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Heydari Z, Moeinvaziri F, Mirazimi SMA, Dashti F, Smirnova O, Shpichka A, Mirzaei H, Timashev P, Vosough M. Alteration in DNA methylation patterns: Epigenetic signatures in gastrointestinal cancers. Eur J Pharmacol 2024; 973:176563. [PMID: 38593929 DOI: 10.1016/j.ejphar.2024.176563] [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: 01/22/2024] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
Abnormalities in epigenetic modifications can cause malignant transformations in cells, leading to cancers of the gastrointestinal (GI) tract, which accounts for 20% of all cancers worldwide. Among the epigenetic alterations, DNA hypomethylation is associated with genomic instability. In addition, CpG methylation and promoter hypermethylation have been recognized as biomarkers for different malignancies. In GI cancers, epigenetic alterations affect genes responsible for cell cycle control, DNA repair, apoptosis, and tumorigenic-specific signaling pathways. Understanding the pattern of alterations in DNA methylation in GI cancers could help scientists discover new molecular-based pharmaceutical treatments. This study highlights alterations in DNA methylation in GI cancers. Understanding epigenetic differences among GI cancers may improve targeted therapies and lead to the discovery of new diagnostic biomarkers.
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Affiliation(s)
- Zahra Heydari
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia
| | - Farideh Moeinvaziri
- Department of Regenerative Medicine, Cell Science Research Centre, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Seyed Mohammad Ali Mirazimi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Kashan University of Medical Sciences, Kashan, Iran
| | - Fatemeh Dashti
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Kashan University of Medical Sciences, Kashan, Iran
| | - Olga Smirnova
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia
| | - Anastasia Shpichka
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| | - Peter Timashev
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia; World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov University, Moscow, Russia; Chemistry Department, Lomonosov Moscow State University, Moscow, Russia.
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Centre, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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Song C, Wang G, Liu M, Xu Z, Liang X, Ding K, Chen Y, Wang W, Lou W, Liu L. Identification of methylation driver genes for predicting the prognosis of pancreatic cancer patients based on whole-genome DNA methylation sequencing technology. Heliyon 2024; 10:e29914. [PMID: 38737285 PMCID: PMC11088258 DOI: 10.1016/j.heliyon.2024.e29914] [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: 05/07/2023] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 05/14/2024] Open
Abstract
This study was based on the use of whole-genome DNA methylation sequencing technology to identify DNA methylation biomarkers in tumor tissue that can predict the prognosis of patients with pancreatic cancer (PCa). TCGA database was used to download PCa-related DNA methylation and transcriptome atlas data. Methylation driver genes (MDGs) were obtained using the MethylMix package. Candidate genes in the MDGs were screened for prognostic relevance to PCa patients by univariate Cox analysis, and a prognostic risk score model was constructed based on the key MDGs. ROC curve analysis was performed to assess the accuracy of the prognostic risk score model. The effects of PIK3C2B knockdown on malignant phenotypes of PCa cells were investigated in vitro. A total of 2737 differentially expressed genes were identified, with 649 upregulated and 2088 downregulated, using 178 PCa samples and 171 normal samples. MethylMix was employed to identify 71 methylation-driven genes (47 hypermethylated and 24 hypomethylated) from 185 TCGA PCa samples. Cox regression analyses identified eight key MDGs (LEF1, ZIC3, VAV3, TBC1D4, FABP4, MAP3K5, PIK3C2B, IGF1R) associated with prognosis in PCa. Seven of them were hypermethylated, while PIK3C2B was hypomethylated. A prognostic risk prediction model was constructed based on the eight key MDGs, which was found to accurately predict the prognosis of PCa patients. In addition, the malignant phenotypes of PANC-1 cells were decreased after the knockdown of PIK3C2B. Therefore, the prognostic risk prediction model based on the eight key MDGs could accurately predict the prognosis of PCa patients.
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Affiliation(s)
- Chao Song
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200000, China
- Department of Pancreatic Surgery, Affiliated Zhongshan Hospital of Fudan University, Shanghai, 200000, China
- Department of General Surgery, Affiliated Zhongshan Hospital of Fudan University, Qingpu Branch, Shanghai, 200000, China
| | - Ganggang Wang
- Department of Hepatobiliary Surgery, Pudong Hospital, Fudan University, Shanghai, 200000, China
| | - Mengmeng Liu
- Department of Gastroenterology, Affiliated Zhongshan Hospital of Fudan University, Qingpu Branch, Shanghai, 200000, China
| | - Zijin Xu
- Department of General Surgery, Affiliated Zhongshan Hospital of Fudan University, Qingpu Branch, Shanghai, 200000, China
| | - Xin Liang
- CAS Key Laboratory of Nutrition, University of Chinese Academy of Sciences, Shanghai, 200000, China
| | - Kai Ding
- CAS Key Laboratory of Nutrition, University of Chinese Academy of Sciences, Shanghai, 200000, China
| | - Yu Chen
- CAS Key Laboratory of Nutrition, University of Chinese Academy of Sciences, Shanghai, 200000, China
| | - Wenquan Wang
- Department of Pancreatic Surgery, Affiliated Zhongshan Hospital of Fudan University, Shanghai, 200000, China
| | - Wenhui Lou
- Department of Pancreatic Surgery, Affiliated Zhongshan Hospital of Fudan University, Shanghai, 200000, China
| | - Liang Liu
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200000, China
- Department of Pancreatic Surgery, Affiliated Zhongshan Hospital of Fudan University, Shanghai, 200000, China
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Gu X, Minko T. Targeted Nanoparticle-Based Diagnostic and Treatment Options for Pancreatic Cancer. Cancers (Basel) 2024; 16:1589. [PMID: 38672671 PMCID: PMC11048786 DOI: 10.3390/cancers16081589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), one of the deadliest cancers, presents significant challenges in diagnosis and treatment due to its aggressive, metastatic nature and lack of early detection methods. A key obstacle in PDAC treatment is the highly complex tumor environment characterized by dense stroma surrounding the tumor, which hinders effective drug delivery. Nanotechnology can offer innovative solutions to these challenges, particularly in creating novel drug delivery systems for existing anticancer drugs for PDAC, such as gemcitabine and paclitaxel. By using customization methods such as incorporating conjugated targeting ligands, tumor-penetrating peptides, and therapeutic nucleic acids, these nanoparticle-based systems enhance drug solubility, extend circulation time, improve tumor targeting, and control drug release, thereby minimizing side effects and toxicity in healthy tissues. Moreover, nanoparticles have also shown potential in precise diagnostic methods for PDAC. This literature review will delve into targeted mechanisms, pathways, and approaches in treating pancreatic cancer. Additional emphasis is placed on the study of nanoparticle-based delivery systems, with a brief mention of those in clinical trials. Overall, the overview illustrates the significant advances in nanomedicine, underscoring its role in transcending the constraints of conventional PDAC therapies and diagnostics.
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Affiliation(s)
- Xin Gu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08554, USA
| | - Tamara Minko
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08554, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
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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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Orlacchio A, Muzyka S, Gonda TA. Epigenetic therapeutic strategies in pancreatic cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 383:1-40. [PMID: 38359967 DOI: 10.1016/bs.ircmb.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal solid malignancies, characterized by its aggressiveness and metastatic potential, with a 5-year survival rate of only 8-11%. Despite significant improvements in PDAC treatment and management, therapeutic alternatives are still limited. One of the main reasons is its high degree of intra- and inter-individual tumor heterogeneity which is established and maintained through a complex network of transcription factors and epigenetic regulators. Epigenetic drugs, have shown promising preclinical results in PDAC and are currently being evaluated in clinical trials both for their ability to sensitize cancer cells to cytotoxic drugs and to counteract the immunosuppressive characteristic of PDAC tumor microenvironment. In this review, we discuss the current status of epigenetic treatment strategies to overcome molecular and cellular PDAC heterogeneity in order to improve response to therapy.
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Affiliation(s)
- Arturo Orlacchio
- Division of Gastroenterology and Hepatology, New York University, New York, NY, United States
| | - Stephen Muzyka
- Division of Gastroenterology and Hepatology, New York University, New York, NY, United States
| | - Tamas A Gonda
- Division of Gastroenterology and Hepatology, New York University, New York, NY, United States.
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Stosic K, Senar OA, Tarfouss J, Bouchart C, Navez J, Van Laethem JL, Arsenijevic T. A Comprehensive Review of the Potential Role of Liquid Biopsy as a Diagnostic, Prognostic, and Predictive Biomarker in Pancreatic Ductal Adenocarcinoma. Cells 2023; 13:3. [PMID: 38201207 PMCID: PMC10778087 DOI: 10.3390/cells13010003] [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: 10/30/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma is one of the most lethal malignant diseases, with a mortality rate being close to incidence. Due to its heterogeneity and plasticity, as well as the lack of distinct symptoms in the early phases, it is very often diagnosed at an advanced stage, resulting in poor prognosis. Traditional tissue biopsies remain the gold standard for making a diagnosis, but have an obvious disadvantage in their inapplicability for frequent sampling. Blood-based biopsies represent a non-invasive method which potentially offers easy and repeated sampling, leading to the early detection and real-time monitoring of the disease and hopefully an accurate prognosis. Given the urgent need for a reliable biomarker that can estimate a patient's condition and response to an assigned treatment, blood-based biopsies are emerging as a potential new tool for improving patients' survival and surveillance. In this article, we discuss the current advances and challenges in using liquid biopsies for pancreatic cancer, focusing on circulating tumour DNA (ctDNA), extracellular vesicles (EVs), and circulating tumour cells (CTCs), and compare the performance and reliability of different biomarkers and combinations of biomarkers.
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Affiliation(s)
- Kosta Stosic
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
| | - Oier Azurmendi Senar
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
| | - Jawad Tarfouss
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
| | - Christelle Bouchart
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Radiation Oncology, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Julie Navez
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Hepato-Biliary-Pancreatic Surgery, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Jean-Luc Van Laethem
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Gastroenterology, Hepatology and Digestive Oncology, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), Route de Lennik 808, 1070 Brussels, Belgium
| | - Tatjana Arsenijevic
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Gastroenterology, Hepatology and Digestive Oncology, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), Route de Lennik 808, 1070 Brussels, Belgium
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Hu H, Wang Y, Liu Y, Zhang C, Li G, Zhang T, Dong B. Comprehensive Analysis of ADAMTS Gene Family in Renal Clear Cell Carcinoma and ADAMTS10 Research Combining Magnetic Resonance Imaging. Mol Biotechnol 2023:10.1007/s12033-023-00915-8. [PMID: 37861954 DOI: 10.1007/s12033-023-00915-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/19/2023] [Indexed: 10/21/2023]
Abstract
Clear cell renal carcinoma (ccRCC) is one of the cancers that posed a severe threat to human life on a global scale. The ADAMTS family has been proven to be involved in a number of tumor types, although it is yet unknown how they relate to ccRCC. The mRNA expression matrix and other clinically relevant information of 607 ccRCC were sourced from TCGA database. The role of ADAMTS family genes in ccRCC was determined by differential gene expression analysis and gene set enrichment analysis (GSEA). Employing stage grading, gene mutation, and survival analysis, the genes most linked to the prognosis of ccRCC were identified. The influence of genes on the pathway was determined by Kyoto Encyclopedia of Genes and Genes (KEGG) analysis. Following that, the gene's impact on ccRCC was verified by qRT-PCR, WB, MTT, Transwell detection, and a wound healing assay. Bioinformatics analysis showed that ADAMTS10 was overexpressed in cancerous tissues of people with ccRCC and its expression increased with tumor grade. Mutation analysis showed that the main cause of mutation in the ADAMTS family gene was amplification. The prognosis and survival of the ADAMTS10 elevated expression group were lower than those of the poorly expressed group, as demonstrated by a survival analysis. On the basis of the findings of MRI, we examined 60 clinical patients and collected their cancer along with the surrounding tissues. The results of qPCR detection showed that the expression of ADAMTS10 was considerably higher in cancerous regions of 60 clinical users than it was in the tissues nearby. Inhibiting ADAMTS10 development prevents cancer cells from proliferating, invading, and migrating. The KEGG analysis links ADAMTS10 to the NF-κB signal pathway. WB experiment confirmed that inhibiting ADAMTS10 expression can inhibit the activation of the NF-κB signal pathway. ADAMTS10 may be a promising prognostic marker for ccRCC that can be employed independently.
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Affiliation(s)
- Haifeng Hu
- Department of Magnetic Resonance Imaging, The Second Affiliated Hospital of Qiqihar Medical College, 64 Zhonghua Xi Lu, Jianhua District, Qiqihar City, Heilongjiang Province, China.
| | - Ying Wang
- Department of Ultrasound, The Second Affiliated Hospital of Qiqihar Medical College, Qiqihar City, China
| | - Ying Liu
- Department of Magnetic Resonance Imaging, The Second Affiliated Hospital of Qiqihar Medical College, 64 Zhonghua Xi Lu, Jianhua District, Qiqihar City, Heilongjiang Province, China
| | - Chunyu Zhang
- Department of Magnetic Resonance Imaging, The Second Affiliated Hospital of Qiqihar Medical College, 64 Zhonghua Xi Lu, Jianhua District, Qiqihar City, Heilongjiang Province, China
| | - Guoan Li
- Department of Magnetic Resonance Imaging, The Second Affiliated Hospital of Qiqihar Medical College, 64 Zhonghua Xi Lu, Jianhua District, Qiqihar City, Heilongjiang Province, China
| | - Tianyu Zhang
- Department of Imaging, The Second Affiliated Hospital of Qiqihar Medical College, Qiqihar City, China
| | - Bo Dong
- Department of Urology, The Second Affiliated Hospital of Qiqihar Medical College, Qiqihar City, China
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García-Ortiz MV, Cano-Ramírez P, Toledano-Fonseca M, Aranda E, Rodríguez-Ariza A. Diagnosing and monitoring pancreatic cancer through cell-free DNA methylation: progress and prospects. Biomark Res 2023; 11:88. [PMID: 37798621 PMCID: PMC10552233 DOI: 10.1186/s40364-023-00528-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/21/2023] [Indexed: 10/07/2023] Open
Abstract
Pancreatic cancer is one of the most challenging cancers due to its high mortality rates. Considering the late diagnosis and the limited survival benefit with current treatment options, it becomes imperative to optimize early detection, prognosis and prediction of treatment response. To address these challenges, significant research efforts have been undertaken in recent years to develop liquid-biopsy-based biomarkers for pancreatic cancer. In particular, an increasing number of studies point to cell-free DNA (cfDNA) methylation analysis as a promising non-invasive approach for the discovery and validation of epigenetic biomarkers with diagnostic or prognostic potential. In this review we provide an update on recent advancements in the field of cfDNA methylation analysis in pancreatic cancer. We discuss the relevance of DNA methylation in the context of pancreatic cancer, recent cfDNA methylation research, its clinical utility, and future directions for integrating cfDNA methylation analysis into routine clinical practice.
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Affiliation(s)
- María Victoria García-Ortiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain.
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain.
| | - Pablo Cano-Ramírez
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain
| | - Marta Toledano-Fonseca
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
| | - Enrique Aranda
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
- Department of Medicine, Faculty of Medicine, University of Córdoba, Córdoba, Spain
| | - Antonio Rodríguez-Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
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9
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Ladel L, Tan WY, Jeyakanthan T, Sailo B, Sharma A, Ahuja N. The Promise of Epigenetics Research in the Treatment of Appendiceal Neoplasms. Cells 2023; 12:1962. [PMID: 37566041 PMCID: PMC10417136 DOI: 10.3390/cells12151962] [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: 04/10/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
Appendiceal cancers (AC) are a rare and heterogeneous group of malignancies. Historically, appendiceal neoplasms have been grouped with colorectal cancers (CRC), and treatment strategies have been modeled after CRC management guidelines due to their structural similarities and anatomical proximity. However, the two have marked differences in biological behavior and treatment response, and evidence suggests significant discrepancies in their respective genetic profiles. In addition, while the WHO classification for appendiceal cancers is currently based on traditional histopathological criteria, studies have demonstrated that histomorphology does not correlate with survival or treatment response in AC. Due to their rarity, appendiceal cancers have not been studied as extensively as other gastrointestinal cancers. However, their incidence has been increasing steadily over the past decade, making it crucial to identify new and more effective strategies for detection and treatment. Recent efforts to map and understand the molecular landscape of appendiceal cancers have unearthed a wealth of information that has made it evident that appendiceal cancers possess a unique molecular profile, distinct from other gastrointestinal cancers. This review focuses on the epigenetic landscape of epithelial appendiceal cancers and aims to provide a comprehensive overview of the current state of knowledge of epigenetic changes across different appendiceal cancer subtypes, highlighting the challenges as well as the promise of employing epigenetics in the quest for the detection of biomarkers, therapeutic targets, surveillance markers, and predictors of treatment response and survival in epithelial appendiceal neoplasms.
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Affiliation(s)
- Luisa Ladel
- Surgical Oncology Research Laboratories, Division of Surgical Oncology, Department of Surgery, Yale School of Medicine, Yale University, New Haven, CT 06519, USA; (L.L.); (W.Y.T.); (T.J.); (B.S.); (A.S.)
- Affiliated Internal Medicine Residency Program at Norwalk Hospital, Department of Internal Medicine, Norwalk Hospital, Yale University, Norwalk, CT 06850, USA
| | - Wan Ying Tan
- Surgical Oncology Research Laboratories, Division of Surgical Oncology, Department of Surgery, Yale School of Medicine, Yale University, New Haven, CT 06519, USA; (L.L.); (W.Y.T.); (T.J.); (B.S.); (A.S.)
- Affiliated Internal Medicine Residency Program at Norwalk Hospital, Department of Internal Medicine, Norwalk Hospital, Yale University, Norwalk, CT 06850, USA
| | - Thanushiya Jeyakanthan
- Surgical Oncology Research Laboratories, Division of Surgical Oncology, Department of Surgery, Yale School of Medicine, Yale University, New Haven, CT 06519, USA; (L.L.); (W.Y.T.); (T.J.); (B.S.); (A.S.)
- Affiliated Internal Medicine Residency Program at Norwalk Hospital, Department of Internal Medicine, Norwalk Hospital, Yale University, Norwalk, CT 06850, USA
| | - Bethsebie Sailo
- Surgical Oncology Research Laboratories, Division of Surgical Oncology, Department of Surgery, Yale School of Medicine, Yale University, New Haven, CT 06519, USA; (L.L.); (W.Y.T.); (T.J.); (B.S.); (A.S.)
| | - Anup Sharma
- Surgical Oncology Research Laboratories, Division of Surgical Oncology, Department of Surgery, Yale School of Medicine, Yale University, New Haven, CT 06519, USA; (L.L.); (W.Y.T.); (T.J.); (B.S.); (A.S.)
| | - Nita Ahuja
- Surgical Oncology Research Laboratories, Division of Surgical Oncology, Department of Surgery, Yale School of Medicine, Yale University, New Haven, CT 06519, USA; (L.L.); (W.Y.T.); (T.J.); (B.S.); (A.S.)
- Department of Pathology, Yale School of Medicine, New Haven, CT 06519, USA
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10
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García-Ortiz MV, Cano-Ramírez P, Toledano-Fonseca M, Cano MT, Inga-Saavedra E, Rodríguez-Alonso RM, Guil-Luna S, Gómez-España MA, Rodríguez-Ariza A, Aranda E. Circulating NPTX2 methylation as a non-invasive biomarker for prognosis and monitoring of metastatic pancreatic cancer. Clin Epigenetics 2023; 15:118. [PMID: 37481552 PMCID: PMC10362605 DOI: 10.1186/s13148-023-01535-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/16/2023] [Indexed: 07/24/2023] Open
Abstract
BACKGROUND Pancreatic cancer is the most lethal cancer with a dismal prognosis mainly due to diagnosis at advanced stage and ineffective treatments. CA19-9 levels and computed tomography (CT) imaging are the main standard criteria for evaluating disease progression and treatment response. In this study we explored liquid biopsy-based epigenetic biomarkers for prognosis and monitoring disease in patients with metastatic pancreatic ductal adenocarcinoma (mPDAC). METHODS Plasma samples were collected from 44 mPDAC patients at the time of diagnosis, and in 15 of them, additional samples were obtained during follow-up of the disease. After cell-free DNA (cfDNA), isolation circulating levels of methylated NPTX2, SPARC, BMP3, SFRP1 and TFPI2 genes were measured using digital droplet PCR (ddPCR). BEAMing technique was performed for quantitation of RAS mutations in cfDNA, and CA19-9 was measured using standard techniques. RESULTS NPTX2 was the most highly and frequently methylated gene in cfDNA samples from mPDAC patients. Higher circulating NPTX2 methylation levels at diagnosis were associated with poor prognosis and efficiently stratified patients for prediction of overall survival (6.06% cut-off, p = 0.0067). Dynamics of circulating NPTX2 methylation levels correlated with disease progression and response to therapy and predicted better than CA19-9 the evolution of disease in mPDAC patients. Remarkably, in many cases the disease progression detected by CT scan was anticipated by an increase in circulating NPTX2 methylation levels. CONCLUSIONS Our study supports circulating NPTX2 methylation levels as a promising liquid biopsy-based clinical tool for non-invasive prognosis, monitoring disease evolution and response to treatment in mPDAC patients.
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Affiliation(s)
- María Victoria García-Ortiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
| | - Pablo Cano-Ramírez
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
| | - Marta Toledano-Fonseca
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
| | - María Teresa Cano
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
| | - Elizabeth Inga-Saavedra
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
| | | | - Silvia Guil-Luna
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
- Department of Anatomy and Comparative Pathology, University of Córdoba, Córdoba, Spain
| | - María Auxiliadora Gómez-España
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
| | - Antonio Rodríguez-Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
| | - Enrique Aranda
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Seville, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
- Department of Medicine, Faculty of Medicine, University of Córdoba, Córdoba, Spain
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11
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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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12
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Wang Y, Douville C, Cohen JD, Mattox A, Curtis S, Silliman N, Popoli M, Ptak J, Dobbyn L, Nehme N, Dudley JC, Summers M, Zhang M, Ho-Pham LT, Tran BNH, Tran TS, Nguyen TV, Bettegowda C, Papadopoulos N, Kinzler KW, Vogelstein B. Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules. Proc Natl Acad Sci U S A 2023; 120:e2220704120. [PMID: 37014860 PMCID: PMC10104560 DOI: 10.1073/pnas.2220704120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/28/2023] [Indexed: 04/05/2023] Open
Abstract
The analysis of cell-free DNA (cfDNA) from plasma offers great promise for the earlier detection of cancer. At present, changes in DNA sequence, methylation, or copy number are the most sensitive ways to detect the presence of cancer. To further increase the sensitivity of such assays with limited amounts of sample, it would be useful to be able to evaluate the same template molecules for all these changes. Here, we report an approach, called MethylSaferSeqS, that achieves this goal, and can be applied to any standard library preparation method suitable for massively parallel sequencing. The innovative step was to copy both strands of each DNA-barcoded molecule with a primer that allows the subsequent separation of the original strands (retaining their 5-methylcytosine residues) from the copied strands (in which the 5-methylcytosine residues are replaced with unmodified cytosine residues). The epigenetic and genetic alterations present in the DNA molecules can then be obtained from the original and copied strands, respectively. We applied this approach to plasma from 265 individuals, including 198 with cancers of the pancreas, ovary, lung, and colon, and found the expected patterns of mutations, copy number alterations, and methylation. Furthermore, we could determine which original template DNA molecules were methylated and/or mutated. MethylSaferSeqS should be useful for addressing a variety of questions relating genetics and epigenetics.
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Affiliation(s)
- Yuxuan Wang
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Christopher Douville
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Joshua D. Cohen
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD21218
| | - Austin Mattox
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Sam Curtis
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Pharmacology and Molecular Science, Johns Hopkins School of Medicine, Baltimore, MD21287
| | - Natalie Silliman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- HHMI, Baltimore, MD21287
| | - Maria Popoli
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Janine Ptak
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- HHMI, Baltimore, MD21287
| | - Lisa Dobbyn
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Nadine Nehme
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Jonathan C. Dudley
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Mahmoud Summers
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Ming Zhang
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Lan T. Ho-Pham
- BioMedical Research Center, Pham Ngoc Thach University of Medicine, Ho Chi Minh City72510, Vietnam
- Clinical Genetics Research Group, Saigon Precision Medicine Research Center, Ho Chi Minh City72512, Vietnam
| | - Bich N. H. Tran
- Clinical Genetics Research Group, Saigon Precision Medicine Research Center, Ho Chi Minh City72512, Vietnam
| | - Thach S. Tran
- Clinical Genetics Research Group, Saigon Precision Medicine Research Center, Ho Chi Minh City72512, Vietnam
- School of Biomedical Engineering, University of Technology, NSW2007, Australia
| | - Tuan V. Nguyen
- Clinical Genetics Research Group, Saigon Precision Medicine Research Center, Ho Chi Minh City72512, Vietnam
- Centre for Health Technologies, University of Technology, NSW2007, Australia
- School of Population Health, University of New South Wales, NSW2003, Australia
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD21298
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- HHMI, Baltimore, MD21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
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13
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Chhoda A, Sharma A, Sailo B, Tang H, Ruzgar N, Tan WY, Ying L, Khatri R, Narayanan A, Mane S, De Kumar B, Wood LD, Iacobuzio-Donahue C, Wolfgang CL, Kunstman JW, Salem RR, Farrell JJ, Ahuja N. Utility of promoter hypermethylation in malignant risk stratification of intraductal papillary mucinous neoplasms. Clin Epigenetics 2023; 15:28. [PMID: 36803844 PMCID: PMC9942382 DOI: 10.1186/s13148-023-01429-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 01/14/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Intraductal papillary mucinous neoplasms (IPMNs), a type of cystic pancreatic cancer (PC) precursors, are increasingly identified on cross-sectional imaging and present a significant diagnostic challenge. While surgical resection of IPMN-related advanced neoplasia, i.e., IPMN-related high-grade dysplasia or PC, is an essential early PC detection strategy, resection is not recommended for IPMN-low-grade dysplasia (LGD) due to minimal risk of carcinogenesis, and significant procedural risks. Based on their promising results in prior validation studies targeting early detection of classical PC, DNA hypermethylation-based markers may serve as a biomarker for malignant risk stratification of IPMNs. This study investigates our DNA methylation-based PC biomarker panel (ADAMTS1, BNC1, and CACNA1G genes) in differentiating IPMN-advanced neoplasia from IPMN-LGDs. METHODS Our previously described genome-wide pharmaco-epigenetic method identified multiple genes as potential targets for PC detection. The combination was further optimized and validated for early detection of classical PC in previous case-control studies. These promising genes were evaluated among micro-dissected IPMN tissue (IPMN-LGD: 35, IPMN-advanced neoplasia: 35) through Methylation-Specific PCR. The discriminant capacity of individual and combination of genes were delineated through Receiver Operating Characteristics curve analysis. RESULTS As compared to IPMN-LGDs, IPMN-advanced neoplasia had higher hypermethylation frequency of candidate genes: ADAMTS1 (60% vs. 14%), BNC1 (66% vs. 3%), and CACGNA1G (25% vs. 0%). We observed Area Under Curve (AUC) values of 0.73 for ADAMTS1, 0.81 for BNC1, and 0.63 for CACNA1G genes. The combination of the BNC1/ CACNA1G genes resulted in an AUC of 0.84, sensitivity of 71%, and specificity of 97%. Combining the methylation status of the BNC1/CACNA1G genes, blood-based CA19-9, and IPMN lesion size enhanced the AUC to 0.92. CONCLUSION DNA-methylation based biomarkers have shown a high diagnostic specificity and moderate sensitivity for differentiating IPMN-advanced neoplasia from LGDs. Addition of specific methylation targets can improve the accuracy of the methylation biomarker panel and enable the development of noninvasive IPMN stratification biomarkers.
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Affiliation(s)
- Ankit Chhoda
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, USA
| | - Anup Sharma
- Department of Surgery, Yale School of Medicine, New Haven, USA
| | - Bethsebie Sailo
- Department of Surgery, Yale School of Medicine, New Haven, USA
| | - Haoyu Tang
- Yale Systems Biology Institute, Yale University, New Haven, USA
| | - Nensi Ruzgar
- Department of Surgery, Yale School of Medicine, New Haven, USA
| | - Wan Ying Tan
- Department of Surgery, Yale School of Medicine, New Haven, USA
| | - Lee Ying
- Department of Surgery, Yale School of Medicine, New Haven, USA
| | - Rishabh Khatri
- Department of Internal Medicine, Temple University Hospital, Philadelphia, USA
| | | | | | | | - Laura D Wood
- Department of Pathology, Johns Hopkins University, Baltimore, USA
| | | | | | - John W Kunstman
- Department of Surgery, Yale School of Medicine, New Haven, USA
| | - Ronald R Salem
- Department of Surgery, Yale School of Medicine, New Haven, USA
| | - James J Farrell
- Section of Digestive Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, USA.
| | - Nita Ahuja
- Department of Surgery, Yale School of Medicine, New Haven, USA.
- Section of Digestive Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, USA.
- Department of Pathology, Yale School of Medicine, New Haven, USA.
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, USA.
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14
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Pancreatic Cancer in Chronic Pancreatitis: Pathogenesis and Diagnostic Approach. Cancers (Basel) 2023; 15:cancers15030761. [PMID: 36765725 PMCID: PMC9913572 DOI: 10.3390/cancers15030761] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
Chronic pancreatitis is one of the main risk factors for pancreatic cancer, but it is a rare event. Inflammation and oncogenes work hand in hand as key promoters of this disease. Tobacco is another co-factor. During alcoholic chronic pancreatitis, the cumulative risk of cancer is estimated at 4% after 15 to 20 years. This cumulative risk is higher in hereditary pancreatitis: 19 and 12% in the case of PRSS1 and SPINK1 mutations, respectively, at an age of 60 years. The diagnosis is difficult due to: (i) clinical symptoms of cancer shared with those of chronic pancreatitis; (ii) the parenchymal and ductal remodeling of chronic pancreatitis rendering imaging analysis difficult; and (iii) differential diagnoses, such as pseudo-tumorous chronic pancreatitis and paraduodenal pancreatitis. Nevertheless, the occurrence of cancer during chronic pancreatitis must be suspected in the case of back pain, weight loss, unbalanced diabetes, and jaundice, despite alcohol withdrawal. Imaging must be systematically reviewed. Endoscopic ultrasound-guided fine-needle biopsy can contribute by targeting suspicious tissue areas with the help of molecular biology (search for KRAS, TP53, CDKN2A, DPC4 mutations). Short-term follow-up of patients is necessary at the clinical and paraclinical levels to try to diagnose cancer at a surgically curable stage. Pancreatic surgery is sometimes necessary if there is any doubt.
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15
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Mazer BL, Lee JW, Roberts NJ, Chu LC, Lennon AM, Klein AP, Eshleman JR, Fishman EK, Canto MI, Goggins MG, Hruban RH. Screening for pancreatic cancer has the potential to save lives, but is it practical? Expert Rev Gastroenterol Hepatol 2023; 17:555-574. [PMID: 37212770 PMCID: PMC10424088 DOI: 10.1080/17474124.2023.2217354] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/21/2023] [Accepted: 05/19/2023] [Indexed: 05/23/2023]
Abstract
INTRODUCTION Most patients with pancreatic cancer present with advanced stage, incurable disease. However, patients with high-grade precancerous lesions and many patients with low-stage disease can be cured with surgery, suggesting that early detection has the potential to improve survival. While serum CA19.9 has been a long-standing biomarker used for pancreatic cancer disease monitoring, its low sensitivity and poor specificity have driven investigators to hunt for better diagnostic markers. AREAS COVERED This review will cover recent advances in genetics, proteomics, imaging, and artificial intelligence, which offer opportunities for the early detection of curable pancreatic neoplasms. EXPERT OPINION From exosomes, to circulating tumor DNA, to subtle changes on imaging, we know much more now about the biology and clinical manifestations of early pancreatic neoplasia than we did just five years ago. The overriding challenge, however, remains the development of a practical approach to screen for a relatively rare, but deadly, disease that is often treated with complex surgery. It is our hope that future advances will bring us closer to an effective and financially sound approach for the early detection of pancreatic cancer and its precursors.
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Affiliation(s)
- Benjamin L. Mazer
- The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jae W. Lee
- The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, MD
| | - Nicholas J. Roberts
- The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Linda C. Chu
- Department of Radiology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anne Marie Lennon
- Department of Medicine, Division of Gastroenterology and Hepatology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alison P. Klein
- The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R. Eshleman
- The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elliot K. Fishman
- Department of Radiology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marcia Irene Canto
- Department of Medicine, Division of Gastroenterology and Hepatology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael G. Goggins
- The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ralph H. Hruban
- The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
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16
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Blood-based DNA methylation signatures in cancer: A systematic review. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166583. [PMID: 36270476 DOI: 10.1016/j.bbadis.2022.166583] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Abstract
DNA methylation profiles are in dynamic equilibrium via the initiation of methylation, maintenance of methylation and demethylation, which control gene expression and chromosome stability. Changes in DNA methylation patterns play important roles in carcinogenesis and primarily manifests as hypomethylation of the entire genome and the hypermethylation of individual loci. These changes may be reflected in blood-based DNA, which provides a non-invasive means for cancer monitoring. Previous blood-based DNA detection objects primarily included circulating tumor DNA/cell-free DNA (ctDNA/cfDNA), circulating tumor cells (CTCs) and exosomes. Researchers gradually found that methylation changes in peripheral blood mononuclear cells (PBMCs) also reflected the presence of tumors. Blood-based DNA methylation is widely used in early diagnosis, prognosis prediction, dynamic monitoring after treatment and other fields of clinical research on cancer. The reversible methylation of genes also makes them important therapeutic targets. The present paper summarizes the changes in DNA methylation in cancer based on existing research and focuses on the characteristics of the detection objects of blood-based DNA, including ctDNA/cfDNA, CTCs, exosomes and PBMCs, and their application in clinical research.
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17
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Heumann TR, Baretti M, Sugar EA, Durham JN, Linden S, Lopez-Vidal TY, Leatherman J, Cope L, Sharma A, Weekes CD, O'Dwyer PJ, Reiss KA, Monga DK, Ahuja N, Azad NS. A randomized, phase II trial of oral azacitidine (CC-486) in patients with resected pancreatic adenocarcinoma at high risk for recurrence. Clin Epigenetics 2022; 14:166. [PMID: 36463226 PMCID: PMC9719150 DOI: 10.1186/s13148-022-01367-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/11/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Of the only 20% of patients with resectable pancreatic ductal adenocarcinoma (rPDA), cancer recurs in 80% of cases. Epigenetic dysregulation is an early hallmark of cancer cells acquiring metastatic potential, and epigenetic modulators may reactivate tumor suppressor genes, delay recurrence, and sensitize PDA to future chemotherapy. METHODS This was a randomized phase II study (NCT01845805) of CC-486 (oral DNA methyltransferase inhibitor azacitidine) vs. observation (OBS) in rPDA patients harboring high-risk features (stage pN1-2, R1 margins, or elevated CA 19-9 level) with no evidence of disease following standard adjuvant therapy. Patients were randomized to oral CC-486 treatment (300 mg daily on days 1-21 on a 28-day cycle) or OBS for up to 12 cycles or until disease relapse/unacceptable toxicities. Following recurrence, records of next-line therapies, imaging, and survival were obtained. The primary endpoint was progression-free survival (PFS)-time from randomization to recurrence (imaging/biopsy confirmed or death). Secondary endpoints included OS and PFS and ORR and metastatic PFS with subsequent next-line systemic therapy in metastatic setting. RESULTS Forty-nine patients (24 in CC-486 arm, 25 in OBS arm) were randomized: median age 66 (range 36-81), 53% male, 73% node positive, 49% elevated CA 19-9, 20% R1 resection, 63% and 100% received perioperative concurrent chemoradiation and chemotherapy, respectively. Median time from surgery to randomization was 9.6 mo (range 2.9-36.8). For the CC-486 arm, median treatment duration was 5.6 mo (range 1.3 to 12.8) with 14 treatment-related grade 3 or 4 AEs among 5 patients (22%) resulting in dose-reduction. Four patients (17%) discontinued therapy due to AEs. With median follow-up of 20.3mo (IQR 12.8, 41.4), 38 (79%) of evaluable patients recurred (34 imaging-confirmed, 4 clinically). Median PFS in imagining-confirmed cases was 9.2 and 8.9mo (HR 0.94, 95% CI 0.46-1.87, p = 0.85) for CC-486 and OBS patients, respectively. Median OS (2-yr OS%) was 33.8 (50%) and 26.4 mo (61%) in CC-486 and OBS patients, respectively. (HR 0.98, 95% CI 0.46-2.05, p = 0.96). ORR with subsequent chemotherapy in the metastatic setting was minimal in both arms. CONCLUSIONS Treatment with CC-486 following adjuvant therapy did not prolong time-to-relapse in patients with high-risk rPDA or improve disease response on 1st-line metastatic therapy.
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Affiliation(s)
- Thatcher R Heumann
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Marina Baretti
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Elizabeth A Sugar
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
- Departments of Biostatistics and Epidemiology, The Bloomberg School of Public Health at Johns Hopkins, Baltimore, MD, USA
| | - Jennifer N Durham
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Sheila Linden
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Tamara Y Lopez-Vidal
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - James Leatherman
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Leslie Cope
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Anup Sharma
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Colin D Weekes
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Peter J O'Dwyer
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Kim A Reiss
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Dulabh K Monga
- Medical Oncology, Allegheny General Hospital, Pittsburgh, PA, USA
| | - Nita Ahuja
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Nilofer S Azad
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA.
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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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Wu H, Guo S, Liu X, Li Y, Su Z, He Q, Liu X, Zhang Z, Yu L, Shi X, Gao S, Wang H, Pan Y, Ma C, Liu R, Dai M, Jin G, Liang Z. Noninvasive detection of pancreatic ductal adenocarcinoma using the methylation signature of circulating tumour DNA. BMC Med 2022; 20:458. [PMID: 36434648 PMCID: PMC9701032 DOI: 10.1186/s12916-022-02647-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/01/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) has the lowest overall survival rate primarily due to the late onset of symptoms and rapid progression. Reliable and accurate tests for early detection are lacking. We aimed to develop a noninvasive test for early PDAC detection by capturing the circulating tumour DNA (ctDNA) methylation signature in blood. METHODS Genome-wide methylation profiles were generated from PDAC and nonmalignant tissues and plasma. Methylation haplotype blocks (MHBs) were examined to discover de novo PDAC markers. They were combined with multiple cancer markers and screened for PDAC classification accuracy. The most accurate markers were used to develop PDACatch, a targeted methylation sequencing assay. PDACatch was applied to additional PDAC and healthy plasma cohorts to train, validate and independently test a PDAC-discriminating classifier. Finally, the classifier was compared and integrated with carbohydrate antigen 19-9 (CA19-9) to evaluate and maximize its accuracy and utility. RESULTS In total, 90 tissues and 546 plasma samples were collected from 232 PDAC patients, 25 chronic pancreatitis (CP) patients and 323 healthy controls. Among 223 PDAC cases with known stage information, 43/119/38/23 cases were of Stage I/II/III/IV. A total of 171 de novo PDAC-specific markers and 595 multicancer markers were screened for PDAC classification accuracy. The top 185 markers were included in PDACatch, from which a 56-marker classifier for PDAC plasma was trained, validated and independently tested. It achieved an area under the curve (AUC) of 0.91 in both the validation (31 PDAC, 26 healthy; sensitivity = 84%, specificity = 89%) and independent tests (74 PDAC, 65 healthy; sensitivity = 82%, specificity = 88%). Importantly, the PDACatch classifier detected CA19-9-negative PDAC plasma at sensitivities of 75 and 100% during the validation and independent tests, respectively. It was more sensitive than CA19-9 in detecting Stage I (sensitivity = 80 and 68%, respectively) and early-stage (Stage I-IIa) PDAC (sensitivity = 76 and 70%, respectively). A combinatorial classifier integrating PDACatch and CA19-9 outperformed (AUC=0.94) either PDACatch (0.91) or CA19-9 (0.89) alone (p < 0.001). CONCLUSIONS The PDACatch assay demonstrated high sensitivity for early PDAC plasma, providing potential utility for noninvasive detection of early PDAC and indicating the effectiveness of methylation haplotype analyses in discovering robust cancer markers.
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Affiliation(s)
- Huanwen Wu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Shiwei Guo
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Xiaoding Liu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Yatong Li
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Qiye He
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Xiaoqian Liu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Zhiwen Zhang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Lianyuan Yu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Xiaohan Shi
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Suizhi Gao
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Huan Wang
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Yaqi Pan
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Chengcheng Ma
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Rui Liu
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China.
| | - Menghua Dai
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China.
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China.
| | - Zhiyong Liang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China.
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Is Cell-Free DNA Testing in Pancreatic Ductal Adenocarcinoma Ready for Prime Time? Cancers (Basel) 2022; 14:cancers14143453. [PMID: 35884515 PMCID: PMC9322623 DOI: 10.3390/cancers14143453] [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: 06/16/2022] [Revised: 07/03/2022] [Accepted: 07/13/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Pancreatic cancer is a deadly cancer with limited treatment options. It is often detected in most people at stages where cure is not possible. There is no good test to know if a person will respond to treatment or if there is any disease beyond what can be seen by available imaging tests. Genetic material from the tumor is expected to float in the blood. Studying the alterations in the genetic material could help detect the tumor early, give an idea about its aggressiveness and response to available treatments, and facilitate the discovery of newer therapies. The focus of the studies so far has been on only one kind of genetic aberration, mutations, which has not given us great results. There is a need to explore another type of change known as methylation that could hold answers for managing pancreatic cancers better. Abstract Cell-free DNA (cfDNA) testing currently does not have a significant role in PDA management: it is insufficient to diagnose PDA, and its use is primarily restricted to identifying targetable mutations (if tissue is insufficient or unavailable). cfDNA testing has the potential to address critical needs in PDA management, such as pre-operative risk stratification (POR), prognostication, and predicting (and monitoring) treatment response. Prior studies have focused primarily on somatic mutations, specifically KRAS variants, and have shown limited success in addressing prognosis and POR. Recent studies have demonstrated the importance of other less prevalent mutations (ERBB2 and TP53), but no studies have provided reliable mutation panels for clinical use. Methylation aberrations in cfDNA (epigenetic markers) in PDA have been relatively less explored. However, early evidence has suggested they offer diagnostic and, to some extent, prognostic value. The inclusion of epigenetic markers of cfDNA adds another dimension to genomic testing and may open new therapeutic avenues beyond addressing critical areas of need in PDA treatment. For cfDNA to substantially influence PDA management, concerted efforts are required to include less frequent mutations and epigenetic markers. Furthermore, relying on KRAS mutations for PDA management will always be inadequate.
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Wu H, Ou S, Zhang H, Huang R, Yu S, Zhao M, Tai S. Advances in biomarkers and techniques for pancreatic cancer diagnosis. Cancer Cell Int 2022; 22:220. [PMID: 35761336 PMCID: PMC9237966 DOI: 10.1186/s12935-022-02640-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/18/2022] [Indexed: 12/31/2022] Open
Abstract
Pancreatic cancer is the most lethal type of malignancy and is characterized by high invasiveness without severe symptoms. It is difficult to detect PC at an early stage because of the low diagnostic accuracy of existing routine methods, such as abdominal ultrasound, CT, MRI, and endoscopic ultrasound (EUS). Therefore, it is of value to develop new diagnostic techniques for early detection with high accuracy. In this review, we aim to highlight research progress on novel biomarkers, artificial intelligence, and nanomaterial applications on the diagnostic accuracy of pancreatic cancer.
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22
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Iyengar D, Tatiparti K, Gavande NS, Sau S, Iyer AK. Nanomedicine for overcoming therapeutic and diagnostic challenges associated with pancreatic cancer. Drug Discov Today 2022; 27:1554-1559. [PMID: 35247592 DOI: 10.1016/j.drudis.2022.02.026] [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: 06/08/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 11/29/2022]
Abstract
Pancreatic cancer is the second leading cause of cancer-related death in the USA. The 5-year survival rate for pancreatic cancer is as low as 10%, making it one of the most deadly cancers. This dismal prognosis is caused, in part, by the lack of early detection and screening options, leading to late-stage detection of the disease, at a point at which chemotherapy is no longer effective. However, nanoparticle (NP) drug delivery systems have increased the efficacy of chemotherapeutics by improving the targeting ability of drugs to the tumor site, while also decreasing the risk of local and systemic toxicity. Such efforts can contribute to the development of early diagnosis and routine screening tests, which will drastically improve the survival rates and prognosis of patients with pancreatic cancer.
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Affiliation(s)
- Disha Iyengar
- Use-inspired Biomaterials & Integrated Nano Delivery (U-BiND) Systems Laboratory, Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Katyayani Tatiparti
- Use-inspired Biomaterials & Integrated Nano Delivery (U-BiND) Systems Laboratory, Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Navnath S Gavande
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Samaresh Sau
- Use-inspired Biomaterials & Integrated Nano Delivery (U-BiND) Systems Laboratory, Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA.
| | - Arun K Iyer
- Use-inspired Biomaterials & Integrated Nano Delivery (U-BiND) Systems Laboratory, Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA; Molecular Imaging Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA.
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23
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Chen G, Long J, Zhu R, Yang G, Qiu J, Zhao F, Liu Y, Tao J, Zhang T, Zhao Y. Identification and Validation of Constructing the Prognostic Model With Four DNA Methylation-Driven Genes in Pancreatic Cancer. Front Cell Dev Biol 2022; 9:709669. [PMID: 35087823 PMCID: PMC8786741 DOI: 10.3389/fcell.2021.709669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 11/29/2021] [Indexed: 12/17/2022] Open
Abstract
Background: Pancreatic cancer (PC) is a highly aggressive gastrointestinal tumor and has a poor prognosis. Evaluating the prognosis validly is urgent for PC patients. In this study, we utilized the RNA-sequencing (RNA-seq) profiles and DNA methylation expression data comprehensively to develop and validate a prognostic signature in patients with PC. Methods: The integrated analysis of RNA-seq, DNA methylation expression profiles, and relevant clinical information was performed to select four DNA methylation-driven genes. Then, a prognostic signature was established by the univariate, multivariate Cox, and least absolute shrinkage and selection operator (LASSO) regression analyses in The Cancer Genome Atlas (TCGA) dataset. GSE62452 cohort was utilized for external validation. Finally, a nomogram model was set up and evaluated by calibration curves. Results: Nine DNA methylation-driven genes that were related to overall survival (OS) were identified. After multivariate Cox and LASSO regression analyses, four of these genes (RIC3, MBOAT2, SEZ6L, and OAS2) were selected to establish the predictive signature. The PC patients were stratified into two groups according to the median risk score, of which the low-risk group displayed a prominently favorable OS compared with the high-risk group, whether in the training (p < 0.001) or validation (p < 0.01) cohort. Then, the univariate and multivariate Cox regression analyses showed that age, grade, risk score, and the number of positive lymph nodes were significantly associated with OS in PC patients. Therefore, we used these clinical variables to construct a nomogram; and its performance in predicting the 1-, 2-, and 3-year OS of patients with PC was assessed via calibration curves. Conclusion: A prognostic risk score signature was built with the four alternative DNA methylation-driven genes. Furthermore, in combination with the risk score, age, grade, and the number of positive lymph nodes, a nomogram was established for conveniently predicting the individualized prognosis of PC patients.
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Affiliation(s)
- Guangyu Chen
- State Key Laboratory of Complex Severe and Rare Diseases, General Surgery Department, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junyu Long
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruizhe Zhu
- State Key Laboratory of Complex Severe and Rare Diseases, General Surgery Department, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Gang Yang
- State Key Laboratory of Complex Severe and Rare Diseases, General Surgery Department, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiangdong Qiu
- State Key Laboratory of Complex Severe and Rare Diseases, General Surgery Department, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fangyu Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, General Surgery Department, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuezhe Liu
- State Key Laboratory of Complex Severe and Rare Diseases, General Surgery Department, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinxin Tao
- State Key Laboratory of Complex Severe and Rare Diseases, General Surgery Department, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Taiping Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, General Surgery Department, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yupei Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, General Surgery Department, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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microRNA-21 Regulates Stemness in Pancreatic Ductal Adenocarcinoma Cells. Int J Mol Sci 2022; 23:ijms23031275. [PMID: 35163198 PMCID: PMC8835847 DOI: 10.3390/ijms23031275] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 02/06/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common and aggressive type of pancreatic cancer (PCa) with a low survival rate. microRNAs (miRs) are endogenous, non-coding RNAs that moderate numerous biological processes. miRs have been associated with the chemoresistance and metastasis of PDAC and the presence of a subpopulation of highly plastic "stem"-like cells within the tumor, known as cancer stem cells (CSCs). In this study, we investigated the role of miR-21, which is highly expressed in Panc-1 and MiaPaCa-2 PDAC cells in association with CSCs. Following miR-21 knockouts (KO) from both MiaPaCa-2 and Panc-1 cell lines, reversed expressions of epithelial-mesenchymal transition (EMT) and CSCs markers were observed. The expression patterns of key CSC markers, including CD44, CD133, CX-C chemokine receptor type 4 (CXCR4), and aldehyde dehydrogenase-1 (ALDH1), were changed depending on miR-21 status. miR-21 (KO) suppressed cellular invasion of Panc-1 and MiaPaCa-2 cells, as well as the cellular proliferation of MiaPaCa-2 cells. Our data suggest that miR-21 is involved in the stemness of PDAC cells, may play roles in mesenchymal transition, and that miR-21 poses as a novel, functional biomarker for PDAC aggressiveness.
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The metabolic stress-activated checkpoint LKB1-MARK3 axis acts as a tumor suppressor in high-grade serous ovarian carcinoma. Commun Biol 2022; 5:39. [PMID: 35017636 PMCID: PMC8752757 DOI: 10.1038/s42003-021-02992-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 12/21/2021] [Indexed: 11/26/2022] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) is the most aggressive gynecological malignancy, resulting in approximately 70% of ovarian cancer deaths. However, it is still unclear how genetic dysregulations and biological processes generate the malignant subtype of HGSOC. Here we show that expression levels of microtubule affinity-regulating kinase 3 (MARK3) are downregulated in HGSOC, and that its downregulation significantly correlates with poor prognosis in HGSOC patients. MARK3 overexpression suppresses cell proliferation and angiogenesis of ovarian cancer cells. The LKB1-MARK3 axis is activated by metabolic stress, which leads to the phosphorylation of CDC25B and CDC25C, followed by induction of G2/M phase arrest. RNA-seq and ATAC-seq analyses indicate that MARK3 attenuates cell cycle progression and angiogenesis partly through downregulation of AP-1 and Hippo signaling target genes. The synthetic lethal therapy using metabolic stress inducers may be a promising therapeutic choice to treat the LKB1-MARK3 axis-dysregulated HGSOCs. Machino et al discover that low expression of microtubule affinity-regulating kinase 3 (MARK3) correlates with poor prognosis in high-grade serous ovarian carcinoma (HGSOC) patients. They find that the LKB1-MARK3 axis is activated by metabolic stress to block the cell cycle at the G2/M checkpoint, and characterise other MARK3 regulated pathways through RNA and ATAC sequencing.
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Stark A, Trick A, Pisanic TR, Wang TH. Droplet Magnetofluidic Assay Platform for Quantitative Methylation-Specific PCR. Methods Mol Biol 2022; 2394:199-209. [PMID: 35094330 DOI: 10.1007/978-1-0716-1811-0_13] [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] [Indexed: 06/14/2023]
Abstract
Early cancer detection requires identification of cellular changes resulting from oncogenesis. Abnormal DNA methylation patterns occurring early in tumor development have been widely identified as early biomarkers for multiple types of cancer tumors. Methylation-Specific PCR (MSP) has permitted highly sensitive detection of these methylation changes at known biomarker locations. MSP requires multiple sample preparation steps including protein digestion, DNA isolation, and bisulfite conversion prior to detection. In this work, we present a streamlined assay platform and instrumentation for integration of all sample processing steps required to obtain quantitative MSP signal from raw biological samples through the use of droplet magnetofluidic principles. In conjunction with this platform, we present a streamlined protocol for solid-phase DNA extraction from cells and bisulfite conversion of genomic DNA, minimizing the processing steps and reagent volume for implementation on a compact assay platform.
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Affiliation(s)
- Alejandro Stark
- Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Alexander Trick
- Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Thomas R Pisanic
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Tza-Huei Wang
- Mechanical & Biomedical Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.
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Liang ZQ, Zhong LY, Li J, Shen JH, Tu XY, Zhong ZH, Zeng JJ, Chen JH, Wei ZX, Dang YW, Huang SN, Chen G. Clinicopathological significance and underlying molecular mechanism of downregulation of basonuclin 1 expression in ovarian carcinoma. Exp Biol Med (Maywood) 2022; 247:106-119. [PMID: 34644201 PMCID: PMC8777474 DOI: 10.1177/15353702211052036] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In this study, we aim to identify the clinical significance of basonuclin 1 (BNC1) expression in ovarian carcinoma (OV) and to explore its latent mechanisms. Via integrating in-house tissue microarrays, gene chips, and RNA-sequencing data, we explored the expression and clinical value of BNC1 in OV. Immunohistochemical staining was utilized to confirm the protein expression status of BNC1. A combined SMD of -2.339 (95% CI: -3.649 to -1.028, P < 0.001) identified that BNC1 was downregulated based on 1346 samples, and the sROC (AUC = 0.93) showed a favorable discriminatory ability of BNC1 in OV patients. We used univariate and multivariate Cox regulation to evaluate the prognostic role of BNC1 for OV patients, and a combined hazard ratio of 0.717 (95% CI: 0.445-0.989, P < 0.001) revealed that BNC1 was a protective factor for OV. Furthermore, the fraction of infiltrating naive B cells, memory B cells, and other immune cells showed statistical differences between the high- and low-BNC1 expression groups through cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm. Enrichment analysis showed that BNC1 may have a relationship with immune-related items in OV. By predicting the potential regulatory transcription factors (TFs) of BNC1, friend leukemia virus integration 1 (FLI1) may be a potential upstream TF of BNC1. Corporately, a decreasing trend of BNC1 may serve as a tumor suppressor and prognostic biomarker in OV patients. Moreover, BNC1 may take part in immune-related pathways and influence the fraction of tumor-infiltrating immune cells.
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Affiliation(s)
- Zi-Qian Liang
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Lu-Yang Zhong
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Jie Li
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Jin-Hai Shen
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Xin-Yue Tu
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Zheng-Hong Zhong
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Jing-Jing Zeng
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Jun-Hong Chen
- Department of Pathology, Maternal and Child Health Hospital of
Guangxi Zhuang Autonomous Region, Nanning 530003, P. R. China
| | - Zhu-Xin Wei
- Department of Radiotherapy, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Su-Ning Huang
- Department of Radiotherapy, Guangxi Medical University Cancer
Hospital, Nanning 530021, P.R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
- Gang Chen.
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A New Survival Model Based on ADAMTSs for Prognostic Prediction in Clear Cell Renal Cell Carcinoma. JOURNAL OF ONCOLOGY 2021; 2021:2606213. [PMID: 34603444 PMCID: PMC8486512 DOI: 10.1155/2021/2606213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 12/15/2022]
Abstract
The main purpose of this study was to explore the genetic variation, gene expression, and clinical significance of ADAMTSs (a disintegrin and metalloprotease domains with thrombospondin motifs) across cancer types. Analysis of data from the TCGA (The Cancer Genome Atlas) database showed that the ADAMTSs have extensive CNV (copy number variation) and SNV (single nucleotide variation) across cancer types. Compared with normal tissues, the methylation of ADAMTSs in cancer tissues is also significantly different, which affects the expression of ADAMTS gene and the prognosis of cancer patients. Through gene expression analysis, we found that ADAMTS family has significant changes in gene expression across cancer types and is closely related to the prognosis of carcinoma, especially in ccRCC (clear cell renal cell carcinoma). LASSO regression analysis was used to establish a prognostic model based on the ADAMTSs to judge the prognosis of patients with ccRCC. Multiple Cox regression analysis suggested that age, grade, stage, and risk score of the prognostic model of ccRCC were independent prognostic factors in patients with renal clear cell carcinoma. These findings indicate that the ADAMTSs-based survival model can accurately predict the prognosis of patients with ccRCC and suggest that ADAMTSs are a potential prognostic biomarker and therapeutic target in ccRCC.
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29
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Ying L, Sharma A, Chhoda A, Ruzgar N, Hasan N, Kwak R, Wolfgang CL, Wang TH, Kunstman JW, Salem RR, Wood LD, Iacobuzio-Donahue C, Schneider EB, Farrell JJ, Ahuja N. Methylation-based Cell-free DNA Signature for Early Detection of Pancreatic Cancer. Pancreas 2021; 50:1267-1273. [PMID: 34860810 DOI: 10.1097/mpa.0000000000001919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVES The potential of DNA methylation alterations in early pancreatic cancer (PC) detection among pancreatic tissue cell-free DNA seems promising. This study investigates the diagnostic capacity of the 4-gene methylation biomarker panel, which included ADAMTS1, BNC1, LRFN5, and PXDN genes, in a case-control study. METHODS A genome-wide pharmacoepigenetic approach identified ADAMTS1, BNC1, LRFN5, and PXDN genes as putative targets. Tissue samples including stage I-IV PC (n = 44), pancreatic intraepithelial neoplasia (n = 15), intraductal papillary mucinous neoplasms (n = 24), and normal pancreas (n = 8), and cell-free DNA, which was acquired through methylation on beads technology from PC (n = 22) and control patients (n = 10), were included. The 2-∆ct was the outcome of interest and underwent receiver operating characteristic analysis to determine the diagnostic accuracy of the panel. RESULTS Receiver operating characteristic analysis revealed an area under the curve of 0.93 among ADAMTS1, 0.76 among BNC1, 0.75 among PXDN, and 0.69 among LRFN5 gene. The combination gene methylation panel (ADAMTS1, BNC1, LRFN5, and PXDN) had an area under the curve of 0.94, with a sensitivity of 100% and specificity of 90%. CONCLUSIONS This methylation-based biomarker panel had promising accuracy for PC detection and warranted further validation in prospective PC surveillance trials.
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Affiliation(s)
| | | | - Ankit Chhoda
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
| | | | | | | | | | - Tza Huei Wang
- Department of Biomedical Engineering and Department of Mechanical Engineering and Institute for NanoBioTechnology, Johns Hopkins University
| | | | | | - Laura D Wood
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD
| | - Christine Iacobuzio-Donahue
- Human Oncology and Pathogenesis Program, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - James J Farrell
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
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30
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Thompson JK, Bednar F. Clinical Utility of Epigenetic Changes in Pancreatic Adenocarcinoma. EPIGENOMES 2021; 5:20. [PMID: 34968245 PMCID: PMC8715475 DOI: 10.3390/epigenomes5040020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022] Open
Abstract
Pancreatic cancer is a molecularly heterogeneous disease. Epigenetic changes and epigenetic regulatory mechanisms underlie at least some of this heterogeneity and contribute to the evolution of aggressive tumor biology in patients and the tumor's intrinsic resistance to therapy. Here we review our current understanding of epigenetic dysregulation in pancreatic cancer and how it is contributing to our efforts in early diagnosis, predictive and prognostic biomarker development and new therapeutic approaches in this deadly cancer.
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Affiliation(s)
| | - Filip Bednar
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA;
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31
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Cardiomyocyte-Specific Circulating Cell-Free Methylated DNA in Esophageal Cancer Patients Treated with Chemoradiation. GASTROINTESTINAL DISORDERS 2021; 3:100-112. [PMID: 35531260 PMCID: PMC9074856 DOI: 10.3390/gidisord3030011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Thoracic high-dose radiation therapy (RT) for cancer has been associated with early and late cardiac toxicity. To assess altered rates of cardiomyocyte cell death due to RT we monitored changes in cardiomyocyte-specific, cell-free methylated DNA (cfDNA) shed into the circulation. Eleven patients with distal esophageal cancer treated with neoadjuvant chemoradiation to 50.4 Gy (RT) and concurrent carboplatin and paclitaxel were enrolled. Subjects underwent fasting blood draws prior to the initiation and after completion of RT as well as 4–6 months following RT. An island of six unmethylated CpGs in the FAM101A locus was used to identify cardiomyocyte-specific cfDNA in serum. After bisulfite treatment this specific cfDNA was quantified by amplicon sequencing at a depth of >35,000 reads/molecule. Cardiomyocyte-specific cfDNA was detectable before RT in the majority of patient samples and showed some distinct changes during the course of treatment and recovery. We propose that patient-specific cardiac damages in response to the treatment are indicated by these changes although co-morbidities may obscure treatment-specific events.
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32
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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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33
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Henriksen SD, Thorlacius-Ussing O. Cell-Free DNA Methylation as Blood-Based Biomarkers for Pancreatic Adenocarcinoma—A Literature Update. EPIGENOMES 2021; 5:epigenomes5020008. [PMID: 34968295 PMCID: PMC8594668 DOI: 10.3390/epigenomes5020008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/14/2022] Open
Abstract
Pancreatic adenocarcinoma has a horrible prognosis, which is partly due to difficulties in diagnosing the disease in an early stage. Additional blood-born biomarkers for pancreatic adenocarcinoma are needed. Epigenetic modifications, as changes in DNA methylation, is a fundamental part of carcinogenesis. The aim of this paper is to do an update on cell-free DNA methylation as blood-based biomarkers for pancreatic adenocarcinoma. The current literature including our studies clearly indicates that cell-free DNA methylation has the potential as blood-based diagnostic and prognostic biomarkers for pancreatic adenocarcinoma. However, still no clinical applicable biomarker for pancreatic adenocarcinoma based on DNA methylation do exist. Further well-designed validation studies are needed.
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Affiliation(s)
- Stine Dam Henriksen
- Department of Gastrointestinal Surgery, Aalborg University Hospital, 9000 Aalborg, Denmark;
- Clinical Cancer Research Center, Aalborg University Hospital, 9000 Aalborg, Denmark
- Correspondence:
| | - Ole Thorlacius-Ussing
- Department of Gastrointestinal Surgery, Aalborg University Hospital, 9000 Aalborg, Denmark;
- Clinical Cancer Research Center, Aalborg University Hospital, 9000 Aalborg, Denmark
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34
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Al-Shaheri FN, Alhamdani MSS, Bauer AS, Giese N, Büchler MW, Hackert T, Hoheisel JD. Blood biomarkers for differential diagnosis and early detection of pancreatic cancer. Cancer Treat Rev 2021; 96:102193. [PMID: 33865174 DOI: 10.1016/j.ctrv.2021.102193] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022]
Abstract
Pancreatic cancer is currently the most lethal tumor entity and case numbers are rising. It will soon be the second most frequent cause of cancer-related death in the Western world. Mortality is close to incidence and patient survival after diagnosis stands at about five months. Blood-based diagnostics could be one crucial factor for improving this dismal situation and is at a stage that could make this possible. Here, we are reviewing the current state of affairs with its problems and promises, looking at various molecule types. Reported results are evaluated in the overall context. Also, we are proposing steps toward clinical utility that should advance the development toward clinical application by improving biomarker quality but also by defining distinct clinical objectives and the respective diagnostic accuracies required to achieve them. Many of the discussed points and conclusions are highly relevant to other solid tumors, too.
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Affiliation(s)
- Fawaz N Al-Shaheri
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Medical Faculty Heidelberg, Heidelberg University, Im Neuenheimer Feld 672, 69120 Heidelberg, Germany.
| | - Mohamed S S Alhamdani
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Andrea S Bauer
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Nathalia Giese
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Markus W Büchler
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Thilo Hackert
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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35
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Satoh K. Molecular Approaches Using Body Fluid for the Early Detection of Pancreatic Cancer. Diagnostics (Basel) 2021; 11:diagnostics11020375. [PMID: 33671729 PMCID: PMC7926932 DOI: 10.3390/diagnostics11020375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most malignant form of gastrointestinal tumor and is the fourth leading cause of deaths due to cancer in Japan. This cancer shows a poor outcome due to the difficulty of its early diagnosis and its rapid growth. Once this disease becomes clinically evident, it is frequently accompanied by distant metastasis at the time of diagnosis. A recent multicenter study in Japan revealed that patients with the early stage of this disease (stage 0 and I) showed favorable prognosis after surgical resection, indicating the importance of early detection for improvement of PDAC prognosis. PDAC develops through a stepwise progression from the precursor lesion, and over the last few decades molecular analyses have shown the detailed genetic alterations that occur in this process. Since advances in molecular technologies have enabled the detection of genetic changes from a very small quantity of samples, a large number of non-invasive molecular approaches have been utilized in an attempt to find precursor or non-invasive carcinoma lesions. In this review, the current efforts in terms of the molecular approaches applied for the early detection of PDAC—especially using body fluids such as pancreatic juice, blood, and saliva—are summarized.
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Affiliation(s)
- Kennichi Satoh
- Division of Gastroenterology, Tohoku Medical and Pharmaceutical University, 1-15-1 Fukumuro, Miyaginoku, Sendai, Miyagi 983-8536, Japan
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36
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Iovanna J. Implementing biological markers as a tool to guide clinical care of patients with pancreatic cancer. Transl Oncol 2020; 14:100965. [PMID: 33248412 PMCID: PMC7704461 DOI: 10.1016/j.tranon.2020.100965] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/04/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
A major obstacle for the effective treatment of PDAC is its molecular heterogeneity. Stratification of PDAC using markers highly specific, reproducible, sensitive, easily measurable and inexpensive is necessary. At the early stages, clinician’s priority lies in rapid diagnosis, so that the patient receives surgery without delay. At advanced disease stages, priority is to determine the tumor subtype and select a suitable effective treatment.
A major obstacle for the effective treatment of pancreatic ductal adenocarcinoma (PDAC) is its molecular heterogeneity, reflected by the diverse clinical outcomes and responses to therapies that occur. The tumors of patients with PDAC must therefore be closely examined and classified before treatment initiation in order to predict the natural evolution of the disease and the response to therapy. To stratify patients, it is absolutely necessary to identify biological markers that are highly specific and reproducible, and easily measurable by inexpensive sensitive techniques. Several promising strategies to find biomarkers are already available or under development, such as the use of liquid biopsies to detect circulating tumor cells, circulating free DNA, methylated DNA, circulating RNA, and exosomes and extracellular vesicles, as well as immunological markers and molecular markers. Such biomarkers are capable of classifying patients with PDAC and predicting their therapeutic sensitivity. Interestingly, developing chemograms using primary cell lines or organoids and analyzing the resulting high-throughput data via artificial intelligence would be highly beneficial to patients. How can exploiting these biomarkers benefit patients with resectable, borderline resectable, locally advanced, and metastatic PDAC? In fact, the utility of these biomarkers depends on the patient's clinical situation. At the early stages of the disease, the clinician's priority lies in rapid diagnosis, so that the patient receives surgery without delay; at advanced disease stages, where therapeutic possibilities are severely limited, the priority is to determine the PDAC tumor subtype so as to estimate the clinical outcome and select a suitable effective treatment.
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Affiliation(s)
- Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France.
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37
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Zhang WH, Wang WQ, Han X, Gao HL, Li TJ, Xu SS, Li S, Xu HX, Li H, Ye LY, Lin X, Wu CT, Long J, Yu XJ, Liu L. Advances on diagnostic biomarkers of pancreatic ductal adenocarcinoma: A systems biology perspective. Comput Struct Biotechnol J 2020; 18:3606-3614. [PMID: 33304458 PMCID: PMC7710502 DOI: 10.1016/j.csbj.2020.11.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 12/26/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy that is usually diagnosed at an advanced stage when curative surgery is no longer an option. Robust diagnostic biomarkers with high sensitivity and specificity for early detection are urgently needed. Systems biology provides a powerful tool for understanding diseases and solving challenging biological problems, allowing biomarkers to be identified and quantified with increasing accuracy, sensitivity, and comprehensiveness. Here, we present a comprehensive overview of efforts to identify biomarkers of PDAC using genomics, transcriptomics, proteomics, metabonomics, and bioinformatics. Systems biology perspective provides a crucial “network” to integrate multi-omics approaches to biomarker identification, shedding additional light on early PDAC detection.
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Affiliation(s)
- Wu-Hu Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Wen-Quan Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xuan Han
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - He-Li Gao
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Tian-Jiao Li
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Shuai-Shuai Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Shuo Li
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Hua-Xiang Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Hao Li
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Long-Yun Ye
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xuan Lin
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Chun-Tao Wu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jiang Long
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xian-Jun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Liang Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
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38
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Early Diagnosis of Pancreatic Cancer: The Key for Survival. Diagnostics (Basel) 2020; 10:diagnostics10110869. [PMID: 33114412 PMCID: PMC7694042 DOI: 10.3390/diagnostics10110869] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/16/2020] [Accepted: 10/23/2020] [Indexed: 02/07/2023] Open
Abstract
Pancreatic cancer (PC) is one of the most aggressive forms of cancer. Negative prognosis is mainly due to the late diagnosis in advanced stages, when the disease is already therapeutically overcome. Studies in recent years have focused on identifying biomarkers that could play a role in early diagnosis, leading to the improvement of morbidity and mortality. Currently, the only biomarker widely used in the diagnosis of PC is carbohydrate antigen 19-9 (CA19.9), which has, however, more of a prognostic role in the follow-up of postoperative recurrence than a diagnostic role. Other biomarkers, recently identified as the methylation status of ADAMTS1 (A disintegrin and metalloproteinase with thrombospondin motifs 1) and BNC1 (zinc finger protein basonuclin-1) in cell-free deoxyribonucleic acid (DNA), may play a role in the early detection of PC. This review focuses on the diagnosis of PC in its early stages.
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Wang X, Shi D, Zhao D, Hu D. Aberrant Methylation and Differential Expression of SLC2A1, TNS4, GAPDH, ATP8A2, and CASZ1 Are Associated with the Prognosis of Lung Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1807089. [PMID: 33029490 PMCID: PMC7532994 DOI: 10.1155/2020/1807089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 02/06/2023]
Abstract
Lung cancer is one of the leading triggers for cancer death worldwide. In this study, the relationship of the aberrantly methylated and differentially expressed genes in lung adenocarcinoma (LUAD) with cancer prognosis was investigated, and 5 feature genes were identified eventually. Specifically, we firstly downloaded the LUAD-related mRNA expression profile (including 57 normal tissue samples and 464 LUAD tissue samples) and Methy450 expression data (including 32 normal tissue samples and 373 LUAD tissue samples) from the TCGA database. The package "limma" was used to screen differentially expressed genes and aberrantly methylated genes, which were intersected for identifying the hypermethylated downregulated genes (DGs Hyper) and the hypomethylated upregulated genes (UGs Hypo). GO annotation and KEGG pathway enrichment analysis were further performed, and it was found that these DGs Hyper and UGs Hypo were predominantly activated in the biological processes and signaling pathways such as the regulation of vasculature development, DNA-binding transcription activator activity, and Ras signaling pathway, indicating that these genes play a vital role in the initiation and progression of LUAD. Additionally, univariate and multivariate Cox regression analyses were conducted to find the genes significantly associated with LUAD prognosis. Five genes including SLC2A1, TNS4, GAPDH, ATP8A2, and CASZ1 were identified, with the former three highly expressed and the latter two poorly expressed in LUAD, indicating poor prognosis of LUAD patients as judged by survival analysis.
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Affiliation(s)
- Xia Wang
- Department of Pneumology, The First People's Hospital of Fuyang, Fuyang, China
| | - Dongming Shi
- Department of Pneumology, The First People's Hospital of Fuyang, Fuyang, China
| | - Dejun Zhao
- Department of Pneumology, The First People's Hospital of Fuyang, Fuyang, China
| | - Danping Hu
- Department of Pneumology, The First People's Hospital of Fuyang, Fuyang, China
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Zhang K, Tian R, Wang G, Zhang J, Ma H, Hu X, Xi J, Wang G. ADAMTS8 Inhibits Cell Proliferation and Invasion, and Induces Apoptosis in Breast Cancer. Onco Targets Ther 2020; 13:8373-8382. [PMID: 32904790 PMCID: PMC7457586 DOI: 10.2147/ott.s248085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/15/2020] [Indexed: 12/22/2022] Open
Abstract
Introduction A disintegrin and metallopeptidase with thrombospondin motifs (ADAMTSs), whose expression is dysregulated in various cancers, is implicated in cancer development. Herein, we aimed to investigate the functional role of ADAMTS8 in breast cancer (BC) and explore the underlying mechanisms. Methods The protein expression of ADAMTS8 in BC cell lines and tumor tissues from BC patients was quantified by Western blot. ADAMTS8 overexpression was induced by transfection with pEZ-M90-ADAMTS8 plasmid using lipofectamine 2000. To generate ADAMTS8 stable knockdown cells, MDA-MB-231 cells were transfected with psi-H1-ADAMTS8siRNA plasmids. Cell counting kit-8 (CCK-8) assay, wound-healing assay, transwell assay and flow cytometry assay were employed to analyze the effects of ADAMTS8 on the proliferation, migration, invasion and apoptosis of BC cells. Chemosensitivity also was assessed using CCK-8 assay. The expressions of β-catenin, MMP-7 and c-Myc were measured by Western blot. Results Our results showed that ADAMTS8 expression was significantly lower in BC tissues than that in adjacent non-tumor tissues. Overexpression of ADAMTS8 in MDA-MB-453 cells could inhibit the cell proliferation, migration and invasion and promote apoptosis. ADAMTS8 knockdown displayed the reverse effect in MDA-MB-231 cells. Consistently, in vivo data showed that ADAMTS8 overexpression led to a reduction in tumor growth. In addition, chemosensitivity testing in MDA-MB-453 cells transfected with pEZ-M90-ADAMTS8 plasmid indicated that cisplatin inhibited cell growth dramatically. Furthermore, attenuated β-catenin, MMP-7 and c-Myc level was detected after ADAMTS8 overexpression. Conclusion These results indicate that increased ADAMTS8 expression could modify the progression of BC by inhibiting cell proliferation and invasion while promoting the apoptosis of BC cells. Thus, ADAMTS8 represents a potential therapeutic target for BC therapy.
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Affiliation(s)
- Kun Zhang
- General Surgical Department, The Third Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Ruoxi Tian
- Basic Medical College, Tianjin Medical University, Tianjin, People's Republic of China
| | - Guanglin Wang
- General Surgical Department, The Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Jianfeng Zhang
- General Surgical Department, The Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Hongqin Ma
- General Surgical Department, The Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Xuhua Hu
- General Surgical Department, The Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Jinchuan Xi
- General Surgical Department, The Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Guiying Wang
- General Surgical Department, The Third Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China.,General Surgical Department, The Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
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Hu Y, Guo M. Synthetic lethality strategies: Beyond BRCA1/2 mutations in pancreatic cancer. Cancer Sci 2020; 111:3111-3121. [PMID: 32639661 PMCID: PMC7469842 DOI: 10.1111/cas.14565] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/15/2020] [Accepted: 07/02/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer cells are often characterized by abnormalities in DNA damage response including defects in cell cycle checkpoints and/or DNA repair. Synthetic lethality between DNA damage repair (DDR) pathways has provided a paradigm for cancer therapy by targeting DDR. The successful example is that cancer cells with BRCA1/2 mutations are sensitized to poly(adenosine diphosphate [ADP]-ribose)polymerase (PARP) inhibitors. Beyond the narrow scope of defects in the BRCA pathway, "BRCAness" provides more opportunities for synthetic lethality strategy. In human pancreatic cancer, frequent mutations were found in cell cycle and DDR genes, including P16, P73, APC, MLH1, ATM, PALB2, and MGMT. Combined DDR inhibitors and chemotherapeutic agents are under preclinical or clinical trials. Promoter region methylation was found frequently in cell cycle and DDR genes. Epigenetics joins the Knudson's "hit" theory and "BRCAness." Aberrant epigenetic changes in cell cycle or DDR regulators may serve as a new avenue for synthetic lethality strategy in pancreatic cancer.
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Affiliation(s)
- Yunlong Hu
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing, China
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing, China.,Henan Key Laboratory for Esophageal Cancer Research, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, Beijing, China
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Xu Z, Gao G, Liu F, Han Y, Dai C, Wang S, Wei G, Kuang Y, Wan D, Zhi Q, Xu Y. Molecular Screening for Nigericin Treatment in Pancreatic Cancer by High-Throughput RNA Sequencing. Front Oncol 2020; 10:1282. [PMID: 32850392 PMCID: PMC7411259 DOI: 10.3389/fonc.2020.01282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/19/2020] [Indexed: 12/18/2022] Open
Abstract
Objectives: Nigericin, an antibiotic derived from Streptomyces hygroscopicus, has been proved to exhibit promising anti-cancer effects on a variety of cancers. Our previous study investigated the potential anti-cancer properties in pancreatic cancer (PC), and demonstrated that nigericin could inhibit the cell viabilities in concentration- and time-dependent manners via differentially expressed circular RNAs (circRNAs). However, the knowledge of nigericin associated with long non-coding RNA (lncRNA) and mRNA in pancreatic cancer (PC) has not been studied. This study is to elucidate the underlying mechanism from the perspective of lncRNA and mRNA. Methods: The continuously varying molecules (lncRNAs and mRNAs) were comprehensively screened by high-throughput RNA sequencing. Results: Our data showed that 76 lncRNAs and 172 mRNAs were common differentially expressed in the nigericin anti-cancer process. Subsequently, the bioinformatics analyses, including Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, coding and non-coding co-expression network, cis- and trans-regulation predictions and protein-protein interaction (PPI) network, were applied to annotate the potential regulatory mechanisms among these coding and non-coding RNAs during the nigericin anti-cancer process. Conclusions: These findings provided new insight into the molecular mechanism of nigericin toward cancer cells, and suggested a possible clinical application in PC.
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Affiliation(s)
- Zhihua Xu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Guanzhuang Gao
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fei Liu
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ye Han
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chen Dai
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Sentai Wang
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Guobang Wei
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuting Kuang
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Daiwei Wan
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Qiaoming Zhi
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Shanghai, China
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Shanghai, China
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Manoochehri M, Wu Y, Giese NA, Strobel O, Kutschmann S, Haller F, Hoheisel JD, Moskalev EA, Hackert T, Bauer AS. SST gene hypermethylation acts as a pan-cancer marker for pancreatic ductal adenocarcinoma and multiple other tumors: toward its use for blood-based diagnosis. Mol Oncol 2020; 14:1252-1267. [PMID: 32243066 PMCID: PMC7266283 DOI: 10.1002/1878-0261.12684] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 03/07/2020] [Accepted: 03/13/2020] [Indexed: 02/06/2023] Open
Abstract
Aberrant DNA methylation is often involved in carcinogenesis. Our initial goal was to identify DNA methylation biomarkers associated with pancreatic cancer. A genomewide methylation study was performed on DNA from pancreatic ductal adenocarcinoma (PDAC) and endocrine pancreas tumors. Validation of DNA methylation patterns and concomitant alterations in expression of gene candidates was performed on patient samples and pancreatic cancer cell lines. Furthermore, validation was done on independent data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Finally, droplet digital PCR was employed to detect DNA methylation marks in cell-free (cf) DNA isolated from plasma samples of PDAC patients and cancer-free blood donors. Hypermethylation of the SST gene (encoding somatostatin) and concomitant downregulation of its expression were discovered in PDAC and endocrine tumor tissues while not being present in chronic pancreatitis (inflamed) tissues and normal pancreas. Fittingly, treatment with a somatostatin agonist (octreotide) reduced cell proliferation and migration of pancreatic cancer cells. Diagnostic performance of SST methylation in a receiver operating characteristic curve analysis was 100% and 89% for tissue and plasma samples, respectively. A large body of TCGA and GEO data confirmed SST hypermethylation and downregulation in PDAC and showed a similar effect in a broad spectrum of other tumor entities. SST promoter methylation represents a sensitive and promising molecular, pan-cancer biomarker detectable in tumor tissue, and liquid biopsy samples.
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Affiliation(s)
- Mehdi Manoochehri
- Division of Functional Genome AnalysisGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Molecular Genetics of Breast CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Yenan Wu
- Division of Functional Genome AnalysisGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | | | - Oliver Strobel
- Department of General SurgeryUniversity Hospital HeidelbergGermany
| | - Stefanie Kutschmann
- Division of Functional Genome AnalysisGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Florian Haller
- Diagnostic Molecular PathologyInstitute of PathologyFriedrich‐Alexander UniversityErlangenGermany
| | - Jörg D. Hoheisel
- Division of Functional Genome AnalysisGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Evgeny A. Moskalev
- Diagnostic Molecular PathologyInstitute of PathologyFriedrich‐Alexander UniversityErlangenGermany
| | - Thilo Hackert
- Department of General SurgeryUniversity Hospital HeidelbergGermany
| | - Andrea S. Bauer
- Division of Functional Genome AnalysisGerman Cancer Research Center (DKFZ)HeidelbergGermany
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Differential methylation landscape of pancreatic ductal adenocarcinoma and its precancerous lesions. Hepatobiliary Pancreat Dis Int 2020; 19:205-217. [PMID: 32312637 DOI: 10.1016/j.hbpd.2020.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 03/18/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Pancreatic cancer is one of the most lethal diseases with an incidence almost equal to the mortality. In addition to having genetic causes, cancer can also be considered an epigenetic disease. DNA methylation is the premier epigenetic modification and patterns of aberrant DNA methylation are recognized to be a common hallmark of human tumor. In the multistage carcinogenesis of pancreas starting from precancerous lesions to pancreatic ductal adenocarcinoma (PDAC), the epigenetic changes play a significant role. DATA SOURCES Relevant studies for this review were derived via an extensive literature search in PubMed via using various keywords such as pancreatic ductal adenocarcinoma, precancerous lesions, methylation profile, epigenetic biomarkers that are relevant directly or closely associated with the concerned area of our interest. The literature search was intensively done considering a time frame of 20 years (1998-2018). RESULT In this review we have highlighted the hypermethylation and hypomethylation of the precancerous PDAC lesions (pancreatic intra-epithelial neoplasia, intraductal papillary mucinous neoplasm, mucinous cystic neoplasm and chronic pancreatitis) and PDAC along with the potential biomarkers. We have also achieved the early epigenetic driver that leads to progression from precancerous lesions to PDAC. A bunch of epigenetic driver genes leads to progression of precancerous lesions to PDAC (ppENK, APC, p14/5/16/17, hMLH1 and MGMT) are also documented. We summarized the importance of these observations in therapeutics and diagnosis of PDAC hence identifying the potential use of epigenetic biomarkers in epigenetic targeted therapy. Epigenetic inactivation occurs by hypermethylation of CpG islands in the promoter regions of tumor suppressor genes. We listed all hyper- and hypomethylation of CpG islands of several genes in PDAC including its precancerous lesions. CONCLUSIONS The concept of the review would help to understand their biological effects, and to determine whether they may be successfully combined with other epigenetic drugs. However, we need to continue our research to develop more specific DNA-demethylating agents, which are the targets for hypermethylated CpG methylation sites.
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Analysis of gene expression profiles of lung cancer subtypes with machine learning algorithms. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165822. [PMID: 32360590 DOI: 10.1016/j.bbadis.2020.165822] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/13/2020] [Accepted: 04/22/2020] [Indexed: 12/14/2022]
Abstract
Lung cancer is one of the most common cancer types worldwide and causes more than one million deaths annually. Lung adenocarcinoma (AC) and lung squamous cell cancer (SCC) are two major lung cancer subtypes and have different characteristics in several aspects. Identifying their differentially expressed genes and different gene expression patterns can deepen our understanding of these two subtypes at the transcriptomic level. In this work, we used several machine learning algorithms to investigate the gene expression profiles of lung AC and lung SCC samples retrieved from Gene Expression Omnibus. First, the profiles were analyzed by using a powerful feature selection method, namely, Monte Carlo feature selection. A feature list, ranking all features according to their importance, and some informative features were obtained. Then, the feature list was used in the incremental feature selection method to extract optimal features, which can allow the support vector machine (SVM) to yield the best performance for classifying lung AC and lung SCC samples. Some top genes (CSTA, TP63, SERPINB13, CLCA2, BICD2, PERP, FAT2, BNC1, ATP11B, FAM83B, KRT5, PARD6G, PKP1) were extensively analyzed to prove that they can be differentially expressed genes between lung AC and lung SCC. Meanwhile, a rule learning procedure was applied on informative features to construct the classification rules. These rules provide a clear procedure of classification and show some different gene expression patterns between lung AC and lung SCC.
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46
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Dhayat SA, Yang Z. Impact of circulating tumor DNA in hepatocellular and pancreatic carcinomas. J Cancer Res Clin Oncol 2020; 146:1625-1645. [PMID: 32338295 PMCID: PMC7256092 DOI: 10.1007/s00432-020-03219-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) and pancreatic cancer (PC) belong to the most lethal malignancies worldwide. Despite advances in surgical techniques and perioperative multidisciplinary management, the prognosis of both carcinoma entities remains poor mainly because of rapid tumor progression and early dissemination with diagnosis in advanced tumor stages with poor sensitivity to current therapy regimens. Both highly heterogeneous visceral carcinomas exhibit unique somatic alterations, but share common driver genes and mutations as well. Recently, circulating tumor DNA (ctDNA) could be identified as a liquid biopsy tool with huge potential as non-invasive biomarker in early diagnosis and prognosis. CtDNA released from necrotic or apoptotic cells of primary tumors, metastasis, and circulating tumor cells can reveal genetic and epigenetic alterations with tumor-specific and individual mutation and methylation profiles. In this article, we focus on clinical impact of ctDNA as potential biomarker in patients with HCC and PC.
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Affiliation(s)
- Sameer A Dhayat
- Department of General, Visceral and Transplantation Surgery, University Hospital Muenster, Albert-Schweitzer-Campus 1 (W1), 48149, Munster, Germany.
| | - Zixuan Yang
- Department of General, Visceral and Transplantation Surgery, University Hospital Muenster, Albert-Schweitzer-Campus 1 (W1), 48149, Munster, Germany
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Singh N, Rashid S, Rashid S, Dash NR, Gupta S, Saraya A. Clinical significance of promoter methylation status of tumor suppressor genes in circulating DNA of pancreatic cancer patients. J Cancer Res Clin Oncol 2020; 146:897-907. [DOI: 10.1007/s00432-020-03169-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 02/27/2020] [Indexed: 12/22/2022]
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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] [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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Crawford HC, Wallace MB, Storz P. Early detection and imaging strategies to reveal and target developing pancreatic cancer. Expert Rev Anticancer Ther 2020; 20:81-83. [PMID: 31986932 DOI: 10.1080/14737140.2020.1720654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Howard C Crawford
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | | | - Peter Storz
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Jacksonville, FL, USA
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Brancaccio M, Natale F, Falco G, Angrisano T. Cell-Free DNA Methylation: The New Frontiers of Pancreatic Cancer Biomarkers' Discovery. Genes (Basel) 2019; 11:E14. [PMID: 31877923 PMCID: PMC7017422 DOI: 10.3390/genes11010014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 12/14/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is among the most lethal cancer types world-wide. Its high mortality is related to the difficulty in the diagnosis, which often occurs when the disease is already advanced. As of today, no early diagnostic tests are available, while only a limited number of prognostic tests have reached clinical practice. The main reason is the lack of reliable biomarkers that are able to capture the early development or the progression of the disease. Hence, the discovery of biomarkers for early diagnosis or prognosis of PDAC remains, de facto, an unmet need. An increasing number of studies has shown that cell-free DNA (cfDNA) methylation analysis represents a promising non-invasive approach for the discovery of biomarkers with diagnostic or prognostic potential. In particular, cfDNA methylation could be utilized for the identification of disease-specific signatures in pre-neoplastic lesions or chronic pancreatitis (CP), representing a sensitive and non-invasive method of early diagnosis of PDAC. In this review, we will discuss the advantages and pitfalls of cfDNA methylation studies. Further, we will present the current advances in the discovery of pancreatic cancer biomarkers with early diagnostic or prognostic potential, focusing on pancreas-specific (e.g., CUX2 or REG1A) or abnormal (e.g., ADAMTS1 or BNC1) cfDNA methylation signatures in high risk pre-neoplastic conditions and PDAC.
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Affiliation(s)
- Mariarita Brancaccio
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Francesco Natale
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Geppino Falco
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
- Biogem Scarl, Istituto di Ricerche Genetiche “Gaetano Salvatore”, Via Camporeale, 83031 Ariano Irpino, Italy
| | - Tiziana Angrisano
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
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