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Zhang L, Li J. Unlocking the secrets: the power of methylation-based cfDNA detection of tissue damage in organ systems. Clin Epigenetics 2023; 15:168. [PMID: 37858233 PMCID: PMC10588141 DOI: 10.1186/s13148-023-01585-8] [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: 06/08/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Detecting organ and tissue damage is essential for early diagnosis, treatment decisions, and monitoring disease progression. Methylation-based assays offer a promising approach, as DNA methylation patterns can change in response to tissue damage. These assays have potential applications in early detection, monitoring disease progression, evaluating treatment efficacy, and assessing organ viability for transplantation. cfDNA released into the bloodstream upon tissue or organ injury can serve as a biomarker for damage. The epigenetic state of cfDNA, including DNA methylation patterns, can provide insights into the extent of tissue and organ damage. CONTENT Firstly, this review highlights DNA methylation as an extensively studied epigenetic modification that plays a pivotal role in processes such as cell growth, differentiation, and disease development. It then presents a variety of highly precise 5-mC methylation detection techniques that serve as powerful tools for gaining profound insights into epigenetic alterations linked with tissue damage. Subsequently, the review delves into the mechanisms underlying DNA methylation changes in organ and tissue damage, encompassing inflammation, oxidative stress, and DNA damage repair mechanisms. Next, it addresses the current research status of cfDNA methylation in the detection of specific organ tissues and organ damage. Finally, it provides an overview of the multiple steps involved in identifying specific methylation markers associated with tissue and organ damage for clinical trials. This review will explore the mechanisms and current state of research on cfDNA methylation-based assay detecting organ and tissue damage, the underlying mechanisms, and potential applications in clinical practice.
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Affiliation(s)
- Lijing Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, No. 1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, No. 1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China.
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, People's Republic of China.
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China.
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2
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Li Z, Gao Y, Zhang J, Han L, Zhao H. DNA methylation meningioma biomarkers: attributes and limitations. Front Mol Neurosci 2023; 16:1182759. [PMID: 37492524 PMCID: PMC10365284 DOI: 10.3389/fnmol.2023.1182759] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/13/2023] [Indexed: 07/27/2023] Open
Abstract
Meningioma, one of the most common primary central nervous system tumors, are classified into three grades by the World Health Organization (WHO) based on histopathology. The gold-standard treatment, surgical resection, is hampered by issues such as incomplete resection in some cases and a high recurrence rate. Alongside genetic alterations, DNA methylation, plays a crucial role in progression of meningiomas in the occurrence and development of meningiomas. The epigenetic landscape of meningioma is instrumental in refining tumor classification, identifying robust molecular markers, determining prognosis, guiding treatment selection, and innovating new therapeutic strategies. Existing classifications lack comprehensive accuracy, and effective therapies are limited. Methylated DNA markers, exhibiting differential characteristics across varying meningioma grades, serve as invaluable diagnostic tools. Particularly, combinatorial methylated markers offer insights into meningioma pathogenesis, tissue origin, subtype classification, and clinical outcomes. This review integrates current research to highlight some of the most promising DNA and promoter methylation markers employed in meningioma diagnostics. Despite their promise, the development and application of DNA methylation biomarkers for meningioma diagnosis and treatment are still in their infancy, with only a handful of DNA methylation inhibitors currently clinically employed for meningioma treatment. Future studies are essential to validate these markers and ascertain their clinical utility. Combinatorial methylated DNA markers for meningiomas have broad implications for understanding tumor development and progression, signaling a paradigm shift in therapeutic strategies for meningiomas.
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Affiliation(s)
- Zhaohui Li
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yufei Gao
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Jinnan Zhang
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Liang Han
- Department of Pathology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Hang Zhao
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, China
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3
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Wang JZ, Nassiri F, Aldape K, von Deimling A, Sahm F. The Epigenetic Landscape of Meningiomas. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1416:175-188. [PMID: 37432627 DOI: 10.1007/978-3-031-29750-2_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Epigenetic changes have been found to be increasingly important in tumor development and progression. These alterations can be present in tumors such as meningiomas in the absence of any gene mutations and alter gene expression without affecting the sequence of the DNA itself. Some examples of these alterations that have been studied in meningiomas include DNA methylation, microRNA interaction, histone packaging, and chromatin restructuring. In this chapter we will describe in detail each of these mechanisms of epigenetic modification in meningiomas and their prognostic significance.
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Affiliation(s)
- Justin Z Wang
- Division of Neurosurgery, Department of Surgery, The University of Toronto, Toronto, ON, Canada
| | - Farshad Nassiri
- Division of Neurosurgery, Department of Surgery, The University of Toronto, Toronto, ON, Canada.
| | - Kenneth Aldape
- Laboratory of Pathology, Center Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andreas von Deimling
- CCU Neuropathology, German Cancer Research Center (DKFZ), University Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- CCU Neuropathology, German Cancer Research Center (DKFZ), University Heidelberg, Heidelberg, Germany
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4
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Why we need new classification models in meningioma management. Acta Neurochir (Wien) 2022; 164:1381-1383. [PMID: 35067786 DOI: 10.1007/s00701-022-05127-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/17/2022] [Indexed: 12/27/2022]
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5
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Shimansky VN, Ryzhova MV, Sultanov RA, Tanyashin SV, Galstyan SA, Telysheva EN, Karnaukhov VV. [The DNA methylation profiling in the study and treatment of patients with meningiomas of the craniovertebral junction]. Arkh Patol 2022; 84:47-51. [PMID: 36469717 DOI: 10.17116/patol20228406147] [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] [Indexed: 06/17/2023]
Abstract
The paper presents the experience of using DNA methylation status in patients with meningiomas of the craniovertebral junction area in a neurosurgical clinic. A clinical case of combined treatment of a patient with meningioma of the craniovertebral junction and the choice of tactics based on the result of DNA methylation analysis of meningioma are described.
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Affiliation(s)
| | - M V Ryzhova
- Burdenko Neurosurgical Center, Moscow, Russia
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Tonogai EJ, Huang S, Botham RC, Berry MR, Joslyn SK, Daniel GB, Chen Z, Rao J, Zhang X, Basuli F, Rossmeisl JH, Riggins GJ, LeBlanc AK, Fan TM, Hergenrother PJ. Evaluation of a procaspase-3 activator with hydroxyurea or temozolomide against high-grade meningioma in cell culture and canine cancer patients. Neuro Oncol 2021; 23:1723-1735. [PMID: 34216463 PMCID: PMC8485451 DOI: 10.1093/neuonc/noab161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND High-grade meningioma is an aggressive type of brain cancer that is often recalcitrant to surgery and radiotherapy, leading to poor overall survival. Currently, there are no FDA-approved drugs for meningioma, highlighting the need for new therapeutic options, but development is challenging due to the lack of predictive preclinical models. METHODS To leverage the known overexpression of procaspase-3 in meningioma, PAC-1, a blood-brain barrier penetrant procaspase-3 activator, was evaluated for its ability to induce apoptosis in meningioma cells. To enhance the effects of PAC-1, combinations with either hydroxyurea or temozolomide were explored in cell culture. Both combinations were further investigated in small groups of canine meningioma patients and assessed by MRI, and the novel apoptosis tracer, [18F]C-SNAT4, was evaluated in patients treated with PAC-1 + HU. RESULTS In meningioma cell lines in culture, PAC-1 + HU are synergistic while PAC-1 + TMZ show additive-to-synergistic effects. In canine meningioma patients, PAC-1 + HU led to stabilization of disease and no change in apoptosis within the tumor, whereas PAC-1 + TMZ reduced tumor burden in all three canine patients treated. CONCLUSIONS Our results suggest PAC-1 + TMZ as a potentially efficacious combination for the treatment of human meningioma, and also demonstrate the utility of including pet dogs with meningioma as a means to assess anticancer strategies for this common brain tumor.
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Affiliation(s)
- Emily J Tonogai
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Shan Huang
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Rachel C Botham
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Matthew R Berry
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Gregory B Daniel
- Radiology, Department of Small Animal Clinical Sciences, Virgina-Maryland College of Veterinary Medicine, Blacksburg, Virginia, USA
| | - Zixin Chen
- Departments of Radiology and Chemistry, Stanford Medicine, Stanford, California, USA
| | - Jianghong Rao
- Departments of Radiology and Chemistry, Stanford Medicine, Stanford, California, USA
| | - Xiang Zhang
- Chemistry and Synthesis Center, NHLBI, NIH, Bethesda, Maryland, USA
| | - Falguni Basuli
- Chemistry and Synthesis Center, NHLBI, NIH, Bethesda, Maryland, USA
| | - John H Rossmeisl
- Neurology and Neurosurgery, Department of Small Animal Clinical Sciences, Virgina-Maryland College of Veterinary Medicine, Blacksburg, Virginia, USA
| | - Gregory J Riggins
- Department of Neurosurgery, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Amy K LeBlanc
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Timothy M Fan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Kurdi M, Shafique Butt N, Baeesa S, Alghamdi B, Maghrabi Y, Bardeesi A, Saeedi R, Al-Sinani T, Alghanmi N, Bari MO, Samkari A, Lary AI. The Impact of IDH1 Mutation and MGMT Promoter Methylation on Recurrence-Free Interval in Glioblastoma Patients Treated With Radiotherapy and Chemotherapeutic Agents. Pathol Oncol Res 2021; 27:1609778. [PMID: 34257620 PMCID: PMC8262235 DOI: 10.3389/pore.2021.1609778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/07/2021] [Indexed: 12/24/2022]
Abstract
The aim of this study is to investigate the relationship between isocitrate dehydrogenase-1 (IDH1) mutation and O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation with recurrence-free interval in glioblastoma patients treated with chemoradiotherapies. Clinical data were collected from 82 patients with totally resected glioblastoma and treated with adjuvant therapies from 2014 to 2019. IDH1 mutation was assessed by immunohistochemistry and MGMT promoter methylation was assessed by different sequencing methods. IDH1 mutation was present in 32 cases and 50 cases were IDH1 wildtype; 54 and 28 patients had unmethylated and methylated MGMT promoter, respectively, Of the 82 patients, 62 patients received chemoradiotherapy while 20 patients only received radiation. Approximately, 61% of patients had a tumor recurrence after 1 year, and 39% showed a recurrence before 1 year of treatment. There was no significant relationship between IDH1 mutation and MGMT promoter methylation (p-value = 0.972). Patients with IDH1 mutation and their age <50 years showed a significant difference in recurrence-free interval (p-value = 0.014). Difference in recurrence-free interval was also statistically observed in patients with unmethylated MGMT promoter and treated with chemoradiotherapies (p-value = 0.031), by which they showed a late tumor recurrence (p-value = 0.016). This revealed that IDH1 mutation and MGMT methylation are independent prognostic factors in glioblastoma. Although IDH1-mutant glioblastomas showed late tumor recurrence in patients less than 50 years old, the type of treatment modalities may not show additional beneficial outcome. Patients with unmethylated MGMT and IDH1 mutation, treated with different chemoradiotherapies, showed a late tumor recurrence.
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Affiliation(s)
- Maher Kurdi
- Department of Pathology, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nadeem Shafique Butt
- Department of Family and Community Medicine, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Saleh Baeesa
- Division of Neurosurgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Badrah Alghamdi
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yazid Maghrabi
- Department of Neuroscience, King Faisal Specialist Hospital, Jeddah, Saudi Arabia
| | - Anas Bardeesi
- Department of Neuroscience, King Faisal Specialist Hospital, Jeddah, Saudi Arabia
| | - Rothaina Saeedi
- Division of Neurosurgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Taghreed Al-Sinani
- Department of Surgery,Division of Neurosurgery, King Fahad General Hospital, Jeddah, Saudi Arabia
| | - Najla Alghanmi
- Department of Pathology, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Mohammed O Bari
- Department of Pathology, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Alaa Samkari
- Department of Pathology and Laboratory Medicine, King Saud Bin Abdulaziz University for Health Science, Jeddah, Saudi Arabia
| | - Ahmed I Lary
- Section of Neurosurgery, Department of Surgery, King Abdulaziz Medical City, Jeddah, Saudi Arabia
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8
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Berg SH, Massoud CM, Jackson-Cook C, Boikos SA, Smith SC, Mochel MC. A Reappraisal of Superficial Pleomorphic Liposarcoma. Am J Clin Pathol 2020; 154:353-361. [PMID: 32525520 DOI: 10.1093/ajcp/aqaa045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Superficial pleomorphic liposarcoma (PL) has a favorable prognosis compared to deeply seated PL. Given developments in the classification of lipomatous neoplasms, we reappraised a series of cases. METHODS Retrospective clinicopathologic evaluation and genome-wide single-nucleotide polymorphism (SNP) microarray studies were performed for cases previously designated superficial PL. RESULTS Four cases were identified (age, 48-70 years). Two were dermally confined, whereas two were superficial subcutaneous; no recurrences or metastases were reported. Tumors demonstrated pleomorphic spindled morphology with variable cellularity. Multivacuolated atypical lipoblasts were focal in 3 and abundant in 1. Dermal tumors demonstrated atypical cells within sclerotic collagen. Genome-wide SNP microarray studies revealed consistent gains and losses, including losses at the 13q14.2 locus encompassing RB1 and DLEU2 and deletion/disruption of the TP53 locus. Although subcutaneous examples showed genomic changes similar to deep PL, the dermal examples showed fewer genetic alterations, including changes reported in the spectrum of atypical spindle cell/pleomorphic lipomatous tumors (ASPLT). All lacked MDM2 amplification. CONCLUSIONS Careful integration of histologic and genetic features may improve classification of lipomatous neoplasms with atypia, allowing reclassification of some superficial PL as ASPLT.
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Affiliation(s)
| | | | - Colleen Jackson-Cook
- Department of Pathology, Virginia Commonwealth University Health System, Richmond
- Department of Human and Molecular Genetics, Virginia Commonwealth University Health System, Richmond
| | - Sosipatros Alexander Boikos
- Department of Hematology, Oncology, and Palliative Care, Virginia Commonwealth University Health System, Richmond
| | | | - Mark Cameron Mochel
- Department of Pathology, Virginia Commonwealth University Health System, Richmond
- Department of Dermatology, Virginia Commonwealth University Health System, Richmond
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Brunetti M, Panagopoulos I, Micci F, Davidson B. MGMT
promoter methylation is a rare epigenetic change in malignant effusions. Cytopathology 2019; 31:12-15. [DOI: 10.1111/cyt.12782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/10/2019] [Accepted: 10/26/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Marta Brunetti
- Section for Cancer CytogeneticsInstitute for Cancer Genetics and InformaticsThe Norwegian Radium HospitalOslo University Hospital Oslo Norway
- Department of PathologyNorwegian Radium HospitalOslo University Hospital Oslo Norway
- Institute of Clinical MedicineFaculty of MedicineUniversity of Oslo Oslo Norway
| | - Ioannis Panagopoulos
- Section for Cancer CytogeneticsInstitute for Cancer Genetics and InformaticsThe Norwegian Radium HospitalOslo University Hospital Oslo Norway
| | - Francesca Micci
- Section for Cancer CytogeneticsInstitute for Cancer Genetics and InformaticsThe Norwegian Radium HospitalOslo University Hospital Oslo Norway
| | - Ben Davidson
- Department of PathologyNorwegian Radium HospitalOslo University Hospital Oslo Norway
- Institute of Clinical MedicineFaculty of MedicineUniversity of Oslo Oslo Norway
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Beltrán-García J, Osca-Verdegal R, Mena-Mollá S, García-Giménez JL. Epigenetic IVD Tests for Personalized Precision Medicine in Cancer. Front Genet 2019; 10:621. [PMID: 31316555 PMCID: PMC6611494 DOI: 10.3389/fgene.2019.00621] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/13/2019] [Indexed: 12/12/2022] Open
Abstract
Epigenetic alterations play a key role in the initiation and progression of cancer. Therefore, it is possible to use epigenetic marks as biomarkers for predictive and precision medicine in cancer. Precision medicine is poised to impact clinical practice, patients, and healthcare systems. The objective of this review is to provide an overview of the epigenetic testing landscape in cancer by examining commercially available epigenetic-based in vitro diagnostic tests for colon, breast, cervical, glioblastoma, lung cancers, and for cancers of unknown origin. We compile current commercial epigenetic tests based on epigenetic biomarkers (i.e., DNA methylation, miRNAs, and histones) that can actually be implemented into clinical practice.
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Affiliation(s)
- Jesús Beltrán-García
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Biomedical Research Institute, Valencia, Spain.,Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain
| | - Rebeca Osca-Verdegal
- INCLIVA Biomedical Research Institute, Valencia, Spain.,Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain
| | - Salvador Mena-Mollá
- Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain.,EpiDisease S.L. Spin-Off of CIBERER (ISCIII), Valencia, Spain
| | - José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Biomedical Research Institute, Valencia, Spain.,Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain.,EpiDisease S.L. Spin-Off of CIBERER (ISCIII), Valencia, Spain
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