Novel Methylated DNA Markers Discriminate Advanced Neoplasia in Pancreatic Cysts: Marker Discovery, Tissue Validation, and Cyst Fluid Testing

Shounak Majumder, William R. Taylor, Tracy C. Yab, Calise K. Berger, Brian A. Dukek, Xiaoming Cao, Patrick H. Foote, Chung Wah Wu, Douglas W. Mahoney, Harry R. Aslanian, Carlos Fernández-Del Castillo, Leona A. Doyle, James J. Farrell, William E. Fisher, Linda S. Lee, Yvonne N. Lee, Walter Park, Clifton Rodrigues, Bonnie Elyssa Gould Rothberg, Ronald R. SalemDiane M. Simeone, Sumithra Urs, George Van Buren, Thomas C. Smyrk, Hatim T. Allawi, Graham P. Lidgard, Massimo Raimondo, Suresh T. Chari, Michael L. Kendrick, John B. Kisiel, Mark D. Topazian, David A. Ahlquist

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1539-1549
Number of pages11
JournalThe American Journal of Gastroenterology
Volume114
Issue number9
DOIs
StatePublished - Sep 1 2019

Fingerprint

Pancreatic Cyst
Cyst Fluid
Genetic Markers
Pancreatic Neoplasms
Neoplasms
ROC Curve
Confidence Intervals
Carcinoembryonic Antigen
Patient Selection
Methylation

ASJC Scopus subject areas

  • Hepatology
  • Gastroenterology

Cite this

Novel Methylated DNA Markers Discriminate Advanced Neoplasia in Pancreatic Cysts : Marker Discovery, Tissue Validation, and Cyst Fluid Testing. / Majumder, Shounak; Taylor, William R.; Yab, Tracy C.; Berger, Calise K.; Dukek, Brian A.; Cao, Xiaoming; Foote, Patrick H.; Wu, Chung Wah; Mahoney, Douglas W.; Aslanian, Harry R.; Fernández-Del Castillo, Carlos; Doyle, Leona A.; Farrell, James J.; Fisher, William E.; Lee, Linda S.; Lee, Yvonne N.; Park, Walter; Rodrigues, Clifton; Gould Rothberg, Bonnie Elyssa; Salem, Ronald R.; Simeone, Diane M.; Urs, Sumithra; Van Buren, George; Smyrk, Thomas C.; Allawi, Hatim T.; Lidgard, Graham P.; Raimondo, Massimo; Chari, Suresh T.; Kendrick, Michael L.; Kisiel, John B.; Topazian, Mark D.; Ahlquist, David A.

In: The American Journal of Gastroenterology, Vol. 114, No. 9, 01.09.2019, p. 1539-1549.

Research output: Contribution to journalArticle

Majumder, S, Taylor, WR, Yab, TC, Berger, CK, Dukek, BA, Cao, X, Foote, PH, Wu, CW, Mahoney, DW, Aslanian, HR, Fernández-Del Castillo, C, Doyle, LA, Farrell, JJ, Fisher, WE, Lee, LS, Lee, YN, Park, W, Rodrigues, C, Gould Rothberg, BE, Salem, RR, Simeone, DM, Urs, S, Van Buren, G, Smyrk, TC, Allawi, HT, Lidgard, GP, Raimondo, M, Chari, ST, Kendrick, ML, Kisiel, JB, Topazian, MD & Ahlquist, DA 2019, 'Novel Methylated DNA Markers Discriminate Advanced Neoplasia in Pancreatic Cysts: Marker Discovery, Tissue Validation, and Cyst Fluid Testing', The American Journal of Gastroenterology, vol. 114, no. 9, pp. 1539-1549. https://doi.org/10.14309/ajg.0000000000000284
Majumder, Shounak ; Taylor, William R. ; Yab, Tracy C. ; Berger, Calise K. ; Dukek, Brian A. ; Cao, Xiaoming ; Foote, Patrick H. ; Wu, Chung Wah ; Mahoney, Douglas W. ; Aslanian, Harry R. ; Fernández-Del Castillo, Carlos ; Doyle, Leona A. ; Farrell, James J. ; Fisher, William E. ; Lee, Linda S. ; Lee, Yvonne N. ; Park, Walter ; Rodrigues, Clifton ; Gould Rothberg, Bonnie Elyssa ; Salem, Ronald R. ; Simeone, Diane M. ; Urs, Sumithra ; Van Buren, George ; Smyrk, Thomas C. ; Allawi, Hatim T. ; Lidgard, Graham P. ; Raimondo, Massimo ; Chari, Suresh T. ; Kendrick, Michael L. ; Kisiel, John B. ; Topazian, Mark D. ; Ahlquist, David A. / Novel Methylated DNA Markers Discriminate Advanced Neoplasia in Pancreatic Cysts : Marker Discovery, Tissue Validation, and Cyst Fluid Testing. In: The American Journal of Gastroenterology. 2019 ; Vol. 114, No. 9. pp. 1539-1549.
@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 Kendrick, {Michael L.} and Kisiel, {John B.} and Topazian, {Mark D.} and Ahlquist, {David A.}",
year = "2019",
month = "9",
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",

}

TY - JOUR

T1 - Novel Methylated DNA Markers Discriminate Advanced Neoplasia in Pancreatic Cysts

T2 - Marker Discovery, Tissue Validation, and Cyst Fluid Testing

AU - Majumder, Shounak

AU - Taylor, William R.

AU - Yab, Tracy C.

AU - Berger, Calise K.

AU - Dukek, Brian A.

AU - Cao, Xiaoming

AU - Foote, Patrick H.

AU - Wu, Chung Wah

AU - Mahoney, Douglas W.

AU - Aslanian, Harry R.

AU - Fernández-Del Castillo, Carlos

AU - Doyle, Leona A.

AU - Farrell, James J.

AU - Fisher, William E.

AU - Lee, Linda S.

AU - Lee, Yvonne N.

AU - Park, Walter

AU - Rodrigues, Clifton

AU - Gould Rothberg, Bonnie Elyssa

AU - Salem, Ronald R.

AU - Simeone, Diane M.

AU - Urs, Sumithra

AU - Van Buren, George

AU - Smyrk, Thomas C.

AU - Allawi, Hatim T.

AU - Lidgard, Graham P.

AU - Raimondo, Massimo

AU - Chari, Suresh T.

AU - Kendrick, Michael L.

AU - Kisiel, John B.

AU - Topazian, Mark D.

AU - Ahlquist, David A.

PY - 2019/9/1

Y1 - 2019/9/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85071787722&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85071787722&partnerID=8YFLogxK

U2 - 10.14309/ajg.0000000000000284

DO - 10.14309/ajg.0000000000000284

M3 - Article

C2 - 31306149

AN - SCOPUS:85071787722

VL - 114

SP - 1539

EP - 1549

JO - American Journal of Gastroenterology

JF - American Journal of Gastroenterology

SN - 0002-9270

IS - 9

ER -