Principal Investigator

John
Kisiel
Awardee Organization

Mayo Clinic Rochester
United States

Fiscal Year
2023
Activity Code
R37
Early Stage Investigator Grants (ESI)
Not Applicable
Project End Date

Multi-site Gastrointestinal Cancer Detection by Stool DNA Methylation

Gastrointestinal (GI) malignancies lead cancer deaths worldwide, killing ~3 million annually. In the U.S., only colorectal cancers (CRC) are screened. Other GI cancers are not screened due to lack of accurate tests or because prevalence is deemed too low for cost-effective screening. Consequently, most patients with GI cancers present at late-stage and cure rates remain abysmally low. Effective early detection is desperately needed to improve outcomes. Our group was central in development and validation of the FDA-approved multi- target stool DNA test for CRC screening. We have begun to expand this approach, showing feasibility to detect supra-colonic GI cancers by stool DNA testing. However, it is critical for a non-invasive molecular test to localize the site of a primary cancer (“site-prediction”). Key preliminary data suggest that this may now be possible. First, we have completed rigorous next-generation sequencing to identify differentially methylated regions (DMRs) which appear highly discriminant for universal and site-specific detection of GI cancers. Second, we prioritized these DMRs by strict filtering criteria and performed a confirmatory study with statistical cross-validation on an independent set of CRC, gastroesophageal and pancreatico-biliary cancer, and normal control tissues. This showed that a panel of 8 selected DMRs could distinguish cancer from normal (95% accuracy) and assign organ site (94-95% accuracy for each category) with overall site-prediction accuracy of 88%. Third, these findings have been confirmed with novel DMRs assayed from stool specimens obtained from CRC and pancreatic cancer patients and normal controls (30, each). Using a 2-stage analysis, cancers were distinguished from controls at 90% specificity in the first stage. At stage 2, the markers accurately classified CRCs from pancreatic cancers with 90% accuracy. It is now our central hypothesis that luminal and ductal adenocarcinomas can be detected and localized by stool assay of universal and site-specific DMRs. This raises 3 key questions: 1) will stool assay of our novel DMRs show the high overall cancer sensitivity and the site-prediction we have seen in preliminary data; 2) will the DMRs be specific for cancer across a wide patient demographic spectrum and in the setting of non-malignant GI diseases; and 3) can sensitivity and specificity be improved by novel assay technology? These will be addressed in the following parallel, integrated, but independent specific aims: 1) Assess panel sensitivity and site-prediction accuracy in stool specimens for adenocarcinoma at esophageal, pancreatic and colorectal sites; 2) Confirm and evaluate DMR specificity in stool; and 3) Optimize novel assay conditions and marker selection for cancer detection and site-prediction at esophageal, pancreatic and colorectal sites. With our team’s strong track record, extensive stool archive, and unique access to a state-of-the art assay platform, we expect to demonstrate in a cost-efficient manner the feasibility of a novel DMR panel for the detection and site prediction of specific GI adenocarcinomas. Results will inform designs of future studies ranging from large- scale case-control studies (phase 2) on early-stage cancer and pre-cursors to pivotal cohort validation (phase 4) of a non-invasive multi-GI cancer screening test. The potential impacts on cancer control are far-reaching.

Publications

  • Voss JK, Ebner DW, Burger KN, Mahoney DW, Devens ME, Lowrie KL, Kisiel JB. Multitarget Stool DNA Testing Has High Positive Predictive Value for Colorectal Neoplasia on the Second Round of Testing. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association. 2023 Aug;21(9):2399-2406. Epub 2023 Jan 6. PMID: 36621751
  • 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. Clinical cancer research : an official journal of the American Association for Cancer Research. 2019 Dec 15;25(24):7396-7404. Epub 2019 Sep 16. PMID: 31527170
  • 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. Hepatology communications. 2021 May 3;5(8):1448-1459. doi: 10.1002/hep4.1730. eCollection 2021 Aug. PMID: 34430788
  • 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 Dec;12(24):2173-2187. Epub 2020 Dec 22. PMID: 33350853
  • Majumder S, Taylor WR, Foote PH, Berger CK, Wu CW, Mahoney DW, Bamlet WR, Burger KN, Postier N, de la Fuente J, Doering KA, Lidgard GP, Allawi HT, Petersen GM, Chari ST, Ahlquist DA, Kisiel JB. High Detection Rates of Pancreatic Cancer Across Stages by Plasma Assay of Novel Methylated DNA Markers and CA19-9. Clinical cancer research : an official journal of the American Association for Cancer Research. 2021 May 1;27(9):2523-2532. Epub 2021 Feb 16. PMID: 33593879
  • Qin Y, Taylor W, Bamlet WR, Ravindran A, Buglioni A, Cao X, Foote PH, Slettedahl SW, Mahoney DW, Albert PS, Kim S, Hu N, Taylor PR, Etemadi A, Sotoudeh M, Malekzadeh R, Abnet CC, Smyrk TC, Katzka D, Topazian MD, Dawsey SM, Ahlquist D, Kisiel JB, Iyer PG. Methylated DNA Markers of Esophageal Squamous Cancer and Dysplasia: An International Study. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2020 Dec;29(12):2642-2650. Epub 2020 Sep 18. PMID: 32948633
  • Marinelli LM, Kisiel JB, Slettedahl SW, Mahoney DW, Lemens MA, Shridhar V, Taylor WR, Staub JK, Cao X, Foote PH, Burger KN, Berger CK, O'Connell MC, Doering KA, Giakoumopoulos M, Berg H, Volkmann C, Solsrud A, Allawi HT, Kaiser M, Vaccaro AM, Albright Crawford C, Moehlenkamp C, Shea G, Deist MS, Schoolmeester JK, Kerr SE, Sherman ME, Bakkum-Gamez JN. Methylated DNA markers for plasma detection of ovarian cancer: Discovery, validation, and clinical feasibility. Gynecologic oncology. 2022 Jun;165(3):568-576. Epub 2022 Mar 31. PMID: 35370009
  • Limburg PJ, Ahlquist DA, Johnson S, Jayasekar Zurn S, Kisiel JB, Smith RA. Multicancer early detection: International summit to Clarify the Roadmap. Cancer. 2022 Feb 15;128 Suppl 4:859-860. PMID: 35133657
  • Kisiel JB, Papadopoulos N, Liu MC, Crosby D, Srivastava S, Hawk ET. Multicancer early detection test: Preclinical, translational, and clinical evidence-generation plan and provocative questions. Cancer. 2022 Feb 15;128 Suppl 4:861-874. PMID: 35133659
  • Iyer PG, Taylor WR, Johnson ML, Lansing RL, Maixner KA, Hemminger LL, Cayer FK, Yab TC, Devens ME, Slettedahl SW, Broderick BT, Mahoney DW, McGlinch MC, Berger CK, Foote PH, Giakomopoulos M, Allawi H, Smyrk TC, Wang KK, Katzka DA, Wolfsen HC, Burke JA, Ahlquist DA, Kisiel JB. Accurate Nonendoscopic Detection of Barrett's Esophagus by Methylated DNA Markers: A Multisite Case Control Study. The American journal of gastroenterology. 2020 Aug;115(8):1201-1209. PMID: 32558685
  • Ebner DW, Burger KN, Broderick B, Mahoney DW, Kellogg TA, Acosta A, Kisiel JB. Positive Predictive Value for Multitarget Stool DNA After Bariatric and Metabolic Surgery. Gastro hep advances. 2023;2(7):902-910. Epub 2023 Jul 1. PMID: 37876832
  • Kisiel JB, Dukek BA, V S R Kanipakam R, 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 GP, Roberts LR, Ahlquist DA. Hepatocellular Carcinoma Detection by Plasma Methylated DNA: Discovery, Phase I Pilot, and Phase II Clinical Validation. Hepatology (Baltimore, Md.). 2019 Mar;69(3):1180-1192. Epub 2019 Feb 5. PMID: 30168613
  • 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. Novel Methylated DNA Markers Discriminate Advanced Neoplasia in Pancreatic Cysts: Marker Discovery, Tissue Validation, and Cyst Fluid Testing. The American journal of gastroenterology. 2019 Sep;114(9):1539-1549. PMID: 31306149
  • Ebner DW, Eckmann JD, Burger KN, Mahoney DW, Bering J, Kahn A, Rodriguez EA, Prichard DO, Wallace MB, Kane SV, Finney Rutten LJ, Gurudu SR, Kisiel JB. Detection of Postcolonoscopy Colorectal Neoplasia by Multi-target Stool DNA. Clinical and translational gastroenterology. 2021 Jun 18;12(6):e00375. PMID: 34140458
  • Iyer PG, Taylor WR, Slettedahl SW, Lansing RL, Hemminger LL, Cayer FK, Mahoney DW, Giakoumopoulos M, Allawi HT, Wu TT, Wang KK, Wolfsen HC, Antpack E, Kisiel JB. Validation of a methylated DNA marker panel for the nonendoscopic detection of Barrett's esophagus in a multisite case-control study. Gastrointestinal endoscopy. 2021 Sep;94(3):498-505. Epub 2021 Apr 20. PMID: 33857451
  • Ebner DW, Eckmann JD, Burger KN, Mahoney DW, Whitaker TJ, Petersen IA, Kisiel JB. High Positive Predictive Value of Multitarget Stool DNA After Aerodigestive Tract Radiotherapy. Gastro hep advances. 2022;1(5):746-754. Epub 2022 May 16. PMID: 36117548
  • Bartemes KR, Gochanour BR, Routman DM, Ma DJ, Doering KA, Burger KN, Foote PH, Taylor WR, Mahoney DW, Berger CK, Cao X, Then SS, Haller TJ, Larish AM, Moore EJ, Garcia JJ, Graham RP, Bakkum-Gamez JN, Kisiel JB, Van Abel KM. Assessing the capacity of methylated DNA markers of cervical squamous cell carcinoma to discriminate oropharyngeal squamous cell carcinoma in human papillomavirus mediated disease. Oral oncology. 2023 Nov;146:106568. Epub 2023 Sep 16. PMID: 37717549
  • Xie H, Mahoney DW, Foote PH, Burger KN, Doering KA, Taylor WR, Then SS, Cao X, McGlinch M, Berger CK, Wu TT, Hubbard JM, Allawi HT, Kaiser MW, Lidgard GP, Ahlquist DA, Kisiel JB. Novel Methylated DNA Markers in the Surveillance of Colorectal Cancer Recurrence. Clinical cancer research : an official journal of the American Association for Cancer Research. 2021 Jan 1;27(1):141-149. Epub 2020 Oct 7. PMID: 33028593
  • Northrop-Albrecht EJ, Taylor WR, Huang BQ, Kisiel JB, Lucien F. Assessment of extracellular vesicle isolation methods from human stool supernatant. Journal of extracellular vesicles. 2022 Apr;11(4):e12208. PMID: 35383410
  • Majumder S, Taylor WR, Foote PH, Gysbers BJ, Cao X, Mahoney DW, Burger KN, Doering KA, Graham RP, Couch FJ, Petersen GM, Kisiel JB. Tissue methylated DNA markers for sporadic pancreatic cancer are strongly associated with familial and genetically predisposed pancreatic cancer. Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]. 2022 Sep;22(6):770-773. Epub 2022 Jun 22. PMID: 35843766
  • Eckmann JD, Ebner DW, Bering J, Kahn A, Rodriguez E, Devens ME, Lowrie KL, Doering K, Then S, Burger KN, Mahoney DW, Prichard DO, Wallace MB, Gurudu SR, Finney LJ, Limburg P, Berger B, Ahlquist DA, Kisiel JB. Multitarget Stool DNA Screening in Clinical Practice: High Positive Predictive Value for Colorectal Neoplasia Regardless of Exposure to Previous Colonoscopy. The American journal of gastroenterology. 2020 Apr;115(4):608-615. PMID: 32068535
  • 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. Detection of endometrial cancer using tampon-based collection and methylated DNA markers. Gynecologic oncology. 2023 Jul;174:11-20. Epub 2023 May 2. PMID: 37141817
  • Sun Z, Behati S, Wang P, Bhagwate A, McDonough S, Wang V, Taylor W, Cunningham J, Kisiel J. Performance comparisons of methylation and structural variants from low-input whole-genome methylation sequencing. Epigenomics. 2023 Jan;15(1):11-19. Epub 2023 Mar 15. PMID: 36919677
  • Zhu M, Taylor WR, Mahoney DW, Then SS, Berger CK, Burger KN, Gonser AM, Doering KA, Xie H, Foote PH, Kaiser MW, Allawi HT, Hubbard JM, Kisiel JB. Plasma Assay of Cell-Free Methylated DNA Markers of Colorectal Cancer: A Tumor-Agnostic Approach to Monitor Recurrence and Response to Anticancer Therapies. Cancers. 2023 Dec 9;15. (24). PMID: 38136324
  • Berger CK, Taylor WR, Mahoney DW, Burger KN, Doering KA, Gonser AM, Cao X, Heilberger J, Gysbers BJ, Foote PH, Kottschade LA, Markovic SN, Lehman JS, Katerov VE, Allawi HT, Kisiel JB, Meves A. Plasma Methylated DNA Markers for Melanoma Surveillance. JCO precision oncology. 2023 Sep;7:e2300389. PMID: 37883729
  • Bramblet RM, Bakkum-Gamez JN, Slettedahl SW, Foote PH, Taylor WR, Berger CK, Gysbers BJ, Arndt J, Chen L, Doering KA, Burger KN, Mahoney DW, Sherman ME, Kisiel JB, Samadder NJ. Methylated DNA Markers for Sporadic Colorectal and Endometrial Cancer Are Strongly Associated with Lynch Syndrome Cancers. Cancer prevention research (Philadelphia, Pa.). 2023 Nov 1;16(11):611-620. PMID: 37728516
  • Ebner DW, Burger KN, Mahoney DW, Broderick BT, Eckmann JD, Devens ME, Lowrie KL, League JB, Bering J, Kahn A, Rodriguez EA, Prichard DO, Wallace MB, Kane SV, Leighton JA, Buttar NS, Rutten LJF, Gurudu SR, Kisiel JB. Neoplasia Diagnosis After Multi-target Stool DNA Is Enhanced Among Lowest Baseline Detectors. Digestive diseases and sciences. 2023 Sep;68(9):3721-3731. Epub 2023 Jul 24. PMID: 37486445