@article{b59a33bda11a4e518e4f804ec5572e30,
title = "Novel Methylated DNA Markers Discriminate Advanced Neoplasia in Pancreatic Cysts: Marker Discovery, Tissue Validation, and Cyst Fluid Testing",
abstract = "OBJECTIVES:Pancreatic cystic lesions (PCLs) may be precancerous. Those likely to harbor high-grade dysplasia (HGD) or pancreatic cancer (PC) are targets for surgical resection. Current algorithms to predict advanced neoplasia (HGD/PC) in PCLs lack diagnostic accuracy. In pancreatic tissue and cyst fluid (CF) from PCLs, we sought to identify and validate novel methylated DNA markers (MDMs) that discriminate HGD/PC from low-grade dysplasia (LGD) or no dysplasia (ND).METHODS:From an unbiased whole-methylome discovery approach using predefined selection criteria followed by multistep validation on case (HGD or PC) and control (ND or LGD) tissues, we identified discriminant MDMs. Top candidate MDMs were then assayed by quantitative methylation-specific polymerase chain reaction on archival CF from surgically resected PCLs.RESULTS:Of 25 discriminant MDMs identified in tissue, 13 were selected for validation in 134 CF samples (21 cases [8 HGD, 13 PC], 113 controls [45 ND, 68 LGD]). A tree-based algorithm using 2 CF-MDMs (TBX15, BMP3) achieved sensitivity and specificity above 90%. Discrimination was significantly better by this CF-MDM panel than by mutant KRAS or carcinoembryonic antigen, with areas under the receiver operating characteristic curve of 0.93 (95% confidence interval: 0.86-0.99), 0.71 (0.57-0.85), and 0.72 (0.60-0.84), respectively. Cutoffs for the MDM panel applied to an independent CF validation set (31 cases, 56 controls) yielded similarly high discrimination, areas under the receiver operating characteristic curve = 0.86 (95% confidence interval: 0.77-0.94, P = 0.2).DISCUSSION:Novel MDMs discovered and validated in tissue accurately identify PCLs harboring HGD/PC. A panel of 2 MDMs assayed in CF yielded results with potential to enhance current risk prediction algorithms. Prospective studies are indicated to optimize and further evaluate CF-MDMs for clinical use.",
author = "Shounak Majumder and Taylor, {William R.} and Yab, {Tracy C.} and Berger, {Calise K.} and Dukek, {Brian A.} and Xiaoming Cao and Foote, {Patrick H.} and Wu, {Chung Wah} and Mahoney, {Douglas W.} and Aslanian, {Harry R.} and {Fern{\'a}ndez-Del Castillo}, Carlos and Doyle, {Leona A.} and Farrell, {James J.} and Fisher, {William E.} and Lee, {Linda S.} and Lee, {Yvonne N.} and Walter Park and Clifton Rodrigues and {Gould Rothberg}, {Bonnie Elyssa} and Salem, {Ronald R.} and Simeone, {Diane M.} and Sumithra Urs and {Van Buren}, George and Smyrk, {Thomas C.} and Allawi, {Hatim T.} and Lidgard, {Graham P.} and Massimo Raimondo and Chari, {Suresh T.} and Michael Kendrick and Kisiel, {John B.} and Topazian, {Mark D.} and Ahlquist, {David A.}",
note = "Funding Information: Carol M. Gatton Foundation (to DAA). Research reported in this publication was also supported by the National Institute of Diabetes And Digestive And Kidney Diseases of the National Institutes of Health under Award Number P30DK084567. The project described was also supported by Award Number P50 CA102701 (Mayo Clinic SPORE in Pancreatic Cancer) and R37CA214679 from the National Cancer Institute. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Cancer Institute or the National Institutes of Health. Exact Sciences (Madison WI) provided funds for sequencing and critical assay reagents. Funding Information: study concept and design; laboratory testing, analysis and interpretation of data; drafting of the manuscript; and critical review of the manuscript for important intellectual content. T.Y.: study concept and design; study supervision; laboratory testing, and interpretation of data; and critical review of the manuscript for important intellectual content. C.B., B.D., X.C., P.F., and C.W.: laboratory testing and interpretation of data. D.M.: study concept and design; analysis and interpretation of data; critical review of the manuscript for important intellectual content; and statistical analysis. H.A. and C.F.-D.C.: acquisition of clinical samples; critical review of the manuscript for important intellectual content. L.D.: pathology interpretation of clinical samples and critical review of the manuscript for important intellectual content. J.F., W F., C.R., L.L., Y.L., W.P., B.R., R.S., D.S., S.U., and G.V.B.: acquisition of clinical samples and critical review of the manuscript for important intellectual content. T.S.: advice on pathology interpretation; analysis and interpretation of data; and critical review of the manuscript for important intellectual content. H.A and G.L.: critical review of the manuscript for important intellectual content. M.R. and M.T.: study concept and design; acquisition of clinical samples; and critical review of the manuscript for important intellectual content. S.C., M.K., and J.K.: study concept and design and critical review of the manuscript for important intellectual content. D.A.: study concept and design; analysis and interpretation of data; drafting of the manuscript; critical review of the manuscript for important intellectual content; statistical analysis; obtained funding; and study supervision. Financial support: Funding was provided by the Carol M. Gatton Foundation (to DAA). Research reported in this publication was also supported by the National Institute of Diabetes And Digestive And Kidney Diseases of the National Institutes of Health under Award Number P30DK084567. The project described was also supported by Award Number P50 CA102701 (Mayo Clinic SPORE in Pancreatic Cancer) and R37CA214679 from the National Cancer Institute. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Cancer Institute or the National Institutes of Health. Exact Sciences (Madison WI) provided funds for sequencing and critical assay reagents. Potential competing interests: Mayo Clinic has licensed intellectual property to Exact Sciences on molecular markers and sample processing techniques for multiple cancers and precancers, including pancreatic cancer. As co-inventors on licensed technologies, several co-authors (D.A.A., J.B.K., S.M., W.R.T., D.W.M., and T.C.Y.) could share potential future royalties to Mayo Clinic from Exact Sciences in accordance with institutional policy and oversight. G.P.L. and H.T.A. are Exact Sciences employees. Exact Sciences provided assay materials and partial funding but had no role in the protocol design, study execution, or analysis of data. The other authors of this manuscript have no conflicts of interest to declare. Publisher Copyright: {\textcopyright} 2019 by The American College of Gastroenterology.",
year = "2019",
month = sep,
day = "1",
doi = "10.14309/ajg.0000000000000284",
language = "English (US)",
volume = "114",
pages = "1539--1549",
journal = "American Journal of Gastroenterology",
issn = "0002-9270",
publisher = "Nature Publishing Group",
number = "9",
}