Detection of endometrial cancer using tampon-based collection and methylated DNA markers

Jamie N. Bakkum-Gamez; Mark E. Sherman; Seth W. Slettedahl; Douglas W. Mahoney; Maureen A. Lemens; Shannon K. Laughlin-Tommaso; Matthew R. Hopkins; Ann VanOosten; Viji Shridhar; Julie K. Staub; Xiaoming Cao; Patrick H. Foote; Megan A. Clarke; Kelli N. Burger; Calise K. Berger; Maria C. O'Connell; Karen A. Doering; Karl C. Podratz; Christopher C. DeStephano; J. Kenneth Schoolmeester; Sarah E. Kerr; Nicolas Wentzensen; William R. Taylor; John B. Kisiel

doi:10.1016/j.ygyno.2023.04.014

Detection of endometrial cancer using tampon-based collection and methylated DNA markers

Jamie N. Bakkum-Gamez, Mark E. Sherman, Seth W. Slettedahl, Douglas W. Mahoney, Maureen A. Lemens, Shannon K. Laughlin-Tommaso, Matthew R. Hopkins, Ann VanOosten, Viji Shridhar, Julie K. Staub, Xiaoming Cao, Patrick H. Foote, Megan A. Clarke, Kelli N. Burger, Calise K. Berger, Maria C. O'Connell, Karen A. Doering, Karl C. Podratz, Christopher C. DeStephano, J. Kenneth SchoolmeesterSarah E. Kerr, Nicolas Wentzensen, William R. Taylor, John B. Kisiel

Research output: Contribution to journal › Article › peer-review

Abstract

Objective: Alterations in DNA methylation are early events in endometrial cancer (EC) development and may have utility in EC detection via tampon-collected vaginal fluid. Methods: For discovery, DNA from frozen EC, benign endometrium (BE), and benign cervicovaginal (BCV) tissues underwent reduced representation bisulfite sequencing (RRBS) to identify differentially methylated regions (DMRs). Candidate DMRs were selected based on receiver operating characteristic (ROC) discrimination, methylation level fold-change between cancers and controls, and absence of background CpG methylation. Methylated DNA marker (MDM) validation was performed using qMSP on DNA from independent EC and BE FFPE tissue sets. Women ≥45 years of age with abnormal uterine bleeding (AUB) or postmenopausal bleeding (PMB) or any age with biopsy-proven EC self-collected vaginal fluid using a tampon prior to clinically indicated endometrial sampling or hysterectomy. Vaginal fluid DNA was assayed by qMSP for EC-associated MDMs. Random forest modeling analysis was performed to generate predictive probability of underlying disease; results were 500-fold in-silico cross-validated. Results: Thirty-three candidate MDMs met performance criteria in tissue. For the tampon pilot, 100 EC cases were frequency matched by menopausal status and tampon collection date to 92 BE controls. A 28-MDM panel highly discriminated between EC and BE (96% (95%CI 89–99%) specificity; 76% (66–84%) sensitivity (AUC 0.88). In PBS/EDTA tampon buffer, the panel yielded 96% (95% CI 87–99%) specificity and 82% (70–91%) sensitivity (AUC 0.91). Conclusion: Next generation methylome sequencing, stringent filtering criteria, and independent validation yielded excellent candidate MDMs for EC. EC-associated MDMs performed with promisingly high sensitivity and specificity in tampon-collected vaginal fluid; PBS-based tampon buffer with added EDTA improved sensitivity. Larger tampon-based EC MDM testing studies are warranted.

Original language	English (US)
Pages (from-to)	11-20
Number of pages	10
Journal	Gynecologic oncology
Volume	174
DOIs	https://doi.org/10.1016/j.ygyno.2023.04.014
State	Published - Jul 2023

Keywords

Cell-free nucleic acids
DNA methylation
Endometrial cancer
Endometrial neoplasm/diagnosis
Endometrial neoplasm/prevention & control
Liquid biopsy

ASJC Scopus subject areas

Oncology
Obstetrics and Gynecology

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10.1016/j.ygyno.2023.04.014

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Bakkum-Gamez, J. N., Sherman, M. E., Slettedahl, S. W., Mahoney, D. W., Lemens, M. A., Laughlin-Tommaso, S. K., Hopkins, M. R., VanOosten, A., Shridhar, V., Staub, J. K., Cao, X., Foote, P. H., Clarke, M. A., Burger, K. N., Berger, C. K., O'Connell, M. C., Doering, K. A., Podratz, K. C., DeStephano, C. C., ... Kisiel, J. B. (2023). Detection of endometrial cancer using tampon-based collection and methylated DNA markers. Gynecologic oncology, 174, 11-20. https://doi.org/10.1016/j.ygyno.2023.04.014

Bakkum-Gamez, JN , Sherman, ME, Slettedahl, SW, Mahoney, DW, Lemens, MA, Laughlin-Tommaso, SK, Hopkins, MR, VanOosten, A, Shridhar, V, Staub, JK, Cao, X, Foote, PH, Clarke, MA, Burger, KN, Berger, CK, O'Connell, MC, Doering, KA, Podratz, KC, DeStephano, CC, Schoolmeester, JK, Kerr, SE, Wentzensen, N, Taylor, WR & Kisiel, JB 2023, 'Detection of endometrial cancer using tampon-based collection and methylated DNA markers', Gynecologic oncology, vol. 174, pp. 11-20. https://doi.org/10.1016/j.ygyno.2023.04.014

@article{084f00967b3c4651b9778f0b89fbf493,

title = "Detection of endometrial cancer using tampon-based collection and methylated DNA markers",

abstract = "Objective: Alterations in DNA methylation are early events in endometrial cancer (EC) development and may have utility in EC detection via tampon-collected vaginal fluid. Methods: For discovery, DNA from frozen EC, benign endometrium (BE), and benign cervicovaginal (BCV) tissues underwent reduced representation bisulfite sequencing (RRBS) to identify differentially methylated regions (DMRs). Candidate DMRs were selected based on receiver operating characteristic (ROC) discrimination, methylation level fold-change between cancers and controls, and absence of background CpG methylation. Methylated DNA marker (MDM) validation was performed using qMSP on DNA from independent EC and BE FFPE tissue sets. Women ≥45 years of age with abnormal uterine bleeding (AUB) or postmenopausal bleeding (PMB) or any age with biopsy-proven EC self-collected vaginal fluid using a tampon prior to clinically indicated endometrial sampling or hysterectomy. Vaginal fluid DNA was assayed by qMSP for EC-associated MDMs. Random forest modeling analysis was performed to generate predictive probability of underlying disease; results were 500-fold in-silico cross-validated. Results: Thirty-three candidate MDMs met performance criteria in tissue. For the tampon pilot, 100 EC cases were frequency matched by menopausal status and tampon collection date to 92 BE controls. A 28-MDM panel highly discriminated between EC and BE (96% (95%CI 89–99%) specificity; 76% (66–84%) sensitivity (AUC 0.88). In PBS/EDTA tampon buffer, the panel yielded 96% (95% CI 87–99%) specificity and 82% (70–91%) sensitivity (AUC 0.91). Conclusion: Next generation methylome sequencing, stringent filtering criteria, and independent validation yielded excellent candidate MDMs for EC. EC-associated MDMs performed with promisingly high sensitivity and specificity in tampon-collected vaginal fluid; PBS-based tampon buffer with added EDTA improved sensitivity. Larger tampon-based EC MDM testing studies are warranted.",

keywords = "Cell-free nucleic acids, DNA methylation, Endometrial cancer, Endometrial neoplasm/diagnosis, Endometrial neoplasm/prevention & control, Liquid biopsy",

author = "Bakkum-Gamez, {Jamie N.} and Sherman, {Mark E.} and Slettedahl, {Seth W.} and Mahoney, {Douglas W.} and Lemens, {Maureen A.} and Laughlin-Tommaso, {Shannon K.} and Hopkins, {Matthew R.} and Ann VanOosten and Viji Shridhar and Staub, {Julie K.} and Xiaoming Cao and Foote, {Patrick H.} and Clarke, {Megan A.} and Burger, {Kelli N.} and Berger, {Calise K.} and O'Connell, {Maria C.} and Doering, {Karen A.} and Podratz, {Karl C.} and DeStephano, {Christopher C.} and Schoolmeester, {J. Kenneth} and Kerr, {Sarah E.} and Nicolas Wentzensen and Taylor, {William R.} and Kisiel, {John B.}",

note = "Publisher Copyright: {\textcopyright} 2023 Elsevier Inc.",

year = "2023",

month = jul,

doi = "10.1016/j.ygyno.2023.04.014",

language = "English (US)",

volume = "174",

pages = "11--20",

journal = "Gynecologic oncology",

issn = "0090-8258",

publisher = "Academic Press Inc.",

}

TY - JOUR

T1 - Detection of endometrial cancer using tampon-based collection and methylated DNA markers

AU - Bakkum-Gamez, Jamie N.

AU - Sherman, Mark E.

AU - Slettedahl, Seth W.

AU - Mahoney, Douglas W.

AU - Lemens, Maureen A.

AU - Laughlin-Tommaso, Shannon K.

AU - Hopkins, Matthew R.

AU - VanOosten, Ann

AU - Shridhar, Viji

AU - Staub, Julie K.

AU - Cao, Xiaoming

AU - Foote, Patrick H.

AU - Clarke, Megan A.

AU - Burger, Kelli N.

AU - Berger, Calise K.

AU - O'Connell, Maria C.

AU - Doering, Karen A.

AU - Podratz, Karl C.

AU - DeStephano, Christopher C.

AU - Schoolmeester, J. Kenneth

AU - Kerr, Sarah E.

AU - Wentzensen, Nicolas

AU - Taylor, William R.

AU - Kisiel, John B.

PY - 2023/7

Y1 - 2023/7

N2 - Objective: Alterations in DNA methylation are early events in endometrial cancer (EC) development and may have utility in EC detection via tampon-collected vaginal fluid. Methods: For discovery, DNA from frozen EC, benign endometrium (BE), and benign cervicovaginal (BCV) tissues underwent reduced representation bisulfite sequencing (RRBS) to identify differentially methylated regions (DMRs). Candidate DMRs were selected based on receiver operating characteristic (ROC) discrimination, methylation level fold-change between cancers and controls, and absence of background CpG methylation. Methylated DNA marker (MDM) validation was performed using qMSP on DNA from independent EC and BE FFPE tissue sets. Women ≥45 years of age with abnormal uterine bleeding (AUB) or postmenopausal bleeding (PMB) or any age with biopsy-proven EC self-collected vaginal fluid using a tampon prior to clinically indicated endometrial sampling or hysterectomy. Vaginal fluid DNA was assayed by qMSP for EC-associated MDMs. Random forest modeling analysis was performed to generate predictive probability of underlying disease; results were 500-fold in-silico cross-validated. Results: Thirty-three candidate MDMs met performance criteria in tissue. For the tampon pilot, 100 EC cases were frequency matched by menopausal status and tampon collection date to 92 BE controls. A 28-MDM panel highly discriminated between EC and BE (96% (95%CI 89–99%) specificity; 76% (66–84%) sensitivity (AUC 0.88). In PBS/EDTA tampon buffer, the panel yielded 96% (95% CI 87–99%) specificity and 82% (70–91%) sensitivity (AUC 0.91). Conclusion: Next generation methylome sequencing, stringent filtering criteria, and independent validation yielded excellent candidate MDMs for EC. EC-associated MDMs performed with promisingly high sensitivity and specificity in tampon-collected vaginal fluid; PBS-based tampon buffer with added EDTA improved sensitivity. Larger tampon-based EC MDM testing studies are warranted.

AB - Objective: Alterations in DNA methylation are early events in endometrial cancer (EC) development and may have utility in EC detection via tampon-collected vaginal fluid. Methods: For discovery, DNA from frozen EC, benign endometrium (BE), and benign cervicovaginal (BCV) tissues underwent reduced representation bisulfite sequencing (RRBS) to identify differentially methylated regions (DMRs). Candidate DMRs were selected based on receiver operating characteristic (ROC) discrimination, methylation level fold-change between cancers and controls, and absence of background CpG methylation. Methylated DNA marker (MDM) validation was performed using qMSP on DNA from independent EC and BE FFPE tissue sets. Women ≥45 years of age with abnormal uterine bleeding (AUB) or postmenopausal bleeding (PMB) or any age with biopsy-proven EC self-collected vaginal fluid using a tampon prior to clinically indicated endometrial sampling or hysterectomy. Vaginal fluid DNA was assayed by qMSP for EC-associated MDMs. Random forest modeling analysis was performed to generate predictive probability of underlying disease; results were 500-fold in-silico cross-validated. Results: Thirty-three candidate MDMs met performance criteria in tissue. For the tampon pilot, 100 EC cases were frequency matched by menopausal status and tampon collection date to 92 BE controls. A 28-MDM panel highly discriminated between EC and BE (96% (95%CI 89–99%) specificity; 76% (66–84%) sensitivity (AUC 0.88). In PBS/EDTA tampon buffer, the panel yielded 96% (95% CI 87–99%) specificity and 82% (70–91%) sensitivity (AUC 0.91). Conclusion: Next generation methylome sequencing, stringent filtering criteria, and independent validation yielded excellent candidate MDMs for EC. EC-associated MDMs performed with promisingly high sensitivity and specificity in tampon-collected vaginal fluid; PBS-based tampon buffer with added EDTA improved sensitivity. Larger tampon-based EC MDM testing studies are warranted.

KW - Cell-free nucleic acids

KW - DNA methylation

KW - Endometrial cancer

KW - Endometrial neoplasm/diagnosis

KW - Endometrial neoplasm/prevention & control

KW - Liquid biopsy

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U2 - 10.1016/j.ygyno.2023.04.014

DO - 10.1016/j.ygyno.2023.04.014

M3 - Article

C2 - 37141817

AN - SCOPUS:85154022933

SN - 0090-8258

VL - 174

SP - 11

EP - 20

JO - Gynecologic oncology

JF - Gynecologic oncology

ER -

Detection of endometrial cancer using tampon-based collection and methylated DNA markers

Abstract

Keywords

ASJC Scopus subject areas

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