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Pellegrini C, Ravaioli F, De Fanti S, Pirazzini C, D’Silva C, Garagnani P, Franceschi C, Bonifazi F, Zinzani PL, Bonafè M, Guarino M, Lodi R, Cortelli P, Tonon C, Mitolo M, Sambati L, Morandi L, Bacalini MG. Detection of Brain-Derived Cell-Free DNA in Plasma. Diagnostics (Basel) 2024; 14:2541. [PMID: 39594207 PMCID: PMC11592591 DOI: 10.3390/diagnostics14222541] [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: 09/24/2024] [Revised: 11/02/2024] [Accepted: 11/05/2024] [Indexed: 11/28/2024] Open
Abstract
Background: Neuronal loss is a major pathological feature of neurodegenerative diseases. The analysis of plasma cell-free DNA (cfDNA) is an emerging approach to track cell death events in a minimally invasive way and from inaccessible areas of the body, such as the brain. Previous studies showed that DNA methylation (DNAm) profiles can be used to map the tissue of origin of cfDNA and to identify molecules released from the brain upon cell death. The aim of the present study is to contribute to this research field, presenting the development and validation of an assay for the detection of brain-derived cfDNA (bcfDNA). Methods: To identify CpG sites with brain-specific DNAm, we compared brain and non-brain tissues for their chromatin state profiles and genome-wide DNAm data, available in public datasets. The selected target genomic regions were experimentally validated by bisulfite sequencing on DNA extracted from 44 different autoptic tissues, including multiple brain regions. Sequencing data were analysed to identify brain-specific epihaplotypes. The developed assay was tested in plasma cfDNA from patients with immune effector cell-associated neurotoxicity syndrome (ICANS) following chimeric antigen receptor T (CAR-T) therapy. Results: We validated five genomic regions with brain-specific DNAm (four hypomethylated and one hypermethylated in the brain). DNAm analysis of the selected genomic regions in plasma samples from CAR-T patients revealed higher levels of bcfDNA in participants with ongoing neurotoxicity syndrome. Conclusions: We developed an assay for the analysis of bcfDNA in plasma. The assay is a promising tool for the early detection of neuronal loss in neurodegenerative diseases.
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Affiliation(s)
- Camilla Pellegrini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (C.P.); (F.R.); (S.D.F.); (M.G.); (R.L.); (P.C.); (C.T.); (L.S.); (L.M.)
| | - Francesco Ravaioli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (C.P.); (F.R.); (S.D.F.); (M.G.); (R.L.); (P.C.); (C.T.); (L.S.); (L.M.)
| | - Sara De Fanti
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (C.P.); (F.R.); (S.D.F.); (M.G.); (R.L.); (P.C.); (C.T.); (L.S.); (L.M.)
| | - Chiara Pirazzini
- Department of Medical and Surgical Sciences—DIMEC, University of Bologna, 40126 Bologna, Italy; (C.P.); (P.G.); (P.L.Z.); (M.B.)
| | - Chiara D’Silva
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy;
| | - Paolo Garagnani
- Department of Medical and Surgical Sciences—DIMEC, University of Bologna, 40126 Bologna, Italy; (C.P.); (P.G.); (P.L.Z.); (M.B.)
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging, Institute of Biology and Biomedicine and Institute of Information Technology, Mathematics and Mechanics, Department of Applied Mathematics, Lobachevsky State University, 603950 Nizhny Novgorod, Russia;
| | - Francesca Bonifazi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Pier Luigi Zinzani
- Department of Medical and Surgical Sciences—DIMEC, University of Bologna, 40126 Bologna, Italy; (C.P.); (P.G.); (P.L.Z.); (M.B.)
- Istituto di Ematologia “Seràgnoli”, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Massimiliano Bonafè
- Department of Medical and Surgical Sciences—DIMEC, University of Bologna, 40126 Bologna, Italy; (C.P.); (P.G.); (P.L.Z.); (M.B.)
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Maria Guarino
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (C.P.); (F.R.); (S.D.F.); (M.G.); (R.L.); (P.C.); (C.T.); (L.S.); (L.M.)
| | - Raffaele Lodi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (C.P.); (F.R.); (S.D.F.); (M.G.); (R.L.); (P.C.); (C.T.); (L.S.); (L.M.)
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40138 Bologna, Italy
| | - Pietro Cortelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (C.P.); (F.R.); (S.D.F.); (M.G.); (R.L.); (P.C.); (C.T.); (L.S.); (L.M.)
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40138 Bologna, Italy
| | - Caterina Tonon
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (C.P.); (F.R.); (S.D.F.); (M.G.); (R.L.); (P.C.); (C.T.); (L.S.); (L.M.)
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40138 Bologna, Italy
| | - Micaela Mitolo
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy;
| | - Luisa Sambati
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (C.P.); (F.R.); (S.D.F.); (M.G.); (R.L.); (P.C.); (C.T.); (L.S.); (L.M.)
| | - Luca Morandi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (C.P.); (F.R.); (S.D.F.); (M.G.); (R.L.); (P.C.); (C.T.); (L.S.); (L.M.)
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40138 Bologna, Italy
| | - Maria Giulia Bacalini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (C.P.); (F.R.); (S.D.F.); (M.G.); (R.L.); (P.C.); (C.T.); (L.S.); (L.M.)
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Ma Y, Zhao Y, Zhang X. Factors affecting neutrophil functions during sepsis: human microbiome and epigenetics. J Leukoc Biol 2024; 116:672-688. [PMID: 38734968 DOI: 10.1093/jleuko/qiae107] [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: 12/07/2023] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 05/13/2024] Open
Abstract
Sepsis is a severe disease that occurs when the body's immune system reacts excessively to infection. The body's response, which includes an intense antibacterial reaction, can damage its tissues and organs. Neutrophils are the major components of white blood cells in circulation, play a vital role in innate immunity while fighting against infections, and are considered a feature determining sepsis classification. There is a plethora of basic research detailing neutrophil functioning, among which, the study of neutrophil extracellular traps is providing novel insights into mechanisms and treatments of sepsis. This review explores their functions, dysfunctions, and influences in the context of sepsis. The interplay between neutrophils and the human microbiome and the impact of DNA methylation on neutrophil function in sepsis are crucial areas of study. The interaction between neutrophils and the human microbiome is complex, particularly in the context of sepsis, where dysbiosis may occur. We highlight the importance of deciphering neutrophils' functional alterations and their epigenetic features in sepsis because it is critical for defining sepsis endotypes and opening up the possibility for novel diagnostic methods and therapy. Specifically, epigenetic signatures are pivotal since they will provide a novel implication for a sepsis diagnostic method when used in combination with the cell-free DNA. Research is exploring how specific patterns of DNA methylation in neutrophils, detectable in cell-free DNA, could serve as biomarkers for the early detection of sepsis.
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Affiliation(s)
- Yina Ma
- Department of Urology Surgery, Beijing Chaoyang Hospital, Capital Medical University, Shijingshan District, Beijing 100043, China
| | - Yu Zhao
- Department of Urology Surgery, Beijing Chaoyang Hospital, Capital Medical University, Shijingshan District, Beijing 100043, China
| | - Xin Zhang
- Department of Urology Surgery, Beijing Chaoyang Hospital, Capital Medical University, Shijingshan District, Beijing 100043, China
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3
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El-Ahmad P, Mendes-Silva AP, Diniz BS. Liquid Biopsy in Neuropsychiatric Disorders: A Step Closer to Precision Medicine. Mol Neurobiol 2024:10.1007/s12035-024-04492-y. [PMID: 39298102 DOI: 10.1007/s12035-024-04492-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 09/11/2024] [Indexed: 09/21/2024]
Abstract
Psychiatric disorders are among the leading causes of disease burden worldwide. Despite their significant impact, their diagnosis remains challenging due to symptom heterogeneity, psychiatric comorbidity, and the lack of objective diagnostic tests and well-defined biomarkers. Leveraging genomic, epigenomic, and fragmentomic technologies, circulating cell-free DNA (ccfDNA)-based liquid biopsies have emerged as a potential non-invasive diagnosis and disease-monitoring tool. ccfDNA is a DNA species released into circulation from all types of cells through passive and active mechanisms and can serve as a biomarker for various diseases, namely, cancer. Despite their potential, the application of ccfDNA in neuropsychiatry remains underdeveloped. In this review, we provide an overview of liquid biopsies and their components, with a particular focus on ccfDNA. With a summary of pre-analytical practices and current ccfDNA technologies, we highlight the current state of research regarding the use of ccfDNA as a biomarker for neuropsychiatric disorders. Finally, we discuss future steps to unlock ccfDNA's potential in clinical practice.
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Affiliation(s)
- Perla El-Ahmad
- UConn Center on Aging, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT, 06030, USA.
| | - Ana Paula Mendes-Silva
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, Canada
- Department of Psychiatry, University of Saskatchewan, Saskatoon, Canada
| | - Breno S Diniz
- UConn Center on Aging, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT, 06030, USA.
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4
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Li S, Jiang J, Zhu W, Wang D, Dong C, Bu Y, Zhang J, Gao D, Hu X, Wan C. Increased cell-free DNA is associated with oxidative damage in patients with schizophrenia. J Psychiatr Res 2024; 175:20-28. [PMID: 38701608 DOI: 10.1016/j.jpsychires.2024.04.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/31/2024] [Accepted: 04/25/2024] [Indexed: 05/05/2024]
Abstract
Cell-free DNA (cfDNA) has been found to be elevated in patients with schizophrenia (SZ), potentially derived from activated apoptosis, but the underlying mechanisms remain unknown. Moreover, whether the concentrations of cfDNA are altered with disease stage has not been investigated, which limits its clinical application as an auxiliary diagnostic marker for SZ. Using an improved fluorescence correlation spectroscopy (FCS) method that does not require DNA extraction, we measured the molar concentrations of cfDNA in plasma samples of 191 patients with SZ, 78 patients with mood disorders (MD) and 65 healthy controls (HC). We also analyzed the cfDNA composition from either the nucleus or mitochondria, oxidation markers and biochemical indexes to explore the potential mechanistic associations of the increased cfDNA levels. We found that in SZ patients, the cfDNA levels were significantly increased (P = 0.003) regardless of the different disease stages or antipsychotic medication use. Furthermore, qPCR revealed that cell-free nuclear DNA (cf-nDNA) (P = 0.041) but not cell-free mitochondrial DNA (cf-mtDNA) was elevated in SZ patients. Moreover, decreased SOD activity in SZ patients (P = 0.005) was negatively correlated with cfDNA levels (P = 0.047), and fasting blood glucose was positively correlated with cfDNA levels in SZ patients (P = 0.013). Our study provides evidence to support that the elevated cfDNA may be a convenient, effective and stable trait indicator of SZ. Further analysis showed that it mainly came from nucleus, suggesting increased apoptosis, and potentially related to oxidative stress and high blood glucose levels in patients.
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Affiliation(s)
- Shuhui Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jie Jiang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wenli Zhu
- The Fourth People's Hospital of Wuhu, Wuhu, 241003, China
| | - Dandan Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Chaoqing Dong
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yangying Bu
- The Fourth People's Hospital of Wuhu, Wuhu, 241003, China
| | - Juan Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Daiyutong Gao
- Department of Mathematics, Nanjing University, Nanjing, 210093, China
| | - Xiaowen Hu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Chunling Wan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Mental Health Center, Shanghai Key Laboratory of Psychiatry Disorders, Shanghai Jiao Tong University, Shanghai, 200030, China.
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5
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López-Otín C, Kroemer G. The missing hallmark of health: psychosocial adaptation. Cell Stress 2024; 8:21-50. [PMID: 38476764 PMCID: PMC10928495 DOI: 10.15698/cst2024.03.294] [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: 01/11/2024] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
The eight biological hallmarks of health that we initially postulated (Cell. 2021 Jan 7;184(1):33-63) include features of spatial compartmentalization (integrity of barriers, containment of local perturbations), maintenance of homeostasis over time (recycling & turnover, integration of circuitries, rhythmic oscillations) and an array of adequate responses to stress (homeostatic resilience, hormetic regulation, repair & regeneration). These hallmarks affect all eight somatic strata of the human body (molecules, organelles, cells, supracellular units, organs, organ systems, systemic circuitries and meta-organism). Here we postulate that mental and socioeconomic factors must be added to this 8×8 matrix as an additional hallmark of health ("psychosocial adaptation") and as an additional stratum ("psychosocial interactions"), hence building a 9×9 matrix. Potentially, perturbation of each of the somatic hallmarks and strata affects psychosocial factors and vice versa. Finally, we discuss the (patho)physiological bases of these interactions and their implications for mental health improvement.
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Affiliation(s)
- Carlos López-Otín
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Facultad de Ciencias de la Vida y la Naturaleza, Universidad Nebrija, Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
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6
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Kwok AJ, Lu J, Huang J, Ip BY, Mok VCT, Lai HM, Ko H. High-resolution omics of vascular ageing and inflammatory pathways in neurodegeneration. Semin Cell Dev Biol 2024; 155:30-49. [PMID: 37380595 DOI: 10.1016/j.semcdb.2023.06.005] [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: 04/29/2023] [Accepted: 06/07/2023] [Indexed: 06/30/2023]
Abstract
High-resolution omics, particularly single-cell and spatial transcriptomic profiling, are rapidly enhancing our comprehension of the normal molecular diversity of gliovascular cells, as well as their age-related changes that contribute to neurodegeneration. With more omic profiling studies being conducted, it is becoming increasingly essential to synthesise valuable information from the rapidly accumulating findings. In this review, we present an overview of the molecular features of neurovascular and glial cells that have been recently discovered through omic profiling, with a focus on those that have potentially significant functional implications and/or show cross-species differences between human and mouse, and that are linked to vascular deficits and inflammatory pathways in ageing and neurodegenerative disorders. Additionally, we highlight the translational applications of omic profiling, and discuss omic-based strategies to accelerate biomarker discovery and facilitate disease course-modifying therapeutics development for neurodegenerative conditions.
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Affiliation(s)
- Andrew J Kwok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Jianning Lu
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Junzhe Huang
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Bonaventure Y Ip
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Vincent C T Mok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hei Ming Lai
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Ho Ko
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Hovhannisyan G, Harutyunyan T, Aroutiounian R, Liehr T. The Diagnostic, Prognostic, and Therapeutic Potential of Cell-Free DNA with a Special Focus on COVID-19 and Other Viral Infections. Int J Mol Sci 2023; 24:14163. [PMID: 37762464 PMCID: PMC10532175 DOI: 10.3390/ijms241814163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Cell-free DNA (cfDNA) in human blood serum, urine, and other body fluids recently became a commonly used diagnostic marker associated with various pathologies. This is because cfDNA enables a much higher sensitivity than standard biochemical parameters. The presence of and/or increased level of cfDNA has been reported for various diseases, including viral infections, including COVID-19. Here, we review cfDNA in general, how it has been identified, where it can derive from, its molecular features, and mechanisms of release and clearance. General suitability of cfDNA for diagnostic questions, possible shortcomings and future directions are discussed, with a special focus on coronavirus infection.
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Affiliation(s)
- Galina Hovhannisyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (G.H.); (T.H.); (R.A.)
| | - Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (G.H.); (T.H.); (R.A.)
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (G.H.); (T.H.); (R.A.)
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, 07747 Jena, Germany
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Kurtulmuş A, Koçana CÇ, Toprak SF, Sözer S. The role of Extracellular Genomic Materials (EGMs) in psychiatric disorders. Transl Psychiatry 2023; 13:262. [PMID: 37464177 PMCID: PMC10354097 DOI: 10.1038/s41398-023-02549-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023] Open
Abstract
Extracellular Genomic Materials (EGMs) are the nucleic acids secreted or released from all types of cells by endogenous or exogenous stimuli through varying mechanisms into the extracellular region and inevitably to all biological fluids. EGMs could be found as free, protein-bound, and/ or with vesicles. EGMs can potentially have immunophenotypic and/or genotypic characteristics of a cell of origin, travel to distant organs, and interact with the new microenvironment. To achieve all, EGMs might bi-directionally transit through varying membranes, including the blood-brain barrier. Such ability provides the transfer of any information related to the pathophysiological changes in psychiatric disorders in the brain to the other distant organ systems or vice versa. In this article, many aspects of EGMs have been elegantly reviewed, including their potential in diagnosis as biomarkers, application in treatment modalities, and functional effects in the pathophysiology of psychiatric disorders. The psychiatric disorders were studied under subgroups of Schizophrenia spectrum disorders, bipolar disorder, depressive disorders, and an autism spectrum disorders. EGMs provide a robust and promising tool in clinics for prognosis and diagnosis. The successful application of EGMs into treatment modalities might further provide encouraging outcomes for researchers and clinicians in psychiatric disorders.
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Affiliation(s)
- Ayşe Kurtulmuş
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
- Institute of Health Sciences, Istanbul University, Istanbul, Turkey
- Istanbul Göztepe Prof.Dr.Süleyman Yalçın City Hospital, Department of Psychiatry, Istanbul, Turkey
| | - Cemal Çağıl Koçana
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
- Institute of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Selin Fulya Toprak
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
- Institute of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Selçuk Sözer
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
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Fisher IF, Shemer R, Dor Y. Epigenetic liquid biopsies: a novel putative biomarker in immunology and inflammation. Trends Immunol 2023; 44:356-364. [PMID: 37012121 DOI: 10.1016/j.it.2023.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
Immune and inflammatory processes occurring within tissues are often undetectable by blood cell counts, standard circulating biomarkers, or imaging, representing an unmet biomedical need. Here, we outline recent advances indicating that liquid biopsies can broadly inform human immune system dynamics. Nucleosome-size fragments of cell-free DNA (cfDNA) released from dying cells into blood contain rich epigenetic information such as methylation, fragmentation, and histone mark patterns. This information allows to infer the cfDNA cell of origin, as well as pre-cell death gene expression patterns. We propose that the analysis of epigenetic features of immune cell-derived cfDNA can shed light on immune cell turnover dynamics in healthy people, and inform the study and diagnosis of cancer, local inflammation, infectious or autoimmune diseases, as well as responses to vaccination.
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Melamud MM, Buneva VN, Ermakov EA. Circulating Cell-Free DNA Levels in Psychiatric Diseases: A Systematic Review and Meta-Analysis. Int J Mol Sci 2023; 24:3402. [PMID: 36834811 PMCID: PMC9963116 DOI: 10.3390/ijms24043402] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
The cell-free DNA (cfDNA) levels are known to increase in biological fluids in various pathological conditions. However, the data on circulating cfDNA in severe psychiatric disorders, including schizophrenia, bipolar disorder (BD), and depressive disorders (DDs), is contradictory. This meta-analysis aimed to analyze the concentrations of different cfDNA types in schizophrenia, BD, and DDs compared with healthy donors. The mitochondrial (cf-mtDNA), genomic (cf-gDNA), and total cfDNA concentrations were analyzed separately. The effect size was estimated using the standardized mean difference (SMD). Eight reports for schizophrenia, four for BD, and five for DDs were included in the meta-analysis. However, there were only enough data to analyze the total cfDNA and cf-gDNA in schizophrenia and cf-mtDNA in BD and DDs. It has been shown that the levels of total cfDNA and cf-gDNA in patients with schizophrenia are significantly higher than in healthy donors (SMD values of 0.61 and 0.6, respectively; p < 0.00001). Conversely, the levels of cf-mtDNA in BD and DDs do not differ compared with healthy individuals. Nevertheless, further research is needed in the case of BD and DDs due to the small sample sizes in the BD studies and the significant data heterogeneity in the DD studies. Additionally, further studies are needed on cf-mtDNA in schizophrenia or cf-gDNA and total cfDNA in BD and DDs due to insufficient data. In conclusion, this meta-analysis provides the first evidence of increases in total cfDNA and cf-gDNA in schizophrenia but shows no changes in cf-mtDNA in BD and DDs. Increased circulating cfDNA in schizophrenia may be associated with chronic systemic inflammation, as cfDNA has been found to trigger inflammatory responses.
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Affiliation(s)
- Mark M. Melamud
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Valentina N. Buneva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Evgeny A. Ermakov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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Bronkhorst AJ, Ungerer V, Oberhofer A, Gabriel S, Polatoglou E, Randeu H, Uhlig C, Pfister H, Mayer Z, Holdenrieder S. New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:2147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
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Affiliation(s)
- Abel J. Bronkhorst
- Munich Biomarker Research Center, Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, D-80636 Munich, Germany
| | | | | | | | | | | | | | | | | | - Stefan Holdenrieder
- Munich Biomarker Research Center, Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, D-80636 Munich, Germany
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