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Iyer PG, Slettedahl SW, Mahoney DW, Giakoumopoulos M, Olson MC, Krockenberger M, Taylor WR, Foote P, Berger C, Leggett C, Wu TT, Antpack E, Falk GW, Ginsberg GG, Abrams JA, Lightdale CJ, Ramirez F, Kahn A, Wolfsen H, Konda V, Trindade AJ, Kisiel JB. Algorithm Training and Testing for a Nonendoscopic Barrett's Esophagus Detection Test in Prospective Multicenter Cohorts. Clin Gastroenterol Hepatol 2024:S1542-3565(24)00284-2. [PMID: 38513982 DOI: 10.1016/j.cgh.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND & AIMS Endoscopic Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) detection is invasive and expensive. Nonendoscopic BE/EAC detection tools are guideline-endorsed alternatives. We previously described a 5-methylated DNA marker (MDM) panel assayed on encapsulated sponge cell collection device (CCD) specimens. We aimed to train a new algorithm using a 3-MDM panel and test its performance in an independent cohort. METHODS Algorithm training and test samples were from 2 prospective multicenter cohorts. All BE cases had esophageal intestinal metaplasia (with or without dysplasia/EAC); control subjects had no endoscopic evidence of BE. The CCD procedure was followed by endoscopy. From CCD cell lysates, DNA was extracted, bisulfite treated, and MDMs were blindly assayed. The algorithm was set and locked using cross-validated logistic regression (training set) and its performance was assessed in an independent test set. RESULTS Training (N = 352) and test (N = 125) set clinical characteristics were comparable. The final panel included 3 MDMs (NDRG4, VAV3, ZNF682). Overall sensitivity was 82% (95% CI, 68%-94%) at 90% (79%-98%) specificity and 88% (78%-94%) sensitivity at 84% (70%-93%) specificity in training and test sets, respectively. Sensitivity was 90% and 68% for all long- and short-segment BE, respectively. Sensitivity for BE with high-grade dysplasia and EAC was 100% in training and test sets. Overall sensitivity for nondysplastic BE was 82%. Areas under the receiver operating characteristic curves for BE detection were 0.92 and 0.94 in the training and test sets, respectively. CONCLUSIONS A locked 3-MDM panel algorithm for BE/EAC detection using a nonendoscopic CCD demonstrated excellent sensitivity for high-risk BE cases in independent validation samples. (Clinical trials.gov: NCT02560623, NCT03060642.).
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Affiliation(s)
- Prasad G Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| | - Seth W Slettedahl
- Division of Clinical Trials, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Douglas W Mahoney
- Division of Clinical Trials, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | | | | | | | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Patrick Foote
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Calise Berger
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Cadman Leggett
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Tsung-Teh Wu
- Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota
| | - Eduardo Antpack
- Department of Surgery, Mayo Clinic Health System, Austin, Minnesota
| | - Gary W Falk
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Gregory G Ginsberg
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Julian A Abrams
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, New York, New York
| | - Charles J Lightdale
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, New York, New York
| | - Francisco Ramirez
- Division of Gastroenterology and Hepatology, Mayo Clinic, Phoenix, Arizona
| | - Allon Kahn
- Division of Gastroenterology and Hepatology, Mayo Clinic, Phoenix, Arizona
| | - Herbert Wolfsen
- Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida
| | - Vani Konda
- Division of Gastroenterology and Hepatology, Baylor University Medical Center, Dallas, Texas
| | - Arvind J Trindade
- Division of Gastroenterology and Hepatology, Zucker School of Medicine at Hofstra/Northwell, Long Island Jewish Medical Center, New Hyde Park, New York
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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Chong ZX, Ho WY, Yeap SK. Delineating the tumour-regulatory roles of EYA4. Biochem Pharmacol 2023; 210:115466. [PMID: 36849065 DOI: 10.1016/j.bcp.2023.115466] [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: 12/29/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
Eyes absent homolog 4 (EYA4) is a protein that regulates many vital cellular processes and organogenesis pathways. It possesses phosphatase, hydrolase, and transcriptional activation functions. Mutations in the Eya4 gene can cause sensorineural hearing loss and heart disease. In most non-nervous system cancers such as those of the gastrointestinal tract (GIT), hematological and respiratory systems, EYA4 acts as a putative tumor suppressor. However, in nervous system tumors such as glioma, astrocytoma, and malignant peripheral nerve sheath tumor (MPNST), it plays a putative tumor-promoting role. EYA4 interacts with various signaling proteins of the PI3K/AKT, JNK/cJUN, Wnt/GSK-3β, and cell cycle pathways to exert its tumor-promoting or tumor-suppressing effect. The tissue expression level and methylation profiles of Eya4 can help predict the prognosis and anti-cancer treatment response among cancer patients. Targeting and altering Eya4 expression and activity could be a potential therapeutic strategy to suppress carcinogenesis. In conclusion, EYA4 may have both putative tumor-promoting and tumor-suppressing roles in different human cancers and has the potential to serve as a prognostic biomarker and therapeutic agent in various cancer types.
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Affiliation(s)
- Zhi Xiong Chong
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
| | - Wan Yong Ho
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia.
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Validation of a methylated DNA marker panel for the nonendoscopic detection of Barrett's esophagus in a multisite case-control study. Gastrointest Endosc 2021; 94:498-505. [PMID: 33857451 PMCID: PMC8380660 DOI: 10.1016/j.gie.2021.03.937] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/30/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS We previously identified a 5 methylated DNA marker (MDM) panel for the detection of nonendoscopic Barrett's esophagus (BE). In this study, we aimed to recalibrate the performance of the 5 MDM panel using a simplified assay in a training cohort, validate the panel in an independent test cohort, and explore the accuracy of an MDM panel with only 3 markers. METHODS Participants were recruited from 3 medical centers. The sponge on a string device (EsophaCap; CapNostics, Concord, NC, USA) was swallowed and withdrawn, followed by endoscopy, in BE cases and control subjects. A 5 MDM panel was blindly assayed using a simplified assay. Random forest modeling analysis was performed, in silico cross-validated in the training set, and then locked down, before test set analysis. RESULTS The training set had 199 patients: 110 BE cases and 89 control subjects, and the test set had 89 patients: 60 BE cases and 29 control subjects. Sensitivity of the 5 MDM panel for BE diagnosis was 93% at 90% specificity in the training set and 93% at 93% specificity in the test set. Areas under the receiver operating characteristic curves were .96 and .97 in the training and test sets, respectively. Model accuracy was not influenced by age, sex, or smoking history. Multiple 3 MDM panels achieved similar accuracy. CONCLUSIONS A 5 MDM panel for BE is highly accurate in training and test sets in a blinded multisite case-control analysis using a simplified assay. This panel may be reduced to only 3 MDMs in the future. (Clinical trial registration number: NCT02560623.).
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Zhu J, Hu LB, Zhao YP, Zhang YQ. Prognostic Role of EYA4 in Lower Grade Glioma with IDH1 Mutation and 1p19q Co-Deletion. World Neurosurg 2021; 149:e1174-e1179. [PMID: 33631386 DOI: 10.1016/j.wneu.2020.07.094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Eyes absent 4 (EYA4) participates in an important role in various cancers. Patients with low EYA4 expression have significantly favorable prognosis compared with those with high EYA4 expression. However, the expression and role of EYA4 in lower grade glioma (LGG) has not been fully elucidated. METHODS The R2 and UCSC Xena browser based on data from 284 cases in GSE16011 from Gene Expression Omnibus datasets and 530 cases of patients with LGG in The Cancer Genome Atlas database were extracted for bioinformatic analyses. The EYA4 expression in different subtypes of LGG was detected. Kaplan-Meier survival curves were generated to explore the association between EYA4 expression and overall survival (OS) in both datasets. RESULTS Patients with LGG with lower EYA4 expression had significantly longer 5- and 10-year OS in 2 datasets (P < 0.001). By matching histological subtypes and gene expression profiles of patients with LGG, oligoastrocytoma and oligodendroglioma groups had lower EYA4 expression and longer OS compared with the astrocytoma group (P < 0.05). Patients with IDH1 mutations and 1p19q co-deletion had longer 5- and 10-year OS (P < 0.001), and EYA4 expression was significantly downregulated in these patients (P < 0.001). CONCLUSIONS This study suggests that EYA4 can be used as a prognostic marker and provide a potential therapeutic target in patients with LGG with IDH1 mutation and 1p19q co-deletion.
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Affiliation(s)
- Jin Zhu
- Department of Functional Neurosurgery, Beijing Institute of Functional Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Li-Bo Hu
- School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Ya-Peng Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu-Qi Zhang
- Department of Neurosurgery, Yuquan Hospital, Tsinghua University, Beijing, China.
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Accurate Nonendoscopic Detection of Barrett's Esophagus by Methylated DNA Markers: A Multisite Case Control Study. Am J Gastroenterol 2020; 115:1201-1209. [PMID: 32558685 PMCID: PMC7415629 DOI: 10.14309/ajg.0000000000000656] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Nonendoscopic Barrett's esophagus (BE) screening may help improve esophageal adenocarcinoma outcomes. We previously demonstrated promising accuracy of methylated DNA markers (MDMs) for the nonendoscopic diagnosis of BE using samples obtained from a capsule sponge-on-string (SOS) device. We aimed to assess the accuracy of these MDMs in an independent cohort using a commercial grade assay. METHODS BE cases had ≥ 1 cm of circumferential BE with intestinal metaplasia; controls had no endoscopic evidence of BE. The SOS device was withdrawn 8 minutes after swallowing, followed by endoscopy (the criterion standard). Highest performing MDMs from a previous study were blindly assessed on extracted bisulfite-converted DNA by target enrichment long-probe quantitative amplified signal (TELQAS) assays. Optimal MDM combinations were selected and analyzed using random forest modeling with in silico cross-validation. RESULTS Of 295 patients consented, 268 (91%) swallowed the SOS device; 112 cases and 89 controls met the pre-established inclusion criteria. The median BE length was 6 cm (interquartile range 4-9), and 50% had no dysplasia. The cross-validated sensitivity and specificity of a 5 MDM random forest model were 92% (95% confidence interval 85%-96%) and 94% (95% confidence interval 87%-98%), respectively. Model performance was not affected by age, gender, or smoking history but was influenced by the BE segment length. SOS administration was well tolerated (median [interquartile range] tolerability 2 [0, 4] on 10 scale grading), and 95% preferred SOS over endoscopy. DISCUSSION Using a minimally invasive molecular approach, MDMs assayed from SOS samples show promise as a safe and accurate nonendoscopic test for BE prediction.
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Azuara D, Aussó S, Rodriguez-Moranta F, Guardiola J, Sanjuan X, Lobaton T, Boadas J, Piqueras M, Monfort D, Guinó E, Moreno V, Capellá G, de Oca J. New Methylation Biomarker Panel for Early Diagnosis of Dysplasia or Cancer in High-Risk Inflammatory Bowel Disease Patients. Inflamm Bowel Dis 2018; 24:2555-2564. [PMID: 30099509 DOI: 10.1093/ibd/izy255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND The risk of developing colorectal cancer (CRC) is increased in patients with inflammatory bowel disease (IBD) of the colon. The aim of the study was to evaluate the effectiveness of selected methylation gene panel for the early detection of CRC in high-risk IBD patients. METHODS In a discovery phase, 73 biopsies of 48 IBD patients (associated or not to CRC) were analyzed from genome-wide DNA methylation analysis using the Illumina Human Methylation 450K BeadChip. The panel of 5 genes selected (EYA4, SLIT2, FLI1, USP44, and SND1) was validated prospectively using methylation-specific melting curve analysis in biopsies of diseased and adjacent healthy tissue of 203 patients: 38 with IBD and associated neoplasia, 81 patients with IBD (25 of them with high risk), 48 with sporadic CRC, and 36 healthy controls. RESULTS The prevalence of methylation was higher in patients with IBD and associated neoplasia (both in diseased and adjacent healthy tissue, 71% and 52%, respectively) than in healthy controls (2/36, 6%; P = 6.72E-05). Methylation in IBD patients at high risk of dysplasia or cancer was more frequently detected than in patients at low risk (92% vs 57%; odds ratio, 8.63; P = 0.001). EYA4 and SLIT2 were the markers most frequently methylated. Differences in methylation levels were more evident in healthy mucosa (82% vs 15% high vs low risk, respectively; P = 1.25E-05). CONCLUSIONS Analysis of this panel of methylation markers may help in the early identification of colorectal dysplasia or cancer in high-risk IBD patients.
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Affiliation(s)
- Daniel Azuara
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL)-CIBERONC, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Susanna Aussó
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, ICO-IDIBELL and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Francisco Rodriguez-Moranta
- Department of Gastroenterology, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jordi Guardiola
- Department of Gastroenterology, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Sanjuan
- Department of Pathology, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Triana Lobaton
- Department of Gastroenterology, Germans Trias i Pujol University Hospital, Badalona, Barcelona, Spain
| | - Jaume Boadas
- Department of Gastroenterology, Hospital of Terrassa, Terrassa Health Consortium (CST), Terrassa, Barcelona, Spain
| | - Marta Piqueras
- Department of Gastroenterology, Hospital of Terrassa, Terrassa Health Consortium (CST), Terrassa, Barcelona, Spain
| | - David Monfort
- Department of Gastroenterology, Hospital of Terrassa, Terrassa Health Consortium (CST), Terrassa, Barcelona, Spain
| | - Elisabet Guinó
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, ICO-IDIBELL and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, ICO-IDIBELL and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Gabriel Capellá
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL)-CIBERONC, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Javier de Oca
- Department of General and Digestive Surgery, Colorectal Unit, University Hospital Bellvitge (HUB-IDIBELL)-CIBERONC, L'Hospitalet de Llobregat, Barcelona, Spain
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Xue M, Shi L, Wang W, Chen S, Wang L. An Overview of Molecular Profiles in Ulcerative Colitis-Related Cancer. Inflamm Bowel Dis 2018; 24:1883-1894. [PMID: 29945208 DOI: 10.1093/ibd/izy221] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Indexed: 12/16/2022]
Abstract
Ulcerative colitis (UC) is an independent risk factor of colorectal cancer (CRC). Both genetic and epigentic events induce a unique molecular profile during the development from UC to UC-related CRC (UCRC). These molecular changes play varied roles in DNA repair, immune response, cell metabolism, and interaction with the microbiota during the carcinogenesis process. This review will systmatically discuss the molecular characteristics of UCRC and point out the future perspectives in this research field.
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Affiliation(s)
- Meng Xue
- Department of Gastroenterology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liuhong Shi
- Department of Ultrasound, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Weijia Wang
- Department of Cardiology, School of Medicine, the Johns Hopkins Hospital, Baltimore, Maryland
| | - Shujie Chen
- Department of Gastroenterology, Sir Runrun Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liangjing Wang
- Department of Gastroenterology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
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Colorectal Cancer Blood-Based Biomarkers. Gastroenterol Res Pract 2017; 2017:2195361. [PMID: 29147109 PMCID: PMC5632863 DOI: 10.1155/2017/2195361] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/16/2017] [Accepted: 09/13/2017] [Indexed: 12/26/2022] Open
Abstract
Mortality and morbidity associated with colorectal cancer (CRC) are increasing globally, partly due to lack of early detection of the disease. The screening is usually performed with colonoscopy, which is invasive and unpleasant, discouraging participation in the screening. As a source of noninvasive and easily accessible biomarkers, liquid biopsies are emerging. Blood-based biomarkers have the potential as diagnostic and prognostic tool in CRC. Early stage detection of CRC with high sensitivity and specificity would likely lead to higher participation in the screening test. It would also improve the prognosis of the disease and improve the recurrence risk. In this review, we summarize the potential biomarkers for early detection and monitoring of CRC.
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Emmett RA, Davidson KL, Gould NJ, Arasaradnam RP. DNA methylation patterns in ulcerative colitis-associated cancer: a systematic review. Epigenomics 2017. [PMID: 28621161 DOI: 10.2217/epi-2017-0025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Evidence points to the role of DNA methylation in ulcerative colitis (UC)-associated cancer (UCC), the most serious complication of ulcerative colitis. A better understanding of the etiology of UCC may facilitate the development of new therapeutic targets and help to identify biomarkers of the disease risk. METHODS A search was performed in three databases following PRISMA protocol. DNA methylation in UCC was compared with sporadic colorectal cancer (SCRC), and individual genes differently methylated in UCC identified. RESULTS While there were some similarities in the methylation patterns of UCC compared with SCRC, generally lower levels of hypermethylation in promoter regions of individual genes was evident in UCC. Certain individual genes are, however, highly methylated in colitis-associated cancer: RUNX3, MINT1, MYOD and p16 exon1 and the promoter regions of EYA4 and ESR. CONCLUSION Patterns of DNA methylation differ between UCC and SCRC. Seven genes appear to be promising putative biomarkers.
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Affiliation(s)
- Ruth A Emmett
- Warwick Medical School, University of Warwick, Coventry, UK
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Chen R, Lai LA, Brentnall TA, Pan S. Biomarkers for colitis-associated colorectal cancer. World J Gastroenterol 2016; 22:7882-7891. [PMID: 27672285 PMCID: PMC5028804 DOI: 10.3748/wjg.v22.i35.7882] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/30/2016] [Accepted: 08/01/2016] [Indexed: 02/06/2023] Open
Abstract
Patients with extensive ulcerative colitis (UC) of more than eight years duration have an increased risk of colorectal cancer. Molecular biomarkers for dysplasia and cancer could have a great clinical value in managing cancer risk in these UC patients. Using a wide range of molecular techniques - including cutting-edge OMICS technologies - recent studies have identified clinically relevant biomarker candidates from a variety of biosamples, including colonic biopsies, blood, stool, and urine. While the challenge remains to validate these candidate biomarkers in multi-center studies and with larger patient cohorts, it is certain that accurate biomarkers of colitis-associated neoplasia would improve clinical management of neoplastic risk in UC patients. This review highlights the ongoing avenues of research in biomarker development for colitis-associated colorectal cancer.
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Towle R, Truong D, Garnis C. Epigenetic mediated silencing of EYA4 contributes to tumorigenesis in oral dysplastic cells. Genes Chromosomes Cancer 2016; 55:568-76. [DOI: 10.1002/gcc.22360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 12/30/2022] Open
Affiliation(s)
- Rebecca Towle
- Department of Integrative Oncology; British Columbia Cancer Research Centre; Vancouver BC V5Z 1L3 Canada
| | - Danielle Truong
- Department of Integrative Oncology; British Columbia Cancer Research Centre; Vancouver BC V5Z 1L3 Canada
| | - Cathie Garnis
- Department of Integrative Oncology; British Columbia Cancer Research Centre; Vancouver BC V5Z 1L3 Canada
- Division of Otolaryngology, Department of Surgery; University of British Columbia; Vancouver BC V5Z 4E3 Canada
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Dai Y, Jiang JB, Wang YL, Jin ZT, Hu SY. Functional and protein‑protein interaction network analysis of colorectal cancer induced by ulcerative colitis. Mol Med Rep 2015; 12:4947-58. [PMID: 26239378 PMCID: PMC4581825 DOI: 10.3892/mmr.2015.4102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 06/17/2015] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer (CRC) is a well‑recognized complication of ulcerative colitis (UC), and patients with UC have a higher incidence of CRC, compared with the general population. However, the properties of CRC induced by UC have not been clarified using an interaction network to analyze and compare gene sets. In the present study, six microarray datasets of CRC and UC were extracted from the Array Express database, and gene signatures were identified using the genome‑wide relative significance (GWRS) method. Functional analysis was performed based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Prediction of the genes and microRNA were performed using a hypergeometric method. A protein‑protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/proteins, and clusters were obtained through the Molecular Complex Detection algorithm. Topological centrality and a novel analyzing method, based on the rank value of GWGS, were used to characterize the biological importance of the clusters. A total of 217 differentially expressed (DE) genes of CRC were identified, 341 DE genes were identified in UC, and 62 common genes existed in the two. Several KEGG pathways were the same in CRC and UC. Collagenase, progesterone, heparin, urokinase, nadh and adenosine drugs demonstrated potential for use in treatment of CRC and UC. In the PPI network of CRC, 210 nodes and 752 edges were observed, wheras 314 nodes and 882 edges were identified in UC. Cluster 3 in UC had the highest GWGS, while the topological centrality of Cluster 3 in UC had the lowest degree and betweenness. PPI network analysis provided an effective way to estimate and understand the likelihood of the potential connections between proteins/genes. The results obtained following the use of GWGS to analyze differences between clusters did not agree with the topological degree and betweenness centrality, which indicated that gene fold change based GWGS was controversial with degree here in CRC and UC.
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Affiliation(s)
- Yong Dai
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Jin-Bo Jiang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Yan-Lei Wang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Zu-Tao Jin
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - San-Yuan Hu
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
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Levenson VV, Melnikov AA. Molecular biomarkers in 2013. Expert Rev Mol Diagn 2013; 13:773-6. [PMID: 24151845 DOI: 10.1586/14737159.2013.850419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Victor V Levenson
- US Biomarkers, Inc., 2201 W. Campbell Park Drive, Ste. 118, Chicago, IL 60612, USA +1 312 626 2886
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