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Bhuvaneshwar K, Gusev Y. Translational bioinformatics and data science for biomarker discovery in mental health: an analytical review. Brief Bioinform 2024; 25:bbae098. [PMID: 38493340 PMCID: PMC10944574 DOI: 10.1093/bib/bbae098] [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: 06/21/2023] [Revised: 01/23/2024] [Accepted: 02/18/2024] [Indexed: 03/18/2024] Open
Abstract
Translational bioinformatics and data science play a crucial role in biomarker discovery as it enables translational research and helps to bridge the gap between the bench research and the bedside clinical applications. Thanks to newer and faster molecular profiling technologies and reducing costs, there are many opportunities for researchers to explore the molecular and physiological mechanisms of diseases. Biomarker discovery enables researchers to better characterize patients, enables early detection and intervention/prevention and predicts treatment responses. Due to increasing prevalence and rising treatment costs, mental health (MH) disorders have become an important venue for biomarker discovery with the goal of improved patient diagnostics, treatment and care. Exploration of underlying biological mechanisms is the key to the understanding of pathogenesis and pathophysiology of MH disorders. In an effort to better understand the underlying mechanisms of MH disorders, we reviewed the major accomplishments in the MH space from a bioinformatics and data science perspective, summarized existing knowledge derived from molecular and cellular data and described challenges and areas of opportunities in this space.
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Affiliation(s)
- Krithika Bhuvaneshwar
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington DC, 20007, USA
| | - Yuriy Gusev
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington DC, 20007, USA
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2
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Shi L, Winchester LM, Westwood S, Baird AL, Anand SN, Buckley NJ, Hye A, Ashton NJ, Bos I, Vos SJB, Kate MT, Scheltens P, Teunissen CE, Vandenberghe R, Gabel S, Meersmans K, Engelborghs S, De Roeck EE, Sleegers K, Frisoni GB, Blin O, Richardson JC, Bordet R, Molinuevo JL, Rami L, Wallin A, Kettunen P, Tsolaki M, Verhey F, Lléo A, Sala I, Popp J, Peyratout G, Martinez-Lage P, Tainta M, Johannsen P, Freund-Levi Y, Frölich L, Dobricic V, Legido-Quigley C, Barkhof F, Andreasson U, Blennow K, Zetterberg H, Streffer J, Lill CM, Bertram L, Visser PJ, Kolb HC, Narayan VA, Lovestone S, Nevado-Holgado AJ. Replication study of plasma proteins relating to Alzheimer's pathology. Alzheimers Dement 2021; 17:1452-1464. [PMID: 33792144 DOI: 10.1002/alz.12322] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/26/2020] [Accepted: 02/05/2021] [Indexed: 12/16/2022]
Abstract
INTRODUCTION This study sought to discover and replicate plasma proteomic biomarkers relating to Alzheimer's disease (AD) including both the "ATN" (amyloid/tau/neurodegeneration) diagnostic framework and clinical diagnosis. METHODS Plasma proteins from 972 subjects (372 controls, 409 mild cognitive impairment [MCI], and 191 AD) were measured using both SOMAscan and targeted assays, including 4001 and 25 proteins, respectively. RESULTS Protein co-expression network analysis of SOMAscan data revealed the relation between proteins and "N" varied across different neurodegeneration markers, indicating that the ATN variants are not interchangeable. Using hub proteins, age, and apolipoprotein E ε4 genotype discriminated AD from controls with an area under the curve (AUC) of 0.81 and MCI convertors from non-convertors with an AUC of 0.74. Targeted assays replicated the relation of four proteins with the ATN framework and clinical diagnosis. DISCUSSION Our study suggests that blood proteins can predict the presence of AD pathology as measured in the ATN framework as well as clinical diagnosis.
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Affiliation(s)
- Liu Shi
- Department of Psychiatry, University of Oxford, Oxford, UK
| | | | - Sarah Westwood
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Alison L Baird
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Sneha N Anand
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Noel J Buckley
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Abdul Hye
- Maurice Wohl Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK
| | - Nicholas J Ashton
- Maurice Wohl Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK.,Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Isabelle Bos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands.,Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | - Stephanie J B Vos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
| | - Mara Ten Kate
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | - Philip Scheltens
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | - Charlotte E Teunissen
- Neurochemistry lab, Department of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | | | - Silvy Gabel
- University Hospital Leuven, Leuven, Belgium.,Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Karen Meersmans
- University Hospital Leuven, Leuven, Belgium.,Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Sebastiaan Engelborghs
- Reference Center for Biological Markers of Dementia (BIODEM), Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Department of Neurology, UZ Brussel and Center for Neurociences (C4N), Vrije Universiteit Brussel, Brussels, Belgium
| | - Ellen E De Roeck
- Reference Center for Biological Markers of Dementia (BIODEM), Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Kristel Sleegers
- Complex Genetics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Institute Born-Bunge, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Giovanni B Frisoni
- University of Geneva, Geneva, Switzerland.,IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Olivier Blin
- AIX marseille university, INS, Ap-hm, Marseille, France
| | | | - Régis Bordet
- Inserm, University of Lille, CHU Lille, Lille, France
| | - José L Molinuevo
- Alzheimer's Disease and Other Cognitive Disorders Unit, Hopsital Clínic-IDIBAPS, Barcelona, Spain.,Barcelona Beta Brain Research Center, Unversitat Pompeu Fabra, Barcelona, Spain
| | - Lorena Rami
- Barcelona Beta Brain Research Center, Unversitat Pompeu Fabra, Barcelona, Spain
| | - Anders Wallin
- Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Petronella Kettunen
- Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Magda Tsolaki
- 1st Department of Neurology, AHEPA University Hospital, Makedonia, Thessaloniki, Greece
| | - Frans Verhey
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
| | - Alberto Lléo
- Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Isabel Sala
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Julius Popp
- University Hospital of Lausanne, Lausanne, Switzerland.,Geriatric Psychiatry, Department of Mental Health and Psychiatry, Geneva University Hospitals, Geneva, Switzerland
| | | | | | | | - Peter Johannsen
- Danish Dementia Research Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Yvonne Freund-Levi
- Maurice Wohl Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK.,Karolinska Institutet Center for Alzheimer Research, Division of Clinical Geriatrics, School of Medical Sciences Örebro University and Department of Neurobiology, Caring Sciences and Society (NVS), Stockholm, Sweden
| | - Lutz Frölich
- Department of Geriatric Psychiatry, Zentralinstitut für Seelische Gesundheit, University of Heidelberg, Mannheim, Germany
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Cristina Legido-Quigley
- Kings College London, London, UK.,The Systems Medicine Group, Steno Diabetes Center, Gentofte, Denmark
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, VU University Medical Center, Amsterdam, the Netherland.,UCL Institutes of Neurology and Healthcare Engineering, London, UK
| | - Ulf Andreasson
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,UK Dementia Research Institute at UCL, London, UK.,Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
| | - Johannes Streffer
- Complex Genetics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,UCB, Braine-l'Alleud, Belgium, formerly Janssen R&D, LLC Beerse, Beerse, Belgium
| | - Christina M Lill
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany.,Ageing Epidemiology Research Unit, School of Public Health, Imperial College, London, UK
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany.,Department of Psychology, University of Oslo, Oslo, Norway
| | - Pieter Jelle Visser
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands.,Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | | | | | - Simon Lovestone
- Department of Psychiatry, University of Oxford, Oxford, UK.,Janssen R&D, Beerse, UK
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3
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Avila J, Perry G. A Multilevel View of the Development of Alzheimer's Disease. Neuroscience 2020; 457:283-293. [PMID: 33246061 DOI: 10.1016/j.neuroscience.2020.11.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/28/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022]
Abstract
Every year the Alzheimer's Association publishes a report that provides facts and figures indicating the public health, social and economic impact of Alzheimer's disease (AD). In addition, there are a number of reviews on the disease for general readers. Also, at congresses, AD is analyzed at different but not always related levels, leading to an "elephant as seen by blind men situation" for many of the participants. The review presented herein seeks to provide readers with a holistic view of how AD develops from various perspectives: the whole human organism, brain, circuits, neurons, cellular hallmarks, and molecular level.
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Affiliation(s)
- Jesús Avila
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), 28049 Madrid, Spain; Network Centre for Biomedical Research in Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain.
| | - George Perry
- College of Sciences, University of Texas at San Antonio, San Antonio, TX, USA.
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4
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Higginbotham L, Ping L, Dammer EB, Duong DM, Zhou M, Gearing M, Hurst C, Glass JD, Factor SA, Johnson ECB, Hajjar I, Lah JJ, Levey AI, Seyfried NT. Integrated proteomics reveals brain-based cerebrospinal fluid biomarkers in asymptomatic and symptomatic Alzheimer's disease. SCIENCE ADVANCES 2020; 6:eaaz9360. [PMID: 33087358 PMCID: PMC7577712 DOI: 10.1126/sciadv.aaz9360] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 09/03/2020] [Indexed: 05/02/2023]
Abstract
Alzheimer's disease (AD) lacks protein biomarkers reflective of its diverse underlying pathophysiology, hindering diagnostic and therapeutic advancements. Here, we used integrative proteomics to identify cerebrospinal fluid (CSF) biomarkers representing a wide spectrum of AD pathophysiology. Multiplex mass spectrometry identified ~3500 and ~12,000 proteins in AD CSF and brain, respectively. Network analysis of the brain proteome resolved 44 biologically diverse modules, 15 of which overlapped with the CSF proteome. CSF AD markers in these overlapping modules were collapsed into five protein panels representing distinct pathophysiological processes. Synaptic and metabolic panels were decreased in AD brain but increased in CSF, while glial-enriched myelination and immunity panels were increased in brain and CSF. The consistency and disease specificity of panel changes were confirmed in >500 additional CSF samples. These panels also identified biological subpopulations within asymptomatic AD. Overall, these results are a promising step toward a network-based biomarker tool for AD clinical applications.
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Affiliation(s)
- Lenora Higginbotham
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Lingyan Ping
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Duc M Duong
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Maotian Zhou
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Marla Gearing
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Cheyenne Hurst
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Jonathan D Glass
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Stewart A Factor
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Erik C B Johnson
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Ihab Hajjar
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - James J Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
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5
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Drummond E, Goñi F, Liu S, Prelli F, Scholtzova H, Wisniewski T. Potential Novel Approaches to Understand the Pathogenesis and Treat Alzheimer's Disease. J Alzheimers Dis 2019; 64:S299-S312. [PMID: 29562516 DOI: 10.3233/jad-179909] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is growing genetic and proteomic data highlighting the complexity of Alzheimer's disease (AD) pathogenesis. Greater use of unbiased "omics" approaches is being increasingly recognized as essential for the future development of effective AD research, that need to better reflect the multiple distinct pathway abnormalities that can drive AD pathology. The track record of success in AD clinical trials thus far has been very poor. In part, this high failure rate has been related to the premature translation of highly successful results in animal models that mirror only limited aspects of AD pathology to humans. We highlight our recent efforts to increase use of human tissue to gain a better understanding of the AD pathogenesis subtype variety and to develop several distinct therapeutic approaches tailored to address this diversity. These therapeutic approaches include the blocking of the Aβ/apoE interaction, stimulation of innate immunity, and the simultaneous blocking of Aβ/tau oligomer toxicity. We believe that future successful therapeutic approaches will need to be combined to better reflect the complexity of the abnormal pathways triggered in AD pathogenesis.
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Affiliation(s)
- Eleanor Drummond
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Fernando Goñi
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Shan Liu
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Frances Prelli
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Henrieta Scholtzova
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
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6
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Wisniewski T, Drummond E. Future horizons in Alzheimer's disease research. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 168:223-241. [PMID: 31699317 DOI: 10.1016/bs.pmbts.2019.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
There are growing genetic, transcriptomic and proteomic data pointing to the complexity of Alzheimer's disease (AD) pathogenesis. Unbiased "omics" approaches are essential for the future development of effective AD research, which will need to be combined and personalized, given that multiple distinct pathways can drive AD pathology. It is essential to gain a better understanding of the AD pathogenesis subtype variety and to develop several distinct therapeutic approaches tailored to address this diversity, as well as the common presence of mixed pathologies. These nonmutually exclusive therapeutic approaches include the targeting of multiple toxic oligomeric species concurrently, targeting the apolipoprotein E/amyloid β interaction and the modulation of innate immunity, as well as more "out of the box" ideas such as targeting infectious agents that may play a role in AD.
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Affiliation(s)
- Thomas Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, United States.
| | - Eleanor Drummond
- Central Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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7
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Lachén-Montes M, González-Morales A, Fernández-Irigoyen J, Santamaría E. Determination of Cerebrospinal Fluid Proteome Variations by Isobaric Labeling Coupled with Strong Cation-Exchange Chromatography and Tandem Mass Spectrometry. Methods Mol Biol 2019; 2044:155-168. [PMID: 31432412 DOI: 10.1007/978-1-4939-9706-0_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cerebrospinal fluid (CSF) is in direct contact with the brain and represents a valuable source of mediators that reflect metabolic processes occurring in the central nervous system (CNS). In this sense, mass spectrometry (MS) methods have proven to be sensitive in quantifying the proteomic profiles of CSF, therefore being able to detect biomarker candidates for neurological disorders. In particular, a key development has been the use of multiplexing technologies to easily identify and quantify complex protein mixtures. This chapter describes a workflow suitable for the analysis of CSF proteome using isobaric labeling coupled to strong cation-exchange chromatography fractionation for its potential use as a biomarker discovery platform. In this case, the isobaric tags for relative and absolute quantitation (iTRAQ) label all proteins in a sample via free amines at the N-terminus and on the side chain of lysine residues. Then, the labeled samples are pooled and chromatographically fractionated. These fractions with the pooled samples are afterward analyzed by tandem mass spectrometry (MS/MS), and proteins are quantified by the relative intensities of the reporter ions in the MS/MS spectra, simultaneously obtaining the amino acid sequence. This method complements the neuroproteomic toolbox to identify new protein biomarkers not only for the early clinical diagnosis and disease staging of CNS-related disorders but also to elucidate the molecular mechanisms related to the pathophysiology of these symptoms.
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Affiliation(s)
- Mercedes Lachén-Montes
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Andrea González-Morales
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Enrique Santamaría
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain.
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8
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Molinuevo JL, Ayton S, Batrla R, Bednar MM, Bittner T, Cummings J, Fagan AM, Hampel H, Mielke MM, Mikulskis A, O'Bryant S, Scheltens P, Sevigny J, Shaw LM, Soares HD, Tong G, Trojanowski JQ, Zetterberg H, Blennow K. Current state of Alzheimer's fluid biomarkers. Acta Neuropathol 2018; 136:821-853. [PMID: 30488277 PMCID: PMC6280827 DOI: 10.1007/s00401-018-1932-x] [Citation(s) in RCA: 331] [Impact Index Per Article: 55.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 12/12/2022]
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative disease with a complex and heterogeneous pathophysiology. The number of people living with AD is predicted to increase; however, there are no disease-modifying therapies currently available and none have been successful in late-stage clinical trials. Fluid biomarkers measured in cerebrospinal fluid (CSF) or blood hold promise for enabling more effective drug development and establishing a more personalized medicine approach for AD diagnosis and treatment. Biomarkers used in drug development programmes should be qualified for a specific context of use (COU). These COUs include, but are not limited to, subject/patient selection, assessment of disease state and/or prognosis, assessment of mechanism of action, dose optimization, drug response monitoring, efficacy maximization, and toxicity/adverse reactions identification and minimization. The core AD CSF biomarkers Aβ42, t-tau, and p-tau are recognized by research guidelines for their diagnostic utility and are being considered for qualification for subject selection in clinical trials. However, there is a need to better understand their potential for other COUs, as well as identify additional fluid biomarkers reflecting other aspects of AD pathophysiology. Several novel fluid biomarkers have been proposed, but their role in AD pathology and their use as AD biomarkers have yet to be validated. In this review, we summarize some of the pathological mechanisms implicated in the sporadic AD and highlight the data for several established and novel fluid biomarkers (including BACE1, TREM2, YKL-40, IP-10, neurogranin, SNAP-25, synaptotagmin, α-synuclein, TDP-43, ferritin, VILIP-1, and NF-L) associated with each mechanism. We discuss the potential COUs for each biomarker.
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Affiliation(s)
- José Luis Molinuevo
- BarcelonaBeta Brain Research Center, Fundació Pasqual Maragall, Universitat Pompeu Fabra, Barcelona, Spain
- Unidad de Alzheimer y otros trastornos cognitivos, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Scott Ayton
- Melbourne Dementia Research Centre, Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Richard Batrla
- Roche Centralised and Point of Care Solutions, Roche Diagnostics International, Rotkreuz, Switzerland
| | - Martin M Bednar
- Neuroscience Therapeutic Area Unit, Takeda Development Centre Americas Ltd, Cambridge, MA, USA
| | - Tobias Bittner
- Genentech, A Member of the Roche Group, Basel, Switzerland
| | - Jeffrey Cummings
- Cleveland Clinic Lou Ruvo Center for Brain Health, Las Vegas, NV, USA
| | - Anne M Fagan
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Harald Hampel
- AXA Research Fund and Sorbonne University Chair, Paris, France
- Sorbonne University, GRC No 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France
- Brain and Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France
- Department of Neurology, Institute of Memory and Alzheimer's Disease (IM2A), Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - Michelle M Mielke
- Departments of Epidemiology and Neurology, Mayo Clinic, Rochester, MN, USA
| | | | - Sid O'Bryant
- Department of Pharmacology and Neuroscience; Institute for Healthy Aging, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Philip Scheltens
- Department of Neurology and Alzheimer Center, VU University Medical Center, Amsterdam, The Netherlands
| | - Jeffrey Sevigny
- Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Leslie M Shaw
- Department of Pathology and Laboratory Medicine, and Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Holly D Soares
- Clinical Development Neurology, AbbVie, North Chicago, IL, USA
| | | | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal Campus, Sahlgrenska University Hospital, 431 80, Mölndal, Sweden
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal Campus, Sahlgrenska University Hospital, 431 80, Mölndal, Sweden.
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Hampel H, O'Bryant SE, Molinuevo JL, Zetterberg H, Masters CL, Lista S, Kiddle SJ, Batrla R, Blennow K. Blood-based biomarkers for Alzheimer disease: mapping the road to the clinic. Nat Rev Neurol 2018; 14:639-652. [PMID: 30297701 PMCID: PMC6211654 DOI: 10.1038/s41582-018-0079-7] [Citation(s) in RCA: 391] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Biomarker discovery and development for clinical research, diagnostics and therapy monitoring in clinical trials have advanced rapidly in key areas of medicine - most notably, oncology and cardiovascular diseases - allowing rapid early detection and supporting the evolution of biomarker-guided, precision-medicine-based targeted therapies. In Alzheimer disease (AD), breakthroughs in biomarker identification and validation include cerebrospinal fluid and PET markers of amyloid-β and tau proteins, which are highly accurate in detecting the presence of AD-associated pathophysiological and neuropathological changes. However, the high cost, insufficient accessibility and/or invasiveness of these assays limit their use as viable first-line tools for detecting patterns of pathophysiology. Therefore, a multistage, tiered approach is needed, prioritizing development of an initial screen to exclude from these tests the high numbers of people with cognitive deficits who do not demonstrate evidence of underlying AD pathophysiology. This Review summarizes the efforts of an international working group that aimed to survey the current landscape of blood-based AD biomarkers and outlines operational steps for an effective academic-industry co-development pathway from identification and assay development to validation for clinical use.
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Affiliation(s)
- Harald Hampel
- AXA Research Fund and Sorbonne University Chair, Paris, France.
- Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France.
- Brain & Spine Institute (ICM), INSERM U 1127, Paris, France.
- Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, AP-HP, Pitié-Salpêtrière Hospital, Paris, France.
| | - Sid E O'Bryant
- University of North Texas Health Science Center, Fort Worth, TX, USA
| | - José L Molinuevo
- Barcelonaβeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | - Colin L Masters
- The Florey Institute, The University of Melbourne, Melbourne, Australia
| | - Simone Lista
- AXA Research Fund and Sorbonne University Chair, Paris, France
- Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France
- Brain & Spine Institute (ICM), INSERM U 1127, Paris, France
- Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Steven J Kiddle
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK
| | | | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.
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