1
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Yang JD, Ghoz H, Aboelsoud MM, Taylor WR, Yab TC, Berger CK, Cao X, Foote PH, Giama NH, Barr Fritcher EG, Mahoney DW, Moser CD, Smyrk TC, Kipp BR, Gores GJ, Roberts LR, Kisiel JB. DNA Methylation Markers for Detection of Cholangiocarcinoma: Discovery, Validation, and Clinical Testing in Biliary Brushings and Plasma. Hepatol Commun 2021; 5:1448-1459. [PMID: 34430788 PMCID: PMC8369938 DOI: 10.1002/hep4.1730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/03/2021] [Accepted: 03/22/2021] [Indexed: 02/04/2023] Open
Abstract
Cholangiocarcinoma (CCA) has poor prognosis due to late-stage, symptomatic presentation. Altered DNA methylation markers may improve diagnosis of CCA. Reduced-representation bisulfite sequencing was performed on DNA extracted from frozen CCA tissues and matched to adjacent benign biliary epithelia or liver parenchyma. Methylated DNA markers (MDMs) identified from sequenced differentially methylated regions were selected for biological validation on DNA from independent formalin-fixed, paraffin-embedded CCA tumors and adjacent hepatobiliary control tissues using methylation-specific polymerase chain reaction. Selected MDMs were then blindly assayed on DNA extracted from independent archival biliary brushing specimens, including 12 perihilar cholangiocarcinoma, 4 distal cholangiocarcinoma cases, and 18 controls. Next, MDMs were blindly assayed on plasma DNA from patients with extrahepatic CCA (eCCA), including 54 perihilar CCA and 5 distal CCA cases and 95 healthy and 22 primary sclerosing cholangitis controls, balanced for age and sex. From more than 3,600 MDMs discovered in frozen tissues, 39 were tested in independent samples. In the clinical pilot of 16 MDMs on cytology brushings, methylated EMX1 (empty spiracles homeobox 1) had an area under the curve (AUC) of 0.98 (95% confidence interval [CI], 0.95-1.0). In the clinical pilot on plasma, a cross-validated recursive partitioning tree prediction model from nine MDMs was accurate for de novo eCCA (AUC, 0.88 [0.81-0.95]) but not for primary sclerosing cholangitis-associated eCCA (AUC, 0.54 [0.35-0.73]). Conclusion: Next-generation DNA sequencing yielded highly discriminant methylation markers for CCA. Confirmation of these findings in independent tissues, cytology brushings, and plasma supports further development of DNA methylation to augment diagnosis of CCA.
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Affiliation(s)
- Ju Dong Yang
- Division of Gastroenterology and HepatologyCedars-Sinai Medical CenterLos AngelesCAUSA
| | - Hassan Ghoz
- Division of Gastroenterology and HepatologyMayo ClinicJacksonvilleFLUSA
| | | | - William R Taylor
- Division of Gastroenterology and HepatologyMayo ClinicRochesterMNUSA
| | - Tracy C Yab
- Division of Gastroenterology and HepatologyMayo ClinicRochesterMNUSA
| | - Calise K Berger
- Division of Gastroenterology and HepatologyMayo ClinicRochesterMNUSA
| | - Xiaoming Cao
- Division of Gastroenterology and HepatologyMayo ClinicRochesterMNUSA
| | - Patrick H Foote
- Division of Gastroenterology and HepatologyMayo ClinicRochesterMNUSA
| | - Nasra H Giama
- Division of Gastroenterology and HepatologyMayo ClinicRochesterMNUSA
| | | | - Douglas W Mahoney
- Department of Biomedical Statistics and InformaticsMayo ClinicRochesterMNUSA
| | - Catherine D Moser
- Department of Pathology and Laboratory MedicineChildren's Healthcare of AtlantaAtlantaGAUSA
| | - Thomas C Smyrk
- Department of Anatomic PathologyMayo ClinicRochesterMNUSA
| | | | - Gregory J Gores
- Division of Gastroenterology and HepatologyMayo ClinicRochesterMNUSA
| | - Lewis R Roberts
- Division of Gastroenterology and HepatologyMayo ClinicRochesterMNUSA
| | - John B Kisiel
- Division of Gastroenterology and HepatologyMayo ClinicRochesterMNUSA
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2
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Janni WJ, Yab TC, Hayes DF, Cristofanilli M, Bidard FC, Ignatiadis M, Regan MM, Alix-Panabières C, Barlow WE, Caldas C, Carey LA, Dirix L, Fehm T, Garcia-Saenz JA, Gazzaniga P, Generali D, Gerratana L, Gisbert-Criado R, Jacot W, Jiang Z, Lianidou E, Magbanua MJ, Manso L, Mavroudis D, Müller V, Munzone E, Pantel K, Pierga JY, Rack B, Riethdorf S, Rugo HS, Sideras K, Sleijfer S, Smerage J, Stebbing J, Terstappen LW, Vidal-Martínez J, Zamarchi R, Giridhar K, Friedl TW, Liu MC. Abstract GS4-08: Clinical utility of repeated circulating tumor cell (CTC) enumeration as early treatment monitoring tool in metastatic breast cancer (MBC) - a global pooled analysis with individual patient data. Cancer Res 2021. [DOI: 10.1158/1538-7445.sabcs20-gs4-08] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background:
Several studies suggest clinical utility of serial circulating tumor cell (CTC) enumeration as a means of assessing response status in metastatic breast cancer (MBC). The aim of this study is to conduct a comprehensive pooled analysis comprising globally available data to further define and explore the role of CTC enumeration as a tool for early treatment monitoring in patients with MBC with a focus on the predictive power in different breast cancer subtypes and clinical settings.
Methods:
In a global effort, peer-reviewed published studies with data on repeated CTC assessments (CellSearch® technology; Menarini Silicon Biosystems; Bologna, Italy) in MBC patients were screened and investigators were asked to provide individual patient data for this pooled analysis. 2761 cases from 32 data sets with data on both baseline and one follow up CTC assessments were included in the analysis (median time interval between the two CTC assessments 35 days). Data were analyzed using log rank tests and Cox regressions to evaluate the association between serial CTC enumeration results and overall survival (OS) in the full patient cohort and defined subgroups.
Results:
588 (21.3%) patients had no CTCs at both time points (neg/neg), 236 (8.5%) patients were CTC negative at baseline and CTC positive at follow up (neg/pos), 712 (25.8%) patients converted from CTC positive at baseline to CTC negative (pos/neg), and 1225 (44.4%) patients had at least one CTC at both time points (pos/pos). Log rank tests showed significant differences in OS between these four CTC change groups (p < 0.0001 for all pairwise comparisons except for the comparison between neg/pos and pos/neg, p = 0.015). Median OS for the neg/neg, neg/pos, pos/neg and pos/pos group was 45.6, 26.1, 34.6, and 17.6 months, respectively. Hazard ratios (HR) (reference group neg/neg) were 1.38 (95% CI 1.16 - 1.64) for the pos/neg group, 1.78 (95% CI 1.43 - 2.22) for the neg/pos group, and 3.06 (95% CI 2.63 - 3.56) for the pos/pos group. Results were similar if a cutoff of 5 CTCs was used for CTC positivity (pos/neg group: HR 1.43, 95% CI 1.25 - 1.63; neg/pos group: HR 2.39, 95% CI 1.91 - 2.99; pos/pos group: HR 3.54, 95% CI 3.12 - 4.02).
In total, 2586 patients could be assigned to different tumor subtypes based on known hormone receptor (ER) and HER2 status of the primary tumor: 1513 (58.5%) patients had a luminal-like tumor (ER positive, HER2 negative), 682 (26.4%) patients had a HER2-positive tumor, and 391 (15.1%) patients had a triple-negative tumor. In patients with luminal-like tumors, the hazard ratios were 1.67 (95% CI 1.29 - 2.17), 2.01 (95% CI 1.45 - 2.77), and 3.87 (95% CI 3.09 - 4.83) for the pos/neg, neg/pos, and pos/pos group, respectively. In patients with HER2-positive tumors, the neg/pos group (HR 1.68, 95% CI 1.12 - 2.53) and the pos/pos group (HR 2.11, 95% CI 1.58 - 2.83) showed significantly worse OS compared to the neg/neg group, while in triple-negative patients, the pos/pos group had a significantly shorter OS compared to the neg/neg group (HR 2.99, 95% CI 2.11 - 4.24).
The results will be up-dated by inclusion of additional large data sets (CALGB 40502, CALGB 40503, COMET, SWOG S0500, TBCRC 001) for the analysis to be presented at SABCS 2020.
Conclusion:
This large pooled analysis confirms that at a median of 35 days after treatment initiation, follow-up CTC assessments strongly predict overall survival. These results suggest potential clinical utility of CTC monitoring as early response marker in MBC, especially in luminal-like tumors.
Citation Format: Wolfgang J Janni, Tracy C. Yab, Daniel F. Hayes, Massimo Cristofanilli, Francois-Clement Bidard, Michail Ignatiadis, Meredith M. Regan, Catherine Alix-Panabières, William E. Barlow, Carlos Caldas, Lisa A. Carey, Luc Dirix, Tanja Fehm, Jose A. Garcia-Saenz, Paola Gazzaniga, Daniele Generali, Lorenzo Gerratana, Rafael Gisbert-Criado, William Jacot, Zefei Jiang, Evi Lianidou, Mark J.M. Magbanua, Luis Manso, Dimitrios Mavroudis, Volkmar Müller, Elisabetta Munzone, Klaus Pantel, Jean-Yves Pierga, Brigitte Rack, Sabine Riethdorf, Hope S. Rugo, Kostandinos Sideras, Stefan Sleijfer, Jeffrey Smerage, Justin Stebbing, Leon W.M.M. Terstappen, José Vidal-Martínez, Rita Zamarchi, Karthik Giridhar, Thomas W.P. Friedl, Minetta C. Liu. Clinical utility of repeated circulating tumor cell (CTC) enumeration as early treatment monitoring tool in metastatic breast cancer (MBC) - a global pooled analysis with individual patient data [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr GS4-08.
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Affiliation(s)
- Wolfgang J Janni
- 1Department of Obstetrics and Gynecology, University Hospital Ulm, Ulm, Germany
| | - Tracy C. Yab
- 2Department of Oncology, Mayo Clinic, Rochester, MN
| | - Daniel F. Hayes
- 3Breast Oncology Program, University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | - Massimo Cristofanilli
- 4Department of Medicine, Division of Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | | | - Michail Ignatiadis
- 6Department of Medical Oncology, Institute Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Meredith M. Regan
- 7Division of Biostatistics, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Catherine Alix-Panabières
- 8Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, Montpellier, France
| | | | - Carlos Caldas
- 10Department of Oncology, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Lisa A. Carey
- 11Division of Hematology-Oncology, University of North Carolina, Chapel Hill, NC
| | - Luc Dirix
- 12University of Antwerp and GZA Sint-Augustinus, Antwerp, Belgium
| | - Tanja Fehm
- 13Department of Gynecology and Obstetrics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Paola Gazzaniga
- 15Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Daniele Generali
- 16Women Cancer Center, Azienda Socio Sanitaria Territoriale di Cremona, University of Trieste, Trieste, Italy
| | - Lorenzo Gerratana
- 17Department of Medicine (DAME) - The University of Udine, Udine, Italy
| | | | - William Jacot
- 19Department of Medical Oncology, Institut du Cancer de Montpellier (ICM), IRCM, INSERM U1194, Université de Montpellier, Montpellier, France
| | - Zefei Jiang
- 20Department of Breast Cancer, The 307th Hospital of Chinese People’s Liberation Army, Beijing, China
| | - Evi Lianidou
- 21Laboratory of Analytical Chemistry, Analysis of Circulating Tumor Cells (ACTC) Lab, Department of Chemistry, University of Athens, Athens, Greece
| | - Mark J.M. Magbanua
- 22University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Luis Manso
- 23Department of Medical Oncology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Dimitrios Mavroudis
- 24Department of Medical Oncology, University General Hospital of Heraklion, Heraklion, Greece
| | - Volkmar Müller
- 25Department of Gynecology and Obstetrics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Elisabetta Munzone
- 26Division of Medical Senology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Klaus Pantel
- 27Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jean-Yves Pierga
- 28Department of Medical Oncology, Institute Curie, Paris & St Cloud, Paris University, Paris, France
| | - Brigitte Rack
- 1Department of Obstetrics and Gynecology, University Hospital Ulm, Ulm, Germany
| | - Sabine Riethdorf
- 27Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hope S. Rugo
- 22University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | | | - Stefan Sleijfer
- 30Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Jeffrey Smerage
- 3Breast Oncology Program, University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | - Justin Stebbing
- 31Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Leon W.M.M. Terstappen
- 32Medical Cell BioPhysics Group, MIRA Institute, Faculty of Science and Technology, University of Twente, Enschede, Netherlands
| | | | - Rita Zamarchi
- 33Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | - Thomas W.P. Friedl
- 1Department of Obstetrics and Gynecology, University Hospital Ulm, Ulm, Germany
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3
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Ballester V, Taylor WR, Slettedahl SW, Mahoney DW, Yab TC, Sinicrope FA, Boland CR, Lidgard GP, Cruz-Correa MR, Smyrk TC, Boardman LA, Ahlquist DA, Kisiel JB. Novel methylated DNA markers accurately discriminate Lynch syndrome associated colorectal neoplasia. Epigenomics 2020; 12:2173-2187. [PMID: 33350853 PMCID: PMC7923255 DOI: 10.2217/epi-2020-0132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: Acquired molecular changes in Lynch syndrome (LS) colorectal tumors have been largely unstudied. We identified methylated DNA markers (MDMs) for discrimination of colorectal neoplasia in LS and determined if these MDMs were comparably discriminant in sporadic patients. Patients & methods: For LS discovery, we evaluated DNA from 53 colorectal case and control tissues using next generation sequencing. For validation, blinded methylation-specific PCR assays to the selected MDMs were performed on 197 cases and controls. Results: OPLAH was the most discriminant MDM with areas under the receiver operating characteristic curve ≥0.97 for colorectal neoplasia in LS and sporadic tissues. ALKBH5, was uniquely hypermethylated in LS neoplasms. Conclusion: Highly discriminant MDMs for colorectal neoplasia in LS were identified with potential use in screening and surveillance.
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Affiliation(s)
- Veroushka Ballester
- Division of Digestive & Liver Diseases, Columbia University, New York, NY 10032, USA
| | - William R Taylor
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | - Tracy C Yab
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Frank A Sinicrope
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | - Marcia R Cruz-Correa
- Comprehensive Cancer Center, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00936, USA
| | - Thomas C Smyrk
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Lisa A Boardman
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - David A Ahlquist
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - John B Kisiel
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN 55905, USA
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4
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Majumder S, Raimondo M, Taylor WR, Yab TC, Berger CK, Dukek BA, Cao X, Foote PH, Wu CW, Devens ME, Mahoney DW, Smyrk TC, Pannala R, Chari ST, Vege SS, Topazian MD, Petersen BT, Levy MJ, Rajan E, Gleeson FC, Dayyeh BA, Nguyen CC, Faigel DO, Woodward TA, Wallace MB, Petersen G, Allawi HT, Lidgard GP, Kisiel JB, Ahlquist DA. Methylated DNA in Pancreatic Juice Distinguishes Patients With Pancreatic Cancer From Controls. Clin Gastroenterol Hepatol 2020; 18:676-683.e3. [PMID: 31323382 PMCID: PMC6984349 DOI: 10.1016/j.cgh.2019.07.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 07/10/2019] [Accepted: 07/12/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Precursors of pancreatic cancer arise in the ductal epithelium; markers exfoliated into pancreatic juice might be used to detect high-grade dysplasia (HGD) and cancer. Specific methylated DNA sequences in pancreatic tissue have been associated with adenocarcinoma. We analyzed these methylated DNA markers (MDMs) in pancreatic juice samples from patients with pancreatic ductal adenocarcinomas (PDACs) or intraductal papillary mucinous neoplasms (IPMNs) with HGD (cases), and assessed their ability to discriminate these patients from individuals without dysplasia or with IPMNs with low-grade dysplasia (controls). METHODS We obtained pancreatic juice samples from 38 patients (35 with biopsy-proven PDAC or pancreatic cystic lesions with invasive cancer and 3 with HGD) and 73 controls (32 with normal pancreas and 41 with benign disease), collected endoscopically from the duodenum after secretin administration from February 2015 through November 2016 at 3 medical centers. Samples were analyzed for the presence of 14 MDMs (in the genes NDRG4, BMP3, TBX15, C13orf18, PRKCB, CLEC11A, CD1D, ELMO1, IGF2BP1, RYR2, ADCY1, FER1L4, EMX1, and LRRC4), by quantitative allele-specific real-time target and signal amplification. We performed area under the receiver operating characteristic curve analyses to determine the ability of each marker, and panels of markers, to distinguish patients with HGD and cancer from controls. MDMs were combined to form a panel for detection using recursive partition trees. RESULTS We identified a group of 3 MDMs (at C13orf18, FER1L4, and BMP3) in pancreatic juice that distinguished cases from controls with an area under the receiver operating characteristic value of 0.90 (95% CI, 0.83-0.97). Using a specificity cut-off value of 86%, this group of MDMs distinguished patients with any stage of pancreatic cancer from controls with 83% sensitivity (95% CI, 66%-93%) and identified patients with stage I or II PDAC or IPMN with HGD with 80% sensitivity (95% CI, 56%-95%). CONCLUSIONS We identified a group of 3 MDMs in pancreatic juice that identify patients with pancreatic cancer with an area under the receiver operating characteristic value of 0.90, including patients with early stage disease or advanced precancer. These DNA methylation patterns might be included in algorithms for early detection of pancreatic cancer, especially in high-risk cohorts. Further optimization and clinical studies are needed.
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Affiliation(s)
- Shounak Majumder
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| | - Massimo Raimondo
- Division of Gastroenterology & Hepatology Mayo Clinic Jacksonville, FL
| | - William R. Taylor
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - Tracy C. Yab
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - Calise K. Berger
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - Brian A. Dukek
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - Xiaoming Cao
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - Patrick H. Foote
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - Chung Wah Wu
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - Mary E. Devens
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - Douglas W. Mahoney
- Department of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN
| | - Thomas C. Smyrk
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN
| | - Rahul Pannala
- Division of Gastroenterology & Hepatology, Mayo Clinic Scottsdale, AZ
| | - Suresh T. Chari
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | | | - Mark D. Topazian
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - Bret T. Petersen
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - Michael J. Levy
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - Elizabeth Rajan
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - Ferga C. Gleeson
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - Barham Abu Dayyeh
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - Cuong C. Nguyen
- Division of Gastroenterology & Hepatology, Mayo Clinic Scottsdale, AZ
| | - Douglas O. Faigel
- Division of Gastroenterology & Hepatology, Mayo Clinic Scottsdale, AZ
| | | | | | - Gloria Petersen
- Department of Health Sciences Research Mayo Clinic, Rochester, MN
| | | | | | - John B. Kisiel
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
| | - David A. Ahlquist
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN
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5
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Qin Y, Wu CW, Taylor WR, Sawas T, Burger KN, Mahoney DW, Sun Z, Yab TC, Lidgard GP, Allawi HT, Buttar NS, Smyrk TC, Iyer PG, Katzka DA, Ahlquist DA, Kisiel JB. Discovery, Validation, and Application of Novel Methylated DNA Markers for Detection of Esophageal Cancer in Plasma. Clin Cancer Res 2019; 25:7396-7404. [PMID: 31527170 DOI: 10.1158/1078-0432.ccr-19-0740] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/20/2019] [Accepted: 09/11/2019] [Indexed: 12/29/2022]
Abstract
PURPOSE The burden of esophageal cancer continues to rise, and noninvasive screening tools are needed. Methylated DNA markers (MDM) assayed from plasma show promise in detection of other cancers. For esophageal cancer detection, we aimed to discover and validate MDMs in tissue, and determine their feasibility when assayed from plasma. EXPERIMENTAL DESIGN Whole-methylome sequencing was performed on DNA extracted from 37 tissues (28 EC; 9 normal esophagus) and 8 buffy coat samples. Top MDMs were validated by methylation specific PCR on tissue from 76 EC (41 adeno, 35 squamous cell) and 17 normal esophagus. Quantitative allele-specific real-time target and signal amplification was used to assay MDMs in plasma from 183 patients (85 EC, 98 controls). Recursive partitioning (rPART) identified MDM combinations predictive of esophageal cancer. Validation was performed in silico by bootstrapping. RESULTS From discovery, 23 candidate MDMs were selected for independent tissue validation; median area under the receiver operating curve (AUC) for individual MDMs was 0.93. Among 12 MDMs advanced to plasma testing, rPART modeling selected a 5 MDM panel (FER1L4, ZNF671, ST8SIA1, TBX15, ARHGEF4) which achieved an AUC of 0.93 (95% CI, 0.89-0.96) on best-fit and 0.81 (95% CI, 0.75-0.88) on cross-validation. At 91% specificity, the panel detected 74% of esophageal cancer overall, and 43%, 64%, 77%, and 92% of stages I, II, III, and IV, respectively. Discrimination was not affected by age, sex, smoking, or body mass index. CONCLUSIONS Novel MDMs assayed from plasma detect esophageal cancer with moderate accuracy. Further optimization and clinical testing are warranted.
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Affiliation(s)
- Yi Qin
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Chung W Wu
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - William R Taylor
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Tarek Sawas
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Kelli N Burger
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Douglas W Mahoney
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Zhifu Sun
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Tracy C Yab
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | | | - Navtej S Buttar
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Thomas C Smyrk
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Prasad G Iyer
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - David A Katzka
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - David A Ahlquist
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - John B Kisiel
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
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6
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Kisiel JB, Klepp P, Allawi HT, Taylor WR, Giakoumopoulos M, Sander T, Yab TC, Moum BA, Lidgard GP, Brackmann S, Mahoney DW, Roseth A, Ahlquist DA. Analysis of DNA Methylation at Specific Loci in Stool Samples Detects Colorectal Cancer and High-Grade Dysplasia in Patients With Inflammatory Bowel Disease. Clin Gastroenterol Hepatol 2019; 17:914-921.e5. [PMID: 29775793 PMCID: PMC6368476 DOI: 10.1016/j.cgh.2018.05.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/08/2018] [Accepted: 05/07/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Patients with inflammatory bowel diseases (IBDs), including ulcerative colitis and Crohn's disease, are at increased risk for colorectal cancer (CRC). Analyses of DNA methylation patterns in stool samples have been reported to detect CRC in patients with IBD. We sought to validate these findings in larger cohorts and assess the accuracy of analysis of DNA methylation patterns in stool for detection of CRC and high-grade dysplasia (HGD) normalized to methylation level at ZDHHC1. METHODS We obtained buffered, frozen stool samples from a US case-control study and from 2 European surveillance cohorts (referral or population based) of patients with chronic ulcerative colitis (n = 248), Crohn's disease (n = 82), indeterminate colitis (n = 2), or IBD with primary sclerosing cholangitis (n = 38). Stool samples were collected before bowel preparation for colonoscopy or at least 1 week after colonoscopy. Among the study samples, stools from individuals with IBD but without neoplasia were used as controls (n = 291). DNA was isolated from stool, exposed to bisulfite, and then assayed by multiplex quantitative allele-specific real-time target and signal amplification. We analyzed methylation levels of BMP3, NDRG4, VAV3, and SFMBT2 relative to the methylation level of ZDHHC1, and compared these between patients with CRC or HGD and controls. RESULTS Levels of methylation at BMP3 and VAV3, relative to ZDHHC1 methylation, identified patients with CRC and HGD with an area under the curve value of 0.91 (95% CI, 0.77-1.00). Methylation levels at specific promotor regions of these genes identified 11 of the 12 patients with CRC and HGD, with 92% sensitivity (95% CI, 60%-100%) and 90% specificity (95% CI, 86%-93%). The proportion of false-positive results did not differ significantly among the case-control, referral cohort, and population cohort studies (P = .60) when the 90% specificity cut-off from the whole sample set was applied. CONCLUSIONS In an analysis of stool samples from 3 independent studies of 332 patients with IBD, we associated levels of methylation at 2 genes (BMP3 and VAV3), relative to level of methylation at ZDHHC1, with detection of CRC and HGD. These methylation patterns identified patients with CRC and HGD with more than 90% specificity, and might be used in CRC surveillance.
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Affiliation(s)
- John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| | - Pasquale Klepp
- Department of Internal Medicine, Lovisenberg Hospital, Oslo, Norway; Clinical Medicine, University Hospital, University of Oslo, Oslo, Norway
| | - Hatim T Allawi
- Department of Gastroenterology, Akershus University Hospital, University of Oslo, Oslo, Norway
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | | | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Bjorn A Moum
- Department of Gastroenterology, Oslo University Hospital, Oslo, Norway
| | | | - Stephan Brackmann
- Department of Gastroenterology, Akershus University Hospital, University of Oslo, Oslo, Norway; Clinical Medicine, University Hospital, University of Oslo, Oslo, Norway
| | - Douglas W Mahoney
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Arne Roseth
- Department of Internal Medicine, Lovisenberg Hospital, Oslo, Norway
| | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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7
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Kisiel JB, Dukek BA, Kanipakam RVSR, Ghoz HM, Yab TC, Berger CK, Taylor WR, Foote PH, Giama NH, Onyirioha K, Abdallah MA, Burger KN, Slettedahl SW, Mahoney DW, Smyrk TC, Lewis JT, Giakoumopoulos M, Allawi HT, Lidgard G, Roberts LR, Ahlquist DA. Hepatocellular Carcinoma Detection by Plasma Methylated DNA: Discovery, Phase I Pilot, and Phase II Clinical Validation. Hepatology 2019; 69:1180-1192. [PMID: 30168613 PMCID: PMC6429916 DOI: 10.1002/hep.30244] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/21/2018] [Indexed: 12/14/2022]
Abstract
Early detection improves hepatocellular carcinoma (HCC) outcomes, but better noninvasive surveillance tools are needed. We aimed to identify and validate methylated DNA markers (MDMs) for HCC detection. Reduced representation bisulfite sequencing was performed on DNA extracted from 18 HCC and 35 control tissues. Candidate MDMs were confirmed by quantitative methylation-specific PCR in DNA from independent tissues (74 HCC, 29 controls). A phase I plasma pilot incorporated quantitative allele-specific real-time target and signal amplification assays on independent plasma-extracted DNA from 21 HCC cases and 30 controls with cirrhosis. A phase II plasma study was then performed in 95 HCC cases, 51 controls with cirrhosis, and 98 healthy controls using target enrichment long-probe quantitative amplified signal (TELQAS) assays. Recursive partitioning identified best MDM combinations. The entire MDM panel was statistically cross-validated by randomly splitting the data 2:1 for training and testing. Random forest (rForest) regression models performed on the training set predicted disease status in the testing set; median areas under the receiver operating characteristics curve (AUCs; and 95% confidence interval [CI]) were reported after 500 iterations. In phase II, a six-marker MDM panel (homeobox A1 [HOXA1], empty spiracles homeobox 1 [EMX1], AK055957, endothelin-converting enzyme 1 [ECE1], phosphofructokinase [PFKP], and C-type lectin domain containing 11A [CLEC11A]) normalized by beta-1,3-galactosyltransferase 6 (B3GALT6) level yielded a best-fit AUC of 0.96 (95% CI, 0.93-0.99) with HCC sensitivity of 95% (88%-98%) at specificity of 92% (86%-96%). The panel detected 3 of 4 (75%) stage 0, 39 of 42 (93%) stage A, 13 of 14 (93%) stage B, 28 of 28 (100%) stage C, and 7 of 7 (100%) stage D HCCs. The AUC value for alpha-fetoprotein (AFP) was 0.80 (0.74-0.87) compared to 0.94 (0.9-0.97) for the cross-validated MDM panel (P < 0.0001). Conclusion: MDMs identified in this study proved to accurately detect HCC by plasma testing. Further optimization and clinical testing of this promising approach are indicated.
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Affiliation(s)
| | | | | | | | - Tracy C. Yab
- Mayo Clinic, 200 First Street SW, Rochester, MN 55905
| | | | | | | | | | | | | | | | | | | | | | | | | | - Hatim T. Allawi
- Exact Sciences Development Company, LLC, 441 Charmany Drive, Madison, WI 53719
| | - Graham Lidgard
- Exact Sciences Development Company, LLC, 441 Charmany Drive, Madison, WI 53719
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8
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Iyer PG, Taylor WR, Johnson ML, Lansing RL, Maixner KA, Yab TC, Simonson JA, Devens ME, Slettedahl SW, Mahoney DW, Berger CK, Foote PH, Smyrk TC, Wang KK, Wolfsen HC, Ahlquist DA. Highly Discriminant Methylated DNA Markers for the Non-endoscopic Detection of Barrett's Esophagus. Am J Gastroenterol 2018; 113:1156-1166. [PMID: 29891853 DOI: 10.1038/s41395-018-0107-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/04/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Minimally invasive methods have been described to detect Barrett's esophagus (BE), but are limited by subjectivity and suboptimal accuracy. We identified methylated DNA markers (MDMs) for BE in tissue and assessed their accuracy on whole esophagus brushings and capsule sponge samples. METHODS Step 1: Unbiased whole methylome sequencing was performed on DNA from BE and normal squamous esophagus (SE) tissue. Discriminant MDM candidates were validated on an independent patient cohort (62 BE cases, 30 controls) by quantitative methylation specific PCR (qMSP). Step 2: Selected MDMs were further evaluated on whole esophageal brushings (49 BE cases, 36 controls). 35 previously sequenced esophageal adenocarcinoma (EAC) MDMs were also evaluated. Step 3: 20 BE cases and 20 controls were randomized to swallow capsules sponges (25 mm, 10 pores or 20 pores per inch (ppi)) followed endoscopy. DNA yield, tolerability, and mucosal injury were compared. Best MDM assays were performed on this cohort. RESULTS Step 1: 19 MDMs with areas under the ROC curve (AUCs) >0.85 were carried forward. Step 2: On whole esophageal brushings, 80% of individual MDM candidates showed high accuracy for BE (AUCs 0.84-0.94). Step 3: The capsule sponge was swallowed and withdrawn in 98% of subjects. Tolerability was superior with the 10 ppi sponge with minimal mucosal injury and abundant DNA yield. A 2-marker panel (VAV3 + ZNF682) yielded excellent BE discrimination (AUC = 1). CONCLUSIONS Identified MDMs discriminate BE with high accuracy. BE detection appears safe and feasible with a capsule sponge. Corroboration in larger studies is warranted. ClinicalTrials.gov number NCT02560623.
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Affiliation(s)
- Prasad G Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - Michele L Johnson
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - Ramona L Lansing
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - Kristyn A Maixner
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - Julie A Simonson
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - Mary E Devens
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - Seth W Slettedahl
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - Douglas W Mahoney
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - Calise K Berger
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - Patrick H Foote
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - Thomas C Smyrk
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - Kenneth K Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - Herbert C Wolfsen
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
| | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA. Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA
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9
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Anderson BW, Suh YS, Choi B, Lee HJ, Yab TC, Taylor WR, Dukek BA, Berger CK, Cao X, Foote PH, Devens ME, Boardman LA, Kisiel JB, Mahoney DW, Slettedahl SW, Allawi HT, Lidgard GP, Smyrk TC, Yang HK, Ahlquist DA. Detection of Gastric Cancer with Novel Methylated DNA Markers: Discovery, Tissue Validation, and Pilot Testing in Plasma. Clin Cancer Res 2018; 24:5724-5734. [PMID: 29844130 DOI: 10.1158/1078-0432.ccr-17-3364] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/09/2018] [Accepted: 05/23/2018] [Indexed: 12/16/2022]
Abstract
Purpose: Gastric adenocarcinoma is the third most common cause of cancer mortality worldwide. Accurate and affordable noninvasive detection methods have potential value for screening and surveillance. Herein, we identify novel methylated DNA markers (MDM) for gastric adenocarcinoma, validate their discrimination for gastric adenocarcinoma in tissues from geographically separate cohorts, explore marker acquisition through the oncogenic cascade, and describe distributions of candidate MDMs in plasma from gastric adenocarcinoma cases and normal controls.Experimental Design: Following discovery by unbiased whole-methylome sequencing, candidate MDMs were validated by blinded methylation-specific PCR in archival case-control tissues from U.S. and South Korean patients. Top MDMs were then assayed by an analytically sensitive method (quantitative real-time allele-specific target and signal amplification) in a blinded pilot study on archival plasma from gastric adenocarcinoma cases and normal controls.Results: Whole-methylome discovery yielded novel and highly discriminant candidate MDMs. In tissue, a panel of candidate MDMs detected gastric adenocarcinoma in 92% to 100% of U.S. and South Korean cohorts at 100% specificity. Levels of most MDMs increased progressively from normal mucosa through metaplasia, adenoma, and gastric adenocarcinoma with variation in points of greatest marker acquisition. In plasma, a 3-marker panel (ELMO1, ZNF569, C13orf18) detected 86% (95% CI, 71-95) of gastric adenocarcinomas at 95% specificity.Conclusions: Novel MDMs appear to accurately discriminate gastric adenocarcinoma from normal controls in both tissue and plasma. The point of aberrant methylation during oncogenesis varies by MDM, which may have relevance to marker selection in clinical applications. Further exploration of these MDMs for gastric adenocarcinoma screening and surveillance is warranted. Clin Cancer Res; 24(22); 5724-34. ©2018 AACR.
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Affiliation(s)
- Bradley W Anderson
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Yun-Suhk Suh
- Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | - Boram Choi
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyuk-Joon Lee
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Brian A Dukek
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Calise K Berger
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Xiaoming Cao
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Patrick H Foote
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Mary E Devens
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Lisa A Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Douglas W Mahoney
- Department of Biomedical Statistics and Information, Mayo Clinic, Rochester, Minnesota
| | - Seth W Slettedahl
- Department of Biomedical Statistics and Information, Mayo Clinic, Rochester, Minnesota
| | | | | | - Thomas C Smyrk
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Han-Kwang Yang
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
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10
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Wu CW, Evans JM, Huang S, Mahoney DW, Dukek BA, Taylor WR, Yab TC, Smyrk TC, Jen J, Kisiel JB, Ahlquist DA. A Comprehensive Approach to Sequence-oriented IsomiR annotation (CASMIR): demonstration with IsomiR profiling in colorectal neoplasia. BMC Genomics 2018; 19:401. [PMID: 29801434 PMCID: PMC5970459 DOI: 10.1186/s12864-018-4794-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/14/2018] [Indexed: 01/14/2023] Open
Abstract
Background MicroRNA (miRNA) profiling is an important step in studying biological associations and identifying marker candidates. miRNA exists in isoforms, called isomiRs, which may exhibit distinct properties. With conventional profiling methods, limitations in assay and analysis platforms may compromise isomiR interrogation. Results We introduce a comprehensive approach to sequence-oriented isomiR annotation (CASMIR) to allow unbiased identification of global isomiRs from small RNA sequencing data. In this approach, small RNA reads are maintained as independent sequences instead of being summarized under miRNA names. IsomiR features are identified through step-wise local alignment against canonical forms and precursor sequences. Through customizing the reference database, CASMIR is applicable to isomiR annotation across species. To demonstrate its application, we investigated isomiR profiles in normal and neoplastic human colorectal epithelia. We also ran miRDeep2, a popular miRNA analysis algorithm to validate isomiRs annotated by CASMIR. With CASMIR, specific and biologically relevant isomiR patterns could be identified. We note that specific isomiRs are often more abundant than their canonical forms. We identify isomiRs that are commonly up-regulated in both colorectal cancer and advanced adenoma, and illustrate advantages in targeting isomiRs as potential biomarkers over canonical forms. Conclusions Studying miRNAs at the isomiR level could reveal new insight into miRNA biology and inform assay design for specific isomiRs. CASMIR facilitates comprehensive annotation of isomiR features in small RNA sequencing data for isomiR profiling and differential expression analysis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4794-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chung Wah Wu
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Jared M Evans
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Shengbing Huang
- Division of Bioinformatics and Computational Biology, University of Minnesota Rochester, Rochester, MN, USA
| | - Douglas W Mahoney
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Brian A Dukek
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Thomas C Smyrk
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jin Jen
- Genome Analysis Core, Medical Genome Facility, Mayo Clinic, Rochester, MN, USA.,Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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11
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Wu CW, Cao X, Berger CK, Foote PH, Mahoney DW, Simonson JA, Anderson BW, Yab TC, Taylor WR, Boardman LA, Kisiel JB, Ahlquist DA. Novel Approach to Fecal Occult Blood Testing by Assay of Erythrocyte-Specific microRNA Markers. Dig Dis Sci 2017; 62:1985-1994. [PMID: 28660489 PMCID: PMC6021130 DOI: 10.1007/s10620-017-4627-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/23/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND Fecal occult blood testing (FOBT) has historically relied on methods to detect hemoglobin with no fundamental innovations in decades. AIM To examine microRNA (miRNA) as a new marker class for FOBT. METHODS Candidate miRNA markers were identified by small RNA sequencing of human whole blood compared to colorectal epithelia. Markers were tested in human blood cell subsets and blood from non-human species. We assessed assay linearity in blood spiking and marker stability in stool over incubation experiments. Levels of candidate erythrocyte markers were explored in stools from colorectal cancer (CRC) cases and controls. RESULTS Based on small RNA sequencing and validation RT-qPCR, expression level of each of the top blood-enriched markers (hsa-miR-144-3p, 144-5p, 451a, 486-5p, 363-3p, 20b-5p) could perfectly discriminate blood from colorectal epithelia. All six markers arose from and showed specificity to human erythrocytes. Marker levels increased linearly with erythrocyte concentration in saline or stool and demonstrated a broader dynamic range than did immunochemical test for hemoglobin. Degradation of markers occurred in stool but was reduced with preservative buffers. Erythrocyte marker candidates for stool testing were selected in an exploratory set of stools (20 CRC, 40 normal). Candidates were then further tested in a feasibility set (29 CRC, 31 advanced adenoma, and 115 normal); a miRNA panel (hsa-miR-451a, 144-5p, and 200b-3p as normalizer) yielded an AUC of 0.89 (95% CI 0.82-0.95, P < .0001) for CRC. CONCLUSIONS A novel miRNA-based approach accurately quantifies fecal blood levels over a broad, clinically relevant range.
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Affiliation(s)
- Chung Wah Wu
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Xiaoming Cao
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Calise K. Berger
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Patrick H. Foote
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Douglas W. Mahoney
- Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Julie A. Simonson
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Bradley W. Anderson
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Tracy C. Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - William R. Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Lisa A. Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - John B. Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - David A. Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
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12
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Hale VL, Chen J, Johnson S, Harrington SC, Yab TC, Smyrk TC, Nelson H, Boardman LA, Druliner BR, Levin TR, Rex DK, Ahnen DJ, Lance P, Ahlquist DA, Chia N. Shifts in the Fecal Microbiota Associated with Adenomatous Polyps. Cancer Epidemiol Biomarkers Prev 2016; 26:85-94. [PMID: 27672054 DOI: 10.1158/1055-9965.epi-16-0337] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 09/02/2016] [Accepted: 09/06/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Adenomatous polyps are the most common precursor to colorectal cancer, the second leading cause of cancer-related death in the United States. We sought to learn more about early events of carcinogenesis by investigating shifts in the gut microbiota of patients with adenomas. METHODS We analyzed 16S rRNA gene sequences from the fecal microbiota of patients with adenomas (n = 233) and without (n = 547). RESULTS Multiple taxa were significantly more abundant in patients with adenomas, including Bilophila, Desulfovibrio, proinflammatory bacteria in the genus Mogibacterium, and multiple Bacteroidetes species. Patients without adenomas had greater abundances of Veillonella, Firmicutes (Order Clostridia), and Actinobacteria (family Bifidobacteriales). Our findings were consistent with previously reported shifts in the gut microbiota of colorectal cancer patients. Importantly, the altered adenoma profile is predicted to increase primary and secondary bile acid production, as well as starch, sucrose, lipid, and phenylpropanoid metabolism. CONCLUSIONS These data hint that increased sugar, protein, and lipid metabolism along with increased bile acid production could promote a colonic environment that supports the growth of bile-tolerant microbes such as Bilophilia and Desulfovibrio In turn, these microbes may produce genotoxic or inflammatory metabolites such as H2S and secondary bile acids, which could play a role in catalyzing adenoma development and eventually colorectal cancer. IMPACT This study suggests a plausible biological mechanism to explain the links between shifts in the microbiota and colorectal cancer. This represents a first step toward resolving the complex interactions that shape the adenoma-carcinoma sequence of colorectal cancer and may facilitate personalized therapeutics focused on the microbiota. Cancer Epidemiol Biomarkers Prev; 26(1); 85-94. ©2016 AACR.
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Affiliation(s)
- Vanessa L Hale
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jun Chen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Stephen Johnson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Sean C Harrington
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Thomas C Smyrk
- Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota
| | - Heidi Nelson
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Lisa A Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Brooke R Druliner
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Theodore R Levin
- Division of Gastroenterology, Kaiser Permanente, Oakland, California
| | - Douglas K Rex
- Division of Gastroenterology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Dennis J Ahnen
- Denver Department of Veterans Affairs Medical Center, University of Colorado Denver School of Medicine, Denver, Colorado
| | - Peter Lance
- University of Arizona Cancer Center, Tucson, Arizona
| | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| | - Nicholas Chia
- Department of Surgery, Mayo Clinic, Rochester, Minnesota.
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
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13
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Giakoumopoulos M, Sander T, Volkmann C, Oliphant A, Flietner E, Aizenstein B, Eckmayer D, Vaccaro A, Rathore V, Carlson J, Berger BM, Yab TC, Taylor WR, Smyrk TC, Edell E, Mahoney DW, Kisiel JB, Ahlquist DA, Lidgard GP, Allawi HT. A methylated DNA marker panel for the sensitive detection of lung cancer in tissue. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.8527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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14
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Redwood DG, Asay ED, Blake ID, Sacco PE, Christensen CM, Sacco FD, Tiesinga JJ, Devens ME, Alberts SR, Mahoney DW, Yab TC, Foote PH, Smyrk TC, Provost EM, Ahlquist DA. Stool DNA Testing for Screening Detection of Colorectal Neoplasia in Alaska Native People. Mayo Clin Proc 2016; 91:61-70. [PMID: 26520415 DOI: 10.1016/j.mayocp.2015.10.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To assess the accuracy of a multitarget stool DNA test (MT-sDNA) compared with fecal immunochemical testing for hemoglobin (FIT) for detection of screening-relevant colorectal neoplasia (SRN) in Alaska Native people, who have among the world's highest rates of colorectal cancer (CRC) and limited access to conventional screening approaches. PATIENTS AND METHODS We performed a prospective, cross-sectional study of asymptomatic Alaska Native adults aged 40-85 years and older undergoing screening or surveillance colonoscopy between February 6, 2012, and August 7, 2014. RESULTS Among 868 enrolled participants, 661 completed the study (403 [61%] women). Overall, SRN detection by MT-sDNA (49%) was superior to that by FIT (28%; P<.001); in the screening group, SRN detection rates were 50% and 31%, respectively (P=.01). Multitarget stool DNA testing detected 62% of adenomas 2 cm or larger vs 29% by FIT (P=.05). Sensitivity by MT-sDNA increased with adenoma size (to 80% for lesions ≥3 cm; P=.01 for trend) and substantially exceeded FIT sensitivity at all adenoma sizes. For sessile serrated polyps larger than 1 cm (n=9), detection was 67% by MT-sDNA vs 11% by FIT (P=.07). For CRC (n=10), detection was 100% by MT-sDNA vs 80% by FIT (P=.48). Specificities were 93% and 96%, respectively (P=.03). CONCLUSION The sensitivity of MT-sDNA for cancer and larger polyps was high and significantly greater than that of FIT for polyps of any size, while specificity was slightly higher with FIT. These findings could translate into high cumulative neoplasm detection rates on serial testing within a screening program. The MT-sDNA represents a potential strategy to expand CRC screening and reduce CRC incidence and mortality, especially where access to endoscopy is limited.
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Affiliation(s)
- Diana G Redwood
- Alaska Native Epidemiology Center, Alaska Native Tribal Health Consortium, Anchorage, AK.
| | - Elvin D Asay
- Alaska Native Epidemiology Center, Alaska Native Tribal Health Consortium, Anchorage, AK
| | - Ian D Blake
- Alaska Native Epidemiology Center, Alaska Native Tribal Health Consortium, Anchorage, AK
| | - Pamela E Sacco
- Alaska Native Epidemiology Center, Alaska Native Tribal Health Consortium, Anchorage, AK
| | - Claudia M Christensen
- Alaska Native Epidemiology Center, Alaska Native Tribal Health Consortium, Anchorage, AK
| | - Frank D Sacco
- Department of Surgery, Alaska Native Medical Center, Anchorage, AK
| | - James J Tiesinga
- Department of Pathology, Alaska Native Medical Center, Anchorage, AK
| | - Mary E Devens
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | | | - Douglas W Mahoney
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN
| | - Tracy C Yab
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Patrick H Foote
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Thomas C Smyrk
- Department of Anatomic Pathology, Mayo Clinic, Rochester, MN
| | - Ellen M Provost
- Alaska Native Epidemiology Center, Alaska Native Tribal Health Consortium, Anchorage, AK
| | - David A Ahlquist
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
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15
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Strauss BB, Yab TC, O'Connor HM, Taylor WR, Mahoney DW, Simonson JA, Christensen J, Chari ST, Ahlquist DA. Fecal Recovery of Ingested Cellular DNA: Implications for Noninvasive Detection of Upper Gastrointestinal Neoplasms. Dig Dis Sci 2016; 61:117-25. [PMID: 26297132 DOI: 10.1007/s10620-015-3845-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 08/04/2015] [Indexed: 12/18/2022]
Abstract
BACKGROUND Stool DNA testing represents a potential noninvasive approach to detect upper gastrointestinal (UGI) neoplasms. However, little is known about fecal recovery efficiency of DNA exfoliated from UGI tumors. AIMS The purpose of this study was to establish a human ingestion model that quantitatively approximates daily cellular shedding from UGI neoplasms and to estimate fecal DNA marker recovery rates. METHODS Healthy volunteers (n = 10) ingested two scheduled doses of raw salmon, 0.3 and 30 g, simulating the mass exfoliated daily from 1 to 4.5 cm lesions. To approach a steady-state, each dose was ingested over three consecutive days in randomized order. Following defecation of an indicator dye ingested with test meals, stools were collected over 48 h. Ingested salmon DNA was captured from stools using probes targeting pathognomonic Salmonidae sequences (SlmII). Captured DNA was quantified using PCR primers to generate 178, 138, 88 and 55 bp amplicons. RESULTS SlmII sequences were recovered from all stools following salmon ingestion; recovery was proportional to amount ingested (p = 0.004). Fecal recovery of ingested salmon varied inversely with amplicon size targeted; mean recovery rates of SlmII were 0.49, 0.91, 3.63, and 7.31 copies per 100,000 copies ingested for 178, 134, 88, and 55 bp amplicons, respectively (p < 0.0001). Longer oro-anal transit was associated with reduced recovery. CONCLUSIONS While recovery efficiencies are low, ingested cellular DNA simulating daily amounts shed from UGI tumors can readily be detected in stool. Assay of shorter-fragment analyte increases recovery. This ingestion model has potential value in studying the effects of perturbations relevant to the fecal recovery of DNA exfoliated from UGI tumors.
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Affiliation(s)
- Benjamin B Strauss
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA.
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA.
| | - Helen M O'Connor
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA.
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, MN, USA.
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA.
| | - Douglas W Mahoney
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA.
| | - Julie A Simonson
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA.
| | - John Christensen
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA
| | - Suresh T Chari
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA.
| | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA.
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Kisiel JB, Raimondo M, Taylor WR, Yab TC, Mahoney DW, Sun Z, Middha S, Baheti S, Zou H, Smyrk TC, Boardman LA, Petersen GM, Ahlquist DA. New DNA Methylation Markers for Pancreatic Cancer: Discovery, Tissue Validation, and Pilot Testing in Pancreatic Juice. Clin Cancer Res 2015; 21:4473-81. [PMID: 26023084 PMCID: PMC4592385 DOI: 10.1158/1078-0432.ccr-14-2469] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 05/12/2015] [Indexed: 12/18/2022]
Abstract
PURPOSE Discriminant markers for pancreatic cancer detection are needed. We sought to identify and validate methylated DNA markers for pancreatic cancer using next-generation sequencing unbiased by known targets. EXPERIMENTAL DESIGN At a referral center, we conducted four sequential case-control studies: discovery, technical validation, biologic validation, and clinical piloting. Candidate markers were identified using variance-inflated logistic regression on reduced-representation bisulfite DNA sequencing results from matched pancreatic cancers, benign pancreas, and normal colon tissues. Markers were validated technically on replicate discovery study DNA and biologically on independent, matched, blinded tissues by methylation-specific PCR. Clinical testing of six methylation candidates and mutant KRAS was performed on secretin-stimulated pancreatic juice samples from 61 patients with pancreatic cancer, 22 with chronic pancreatitis, and 19 with normal pancreas on endoscopic ultrasound. Areas under receiver-operating characteristics curves (AUC) for markers were calculated. RESULTS Sequencing identified >500 differentially hyper-methylated regions. On independent tissues, AUC on 19 selected markers ranged between 0.73 and 0.97. Pancreatic juice AUC values for CD1D, KCNK12, CLEC11A, NDRG4, IKZF1, PKRCB, and KRAS were 0.92*, 0.88, 0.85, 0.85, 0.84, 0.83, and 0.75, respectively, for pancreatic cancer compared with normal pancreas and 0.92*, 0.73, 0.76, 0.85*, 0.73, 0.77, and 0.62 for pancreatic cancer compared with chronic pancreatitis (*, P = 0.001 vs. KRAS). CONCLUSIONS We identified and validated novel DNA methylation markers strongly associated with pancreatic cancer. On pilot testing in pancreatic juice, best markers (especially CD1D) highly discriminated pancreatic cases from controls.
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Affiliation(s)
- John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| | - Massimo Raimondo
- Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Douglas W Mahoney
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Zhifu Sun
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Sumit Middha
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Saurabh Baheti
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Hongzhi Zou
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Lisa A Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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17
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Kisiel JB, Yab TC, Taylor WR, Mahoney DW, Ahlquist DA. Stool methylated DNA markers decrease following colorectal cancer resection--implications for surveillance. Dig Dis Sci 2014; 59:1764-7. [PMID: 24993691 PMCID: PMC4220675 DOI: 10.1007/s10620-014-3265-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 06/20/2014] [Indexed: 01/05/2023]
Abstract
BACKGROUND Molecular changes associated with colorectal cancer (CRC) are detected by stool deoxyribonucleic acid testing but could persist following tumor resection. AIMS We sought to determine whether methylated gene markers in stool normalize after CRC resection. METHODS We studied stools from 22 CRC cases before and after subtotal resection and from 80 colonoscopy-normal controls. In blinded fashion, target genes (methylated NDRG4 and BMP3) were captured from stool supernatant, bisulfite-treated, and assayed by quantitative allele-specific real-time target and signal amplification. Results were dichotomized at 95% specificity cutoffs. RESULTS Among CRC cases, median methylated NDRG4 and BMP3 levels decreased dramatically (4- to 15-fold) following resection, p = 0.003 and p < 0.0001, respectively. Among the 14 cases with elevated preoperative levels, 13 (93%) fell into the normal range after surgery, p = 0.0002. A case whose stool methylated NDRG4 level increased sharply after surgery was found to have recurrent CRC. CONCLUSIONS Methylated gene marker levels clear from stool following CRC resection unless disease is present. Postoperative stool marker levels are informative and may be of value in surveillance.
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Affiliation(s)
- John B. Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - Tracy C. Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - William R. Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | | | - David A. Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
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18
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Heigh RI, Yab TC, Taylor WR, Hussain FTN, Smyrk TC, Mahoney DW, Domanico MJ, Berger BM, Lidgard GP, Ahlquist DA. Detection of colorectal serrated polyps by stool DNA testing: comparison with fecal immunochemical testing for occult blood (FIT). PLoS One 2014; 9:e85659. [PMID: 24465639 PMCID: PMC3896420 DOI: 10.1371/journal.pone.0085659] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 11/29/2013] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Precursors to 1/3 of colorectal cancer (CRC), serrated polyps have been under-detected by screening due to their inconspicuous, non-hemorrhagic, and proximal nature. A new multi-target stool DNA test (multi-target sDNA) shows high sensitivity for both CRC and advanced adenomas. Screen detection of serrated polyps by this approach requires further validation. We sought to assess and compare noninvasive detection of sessile serrated polyps (SSP) ≥ 1 cm by sDNA and an occult blood fecal immunochemical test (FIT). METHODS In a blinded prospective study, a single stool sample used for both tests was collected from 456 asymptomatic adults prior to screening or surveillance colonoscopy (criterion standard). All 29 patients with SSP ≥ 1 cm were included as cases and all 232 with no neoplastic findings as controls. Buffered stool samples were processed and frozen on receipt; Exact Sciences performed sDNA in batches using optimized analytical methods. The sDNA multi-marker panel targets methylated BMP3 (mBMP3) and NDRG4, mutant KRAS, β-actin, and hemoglobin. FIT (Polymedco OC-FIT Check) was performed in separate lab ≤ 2 days post defecation and evaluated at cutoffs of 50 (FIT-50) and 100 ng/ml (FIT-100). RESULTS MEDIAN AGES: cases 61 (range 57-77), controls 62 (52-70), p = NS. Women comprised 59% and 51%, p = NS, respectively. SSP median size was 1.2 cm (1-3 cm), 93% were proximal, and 64% had synchronous diminutive polyps. Among multi-target sDNA markers, mBMP3 proved highly discriminant for detection of SSP ≥ 1 cm (AUC = 0.87, p<0.00001); other DNA markers provided no incremental sensitivity. Hemoglobin alone showed no discrimination (AUC = 0.50, p = NS). At matched specificities, detection of SSP ≥ 1 cm by stool mBMP3 was significantly greater than by FIT-50 (66% vs 10%, p = 0.0003) or FIT-100 (63% vs 0%, p<0.0001). CONCLUSIONS In a screening and surveillance setting, SSP ≥ 1 cm can be detected noninvasively by stool assay of exfoliated DNA markers, especially mBMP3. FIT appears to have no value in SSP detection.
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Affiliation(s)
- Russell I. Heigh
- Division of Gastroenterology at Mayo Clinic, Scottsdale, Arizona, United States of America
- * E-mail:
| | - Tracy C. Yab
- Division of Gastroenterology and Hepatology at Mayo Clinic, Rochester, Minnesota, United States of America
| | - William R. Taylor
- Division of Gastroenterology and Hepatology at Mayo Clinic, Rochester, Minnesota, United States of America
| | | | - Thomas C. Smyrk
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester Minnesota, United States of America
| | - Douglas W. Mahoney
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester Minnesota, United States of America
| | | | - Barry M. Berger
- Exact Sciences Corporation, Madison, Wisconsin, United States of America
| | - Graham P. Lidgard
- Exact Sciences Corporation, Madison, Wisconsin, United States of America
| | - David A. Ahlquist
- Division of Gastroenterology and Hepatology at Mayo Clinic, Rochester, Minnesota, United States of America
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Lidgard GP, Domanico MJ, Bruinsma JJ, Light J, Gagrat ZD, Oldham-Haltom RL, Fourrier KD, Allawi H, Yab TC, Taylor WR, Simonson JA, Devens M, Heigh RI, Ahlquist DA, Berger BM. Clinical performance of an automated stool DNA assay for detection of colorectal neoplasia. Clin Gastroenterol Hepatol 2013; 11:1313-8. [PMID: 23639600 DOI: 10.1016/j.cgh.2013.04.023] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 03/28/2013] [Accepted: 04/06/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Colorectal cancer (CRC) and advanced precancers can be detected noninvasively by analyses of exfoliated DNA markers and hemoglobin in stool. Practical and cost-effective application of a stool DNA-based (sDNA) test for general CRC screening requires high levels of accuracy and high-capacity throughput. We optimized an automated sDNA assay and evaluated its clinical performance. METHODS In a blinded, multicenter, case-control study, we collected stools from 459 asymptomatic patients before screening or surveillance colonoscopies and from 544 referred patients. Cases included CRC (n = 93), advanced adenoma (AA) (n = 84), or sessile serrated adenoma ≥1 cm (SSA) (n = 30); controls included nonadvanced polyps (n = 155) or no colonic lesions (n = 641). Samples were analyzed by using an automated multi-target sDNA assay to measure β-actin (a marker of total human DNA), mutant KRAS, aberrantly methylated BMP3 and NDRG4, and fecal hemoglobin. Data were analyzed by a logistic algorithm to categorize patients as positive or negative for advanced colorectal neoplasia (CRC, advanced adenoma, and/or SSA ≥1 cm). RESULTS At 90% specificity, sDNA analysis identified individuals with CRC with 98% sensitivity. Its sensitivity for stage I cancer was 95%, for stage II cancer it was 100%, for stage III cancer it was 96%, for stage IV cancer it was 100%, and for stages I-III cancers it was 97% (nonsignificant P value). Its sensitivity for advanced precancers (AA and SSA) ≥1 cm was 57%, for >2 cm it was 73%, and for >3 cm it was 83%. The assay detected AA with high-grade dysplasia with 83% sensitivity. CONCLUSIONS We developed an automated, multi-target sDNA assay that detects CRC and premalignant lesions with levels of accuracy previously demonstrated with a manual process. This automated high-throughput system could be a widely accessible noninvasive approach to general CRC screening.
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Kisiel JB, Yab TC, Hussain FTN, Taylor WR, Garrity-Park MM, Sandborn WJ, Loftus EV, Wolff BG, Smyrk TC, Itzkowitz SH, Rubin DT, Zou H, Mahoney DW, Ahlquist DA. Stool DNA testing for the detection of colorectal neoplasia in patients with inflammatory bowel disease. Aliment Pharmacol Ther 2013; 37:546-54. [PMID: 23347191 PMCID: PMC3869396 DOI: 10.1111/apt.12218] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 12/29/2012] [Accepted: 01/02/2013] [Indexed: 12/12/2022]
Abstract
BACKGROUND Current approaches to the detection of colorectal neoplasia associated with inflammatory bowel disease (IBD-CRN) are suboptimal. AIM To test the feasibility of using stool assay of exfoliated DNA markers to detect IBD-CRN. METHODS This investigation comprised tissue and stool studies. In the tissue study, gene sequencing and methylation assays were performed on candidate genes using tissue DNA from 25 IBD-CRNs and from 25 IBD mucosae without CRN. Mutations on p53, APC, KRAS, BRAF or PIK3CA genes were insufficiently informative, but several aberrantly methylated genes were highly discriminant. In the stool study, we evaluated candidate methylated genes (vimentin, EYA4, BMP3, NDRG4) in a prospective blinded study on buffered stools from 19 cases with known IBD-CRN and 35 age- and sex-matched IBD controls without CRN. From stool-extracted DNA, target genes were assayed using quantitative allele-specific real-time target and signal amplification method. RESULTS IBD-CRN cases included 17 with ulcerative colitis (UC) and two with Crohn's disease (CD); nine had cancer and 10 had dysplasia. Controls included 25 with UC and 10 with CD. Individually, BMP3, vimentin, EYA4 and NDRG4 markers showed high discrimination in stools with respective areas under the ROC curve of 0.91, 0.91, 0.85 and 0.84 for total IBD-CRN and of 0.97, 0.97, 0.95 and 0.85 for cancer. At 89% specificity, the combination of BMP3 and mNDRG4 detected 9/9 (100%) of CRC and 80% of dysplasia, 4/4 (100%) of high grade and 4/6 (67%) of low grade. CONCLUSION These findings demonstrate the feasibility of stool DNA testing for non-invasive detection of colorectal neoplasia associated with inflammatory bowel disease.
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Affiliation(s)
- John B. Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester Minnesota, USA
| | - Tracy C. Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester Minnesota, USA
| | | | - William R. Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester Minnesota, USA
| | - Megan M. Garrity-Park
- Division of Experimental Pathology and Lab Medicine, Mayo Clinic, Rochester Minnesota, USA
| | - William J. Sandborn
- Division of Gastroenterology, University of California San Diego, La Jolla California, USA
| | - Edward V. Loftus
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester Minnesota, USA
| | - Bruce G. Wolff
- Division of Colon and Rectal Surgery, Mayo Clinic, Rochester Minnesota, USA
| | - Thomas C. Smyrk
- Division of Anatomic Pathology, Mayo Clinic, Rochester Minnesota, USA
| | - Steven H. Itzkowitz
- Dr. Henry D. Janowitz Division of Gastroenterology, Mount Sinai School of Medicine, New York New York, USA
| | - David T. Rubin
- University of Chicago Inflammatory Bowel Disease Center, Chicago Illinois, USA
| | - Hongzhi Zou
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester Minnesota, USA
| | - Douglas W. Mahoney
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester Minnesota, USA
| | - David A. Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester Minnesota, USA
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Heigh RI, Mahoney DW, Yab TC, Simonson JA, Boardman LA, Domanico MJ, Berger BM, Lidgard GP, Ahlquist DA. Screen detection of serrated polyps by stool DNA multi-target testing (sDNA-MT): Comparison against fecal immunochemical occult blood testing (FIT). J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.4_suppl.341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
341 Background: Precursors to 1/3 of colorectal cancer (CRC), serrated polyps have historically been underdetected by screening due to their inconspicuous, nonhemorrhagic, and proximal nature. New generation sDNA-MT show high sensitivity for both CRC and advanced adenomas (Gastroenterology 2012;142:248), but screen detection of serrated polyps by this approach requires further validation. Aim: To assess and compare noninvasive detection of sessile serrated polyps >1cm (SSP) by sDNA-MT and a commercial quantitative FIT. Methods: In a blinded prospective study, a single stool sample used for both tests was collected from 456 asymptomatic adults prior to screening or surveillance colonoscopy (criterion standard). All 29 patients with SSP were included as cases and all 232 with no neoplastic findings as controls. Buffered stool samples were processed and frozen on receipt; Exact Sciences performed sDNA-MT in batches using optimized analytical methods (Gastroenterology 2012;142:S770). The sDNA-MT panel targets methylated BMP3 (mBMP3) and NDRG4, mutant KRAS, β-actin, and hemoglobin. FIT (Polymedco OC-FIT Check) was performed in separate lab <2 days post defecation and evaluated at cutoffs of 50 (FIT-50) and 100 ng/ml (FIT-100). Results: Age/sex distributions were similar in cases and controls: 40% vs 45% > 65 years and 51% vs 59% women, p=NS respectively. SSP median size was 1.2cm (range 1-3cm), 93% were proximal, and 64% had synchronous diminutive polyps. Among sDNA-MT markers, mBMP3 proved highly discriminant for SSP detection (AUC=0.87, p<0.00001); other DNA markers were less informative and provided no incremental sensitivity. Hemoglobin alone showed no discrimination (AUC=0.50, p=NS). At matched specificities, SSP detection by stool mBMP3 was significantly greater than by either FIT-50 or FIT-100 (Table). Conclusions: From a screening and surveillance setting, SSP can be detected noninvasively by stool assay of exfoliated DNA markers, especially mBMP3. FIT appears to have no value in SSP detection. [Table: see text]
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Lidgard GP, Domanico MJ, Bruinsma JJ, Light J, Gagrat ZD, Oldham-Haltom RL, Fourrier KD, Allawi H, Yab TC, Simonson JA, Devens M, Heigh RI, Ahlquist DA, Berger BM. Abstract B12: An optimized molecular stool test for colorectal cancer screening: Evaluation of an automated analytic platform and logistic algorithm. Cancer Prev Res (Phila) 2012. [DOI: 10.1158/1940-6207.prev-12-b12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
We have demonstrated that colorectal cancer (CRC) and advanced pre-cancers can be detected non-invasively by a manual multi-target stool DNA-based test (sDNA-MT) comprising exfoliated DNA markers (methylated BMP3 and NDRG4, mutant KRAS (7 mutations, codons 12, 13), plus β-actin) and fecal hemoglobin (Hb) (Lidgard, Gastroenterology 2012;142(5);S-770). We now report the clinical performance of this sDNA-MT test using an optimized automated analytic platform and logistic algorithm. This platform could facilitate the routine performance of sDNA-MT for CRC screening by molecular diagnostics capable clinical laboratories.
Method: Stool samples were collected from 1003 subjects at 36 study sites after informed consent and prior to colonoscopy bowel preparation from those presenting for average risk CRC screening (283) or surveillance (176) at 2 sites. From referred subjects with CRC, Advanced Adenoma (AA) or Sessile Serrate Adenoma ≥ 1 cm, (SSA) stool was collected at least 7 days post-colonoscopy and prior to surgery or chemo-radiation (135; 21 sites) and similarly for subjects with no neoplastic findings on colonoscopy (Neg) (409; 13 sites). The study population included: cases (207), 58% male, median age 65 yrs. (38-87), CRC (93), AA (84), SSA ≥ 1 cm (30) and controls (796), 42% male, median age 65 yrs. (50-84), Neg (641) and non-advanced adenomas (NA) (155).
Stool sample collection and DNA isolation were previously described. Automated methylation, mutation and actin assays were performed with a Hamilton STARlet fluid handler (Hamilton Robotics, Reno NV), and QuARTS (Quantitative Allele-specific Real-time Target and Signal amplification) run on an ABI 7500 FastDx real time thermal cycler (Applied Biosystems, Foster City, CA). Fecal Hb (ng/ml buffer) analysis was performed by automated sandwich ELISA. A “Positive” or “Negative” result was determined with an algorithm that included the methylation and mutation results and a logistic regression score, which combines DNA marker results with Hb and actin results. Algorithm results exceeding a threshold were called “Positive”. The algorithm provided good discriminative ability, stability, sensitivity and specificity. Robustness was tested with computer simulations and statistical techniques (leave-one-out and 10-fold cross validation).
Results: At a 90% nominal specificity, sDNA-MT sensitivity was 98% for CRC (91/93) [Stage: I, 95% (20/21), II, 100% (23/23), III 96% (26/27), IV 100% (7/7) and I-III combined 97% (69/71)], 57% (65/114) for precursors ≥1 cm (AA, SSA), and 86% (12/14) for precursors with high grade dysplasia. CRC patients were typically referred to colonoscopy for symptoms and test sensitivity may be elevated relative to that seen with screening.
Conclusion: With this study using a novel automated sDNA-MT analytic platform with logistic algorithm, we corroborate our earlier findings using a manual process and demonstrate a platform that allows testing to be performed routinely by molecular diagnostic capable laboratories. The high sensitivity of sDNA-MT for CRC across all stages and for advanced precursors with high-grade dysplasia could lead to improved non-invasive CRC screening performance with wide accessibility to patients. A large multi-site pivotal CRC screening study (DeeP-C study clinicaltrials.gov, NCT01397747) to support such use is underway.
Citation Format: Graham P. Lidgard, Michael J. Domanico, Janelle J. Bruinsma, James Light, Zubin D. Gagrat, Rebecca L. Oldham-Haltom, Keith D. Fourrier, Hatim Allawi, Tracy C. Yab, Julie A. Simonson, Mary Devens, Russell I. Heigh, David A. Ahlquist, Barry M. Berger. An optimized molecular stool test for colorectal cancer screening: Evaluation of an automated analytic platform and logistic algorithm. [abstract]. In: Proceedings of the Eleventh Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2012 Oct 16-19; Anaheim, CA. Philadelphia (PA): AACR; Cancer Prev Res 2012;5(11 Suppl):Abstract nr B12.
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Affiliation(s)
- Graham P. Lidgard
- 1Exact Sciences Corporation, Madison, Wisconsin, 2Mayo Clinic, Rochester, Minnesota, 3Mayo Clinic, Scottsdale, Arizona
| | - Michael J. Domanico
- 1Exact Sciences Corporation, Madison, Wisconsin, 2Mayo Clinic, Rochester, Minnesota, 3Mayo Clinic, Scottsdale, Arizona
| | - Janelle J. Bruinsma
- 1Exact Sciences Corporation, Madison, Wisconsin, 2Mayo Clinic, Rochester, Minnesota, 3Mayo Clinic, Scottsdale, Arizona
| | - James Light
- 1Exact Sciences Corporation, Madison, Wisconsin, 2Mayo Clinic, Rochester, Minnesota, 3Mayo Clinic, Scottsdale, Arizona
| | - Zubin D. Gagrat
- 1Exact Sciences Corporation, Madison, Wisconsin, 2Mayo Clinic, Rochester, Minnesota, 3Mayo Clinic, Scottsdale, Arizona
| | - Rebecca L. Oldham-Haltom
- 1Exact Sciences Corporation, Madison, Wisconsin, 2Mayo Clinic, Rochester, Minnesota, 3Mayo Clinic, Scottsdale, Arizona
| | - Keith D. Fourrier
- 1Exact Sciences Corporation, Madison, Wisconsin, 2Mayo Clinic, Rochester, Minnesota, 3Mayo Clinic, Scottsdale, Arizona
| | - Hatim Allawi
- 1Exact Sciences Corporation, Madison, Wisconsin, 2Mayo Clinic, Rochester, Minnesota, 3Mayo Clinic, Scottsdale, Arizona
| | - Tracy C. Yab
- 1Exact Sciences Corporation, Madison, Wisconsin, 2Mayo Clinic, Rochester, Minnesota, 3Mayo Clinic, Scottsdale, Arizona
| | - Julie A. Simonson
- 1Exact Sciences Corporation, Madison, Wisconsin, 2Mayo Clinic, Rochester, Minnesota, 3Mayo Clinic, Scottsdale, Arizona
| | - Mary Devens
- 1Exact Sciences Corporation, Madison, Wisconsin, 2Mayo Clinic, Rochester, Minnesota, 3Mayo Clinic, Scottsdale, Arizona
| | - Russell I. Heigh
- 1Exact Sciences Corporation, Madison, Wisconsin, 2Mayo Clinic, Rochester, Minnesota, 3Mayo Clinic, Scottsdale, Arizona
| | - David A. Ahlquist
- 1Exact Sciences Corporation, Madison, Wisconsin, 2Mayo Clinic, Rochester, Minnesota, 3Mayo Clinic, Scottsdale, Arizona
| | - Barry M. Berger
- 1Exact Sciences Corporation, Madison, Wisconsin, 2Mayo Clinic, Rochester, Minnesota, 3Mayo Clinic, Scottsdale, Arizona
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Ahlquist DA, Taylor WR, Yab TC, Devens ME, Mahoney DW, Boardman LA, Thibodeau SN, Zou H, Michael D, Berger BM, Lidgard GP. Abstract 3572: Methylated gene marker levels in stool: effects of demographic, drug, and body mass and other patient characteristics. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-3572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Aberrantly methylated genes represent attractive and broadly informative markers for colorectal cancer (CRC). As demographics, numerous ingestants, environmental exposures, and obesity variably influence both gene methylation rates and CRC incidence, it is important to understand the effects of such covariates on the clinical performance of CRC screening tests that incorporate assay of methylated gene markers. Based on a recent multicenter study (Ahlquist et al. Gastroenterology 2012 (in press)), stool assay of carefully selected methylated gene marker candidates (NDRG4, BMP3, vimentin, TFPI2), alone or in combination, yield high detection rates of both CRC and large adenomas. Aim: To assess the impact of demographic, exposure, body mass, and other patient variables on stool levels of the above 4 methylated gene markers. Methods: We studied buffered stools collected within 3 years of a normal colonoscopy from 500 patients undergoing average-risk screening or polyp surveillance (median age 64 (range 44-85); 53% women). Upon receipt, stools were promptly homogenized, aliquoted, and frozen at –80°C. On supernatants from thawed/spun aliquots, target genes were purified by hybrid capture, bisulfite treated, and assayed using the analytically-sensitive QuARTS method (quantitative allele-specific real-time target and signal amplification), as described (above citation). The reference gene β-actin was assayed along with methylation of NDRG4, BMP3, vimentin, TFPI2. Log-converted data were normalized to allow comparison of effects between markers, and effect size was expressed as % change relative to standard deviation for each marker (standardized relative change (SRβ)). Results: The only patient characteristic that significantly influenced all methylated marker levels in stool was age (p<0.0001 for each marker); SRΔ was greatest with TFPI2 at +91.3 (p<0.001 vs other markers), least with BMP3 at +29.7 (p<0.001 vs others), and intermediate with vimentin at +46.0 and NDRG4 at +45.1. In contrast to methylation markers, levels of β-actin did not change across age. The other demographic variables of sex, race, and geographic residence had no effect on methylation markers. Marker levels were also not affected by exposure variables (smoking, alcohol consumption, or analgesic use), by family history of CRC or polyps, or by personal history of polyps. Finally, neither overweight status (n=176) nor obesity (n=148) had an effect on marker levels. Conclusions: Age significantly affects stool levels of tumor-associated methylated gene markers in colonoscopy-normal patients, and the degree of this age effect differs across markers. In contrast, other key patient variables had no effect on stool marker levels. Comment: Optimal use of these methylation markers for stool screening of CRC may require age-adjustment of normal cutoff levels to maximize test specificity.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3572. doi:1538-7445.AM2012-3572
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Ahlquist DA, Zou H, Domanico M, Mahoney DW, Yab TC, Taylor WR, Butz ML, Thibodeau SN, Rabeneck L, Paszat LF, Kinzler KW, Vogelstein B, Bjerregaard NC, Laurberg S, Sørensen HT, Berger BM, Lidgard GP. Next-generation stool DNA test accurately detects colorectal cancer and large adenomas. Gastroenterology 2012; 142:248-56; quiz e25-6. [PMID: 22062357 PMCID: PMC4017869 DOI: 10.1053/j.gastro.2011.10.031] [Citation(s) in RCA: 218] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 10/18/2011] [Accepted: 10/24/2011] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Technical advances have led to stool DNA (sDNA) tests that might accurately detect neoplasms on both sides of the colorectum. We assessed colorectal neoplasm detection by a next-generation sDNA test and effects of covariates on test performance. METHODS We performed a blinded, multicenter, case-control study using archived stool samples collected in preservative buffer from 252 patients with colorectal cancer (CRC), 133 with adenomas ≥ 1 cm, and 293 individuals with normal colonoscopy results (controls); two-thirds were randomly assigned to a training set and one-third to a test set. The sDNA test detects 4 methylated genes, a mutant form of KRAS, and the α-actin gene (as a reference value) using quantitative, allele-specific, real-time target and signal amplification; it also quantifies hemoglobin. We used a logistical model to analyze data. RESULTS The sDNA test identified 85% of patients with CRC and 54% of patients with adenomas ≥1 cm with 90% specificity. The test had a high rate of detection for all nonmetastatic stages of CRC (aggregate 87% detection rate for CRC stages I-III). Detection rates increased with adenoma size: 54% ≥ 1 cm, 63% >1 cm, 77% >2 cm, 86% >3 cm, and 92% >4 cm (P < .0001). Based on receiver operating characteristic analysis, the rate of CRC detection was slightly greater for the training than the test set (P = .04), whereas the rate of adenoma detection was comparable between sets. Sensitivities for detection of CRC and adenoma did not differ with lesion site. CONCLUSIONS Early-stage CRC and large adenomas can be detected throughout the colorectum and with high levels of accuracy by the sDNA test. Neoplasm size, but not anatomical site, affected detection rates. Further studies are needed to validate the findings in a larger population and optimize the sDNA test.
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Affiliation(s)
- David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905, USA.
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Kisiel JB, Yab TC, Taylor WR, Chari ST, Petersen GM, Mahoney DW, Ahlquist DA. Stool DNA testing for the detection of pancreatic cancer: assessment of methylation marker candidates. Cancer 2011. [PMID: 22083596 DOI: 10.1002/cncr/26558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Pancreatic cancer (PanC) presents at late stage with high mortality. Effective early detection methods are needed. Aberrantly methylated genes are unexplored as markers for noninvasive detection by stool testing. The authors aimed to select discriminant methylated genes and to assess accuracy of these and mutant KRAS in stool to detect PanC. METHODS Nine target genes were assayed by real-time methylation-specific polymerase chain reaction (MSP) in bisulfite-treated DNA from microdissected frozen specimens of 24 PanC cases and 30 normal colon controls. Archived stools from 58 PanC cases and 65 controls matched on sex, age, and smoking were analyzed. Target genes from fecal supernatants were enriched by hybrid capture, bisulfite-treated, and assayed by MSP. KRAS mutations were assayed using the QuARTS technique. RESULTS Areas under the receiver operating characteristics curves (AUCs) for tissue BMP3, NDRG4, EYA4, UCHL1, MDFI, Vimentin, CNTNAP2, SFRP2, and TFPI2 were 0.90, 0.79, 0.78, 0.78, 0.77, 0.77, 0.69, 0.67, and 0.66, respectively. The top 4 markers and mutant KRAS were evaluated in stool. BMP3 was the most discriminant methylation marker in stool. At 90% specificity, methylated BMP3 alone detected 51% of PanCs, mutant KRAS detected 50%, and combination detected 67%. AUCs for methylated BMP3, mutant KRAS, and combination in stool were 0.73, 0.75, and 0.85, respectively. CONCLUSIONS This study demonstrates that stool assay of a methylated gene marker can detect PanC. Among candidate methylated markers discriminant in tissue, BMP3 alone performed well in stool. Combining methylated BMP3 and mutant KRAS increased stool detection over either marker alone.
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Affiliation(s)
- John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
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Kisiel JB, Yab TC, Taylor WR, Chari ST, Petersen GM, Mahoney DW, Ahlquist DA. Stool DNA testing for the detection of pancreatic cancer: assessment of methylation marker candidates. Cancer 2011; 118:2623-31. [PMID: 22083596 DOI: 10.1002/cncr.26558] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 08/10/2011] [Indexed: 12/21/2022]
Abstract
BACKGROUND Pancreatic cancer (PanC) presents at late stage with high mortality. Effective early detection methods are needed. Aberrantly methylated genes are unexplored as markers for noninvasive detection by stool testing. The authors aimed to select discriminant methylated genes and to assess accuracy of these and mutant KRAS in stool to detect PanC. METHODS Nine target genes were assayed by real-time methylation-specific polymerase chain reaction (MSP) in bisulfite-treated DNA from microdissected frozen specimens of 24 PanC cases and 30 normal colon controls. Archived stools from 58 PanC cases and 65 controls matched on sex, age, and smoking were analyzed. Target genes from fecal supernatants were enriched by hybrid capture, bisulfite-treated, and assayed by MSP. KRAS mutations were assayed using the QuARTS technique. RESULTS Areas under the receiver operating characteristics curves (AUCs) for tissue BMP3, NDRG4, EYA4, UCHL1, MDFI, Vimentin, CNTNAP2, SFRP2, and TFPI2 were 0.90, 0.79, 0.78, 0.78, 0.77, 0.77, 0.69, 0.67, and 0.66, respectively. The top 4 markers and mutant KRAS were evaluated in stool. BMP3 was the most discriminant methylation marker in stool. At 90% specificity, methylated BMP3 alone detected 51% of PanCs, mutant KRAS detected 50%, and combination detected 67%. AUCs for methylated BMP3, mutant KRAS, and combination in stool were 0.73, 0.75, and 0.85, respectively. CONCLUSIONS This study demonstrates that stool assay of a methylated gene marker can detect PanC. Among candidate methylated markers discriminant in tissue, BMP3 alone performed well in stool. Combining methylated BMP3 and mutant KRAS increased stool detection over either marker alone.
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Affiliation(s)
- John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
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