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de Souza HMR, Pereira TTP, de Sá HC, Alves MA, Garrett R, Canuto GAB. Critical Factors in Sample Collection and Preparation for Clinical Metabolomics of Underexplored Biological Specimens. Metabolites 2024; 14:36. [PMID: 38248839 PMCID: PMC10819689 DOI: 10.3390/metabo14010036] [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: 11/24/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
This review article compiles critical pre-analytical factors for sample collection and extraction of eight uncommon or underexplored biological specimens (human breast milk, ocular fluids, sebum, seminal plasma, sweat, hair, saliva, and cerebrospinal fluid) under the perspective of clinical metabolomics. These samples are interesting for metabolomics studies as they reflect the status of living organisms and can be applied for diagnostic purposes and biomarker discovery. Pre-collection and collection procedures are critical, requiring protocols to be standardized to avoid contamination and bias. Such procedures must consider cleaning the collection area, sample stimulation, diet, and food and drug intake, among other factors that impact the lack of homogeneity of the sample group. Precipitation of proteins and removal of salts and cell debris are the most used sample preparation procedures. This review intends to provide a global view of the practical aspects that most impact results, serving as a starting point for the designing of metabolomic experiments.
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Affiliation(s)
- Hygor M. R. de Souza
- Instituto de Química, Universidade Federal do Rio de Janeiro, LabMeta—LADETEC, Rio de Janeiro 21941-598, Brazil;
| | - Tássia T. P. Pereira
- Departamento de Genética, Ecologia e Evolucao, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil
| | - Hanna C. de Sá
- Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Salvador 40170-115, Brazil;
| | - Marina A. Alves
- Instituto de Pesquisa de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil;
| | - Rafael Garrett
- Instituto de Química, Universidade Federal do Rio de Janeiro, LabMeta—LADETEC, Rio de Janeiro 21941-598, Brazil;
- Department of Laboratory Medicine, Boston Children’s Hospital—Harvard Medical School, Boston, MA 02115, USA
| | - Gisele A. B. Canuto
- Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Salvador 40170-115, Brazil;
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Robinson O, Lau CE. How do metabolic processes age: Evidence from human metabolomic studies. Curr Opin Chem Biol 2023; 76:102360. [PMID: 37393706 DOI: 10.1016/j.cbpa.2023.102360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/16/2023] [Accepted: 06/06/2023] [Indexed: 07/04/2023]
Abstract
Metabolomics, the global profiling of small molecules in the body, has emerged as a promising analytical approach for assessing molecular changes associated with ageing at the population level. Understanding root metabolic ageing pathways may have important implications for managing age-related disease risk. In this short review, relevant studies published in the last few years that have made valuable contributions to this field will be discussed. These include large-scale studies investigating metabolic changes with age, metabolomic clocks, and metabolic pathways associated with ageing phenotypes. Recent significant advances include the use of longitudinal study designs, populations spanning the whole life course, standardised analytical platforms of enhanced metabolome coverage and development of multivariate analyses. While many challenges remain, recent studies have demonstrated the considerable promise of this field.
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Affiliation(s)
- Oliver Robinson
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, United Kingdom; Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, United Kingdom.
| | - ChungHo E Lau
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, United Kingdom
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Neutzner M, Kohler C, Frank S, Killer HE, Neutzner A. Impact of aging on meningeal gene expression. Fluids Barriers CNS 2023; 20:12. [PMID: 36747230 PMCID: PMC9903605 DOI: 10.1186/s12987-023-00412-9] [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: 11/07/2022] [Accepted: 01/25/2023] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The three-layered meninges cover and protect the central nervous system and form the interface between cerebrospinal fluid and the brain. They are host to a lymphatic system essential for maintaining fluid dynamics inside the cerebrospinal fluid-filled subarachnoid space and across the brain parenchyma via their connection to glymphatic structures. Meningeal fibroblasts lining and traversing the subarachnoid space have direct impact on the composition of the cerebrospinal fluid through endocytotic uptake as well as extensive protein secretion. In addition, the meninges are an active site for immunological processes and act as gatekeeper for immune cells entering the brain. During aging in mice, lymphatic drainage from the brain is less efficient contributing to neurodegenerative processes. Aging also affects the immunological status of the meninges, with increasing numbers of T cells, changing B cell make-up, and altered macrophage complement. METHODS We employed RNASeq to measure gene expression and to identify differentially expressed genes in meninges isolated from young and aged mice. Using Ingenuity pathway, GO term, and MeSH analyses, we identified regulatory pathways and cellular functions in meninges affected by aging. RESULTS Aging had profound impact on meningeal gene expression. Pathways related to innate as well as adaptive immunity were affected. We found evidence for increasing numbers of T and B lymphocytes and altered activity profiles for macrophages and other myeloid cells. Furthermore, expression of pro-inflammatory cytokine and chemokine genes increased with aging. Similarly, the complement system seemed to be more active in meninges of aged mice. Altered expression of solute carrier genes pointed to age-dependent changes in cerebrospinal fluid composition. In addition, gene expression for secreted proteins showed age-dependent changes, in particular, genes related to extracellular matrix composition and organization were affected. CONCLUSIONS Aging has profound effects on meningeal gene expression; thereby affecting the multifaceted functions meninges perform to maintain the homeostasis of the central nervous system. Thus, age-dependent neurodegenerative processes and cognitive decline are potentially in part driven by altered meningeal function.
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Affiliation(s)
- Melanie Neutzner
- grid.6612.30000 0004 1937 0642Department of Biomedicine, University Hospital Basel, University of Basel, Hebelstrasse 20, 4031 Basel, Switzerland
| | - Corina Kohler
- grid.6612.30000 0004 1937 0642Department of Biomedicine, University Hospital Basel, University of Basel, Hebelstrasse 20, 4031 Basel, Switzerland
| | - Stephan Frank
- grid.6612.30000 0004 1937 0642Department of Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Hanspeter E. Killer
- grid.6612.30000 0004 1937 0642Department of Biomedicine, University Hospital Basel, University of Basel, Hebelstrasse 20, 4031 Basel, Switzerland
| | - Albert Neutzner
- Department of Biomedicine, University Hospital Basel, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland.
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Panyard DJ, Yu B, Snyder MP. The metabolomics of human aging: Advances, challenges, and opportunities. SCIENCE ADVANCES 2022; 8:eadd6155. [PMID: 36260671 PMCID: PMC9581477 DOI: 10.1126/sciadv.add6155] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
As the global population becomes older, understanding the impact of aging on health and disease becomes paramount. Recent advancements in multiomic technology have allowed for the high-throughput molecular characterization of aging at the population level. Metabolomics studies that analyze the small molecules in the body can provide biological information across a diversity of aging processes. Here, we review the growing body of population-scale metabolomics research on aging in humans, identifying the major trends in the field, implicated biological pathways, and how these pathways relate to health and aging. We conclude by assessing the main challenges in the research to date, opportunities for advancing the field, and the outlook for precision health applications.
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Affiliation(s)
- Daniel J. Panyard
- Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
- Corresponding author. (D.J.P.); (M.P.S.)
| | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
- Corresponding author. (D.J.P.); (M.P.S.)
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Mehta NH, Suss RA, Dyke JP, Theise ND, Chiang GC, Strauss S, Saint-Louis L, Li Y, Pahlajani S, Babaria V, Glodzik L, Carare RO, de Leon MJ. Quantifying cerebrospinal fluid dynamics: A review of human neuroimaging contributions to CSF physiology and neurodegenerative disease. Neurobiol Dis 2022; 170:105776. [PMID: 35643187 PMCID: PMC9987579 DOI: 10.1016/j.nbd.2022.105776] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/21/2022] [Indexed: 01/13/2023] Open
Abstract
Cerebrospinal fluid (CSF), predominantly produced in the ventricles and circulating throughout the brain and spinal cord, is a key protective mechanism of the central nervous system (CNS). Physical cushioning, nutrient delivery, metabolic waste, including protein clearance, are key functions of the CSF in humans. CSF volume and flow dynamics regulate intracranial pressure and are fundamental to diagnosing disorders including normal pressure hydrocephalus, intracranial hypotension, CSF leaks, and possibly Alzheimer's disease (AD). The ability of CSF to clear normal and pathological proteins, such as amyloid-beta (Aβ), tau, alpha synuclein and others, implicates it production, circulation, and composition, in many neuropathologies. Several neuroimaging modalities have been developed to probe CSF fluid dynamics and better relate CSF volume and flow to anatomy and clinical conditions. Approaches include 2-photon microscopic techniques, MRI (tracer-based, gadolinium contrast, endogenous phase-contrast), and dynamic positron emission tomography (PET) using existing approved radiotracers. Here, we discuss CSF flow neuroimaging, from animal models to recent clinical-research advances, summarizing current endeavors to quantify and map CSF flow with implications towards pathophysiology, new biomarkers, and treatments of neurological diseases.
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Affiliation(s)
- Neel H Mehta
- Department of Biology, Cornell University, Ithaca, NY, USA
| | - Richard A Suss
- Division of Neuroradiology, Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan P Dyke
- Citigroup Biomedical Imaging Center, Weill Cornell Medicine, New York, NY, USA
| | - Neil D Theise
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Gloria C Chiang
- Division of Neuroradiology, Department of Radiology, Weill Cornell Medicine, New York, NY, USA
| | - Sara Strauss
- Division of Neuroradiology, Department of Radiology, Weill Cornell Medicine, New York, NY, USA
| | | | - Yi Li
- Brain Health Imaging Institute, Department of Radiology, Weill Cornell Medicine, New York, NY, USA
| | - Silky Pahlajani
- Brain Health Imaging Institute, Department of Radiology, Weill Cornell Medicine, New York, NY, USA
| | - Vivek Babaria
- Orange County Spine and Sports, Interventional Physiatry, Newport Beach, CA, USA
| | - Lidia Glodzik
- Brain Health Imaging Institute, Department of Radiology, Weill Cornell Medicine, New York, NY, USA
| | - Roxana O Carare
- Department of Medicine, University of Southampton, Southampton, UK
| | - Mony J de Leon
- Brain Health Imaging Institute, Department of Radiology, Weill Cornell Medicine, New York, NY, USA.
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