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Stolfi F, Abreu H, Sinella R, Nembrini S, Centonze S, Landra V, Brasso C, Cappellano G, Rocca P, Chiocchetti A. Omics approaches open new horizons in major depressive disorder: from biomarkers to precision medicine. Front Psychiatry 2024; 15:1422939. [PMID: 38938457 PMCID: PMC11210496 DOI: 10.3389/fpsyt.2024.1422939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 05/28/2024] [Indexed: 06/29/2024] Open
Abstract
Major depressive disorder (MDD) is a recurrent episodic mood disorder that represents the third leading cause of disability worldwide. In MDD, several factors can simultaneously contribute to its development, which complicates its diagnosis. According to practical guidelines, antidepressants are the first-line treatment for moderate to severe major depressive episodes. Traditional treatment strategies often follow a one-size-fits-all approach, resulting in suboptimal outcomes for many patients who fail to experience a response or recovery and develop the so-called "therapy-resistant depression". The high biological and clinical inter-variability within patients and the lack of robust biomarkers hinder the finding of specific therapeutic targets, contributing to the high treatment failure rates. In this frame, precision medicine, a paradigm that tailors medical interventions to individual characteristics, would help allocate the most adequate and effective treatment for each patient while minimizing its side effects. In particular, multi-omic studies may unveil the intricate interplays between genetic predispositions and exposure to environmental factors through the study of epigenomics, transcriptomics, proteomics, metabolomics, gut microbiomics, and immunomics. The integration of the flow of multi-omic information into molecular pathways may produce better outcomes than the current psychopharmacological approach, which targets singular molecular factors mainly related to the monoamine systems, disregarding the complex network of our organism. The concept of system biomedicine involves the integration and analysis of enormous datasets generated with different technologies, creating a "patient fingerprint", which defines the underlying biological mechanisms of every patient. This review, centered on precision medicine, explores the integration of multi-omic approaches as clinical tools for prediction in MDD at a single-patient level. It investigates how combining the existing technologies used for diagnostic, stratification, prognostic, and treatment-response biomarkers discovery with artificial intelligence can improve the assessment and treatment of MDD.
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Affiliation(s)
- Fabiola Stolfi
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Disease (CAAD), Università del Piemonte Orientale, Novara, Italy
| | - Hugo Abreu
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Disease (CAAD), Università del Piemonte Orientale, Novara, Italy
| | - Riccardo Sinella
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Disease (CAAD), Università del Piemonte Orientale, Novara, Italy
| | - Sara Nembrini
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Disease (CAAD), Università del Piemonte Orientale, Novara, Italy
| | - Sara Centonze
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Disease (CAAD), Università del Piemonte Orientale, Novara, Italy
| | - Virginia Landra
- Department of Neuroscience “Rita Levi Montalcini”, University of Turin, Turin, Italy
| | - Claudio Brasso
- Department of Neuroscience “Rita Levi Montalcini”, University of Turin, Turin, Italy
| | - Giuseppe Cappellano
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Disease (CAAD), Università del Piemonte Orientale, Novara, Italy
| | - Paola Rocca
- Department of Neuroscience “Rita Levi Montalcini”, University of Turin, Turin, Italy
| | - Annalisa Chiocchetti
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Disease (CAAD), Università del Piemonte Orientale, Novara, Italy
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Hachem M, Ahmmed MK, Nacir-Delord H. Phospholipidomics in Clinical Trials for Brain Disorders: Advancing our Understanding and Therapeutic Potentials. Mol Neurobiol 2024; 61:3272-3295. [PMID: 37981628 PMCID: PMC11087356 DOI: 10.1007/s12035-023-03793-y] [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: 05/19/2023] [Accepted: 10/31/2023] [Indexed: 11/21/2023]
Abstract
Phospholipidomics is a specialized branch of lipidomics that focuses on the characterization and quantification of phospholipids. By using sensitive analytical techniques, phospholipidomics enables researchers to better understand the metabolism and activities of phospholipids in brain disorders such as Alzheimer's and Parkinson's diseases. In the brain, identifying specific phospholipid biomarkers can offer valuable insights into the underlying molecular features and biochemistry of these diseases through a variety of sensitive analytical techniques. Phospholipidomics has emerged as a promising tool in clinical studies, with immense potential to advance our knowledge of neurological diseases and enhance diagnosis and treatment options for patients. In the present review paper, we discussed numerous applications of phospholipidomics tools in clinical studies, with a particular focus on the neurological field. By exploring phospholipids' functions in neurological diseases and the potential of phospholipidomics in clinical research, we provided valuable insights that could aid researchers and clinicians in harnessing the full prospective of this innovative practice and improve patient outcomes by providing more potent treatments for neurological diseases.
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Affiliation(s)
- Mayssa Hachem
- Department of Chemistry and Healthcare Engineering Innovation Center, Khalifa University of Sciences and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates.
| | - Mirja Kaizer Ahmmed
- Department of Fishing and Post-Harvest Technology, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Houda Nacir-Delord
- Department of Chemistry, Khalifa University of Sciences and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates
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Uras I, Karayel-Basar M, Sahin B, Baykal AT. Detection of early proteomic alterations in 5xFAD Alzheimer's disease neonatal mouse model via MALDI-MSI. Alzheimers Dement 2023; 19:4572-4589. [PMID: 36934297 DOI: 10.1002/alz.13008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 03/20/2023]
Abstract
Alzheimer's disease (AD) is a debilitating neurodegenerative disorder, characterized by memory deficit and dementia. AD is considered a multifactorial disorder where multiple processes like amyloid-beta and tau accumulation, axonal degeneration, synaptic plasticity, and autophagic processes plays an important role. In this study, the spatial proteomic differences in the neonatal 5xFAD brain tissue were investigated using MALDI-MSI coupled to LC-MS/MS, and the statistically significantly altered proteins were associated with AD. Thirty-five differentially expressed proteins (DEPs) between the brain tissues of neonatal 5xFAD and their littermate mice were detected via MALDI-MSI technique. Among the 35 proteins identified, 26 of them were directly associated with AD. Our results indicated a remarkable resemblance in the protein expression profiles of neonatal 5xFAD brain when compared to AD patient specimens or AD mouse models. These findings showed that the molecular alterations in the AD brain existed even at birth and that some proteins are neurodegenerative presages in neonatal AD brain. HIGHLIGHTS: Spatial proteomic alterations in the 5xFAD mouse brain compared to the littermate. 26 out of 35 differentially expressed proteins associated with Alzheimer's disease (AD). Molecular alterations and neurodegenerative presages in neonatal AD brain. Alterations in the synaptic function an early and common neurobiological thread.
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Affiliation(s)
- Irep Uras
- Department of Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Merve Karayel-Basar
- Department of Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Betul Sahin
- Acibadem Labmed Clinical Laboratories, Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
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Zhou Y, Jiang X, Wang X, Huang J, Li T, Jin H, He J. Promise of spatially resolved omics for tumor research. J Pharm Anal 2023; 13:851-861. [PMID: 37719191 PMCID: PMC10499658 DOI: 10.1016/j.jpha.2023.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 09/19/2023] Open
Abstract
Tumors are spatially heterogeneous tissues that comprise numerous cell types with intricate structures. By interacting with the microenvironment, tumor cells undergo dynamic changes in gene expression and metabolism, resulting in spatiotemporal variations in their capacity for proliferation and metastasis. In recent years, the rapid development of histological techniques has enabled efficient and high-throughput biomolecule analysis. By preserving location information while obtaining a large number of gene and molecular data, spatially resolved metabolomics (SRM) and spatially resolved transcriptomics (SRT) approaches can offer new ideas and reliable tools for the in-depth study of tumors. This review provides a comprehensive introduction and summary of the fundamental principles and research methods used for SRM and SRT techniques, as well as a review of their applications in cancer-related fields.
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Affiliation(s)
- Yanhe Zhou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xinyi Jiang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xiangyi Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jianpeng Huang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Tong Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Hongtao Jin
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Beijing, 10050, China
| | - Jiuming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
- NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Beijing, 10050, China
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Cappuccio G, Khalil SM, Osenberg S, Li F, Maletic-Savatic M. Mass spectrometry imaging as an emerging tool for studying metabolism in human brain organoids. Front Mol Biosci 2023; 10:1181965. [PMID: 37304070 PMCID: PMC10251497 DOI: 10.3389/fmolb.2023.1181965] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
Human brain organoids are emerging models to study human brain development and pathology as they recapitulate the development and characteristics of major neural cell types, and enable manipulation through an in vitro system. Over the past decade, with the advent of spatial technologies, mass spectrometry imaging (MSI) has become a prominent tool for metabolic microscopy, providing label-free, non-targeted molecular and spatial distribution information of the metabolites within tissue, including lipids. This technology has never been used for studies of brain organoids and here, we set out to develop a standardized protocol for preparation and mass spectrometry imaging of human brain organoids. We present an optimized and validated sample preparation protocol, including sample fixation, optimal embedding solution, homogenous deposition of matrices, data acquisition and processing to maximize the molecular information derived from mass spectrometry imaging. We focus on lipids in organoids, as they play critical roles during cellular and brain development. Using high spatial and mass resolution in positive- and negative-ion modes, we detected 260 lipids in the organoids. Seven of them were uniquely localized within the neurogenic niches or rosettes as confirmed by histology, suggesting their importance for neuroprogenitor proliferation. We observed a particularly striking distribution of ceramide-phosphoethanolamine CerPE 36:1; O2 which was restricted within rosettes and of phosphatidyl-ethanolamine PE 38:3, which was distributed throughout the organoid tissue but not in rosettes. This suggests that ceramide in this particular lipid species might be important for neuroprogenitor biology, while its removal may be important for terminal differentiation of their progeny. Overall, our study establishes the first optimized experimental pipeline and data processing strategy for mass spectrometry imaging of human brain organoids, allowing direct comparison of lipid signal intensities and distributions in these tissues. Further, our data shed new light on the complex processes that govern brain development by identifying specific lipid signatures that may play a role in cell fate trajectories. Mass spectrometry imaging thus has great potential in advancing our understanding of early brain development as well as disease modeling and drug discovery.
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Affiliation(s)
- Gerarda Cappuccio
- Department of Pediatrics–Neurology, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
| | - Saleh M. Khalil
- Department of Pediatrics–Neurology, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
| | - Sivan Osenberg
- Department of Pediatrics–Neurology, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
| | - Feng Li
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, United States
| | - Mirjana Maletic-Savatic
- Department of Pediatrics–Neurology, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
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Brožová K, Hantusch B, Kenner L, Kratochwill K. Spatial Proteomics for the Molecular Characterization of Breast Cancer. Proteomes 2023; 11:17. [PMID: 37218922 PMCID: PMC10204503 DOI: 10.3390/proteomes11020017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/30/2023] [Accepted: 04/23/2023] [Indexed: 05/24/2023] Open
Abstract
Breast cancer (BC) is a major global health issue, affecting a significant proportion of the female population and contributing to high rates of mortality. One of the primary challenges in the treatment of BC is the disease's heterogeneity, which can lead to ineffective therapies and poor patient outcomes. Spatial proteomics, which involves the study of protein localization within cells, offers a promising approach for understanding the biological processes that contribute to cellular heterogeneity within BC tissue. To fully leverage the potential of spatial proteomics, it is critical to identify early diagnostic biomarkers and therapeutic targets, and to understand protein expression levels and modifications. The subcellular localization of proteins is a key factor in their physiological function, making the study of subcellular localization a major challenge in cell biology. Achieving high resolution at the cellular and subcellular level is essential for obtaining an accurate spatial distribution of proteins, which in turn can enable the application of proteomics in clinical research. In this review, we present a comparison of current methods of spatial proteomics in BC, including untargeted and targeted strategies. Untargeted strategies enable the detection and analysis of proteins and peptides without a predetermined molecular focus, whereas targeted strategies allow the investigation of a predefined set of proteins or peptides of interest, overcoming the limitations associated with the stochastic nature of untargeted proteomics. By directly comparing these methods, we aim to provide insights into their strengths and limitations and their potential applications in BC research.
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Affiliation(s)
- Klára Brožová
- Core Facility Proteomics, Medical University of Vienna, 1090 Vienna, Austria
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
- Division of Molecular and Structural Preclinical Imaging, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1210 Vienna, Austria
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine, 1090 Vienna, Austria
| | - Brigitte Hantusch
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
| | - Lukas Kenner
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine, 1090 Vienna, Austria
- CBmed GmbH—Center for Biomarker Research in Medicine, 8010 Graz, Austria
- Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna, 1090 Vienna, Austria
| | - Klaus Kratochwill
- Core Facility Proteomics, Medical University of Vienna, 1090 Vienna, Austria
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
- Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
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Investigation of Phospholipid Differences in Valproic Acid-Induced Autistic Mouse Model Brain Using Mass Spectrometry Imaging. Metabolites 2023; 13:metabo13020178. [PMID: 36837796 PMCID: PMC9966147 DOI: 10.3390/metabo13020178] [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: 12/26/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
Autism is a neurodevelopmental disorder for which the cause and treatment have yet not been determined. The polyunsaturated fatty acid (PUFA) levels change rapidly in the blood or cerebrospinal fluid of autistic children and PUFAs are closely related to autism spectrum disorder (ASD). This finding suggests that changes in lipid metabolism are associated with ASD and result in an altered distribution of phospholipids in cell membranes. To further understand ASD, it is necessary to analyze phospholipids in organs consisting of nerve cells, such as the brain. In this study, we investigated the phospholipid distribution in the brain tissue of valproic acid-induced autistic mice using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Phospholipids including phosphatidylcholine, phosphatidylethanolamine, and phosphatidylserine were identified in each brain region and exhibited differences between the ASD and control groups. These phospholipids contain docosahexaenoic acid and arachidonic acid, which are important PUFAs for cell signaling and brain growth. We expect that the differences in phospholipids identified in the brain tissue of the ASD model with MALDI-MSI, in conjunction with conventional biological fluid analysis, will help to better understand changes in lipid metabolism in ASD.
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Hristova J, Svinarov D. Enhancing precision medicine through clinical mass spectrometry platform. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2053342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Julieta Hristova
- Alexander University Hospital, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Dobrin Svinarov
- Alexander University Hospital, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
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9
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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Bokhari RS, Beheshti A, Blutt SE, Bowles DE, Brenner D, Britton R, Bronk L, Cao X, Chatterjee A, Clay DE, Courtney C, Fox DT, Gaber MW, Gerecht S, Grabham P, Grosshans D, Guan F, Jezuit EA, Kirsch DG, Liu Z, Maletic-Savatic M, Miller KM, Montague RA, Nagpal P, Osenberg S, Parkitny L, Pierce NA, Porada C, Rosenberg SM, Sargunas P, Sharma S, Spangler J, Tavakol DN, Thomas D, Vunjak-Novakovic G, Wang C, Whitcomb L, Young DW, Donoviel D. Looking on the horizon; potential and unique approaches to developing radiation countermeasures for deep space travel. LIFE SCIENCES IN SPACE RESEARCH 2022; 35:105-112. [PMID: 36336356 DOI: 10.1016/j.lssr.2022.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/29/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023]
Abstract
Future lunar missions and beyond will require new and innovative approaches to radiation countermeasures. The Translational Research Institute for Space Health (TRISH) is focused on identifying and supporting unique approaches to reduce risks to human health and performance on future missions beyond low Earth orbit. This paper will describe three funded and complementary avenues for reducing the risk to humans from radiation exposure experienced in deep space. The first focus is on identifying new therapeutic targets to reduce the damaging effects of radiation by focusing on high throughput genetic screens in accessible, sometimes called lower, organism models. The second focus is to design innovative approaches for countermeasure development with special attention to nucleotide-based methodologies that may constitute a more agile way to design therapeutics. The final focus is to develop new and innovative ways to test radiation countermeasures in a human model system. While animal studies continue to be beneficial in the study of space radiation, they can have imperfect translation to humans. The use of three-dimensional (3D) complex in vitro models is a promising approach to aid the development of new countermeasures and personalized assessments of radiation risks. These three distinct and unique approaches complement traditional space radiation efforts and should provide future space explorers with more options to safeguard their short and long-term health.
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Affiliation(s)
- Rihana S Bokhari
- Agile Decision Sciences, NRESS, Arlington, VA 22202, United States of America.
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, United States of America; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States of America
| | - Sarah E Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States of America; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States of America
| | - Dawn E Bowles
- Division of Surgical Sciences, Department of Surgery, Duke University, Durham NC, United States of America
| | - David Brenner
- Columbia University, New York, NY, 10027, United States of America
| | - Robert Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States of America
| | - Lawrence Bronk
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States of America
| | - Xu Cao
- Stanford University School of Medicine, Stanford, CA 94305, United States of America
| | - Anushree Chatterjee
- Sachi Bioworks, Louisville, CO 80027, United States of America; University of Colorado Boulder, Boulder, CO 80303, United States of America
| | - Delisa E Clay
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, United States of America
| | | | - Donald T Fox
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, United States of America
| | - M Waleed Gaber
- Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States of America
| | - Sharon Gerecht
- Chemical and Biomolecular Engineering and Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218 United States of America; Biomedical Engineering, Duke University, Durham, NC 27708, United States of America
| | - Peter Grabham
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University, New York, NY 10027 United States of America
| | - David Grosshans
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States of America
| | - Fada Guan
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States of America
| | - Erin A Jezuit
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, United States of America
| | - David G Kirsch
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, United States of America
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States of America; Jan and Dan Duncan Neurological Research Institute, 1250 Moursund St. Houston, TX 77030, United States of America
| | - Mirjana Maletic-Savatic
- Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States of America; Jan and Dan Duncan Neurological Research Institute, 1250 Moursund St. Houston, TX 77030, United States of America
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas, Austin, TX 78712, United States of America
| | - Ruth A Montague
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, United States of America
| | - Prashant Nagpal
- Sachi Bioworks, Louisville, CO 80027, United States of America
| | - Sivan Osenberg
- Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States of America; Jan and Dan Duncan Neurological Research Institute, 1250 Moursund St. Houston, TX 77030, United States of America
| | - Luke Parkitny
- Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States of America; Jan and Dan Duncan Neurological Research Institute, 1250 Moursund St. Houston, TX 77030, United States of America
| | - Niles A Pierce
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States of America; Division of Engineering & Applied Science, California Institute of Technology, Pasadena, CA 91125, United States of America; Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Christopher Porada
- Wake Forest Institute for Regenerative Medicine, Fetal Research and Therapy Program Wake Forest School of Medicine, Winston-Salem, NC 27157, United States of America
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77303, United States of America; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77303, United States of America; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77303, United States of America; Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77303, United States of America
| | - Paul Sargunas
- Chemical and Biomolecular Engineering and Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218 United States of America
| | - Sadhana Sharma
- Sachi Bioworks, Louisville, CO 80027, United States of America
| | - Jamie Spangler
- Chemical and Biomolecular Engineering and Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218 United States of America
| | | | - Dilip Thomas
- Stanford University School of Medicine, Stanford, CA 94305, United States of America
| | | | - Chunbo Wang
- Division of Surgical Sciences, Department of Surgery, Duke University, Durham NC, United States of America
| | - Luke Whitcomb
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, United States of America
| | - Damian W Young
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, United States of America
| | - Dorit Donoviel
- Translational Research Institute for Space Health, Houston, TX 77030, United States of America; Center for Space Medicine, Baylor College of Medicine, Houston, TX 77030, United States of America.
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11
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Chen D, Bu XM, Zhang MY, Xu XL, Wang B, Gan YM, Li KX, Xu X, Han J, Shi N. On-tissue pyrene-1-boronic acid labeling assisted MALDI imaging of catecholamines in porcine adrenal gland. J Chromatogr A 2022; 1678:463361. [PMID: 35914408 DOI: 10.1016/j.chroma.2022.463361] [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: 05/01/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 10/16/2022]
Abstract
In this study, an on-tissue chemical labeling - matrix assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) method was developed for visualization of the distribution of three catecholamine (CA) compounds (dopamine, epinephrine and norepinephrine) in porcine adrenal gland. Commercially available pyrene-1-boronic acid (PBA) was employed as an effective in situ derivatizing reagent dissolved in acetonitrile containing 0.1% pyridine for the chemical labeling and the matrix coating. Without extra matrix coating, the tissue section was directly analyzed by MALDI-MS. The detection specificity and sensitivity were greatly improved with the on-tissue PBA labeling and successful imaging of the three CAs in porcine adrenal gland was achieved. Compared with previously reported methods for MALDI-MSI of the CAs, the analytical strategy proposed in the study provided a robust, easy-to-use and low-cost on-tissue chemical derivatization method that facilitated simultaneous molecular imaging of the three compounds.
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Affiliation(s)
- Di Chen
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Xin-Miao Bu
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Man-Yu Zhang
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Xin-Li Xu
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Bin Wang
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Yu-Mei Gan
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Kai-Xuan Li
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Xia Xu
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases of Henan Province; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China.
| | - Jun Han
- University of Victoria - Genome British Columbia Proteomics Centre, Victoria, BC V8Z 7X8, Canada; Division of Medical Sciences, University of Victoria, Victoria, BC V8P 5C2, Canada.
| | - Nian Shi
- Physics Diagnostic Division, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China.
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12
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Spruill ML, Maletic-Savatic M, Martin H, Li F, Liu X. Spatial analysis of drug absorption, distribution, metabolism, and toxicology using mass spectrometry imaging. Biochem Pharmacol 2022; 201:115080. [PMID: 35561842 PMCID: PMC9744413 DOI: 10.1016/j.bcp.2022.115080] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 12/14/2022]
Abstract
Mass spectrometry imaging (MSI) is emerging as a powerful analytical tool for detection, quantification, and simultaneous spatial molecular imaging of endogenous and exogenous molecules via in situ mass spectrometry analysis of thin tissue sections without the requirement of chemical labeling. The MSI generates chemically specific and spatially resolved ion distribution information for administered drugs and metabolites, which allows numerous applications for studies involving various stages of drug absorption, distribution, metabolism, excretion, and toxicity (ADMET). MSI-based pharmacokinetic imaging analysis provides a histological context and cellular environment regarding dynamic drug distribution and metabolism processes, and facilitates the understanding of the spatial pharmacokinetics and pharmacodynamic properties of drugs. Herein, we discuss the MSI's current technological developments that offer qualitative, quantitative, and spatial location information of small molecule drugs, antibody, and oligonucleotides macromolecule drugs, and their metabolites in preclinical and clinical tissue specimens. We highlight the macro and micro drug-distribution in the whole-body, brain, lung, liver, kidney, stomach, intestine tissue sections, organoids, and the latest applications of MSI in pharmaceutical ADMET studies.
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Affiliation(s)
- Michelle L Spruill
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, USA
| | - Mirjana Maletic-Savatic
- Department of Pediatrics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | | | - Feng Li
- Center for Drug Discovery and Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA; NMR and Drug Metabolism Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Xinli Liu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, USA.
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13
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Han X, Gross RW. The foundations and development of lipidomics. J Lipid Res 2022; 63:100164. [PMID: 34953866 PMCID: PMC8953652 DOI: 10.1016/j.jlr.2021.100164] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/15/2022] Open
Abstract
For over a century, the importance of lipid metabolism in biology was recognized but difficult to mechanistically understand due to the lack of sensitive and robust technologies for identification and quantification of lipid molecular species. The enabling technological breakthroughs emerged in the 1980s with the development of soft ionization methods (Electrospray Ionization and Matrix Assisted Laser Desorption/Ionization) that could identify and quantify intact individual lipid molecular species. These soft ionization technologies laid the foundations for what was to be later named the field of lipidomics. Further innovative advances in multistage fragmentation, dramatic improvements in resolution and mass accuracy, and multiplexed sample analysis fueled the early growth of lipidomics through the early 1990s. The field exponentially grew through the use of a variety of strategic approaches, which included direct infusion, chromatographic separation, and charge-switch derivatization, which facilitated access to the low abundance species of the lipidome. In this Thematic Review, we provide a broad perspective of the foundations, enabling advances, and predicted future directions of growth of the lipidomics field.
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Affiliation(s)
- Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA; Departments of Medicine - Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - Richard W Gross
- Division of Bioorganic Chemistry and Molecular Pharmacology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Chemistry, Washington University, St. Louis, MO, USA
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14
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Agrawal I, Tripathi P, Biswas S. Mass Spectrometry Based Protein Biomarkers and Drug Target Discovery and Clinical Diagnosis in Age-Related Progressing Neurodegenerative Diseases. Drug Metab Rev 2022; 54:22-36. [PMID: 35038284 DOI: 10.1080/03602532.2022.2029475] [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: 12/30/2022]
Abstract
Neurodegenerative diseases correspond to overly complex health disorders that are driven by intersecting pathophysiology that are often trapped in vicious cycles of degeneration and cognitive decline. The usual diagnostic route of these diseases is based on postmortem examination that involves identifying pathology that is specific to the disease in the brain. However, in such cases, accurate diagnosis of the specific disease is limited because clinical disease presentations are often complex that do not easily allow to discriminate patient's cognitive, behavioral, and functional impairment profiles. Additionally, an early identification and therapeutic intervention of these diseases is pivotal to slow the progression of neurodegeneration and extend healthy life span. Mass spectrometry-based techniques have proven to be hugely promising in biological sample analysis and discovery of biomarkers including protein and peptide biomarkers for potential drug target discovery. Recent studies on these biomarkers have demonstrated their potential for applications in early diagnostics and identifying therapeutic targets to battle against neurodegenerative diseases. In this review, we have presented principles of mass spectrometry (MS) and the associated workflows in analyzing and imaging biological samples for discovery of biomarkers. We have especially focused on age- related progressing neurodegenerative diseases such as Alzheimer's (AD) and Parkinson's disease (PD), Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal dementia (FTD) and the related MS-based biomarkers developments for these diseases. Finally, we present a future perspective discussing the potential research directions ahead.
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Affiliation(s)
- Ishita Agrawal
- Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Pallavi Tripathi
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK
| | - Shyamasri Biswas
- USA Prime Biotech LLC, 1330 NW 6th St., Suite A-2, Gainesville, FL 32601, USA
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15
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Schnackenberg LK, Thorn DA, Barnette D, Jones EE. MALDI imaging mass spectrometry: an emerging tool in neurology. Metab Brain Dis 2022; 37:105-121. [PMID: 34347208 DOI: 10.1007/s11011-021-00797-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/11/2021] [Indexed: 12/24/2022]
Abstract
Neurological disease and disorders remain a large public health threat. Thus, research to improve early detection and/or develop more effective treatment approaches are necessary. Although there are many common techniques and imaging modalities utilized to study these diseases, existing approaches often require a label which can be costly and time consuming. Matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) is a label-free, innovative and emerging technique that produces 2D ion density maps representing the distribution of an analyte(s) across a tissue section in relation to tissue histopathology. One main advantage of MALDI IMS over other imaging modalities is its ability to determine the spatial distribution of hundreds of analytes within a single imaging run, without the need for a label or any a priori knowledge. Within the field of neurology and disease there have been several impactful studies in which MALDI IMS has been utilized to better understand the cellular pathology of the disease and or severity. Furthermore, MALDI IMS has made it possible to map specific classes of analytes to regions of the brain that otherwise may have been lost using more traditional methods. This review will highlight key studies that demonstrate the potential of this technology to elucidate previously unknown phenomenon in neurological disease.
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Affiliation(s)
- Laura K Schnackenberg
- Division of Systems Biology, National Center for Toxicological Research/FDA, 3900 NCTR Rd, Jefferson, AR, USA
| | - David A Thorn
- Division of Systems Biology, National Center for Toxicological Research/FDA, 3900 NCTR Rd, Jefferson, AR, USA
| | - Dustyn Barnette
- Division of Systems Biology, National Center for Toxicological Research/FDA, 3900 NCTR Rd, Jefferson, AR, USA
| | - E Ellen Jones
- Division of Systems Biology, National Center for Toxicological Research/FDA, 3900 NCTR Rd, Jefferson, AR, USA.
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16
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Recent Advances of Ambient Mass Spectrometry Imaging and Its Applications in Lipid and Metabolite Analysis. Metabolites 2021; 11:metabo11110780. [PMID: 34822438 PMCID: PMC8625079 DOI: 10.3390/metabo11110780] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 01/02/2023] Open
Abstract
Ambient mass spectrometry imaging (AMSI) has attracted much attention in recent years. As a kind of unlabeled molecular imaging technique, AMSI can enable in situ visualization of a large number of compounds in biological tissue sections in ambient conditions. In this review, the developments of various AMSI techniques are discussed according to one-step and two-step ionization strategies. In addition, recent applications of AMSI for lipid and metabolite analysis (from 2016 to 2021) in disease diagnosis, animal model research, plant science, drug metabolism and toxicology research, etc., are summarized. Finally, further perspectives of AMSI in spatial resolution, sensitivity, quantitative ability, convenience and software development are proposed.
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17
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Francischini DS, Arruda MA. When a picture is worth a thousand words: Molecular and elemental imaging applied to environmental analysis – A review. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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18
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Taira S, Kiriake‐Yoshinaga A, Shikano H, Ikeda R, Kobayashi S, Yoshinaga K. Localization analysis of essential oils in perilla herb ( Perilla frutescens var. crispa) using derivatized mass spectrometry imaging. Food Sci Nutr 2021; 9:2779-2784. [PMID: 34026091 PMCID: PMC8116838 DOI: 10.1002/fsn3.2232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/24/2021] [Accepted: 02/27/2021] [Indexed: 11/10/2022] Open
Abstract
The localization of essential oils, including flavor components, in perilla herb (Perilla frutescens var. crispa) were visually determined using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) imaging. The surface of a perilla leaf was peeled using a cyanoacrylate adhesion compound and contained oil glands that retained their morphology and chemical properties. We imaged the three essential oils perillaldehyde, β-caryophyllene, and rosmarinic acid (RA). Perillaldehyde was derivatized using glycine to prevent evaporation and allow its detection and imaging while localized in oil glands. β-caryophyllene also localized in the oil glands and not in the epidermis region. RA was detected throughout the leaf, including the oil glands. Quantitative data for the three essential oils were obtained by gas chromatography- or liquid chromatography-MS. The concentrations of perillaldehyde, β-caryophyllene, and RA were 12.6 ± 0.62, 0.27 ± 0.02, and 0.16 ± 0.02 [mg/g] in the paste sample of perilla herb. Peeling using a cyanoacrylate adhesion compound, and derivatization of a target such as an aroma component have great potential for mass spectrometry imaging for multiple essential oils.
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Affiliation(s)
- Shu Taira
- Faculty of Food and Agricultural SciencesFukushima UniversityFukushimaJapan
| | | | - Hitomi Shikano
- Faculty of Food and Agricultural SciencesFukushima UniversityFukushimaJapan
| | - Ryuzoh Ikeda
- Faculty of Food and Agricultural SciencesFukushima UniversityFukushimaJapan
| | - Shoko Kobayashi
- Research Center for Food SafetyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Kazuaki Yoshinaga
- Faculty of Food and Agricultural SciencesFukushima UniversityFukushimaJapan
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19
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Mechanistic Insights into Alzheimer's Disease Unveiled through the Investigation of Disturbances in Central Metabolites and Metabolic Pathways. Biomedicines 2021; 9:biomedicines9030298. [PMID: 33799385 PMCID: PMC7998757 DOI: 10.3390/biomedicines9030298] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 11/17/2022] Open
Abstract
Hydrophilic metabolites are closely involved in multiple primary metabolic pathways and, consequently, play an essential role in the onset and progression of multifactorial human disorders, such as Alzheimer’s disease. This review article provides a comprehensive revision of the literature published on the use of mass spectrometry-based metabolomics platforms for approaching the central metabolome in Alzheimer’s disease research, including direct mass spectrometry, gas chromatography-mass spectrometry, hydrophilic interaction liquid chromatography-mass spectrometry, and capillary electrophoresis-mass spectrometry. Overall, mounting evidence points to profound disturbances that affect a multitude of central metabolic pathways, such as the energy-related metabolism, the urea cycle, the homeostasis of amino acids, fatty acids and nucleotides, neurotransmission, and others.
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20
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Saigusa D, Matsukawa N, Hishinuma E, Koshiba S. Identification of biomarkers to diagnose diseases and find adverse drug reactions by metabolomics. Drug Metab Pharmacokinet 2020; 37:100373. [PMID: 33631535 DOI: 10.1016/j.dmpk.2020.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022]
Abstract
Metabolomics has been widely used for investigating the biological functions of disease expression and has the potential to discover biomarkers in circulating biofluids or tissue extracts that reflect in phenotypic changes. Metabolic profiling has advantages because of the use of unbiased techniques, including multivariate analysis, and has been applied in pharmacological studies to predict therapeutic and adverse reactions of drugs, which is called pharmacometabolomics (PMx). Nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based metabolomics has contributed to the discovery of recent disease biomarkers; however, the optimal strategy for the study purpose must be selected from many established protocols, methodologies and analytical platforms. Additionally, information on molecular localization in tissue is essential for further functional analyses related to therapeutic and adverse effects of drugs in the process of drug development. MS imaging (MSI) is a promising technology that can visualize molecules on tissue surfaces without labeling and thus provide localized information. This review summarizes recent uses of MS-based global and wide-targeted metabolomics technologies and the advantages of the MSI approach for PMx and highlights the PMx technique for the biomarker discovery of adverse drug effects.
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Affiliation(s)
- Daisuke Saigusa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
| | - Naomi Matsukawa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
| | - Eiji Hishinuma
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
| | - Seizo Koshiba
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
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21
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Metabolomic and Imaging Mass Spectrometric Assays of Labile Brain Metabolites: Critical Importance of Brain Harvest Procedures. Neurochem Res 2020; 45:2586-2606. [PMID: 32949339 DOI: 10.1007/s11064-020-03124-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/29/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022]
Abstract
Metabolomic technologies including imaging mass spectrometry (IMS; also called mass spectrometry imaging, MSI, or matrix-assisted laser desorption/ionization-mass spectrometry imaging, MALDI MSI) are important methods to evaluate levels of many compounds in brain with high spatial resolution, characterize metabolic phenotypes of brain disorders, and identify disease biomarkers. ATP is central to brain energetics, and reports of its heterogeneous distribution in brain and regional differences in ATP/ADP ratios reported in IMS studies conflict with earlier studies. These discordant data were, therefore, analyzed and compared with biochemical literature that used rigorous methods to preserve labile metabolites. Unequal, very low regional ATP levels and low ATP/ADP ratios are explained by rapid metabolism during postmortem ischemia. A critical aspect of any analysis of brain components is their stability during and after tissue harvest so measured concentrations closely approximate their physiological levels in vivo. Unfortunately, the requirement for inactivation of brain enzymes by freezing or heating is not widely recognized outside the neurochemistry discipline, and procedures that do not prevent postmortem autolysis, including decapitation, brain removal/dissection, and 'snap freezing' are commonly used. Strong emphasis is placed on use of supplementary approaches to calibrate metabolite abundance in units of concentration in IMS studies and comparison of IMS results with biochemical data obtained by different methods to help identify potential artifacts.
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22
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Lipidomic UPLC-MS/MS Profiles of Normal-Appearing White Matter Differentiate Primary and Secondary Progressive Multiple Sclerosis. Metabolites 2020; 10:metabo10090366. [PMID: 32911763 PMCID: PMC7569864 DOI: 10.3390/metabo10090366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 09/07/2020] [Indexed: 01/20/2023] Open
Abstract
Multiple sclerosis (MS) is a neurodegenerative inflammatory disease where an autoimmune response to components of the central nervous system leads to a loss of myelin and subsequent neurological deterioration. People with MS can develop primary or secondary progressive disease (PPMS, SPMS) and differentiation of the specific differences in the pathogenesis of these two courses, at the molecular level, is currently unclear. Recently, lipidomics studies using human biofluids, mainly plasma and cerebrospinal fluid, have highlighted a possible role for lipids in the initiation and progression of MS. However, there is a lack of lipidomics studies in MS on CNS tissues, such as normal-appearing white matter (NAWM), where local inflammation initially occurs. Herein, we developed an untargeted reverse phase ultra-performance liquid chromatography time of flight tandem mass spectrometry (RP-UPLC-TOF MSE)-based workflow, in combination with multivariate and univariate statistical analysis, to assess significant differences in lipid profiles in brain NAWM from post-mortem cases of PPMS, SPMS and controls. Groups of eight control, nine PPMS and seven SPMS NAWM samples were used. Correlation analysis of the identified lipids by RP-UPLC-TOF MSE was undertaken to remove those lipids that correlated with age, gender and post-mortem interval as confounding factors. We demonstrate that there is a significantly altered lipid profile of control cases compared with MS cases and that progressive disease, PPMS and SPMS, can be differentiated on the basis of the lipidome of NAWM with good sensitivity, specificity and prediction accuracy based on receiver operating characteristic (ROC) curve analysis. Metabolic pathway analysis revealed that the most altered lipid pathways between PPMS and SPMS were glycerophospholipid metabolism, glycerophosphatidyl inositol (GPI) anchor synthesis and linoleic acid metabolism. Further understanding of the impact of these lipid alterations described herein associated with progression will provide an increased understanding of the mechanisms underpinning progression and highlight possible new therapeutic targets.
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23
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Islam A, Takeyama E, Mamun MA, Sato T, Horikawa M, Takahashi Y, Kikushima K, Setou M. Green Nut Oil or DHA Supplementation Restored Decreased Distribution Levels of DHA Containing Phosphatidylcholines in the Brain of a Mouse Model of Dementia. Metabolites 2020; 10:metabo10040153. [PMID: 32316172 PMCID: PMC7240946 DOI: 10.3390/metabo10040153] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/10/2020] [Accepted: 04/14/2020] [Indexed: 02/06/2023] Open
Abstract
Dementia is a major public health concern nowadays. Reduced levels of brain docosahexaenoic acid (DHA) and DHA-phosphatidylcholines (DHA-PCs) in dementia patients were reported previously. Recently, we have reported that supplementation of green nut oil (GNO) or DHA improves memory function and distribution levels of brain DHA in senescence accelerated mice P8 (SAMP8). GNO is extracted from Plukenetia volubilis seeds, and SAMP8 is a well-known model mouse of dementia. In this current study, we examined the results of GNO or DHA supplementation in the distribution levels of brain DHA-PCs in same model mouse of dementia using desorption electrospray ionization (DESI) mass spectrometry imaging (MSI). We observed significantly decreased distribution of brain DHA-PCs, PC (16:0_22:6), and PC (18:0_22:6) in SAMP8 mice compared to wild type mice, and GNO or DHA treatment restored the decreased distribution levels of PC (16:0_22:6) and PC (18:0_22:6) in the brain of SAMP8 mice. These results indicate that GNO or DHA supplementation can ameliorate the decreased distribution of brain DHA-PCs in dementia, and could be potentially used for the prevention and treatment of dementia.
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Affiliation(s)
- Ariful Islam
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; (A.I.); (M.A.M.); (T.S.); (M.H.); (Y.T.); (K.K.)
| | - Emiko Takeyama
- Department of Food Science and Nutrition, Graduate School of Human Life Sciences, Showa Women’s University, Taishido, Setagaya-ku, Tokyo 154-8533, Japan;
- Institute of Women’s Health Sciences, Showa Women’s University, Taishido, Setagaya-ku, Tokyo 154-8533, Japan
| | - Md. Al Mamun
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; (A.I.); (M.A.M.); (T.S.); (M.H.); (Y.T.); (K.K.)
| | - Tomohito Sato
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; (A.I.); (M.A.M.); (T.S.); (M.H.); (Y.T.); (K.K.)
- International Mass Imaging Center, Hamamatsu University School of Medicine, Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Makoto Horikawa
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; (A.I.); (M.A.M.); (T.S.); (M.H.); (Y.T.); (K.K.)
- International Mass Imaging Center, Hamamatsu University School of Medicine, Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Yutaka Takahashi
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; (A.I.); (M.A.M.); (T.S.); (M.H.); (Y.T.); (K.K.)
| | - Kenji Kikushima
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; (A.I.); (M.A.M.); (T.S.); (M.H.); (Y.T.); (K.K.)
- International Mass Imaging Center, Hamamatsu University School of Medicine, Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Mitsutoshi Setou
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; (A.I.); (M.A.M.); (T.S.); (M.H.); (Y.T.); (K.K.)
- International Mass Imaging Center, Hamamatsu University School of Medicine, Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
- Department of Systems Molecular Anatomy, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
- Correspondence: ; Tel.: +81-053-435-2086
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Damiani C, Gaglio D, Sacco E, Alberghina L, Vanoni M. Systems metabolomics: from metabolomic snapshots to design principles. Curr Opin Biotechnol 2020; 63:190-199. [PMID: 32278263 DOI: 10.1016/j.copbio.2020.02.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/11/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
Abstract
Metabolomics is a rapidly expanding technology that finds increasing application in a variety of fields, form metabolic disorders to cancer, from nutrition and wellness to design and optimization of cell factories. The integration of metabolic snapshots with metabolic fluxes, physiological readouts, metabolic models, and knowledge-informed Artificial Intelligence tools, is required to obtain a system-level understanding of metabolism. The emerging power of multi-omic approaches and the development of integrated experimental and computational tools, able to dissect metabolic features at cellular and subcellular resolution, provide unprecedented opportunities for understanding design principles of metabolic (dis)regulation and for the development of precision therapies in multifactorial diseases, such as cancer and neurodegenerative diseases.
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Affiliation(s)
- Chiara Damiani
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy; ISBE.IT, SYSBIO Centre of Systems Biology, Piazza della Scienza 2, Milan 20126, Italy
| | - Daniela Gaglio
- ISBE.IT, SYSBIO Centre of Systems Biology, Piazza della Scienza 2, Milan 20126, Italy; Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Segrate, Milan, Italy
| | - Elena Sacco
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy; ISBE.IT, SYSBIO Centre of Systems Biology, Piazza della Scienza 2, Milan 20126, Italy
| | - Lilia Alberghina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy; ISBE.IT, SYSBIO Centre of Systems Biology, Piazza della Scienza 2, Milan 20126, Italy
| | - Marco Vanoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy; ISBE.IT, SYSBIO Centre of Systems Biology, Piazza della Scienza 2, Milan 20126, Italy.
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25
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Sample preparation of formalin-fixed paraffin-embedded tissue sections for MALDI-mass spectrometry imaging. Anal Bioanal Chem 2020; 412:1263-1275. [PMID: 31989198 PMCID: PMC7021751 DOI: 10.1007/s00216-019-02296-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/06/2019] [Accepted: 11/20/2019] [Indexed: 12/11/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MALDI MSI) has become a powerful tool with a high potential relevance for the analysis of biomolecules in tissue samples in the context of diseases like cancer and cardiovascular or cardiorenal diseases. In recent years, significant progress has been made in the technology of MALDI MSI. However, a more systematic optimization of sample preparation would likely achieve an increase in the molecular information derived from MALDI MSI. Therefore, we have employed a systematic approach to develop, establish and validate an optimized "standard operating protocol" (SOP) for sample preparation in MALDI MSI of formalin-fixed paraffin-embedded (FFPE) tissue sample analyses within this study. The optimized parameters regarding the impact on the resulting signal-to-noise (S/N) ratio were as follows: (i) trypsin concentration, solvents, deposition method, and incubation time; (ii) tissue washing procedures and drying processes; and (iii) spray flow rate, number of layers of trypsin deposition, and grid size. The protocol was evaluated on interday variability and its applicability for analyzing the mouse kidney, aorta, and heart FFPE tissue samples. In conclusion, an optimized SOP for MALDI MSI of FFPE tissue sections was developed to generate high sensitivity, to enhance spatial resolution and reproducibility, and to increase its applicability for various tissue types. This optimized SOP will further increase the molecular information content and intensify the use of MSI in future basic research and diagnostic applications. Graphical Abstract.
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Mussap M, Loddo C, Fanni C, Fanos V. Metabolomics in pharmacology - a delve into the novel field of pharmacometabolomics. Expert Rev Clin Pharmacol 2020; 13:115-134. [PMID: 31958027 DOI: 10.1080/17512433.2020.1713750] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: Pharmacometabolomics is an emerging science pursuing the application of precision medicine. Combining both genetic and environmental factors, the so-called pharmacometabolomic approach guides patient selection and stratification in clinical trials and optimizes personalized drug dosage, improving efficacy and safety.Areas covered: This review illustrates the progressive introduction of pharmacometabolomics as an innovative solution for enhancing the discovery of novel drugs and improving research and development (R&D) productivity of the pharmaceutical industry. An extended analysis on published pharmacometabolomics studies both in animal models and humans includes results obtained in several areas such as hepatology, gastroenterology, nephrology, neuropsychiatry, oncology, drug addiction, embryonic cells, neonatology, and microbiomics.Expert opinion: a tailored, individualized therapy based on the optimization of pharmacokinetics and pharmacodynamics, the improvement of drug efficacy, and the abolition of drug toxicity and adverse drug reactions is a key issue in precision medicine. Genetics alone has become insufficient for deciphring intra- and inter-individual variations in drug-response, since they originate both from genetic and environmental factors, including human microbiota composition. The association between pharmacogenomics and pharmacometabolomics may be considered the new strategy for an in-deep knowledge on changes and alterations in human and microbial metabolic pathways due to the action of a drug.
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Affiliation(s)
- Michele Mussap
- Laboratory Unit, Department of Surgical Sciences, University of Cagliari, Cagliari, Italy
| | | | - Claudia Fanni
- Division of Pediatrics, Rovigo Hospital, Rovigo, Italy
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Neonatal Pathology and Neonatal Section, Department of Surgical Sciences, University of Cagliari, Cagliari, Italy
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