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Hartwig C, Müller J, Klett H, Kouhestani D, Mittelstädt A, Anthuber A, David P, Brunner M, Jacobsen A, Glanz K, Swierzy I, Roßdeutsch L, Klösch B, Grützmann R, Wittenberger T, Sohn K, Weber GF. Discrimination of pancreato-biliary cancer and pancreatitis patients by non-invasive liquid biopsy. Mol Cancer 2024; 23:28. [PMID: 38308296 PMCID: PMC10836044 DOI: 10.1186/s12943-024-01943-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/19/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Current diagnostics for the detection of pancreato-biliary cancers (PBCs) need to be optimized. We therefore propose that methylated cell-free DNA (cfDNA) derived from non-invasive liquid biopsies serves as a novel biomarker with the ability to discriminate pancreato-biliary cancers from non-cancer pancreatitis patients. METHODS Differentially methylated regions (DMRs) from plasma cfDNA between PBCs, pancreatitis and clinical control samples conditions were identified by next-generation sequencing after enrichment using methyl-binding domains and database searches to generate a discriminatory panel for a hybridization and capture assay with subsequent targeted high throughput sequencing. RESULTS The hybridization and capture panel, covering around 74 kb in total, was applied to sequence a cohort of 25 PBCs, 25 pancreatitis patients, 25 clinical controls, and seven cases of Intraductal Papillary Mucinous Neoplasia (IPMN). An unbiased machine learning approach identified the 50 most discriminatory methylation markers for the discrimination of PBC from pancreatitis and controls resulting in an AUROC of 0.85 and 0.88 for a training (n = 45) and a validation (n = 37) data set, respectively. The panel was also able to distinguish high grade from low grade IPMN samples. CONCLUSIONS We present a proof of concept for a methylation biomarker panel with better performance and improved discriminatory power than the current clinical marker CA19-9 for the discrimination of pancreato-biliary cancers from non-cancerous pancreatitis patients and clinical controls. This workflow might be used in future diagnostics for the detection of precancerous lesions, e.g. the identification of high grade IPMNs vs. low grade IPMNs.
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Affiliation(s)
- Christina Hartwig
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
- Institute for Interfacial Engineering and Plasma Technology IGVP, University of Stuttgart, Stuttgart, Germany
| | - Jan Müller
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | | | - Dina Kouhestani
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Anke Mittelstädt
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Anna Anthuber
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Paul David
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Maximilian Brunner
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Anne Jacobsen
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Karolina Glanz
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Izabela Swierzy
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Lotta Roßdeutsch
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Bettina Klösch
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Robert Grützmann
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
- Comprehensive Cancer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), Erlangen, Germany
| | | | - Kai Sohn
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany.
| | - Georg F Weber
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany.
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany.
- Comprehensive Cancer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany.
- Bavarian Cancer Research Center (BZKF), Erlangen, Germany.
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Petit J, Carroll G, Williams H, Pockney P, Scott RJ. Evaluation of a Multi-Gene Methylation Blood-Test for the Detection of Colorectal Cancer. Med Sci (Basel) 2023; 11:60. [PMID: 37755164 PMCID: PMC10534804 DOI: 10.3390/medsci11030060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 09/28/2023] Open
Abstract
Circulating tumour DNA biomarkers are an expanding field in oncology research that offer great potential but are currently often limited in value by overall cost. The aim of this study was to evaluate the efficacy of a novel multi-gene methylation blood test for the identification of colorectal cancer and throughout the spectrum of colorectal disease. Participants were recruited either prior to resection for known CRC or prior to screening colonoscopy after a positive faecal immunochemical test. Blood was collected from participants prior to their procedure being performed. The plasma was separated, and multiplex MethylLight droplet digital PCR was used to analyse for the presence of four methylated genes: SDC2, NPY, IKZF1 and SEPT9. A total of 537 participants underwent analysis. The SDC2/NPY genes showed a sensitivity of 33-54% and a specificity of 72-96%, whilst the IKZF1/SEPT9 genes showed a sensitivity of 19-42% and a specificity of 88-96%. Combining the two tests did not significantly increase the test accuracy. The sensitivity for advanced adenoma was 2-15%. There was a significant difference in the frequency of detectable methylation between the participants with CRC and those without CRC. However, neither the sensitivity nor the specificity was superior to current diagnostic screening tests.
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Affiliation(s)
- Joel Petit
- Division of Surgery, John Hunter Hospital, Newcastle, NSW 2305, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW 2305, Australia
- Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia
| | - Georgia Carroll
- Division of Surgery, John Hunter Hospital, Newcastle, NSW 2305, Australia
- Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW 2305, Australia
| | - Henry Williams
- Division of Surgery, John Hunter Hospital, Newcastle, NSW 2305, Australia
| | - Peter Pockney
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW 2305, Australia
- Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia
| | - Rodney J. Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW 2305, Australia
- Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia
- Pathology North, Newcastle, NSW 2305, Australia
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3
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Peller MT, Das KK. Blood-Based Biomarkers in the Diagnosis and Risk Stratification of Pancreatic Cysts. Gastrointest Endosc Clin N Am 2023; 33:559-581. [PMID: 37245936 DOI: 10.1016/j.giec.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The use of blood-based biomarkers for the assessment of pancreatic cystic lesions is a rapidly growing field with incredible potential. CA 19-9 remains the only blood-based marker in common use, while many novel biomarkers are in early stages of development and validation. We highlight current work in the fields of proteomics, metabolomics, cell-free DNA/circulating tumor DNA, extracellular vesicles, and microRNA among others, as well as barriers to development and future directions in the work of blood-based biomarkers for pancreatic cystic lesions.
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Affiliation(s)
- Matthew T Peller
- Division of Gastroenterology, Washington University School of Medicine, 660 South Euclid Avenue Campus Box 8124, Saint Louis, MO 63110, USA
| | - Koushik K Das
- Division of Gastroenterology, Washington University School of Medicine, 660 South Euclid Avenue Campus Box 8124, Saint Louis, MO 63110, USA.
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4
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Bararia A, Chakraborty P, Roy P, Chattopadhay BK, Das A, Chatterjee A, Sikdar N. Emerging role of non-invasive and liquid biopsy biomarkers in pancreatic cancer. World J Gastroenterol 2023; 29:2241-2260. [PMID: 37124888 PMCID: PMC10134423 DOI: 10.3748/wjg.v29.i15.2241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/02/2023] [Accepted: 03/16/2023] [Indexed: 04/14/2023] Open
Abstract
A global increase in the incidence of pancreatic cancer (PanCa) presents a major concern and health burden. The traditional tissue-based diagnostic techniques provided a major way forward for molecular diagnostics; however, they face limitations based on diagnosis-associated difficulties and concerns surrounding tissue availability in the clinical setting. Late disease development with asymptomatic behavior is a drawback in the case of existing diagnostic procedures. The capability of cell free markers in discriminating PanCa from autoimmune pancreatitis and chronic pancreatitis along with other precancerous lesions can be a boon to clinicians. Early-stage diagnosis of PanCa can be achieved only if these biomarkers specifically discriminate the non-carcinogenic disease stage from malignancy with respect to tumor stages. In this review, we comprehensively described the non-invasive disease detection approaches and why these approaches are gaining popularity for their early-stage diagnostic capability and associated clinical feasibility.
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Affiliation(s)
- Akash Bararia
- Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Prosenjeet Chakraborty
- Department of Molecular Biosciences, SVYASA School of Yoga and Naturopathy, Bangalore 560105, India
| | - Paromita Roy
- Department of Pathology, Tata Medical Center, Kolkata 700160, India
| | | | - Amlan Das
- Department of Biochemistry, Royal Global University, Assam 781035, India
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9061, New Zealand
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun 248007, India
| | - Nilabja Sikdar
- Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, India
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5
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Guan H, Tian K, Luo W, Li M. m 6A-modified circRNA MYO1C participates in the tumor immune surveillance of pancreatic ductal adenocarcinoma through m 6A/PD-L1 manner. Cell Death Dis 2023; 14:120. [PMID: 36781839 PMCID: PMC9925427 DOI: 10.1038/s41419-023-05570-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 02/15/2023]
Abstract
Emerging evidence indicates the critical roles of N6-methyladenosine (m6A) modification in human cancers. Herein, our work reported that a novel m6A-modified circRNA from the MYO1C gene, circMYO1C, upregulated in the pancreatic ductal adenocarcinoma (PDAC). Our findings demonstrated that circMYO1C is highly expressed in PDAC tissues. Functionally, circMYO1C promoted the proliferation and migration of PDAC cells in vitro and its silencing reduced the tumor growth in vivo. Mechanistically, circMYO1C cyclization was mediated by m6A methyltransferase METTL3. Moreover, methylated RNA immunoprecipitation sequencing (MeRIP-seq) unveiled the remarkable m6A modification on PD-L1 mRNA. Moreover, circMYO1C targeted the m6A site of PD-L1 mRNA to enhance its stability by cooperating with IGF2BP2, thereby accelerating PDAC immune escape. In conclusion, these findings highlight the oncogenic role of METTL3-induced circMYO1C in PDAC tumorigenesis via an m6A-dependent manner, inspiring a novel strategy to explore PDAC epigenetic therapy.
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Affiliation(s)
- Hua Guan
- Department of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan China
| | - Kun Tian
- grid.54549.390000 0004 0369 4060Department of Stomatology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan China
| | - Wei Luo
- Department of Stomatology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
| | - Mingfei Li
- Department of Hepatobiliary Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
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Elrakaybi A, Ruess DA, Lübbert M, Quante M, Becker H. Epigenetics in Pancreatic Ductal Adenocarcinoma: Impact on Biology and Utilization in Diagnostics and Treatment. Cancers (Basel) 2022; 14:cancers14235926. [PMID: 36497404 PMCID: PMC9738647 DOI: 10.3390/cancers14235926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive malignancies with high potential of metastases and therapeutic resistance. Although genetic mutations drive PDAC initiation, they alone do not explain its aggressive nature. Epigenetic mechanisms, including aberrant DNA methylation and histone modifications, significantly contribute to inter- and intratumoral heterogeneity, disease progression and metastasis. Thus, increased understanding of the epigenetic landscape in PDAC could offer new potential biomarkers and tailored therapeutic approaches. In this review, we shed light on the role of epigenetic modifications in PDAC biology and on the potential clinical applications of epigenetic biomarkers in liquid biopsy. In addition, we provide an overview of clinical trials assessing epigenetically targeted treatments alone or in combination with other anticancer therapies to improve outcomes of patients with PDAC.
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Affiliation(s)
- Asmaa Elrakaybi
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Department of Clinical Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Dietrich A. Ruess
- Department of General and Visceral Surgery, Center of Surgery, Medical Center University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
| | - Michael Quante
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
- Department of Gastroenterology and Hepatology, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Heiko Becker
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
- Correspondence: ; Tel.: +49-761-270-36000
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7
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DNA methylome in pancreatic cancer identified novel promoter hyper-methylation in NPY and FAIM2 genes associated with poor prognosis in Indian patient cohort. Cancer Cell Int 2022; 22:334. [PMID: 36329447 PMCID: PMC9635159 DOI: 10.1186/s12935-022-02737-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/17/2022] [Indexed: 11/06/2022] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is one of the leading cancers worldwide and has a poor survival, with a 5-year survival rate of only 8.5%. In this study we investigated altered DNA methylation associated with PDAC severity and prognosis. Methods Methylome data, generated using 450 K bead array, was compared between paired PDAC and normal samples in the TCGA cohort (n = 9) and our Indian cohort (n = 7). The total Indian Cohort (n = 75) was split into cohort 1 (n = 7), cohort 2 (n = 22), cohort 3 (n = 26) and cohort 4 (n = 20).Validation of differential methylation (6 selected CpG loci) and associated gene expression for differentially methylated genes (10 selected gDMs) were carried out in separate validation cohorts, using MSP, RT-PCR and IHC correlations between methylation and gene expression were observed in TCGA, GTEx cohorts and in validation cohorts. Kaplan–Meier survival analysis was done to study differential prognosis, during 2–5 years of follow-up. Results We identified 156 DMPs, mapped to 91 genes (gDMs), in PDAC; 68 (43.5%) DMPs were found to be differentially methylated both in TCGA cohort and our cohort, with significant concordance at hypo- and hyper-methylated loci. Enrichments of “regulation of ion transport”, “Interferon alpha/beta signalling”, “morphogenesis and development” and “transcriptional dysregulation” pathways were observed among 91 gDMs. Hyper-methylation of NPY and FAIM2 genes with down-regulated expression in PDAC, were significantly associated with poor prognosis in the Indian patient cohort. Conclusions Ethnic variations among populations may determine the altered epigenetic landscape in the PDAC patients of the Indian cohort. Our study identified novel differentially methylated genes (mainly NPY and FAIM2) and also validated the previously identified differentially methylated CpG sites associated with PDAC cancer patient’s survival. Comparative analysis of our data with TCGA and CPTAC cohorts showed that both NPY and FAIM2 hyper-methylation and down-regulations can be novel epigenetically regulated genes in the Indian patient population, statistically significantly associated with poor survival and advanced tumour stages. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02737-1.
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Ganji C, Farran B. Current clinical trials for epigenetic targets and therapeutic inhibitors for pancreatic cancer therapy. Drug Discov Today 2022; 27:1404-1410. [PMID: 34952224 DOI: 10.1016/j.drudis.2021.12.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/08/2021] [Accepted: 12/17/2021] [Indexed: 02/06/2023]
Abstract
Pancreatic cancer (PC) is an aggressive disease characterized by high mortality. Diagnosis at advanced stage, resistance, and recurrence are major hurdles for PC therapy and contribute to poor survival rate. Mutations in tumor-promoting kinases and epigenetic dysregulation in tumor suppressor genes are hallmarks of PC and can be used for diagnosis and therapy. In this review, we highlight dysregulated genes associated with epigenetic mechanisms, including DNA methylation and histone acetylation, involved in PC progression and resistance. We also explore epigenetic drugs currently in clinical trials. Combining epigenetic drugs and targeted therapies might represent a promising approach for PC.
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Affiliation(s)
| | - Batoul Farran
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA.
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Vrba L, Futscher BW, Oshiro M, Watts GS, Menashi E, Hu C, Hammad H, Pennington DR, Golconda U, Gavini H, Roe DJ, Shroff RT, Nelson MA. Liquid biopsy, using a novel DNA methylation signature, distinguishes pancreatic adenocarcinoma from benign pancreatic disease. Clin Epigenetics 2022; 14:28. [PMID: 35193708 PMCID: PMC8864826 DOI: 10.1186/s13148-022-01246-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/09/2022] [Indexed: 12/17/2022] Open
Abstract
We tested the ability of a novel DNA methylation biomarker set to distinguish metastatic pancreatic cancer cases from benign pancreatic cyst patients and to monitor tumor dynamics using quantitative DNA methylation analysis of cell-free DNA (cfDNA) from blood samples. The biomarkers were able to distinguish malignant cases from benign disease with high sensitivity and specificity (AUC = 0.999). Furthermore, the biomarkers detected a consistent decline in tumor-derived cfDNA in samples from patients undergoing chemotherapy. The study indicates that our liquid biopsy assay could be useful for management of pancreatic cancer patients.
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Affiliation(s)
- Lukas Vrba
- The University of Arizona Cancer Center, Tucson, AZ, USA.,Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, USA
| | - Bernard W Futscher
- The University of Arizona Cancer Center, Tucson, AZ, USA.,Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, USA.,Precision Epigenomics Inc, Tucson, AZ, USA
| | - Marc Oshiro
- The University of Arizona Cancer Center, Tucson, AZ, USA
| | - George S Watts
- The University of Arizona Cancer Center, Tucson, AZ, USA.,Department of Medical Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, USA
| | | | - Charles Hu
- Dignity Health Chandler Regional Medical Center, Chandler, AZ, USA
| | - Hytham Hammad
- The University of Arizona Cancer Center, Tucson, AZ, USA.,Division of Hematology/Oncology, Department of Medicine, University of Arizona Caner Center, Tucson, AZ, USA
| | - Daniel R Pennington
- The University of Arizona Cancer Center, Tucson, AZ, USA.,Division of Hematology/Oncology, Department of Medicine, University of Arizona Caner Center, Tucson, AZ, USA
| | | | - Hemanth Gavini
- Division of Hematology/Oncology, Department of Medicine, University of Arizona Caner Center, Tucson, AZ, USA
| | - Denise J Roe
- The University of Arizona Cancer Center, Tucson, AZ, USA
| | - Rachna T Shroff
- The University of Arizona Cancer Center, Tucson, AZ, USA.,Division of Hematology/Oncology, Department of Medicine, University of Arizona Caner Center, Tucson, AZ, USA
| | - Mark A Nelson
- The University of Arizona Cancer Center, Tucson, AZ, USA. .,Department of Pathology, College of Medicine, University of Arizona, Tucson, AZ, USA. .,Precision Epigenomics Inc, Tucson, AZ, USA.
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10
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Henriksen SD, Stubbe BE, Madsen PH, Johansen JS, Jensen BV, Hansen CP, Johansen MN, Pedersen IS, Krarup H, Thorlacius-Ussing O. Cell-free DNA promoter hypermethylation as a diagnostic marker for pancreatic ductal adenocarcinoma - An external validation study. Pancreatology 2021; 21:S1424-3903(21)00154-X. [PMID: 33994313 DOI: 10.1016/j.pan.2021.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/27/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND We recently identified a diagnostic prediction model based on promoter hypermethylation of eight selected genes in plasma cell-free (cf) DNA, which showed promising results as a diagnostic biomarker for pancreatic ductal adenocarcinoma (PDAC). The aim of the present study was to validate this biomarker profile in an external patient cohort and examine any additional effect of serum CA 19-9. METHODS Patients with PDAC (n = 346, stage I-IV) and chronic pancreatitis (n = 25) were included. Methylation-specific PCR of a 28-gene panel was performed on serum cfDNA samples. The previously developed diagnostic prediction model (age>65 years, BMP3, RASSF1A, BNC1, MESTv2, TFPI2, APC, SFRP1 and SFRP2) was validated alone and in combination with serum CA 19-9 in this external patient cohort. RESULTS Patients with PDAC had a higher number of hypermethylated genes (mean 8.11, 95% CI 7.70-8.52) than patients with chronic pancreatitis (mean 5.60, 95% CI 4.42-6.78, p = 0.011). Validation of the diagnostic prediction model yielded an AUC of 0.77 (95% CI 0.69-0.84). The combination of serum CA 19-9 and our test had an AUC of 0.93 (95% CI 0.89-0.96) in the primary study and 0.85 (95% CI 0.79-0.91) in the validation study. CONCLUSION In this validation study, PDAC was associated with a higher number of hypermethylated genes in serum cfDNA than chronic pancreatitis. Our diagnostic test was superior to the predictive value of serum CA 19-9 alone in both the primary and the validation study. The combination of our test with CA 19-9 may serve as a clinically useful diagnostic biomarker for PDAC.
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Affiliation(s)
- Stine D Henriksen
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Denmark; Department of Clinical Medicine, Aalborg University, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Denmark.
| | - Benjamin E Stubbe
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Denmark
| | - Poul H Madsen
- Department of Molecular Diagnostics, Aalborg University Hospital, Denmark
| | - Julia S Johansen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark; Department of Medicine, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Benny V Jensen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Carsten P Hansen
- Department of Surgery, Rigshospitalet, Copenhagen University Hospital, Denmark
| | - Martin N Johansen
- Unit of Clinical Biostatistics, Aalborg University Hospital, Denmark
| | - Inge S Pedersen
- Department of Clinical Medicine, Aalborg University, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Denmark; Department of Molecular Diagnostics, Aalborg University Hospital, Denmark
| | - Henrik Krarup
- Clinical Cancer Research Center, Aalborg University Hospital, Denmark; Department of Molecular Diagnostics, Aalborg University Hospital, Denmark
| | - Ole Thorlacius-Ussing
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Denmark; Department of Clinical Medicine, Aalborg University, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Denmark
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