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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 (Basel) 2023; 15:5778. [PMID: 38136324 PMCID: PMC10742045 DOI: 10.3390/cancers15245778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Radiographic surveillance of colorectal cancer (CRC) after curative-intent therapy is costly and unreliable. Methylated DNA markers (MDMs) detected primary CRC and metastatic recurrence with high sensitivity and specificity in cross-sectional studies. This study evaluated using serial MDMs to detect recurrence and monitor the treatment response to anti-cancer therapies. METHODS A nested case-control study was drawn from a prospective cohort of patients with CRC who completed curative-intent therapy for CRC of all stages. Plasma MDMs were assayed vis target enrichment long-probe quantitative-amplified signal assays, normalized to B3GALT6, and analyzed in combination with serum carcinoembryonic antigen to yield an MDM score. Clinical information, including treatment and radiographic measurements of the tumor burden, were longitudinally collected. RESULTS Of the 35 patients, 18 had recurrence and 17 had no evidence of disease during the study period. The MDM score was positive in 16 out of 18 patients who recurred and only 2 of the 17 patients without recurrence. The MDM score detected recurrence in 12 patients preceding clinical or radiographic detection of recurrent CRC by a median of 106 days (range 90-232 days). CONCLUSIONS Plasma MDMs can detect recurrent CRC prior to radiographic detection; this tumor-agnostic liquid biopsy approach may assist cancer surveillance and monitoring.
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Affiliation(s)
- Mojun Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA (H.X.)
| | - William R. Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA (A.M.G.); (K.A.D.); (P.H.F.)
| | - Douglas W. Mahoney
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN 55905, USA
| | - Sara S. Then
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA (A.M.G.); (K.A.D.); (P.H.F.)
| | - Calise K. Berger
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA (A.M.G.); (K.A.D.); (P.H.F.)
| | - Kelli N. Burger
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN 55905, USA
| | - Anna M. Gonser
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA (A.M.G.); (K.A.D.); (P.H.F.)
| | - Karen A. Doering
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA (A.M.G.); (K.A.D.); (P.H.F.)
| | - Hao Xie
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA (H.X.)
| | - Patrick H. Foote
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA (A.M.G.); (K.A.D.); (P.H.F.)
| | | | - Hatim T. Allawi
- Exact Sciences Corporation, Madison, WI 53719, USA; (M.W.K.)
| | | | - John B. Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA (A.M.G.); (K.A.D.); (P.H.F.)
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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 Oncol 2023; 146:106568. [PMID: 37717549 PMCID: PMC10591712 DOI: 10.1016/j.oraloncology.2023.106568] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 06/02/2023] [Revised: 08/11/2023] [Accepted: 09/06/2023] [Indexed: 09/19/2023]
Abstract
OBJECTIVE Early identification of human papillomavirus associated oropharyngeal squamous cell carcinoma (HPV(+)OPSCC) is challenging and novel biomarkers are needed. We hypothesized that a panel of methylated DNA markers (MDMs) found in HPV(+) cervical squamous cell carcinoma (CSCC) will have similar discrimination in HPV(+)OPSCC tissues. MATERIALS AND METHODS Formalin-fixed, paraffin-embedded tissues were obtained from patients with primary HPV(+)OPSCC or HPV(+)CSCC; control tissues included normal oropharynx palatine tonsil (NOP) and cervix (NCS). Using a methylation-specific polymerase chain reaction, 21 previously validated cervical MDMs were evaluated on tissue-extracted DNA. Discrimination between case and control cervical and oropharynx tissue was assessed using area under the curve (AUC). RESULTS 34 HPV(+)OPSCC, 36 HPV(+)CSCC, 26 NOP, and 24 NCS patients met inclusion criteria. Within HPV(+)CSCC, 18/21 (86%) of MDMs achieved an AUC ≥ 0.9 and all MDMs exhibited better than chance classifications relative to control cervical tissue (all p < 0.001). In contrast, within HPV(+)OPSCC only 5/21 (24%) MDMs achieved an AUC ≥ 0.90 but 19/21 (90%) exhibited better than chance classifications relative to control tonsil tissue (all p < 0.001). Overall, 13/21 MDMs had statistically significant lower AUCs in the oropharyngeal cohort compared to the cervical cohort, and only 1 MDM exhibited a statistically significant increase in AUC. CONCLUSIONS Previously validated MDMs exhibited robust performance in independent HPV(+)CSCC patients. However, most of these MDMs exhibited higher discrimination for HPV(+)CSCC than for HPV(+)OPSCC. This suggests that each SCC subtype requires a unique set of MDMs for optimal discrimination. Future studies are necessary to establish an MDM panel for HPV(+)OPSCC.
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Affiliation(s)
- Kathleen R Bartemes
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, MN, USA
| | | | | | - Daniel J Ma
- Department of Radiation Oncology, Rochester, MN, USA
| | | | - Kelli N Burger
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | | | - Douglas W Mahoney
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | - Xiaoming Cao
- Department of Gastroenterology, Rochester, MN, USA
| | - Sara S Then
- Department of Gastroenterology, Rochester, MN, USA
| | - Travis J Haller
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, MN, USA
| | - Alyssa M Larish
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, USA
| | - Eric J Moore
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, MN, USA
| | - Joaquin J Garcia
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rondell P Graham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Kathryn M Van Abel
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, MN, USA.
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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 Prev Res (Phila) 2023; 16:611-620. [PMID: 37728516 PMCID: PMC10870731 DOI: 10.1158/1940-6207.capr-23-0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/25/2023] [Revised: 07/21/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023]
Abstract
Lynch syndrome (LS) markedly increases risks of colorectal and endometrial cancers. Early detection biomarkers for LS cancers could reduce the needs for invasive screening and surgical prophylaxis.To validate a panel of methylated DNA markers (MDM) previously identified in sporadic colorectal cancer and endometrial cancer for discrimination of these cancers in LS.In a case-control design, previously identified MDMs for the detection of colorectal cancer and endometrial cancer were assayed by qMSP on tissue-extracted DNA. Results were normalized to ACTB values within each sample. Least absolute shrinkage and selection operator models to classify colorectal cancer and endometrial cancer were trained on sporadic cases and controls and then applied to classify colorectal cancer and endometrial cancer, in those with LS, and cross-validated.We identified colorectal cancer cases (23 with LS, 48 sporadic), colorectal controls (32 LS, 48 sporadic), endometrial cancer cases (30 LS, 48 sporadic), and endometrial controls (29 LS, 37 sporadic). A 3-MDM panel (LASS4, LRRC4, and PPP2R5C) classified LS-CRC from LS controls with an AUC of 0.92 (0.84-0.99); results were similar for sporadic colorectal cancer. A 6-MDM panel (SFMBT2, MPZ, CYTH2, DIDO1, chr10.4479, and EMX2OS) discriminated LS-EC from LS controls with an AUC of 0.92 (0.83-1.0); the AUC for sporadic endometrial cancer versus sporadic controls was nominally higher, 0.99 (0.96-1.0).MDMs previously identified in sporadic endometrial cancer and colorectal cancer discriminate between endometrial cancer and benign endometrium and colorectal cancer and benign colorectum in LS. This supports the inclusion of patients with LS within future prospective clinical trials evaluating endometrial cancer and colorectal cancer MDMs and may provide a new avenue for cancer screening or surveillance in this high-risk population. PREVENTION RELEVANCE Lynch syndrome (LS) markedly increases risks of colorectal and endometrial cancers. Early detection biomarkers for LS cancers could reduce the needs for invasive screening and surgery. Methylated DNA markers previously identified in sporadic endometrial cancer and colorectal cancer discriminate between benign and cancer tissue in LS.
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Affiliation(s)
| | | | | | - Patrick H. Foote
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - William R. Taylor
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Calise K. Berger
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Brianna J. Gysbers
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Jacquelyn Arndt
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Longwen Chen
- Division of Anatomic Pathology, Mayo Clinic, Scottsdale, AZ
| | - Karen A. Doering
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Kelli N. Burger
- Department of Quantitative Health Sciences, Mayo Clinic Rochester, MN
| | | | - Mark E. Sherman
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL
| | - John B. Kisiel
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - N. Jewel Samadder
- Department of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, AZ
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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 Precis Oncol 2023; 7:e2300389. [PMID: 37883729 PMCID: PMC10861016 DOI: 10.1200/po.23.00389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/21/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 10/28/2023] Open
Abstract
PURPOSE Surveillance after primary melanoma treatment aims to detect early signs of low-volume systemic disease. The current standard of care, surveillance imaging, is costly and difficult to access. We therefore sought to develop methylated DNA markers (MDMs) as promising alternatives for disease surveillance. METHODS We used reduced representation bisulfite sequencing (RRBS) to identify MDMs in DNA samples obtained from metastatic melanoma, benign nevi, and normal skin tissues. The identified MDMs underwent validation in an independent cohort of tissue and buffy coat DNA samples. Subsequently, we tested the validated MDMs in the plasma DNA of patients with metastatic melanoma undergoing surveillance with total body imaging and compared them with cancer-free controls. To estimate the overall predictive accuracy of the MDMs, we used random forest modeling with bootstrap cross-validation. RESULTS Forty MDMs demonstrated discrimination between melanoma cases and controls consisting of benign nevi and normal skin. Nine MDMs passing biological validation in tissue were run on 77 plasma samples from individuals with a history of metastatic melanoma, 49 of whom had evidence of disease detected by imaging at the time of blood draw, and 100 cancer-free controls. The cross-validated sensitivity of the panel for imaging-positive disease was 80% with a specificity of 100% in cancer-free controls, resulting in an overall AUC of 0.88 (95% CI, 0.81 to 0.96). The survival estimates for patients with melanoma who tested positive for the panel at 6 months and 1 year were 67% and 56%, respectively, while those who tested negative had survival rates of 100% and 92%. CONCLUSION MDMs identified by RRBS demonstrate a high degree of concordance with imaging results in the plasma of patients with metastatic melanoma. Further prospective studies in larger intended use cohorts are needed to confirm these findings.
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Affiliation(s)
- Calise K. Berger
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - William R. Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Douglas W. Mahoney
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN
| | - Kelli N. Burger
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN
| | - Karen A. Doering
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Anna M. Gonser
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Xiaoming Cao
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | | | | | - Patrick H. Foote
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | | | | | - Julia S. Lehman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
- Department of Dermatology, Mayo Clinic, Rochester, MN
| | | | | | - John B. Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
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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. Gynecol Oncol 2023; 174:11-20. [PMID: 37141817 DOI: 10.1016/j.ygyno.2023.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 04/16/2023] [Accepted: 04/16/2023] [Indexed: 05/06/2023]
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.
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Affiliation(s)
- Jamie N Bakkum-Gamez
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology Surgery, Mayo Clinic, Rochester, MN, United States of America.
| | - Mark E Sherman
- Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, United States of America
| | - Seth W Slettedahl
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States of America
| | - Douglas W Mahoney
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States of America
| | - Maureen A Lemens
- Surgery Research, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Shannon K Laughlin-Tommaso
- Department of Obstetrics and Gynecology, Division of Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Matthew R Hopkins
- Department of Obstetrics and Gynecology, Division of Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Ann VanOosten
- Surgery Research, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Viji Shridhar
- Department of Laboratory Medicine and Pathology, Experimental Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Julie K Staub
- Department of Laboratory Medicine and Pathology, Experimental Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Xiaoming Cao
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Patrick H Foote
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Megan A Clarke
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Kelli N Burger
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Calise K Berger
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Maria C O'Connell
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Karen A Doering
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Karl C Podratz
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology Surgery, Mayo Clinic, Rochester, MN, United States of America
| | - Christopher C DeStephano
- Department of Obstetrics and Gynecology, Division of Minimally Invasive Gynecology, Mayo Clinic, Jacksonville, FL, United States of America
| | - J Kenneth Schoolmeester
- Department of Laboratory Medicine and Pathology, Anatomic Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Sarah E Kerr
- Hospital Pathology Associates, Minneapolis, MN, United States of America
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - William R Taylor
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - John B Kisiel
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
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Witzig TE, Taylor WR, Mahoney DW, Bamlet WR, Foote PH, Burger K, Doering KA, Devens ME, Arndt JR, O'Connell M, Berger CK, Novak A, Cerhan JR, Hennek J, Katerov VE, Allawi HT, Jevremovic D, Dao LN, Graham RP, Kisiel JB. Methylated DNA markers in early detection of lymphoma: Discovery, validation, and clinical pilot. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.7562] [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
7562 Background: Lymphoma is the 6th most common cancer and a top 10 cause of cancer deaths. To date, there are no blood test approaches to population screening, and accurate surveillance markers are limited. Methylated DNA markers (MDMs) are broadly informative for early detection of cancer but have not been extensively studied for lymphomas. We sought to discover and validate MDMs in DNA extracted from lymphoma tissue, then test these MDMs in archival blood plasma specimens. Methods: Reduced representation bisulfite sequencing (RRBS) was performed on DNA extracted from a discovery set of frozen tissues of classic Hodgkin lymphoma (CHL, n=24), non-Hodgkin lymphoma (NHL, n=78: T-cell-TCL (8); diffuse large B-cell-DLBCL (18); follicular-FL (12); mantle cell-MCL (20); marginal zone-MZL (15)), and lymphoma cell line samples (27); controls included benign lymph node (n=11) and healthy donor buffy coat (n=30). 30 MDMs were ranked by fold-change and AUC and used to design methylation-specific PCR assays for biological validation on independent DNA samples extracted from FFPE tissue from 13 normal lymph node and 63 lymphoma samples and 36 buffy coats from healthy patients. Target enrichment long-probe quantitative-amplified signal assays were developed for 16 MDMs and then assayed in plasma-extracted, bisulfite-converted DNA samples from 390 independent treatment-naïve lymphoma patients (100 CHL and 290 NHL:100 DLBCL, 73 FL, 41 MCL, 41 MZL, 35 TCL), and 210 controls without cancer. Lymphoma plasma samples and 159 controls were provided by the Lymphoma SPORE (CA97274); 51 controls came from a 7-county population archive. Classification of lymphoma cases vs controls was modeled with random forest method and cross-validated across 500 bootstrap samples of each dataset. Results: For MDMs tested in DNA from independent biological validation samples, cross-validated random forest models identified 60/63 cases (95% sensitivity) and 12/13 normal controls (92% specificity). In plasmas, a panel of 16 MDMs ( ZNF503, VWA5B1, HOXA9_5195, GABRG3, ITGA5, MAX_chr17_793, BNC1_2407, CDK20, MAX_chr4_184, TPBG, DNAH14, SYT2, CACNG8, FAM110B, and NRN1) detected 78% (95% CI, 74-82%) of lymphoma cases at 90% specificity. Excluding MZL and TCL, sensitivity increased to 84% (80-88%) including 26/49 (53% (38-67%)) of stage I and 59/71 (83% (71-90%)) of stage II cases. Conclusions: MDMs show promise to detect lymphoma. These markers could be evaluated as part of multicancer early detection testing and could also be evaluated as response markers to treatment and subsequent surveillance.[Table: see text]
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Linda N Dao
- Anatomic Pathology, Mayo Clinic, Rochester, MN
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7
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Weng J, Bakkum-Gamez JN, Slettedahl S, Mahoney DW, Cao X, Foote PH, Burger K, Berger CK, O'Connell M, Arndt JR, Doering KA, Sherman ME, Taylor WR, Chen L, Couch F, Kisiel JB, Samadder J. Methylated DNA markers discriminate ovarian cancer from benign tissue in BRCA carriers. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.e17610] [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
e17610 Background: Methylated DNA markers (MDMs) associated with sporadic ovarian cancer (OC) are detected in plasma from patients with treatment naïve tumors, but not cancer-free controls. To assess potential benefits to patients at risk for hereditary OC, the aim of this study was to measure the performance of validated sporadic OC MDMs in OC and benign ovarian tissue (BOT), surgically obtained from germline BRCA1 or BRCA2 ( BRCA1/2) mutation carriers. Methods: BRCA1/2 carriers with OC and BRCA1/2 carriers who had undergone risk-reducing salpingo-oophorectomy (SO) were identified at a comprehensive cancer center. BRCA1/2 carriers in both OC and BOT groups were balanced on age and year of surgery with non- BRCA carriers with sporadic OC or benign indications for SO. OC and BOT formalin fixed paraffin embedded (FFPE) tissues were macrodissected following pathologist selection of representative sites; DNA was extracted, and bisulfite converted. 15 OC MDMs ( GDF6, IFFO1, MAX.chr1.147790358, MAX.chr6.10382190, MAX.chr11.14926602, C2CD4D, PDRM14, NCOR2, SKI, DSCR6, SIM2, PALLD, CDO1, GPRIN1, BCAT1) previously identified in sporadic OC were assayed by quantitative methylation specific PCR, normalized by β-actin, by blinded personnel. Areas under the receiver operating characteristic curve (AUC) were generated for each MDM to assess discrimination of OC from benign tissue and compared between BRCA1/2 and sporadic (non- BRCA) patients, using a z-test. Results: Among BRCA1/2 carriers, there were 48 OC ( BRCA-OC) and 48 BOT ( BRCA-BOT); among non- BRCA, we matched 48 OC (Sporadic-OC) and 48 BOT (non- BRCA-BOT). The median AUC for OC MDM discriminated between OC and BOT with AUCs in BRCA1/2 carriers was 0.87, (IQR, 0.83-0.93). Sporadic-OC vs non- BRCA-BOT median AUC was 0.88 (IQR, 0.83-0.92). AUCs were not significantly different for each MDM when stratified by BRCA or sporadic status. MDMs with an AUC of ≥0.9 in either group are shown (Table). Conclusions: OC MDMs identified and validated in sporadic OC are highly discriminant for OC from BOT in DNA extracted from tissues of people who carry a BRCA1/2 mutation. Testing the performance of these OC MDMs in plasma from BRCA1/2 carriers with and without OC may be of clinical value for high-risk patients and inform multi-cancer early detection testing strategies.[Table: see text]
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Affiliation(s)
- Jessica Weng
- Mayo Clinic Alix School of Medicine, Rochester, MN
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Fergus Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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8
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Zhu M, Taylor WR, Mahoney DW, Then SS, Berger CK, Burger K, Gonser AM, Doering KA, Foote PH, Kaiser MW, Allawi HT, Hubbard JM, Kisiel JB. Plasma methylated DNA markers detect recurrence and response to therapy in colorectal cancer. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.e15567] [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
e15567 Background: Radiographic surveillance of colorectal cancer (CRC) after therapy is costly and insensitive. We have reported high cross-sectional performance of methylated DNA markers (MDMs) for detection of primary CRC and metastatic recurrence. This study evaluated MDMs to detect recurrence and measure response to anti-cancer therapy in a longitudinal cohort. Methods: This was a nested case-control study drawn from a prospective cohort of adult patients with CRC who completed definitive treatment and followed forward from the start of surveillance by cross-sectional imaging (CT or MRI) and carcinoembryonic antigen (CEA), collected every 3-6 months under routine care. Blood was collected in LBgard® tubes (Biomatrica, San Diego CA). Cases had recurrent CRC (defined by RECIST v1.1 or radiographic findings that justify re-initiation of anti-cancer therapy as determined by treating clinicians). Controls remained NED (no radiographic recurrence and off therapy for ≥4 surveillance visits). From 6mL of plasma, MDMs ( CNNM1, ANKRD13B, FER1L4, ZNF568, CHST2, ZNF671, VAV3, QKI, GRIN2D, DTX1, PDGFD, SFMBT2, JAM3) were measured by target enrichment long-probe quantitative-amplified signal assays, normalized to B3GALT6, in blinded fashion. Previously published random forest models of MDMs +/- CEA, developed on independent patients with intact primary tumors, were used to develop a summary score. Results: With a median follow-up of 276 days (IQR 187-343) and 3 visits per patient (54 visits total), 18 patients had recurrence after start of surveillance. Another 18 patients remained NED after median 555 days (IRQ 469-662) and 4 surveillance visits per patient (76 visits total). Using a 90th %-ile cut-off summary score from 60 NED patients in a prior cross-sectional measurement, the MDM panel was positive in 15 of 18 patients who recurred and only 2 of the 18 NED patients (Table). Of the 76 patient visits for NED patients, 67 (88%) were below the threshold. The MDM panel score crossed the positivity threshold by a median of 127 days (IRQ 0-233) preceding clinical or radiographic documentation of recurrence. A random forest model with CEA was more sensitive but less specific (Table). In patients who resumed therapy, the MDM panel scores correlated closely with subsequent RECIST scores (not shown). Conclusions: Plasma MDMs rise in anticipation of recurrent CRC prior to radiographic detection and remain low in patients without radiographic disease over serial measurements, warranting further development of this tumor-agnostic liquid biopsy approach as a cost-effective tool to assist cancer surveillance.[Table: see text]
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9
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Meves A, Taylor WR, Berger CK, Mahoney DW, Burger K, Quattrocchi E, Doering KA, Gonser AM, Cao X, Heilberger J, Gysbers BJ, Foote PH, Katerov VE, Allawi HT, Kisiel JB. Plasma methylated DNA markers of cutaneous melanoma: Association with PET/CT-positive disease. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.9567] [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
9567 Background: Cutaneous melanoma surveillance is important to identify low-volume systemic disease, but imaging is costly and poorly accessible to patients; frequent skin checks lack sensitivity and specificity. We aimed to establish clinical feasibility of a liquid biopsy blood test, which quantifies validated, melanoma-specific, methylated DNA markers (MDMs), previously discovered, and reported by our team, using tissue extracted DNA. Methods: We prospectively collected blood from adult patients with histologically confirmed melanoma metastases and no other internal malignancies (within 5-years) who underwent surveillance by FDG-PET/CT (N = 88). Blood from age- and sex balanced cancer-free controls (N = 100) were compared. From PET/CT, we extracted the number of organs involved, SUV-max, and largest tumor diameter. Unequivocal metastasis was defined as SUV ≥ 4 and largest diameter > 5 mm. Because PET/CT is inadequate for the screening of brain metastases, we excluded the brain from the analysis. MDMs ( chr11.149, HOXA9, chr20.210, FLJ22536, CLIC5, SIX4, chr7.155, chr17.730, chr1.110) were assayed using target enrichment long-probe quantitative-amplified signal assays, normalized to B3GALT6, in blinded fashion. Using a logistic regression approach and nine candidate MDMs, we calculated the sensitivity for detecting patients with metastasis on PET/CT at 100% specificity. Results: 52/88 (59%) of melanoma patients showed evidence of metastasis on PET/CT at the time of blood draw. At 100% specificity, a panel of 4 MDMs ( HOXA9, chr20.210, chr17.730, chr1.110) yielded a sensitivity of 86.5% (45/52 cases) vs. 100 cancer-free controls. When applying this model to the 36 PET/CT-negative patients, specificity was as high as 97.2% (35/36 cases) while maintaining a sensitivity of 86.5% (one patient with a positive test result had a complete metabolic response to binimetinib / encorafenib prior to negative PET/CT). For patients with ≥ 2 organs involved by metastasis, sensitivity was 100% (29/29 cases). False-negative cases had metastasis in single organs and were characterized by minimal tumor burden and oral corticosteroid use. One false-negative patient had localized stage III disease without known primary melanoma. Conclusions: Plasma MDM levels appear highly concordant with FDG-PET/CT in patients with metastatic cutaneous melanoma. A liquid biopsy approach has potential to lower cost and improve patient access to surveillance. Additional prospective studies in larger intended use cohorts are needed to validate our results.
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10
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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. Gynecol Oncol 2022; 165:568-576. [DOI: 10.1016/j.ygyno.2022.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 11/25/2022]
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11
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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] [Grants] [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
| | | | | | - 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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12
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Bakkum-Gamez JN, Graham RP, Broderick BT, Slettedahl S, Mahoney DW, Lemens M, Cao X, Foote PH, Burger K, Berger CK, O'Connell M, Doering KA, Schoolmeester JK, Kerr S, Taylor WR, Sherman ME, Kisiel JB. Discovery and validation of novel methylated DNA markers of cervical cancer. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.5526] [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
5526 Background: HR-HPV DNA testing, with or without cervical cytology, provides excellent sensitivity for detection of cervical cancer (CC) and its precursors; negative test results indicate that risk of disease is extremely low and enable women to undergo reduced screening with safety. However, management of women who screen positive remains challenging as many will prove to have self-limited HR-HPV infections. DNA methylation is an early event in carcinogenesis that could enhance CC screening specificity. Methods: For discovery, DNA from 70 FFPE CC (36 squamous, 34 adenocarcinoma) tissues that were reviewed microscopically, 18 fresh frozen benign cervicovaginal (BCV) tissues collected at the time of benign hysterectomy, and 18 buffy coats from cancer-free women underwent reduced representation bisulfite sequencing (RRBS) to identify MDMs associated with CC. Candidate MDM selection was based on area under the receiver operating characteristic curve (AUC) discrimination, methylation fold change, and low background methylation among benign controls. Candidate MDMs were re-tested using methylation-specific PCR (MSP) to confirm performance. Blinded biological validation was performed using MSP on DNA extracted from independent FFPE CC (38 squamous, 43 adenocarcinoma) and BCV (40) tissues. The performance of CC MDMs was also tested in DNA extracted from cervical dysplasia (36 adenocarcinoma in situ (AIS), 32 cervical intraepithelial neoplasia (CIN) 2/3, 11 CIN 1) FFPE tissues. Results: From RRBS discovery and technical validation via MSP, 30 candidate MDMs showed marked methylation fold changes (10 to >1000) across both CC histologies compared to BCV tissue from cancer-free women. Each of the 30 MDMs highly discriminated CC from BCV tissue with 9 MDMs having an AUC >0.90 (Table). CC MDMs also highly discriminated AIS from BCV but did not perform well in CIN 2/3 and CIN 1 (Table). Conclusions: Whole methylome sequencing, stringent filtering criteria, and biological validation have yielded outstanding candidate MDMs for CC that highly discriminate CC from BCV, notably with high specificity. Performance in cervical dysplasias varied with higher positivity rates in AIS than in CIN 2/3 and CIN 1. Translation to testing these novel MDMs in lower genital tract biospecimens and the addition of HR-HPV to the CC panel are warranted.[Table: see text]
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Sarah Kerr
- Hospital Pathology Associates, Minneapolis, MN
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13
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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. Clin Cancer Res 2021; 27:2523-2532. [PMID: 33593879 DOI: 10.1158/1078-0432.ccr-20-0235] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 09/03/2020] [Accepted: 02/11/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE We have previously identified tissue methylated DNA markers (MDMs) associated with pancreatic ductal adenocarcinoma (PDAC). In this case-control study, we aimed to assess the diagnostic performance of plasma MDMs for PDAC. EXPERIMENTAL DESIGN Thirteen MDMs (GRIN2D, CD1D, ZNF781, FER1L4, RYR2, CLEC11A, AK055957, LRRC4, GH05J042948, HOXA1, PRKCB, SHISA9, and NTRK3) were identified on the basis of selection criteria applied to results of prior tissue experiments and assays were optimized in plasma. Next, 340 plasma samples (170 PDAC cases and 170 controls) were assayed using target enrichment long-probe quantitative amplified signal method. Initially, 120 advanced-stage PDAC cases and 120 healthy controls were used to train a prediction algorithm at 97.5% specificity using random forest modeling. Subsequently, the locked algorithm derived from the training set was applied to an independent blinded test set of 50 early-stage PDAC cases and 50 controls. Finally, data from all 340 patients were combined, and cross-validated. RESULTS The cross-validated area under the receiver operating characteristic curve (AUC) for the training set was 0.93 (0.89-0.96) for the MDM panel alone, 0.91 (95% confidence interval, 0.87-0.96) for carbohydrate antigen 19-9 (CA19-9) alone, and 0.99 (0.98-1) for the combined MDM-CA19-9 panel. In the test set of early-stage PDAC, the AUC for MDMs alone was 0.84 (0.76-0.92), CA19-9 alone was 0.87 (0.79-0.94), and combined MDM-CA19-9 panel was 0.90 (0.84-0.97) significantly better compared with either MDMs alone or CA19-9 alone (P = 0.0382 and 0.0490, respectively). At a preset specificity of 97.5%, the sensitivity for the combined panel in the test set was 80% (28%-99%) for stage I disease and 82% (68%-92%) for stage II disease. Using the combined datasets, the cross-validated AUC was 0.9 (0.86-0.94) for the MDM panel alone and 0.89 for CA19-9 alone (0.84-0.93) versus 0.97 (0.94-0.99) for the combined MDM-CA19-9 panel (P ≤ 0.0001). Overall, cross-validated sensitivity of MDM-CA19-9 panel was 92% (83%-98%), with an observed specificity of 92% at the preset specificity of 97.5%. CONCLUSIONS Plasma MDMs in combination with CA19-9 detect PDAC with significantly higher accuracy compared with either biomarker individually.
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Affiliation(s)
- Shounak Majumder
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota.
| | - William R Taylor
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Patrick H Foote
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Calise K Berger
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Chung Wah Wu
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Douglas W Mahoney
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - William R Bamlet
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Kelli N Burger
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Neil Postier
- Department of Chemistry, Wheaton College, Wheaton, Illinois
| | - Jaime de la Fuente
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Karen A Doering
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | | | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Suresh T Chari
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota
| | - David A Ahlquist
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota
| | - John B Kisiel
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota
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14
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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. Clin Cancer Res 2020; 27:141-149. [PMID: 33028593 DOI: 10.1158/1078-0432.ccr-20-2589] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 07/06/2020] [Revised: 09/04/2020] [Accepted: 10/01/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE We aimed to assess the concordance of colorectal cancer-associated methylated DNA markers (MDM) in primary and metastatic colorectal cancer for feasibility in detection of distantly recurrent/metastatic colorectal cancer in plasma. EXPERIMENTAL DESIGN A panel of previously discovered colorectal cancer-associated MDMs was selected. MDMs from primary and paired metastatic colorectal cancer tissue were assayed with quantitative methylation-specific PCR. Plasma MDMs were measured blindly by target enrichment long-probe quantitative-amplified signal assays. Random forest modeling was used to derive a prediction algorithm of MDMs in archival plasma samples from primary colorectal cancer cases. This algorithm was validated in prospectively collected plasma samples from recurrent colorectal cancer cases. The accuracy of the algorithm was summarized as sensitivity, specificity, and area under the curve (AUC). RESULTS Of the 14 selected MDMs, the concordance between primary and metastatic tissue was considered moderate or higher for 12 MDMs (86%). At a preset specificity of 95% (91%-98%), a panel of 13 MDMs, in plasma from 97 colorectal cancer cases and 200 controls, detected stage IV colorectal cancer with 100% (80%-100%) sensitivity and all stages of colorectal cancer with an AUC of 0.91 (0.87-0.95), significantly higher than carcinoembryonic antigen [AUC, 0.72 (0.65-0.79)]. This panel, in plasma from 40 cases and 60 healthy controls, detected recurrent/metastatic colorectal cancer with 90% (76%-97%) sensitivity, 90% (79%-96%) specificity, and an AUC of 0.96 (0.92-1.00). The panel was positive in 0.30 (0.19-0.43) of 60 patients with no evidence of disease in post-operative patients with colorectal cancer. CONCLUSIONS Plasma assay of novel colorectal cancer-associated MDMs can reliably detect both primary colorectal cancer and distantly recurrent colorectal cancer with promising accuracy.
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Affiliation(s)
- Hao Xie
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Douglas W Mahoney
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Patrick H Foote
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Kelli N Burger
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Karen A Doering
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Sara S Then
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Xiaoming Cao
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Maria McGlinch
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Calise K Berger
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Tsung-Teh Wu
- Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
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15
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Majumder S, Berger CK, Foote PH, Cao X, McGlinch M, Gysbers B, Halfdanarson TR, Graham RP, de la Fuente J, Robran MJ, Doering KA, Burger K, Mahoney DW, Taylor WR, Petersen GM, Ahlquist DA, Kisiel JB. Molecular detection of pancreatic neuroendocrine tumors using methylated DNA markers: Discovery and tissue validation. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e16705] [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
e16705 Background: The prevalence of pancreatic neuroendocrine tumors (PNETs) has increased in the last decade. Despite being clinically asymptomatic PNETs can be biologically aggressive. There is currently no reliable non-invasive diagnostic biomarker for PNETs. In this study we aimed to identify and validate methylated DNA marker (MDM) candidates that differentiate PNET from normal pancreas. Methods: For discovery, reduced representation bisulfite sequencing (RRBS) was performed on DNA extracted from frozen normal pancreas (n = 13) and PNET (n = 51) tissues. Area under the receiver operator characteristic curve (AUC), fold-change, and p-value criteria selected candidates MDMs for blinded validation in independent FFPE tissues from primary PNET (n = 67; solid = 50, cystic = 17), normal pancreas controls (n = 24), and normal buffy coat (n = 36) using methylation specific PCR. MDM distributions in primary PNETs were compared to primary lung (n = 36) and small bowel (n = 36) NETs and metastatic PNET tissue (n = 25). The discrimination accuracy of candidate markers was summarized as the AUC with corresponding 95% confidence intervals (CI). Results: From the RRBS discovery, 31 candidate MDMs were selected for validation. Four MDMs ( SRRM3, HCN2, SPTBN4 and TMC6) achieved individual AUCs ≥0.95 in the validation set (Table). These MDMs were similarly discriminant in metastatic PNET tissue and in primary lung and small bowel NETs. Three out of these 4 MDMs perfectly differentiated PNET tissue from buffy coat with AUC of 1 and may be ideally suited for further development of a blood-based assay. Conclusions: We identified and validated novel MDMs in tissue that discriminate PNETs from controls with normal pancreas and buffy coat with high accuracy. These MDMs also differentiated metastatic PNETs from normal pancreas tissue. Further exploration of these candidate tissue MDMs in plasma can potentially guide diagnosis and management of PNETs. Funding: P30DK084567. [Table: see text]
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16
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Bakkum-Gamez JN, Marinelli L, Ahlquist DA, Slettedahl S, Mahoney DW, Taylor WR, Burger K, Berger CK, Doering KA, Lemens M, Shridhar V, Allawi HT, Berg H, Giakoumopoulos M, Kaiser MW, Schoolmeester JK, Kerr S, Sherman ME, Kisiel JB. Methylated DNA markers for plasma detection of ovarian cancer: Discovery, validation, and clinical feasibility. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.6072] [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
6072 Background: Effective screening tests for ovarian cancer (OC) are lacking; most cases present at advanced stage and portend poor prognosis. DNA methylation is an early event in carcinogenesis and can be detected in blood plasma samples from cancer patients. In DNA extracted from tissues, we first discovered, then validated discriminant methylated DNA marker (MDM) candidates for OC and subsequently tested independent plasma from women with and without OC. Methods: For discovery, DNA from 67 frozen tissues (18 high grade serous (HGS), 18 endometrioid, 15 clear cell (CC), 6 mucinous OCs; 10 benign fallopian tube epithelium (FT); and 19 buffy coats from cancer-free women underwent reduced representation bisulfite sequencing (RRBS) to identify MDMs associated with OC. Candidate MDM selection was based on receiver operating characteristic (ROC) discrimination, methylation fold change, and low background methylation among controls. Blinded biological validation was performed using methylated specific PCR on DNA extracted from independent FFPE tissues from OCs (36 HGS, 22 endometrioid, 21 CC, and 14 mucinous) and 29 FT. Top performing MDMs in tissue were tested using long-probe quantitative amplified signal assays in independent pre-treatment plasma samples from women newly-diagnosed with OC and population-sampled healthy women. A random forest modeling analysis was performed to generate predictive probability of disease; results were 500-fold in silico cross-validated. Results: After RRBS discovery and biological validation, 33 MDMs showed marked methylation fold changes (10 to > 1000) across all OC histologies vs FT. The top 11 MDMs ( GPRIN1, CDO1, SRC, SIM2, AGRN, FAIM2, CELF2, DSCR6, GYPC, CAPN2, BCAT1) were tested on plasma from 91 women with OC (76 (84%) HGS) and 91 without OC; the cross-validated 11-MDM panel highly discriminated OC from controls (96% (95%CI 89-99%) specificity; 79% (69-87%) sensitivity, and AUC 0.91 (0.86 - 0.96)). Among HGS, the panel correctly identified 83%, including 5/6 stage I/II, and the majority of other subtypes (Table). Conclusions: Whole methylome sequencing, stringent filtering criteria, and biological validation yielded outstanding candidate MDMs for OC that performed with promisingly high sensitivity and specificity in plasma. Larger plasma-based OC MDM testing studies, with larger numbers of non-HGS histologies are warranted. [Table: see text]
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Viji Shridhar
- Mayo Clinic, Department of Experimental Pathology, Rochester, MN
| | | | | | | | | | | | - Sarah Kerr
- Hospital Pathology Associates, Minneapolis, MN
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17
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Xie H, Mahoney DW, Foote PH, Burger K, Doering KA, Taylor WR, Cao X, McGlinch M, Berger CK, Hubbard JM, Allawi HT, Lidgard GP, Ahlquist DA, Kisiel JB. Novel methylated DNA markers in plasma detect distant recurrence of colorectal cancer. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.4088] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
4088 Background: Methylated DNA markers (MDMs) are broadly informative for early detection of colorectal cancer (CRC) but have not been extensively studied for post-treatment surveillance and disease monitoring. We aimed to assess the feasibility of novel CRC-associated MDMs for detection of distant recurrent CRC (rCRC) in plasma. Methods: A panel of 13 MDMs previously identified to be discriminant for primary CRC was selected. In a cross-sectional analysis of plasma samples, MDMs were assayed blindly (by target enrichment long-probe quantitative amplified signal assay) from 160 age/sex-balanced patients (60 healthy controls, 60 with resected CRC and no evidence of disease (NED), and 40 rCRC after primary tumor resection). Plasma-derived carcinoembryonic antigen (CEA) was measured on all patients. Random forest modeling was used to derive a prediction algorithm of MDMs (with and without CEA) for the endpoint of rCRC relative to healthy controls. The accuracy of the algorithm was summarized as sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) with 95% confidence intervals (CI) in the test set. Results: Median patient age was 55 (interquartile range: 49-64) years. As shown in the Table below, a single MDM with the highest AUC was significantly better than CEA ( p= 0.02). On cross validation, CEA provided no additional improvement to the performance of the panel of 13 MDMs ( p= 0.2). The cross-validated panel of MDMs detected rCRC liver metastases with 96% (79-100%) sensitivity, lung metastases with 78% (40-97%) sensitivity, and peritoneal/nodal metastases with 57% (18-90%) sensitivity. Lesions with Response Evaluation Criteria in Solid Tumors sum > 4 cm were detected with 94% (73-100%) sensitivity and ≤4 cm with 78% (52-94%) sensitivity. Conclusions: Novel MDMs in plasma detect rCRC with promising accuracy. The clinical utility of MDMs for non-invasive post-treatment surveillance and treatment monitoring in CRC warrants further evaluation in longitudinal studies with sufficient follow-up to exclude sub-clinical recurrence in those with NED. [Table: see text]
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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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Xie H, Mahoney DW, Peterson MM, Foote PH, Burger K, Doering KA, Taylor WR, Cao X, McGlinch M, Berger CK, Wu TT, Hubbard JM, Ahlquist DA, Kisiel JB. Methylated DNA markers (MDMs) in primary (pCRC) and metastatic colorectal cancers (mCRC). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.3599] [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
3599 Background: Existing tools for post-treatment CRC surveillance and monitoring are insensitive and expensive. MDMs are broadly informative for early detection of CRC but have not been extensively studied for disease monitoring. As a first step, we sought to assess the concordance of novel CRC-associated MDMs in pCRC and mCRC. Methods: A panel of 14 MDMs previously identified to be highly discriminant for pCRC was selected on the basis of high median fold-change of MDM levels relative to buffy coat (682 (IQR: 132-19347)). Surgically resected pCRC and paired mCRC were identified from institutional pathology databases. Quantitative methylation-specific PCR was used to assay MDMs. 30 paired samples per metastatic subtype were calculated to be sufficient. MDM levels were compared using two-sample and paired Wilcoxon rank sum tests. Results: 87 patients with paired pCRC and mCRC including 57 synchronous and 30 metachronous metastases were included. 41/87 (47%) had neoadjuvant and 59/87 (68%) had adjuvant chemotherapy. All synchronous metastases were to liver. Metachronous metastases were to liver in 19/30 (63%) and to lung in 11/30 (37%). The levels of 14 selected MDMs were remarkably similar between paired pCRC and mCRC (Table). Individual MDM levels and the average level of all MDMs combined were not significantly different ( p> 0.0018 by Bonferroni correction). Conclusions: MDM levels are highly concordant in pCRC and mCRC. Thus, MDMs discovered from pCRC should be further studied for non-invasive surveillance after surgical resection and monitoring of treatment response in mCRC. [Table: see text]
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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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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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22
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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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23
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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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Foà PP, Melli M, Berger CK, Billinger D, Guidotti GG. Action of insulin on chick embryo heart. Fed Proc 1965; 24:1046-50. [PMID: 5838174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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