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de Boer SC, Riedl L, Fenoglio C, Rue I, Landin-Romero R, Matis S, Chatterton Z, Galimberti D, Halliday G, Diehl-Schmid J, Piguet O, Pijnenburg YA, Ducharme S. Rationale and Design of the "DIagnostic and Prognostic Precision Algorithm for behavioral variant Frontotemporal Dementia" (DIPPA-FTD) Study: A Study Aiming to Distinguish Early Stage Sporadic FTD from Late-Onset Primary Psychiatric Disorders. J Alzheimers Dis 2024; 97:963-973. [PMID: 38143357 PMCID: PMC10836537 DOI: 10.3233/jad-230829] [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] [Accepted: 11/06/2023] [Indexed: 12/26/2023]
Abstract
BACKGROUND The behavioral variant of frontotemporal dementia (bvFTD) is very heterogeneous in pathology, genetics, and disease course. Unlike Alzheimer's disease, reliable biomarkers are lacking and sporadic bvFTD is often misdiagnosed as a primary psychiatric disorder (PPD) due to overlapping clinical features. Current efforts to characterize and improve diagnostics are centered on the minority of genetic cases. OBJECTIVE The multi-center study DIPPA-FTD aims to develop diagnostic and prognostic algorithms to help distinguish sporadic bvFTD from late-onset PPD in its earliest stages. METHODS The prospective DIPPA-FTD study recruits participants with late-life behavioral changes, suspect for bvFTD or late-onset PPD diagnosis with a negative family history for FTD and/or amyotrophic lateral sclerosis. Subjects are invited to participate after diagnostic screening at participating memory clinics or recruited by referrals from psychiatric departments. At baseline visit, participants undergo neurological and psychiatric examination, questionnaires, neuropsychological tests, and brain imaging. Blood is obtained to investigate biomarkers. Patients are informed about brain donation programs. Follow-up takes place 10-14 months after baseline visit where all examinations are repeated. Results from the DIPPA-FTD study will be integrated in a data-driven approach to develop diagnostic and prognostic models. CONCLUSIONS DIPPA-FTD will make an important contribution to early sporadic bvFTD identification. By recruiting subjects with ambiguous or prodromal diagnoses, our research strategy will allow the characterization of early disease stages that are not covered in current sporadic FTD research. Results will hopefully increase the ability to diagnose sporadic bvFTD in the early stage and predict progression rate, which is pivotal for patient stratification and trial design.
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Affiliation(s)
- Sterre C.M. de Boer
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- School of Psychology and Brain & Mind Centre, The University of Sydney, Sydney, Australia
| | - Lina Riedl
- Department of Psychiatry and Psychotherapy, School of Medicine, Technical University of Munich, Munich, Germany
| | - Chiara Fenoglio
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Ishana Rue
- Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, Canada
| | - Ramon Landin-Romero
- Faculty of Medicine and Health, School of Health Sciences & Brain and Mind Sciences, The University of Sydney, Sydney, Australia
| | - Sophie Matis
- Faculty of Medicine and Health, School of Health Sciences & Brain and Mind Sciences, The University of Sydney, Sydney, Australia
| | - Zac Chatterton
- Brain and Mind Centre and Faculty of Medicine and Health School of Medical Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Daniela Galimberti
- University of Milan, Milan, Italy
- Fondazione Ca’ Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Glenda Halliday
- School of Medical Sciences & Brain and Mind Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Janine Diehl-Schmid
- Department of Psychiatry and Psychotherapy, School of Medicine, Technical University of Munich, Munich, Germany
- kbo-Inn-Salzach-Klinikum, Clinical Center for Psychiatry, Psychotherapy, Psychosomatic Medicine, Geriatrics and Neurology, Wasserburg/Inn, Germany
| | - Olivier Piguet
- School of Psychology and Brain & Mind Centre, The University of Sydney, Sydney, Australia
| | - Yolande A.L. Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Simon Ducharme
- Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada
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2
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Gaitsch H, Franklin RJM, Reich DS. Cell-free DNA-based liquid biopsies in neurology. Brain 2023; 146:1758-1774. [PMID: 36408894 PMCID: PMC10151188 DOI: 10.1093/brain/awac438] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/26/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022] Open
Abstract
This article reviews recent developments in the application of cell-free DNA-based liquid biopsies to neurological diseases. Over the past few decades, an explosion of interest in the use of accessible biofluids to identify and track molecular disease has revolutionized the fields of oncology, prenatal medicine and others. More recently, technological advances in signal detection have allowed for informative analysis of biofluids that are typically sparse in cells and other circulating components, such as CSF. In parallel, advancements in epigenetic profiling have allowed for novel applications of liquid biopsies to diseases without characteristic mutational profiles, including many degenerative, autoimmune, inflammatory, ischaemic and infectious disorders. These events have paved the way for a wide array of neurological conditions to benefit from enhanced diagnostic, prognostic, and treatment abilities through the use of liquid biomarkers: a 'liquid biopsy' approach. This review includes an overview of types of liquid biopsy targets with a focus on circulating cell-free DNA, methods used to identify and probe potential liquid biomarkers, and recent applications of such biomarkers to a variety of complex neurological conditions including CNS tumours, stroke, traumatic brain injury, Alzheimer's disease, epilepsy, multiple sclerosis and neuroinfectious disease. Finally, the challenges of translating liquid biopsies to use in clinical neurology settings-and the opportunities for improvement in disease management that such translation may provide-are discussed.
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Affiliation(s)
- Hallie Gaitsch
- NIH-Oxford-Cambridge Scholars Program, Wellcome-MRC Cambridge Stem Cell Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 1TN, UK
| | | | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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3
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Verebi C, Nectoux J, Gorwood P, Le Strat Y, Duriez P, Ramoz N, Bienvenu T. A systematic literature review and meta-analysis of circulating nucleic acids as biomarkers in psychiatry. Prog Neuropsychopharmacol Biol Psychiatry 2023; 125:110770. [PMID: 37068545 DOI: 10.1016/j.pnpbp.2023.110770] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/14/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023]
Abstract
Common mental disorders (CMDs) such as depression, anxiety and post-traumatic stress disorders account for 40% of the global burden of disease. In most psychiatric disorders, both diagnosis and monitoring can be challenging, frequently requiring long-term investigation and follow-up. The discovery of better methods to facilitate accurate and fast diagnosis and monitoring of psychiatric disorders is therefore crucial. Circulating nucleic acids (CNAs) are among these new tools. CNAs (DNA or RNA) can be found circulating in body biofluids, and can be isolated from biological samples such as plasma. They can serve as biomarkers for diagnosis and prognoses. They appear to be promising for disorders (such as psychiatric disorders) that involve organs or structures that are difficult to assess. This review presents an accurate assessment of the current literature about the use of plasma and serum cell-free DNA (cfDNA) as biomarkers for several aspects of psychiatric disorders: diagnosis, prognosis, treatment response, and monitor disease progression. For each psychiatric disorder, we examine the effect sizes to give insights on the efficacy of CNAs as biomarkers. The global effect size for plasma nuclear and mitochondrial cfDNA studies was generally moderate for psychiatric disorders. In addition, we discuss future applications of CNAs and particularly cfDNA as non-invasive biomarkers for these diseases.
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Affiliation(s)
- Camille Verebi
- Service de Médecine Génomique des Maladies de Système et d'Organe, Hôpital Cochin, AP.HP.CUP, Paris, France; INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France
| | - Juliette Nectoux
- Service de Médecine Génomique des Maladies de Système et d'Organe, Hôpital Cochin, AP.HP.CUP, Paris, France
| | - Philip Gorwood
- INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France; Université Paris Cité, GHU Paris Psychiatrie et Neurosciences (CMME), Paris, France
| | - Yann Le Strat
- AP-HP, Department of Psychiatry, Louis Mourier Hospital, Université Paris Cité, Faculté de Médecine, Colombes, France
| | - Philibert Duriez
- INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France; Université Paris Cité, GHU Paris Psychiatrie et Neurosciences (CMME), Paris, France
| | - Nicolas Ramoz
- INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France
| | - Thierry Bienvenu
- Service de Médecine Génomique des Maladies de Système et d'Organe, Hôpital Cochin, AP.HP.CUP, Paris, France; INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Paris, France.
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4
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Chatterton Z, Lamichhane P, Ahmadi Rastegar D, Fitzpatrick L, Lebhar H, Marquis C, Halliday G, Kwok JB. Single-cell DNA methylation sequencing by combinatorial indexing and enzymatic DNA methylation conversion. Cell Biosci 2023; 13:2. [PMID: 36600255 PMCID: PMC9811750 DOI: 10.1186/s13578-022-00938-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/07/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND DNA methylation is a critical molecular mark involved in cellular differentiation and cell-specific processes. Single-cell whole genome DNA methylation profiling methods hold great potential to resolve the DNA methylation profiles of individual cell-types. Here we present a method that couples single-cell combinatorial indexing (sci) with enzymatic conversion (sciEM) of unmethylated cytosines. RESULTS The sciEM method facilitates DNA methylation profiling of single-cells that is highly correlated with single-cell bisulfite-based workflows (r2 > 0.99) whilst improving sequencing alignment rates, reducing adapter contamination and over-estimation of DNA methylation levels (CpG and non-CpG). As proof-of-concept we perform sciEM analysis of the temporal lobe, motor cortex, hippocampus and cerebellum of the human brain to resolve single-cell DNA methylation of all major cell-types. CONCLUSION To our knowledge sciEM represents the first non-bisulfite single-cell DNA methylation sequencing approach with single-base resolution.
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Affiliation(s)
- Zac Chatterton
- grid.1013.30000 0004 1936 834XBrain and Mind Centre, The University of Sydney, Camperdown, Australia ,grid.1013.30000 0004 1936 834XSchool of Medical Science, The University of Sydney, Camperdown, Australia
| | - Praves Lamichhane
- grid.1013.30000 0004 1936 834XBrain and Mind Centre, The University of Sydney, Camperdown, Australia ,grid.1013.30000 0004 1936 834XSchool of Medical Science, The University of Sydney, Camperdown, Australia
| | - Diba Ahmadi Rastegar
- grid.1013.30000 0004 1936 834XBrain and Mind Centre, The University of Sydney, Camperdown, Australia ,grid.1013.30000 0004 1936 834XSchool of Medical Science, The University of Sydney, Camperdown, Australia
| | - Lauren Fitzpatrick
- grid.1013.30000 0004 1936 834XBrain and Mind Centre, The University of Sydney, Camperdown, Australia ,grid.1013.30000 0004 1936 834XSchool of Medical Science, The University of Sydney, Camperdown, Australia
| | - Hélène Lebhar
- grid.1005.40000 0004 4902 0432Recombinant Products Facility, University of New South Wales, Kensington, Australia
| | - Christopher Marquis
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, Australia
| | - Glenda Halliday
- grid.1013.30000 0004 1936 834XBrain and Mind Centre, The University of Sydney, Camperdown, Australia ,grid.1013.30000 0004 1936 834XSchool of Medical Science, The University of Sydney, Camperdown, Australia
| | - John B. Kwok
- grid.1013.30000 0004 1936 834XBrain and Mind Centre, The University of Sydney, Camperdown, Australia ,grid.1013.30000 0004 1936 834XSchool of Medical Science, The University of Sydney, Camperdown, Australia
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Martins-Ferreira R, Leal B, Chaves J, Ciudad L, Samões R, Martins da Silva A, Pinho Costa P, Ballestar E. Circulating cell-free DNA methylation mirrors alterations in cerebral patterns in epilepsy. Clin Epigenetics 2022; 14:188. [PMID: 36575526 PMCID: PMC9795776 DOI: 10.1186/s13148-022-01416-2] [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: 08/08/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND DNA methylation profiling of circulating cell-free DNA (cfDNA) has rapidly become a promising strategy for biomarker identification and development. The cell-type-specific nature of DNA methylation patterns and the direct relationship between cfDNA and apoptosis can potentially be used non-invasively to predict local alterations. In addition, direct detection of altered DNA methylation patterns performs well as a biomarker. In a previous study, we demonstrated marked DNA methylation alterations in brain tissue from patients with mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS). RESULTS We performed DNA methylation profiling in cfDNA isolated from the serum of MTLE patients and healthy controls using BeadChip arrays followed by systematic bioinformatic analysis including deconvolution analysis and integration with DNase accessibility data sets. Differential cfDNA methylation analysis showed an overrepresentation of gene ontology terms and transcription factors related to central nervous system function and regulation. Deconvolution analysis of the DNA methylation data sets ruled out the possibility that the observed differences were due to changes in the proportional contribution of cortical neurons in cfDNA. Moreover, we found no overrepresentation of neuron- or glia-specific patterns in the described cfDNA methylation patterns. However, the MTLE-HS cfDNA methylation patterns featured a significant overrepresentation of the epileptic DNA methylation alterations previously observed in the hippocampus. CONCLUSIONS Our results support the use of cfDNA methylation profiling as a rational approach to seeking non-invasive and reproducible epilepsy biomarkers.
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Affiliation(s)
- Ricardo Martins-Ferreira
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona Spain ,grid.5808.50000 0001 1503 7226Immunogenetics Laboratory, Molecular Pathology and Immunology Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal
| | - Bárbara Leal
- grid.5808.50000 0001 1503 7226Immunogenetics Laboratory, Molecular Pathology and Immunology Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal
| | - João Chaves
- Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal ,grid.413438.90000 0004 0574 5247Neurology Service, Hospital de Santo António - Centro Hospitalar Universitário do Porto (HSA-CHUP), Porto, Portugal
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona Spain
| | - Raquel Samões
- grid.413438.90000 0004 0574 5247Neurology Service, Hospital de Santo António - Centro Hospitalar Universitário do Porto (HSA-CHUP), Porto, Portugal
| | - António Martins da Silva
- Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal ,Neurophysiology Service, HSA-CHUP, Porto, Portugal
| | - Paulo Pinho Costa
- grid.5808.50000 0001 1503 7226Immunogenetics Laboratory, Molecular Pathology and Immunology Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal ,grid.422270.10000 0001 2287 695XDepartment of Human Genetics, Instituto Nacional de Saúde Dr. Ricardo Jorge, Porto, Portugal
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona Spain ,grid.22069.3f0000 0004 0369 6365Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, 200241 China
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Southwood D, Singh S, Chatterton Z. Brain-derived cell-free DNA. Neural Regen Res 2022; 17:2213-2214. [PMID: 35259835 PMCID: PMC9083148 DOI: 10.4103/1673-5374.335794] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/30/2021] [Accepted: 11/09/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Dean Southwood
- Brain and Mind Center, School of Medical Sciences, Department of Neuroscience, The University of Sydney, Camperdown, NSW, Australia
| | - Sanyukta Singh
- Brain and Mind Center, School of Medical Sciences, Department of Neuroscience, The University of Sydney, Camperdown, NSW, Australia
| | - Zac Chatterton
- Brain and Mind Center, School of Medical Sciences, Department of Neuroscience, The University of Sydney, Camperdown, NSW, Australia
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Gong W, Pan X, Xu D, Ji G, Wang Y, Tian Y, Cai J, Li J, Zhang Z, Yuan X. Benchmarking DNA Methylation Analysis of 14 Alignment Algorithms for Whole Genome Bisulfite Sequencing in Mammals. Comput Struct Biotechnol J 2022; 20:4704-4716. [PMID: 36147684 PMCID: PMC9465269 DOI: 10.1016/j.csbj.2022.08.051] [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: 03/25/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 01/10/2023] Open
Abstract
Whole genome bisulfite sequencing (WGBS) is an essential technique for methylome studies. Although a series of tools have been developed to overcome the mapping challenges caused by bisulfite treatment, the latest available tools have not been evaluated on the performance of reads mapping as well as on biological insights in multiple mammals. Herein, based on the real and simulated WGBS data of 14.77 billion reads, we undertook 936 mappings to benchmark and evaluate 14 wildly utilized alignment algorithms from reads mapping to biological interpretation in humans, cattle and pigs: Bwa-meth, BSBolt, BSMAP, Walt, Abismal, Batmeth2, Hisat_3n, Hisat_3n_repeat, Bismark-bwt2-e2e, Bismark-his2, BSSeeker2-bwt, BSSeeker2-soap2, BSSeeker2-bwt2-e2e and BSSeeker2-bwt2-local. Specifically, Bwa-meth, BSBolt, BSMAP, Bismark-bwt2-e2e and Walt exhibited higher uniquely mapped reads, mapped precision, recall and F1 score than other nine alignment algorithms, and the influences of distinct alignment algorithms on the methylomes varied considerably at the numbers and methylation levels of CpG sites, the calling of differentially methylated CpGs (DMCs) and regions (DMRs). Moreover, we reported that BSMAP showed the highest accuracy at the detection of CpG coordinates and methylation levels, the calling of DMCs, DMRs, DMR-related genes and signaling pathways. These results suggested that careful selection of algorithms to profile the genome-wide DNA methylation is required, and our works provided investigators with useful information on the choice of alignment algorithms to effectively improve the DNA methylation detection accuracy in mammals.
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Affiliation(s)
- Wentao Gong
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiangchun Pan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Dantong Xu
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Guanyu Ji
- Shenzhen Gendo Health Technology CO,. Ltd, Shenzhen 518122, China
| | - Yifei Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yuhan Tian
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiali Cai
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiaqi Li
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhe Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Corresponding authors.
| | - Xiaolong Yuan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Corresponding authors.
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CfDNA Measurement as a Diagnostic Tool for the Detection of Brain Somatic Mutations in Refractory Epilepsy. Int J Mol Sci 2022; 23:ijms23094879. [PMID: 35563270 PMCID: PMC9102996 DOI: 10.3390/ijms23094879] [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: 03/31/2022] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 02/04/2023] Open
Abstract
Epilepsy is a neurological disorder that affects more than 50 million people. Its etiology is unknown in approximately 60% of cases, although the existence of a genetic factor is estimated in about 75% of these individuals. Hundreds of genes involved in epilepsy are known, and their number is increasing progressively, especially with next-generation sequencing techniques. However, there are still many cases in which the results of these molecular studies do not fully explain the phenotype of the patients. Somatic mutations specific to brain tissue could contribute to the phenotypic spectrum of epilepsy. Undetectable in the genomic DNA of blood cells, these alterations can be identified in cell-free DNA (cfDNA). We aim to review the current literature regarding the detection of somatic variants in cfDNA to diagnose refractory epilepsy, highlighting novel research directions and suggesting further studies.
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9
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Guemri J, Pierre-Jean M, Brohard S, Oussada N, Horgues C, Bonnet E, Mauger F, Deleuze JF. Methylated ccfDNA from plasma biomarkers of Alzheimer's disease using targeted bisulfite sequencing. Epigenomics 2022; 14:451-468. [PMID: 35416052 DOI: 10.2217/epi-2021-0491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Noninvasive biomarkers such as methylated ccfDNA from plasma could help to support the diagnosis of Alzheimer's disease (AD). Methods: A targeted sequencing protocol was developed to identify candidate biomarkers of AD in methylated ccfDNA extracted from plasma. Results: The authors identified differentially methylated CpGs, regions of which were the same as those identified in previous AD studies. Specifically, a differentially methylated CpG of the LHX2 gene previously identified in a plasma study of AD was replicated in the study. The MBP and DUSP22 regions have been identified in other brain studies of AD and in the authors' study. Conclusion: Although these biomarkers must be validated in other cohorts, methylated ccfDNA could be a relevant noninvasive biomarker in AD.
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Affiliation(s)
- Julien Guemri
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Morgane Pierre-Jean
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Solène Brohard
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Nouara Oussada
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Caroline Horgues
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Eric Bonnet
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Florence Mauger
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Jean-François Deleuze
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
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10
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Martins-Ferreira R, Leal BG, Costa PP. The Potential of Circulating Cell-Free DNA Methylation as an Epilepsy Biomarker. Front Cell Neurosci 2022; 16:852151. [PMID: 35401115 PMCID: PMC8987989 DOI: 10.3389/fncel.2022.852151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/24/2022] [Indexed: 12/03/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) are highly degraded DNA fragments shed into the bloodstream. Apoptosis is likely to be the main source of cfDNA due to the matching sizes of cfDNA and apoptotic DNA cleavage fragments. The study of cfDNA in liquid biopsies has served clinical research greatly. Genetic analysis of these circulating fragments has been used in non-invasive prenatal testing, detection of graft rejection in organ transplants, and cancer detection and monitoring. cfDNA sequencing is, however, of limited value in settings in which genetic association is not well-established, such as most neurodegenerative diseases.Recent studies have taken advantage of the cell-type specificity of DNA methylation to determine the tissue of origin, thus detecting ongoing cell death taking place in specific body compartments. Such an approach is yet to be developed in the context of epilepsy research. In this article, we review the different approaches that have been used to monitor cell-type specific death through DNA methylation analysis, and recent data detecting neuronal death in neuropathological settings. We focus on the potential relevance of these tools in focal epilepsies, like Mesial Temporal Lobe Epilepsy with Hippocampal Sclerosis (MTLE-HS), characterized by severe neuronal loss. We speculate on the potential relevance of cfDNA methylation screening for the detection of neuronal cell death in individuals with high risk of epileptogenesis that would benefit from early diagnosis and consequent early treatment.
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Affiliation(s)
- Ricardo Martins-Ferreira
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
- Immunogenetics Lab, Molecular Pathology and Immunology, Instituto de Ciências Biomédicas Abel Salazar—Universidade do Porto (ICBAS-UPorto), Porto, Portugal
- Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - Bárbara Guerra Leal
- Immunogenetics Lab, Molecular Pathology and Immunology, Instituto de Ciências Biomédicas Abel Salazar—Universidade do Porto (ICBAS-UPorto), Porto, Portugal
- Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
- *Correspondence: Bárbara Guerra Leal
| | - Paulo Pinho Costa
- Immunogenetics Lab, Molecular Pathology and Immunology, Instituto de Ciências Biomédicas Abel Salazar—Universidade do Porto (ICBAS-UPorto), Porto, Portugal
- Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
- Instituto Nacional de Saúde Dr. Ricardo Jorge, Department of Human Genetics, Porto, Portugal
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