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Cornelli L, Van Paemel R, Ferro Dos Santos MR, Roelandt S, Willems L, Vandersteene J, Baert E, Mus LM, Van Roy N, De Wilde B, De Preter K. Diagnosis of pediatric central nervous system tumors using methylation profiling of cfDNA from cerebrospinal fluid. Clin Epigenetics 2024; 16:87. [PMID: 38970137 PMCID: PMC11225235 DOI: 10.1186/s13148-024-01696-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/17/2024] [Indexed: 07/07/2024] Open
Abstract
Pediatric central nervous system tumors remain challenging to diagnose. Imaging approaches do not provide sufficient detail to discriminate between different tumor types, while the histopathological examination of tumor tissue shows high inter-observer variability. Recent studies have demonstrated the accurate classification of central nervous system tumors based on the DNA methylation profile of a tumor biopsy. However, a brain biopsy holds significant risk of bleeding and damaging the surrounding tissues. Liquid biopsy approaches analyzing circulating tumor DNA show high potential as an alternative and less invasive tool to study the DNA methylation pattern of tumors. Here, we explore the potential of classifying pediatric brain tumors based on methylation profiling of the circulating cell-free DNA (cfDNA) in cerebrospinal fluid (CSF). For this proof-of-concept study, we collected cerebrospinal fluid samples from 19 pediatric brain cancer patients via a ventricular drain placed for reasons of increased intracranial pressure. Analyses on the cfDNA showed high variability of cfDNA quantities across patients ranging from levels below the limit of quantification to 40 ng cfDNA per milliliter of CSF. Classification based on methylation profiling of cfDNA from CSF was correct for 7 out of 20 samples in our cohort. Accurate results were mostly observed in samples of high quality, more specifically those with limited high molecular weight DNA contamination. Interestingly, we show that centrifugation of the CSF prior to processing increases the fraction of fragmented cfDNA to high molecular weight DNA. In addition, classification was mostly correct for samples with high tumoral cfDNA fraction as estimated by computational deconvolution (> 40%). In summary, analysis of cfDNA in the CSF shows potential as a tool for diagnosing pediatric nervous system tumors especially in patients with high levels of tumoral cfDNA in the CSF. Further optimization of the collection procedure, experimental workflow and bioinformatic approach is required to also allow classification for patients with low tumoral fractions in the CSF.
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Affiliation(s)
- Lotte Cornelli
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Ruben Van Paemel
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Maísa R Ferro Dos Santos
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Sofie Roelandt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Leen Willems
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | | | - Edward Baert
- Department of Neurosurgery, Ghent University Hospital, Ghent, Belgium
| | - Liselot M Mus
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Nadine Van Roy
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Bram De Wilde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.
- Cancer Research Institute Ghent, Ghent, Belgium.
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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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3
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Noushmehr H, Herrgott G, Morosini NS, Castro AV. Noninvasive approaches to detect methylation-based markers to monitor gliomas. Neurooncol Adv 2022; 4:ii22-ii32. [PMID: 36380867 PMCID: PMC9650474 DOI: 10.1093/noajnl/vdac021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023] Open
Abstract
In this review, we summarize the current approaches used to detect glioma tissue-derived DNA methylation markers in liquid biopsy specimens with the aim to diagnose, prognosticate and potentially track treatment response and evolution of patients with gliomas.
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Affiliation(s)
- Houtan Noushmehr
- Department of Neurosurgery, Omics Laboratory, Henry Ford Health System, Detroit, Michigan, USA
| | - Grayson Herrgott
- Department of Neurosurgery, Omics Laboratory, Henry Ford Health System, Detroit, Michigan, USA
| | - Natalia S Morosini
- Department of Neurosurgery, Omics Laboratory, Henry Ford Health System, Detroit, Michigan, USA
| | - Ana Valeria Castro
- Department of Neurosurgery, Omics Laboratory, Henry Ford Health System, Detroit, Michigan, USA
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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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Dai X, Shen L. Advances and Trends in Omics Technology Development. Front Med (Lausanne) 2022; 9:911861. [PMID: 35860739 PMCID: PMC9289742 DOI: 10.3389/fmed.2022.911861] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/09/2022] [Indexed: 12/11/2022] Open
Abstract
The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.
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Mair R, Mouliere F. Cell-free DNA technologies for the analysis of brain cancer. Br J Cancer 2022; 126:371-378. [PMID: 34811503 PMCID: PMC8811068 DOI: 10.1038/s41416-021-01594-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/07/2021] [Accepted: 10/06/2021] [Indexed: 11/08/2022] Open
Abstract
Survival for glioma patients has shown minimal improvement over the past 20 years. The ability to detect and monitor gliomas relies primarily upon imaging technologies that lack sensitivity and specificity, especially during the post-surgical treatment phase. Treatment-response monitoring with an effective liquid-biopsy paradigm may also provide the most facile clinical scenario for liquid-biopsy integration into brain-tumour care. Conceptually, liquid biopsy is advantageous when compared with both tissue sampling (less invasive) and imaging (more sensitive and specific), but is hampered by technical and biological problems. These problems predominantly relate to low concentrations of tumour-derived DNA in the bloodstream of glioma patients. In this review, we highlight methods by which the neuro-oncological scientific and clinical communities have attempted to circumvent this limitation. The use of novel biological, technological and computational approaches will be explored. The utility of alternate bio-fluids, tumour-guided sequencing, epigenomic and fragmentomic methods may eventually be leveraged to provide the biological and technological means to unlock a wide range of clinical applications for liquid biopsy in glioma.
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Affiliation(s)
- Richard Mair
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE, Cambridge, UK.
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE, Cambridge, UK.
- Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, CB2 0QQ, Cambridge, UK.
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, 1081 HV, Amsterdam, The Netherlands.
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