. We and others previously discovered that zinc finger E-box-binding homeobox 1 (ZEB1) is a massive driver causing these resistance. However, how to dynamically modulate the intrinsic expression of ZEB1 during cell cycle progression is elusive. Here integrated affinity purification combined with mass spectrometry and TCGA analysis identify a cell cycle-related E3 ubiquitin ligase, checkpoint with forkhead and ring finger domains (CHFR), as a key negative regulator of ZEB1 in TNBC. Functional studies reveal that CHFR associates with and decreases ZEB1 expression in a ubiquitinating-dependent manner and that CHFR represses fatty acid synthase (FASN) expression through ZEB1, leading to significant cell death of TNBC under chemotherapy. Intriguingly, a small-molecule inhibitor of HDAC under clinical trial, Trichostatin A (TSA), increases the expression of CHFR independent of histone acetylation, thereby destabilizes ZEB1 and sensitizes the resistant TNBC cells to conventional chemotherapy. In patients with basal-like breast cancers, CHFR levels significantly correlates with survival. These findings suggest the therapeutic potential for targeting CHFR-ZEB1 signaling in resistant malignant breast cancers.
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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Baretti M, Karunasena E, Zahurak M, Walker R, Zhao Y, Pisanic TR, Wang TH, Greten TF, Duffy AG, Gootjes E, Meijer G, Verheul HMW, Ahuja N, Herman JG, Azad NS. A phase 2 trial of gemcitabine and docetaxel in patients with metastatic colorectal adenocarcinoma with methylated checkpoint with forkhead and ring finger domain promoter and/or microsatellite instability phenotype. Clin Transl Sci 2021; 14:954-963. [PMID: 33811727 PMCID: PMC8212722 DOI: 10.1111/cts.12960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/17/2020] [Accepted: 11/22/2020] [Indexed: 12/13/2022] Open
Abstract
Abstract We previously reported CHFR methylation in a subset of colorectal cancer (CRC; ∼30%) with high concordance with microsatellite instability (MSI). We also showed that CHFR methylation predicted for sensitivity to docetaxel, whereas the MSI‐high phenotypes were sensitive to gemcitabine. We hypothesized that this subset of patients with CRC would be selectively sensitive to gemcitabine and docetaxel. We enrolled a Phase 2 trial of gemcitabine and docetaxel in patients with MSI‐high and/or CHFR methylated CRC. The primary objective was Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 response rate. Enrolled patients were treated with gemcitabine 800 mg/m2 on days 1 and 8 and docetaxel 70 mg/m2 on day 8 of each 21‐day cycle. A total of 6 patients with CHFR‐methylated, MSI‐high CRC were enrolled from September 2012 to August 2016. The study was closed in September of 2017 due to poor accrual prior to reaching the first interim assessment of response rate, which would have occurred at 10 patients. No RECIST criteria tumor responses were observed, with 3 patients (50%) having stable disease as best response, 1 lasting more than 9 months. Median progression‐free survival (PFS) was 1.79 months (95% confidence interval [CI] = 1.28, not available [NA]) and median overall survival (OS) was 15.67 months (95% CI = 4.24, NA). Common grade 3 toxicities were lymphopenia (67%), leukopenia (33%), and anemia (33%). Although negative, this study establishes a proof‐of‐concept for the implementation of epigenetic biomarkers (CHFR methylation/MSI) as inclusion criteria in a prospective clinical trial to optimize combinatorial strategies in the era of personalized medicine. Study Highlights WHAT IS THE CURRENT KNOWLEDGE ON THE TOPIC?
CHFR silencing via DNA methylation has been suggested to be predictive of taxane sensitivity in diverse tumors. The frequent association of CHFR methylation with microsatellite instability (MSI) suggested a possible combination therapy with gemcitabine, because the MSI phenotype may result in sensitivity to nucleoside analogues.
WHAT QUESTION DID THIS STUDY ADDRESS?
We hypothesized that metastatic colorectal cancer (mCRC), which have CHFR methylation and MSI phenotype were sensitive to gemcitabine and docetaxel, and have designed this Phase 2 trial in biomarker‐selected mCRC to test this prediction.
WHAT DOES THIS STUDY ADD TO OUR KNOWLEDGE?
The study enrolled a molecularly defined subgroup of patients with colorectal cancer (CRC) and showed that the combination is safe in this population. Nevertheless, due to poor enrollment and early termination, no conclusions on the primary and secondary end points could be made.
HOW MIGHT THIS CHANGE CLINICAL PHARMACOLOGY OR TRANSLATIONAL SCIENCE?
This study supports the feasibility of implementing DNA methylation markers in a prospective clinical trial and further efforts toward their application as predictive biomarkers for therapeutic agents in defined subsets of patients are warranted.
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Affiliation(s)
- Marina Baretti
- Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Enusha Karunasena
- Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Marianna Zahurak
- Department of Oncology, Biostatistics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rosalind Walker
- Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Yang Zhao
- Johns Hopkins Institute for NanoBioTechnology, Baltimore, Maryland, USA
| | - Thomas R Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Baltimore, Maryland, USA
| | - Tza-Huei Wang
- Johns Hopkins Institute for NanoBioTechnology, Baltimore, Maryland, USA
| | - Tim F Greten
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Austin G Duffy
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Elske Gootjes
- Amsterdam University Medical Center, location VUMC, Amsterdam and Radboud UMC, Nijmegen, The Netherlands
| | - Gerrit Meijer
- Amsterdam University Medical Center, location VUMC, Amsterdam and Radboud UMC, Nijmegen, The Netherlands
| | - Henk M W Verheul
- Amsterdam University Medical Center, location VUMC, Amsterdam and Radboud UMC, Nijmegen, The Netherlands
| | - Nita Ahuja
- Oncology and Pathology, Smilow Cancer Hospital, Yale University School of Medicine, New Haven, Connecticut, USA
| | - James G Herman
- Department of Medicine, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Nilofer S Azad
- Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
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Use of DNA methylation profiling in translational oncology. Semin Cancer Biol 2020; 83:523-535. [PMID: 33352265 DOI: 10.1016/j.semcancer.2020.12.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023]
Abstract
DNA methylation is a highly regulated process that has a critical role in human development and homeostatic control of the cell. The number of genes affected by anomalous DNA methylation in cancer-associated pathways is swiftly accelerating and with the advancement of molecular technologies, new layers of complexity are opening up and refining our strategies to combat cancer. DNA methylation profiling is an essential facet to understanding malignant transformation and is becoming an increasingly important tool for cancer diagnosis, prognosis and therapy monitoring. In this review, the role of DNA methylation in normal cellular function is discussed, as well as how epigenetic aberrations override normal cellular cues that lead to tumor initiation and propagation. The review also focuses on the latest advancements in DNA methylation profiling as a biomarker for early cancer detection, predicting patient clinical outcomes and responses to treatment and provides new insights into epigenetic-based therapy in clinical oncology.
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Wu C, Wu Z, Tian B. Five gene signatures were identified in the prediction of overall survival in resectable pancreatic cancer. BMC Surg 2020; 20:207. [PMID: 32943033 PMCID: PMC7499920 DOI: 10.1186/s12893-020-00856-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/26/2020] [Indexed: 02/07/2023] Open
Abstract
Background Although genes have been previously detected in pancreatic cancer (PC), aberrant genes that play roles in resectable pancreatic cancer should be further assessed. Methods Messenger RNA samples and clinicopathological data corrected with PC were downloaded from The Cancer Genome Atlas (TCGA). Resectable PC patients were randomly divided into a primary set and a validation set. Univariable Cox regression analysis, lasso-penalized Cox regression analysis, and multivariable Cox analysis were implemented to distinguish survival-related genes (SRGs). A risk score based on the SRGs was calculated by univariable Cox regression analysis. A genomic-clinical nomogram was established by integrating the risk score and clinicopathological data to predict overall survival (OS) in resectable PC. Results Five survival-related genes (AADAC, DEF8, HIST1H1C, MET, and CHFR) were significantly correlated with OS in resectable PC. The resectable PC patients, based on risk score, were sorted into a high-risk group that showed considerably unfavorable OS (p < 0.001) than the low-risk group, in both the primary set and the validation set. The concordance index (C-index) was calculated to evaluate the predictive performance of the nomogram were respectively in the primary set [0.696 (0.608–0.784)] and the validation set [0.682 (0.606–0.758)]. Additionally, gene set enrichment Analysis discovered several meaningful enriched pathways. Conclusion Our study identified five prognostic gene biomarkers for OS prediction and which facilitate postoperative molecular target therapy for the resectable PC, especially the nomic-clinical nomogram which may be used as an effective model for the postoperative OS evaluation and also an optimal therapeutic tool for the resectable PC.
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Affiliation(s)
- Chao Wu
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Zuowei Wu
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Bole Tian
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China.
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Li Y, Shi Y, Wang X, Yu X, Wu C, Ding S. Silencing of CHFR Sensitizes Gastric Carcinoma to PARP Inhibitor Treatment. Transl Oncol 2019; 13:113-121. [PMID: 31812083 PMCID: PMC6909066 DOI: 10.1016/j.tranon.2019.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 01/11/2023] Open
Abstract
CHFR is a tumor suppressor that not only recognizes poly(ADP-ribosylation) (PARylation) signals at the sites of DNA damage but also is downregulated in many types of cancer. However, the underlying mechanism linking its role in PARylation-mediated DNA damage repair and tumor suppression is unclear. Here, we examined a panel of gastric cancer cell lines as well as primary tissue samples from gastric cancer patients, and found that CHFR expression was silenced by DNA hypermethylation in gastric cancer including 38.46% of primary gastric cancers. DNMT1 was associated with aberrant methylation of CHFR, and the expression of CHFR was restored by DNMT1 inhibitor 5-aza-2-deoxycytidine (5-aza-CdR) treatment. Moreover, we found that loss of CHFR abolished DNA damage repair and sensitized gastric tumor cells to PARP inhibitor treatment. Thus, our study reveals a potential therapeutic approach for treating gastric cancer with PARP inhibitor and lacking CHFR can serve as a biomarker for predicting the efficacy of PARP inhibitor on the gastric tumor treatment in future.
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Affiliation(s)
- Yuan Li
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 10091, China
| | - Yanyan Shi
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
| | - Xiumin Wang
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, PR China
| | - Xiaochun Yu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 E. Duarte Rd, Duarte, CA, 91010, USA.
| | - Chen Wu
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, PR China.
| | - Shigang Ding
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 10091, China.
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Pan-Cancer Landscape of Aberrant DNA Methylation across Human Tumors. Cell Rep 2019; 25:1066-1080.e8. [PMID: 30355485 DOI: 10.1016/j.celrep.2018.09.082] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 08/29/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022] Open
Abstract
The discovery of cancer-associated alterations has primarily focused on genetic variants. Nonetheless, altered epigenomes contribute to deregulate transcription and promote oncogenic pathways. Here, we designed an algorithmic approach (RESET) to identify aberrant DNA methylation and associated cis-transcriptional changes across >6,000 human tumors. Tumors exhibiting mutations of chromatin remodeling factors and Wnt signaling displayed DNA methylation instability, characterized by numerous hyper- and hypo-methylated loci. Most silenced and enhanced genes coalesced in specific pathways including apoptosis, DNA repair, and cell metabolism. Cancer-germline antigens (CG) were frequently epigenomically enhanced and their expression correlated with response to anti-PD-1, but not anti-CTLA4, in skin melanoma. Finally, we demonstrated the potential of our approach to explore DNA methylation changes in pediatric tumors, which frequently lack genetic drivers and exhibit epigenomic modifications. Our results provide a pan-cancer map of aberrant DNA methylation to inform functional and therapeutic studies.
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Cha Y, Kim SY, Yeo HY, Baek JY, Choi MK, Jung KH, Dong SM, Chang HJ. Association of CHFR Promoter Methylation with Treatment Outcomes of Irinotecan-Based Chemotherapy in Metastatic Colorectal Cancer. Neoplasia 2018; 21:146-155. [PMID: 30562637 PMCID: PMC6297269 DOI: 10.1016/j.neo.2018.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/27/2018] [Indexed: 02/08/2023] Open
Abstract
Aberrant promoter methylation plays a vital role in colorectal carcinogenesis. However, its role in treatment responses is unclear, especially for metastatic disease. Here, we investigated the association between promoter methylation and treatment outcomes of irinotecan-based chemotherapy in 102 patients with metastatic colorectal cancer. Promoter methylation was examined by methylation-specific polymerase chain reaction for three loci (CHFR, WRN, and SULF2) associated with chemotherapy response and five CpG island methylator phenotype (CIMP)–specific markers (CACNA1G, IGF2, NEUROG1, RUNX3, and SOCS1). Association between CHFR methylation and in vitro sensitivity to irinotecan was also evaluated. Promoter methylation of CHFR, WRN, and SULF2 was identified in 16 (15.7%), 24 (23.5%), and 33 (32.4%) patients, respectively. CIMP status was positive in 22 (21.6%) patients. CHFR methylation was associated with a significantly longer time to progression (TTP) (median: 8.77 vs. 4.43 months, P = .019), with trends favoring higher overall survival (OS) (median: 22.83 vs. 20.17 months, P = .300) and response rates (31.3% vs. 17.4%, P = .300). For patients with unmethylated CHFR, TTP (median: 5.60 vs. 3.53, P = .020) and OS (median: 20.57 vs. 9.23, P = .006) were significantly different according to CIMP status. Colorectal cancer cell lines with CHFR methylation demonstrated increased sensitivity to irinotecan. Both CHFR overexpression and combination with 5-aza-2′-deoxycytidine reversed irinotecan sensitivity in CHFR-methylated cell lines, whereas CHFR knockdown in unmethylated cells restored sensitivity to irinotecan. These data suggest that CHFR methylation may be associated with favorable treatment outcomes of irinotecan-based chemotherapy in patients with metastatic colorectal cancer.
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Affiliation(s)
- Yongjun Cha
- Center for Colorectal Cancer, National Cancer Center, Goyang, Korea; Precision Medicine Branch, Division of Precision Medicine, Research Institute of National Cancer Center, Goyang, Korea
| | - Sun Young Kim
- Center for Colorectal Cancer, National Cancer Center, Goyang, Korea
| | - Hyun Yang Yeo
- Precision Medicine Branch, Division of Precision Medicine, Research Institute of National Cancer Center, Goyang, Korea
| | - Ji Yeon Baek
- Center for Colorectal Cancer, National Cancer Center, Goyang, Korea; Translational Research Branch, Division of Translational Science, Research Institute of National Cancer Center, Goyang, Korea
| | - Moon Ki Choi
- Center for Colorectal Cancer, National Cancer Center, Goyang, Korea
| | - Kyung Hae Jung
- Center for Colorectal Cancer, National Cancer Center, Goyang, Korea
| | - Seung Myung Dong
- Molecular Epidemiology Branch, Division of Cancer Epidemiology and Prevention, Research Institute of National Cancer Center, Goyang, Korea.
| | - Hee Jin Chang
- Center for Colorectal Cancer, National Cancer Center, Goyang, Korea; Precision Medicine Branch, Division of Precision Medicine, Research Institute of National Cancer Center, Goyang, Korea.
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13
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The inhibition of UBC13 expression and blockage of the DNMT1-CHFR-Aurora A pathway contribute to paclitaxel resistance in ovarian cancer. Cell Death Dis 2018; 9:93. [PMID: 29367628 PMCID: PMC5833742 DOI: 10.1038/s41419-017-0137-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 09/03/2017] [Accepted: 11/08/2017] [Indexed: 12/14/2022]
Abstract
Paclitaxel is widely used as a first-line chemotherapeutic drug for patients with ovarian cancer and other solid cancers, but drug resistance occurs frequently, resulting in ovarian cancer still presenting as the highest lethality among all gynecological tumors. Here, using DIGE quantitative proteomics, we identified UBC13 as down-regulated in paclitaxel-resistant ovarian cancer cells, and it was further revealed by immunohistochemical staining that UBC13 low-expression was associated with poorer prognosis and shorter survival of the patients. Through gene function experiments, we found that paclitaxel exposure induced UBC13 down-regulation, and the enforced change in UBC13 expression altered the sensitivity to paclitaxel. Meanwhile, the reduction of UBC13 increased DNMT1 levels by attenuating its ubiquitination, and the up-regulated DNMT1 enhanced the CHFR promoter DNA methylation levels, leading to a reduction of CHFR expression, and an increased in the levels of Aurora A. Our findings revealed a novel function for UBC13 in regulating paclitaxel sensitivity through a DNMT1-CHFR-Aurora A pathway in ovarian cancer cells. UBC13 could potentially be employed as a therapeutic molecular drug for reversing paclitaxel resistance in ovarian cancer patients.
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14
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Zhang D, Xu XL, Li F, Sun HC, Cui YQ, Liu S, Xu PY. Upregulation of the checkpoint protein CHFR is associated with tumor suppression in pancreatic cancers. Oncol Lett 2018; 14:8042-8050. [PMID: 29344247 PMCID: PMC5755226 DOI: 10.3892/ol.2017.7239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/27/2017] [Indexed: 12/24/2022] Open
Abstract
The checkpoint with forkhead-associated (FHA) domain and RING-finger (CHFR) protein was identified as a cell cycle checkpoint protein and E3 ubiquitin ligase. In the present study, the potential functions of CHFR in pancreatic cancer were investigated. CHFR expression was measured in five pancreatic cancer cell lines by reverse transcription- quantitative polymerase chain reaction and western blotting. Capan-1 cells stably expressing CHFR were established by lentiviral vector transfection. Cell proliferation was assessed using Cell Counting Kit-8, and cell migration/invasion assay was determined using Transwell assays. Cell cycle and apoptosis induced by gemcitabine or docetaxel were evaluated using flow cytometry. CHFR expression levels were also evaluated in pancreatic ductal adenocarcinoma (PDAC) tumor samples as well as adjacent non-tumor tissues by immunohistochemistry. The significance of CHFR expression was determined, with respect to clinicopathological features and overall survival. Overexpression of CHFR in Capan-1 cells led to a decreased proliferative rate and reduced cell migration and invasion abilities. Results also indicated an increase in G1 phase cells in Capan-1 cells overexpressing CHFR. Docetaxel-induced apoptosis was inhibited in Capan-1 cells with CHFR-overexpression. A reduction in CHFR expression was detected in 51.9% of patients with PDAC, which significantly correlated with later T-stage. The results show CHFR functions as a tumor suppressor in pancreatic cancer, suggests its potential role in controlling the cell cycle of pancreatic cancer cells; however, CHFR overexpression is not a favorable factor in apoptosis induced by docetaxel.
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Affiliation(s)
- Di Zhang
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, P.R. China
| | - Xiao-Lan Xu
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Fei Li
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, P.R. China
| | - Hai-Chen Sun
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, P.R. China
| | - Ye-Qing Cui
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, P.R. China
| | - Shuang Liu
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, P.R. China
| | - Ping-Yong Xu
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China
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15
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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: 0.7] [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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16
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Wang C, Ma W, Wei R, Zhang X, Shen N, Shang L, E L, Wang Y, Gao L, Li X, Wang B, Zhang Y, Du A. Clinicopathological significance of CHFR methylation in non-small cell lung cancer: a systematic review and meta-analysis. Oncotarget 2017; 8:109732-109739. [PMID: 29312643 PMCID: PMC5752556 DOI: 10.18632/oncotarget.21962] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/25/2017] [Indexed: 11/25/2022] Open
Abstract
Checkpoint with Forkhead-associated and Ring finger domains (CHFR) is a G2/M checkpoint and tumor-suppressor gene. Recent publications showed the correlation of CHFR promoter methylation with clinicopathological significance of non-small cell lung cancer (NSCLC), however, the results remain inconsistent. The aim of this study is to investigate the Clinicopathological significance of CHFR promoter methylation in NSCLC with a meta-analysis. A total of nine studies were included in the meta-analysis that 816 patients were involved. Our data indicated that the frequency of CHFR promoter methylation was higher in NSCLC than in normal lung tissue, Odd Ratios (OR) was 9.92 with 95% corresponding confidence interval (CI) 2.17-45.23, p = 0.003. Further subgroup analysis revealed that CHFR promoter was more frequently methylated in squamous cell carcinoma (SCC) than in adenocarcinoma (ADC), OR was 4.46 with 95% CI 1.65-12.05, p = 0.003, suggesting the mechanism of SCC pathogenesis is different from ADC. Notably, CHFR promoter methylation was correlated with smoking behavior in NSCLC. In conclusion, CHFR could be a biomarker for diagnosis of NSCLC, and a promising drug target for development of gene therapy in SCC. CHFR promoter methylation is potentially associated with poor overall survival, additional studies need to be carried out for confirmation in future.
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Affiliation(s)
- Chen Wang
- Department of Pathology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P.R. China
| | - Wenxia Ma
- Department of Pathology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P.R. China
| | - Rong Wei
- Department of Pathology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P.R. China
| | - Xiaoqin Zhang
- Department of Pathology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P.R. China
| | - Ningning Shen
- Department of Pathology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P.R. China
| | - Lifang Shang
- Department of Pathology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P.R. China
| | - Li E
- Department of Pathology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P.R. China
| | - Ying Wang
- Department of Pathology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P.R. China
| | - Lifang Gao
- Department of Pathology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P.R. China
| | - Xin Li
- Department of Pathology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P.R. China
| | - Bin Wang
- Department of Pathology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P.R. China
| | - Yaping Zhang
- Department of Pathology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P.R. China
| | - Aiping Du
- Department of Pathology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P.R. China
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17
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Luebeck EG, Curtius K, Hazelton WD, Maden S, Yu M, Thota PN, Patil DT, Chak A, Willis JE, Grady WM. Identification of a key role of widespread epigenetic drift in Barrett's esophagus and esophageal adenocarcinoma. Clin Epigenetics 2017; 9:113. [PMID: 29046735 PMCID: PMC5644061 DOI: 10.1186/s13148-017-0409-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/24/2017] [Indexed: 12/13/2022] Open
Abstract
Background Recent studies have identified age-related changes in DNA methylation patterns in normal and cancer tissues in a process that is called epigenetic drift. However, the evolving patterns, functional consequences, and dynamics of epigenetic drift during carcinogenesis remain largely unexplored. Here we analyze the evolution of epigenetic drift patterns during progression from normal squamous esophagus tissue to Barrett’s esophagus (BE) to esophageal adenocarcinoma (EAC) using 173 tissue samples from 100 (nonfamilial) BE patients, along with publically available datasets including The Cancer Genome Atlas (TCGA). Results Our analysis reveals extensive methylomic drift between normal squamous esophagus and BE tissues in nonprogressed BE patients, with differential drift affecting 4024 (24%) of 16,984 normally hypomethylated cytosine-guanine dinucleotides (CpGs) occurring in CpG islands. The majority (63%) of islands that include drift CpGs are associated with gene promoter regions. Island CpGs that drift have stronger pairwise correlations than static islands, reflecting collective drift consistent with processive DNA methylation maintenance. Individual BE tissues are extremely heterogeneous in their distribution of methylomic drift and encompass unimodal low-drift to bimodal high-drift patterns, reflective of differences in BE tissue age. Further analysis of longitudinally collected biopsy samples from 20 BE patients confirm the time-dependent evolution of these drift patterns. Drift patterns in EAC are similar to those in BE, but frequently exhibit enhanced bimodality and advanced mode drift. To better understand the observed drift patterns, we developed a multicellular stochastic model at the CpG island level. Importantly, we find that nonlinear feedback in the model between mean island methylation and CpG methylation rates is able to explain the widely heterogeneous collective drift patterns. Using matched gene expression and DNA methylation data in EAC from TCGA and other publically available data, we also find that advanced methylomic drift is correlated with significant transcriptional repression of ~ 200 genes in important regulatory and developmental pathways, including several checkpoint and tumor suppressor-like genes. Conclusions Taken together, our findings suggest that epigenetic drift evolution acts to significantly reduce the expression of developmental genes that may alter tissue characteristics and improve functional adaptation during BE to EAC progression. Electronic supplementary material The online version of this article (10.1186/s13148-017-0409-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- E Georg Luebeck
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Kit Curtius
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - William D Hazelton
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Sean Maden
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Prashanthi N Thota
- Department of Gastroenterology, Digestive Disease & Surgery Institute, Cleveland Clinic, Cleveland, OH 44195 USA
| | - Deepa T Patil
- Department of Pathology, Cleveland Clinic, Cleveland, OH 44195 USA
| | - Amitabh Chak
- University Hospitals Case Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - Joseph E Willis
- University Hospitals Case Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA.,Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195 USA
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18
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Abstract
The epigenetic phenomena refer to heritable changes in gene expression other than those in the DNA sequence, such as DNA methylation and histone modifications. Major research progress in the last few years has provided further proof that environmental factors, including diet and nutrition, can influence physiologic and pathologic processes through epigenetic alterations, which in turn influence gene expression. This influence is termed nutritional epigenetics, and one prominent example is the regulation of gene transcription by vitamin A through interaction to its nuclear receptor. Vitamin A is critical throughout life. Together with its derivatives, it regulates diverse processes including reproduction, embryogenesis, vision, growth, cellular differentiation and proliferation, maintenance of epithelial cellular integrity and immune function. Here we review the epigenetic role of vitamin A in cancer, stem cells differentiation, proliferation, and immunity. The data presented here show that retinoic acid is a potent agent capable of inducing alterations in epigenetic modifications that produce various effects on the phenotype. Medical benefits of vitamin A as an epigenetic modulator, especially with respect to its chronic use as nutritional supplement, should rely on our further understanding of its epigenetic effects during health and disease, as well as through different generations.
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Affiliation(s)
- Shimrit Bar-El Dadon
- a The Robert H. Smith Faculty of Agricultural, Food, and Nutritional Sciences, The Hebrew University of Jerusalem , Rehovot , Israel
| | - Ram Reifen
- a The Robert H. Smith Faculty of Agricultural, Food, and Nutritional Sciences, The Hebrew University of Jerusalem , Rehovot , Israel
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19
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Sun Z, Liu J, Jing H, Dong SX, Wu J. The diagnostic and prognostic value of CHFR hypermethylation in colorectal cancer, a meta-analysis and literature review. Oncotarget 2017; 8:89142-89148. [PMID: 29179506 PMCID: PMC5687676 DOI: 10.18632/oncotarget.19408] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/24/2017] [Indexed: 12/19/2022] Open
Abstract
The Checkpoint with Forkhead-associated and Ring finger domains (CHFR) is a mitotic checkpoint and tumor-suppressor gene, its loss contributes tumorigenesis of epithelial cancers including colorectal carcinoma (CRC). The diagnostic and prognostic value of CHFR promoter hypermethylation in CRC remains unclear. This study aimed to conduct a meta-analysis and literature review and investigate clinicopathological significance of CHFR promoter hypermethylation in CRC. The following online database were used: PubMed, EMBASE, and Web of Science up to March 2017. Odds Ratios (OR) and Hazard Ratios (HR) with 95% corresponding confidence intervals (CIs) were calculated. A total of seven relevant articles were available for meta-analysis which included 966 patients. The frequency of CHFR promoter hypermethylation significantly increased in CRC compared to normal colorectal mucosa tissue, pooled OR was 8.35, p < 0.00001. CHFR promoter hypermethylation was not significantly correlated to stage, OR was 1.16, p = 0.63. However, CHFR promoter hypermethylation was more frequently observed in CRC with positive lymph nodes metastasis than CRC with negative lymph nodes metastasis, OR was 0.46, p = 0.03. Additionally CHFR promoter hypermethylation was significantly related to poor overall survival in patients with CRC, HR was 0.62, p = 0.008. Based on these results, tumor CHFR promoter hypermethylation is not only a diagnostic biomarker for CRC, but also a prognostic marker. CHFR promoter hypermethylation is significantly associated with worse overall survival in patients with CRC. Our data suggested that CHFR could be a potential drug target for development of demethylation treatment for patients with CRC.
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Affiliation(s)
- Zhulei Sun
- Department of Pathology, Huaihe Hospital, Henan University, 8 Bao Bei Lu, GuLou Qu, Kaifeng 475000, China
| | - Juncai Liu
- Department of Radiotherapy, Huaihe Hospital, Henan University, Kaifeng 475000, China
| | - Hong Jing
- Department of Pathology, Huaihe Hospital, Henan University, 8 Bao Bei Lu, GuLou Qu, Kaifeng 475000, China
| | - Shu-Xiao Dong
- Department of Gastrointestinal Surgery, Linyi People's Hospital, Linyi 276001, Shandong, China
| | - Jiang Wu
- Department of Pathology, Huaihe Hospital, Henan University, 8 Bao Bei Lu, GuLou Qu, Kaifeng 475000, China
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20
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Clark DJ, Mao L. Understanding the Surgical Margin: A Molecular Assessment. Oral Maxillofac Surg Clin North Am 2017; 29:245-258. [PMID: 28528739 DOI: 10.1016/j.coms.2017.03.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The inclusion of molecular characteristics into surgical margin analysis may not only yield a more sensitive and accurate assessment of the cells in these margins, but may also provide insight into their impacts on patients' postoperative prognosis. This concept of the "molecular surgical margin" is advantageous, as it integrates recent advances in our understanding of head and neck carcinogenesis, while also retaining the established methodology of histopathology. This multidisciplinary approach may facilitate the development of a uniform criterion for defining the surgical margin, which will likely result in a reduced recurrence rate and improved overall patient survival.
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Affiliation(s)
- David J Clark
- Department of Pathology, Johns Hopkins Medical Institute, 400 North Broadway, Baltimore, MD 21231, USA
| | - Li Mao
- Department of Oncology and Diagnostic Sciences, University of Maryland School of Dentistry, 650 West Baltimore Street, Baltimore, MD 21201, USA.
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21
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Takane K, Akagi K, Fukuyo M, Yagi K, Takayama T, Kaneda A. DNA methylation epigenotype and clinical features of NRAS-mutation(+) colorectal cancer. Cancer Med 2017; 6:1023-1035. [PMID: 28378457 PMCID: PMC5430106 DOI: 10.1002/cam4.1061] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/15/2017] [Accepted: 02/26/2017] [Indexed: 12/28/2022] Open
Abstract
Sporadic colorectal cancer (CRC) is classified into several molecular subtypes. We previously established two groups of DNA methylation markers through genome‐wide DNA methylation analysis to classify CRC into distinct subgroups: high‐, intermediate‐, and low‐methylation epigenotypes (HME, IME, and LME, respectively). HME CRC, also called CpG island methylator phenotype (CIMP)‐high CRC, shows methylation of both Group 1 markers (CIMP markers) and Group 2 markers, while IME/CIMP‐low CRC shows methylation of Group 2, but not of Group 1 markers, and LME CRC shows no methylation of either Group 1 or Group 2 markers. While BRAF‐ and KRAS‐mutation(+) CRC strongly correlated with HME and IME, respectively, clinicopathological features of NRAS‐mutation(+) CRC, including association with DNA methylation, remain unclear. To characterize NRAS‐mutation(+) CRC, the methylation levels of 19 methylation marker genes (6 Group 1 and 13 Group 2) were analyzed in 61 NRAS‐mutation(+) and 144 NRAS‐mutation(−) CRC cases by pyrosequencing, and their correlation with clinicopathological features was investigated. Different from KRAS‐mutation(+) CRC,NRAS‐mutation(+) CRC significantly correlated with LME. NRAS‐mutation(+) CRC showed significantly better prognosis than KRAS‐mutation(+) CRC (P = 3 × 10−4). NRAS‐mutation(+) CRC preferentially occurred in elder patients (P = 0.02) and at the distal colon (P = 0.006), showed significantly less lymph vessel invasion (P = 0.002), and correlated with LME (P = 8 × 10−5). DNA methylation significantly accumulated at the proximal colon. NRAS‐mutation(+) CRC may constitute a different subgroup from KRAS‐mutation(+) CRC, showing significant correlation with LME, older age, distal colon, and relatively better prognosis.
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Affiliation(s)
- Kiyoko Takane
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Digestive Surgery and Pathology, Nihon University School of Medicine, Tokyo, Japan
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Koichi Yagi
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tadatoshi Takayama
- Department of Digestive Surgery and Pathology, Nihon University School of Medicine, Tokyo, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
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22
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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: 0.9] [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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23
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CHFR negatively regulates SIRT1 activity upon oxidative stress. Sci Rep 2016; 6:37578. [PMID: 27883020 PMCID: PMC5121620 DOI: 10.1038/srep37578] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 11/01/2016] [Indexed: 11/20/2022] Open
Abstract
SIRT1, the NAD+-dependent protein deacetylase, controls cell-cycle progression and apoptosis by suppressing p53 tumour suppressor. Although SIRT1 is known to be phosphorylated by JNK1 upon oxidative stress and subsequently down-regulated, it still remains elusive how SIRT1 stability and activity are controlled. Here, we have unveiled that CHFR functions as an E3 Ub-ligase of SIRT1, responsible for its proteasomal degradation under oxidative stress conditions. CHFR interacts with and destabilizes SIRT1 by ubiquitylation and subsequent proteolysis. Such CHFR-mediated SIRT1 inhibition leads to the increase of p53 acetylation and its target gene transcription. Notably, CHFR facilitates SIRT1 destabilization when SIRT1 is phosphorylated by JNK1 upon oxidative stress, followed by prominent apoptotic cell death. Meanwhile, JNK inhibitor prevents SIRT1 phosphorylation, leading to elevated SIRT1 protein levels even in the presence of H2O2. Taken together, our results indicate that CHFR plays a crucial role in the cellular stress response pathway by controlling the stability and function of SIRT1.
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Costa G, Barra V, Lentini L, Cilluffo D, Di Leonardo A. DNA demethylation caused by 5-Aza-2'-deoxycytidine induces mitotic alterations and aneuploidy. Oncotarget 2016; 7:3726-39. [PMID: 26771138 PMCID: PMC4826165 DOI: 10.18632/oncotarget.6897] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 12/18/2015] [Indexed: 01/19/2023] Open
Abstract
Aneuploidy, the unbalanced number of chromosomes in a cell, is considered a prevalent form of genetic instability and is largely acknowledged as a condition implicated in tumorigenesis. Epigenetic alterations like DNA hypomethylation have been correlated with cancer initiation/progression. Furthermore, a growing body of evidence suggests the involvement of epigenome-wide disruption as a cause of global DNA hypomethylation in aneuploidy generation. Here, we report that the DNA hypomethylating drug 5-aza-2′-deoxycytidine (DAC), affects the correct ploidy of nearly diploid HCT-116 human cells by altering the methylation pattern of the chromosomes. Specifically, we show that a DAC-induced reduction of 5-Methyl Cytosine at the pericentromeric region of chromosomes correlates with aneuploidy and mitotic defects. Our results suggest that DNA hypomethylation leads to aneuploidy by altering the DNA methylation landscape at the centromere that is necessary to ensure proper chromosomes segregation by recruiting the proteins necessary to build up a functional kinetochore.
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Affiliation(s)
- Giuseppe Costa
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Palermo, Italy
| | - Viviana Barra
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Palermo, Italy
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Palermo, Italy
| | - Danilo Cilluffo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Palermo, Italy
| | - Aldo Di Leonardo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Palermo, Italy.,Centro di OncoBiologia Sperimentale (COBS), Palermo, Italy
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Arsenic trioxide induces cell cycle arrest and alters DNA methylation patterns of cell cycle regulatory genes in colorectal cancer cells. Life Sci 2016; 167:67-77. [PMID: 27769816 DOI: 10.1016/j.lfs.2016.10.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/06/2016] [Accepted: 10/17/2016] [Indexed: 12/16/2022]
Abstract
AIMS Cell cycle dysregulation is important in tumorigenesis. Transcriptional silencing of cell cycle regulatory genes, due to DNA methylation, is a common epigenetic event in malignancies. As2O3 has been shown to induce cell cycle arrest and also to be a potential hypomethylating agent. Our study aimed to investigate DNA methylation patterns of cell cycle regulatory genes promoters, the effects of Arsenic trioxide (As2O3) on the methylated genes and cell cycle distribution in colorectal cancer (CRC) cell lines. MAIN METHODS The methylation-specific PCR (MSP) and/or restriction enzyme-based methods were used to study the promoter methylation patterns of 24 cell cycle regulatory genes in CRC cell lines. Gene expression level and cell cycle distribution were determined by Real-time PCR and flow cytometric analyses, respectively. KEY FINDINGS Our methylation analysis indicated that only promoters of RBL1 (p107), CHFR and p16 genes were aberrantly methylated in three cell lines. As2O3 significantly decreased DNA methylation in promoter regions of these genes and restored their expression. We found that As2O3 significantly reduced the expression of DNA methyltransferase 1 (DNMT1) and increased arsenic methyltransferase (AS3MT). Furthermore, As2O3 altered transcriptional activity of several unmethylated cell cycle regulatory genes including cyclin B1, E1, D1, GADD45A and p21. Cell cycle flow cytometry analysis showed As2O3 induced G2/M arrest in all three cell lines. SIGNIFICANCE These data suggest that demethylation and alteration in the expression level of the cell cycle-related genes may be possible mechanisms in As2O3-induced cell cycle arrest in colorectal cancer cells.
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Defining, distinguishing and detecting the contribution of heterogeneous methylation to cancer heterogeneity. Semin Cell Dev Biol 2016; 64:5-17. [PMID: 27582426 DOI: 10.1016/j.semcdb.2016.08.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 08/24/2016] [Indexed: 01/07/2023]
Abstract
DNA methylation is a fundamental means of epigenetic gene regulation that occurs in virtually all cell types. In many higher organisms, including humans, it plays vital roles in cell differentiation and homeostatic maintenance of cell phenotype. The control of DNA methylation has traditionally been attributed to a highly coordinated, linear process, whose dysregulation has been associated with numerous pathologies including cancer, where it occurs early in, and even prior to, the development of neoplastic tissues. Recent experimental evidence has demonstrated that, contrary to prevailing paradigms, methylation patterns are actually maintained through inexact, dynamic processes. These processes normally result in minor stochastic differences between cells that accumulate with age. However, various factors, including cancer itself, can lead to substantial differences in intercellular methylation patterns, viz. methylation heterogeneity. Advancements in molecular biology techniques are just now beginning to allow insight into how this heterogeneity contributes to clonal evolution and overall cancer heterogeneity. In the current review, we begin by presenting a didactic overview of how the basal bimodal methylome is established and maintained. We then provide a synopsis of some of the factors that lead to the accrual of heterogeneous methylation and how this heterogeneity may lead to gene silencing and impact the development of cancerous phenotypes. Lastly, we highlight currently available methylation assessment techniques and discuss their suitability to the study of heterogeneous methylation.
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Sakaguchi H, Muramatsu H, Okuno Y, Makishima H, Xu Y, Furukawa-Hibi Y, Wang X, Narita A, Yoshida K, Shiraishi Y, Doisaki S, Yoshida N, Hama A, Takahashi Y, Yamada K, Miyano S, Ogawa S, Maciejewski JP, Kojima S. Aberrant DNA Methylation Is Associated with a Poor Outcome in Juvenile Myelomonocytic Leukemia. PLoS One 2015; 10:e0145394. [PMID: 26720758 PMCID: PMC4697810 DOI: 10.1371/journal.pone.0145394] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/03/2015] [Indexed: 12/18/2022] Open
Abstract
Juvenile myelomonocytic leukemia (JMML), an overlap of myelodysplastic / myeloproliferative neoplasm, is an intractable pediatric myeloid neoplasm. Epigenetic regulation of transcription, particularly by CpG methylation, plays an important role in tumor progression, mainly by repressing tumor-suppressor genes. To clarify the clinical importance of aberrant DNA methylation, we studied the hypermethylation status of 16 target genes in the genomes of 92 patients with JMML by bisulfite conversion and the pryosequencing technique. Among 16 candidate genes, BMP4, CALCA, CDKN2A, and RARB exhibited significant hypermethylation in 72% (67/92) of patients. Based on the number of hypermethylated genes, patients were stratified into three cohorts based on an aberrant methylation score (AMS) of 0, 1–2, or 3–4. In the AMS 0 cohort, the 5-year overall survival (OS) and transplantation-free survival (TFS) were good (69% and 76%, respectively). In the AMS 1–2 cohort, the 5-year OS was comparable to that in the AMS 0 cohort (68%), whereas TFS was poor (6%). In the AMS 3–4 cohort, 5-year OS and TFS were markedly low (8% and 0%, respectively). Epigenetic analysis provides helpful information for clinicians to select treatment strategies for patients with JMML. For patients with AMS 3–4 in whom hematopoietic stem cell transplantation does not improve the prognosis, alternative therapies, including DNA methyltransferase inhibitors and new molecular-targeting agents, should be established as treatment options.
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Affiliation(s)
- Hirotoshi Sakaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Hematology and Oncology, Children’s Medical Center, Japanese Red Cross Nagoya First Hospital, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideki Makishima
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yinyan Xu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoko Furukawa-Hibi
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Xinan Wang
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Sayoko Doisaki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nao Yoshida
- Department of Hematology and Oncology, Children’s Medical Center, Japanese Red Cross Nagoya First Hospital, Nagoya, Japan
| | - Asahito Hama
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kiyofumi Yamada
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoru Miyano
- Laboratory of DNA information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jaroslaw P. Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- * E-mail:
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Derks S, Cleven AHG, Melotte V, Smits KM, Brandes JC, Azad N, van Criekinge W, de Bruïne AP, Herman JG, van Engeland M. Emerging evidence for CHFR as a cancer biomarker: from tumor biology to precision medicine. Cancer Metastasis Rev 2015; 33:161-71. [PMID: 24375389 PMCID: PMC3988518 DOI: 10.1007/s10555-013-9462-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Novel insights in the biology of cancer have switched the paradigm of a “one-size-fits-all” cancer treatment to an individualized biology-driven treatment approach. In recent years, a diversity of biomarkers and targeted therapies has been discovered. Although these examples accentuate the promise of personalized cancer treatment, for most cancers and cancer subgroups no biomarkers and effective targeted therapy are available. The great majority of patients still receive unselected standard therapies with no use of their individual molecular characteristics. Better knowledge about the underlying tumor biology will lead the way toward personalized cancer treatment. In this review, we summarize the evidence for a promising cancer biomarker: checkpoint with forkhead and ring finger domains (CHFR). CHFR is a mitotic checkpoint and tumor suppressor gene, which is inactivated in a diverse group of solid malignancies, mostly by promoter CpG island methylation. CHFR inactivation has shown to be an indicator of poor prognosis and sensitivity to taxane-based chemotherapy. Here we summarize the current knowledge of altered CHFR expression in cancer, the impact on tumor biology and implications for personalized cancer treatment.
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Affiliation(s)
- Sarah Derks
- Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Arjen H. G. Cleven
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Veerle Melotte
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Kim M. Smits
- Department of Radiation Oncology (MAASTRO Clinic), GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Johann C. Brandes
- Department of Hematology and Oncology, Atlanta VA Medical Center Winship Cancer Institute, Emory University, Atlanta, GA USA
| | - Nilofer Azad
- Department of Gastrointestinal Oncology, The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Wim van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
- MDxHealth, Irvine, CA USA
| | - Adriaan P. de Bruïne
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - James G. Herman
- Department of Tumor Biology, The Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Manon van Engeland
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
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Omura K, Uehara T, Morikawa Y, Hayashi H, Mitsumori K, Minami K, Kanki M, Yamada H, Ono A, Urushidani T. Comprehensive analysis of DNA methylation and gene expression of rat liver in a 2-stage hepatocarcinogenesis model. J Toxicol Sci 2015; 39:837-48. [PMID: 25374375 DOI: 10.2131/jts.39.837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Recent studies have shown that epigenetic alterations correlate with carcinogenesis in various tissues. Identification of these alterations might help characterize the early stages of carcinogenesis. We comprehensively analyzed DNA methylation and gene expression in livers obtained from rats exposed to nitrosodiethylamine (DEN) followed by a promoter of hepatic carcinogenesis, phenobarbital (PB). The combination of DEN and PB induced marked increases in number and area of glutathione S-transferase-placental form (GST-P)-positive foci in the liver. In the liver of rats that received 30 mg/kg of DEN, pathway analysis revealed alterations of common genes in terms of gene expression and DNA methylation, and that these alterations were related to immune responses. Hierarchical clustering analysis of the expression of common genes from public data obtained through the Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system (TG-GATEs) showed that carcinogenic compounds clustered together. MBD-seq and GeneChip analysis indicated that major histocompatibility complex class Ib gene RT1-CE5, which has an important role in antigen presentation, was hypomethylated around the promoter region and specifically induced in the livers of DEN-treated rats. Further, immunohistochemical analysis indicated that the co-localization of GST-P and protein homologous to RT1-CE5 was present at the foci of some regions. These results suggest that common genes were altered in terms of both DNA methylation and expression in livers, with preneoplastic foci indicating carcinogenic potential, and that immune responses are involved in early carcinogenesis. In conclusion, the present study identified a specific profile of DNA methylation and gene expression in livers with preneoplastic foci. Early epigenetic perturbations of immune responses might correlate with the early stages of hepatocarcinogenesis.
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Affiliation(s)
- Ko Omura
- Drug Safety Research Laboratories, Astellas Pharma Inc
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Perdereau D, Cailliau K, Browaeys-Poly E, Lescuyer A, Carré N, Benhamed F, Goenaga D, Burnol AF. Insulin-induced cell division is controlled by the adaptor Grb14 in a Chfr-dependent manner. Cell Signal 2015; 27:798-806. [PMID: 25578860 DOI: 10.1016/j.cellsig.2015.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/03/2015] [Indexed: 01/02/2023]
Abstract
Beyond its key role in the control of energy metabolism, insulin is also an important regulator of cell division and neoplasia. However, the molecular events involved in insulin-driven cell proliferation are not fully elucidated. Here, we show that the ubiquitin ligase Chfr, a checkpoint protein involved in G2/M transition, is a new effector involved in the control of insulin-induced cell proliferation. Chfr is identified as a partner of the molecular adapter Grb14, an inhibitor of insulin signalling. Using mammalian cell lines and the Xenopus oocyte as a model of G2/M transition, we demonstrate that Chfr potentiates the inhibitory effect of Grb14 on insulin-induced cell division. Insulin stimulates Chfr binding to the T220 residue of Grb14. Both Chfr binding site and Grb14 C-ter BPS-SH2 domain, mediating IR binding and inhibition, are required to prevent insulin-induced cell division. Targeted mutagenesis revealed that Chfr ligase activity and phosphorylation of its T39 residue, a target of Akt, are required to potentiate Grb14 inhibitory activity. In the presence of insulin, the binding of Chfr to Grb14 activates its ligase activity, leading to Aurora A and Polo-like kinase degradation and blocking cell division. Collectively, our results show that Chfr and Grb14 collaborate in a negative feedback loop controlling insulin-stimulated cell division.
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Affiliation(s)
- Dominique Perdereau
- INSERM, U1016, Institut Cochin, Paris, France; CNRS, UMR8104, Paris, France; Université Paris Descartes, Sorbonne Paris Cité; 24, Rue du Faubourg Saint Jacques, Paris 75014, France
| | - Katia Cailliau
- Laboratoire de Régulation des Signaux de Division, Université de Lille 1, UE 4479, IFR 147, Villeneuve d'Ascq 59655, France
| | - Edith Browaeys-Poly
- Laboratoire de Régulation des Signaux de Division, Université de Lille 1, UE 4479, IFR 147, Villeneuve d'Ascq 59655, France
| | - Arlette Lescuyer
- Laboratoire de Régulation des Signaux de Division, Université de Lille 1, UE 4479, IFR 147, Villeneuve d'Ascq 59655, France
| | - Nadège Carré
- INSERM, U1016, Institut Cochin, Paris, France; CNRS, UMR8104, Paris, France; Université Paris Descartes, Sorbonne Paris Cité; 24, Rue du Faubourg Saint Jacques, Paris 75014, France
| | - Fadila Benhamed
- INSERM, U1016, Institut Cochin, Paris, France; CNRS, UMR8104, Paris, France; Université Paris Descartes, Sorbonne Paris Cité; 24, Rue du Faubourg Saint Jacques, Paris 75014, France
| | - Diana Goenaga
- INSERM, U1016, Institut Cochin, Paris, France; CNRS, UMR8104, Paris, France; Université Paris Descartes, Sorbonne Paris Cité; 24, Rue du Faubourg Saint Jacques, Paris 75014, France
| | - Anne-Françoise Burnol
- INSERM, U1016, Institut Cochin, Paris, France; CNRS, UMR8104, Paris, France; Université Paris Descartes, Sorbonne Paris Cité; 24, Rue du Faubourg Saint Jacques, Paris 75014, France.
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Brinkmann K, Schell M, Hoppe T, Kashkar H. Regulation of the DNA damage response by ubiquitin conjugation. Front Genet 2015; 6:98. [PMID: 25806049 PMCID: PMC4354423 DOI: 10.3389/fgene.2015.00098] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/23/2015] [Indexed: 12/12/2022] Open
Abstract
In response to DNA damage, cells activate a highly conserved and complex kinase-based signaling network, commonly referred to as the DNA damage response (DDR), to safeguard genomic integrity. The DDR consists of a set of tightly regulated events, including detection of DNA damage, accumulation of DNA repair factors at the site of damage, and finally physical repair of the lesion. Upon overwhelming damage the DDR provokes detrimental cellular actions by involving the apoptotic machinery and inducing a coordinated demise of the damaged cells (DNA damage-induced apoptosis, DDIA). These diverse actions involve transcriptional activation of several genes that govern the DDR. Moreover, recent observations highlighted the role of ubiquitylation in orchestrating the DDR, providing a dynamic cellular regulatory circuit helping to guarantee genomic stability and cellular homeostasis (Popovic et al., 2014). One of the hallmarks of human cancer is genomic instability (Hanahan and Weinberg, 2011). Not surprisingly, deregulation of the DDR can lead to human diseases, including cancer, and can induce resistance to genotoxic anti-cancer therapy (Lord and Ashworth, 2012). Here, we summarize the role of ubiquitin-signaling in the DDR with special emphasis on its role in cancer and highlight the therapeutic value of the ubiquitin-conjugation machinery as a target in anti-cancer treatment strategy.
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Affiliation(s)
- Kerstin Brinkmann
- Centre for Molecular Medicine Cologne and Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of CologneCologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University Hospital of CologneCologne, Germany
| | - Michael Schell
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University Hospital of CologneCologne, Germany
- Institute for Genetics, University of CologneCologne, Germany
| | - Thorsten Hoppe
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University Hospital of CologneCologne, Germany
- Institute for Genetics, University of CologneCologne, Germany
| | - Hamid Kashkar
- Centre for Molecular Medicine Cologne and Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of CologneCologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University Hospital of CologneCologne, Germany
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Song A, Ye J, Zhang K, Yu H, Gao Y, Wang H, Sun L, Xing X, Yang K, Zhao M. Aberrant expression of the CHFR prophase checkpoint gene in human B-cell non-Hodgkin lymphoma. Leuk Res 2015; 39:536-43. [PMID: 25798877 DOI: 10.1016/j.leukres.2015.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 01/22/2015] [Accepted: 02/15/2015] [Indexed: 10/23/2022]
Abstract
Checkpoint with FHA and Ring Finger (CHFR) is a checkpoint protein that reportedly initiates a cell cycle delay in response to microtubule stress during prophase in mitosis, which has become an interesting target for understanding cancer pathogenesis. Recently, aberrant methylation of the CHFR gene associated with gene silencing has been reported in several cancers. In the present study, we examined the expression of CHFR in B-cell non-Hodgkin lymphoma (B-NHL) in vitro and in vivo. Our results showed that the expression level of CHFR mRNA and protein was reduced in B-NHL tissue samples and B cell lines. Furthermore, CHFR methylation was detected in 39 of 122 B-NHL patients, which was not found in noncancerous reactive hyperplasia of lymph node (RH) tissues. CHFR methylation correlated with the reduced expression of CHFR, high International Prognostic Index (IPI) scores and later pathologic Ann Arbor stages of B-NHL. Treatment with demethylation reagent, 5-Aza-dC, could eliminate the hypermethylation of CHFR, enhance CHFR expression and cell apoptosis and inhibit the cell proliferation of Raji cells, which could be induced by high expression of CHFR in Raji cells. Our results indicated that aberrant methylation of CHFR may be associated with the pathogenesis, progression for B-NHL, which might be a novel molecular marker as prognosis and treatment for B-NHL.
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Affiliation(s)
- Aiqin Song
- Department of Pediatric Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China.
| | - Junli Ye
- Department of Pathophysiology, Medical College of Qingdao University, Qingdao, Shangdong 266021, China
| | - Kunpeng Zhang
- Department of Pediatric Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Hongsheng Yu
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Yanhua Gao
- Department of Hematology, Qingdao Women and Children's Medical Care Center, Qingdao, 266011, China
| | - Hongfang Wang
- Department of Pediatric Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Lirong Sun
- Department of Pediatric Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Xiaoming Xing
- Department of Pathology, Affiliated Hospital of Qingdao University, Qingdao, Shangdong 266003, China
| | - Kun Yang
- Center Laboratory, Affiliated Hospital of Qingdao University, Qingdao, Shangdong 266003, China
| | - Min Zhao
- Department of Pediatric Hematology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
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p16INK4A and p14ARF gene promoter hypermethylation as prognostic biomarker in oral and oropharyngeal squamous cell carcinoma: a review. DISEASE MARKERS 2014; 2014:260549. [PMID: 24803719 PMCID: PMC3997957 DOI: 10.1155/2014/260549] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/17/2014] [Indexed: 12/18/2022]
Abstract
Head and neck squamous cell carcinoma is a heterogeneous group of tumors with each subtype having a distinct histopathological and molecular profile. Most tumors share, to some extent, the same multistep carcinogenic pathways, which include a wide variety of genetic and epigenetic changes. Epigenetic alterations represent all changes in gene expression patterns that do not alter the actual DNA sequence. Recently, it has become clear that silencing of cancer related genes is not exclusively a result of genetic changes such as mutations or deletions, but it can also be regulated on epigenetic level, mostly by means of gene promoter hypermethylation. Results from recent studies have demonstrated that DNA methylation patterns contain tumor-type-specific signatures, which could serve as biomarkers for clinical outcome in the near future. The topic of this review discusses gene promoter hypermethylation in oral and oropharyngeal squamous cell carcinoma (OSCC). The main objective is to analyse the available data on gene promoter hypermethylation of the cell cycle regulatory proteins p16INK4A and p14ARF and to investigate their clinical significance as novel biomarkers in OSCC. Hypermethylation of both genes seems to possess predictive properties for several clinicopathological outcomes. We conclude that the methylation status of p16INK4A is definitely a promising candidate biomarker for predicting clinical outcome of OSCC, especially for recurrence-free survival.
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Chopra A, Anderson A, Giardina C. Novel piperazine-based compounds inhibit microtubule dynamics and sensitize colon cancer cells to tumor necrosis factor-induced apoptosis. J Biol Chem 2013; 289:2978-91. [PMID: 24338023 DOI: 10.1074/jbc.m113.499319] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We recently identified a series of mitotically acting piperazine-based compounds that potently increase the sensitivity of colon cancer cells to apoptotic ligands. Here we describe a structure-activity relationship study on this compound class and identify a highly active derivative ((4-(3-chlorophenyl)piperazin-1-yl)(2-ethoxyphenyl)methanone), referred to as AK301, the activity of which is governed by the positioning of functional groups on the phenyl and benzoyl rings. AK301 induced mitotic arrest in HT29 human colon cancer cells with an ED50 of ≈115 nm. Although AK301 inhibited growth of normal lung fibroblast cells, mitotic arrest was more pronounced in the colon cancer cells (50% versus 10%). Cells arrested by AK301 showed the formation of multiple microtubule organizing centers with Aurora kinase A and γ-tubulin. Employing in vitro and in vivo assays, tubulin polymerization was found to be slowed (but not abolished) by AK301. In silico molecular docking suggests that AK301 binds to the colchicine-binding domain on β-tubulin, but in a novel orientation. Cells arrested by AK301 expressed elevated levels of TNFR1 on their surface and more readily activated caspases-8, -9, and -3 in the presence of TNF. Relative to other microtubule destabilizers, AK301 was the most active TNF-sensitizing agent and also stimulated Fas- and TRAIL-induced apoptosis. In summary, we report a new class of mitosis-targeting agents that effectively sensitizes cancer cells to apoptotic ligands. These compounds should help illuminate the role of microtubules in regulating apoptotic ligand sensitivity and may ultimately be useful for developing agents that augment the anti-cancer activities of the immune response.
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Shinde SR, Gangula NR, Kavela S, Pandey V, Maddika S. TOPK and PTEN participate in CHFR mediated mitotic checkpoint. Cell Signal 2013; 25:2511-7. [PMID: 24012691 PMCID: PMC3819987 DOI: 10.1016/j.cellsig.2013.08.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 08/24/2013] [Indexed: 01/15/2023]
Abstract
Mitotic progression is regulated by co-ordinated action of several proteins and is crucial for the maintenance of genomic stability. CHFR (Check point protein with FHA and RING domains) is an E3 ubiquitin ligase and a checkpoint protein that regulates entry into mitosis. But the molecular players involved in CHFR mediated mitotic checkpoint are not completely understood. In this study, we identified TOPK/PBK, a serine/threonine kinase and PTEN, a lipid phosphatase to play an important role in CHFR mediated mitotic transitions. We demonstrated that CHFR ubiquitinates and regulates TOPK levels, which is essential for its checkpoint function. Moreover, TOPK phosphorylates and inactivates PTEN, which in turn activates Akt that leads to proper G2/M progression. Collectively, our results reveal TOPK and PTEN as new players in CHFR mediated mitotic checkpoint. TOPK is identified as a novel CHFR associated protein. TOPK is a substrate of CHFR. TOPK participates in CHFR mediated mitotic stress check point. PTEN is phosphorylated by TOPK and is required for mitotic entry.
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Affiliation(s)
- Swapnil R Shinde
- Laboratory of Cell Death & Cell Survival, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, India
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CHFR is negatively regulated by SUMOylation-mediated ubiquitylation. Biochem Biophys Res Commun 2013; 433:194-9. [DOI: 10.1016/j.bbrc.2013.02.080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 02/20/2013] [Indexed: 12/30/2022]
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Koga T, Takeshita M, Ijichi K, Yano T, Maehara Y, Sueishi K. CHFR aberrant methylation involves a subset of human lung adenocarcinoma associated with poor clinical outcomes. Hum Pathol 2013; 44:1382-90. [PMID: 23415374 DOI: 10.1016/j.humpath.2012.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 11/26/2012] [Accepted: 11/28/2012] [Indexed: 12/20/2022]
Abstract
Excluding epidermal growth factor receptor (EGFR) mutation, v-Ki-ras2/Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation, and echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) fusion, the genetic alterations involved in lung adenocarcinogenesis, especially those linked to poor clinical outcomes, are still unknown. In this study, we analyzed abnormal checkpoint gene with forkhead-associated domain and ring finger (CHFR) methylation along with the above 3 mutations in 165 lung adenocarcinomas, evaluated the spectrum of each molecular abnormality, and correlated the results with clinical and pathologic variables. Reverse transcription-polymerase chain reaction assay, reverse transcription-polymerase chain reaction followed by direct DNA sequencing, and methylation-specific polymerase chain reaction were performed to detect these 3 mutations and CHFR hypermethylation. The EML4-ALK transcript or CHFR hypermethylation was found in 11 (6.7%) or 16 (10%) adenocarcinomas, respectively, whereas EGFR or KRAS mutation was detected in 48 (29%) or 13 (8%) cases, respectively. EGFR mutations occurred in patients who were negative for both CHFR hypermethylation and KRAS mutation. Among the 4 genetic or epigenetic abnormalities, only CHFR hypermethylation was significantly correlated with poor prognosis and lymphatic vessel invasion (P = .024). Histopathologically, the molecular abnormality that correlated with alveolar-destructive growth was the CHFR hypermethylation rather than the EGFR mutation (P = .03). Our results demonstrate that CHFR hypermethylation maybe one of the molecular abnormalities involved in a subset of lung adenocarcinomas with poor prognoses that might be induced by destructive growth and lymphatic vessel invasion of carcinoma cells. Thus, CHFR abnormality might be pursued as a novel therapeutic target against lung adenocarcinoma without an already-known mutation.
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Affiliation(s)
- Takaomi Koga
- Department of Pathology, Division of Pathophysiological and Experimental Pathology, Graduate School of Medical Sciences, Kyushu University 812-8582, Fukuoka, Japan.
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Pillai RN, Brodie SA, Sica GL, Shaojin Y, Li G, Nickleach DC, Yuan L, Varma VA, Bonta D, Herman JG, Brock MV, Ribeiro MJA, Ramalingam SS, Owonikoko TK, Khuri FR, Brandes JC. CHFR protein expression predicts outcomes to taxane-based first line therapy in metastatic NSCLC. Clin Cancer Res 2013; 19:1603-11. [PMID: 23386692 DOI: 10.1158/1078-0432.ccr-12-2995] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
PURPOSE Currently, there is no clinically validated test for the prediction of response to tubulin-targeting agents in non-small cell lung cancer (NSCLC). Here, we investigated the significance of nuclear expression of the mitotic checkpoint gene checkpoint with forkhead and ringfinger domains (CHFR) as predictor of response and overall survival with taxane-based first-line chemotherapy in advanced stage NSCLC. METHODS We studied a cohort of 41 patients (median age 63 years) with advanced NSCLC treated at the Atlanta VAMC between 1999 and 2010. CHFR expression by immunohistochemistry (score 0-4) was correlated with clinical outcome using chi-square test and Cox proportional models. A cutoff score of "3" was determined by receiver operator characteristics analysis for "low" CHFR expression. Results were validated in an additional 20 patients who received taxane-based chemotherapy at Emory University Hospital and the Atlanta VAMC. RESULTS High expression (score = 4) of CHFR is strongly associated with adverse outcomes: the risk for progressive disease after first-line chemotherapy with carboplatin-paclitaxel was 52% in patients with CHFR-high versus only 19% in those with CHFR-low tumors (P = 0.033). Median overall survival was strongly correlated with CHFR expression status (CHFR low: 9.9 months; CHFR high: 6.2 months; P = 0.002). After multivariate adjustment, reduced CHFR expression remained a powerful predictor of improved overall survival (HR = 0.24; 95% CI, 0.1-0.58%; P = 0.002). In the validation set, low CHFR expression was associated with higher likelihood of clinical benefit (P = 0.03) and improved overall survival (P = 0.038). CONCLUSIONS CHFR expression is a novel predictive marker of response and overall survival in NSCLC patients treated with taxane-containing chemotherapy.
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Affiliation(s)
- Rathi N Pillai
- Department of Hematology and Oncology, Emory University, Atlanta, Georgia 30322, USA
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Kobayashi Y, Banno K, Shimizu T, Ueki A, Tsuji K, Masuda K, Kisu I, Nomura H, Tominaga E, Nagano O, Saya H, Aoki D. Gene expression profile of a newly established choriocarcinoma cell line, iC3-1, compared to existing choriocarcinoma cell lines and normal placenta. Placenta 2013. [DOI: 10.1016/j.placenta.2012.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Giovinazzi S, Morozov VM, Summers MK, Reinhold WC, Ishov AM. USP7 and Daxx regulate mitosis progression and taxane sensitivity by affecting stability of Aurora-A kinase. Cell Death Differ 2013; 20:721-31. [PMID: 23348568 DOI: 10.1038/cdd.2012.169] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A large number of patients are resistant to taxane-based chemotherapy. Functional mitotic checkpoints are essential for taxane sensitivity. Thus, mitotic regulators are potential markers for therapy response and could be targeted for anticancer therapy. In this study, we identified a novel function of ubiquitin (Ub)-specific processing protease-7 (USP7) that interacts and cooperates with protein death domain-associated protein (Daxx) in the regulation of mitosis and taxane resistance. Depletion of USP7 impairs mitotic progression, stabilizes cyclin B and reduces stability of the mitotic E3 Ub ligase, checkpoint with forkhead and Ring-finger (CHFR). Consequently, cells with depleted USP7 accumulate Aurora-A kinase, a CHFR substrate, thus elevating multipolar mitoses. We further show that these effects are independent of the USP7 substrate p53. Thus, USP7 and Daxx are necessary to regulate proper execution of mitosis, partially via regulation of CHFR and Aurora-A kinase stability. Results from colony formation assay, in silico analysis across the NCI60 platform and in breast cancer patients suggest that USP7 levels inversely correlate with response to taxanes, pointing at the USP7 protein as a potential predictive factor for taxane response in cancer patients. In addition, we demonstrated that inhibition of Aurora-A attenuates USP7-mediated taxane resistance, suggesting that combinatorial drug regimens of Taxol and Aurora-A inhibitors may improve the outcome of chemotherapy response in cancer patients resistant to taxane treatment. Finally, our study offers novel insights on USP7 inhibition as cancer therapy.
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Affiliation(s)
- S Giovinazzi
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610, USA
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Colacino JA, Dolinoy DC, Duffy SA, Sartor MA, Chepeha DB, Bradford CR, McHugh JB, Patel DA, Virani S, Walline HM, Bellile E, Terrell JE, Stoerker JA, Taylor JMG, Carey TE, Wolf GT, Rozek LS. Comprehensive analysis of DNA methylation in head and neck squamous cell carcinoma indicates differences by survival and clinicopathologic characteristics. PLoS One 2013; 8:e54742. [PMID: 23358896 PMCID: PMC3554647 DOI: 10.1371/journal.pone.0054742] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 12/14/2012] [Indexed: 01/01/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the eighth most commonly diagnosed cancer in the United States. The risk of developing HNSCC increases with exposure to tobacco, alcohol and infection with human papilloma virus (HPV). HPV-associated HNSCCs have a distinct risk profile and improved prognosis compared to cancers associated with tobacco and alcohol exposure. Epigenetic changes are an important mechanism in carcinogenic progression, but how these changes differ between viral- and chemical-induced cancers remains unknown. CpG methylation at 1505 CpG sites across 807 genes in 68 well-annotated HNSCC tumor samples from the University of Michigan Head and Neck SPORE patient population were quantified using the Illumina Goldengate Methylation Cancer Panel. Unsupervised hierarchical clustering based on methylation identified 6 distinct tumor clusters, which significantly differed by age, HPV status, and three year survival. Weighted linear modeling was used to identify differentially methylated genes based on epidemiological characteristics. Consistent with previous in vitro findings by our group, methylation of sites in the CCNA1 promoter was found to be higher in HPV(+) tumors, which was validated in an additional sample set of 128 tumors. After adjusting for cancer site, stage, age, gender, alcohol consumption, and smoking status, HPV status was found to be a significant predictor for DNA methylation at an additional 11 genes, including CASP8 and SYBL1. These findings provide insight into the epigenetic regulation of viral vs. chemical carcinogenesis and could provide novel targets for development of individualized therapeutic and prevention regimens based on environmental exposures.
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Affiliation(s)
- Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Sonia A. Duffy
- School of Nursing, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Douglas B. Chepeha
- Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Carol R. Bradford
- Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jonathan B. McHugh
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Divya A. Patel
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University, New Haven, Connecticut, United States of America
| | - Shama Virani
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Heather M. Walline
- Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Emily Bellile
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jeffrey E. Terrell
- Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jay A. Stoerker
- Sequenom Center for Molecular Medicine, San Diego, California, United States of America
| | - Jeremy M. G. Taylor
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Thomas E. Carey
- Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Gregory T. Wolf
- Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Laura S. Rozek
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
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SUMOylation negatively regulates the stability of CHFR tumor suppressor. Biochem Biophys Res Commun 2013; 430:213-7. [DOI: 10.1016/j.bbrc.2012.10.111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 10/25/2012] [Indexed: 12/24/2022]
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Liu C, Wu J, Paudyal SC, You Z, Yu X. CHFR is important for the first wave of ubiquitination at DNA damage sites. Nucleic Acids Res 2012; 41:1698-710. [PMID: 23268447 PMCID: PMC3561977 DOI: 10.1093/nar/gks1278] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Protein ubiquitination plays an important role in activating the DNA damage response and maintaining genomic stability. In response to DNA double-strand breaks (DSBs), a ubiquitination cascade occurs at DNA lesions. Here, we show that checkpoint with Forkhead-associated (FHA) and RING finger domain protein (CHFR), an E3 ubiquitin ligase, is recruited to DSBs by poly(ADP-ribose) (PAR). At DSBs, CHFR regulates the first wave of protein ubiquitination. Moreover, CHFR ubiquitinates PAR polymerase 1 (PARP1) and regulates chromatin-associated PARP1 in vivo. Thus, these results demonstrate that CHFR is an important E3 ligase in the early stage of the DNA damage response, which mediates the crosstalk between ubiquitination and poly-ADP-ribosylation.
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Affiliation(s)
- Chao Liu
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Abstract
Knowledge of epigenetic alterations in disease is rapidly increasing owing to the development of genome-wide techniques for their identification. The ever-growing number of genes that show epigenetic alterations in disease emphasizes the crucial role of these epigenetic alterations - particularly DNA methylation - for future diagnosis, prognosis and prediction of response to therapies. This Review focuses on epigenetic profiling, which has started to be of clinical value in cancer and may in the future be extended to other diseases, such as neurological and autoimmune disorders.
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Yasui H, Ishida T, Maruyama R, Nojima M, Ikeda H, Suzuki H, Hayashi T, Shinomura Y, Imai K. Model of translational cancer research in multiple myeloma. Cancer Sci 2012; 103:1907-12. [PMID: 22809142 PMCID: PMC3533800 DOI: 10.1111/j.1349-7006.2012.02384.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Revised: 07/09/2012] [Accepted: 07/11/2012] [Indexed: 11/30/2022] Open
Abstract
Recently, intensive laboratory and preclinical studies have identified and validated therapeutic molecular targets in multiple myeloma (MM). The introduction of novel agents such as the proteasome inhibitor bortezomib and the immunomodulatory drugs thalidomide and lenalidomide, which were rapidly translated from preclinical studies at the Dana-Farber Cancer Institute into clinical trials, has changed the treatment paradigm and markedly extended overall survival; MM has therefore become a remarkable example of translational cancer research in new drug development. In this article, with the aim of determining the key factors underlying success in translational research, we focus on our studies of MM at Dana-Farber Cancer Institute as well as at our institutes. The identification of these key factors will help to promote translational cancer research not only in MM but also in other hematologic malignancies and solid tumors, to develop novel therapies, to overcome drug resistance, and to thereby improve the prognosis of cancer patients. (Cancer Sci, doi: 10.1111/j.1349-7006.2012.02384.x, 2012)
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Affiliation(s)
- Hiroshi Yasui
- First Department of Internal Medicine, Sapporo Medical University, Sapporo, Japan; Department of Regional Health Care and Medicine, Sapporo Medical University, Sapporo, Japan.
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Egeberg DL, Lethan M, Manguso R, Schneider L, Awan A, Jørgensen TS, Byskov AG, Pedersen LB, Christensen ST. Primary cilia and aberrant cell signaling in epithelial ovarian cancer. Cilia 2012; 1:15. [PMID: 23351307 PMCID: PMC3555760 DOI: 10.1186/2046-2530-1-15] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 05/01/2012] [Indexed: 12/14/2022] Open
Abstract
Background Ovarian cancer is the fourth leading cause of cancer-related deaths among women in Denmark, largely due to the advanced stage at diagnosis in most patients. Approximately 90% of ovarian cancers originate from the single-layered ovarian surface epithelium (OSE). Defects in the primary cilium, a solitary sensory organelle in most cells types including OSE, were recently implicated in tumorigenesis, mainly due to deregulation of ciliary signaling pathways such as Hedgehog (Hh) signaling. However, a possible link between primary cilia and epithelial ovarian cancer has not previously been investigated. Methods The presence of primary cilia was analyzed in sections of fixed human ovarian tissue as well as in cultures of normal human ovarian surface epithelium (OSE) cells and two human OSE-derived cancer cell lines. We also used immunofluorescence microscopy, western blotting, RT-PCR and siRNA to investigate ciliary signaling pathways in these cells. Results We show that ovarian cancer cells display significantly reduced numbers of primary cilia. The reduction in ciliation frequency in these cells was not due to a failure to enter growth arrest, and correlated with persistent centrosomal localization of aurora A kinase (AURA). Further, we demonstrate that ovarian cancer cells have deregulated Hh signaling and platelet-derived growth factor receptor alpha (PDGFRα) expression and that promotion of ciliary formation/stability by AURA siRNA depletion decreases Hh signaling in ovarian cancer cells. Lastly, we show that the tumor suppressor protein and negative regulator of AURA, checkpoint with forkhead-associated and ring finger domains (CHFR), localizes to the centrosome/primary cilium axis. Conclusions Our results suggest that primary cilia play a role in maintaining OSE homeostasis and that the low frequency of primary cilia in cancer OSE cells may result in part from over-expression of AURA, leading to aberrant Hh signaling and ovarian tumorigenesis.
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Affiliation(s)
- Dorte L Egeberg
- Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
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47
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Promoter hypermethylation of DNA damage response genes in hepatocellular carcinoma. Cell Biol Int 2012; 36:427-32. [PMID: 21864295 DOI: 10.1042/cbi20100851] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Aberrant methylation of promoter CpG islands is a major inactivation mechanism of tumour-related genes that play a crucial role in the progression of silencing in human cancers, including HCC (hepatocellular carcinoma). We have examined the promoter methylation status of five important DNA damage response genes in fresh-frozen HCC tissues and cell lines, as well as the possible correlation between methylation patterns and clinical features of the carcinoma. Promoter methylation status of RASSF1A (Ras association domain family 1), CHFR (checkpoint with forkhead and ring finger domains), GSTP1 (glutathione-S-transferase-pi gene), MGMT [O(6)-methylguanine-DNA methyltransferase] and hMLH1 (human mutL homologue 1) were examined by the MSP (methylation-specific PCR) in 70 HCC tissues and five HCC cell lines. The mRNA expression levels of these genes were measured by RT-PCR (reverse transcription-PCR). Methylation frequencies of these genes tested in HCC were 54 (78%) for RASSF1A, 30 (43%) for CHFR, 26 (38%) for GSTP1 and 22 (32%) for MGMT. No hypermethylation was detected for hMLH1 in any case of HCC or HCC cell lines. Moreover, promoter hypermethylation of RASSF1A, CHFR and GSTP1 in both HepG2 and SNU398 cells, and hypermethylation of MGMT in Huh7 cells, were detected. Treatment of three cell lines with 5Aza-dC (5-aza-20-deoxycytidine) restored or increased the expression of these genes, implicating aberrant DNA methylation in transcriptional silencing. Hypermethylation of RASSF1A and patient age were significantly associated. CHFR methylation status showed a statistically significant correlation with HCC progression. Methylation of the RASSF1A, CHFR, GSTP1 and MGMT genes seem therefore to play an important role in the pathogenesis of HCC. These epigenetic changes may have prognostic importance for patients with HCC.
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Banno K, Kisu I, Yanokura M, Masuda K, Ueki A, Kobayashi Y, Susumu N, Aoki D. Epigenetics and genetics in endometrial cancer: new carcinogenic mechanisms and relationship with clinical practice. Epigenomics 2012; 4:147-62. [PMID: 22449187 DOI: 10.2217/epi.12.13] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Endometrial cancer is the seventh most common cancer worldwide among females. An increased incidence and a younger age of patients are also predicted to occur, and therefore elucidation of the pathological mechanisms is important. However, several aspects of the mechanism of carcinogenesis in the endometrium remain unclear. Associations with genetic mutations of cancer-related genes have been shown, but these do not provide a complete explanation. Therefore, epigenetic mechanisms have been examined. Silencing of genes by DNA hypermethylation, hereditary epimutation of DNA mismatch repair genes and regulation of gene expression by miRNAs may underlie carcinogenesis in endometrial cancer. New therapies include targeting epigenetic changes using histone deacetylase inhibitors. Some cases of endometrial cancer may also be hereditary. Thus, patients with Lynch syndrome which is a hereditary disease, have a higher risk for developing endometrial cancer than the general population. Identification of such disease-related genes may contribute to early detection and prevention of endometrial cancer.
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Affiliation(s)
- Kouji Banno
- Department of Obstetrics & Gynecology, School of Medicine, Keio University, Shinanomachi 35 Shinjuku-ku, Tokyo 160-8582, Japan.
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Sanbhnani S, Yeong FM. CHFR: a key checkpoint component implicated in a wide range of cancers. Cell Mol Life Sci 2012; 69:1669-87. [PMID: 22159584 PMCID: PMC11114665 DOI: 10.1007/s00018-011-0892-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2011] [Revised: 11/13/2011] [Accepted: 11/16/2011] [Indexed: 02/06/2023]
Abstract
CHFR (Checkpoint with Forkhead-associated and RING finger domains) has been implicated in a checkpoint regulating entry into mitosis. However, the details underlying its roles and regulation are unclear due to conflicting lines of evidence supporting different notions of its functions. We provide here an overview of how CHFR is thought to contribute towards regulating mitotic entry and present possible explanations for contradictory observations published on the functions and regulation of CHFR. Furthermore, we survey key data showing correlations between promoter hypermethylation or down-regulation of CHFR and cancers, with a view on the likely reasons why different extents of correlations have been reported. Lastly, we explore the possibilities of exploiting CHFR promoter hypermethylation status in diagnostics and therapeutics for cancer patients. With keen interest currently focused on the association between hypermethylation of CHFR and cancers, details of how CHFR functions require further study to reveal how its absence might possibly contribute to tumorigenesis.
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Affiliation(s)
- Sheru Sanbhnani
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore
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Tainaka K, Okamoto A. ICON probes: synthesis and DNA methylation typing. ACTA ACUST UNITED AC 2012; Chapter 8:Unit 8.7.1-17. [PMID: 22147422 DOI: 10.1002/0471142700.nc0807s47] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
DNA methylation and demethylation significantly affect the deactivation and activation processes of gene expression, respectively. The determination of the location and frequency of DNA methylation is important for the elucidation of the mechanisms of cell differentiation and carcinogenesis and may be a useful and effective index for cancer diagnosis. We have developed an artificial DNA probe that induces a methylation detection reaction of a target cytosine in a long DNA sequence (ICON probe). This artificial DNA allows the rapid detection of a methyl group attached at the C5 position of the target cytosine. In addition, there is no nonspecific cleavage of genomic DNA in this reaction. The ICON probe also facilitates the quantification of methylation at the target cytosine using a small amount of genomic DNA sample. This unit provides a procedure for synthesizing bipyridine-modified adenosine phosphoramidite and preparation of ICON probes. Additionally, the protocol for the methylation quantification experiments by quantitative PCR utilizing ICON probes is also presented.
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Affiliation(s)
- Kazuki Tainaka
- Advanced Science Institute, RIKEN, The Institute of Physical and Chemical Research, Wako, Saitama, Japan
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