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Pessei V, Macagno M, Mariella E, Congiusta N, Battaglieri V, Battuello P, Viviani M, Gionfriddo G, Lamba S, Lorenzato A, Oddo D, Idrees F, Cavaliere A, Bartolini A, Guarrera S, Linnebacher M, Monteonofrio L, Cardone L, Milella M, Bertotti A, Soddu S, Grassi E, Crisafulli G, Bardelli A, Barault L, Di Nicolantonio F. DNA demethylation triggers cell free DNA release in colorectal cancer cells. Genome Med 2024; 16:118. [PMID: 39385243 DOI: 10.1186/s13073-024-01386-5] [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: 07/31/2023] [Accepted: 09/18/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Liquid biopsy based on cell-free DNA (cfDNA) analysis holds significant promise as a minimally invasive approach for the diagnosis, genotyping, and monitoring of solid malignancies. Human tumors release cfDNA in the bloodstream through a combination of events, including cell death, active and passive release. However, the precise mechanisms leading to cfDNA shedding remain to be characterized. Addressing this question in patients is confounded by several factors, such as tumor burden extent, anatomical and vasculature barriers, and release of nucleic acids from normal cells. In this work, we exploited cancer models to dissect basic mechanisms of DNA release. METHODS We measured cell loss ratio, doubling time, and cfDNA release in the supernatant of a colorectal cancer (CRC) cell line collection (N = 76) representative of the molecular subtypes previously identified in cancer patients. Association analyses between quantitative parameters of cfDNA release, cell proliferation, and molecular features were evaluated. Functional experiments were performed to test the impact of modulating DNA methylation on cfDNA release. RESULTS Higher levels of supernatant cfDNA were significantly associated with slower cell cycling and increased cell death. In addition, a higher cfDNA shedding was found in non-CpG Island Methylator Phenotype (CIMP) models. These results indicate a positive correlation between lower methylation and increased cfDNA levels. To explore this further, we exploited methylation microarrays to identify a subset of probes significantly associated with cfDNA shedding and derive a methylation signature capable of discriminating high from low cfDNA releasers. We applied this signature to an independent set of 176 CRC cell lines and patient derived organoids to select 14 models predicted to be low or high releasers. The methylation profile successfully predicted the amount of cfDNA released in the supernatant. At the functional level, genetic ablation of DNA methyl-transferases increased chromatin accessibility and DNA fragmentation, leading to increased cfDNA release in isogenic CRC cell lines. Furthermore, in vitro treatment of five low releaser CRC cells with a demethylating agent was able to induce a significant increase in cfDNA shedding. CONCLUSIONS Methylation status of cancer cell lines contributes to the variability of cfDNA shedding in vitro. Changes in methylation pattern are associated with cfDNA release levels and might be exploited to increase sensitivity of liquid biopsy assays.
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Affiliation(s)
- Valeria Pessei
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Marco Macagno
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Elisa Mariella
- Department of Oncology, University of Torino, Turin, Italy
- IFOM, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Noemi Congiusta
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Vittorio Battaglieri
- Department of Oncology, University of Torino, Turin, Italy
- IFOM, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Paolo Battuello
- Department of Oncology, University of Torino, Turin, Italy
- IFOM, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Marco Viviani
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Giulia Gionfriddo
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Simona Lamba
- Department of Oncology, University of Torino, Turin, Italy
| | | | - Daniele Oddo
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Fariha Idrees
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Alessandro Cavaliere
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Alice Bartolini
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Simonetta Guarrera
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
- IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, Turin, Italy
| | - Michael Linnebacher
- Clinic of General Surgery, Molecular Oncology and Immunotherapy, UMR, Rostock, Germany
| | - Laura Monteonofrio
- Department of Research and Advanced Technologies, Regina Elena National Cancer Institute IRCCS, Rome, Italy
| | - Luca Cardone
- Department of Research and Advanced Technologies, Regina Elena National Cancer Institute IRCCS, Rome, Italy
| | - Michele Milella
- Section of Innovation Biomedicine - Oncology Area, Department of Engineering for Innovation Medicine, University of Verona and Verona University and Hospital Trust, Verona, Italy
| | - Andrea Bertotti
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | - Silvia Soddu
- Department of Research and Advanced Technologies, Regina Elena National Cancer Institute IRCCS, Rome, Italy
| | - Elena Grassi
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
- Department of Oncology, University of Torino, Turin, Italy
| | | | - Alberto Bardelli
- Department of Oncology, University of Torino, Turin, Italy
- IFOM, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Ludovic Barault
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy.
- Department of Oncology, University of Torino, Turin, Italy.
| | - Federica Di Nicolantonio
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy.
- Department of Oncology, University of Torino, Turin, Italy.
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Bustamante P, Coblentz J, Mastromonaco C, Youhnovska E, Ito H, Proença RP, Fonseca C, Dickinson K, Marcotte E, MacDonald M, Toledo-Dias AB, Bergeron S, Goyeneche A, Schmidt Andujar RA, Tsering T, Laskaris A, Jin E, Nadeau A, Porraccio T, Burnier MN, Burnier JV. Comprehensive clinical imaging, histopathological analysis and liquid biopsy-based surveillance of human uveal melanoma in a prolonged rabbit xenograft model. Melanoma Res 2024; 34:285-295. [PMID: 38847739 DOI: 10.1097/cmr.0000000000000964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Uveal melanoma is the most common intraocular tumor in adults. Our group has previously developed a human uveal melanoma animal model; however, adverse effects caused by the immunosuppressive agent, cyclosporine A, prevented animals from surviving more than 12 weeks. In this study, we tested multiple cyclosporine A doses over an extended disease course up to 20 weeks, providing complete clinical imaging of intraocular tumors, histopathological analysis and liquid biopsy biomarker analysis. Twenty albino rabbits were divided into four groups with different daily cyclosporine A schedules (0-10 mg/kg) and inoculated with human uveal melanoma cell lines, 92.1 or MP41, into the suprachoroidal space. Rabbits were monitored with fundoscopy, ultrasound and optical coherence tomography. Intraocular tumors (macroscopic or microscopic) were detected in all study animals. Tumor size and growth were correlated to cyclosporine A dose, with tumors regressing when cyclosporine A was arrested. All tumors expressed HMB-45 and MelanA; however, tumor size, pigmentation and cell morphology differed in 92.1 vs. MP41 tumors. Finally, across all groups, circulating tumor DNA from plasma and aqueous humor was detected earlier than tumor detection by imaging and correlated to tumor growth. In conclusion, using three clinically relevant imaging modalities (fundoscopy, ultrasonography and optical coherence tomography) and liquid biopsy, we were successfully able to monitor tumor progression in our rabbit xenograft model of human uveal melanoma.
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Affiliation(s)
- Prisca Bustamante
- Cancer Research Program, Research Institute of the McGill University Health Centre
- McGill University Ocular Pathology and Translational Research Laboratory, McGill University
- Department of Pathology, McGill University, Montréal, Canada
| | - Jacqueline Coblentz
- Cancer Research Program, Research Institute of the McGill University Health Centre
- McGill University Ocular Pathology and Translational Research Laboratory, McGill University
| | - Christina Mastromonaco
- McGill University Ocular Pathology and Translational Research Laboratory, McGill University
| | - Emma Youhnovska
- Cancer Research Program, Research Institute of the McGill University Health Centre
| | - Hiroaki Ito
- McGill University Ocular Pathology and Translational Research Laboratory, McGill University
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Rita Pinto Proença
- McGill University Ocular Pathology and Translational Research Laboratory, McGill University
- Coimbra University Hospital Center, Coimbra
- Faculty of Medicine, University of Lisbon, Lisbon
- Hospital CUF Cascais, Cascais, Portugal
| | - Cristina Fonseca
- McGill University Ocular Pathology and Translational Research Laboratory, McGill University
- Coimbra University Hospital Center, Coimbra
| | - Kyle Dickinson
- Cancer Research Program, Research Institute of the McGill University Health Centre
| | - Emily Marcotte
- Cancer Research Program, Research Institute of the McGill University Health Centre
- McGill University Ocular Pathology and Translational Research Laboratory, McGill University
| | - Myriam MacDonald
- McGill University Ocular Pathology and Translational Research Laboratory, McGill University
| | | | - Sabrina Bergeron
- McGill University Ocular Pathology and Translational Research Laboratory, McGill University
| | - Alicia Goyeneche
- McGill University Ocular Pathology and Translational Research Laboratory, McGill University
| | | | - Thupten Tsering
- Cancer Research Program, Research Institute of the McGill University Health Centre
- Department of Pathology, McGill University, Montréal, Canada
| | - Alexander Laskaris
- Cancer Research Program, Research Institute of the McGill University Health Centre
- Department of Pathology, McGill University, Montréal, Canada
| | - Eva Jin
- Cancer Research Program, Research Institute of the McGill University Health Centre
- Department of Pathology, McGill University, Montréal, Canada
| | - Amélie Nadeau
- Cancer Research Program, Research Institute of the McGill University Health Centre
- Department of Pathology, McGill University, Montréal, Canada
| | - Tiffany Porraccio
- McGill University Ocular Pathology and Translational Research Laboratory, McGill University
| | - Miguel N Burnier
- Cancer Research Program, Research Institute of the McGill University Health Centre
- McGill University Ocular Pathology and Translational Research Laboratory, McGill University
- Department of Pathology, McGill University, Montréal, Canada
| | - Julia V Burnier
- Cancer Research Program, Research Institute of the McGill University Health Centre
- Department of Pathology, McGill University, Montréal, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Canada
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Megquier K, Husted C, Rhoades J, White ME, Genereux DP, Chen FL, Xiong K, Kwon E, Swofford R, Painter C, Adalsteinsson V, London CA, Gardner HL, Karlsson EK. Impact of preanalytical factors on liquid biopsy in the canine cancer model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.29.605605. [PMID: 39131379 PMCID: PMC11312437 DOI: 10.1101/2024.07.29.605605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
While liquid biopsy has potential to transform cancer diagnostics through minimally-invasive detection and monitoring of tumors, the impact of preanalytical factors such as the timing and anatomical location of blood draw is not well understood. To address this gap, we leveraged pet dogs with spontaneous cancer as a model system, as their compressed disease timeline facilitates rapid diagnostic benchmarking. Key liquid biopsy metrics from dogs were consistent with existing reports from human patients. The tumor content of samples was higher from venipuncture sites closer to the tumor and from a central vein. Metrics also differed between lymphoma and non-hematopoietic cancers, urging cancer-type-specific interpretation. Liquid biopsy was highly sensitive to disease status, with changes identified soon after post chemotherapy administration, and trends of increased tumor fraction and other metrics observed prior to clinical relapse in dogs with lymphoma or osteosarcoma. These data support the utility of pet dogs with cancer as a relevant system for advancing liquid biopsy platforms.
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Affiliation(s)
- Kate Megquier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher Husted
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA, USA
| | | | | | | | - Frances L. Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, USA
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Euijin Kwon
- Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA, USA
| | - Ross Swofford
- Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, USA
| | | | | | - Cheryl A. London
- Tufts Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | | | - Elinor K. Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
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4
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Abstract
With the rapid development of science and technology, cell-free DNA (cfDNA) is rapidly becoming an important biomarker for tumor diagnosis, monitoring and prognosis, and this cfDNA-based liquid biopsy technology has great potential to become an important part of precision medicine. cfDNA is the total amount of free DNA in the systemic circulation, including DNA fragments derived from tumor cells and all other somatic cells. Tumor cells release fragments of DNA into the bloodstream, and this source of cfDNA is called circulating tumor DNA (ctDNA). cfDNA detection has become a major focus in the field of tumor research in recent years, which provides a new opportunity for non-invasive diagnosis and prognosis of cancer. In this paper, we discuss the limitations of the study on the origin and dynamics analysis of ctDNA, and how to solve these problems in the future. Although the future faces major challenges, it also contains great potential.
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Liu SC. Circulating tumor DNA in liquid biopsy: Current diagnostic limitation. World J Gastroenterol 2024; 30:2175-2178. [PMID: 38681986 PMCID: PMC11045476 DOI: 10.3748/wjg.v30.i15.2175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/07/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
With the rapid development of science and technology, cell-free DNA (cfDNA) is rapidly becoming an important biomarker for tumor diagnosis, monitoring and prognosis, and this cfDNA-based liquid biopsy technology has great potential to become an important part of precision medicine. cfDNA is the total amount of free DNA in the systemic circulation, including DNA fragments derived from tumor cells and all other somatic cells. Tumor cells release fragments of DNA into the bloodstream, and this source of cfDNA is called circulating tumor DNA (ctDNA). cfDNA detection has become a major focus in the field of tumor research in recent years, which provides a new opportunity for non-invasive diagnosis and prognosis of cancer. In this paper, we discuss the limitations of the study on the origin and dynamics analysis of ctDNA, and how to solve these problems in the future. Although the future faces major challenges, it also contains great potential.
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Affiliation(s)
- Shi-Cai Liu
- School of Medical Information, Wannan Medical College, Wuhu 241002, Anhui Province, China
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6
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Mahmoudian RA, Farshchian M, Golyan FF, Mahmoudian P, Alasti A, Moghimi V, Maftooh M, Khazaei M, Hassanian SM, Ferns GA, Mahaki H, Shahidsales S, Avan A. Preclinical tumor mouse models for studying esophageal cancer. Crit Rev Oncol Hematol 2023; 189:104068. [PMID: 37468084 DOI: 10.1016/j.critrevonc.2023.104068] [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: 05/10/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023] Open
Abstract
Preclinical models are extensively employed in cancer research because they can be manipulated in terms of their environment, genome, molecular biology, organ systems, and physical activity to mimic human behavior and conditions. The progress made in in vivo cancer research has resulted in significant advancements, enabling the creation of spontaneous, metastatic, and humanized mouse models. Most recently, the remarkable and extensive developments in genetic engineering, particularly the utilization of CRISPR/Cas9, transposable elements, epigenome modifications, and liquid biopsies, have further facilitated the design and development of numerous mouse models for studying cancer. In this review, we have elucidated the production and usage of current mouse models, such as xenografts, chemical-induced models, and genetically engineered mouse models (GEMMs), for studying esophageal cancer. Additionally, we have briefly discussed various gene-editing tools that could potentially be employed in the future to create mouse models specifically for esophageal cancer research.
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Affiliation(s)
- Reihaneh Alsadat Mahmoudian
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Moein Farshchian
- Division of Oncology, Laboratory of Cellular Therapy, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Fatemeh Fardi Golyan
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parvaneh Mahmoudian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Alasti
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vahid Moghimi
- Department of Biology, Faculty of Science, Hakim Sabzevari University, Sabzevar, Iran
| | - Mina Maftooh
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Department of Medical Education, Falmer, Brighton, Sussex BN1 9PH, UK
| | - Hanie Mahaki
- Vascular & Endovascular Surgery Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; College of Medicine, University of Warith Al-Anbiyaa, Karbala, Iraq; Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.
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