1
|
Gómez-Pascual A, Naccache T, Xu J, Hooshmand K, Wretlind A, Gabrielli M, Lombardo MT, Shi L, Buckley NJ, Tijms BM, Vos SJB, Ten Kate M, Engelborghs S, Sleegers K, Frisoni GB, Wallin A, Lleó A, Popp J, Martinez-Lage P, Streffer J, Barkhof F, Zetterberg H, Visser PJ, Lovestone S, Bertram L, Nevado-Holgado AJ, Gualerzi A, Picciolini S, Proitsi P, Verderio C, Botía JA, Legido-Quigley C. Paired plasma lipidomics and proteomics analysis in the conversion from mild cognitive impairment to Alzheimer's disease. Comput Biol Med 2024; 176:108588. [PMID: 38761503 DOI: 10.1016/j.compbiomed.2024.108588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/09/2024] [Accepted: 05/09/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND Alzheimer's disease (AD) is a neurodegenerative condition for which there is currently no available medication that can stop its progression. Previous studies suggest that mild cognitive impairment (MCI) is a phase that precedes the disease. Therefore, a better understanding of the molecular mechanisms behind MCI conversion to AD is needed. METHOD Here, we propose a machine learning-based approach to detect the key metabolites and proteins involved in MCI progression to AD using data from the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery Study. Proteins and metabolites were evaluated separately in multiclass models (controls, MCI and AD) and together in MCI conversion models (MCI stable vs converter). Only features selected as relevant by 3/4 algorithms proposed were kept for downstream analysis. RESULTS Multiclass models of metabolites highlighted nine features further validated in an independent cohort (0.726 mean balanced accuracy). Among these features, one metabolite, oleamide, was selected by all the algorithms. Further in-vitro experiments in rodents showed that disease-associated microglia excreted oleamide in vesicles. Multiclass models of proteins stood out with nine features, validated in an independent cohort (0.720 mean balanced accuracy). However, none of the proteins was selected by all the algorithms. Besides, to distinguish between MCI stable and converters, 14 key features were selected (0.872 AUC), including tTau, alpha-synuclein (SNCA), junctophilin-3 (JPH3), properdin (CFP) and peptidase inhibitor 15 (PI15) among others. CONCLUSIONS This omics integration approach highlighted a set of molecules associated with MCI conversion important in neuronal and glia inflammation pathways.
Collapse
Affiliation(s)
- Alicia Gómez-Pascual
- Department of Information and Communications Engineering Faculty of Informatics, University of Murcia, Murcia, Spain; Steno Diabetes Center Copenhagen, Herlev, Denmark
| | - Talel Naccache
- Department of Data Science, City University of London, United Kingdom
| | - Jin Xu
- Institute of Pharmaceutical Science, King's College London, London, United Kingdom
| | | | | | | | - Marta Tiffany Lombardo
- CNR Institute of Neuroscience, 20854, Vedano al Lambro, Italy; School of Medicine and Surgery, University of Milano-Bicocca, 20126, Italy
| | - Liu Shi
- Novo Nordisk Research Centre Oxford (NNRCO), Oxford, United Kingdom
| | - Noel J Buckley
- Department of Psychiatry, University of Oxford, United Kingdom; Kavli Institute for Nanoscience Discovery, Denmark
| | - Betty M Tijms
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | - Stephanie J B Vos
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
| | - Mara Ten Kate
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | - Sebastiaan Engelborghs
- Reference Center for Biological Markers of Dementia (BIODEM), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Department of Neurology and Bru-BRAIN, UZ Brussel and Center for Neurosciences (C4N), Vrije Universiteit Brussel, Brussels, 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
| | - Anders Wallin
- Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Alberto Lleó
- Neurology Department, Hospital Sant Pau, Barcelona, Spain, Centro de Investigación en Red en enfermedades neurodegenerativas (CIBERNED)
| | - Julius Popp
- Old age psychiatry, University Hospital of Lausanne, University of Lausanne, Switzerland; Department of Geriatric Psychiatry, University Hospital of Psychiatry Zürich, University of Zürich, Switzerland
| | | | - Johannes Streffer
- AC Immune SA, Lausanne, Switzerland, formerly Janssen R&D, LLC. Beerse, Belgium at the time of study conduct
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, Vrije Universiteit, the Netherlands; Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, United Kingdom
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden; Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden; UK Dementia Research Institute at UCL, London, United Kingdom; Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom
| | - Pieter Jelle Visser
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands; Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
| | - Simon Lovestone
- Department of Psychiatry, University of Oxford, United Kingdom; Janssen Medical (UK), High Wycombe, United Kingdom
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany; Department of Psychology, University of Oslo, Oslo, Norway
| | | | - Alice Gualerzi
- IRCCS Fondazione Don Carlo Gnocchi ONLUS in Milan, Italy
| | | | - Petroula Proitsi
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | | | - Juan A Botía
- Department of Information and Communications Engineering Faculty of Informatics, University of Murcia, Murcia, Spain
| | - Cristina Legido-Quigley
- Steno Diabetes Center Copenhagen, Herlev, Denmark; Institute of Pharmaceutical Science, King's College London, London, United Kingdom.
| |
Collapse
|
2
|
Timsina J, Dinasarapu A, Kilic-Berkmen G, Budde J, Sung YJ, Klein AM, Cruchaga C, Jinnah HA. Blood-Based Proteomics for Adult-Onset Focal Dystonias. Ann Neurol 2024. [PMID: 38578115 DOI: 10.1002/ana.26929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/27/2024] [Accepted: 03/10/2024] [Indexed: 04/06/2024]
Abstract
OBJECTIVES The adult-onset focal dystonias are characterized by over-active muscles leading to abnormal movements. For most cases, the etiology and pathogenesis remain unknown. In the current study, unbiased proteomics methods were used to identify potential changes in blood plasma proteins. METHODS A large-scale unbiased proteomics screen was used to compare proteins (N = 6,345) in blood plasma of normal healthy controls (N = 49) with adult-onset focal dystonia (N = 143) consisting of specific subpopulations of cervical dystonia (N = 45), laryngeal dystonia (N = 49), and blepharospasm (N = 49). Pathway analyses were conducted to identify relevant biological pathways. Finally, protein changes were used to build a prediction model for dystonia. RESULTS After correction for multiple comparisons, 15 proteins were associated with adult-onset focal dystonia. Subgroup analyses revealed some proteins were shared across the dystonia subgroups while others were unique to 1 subgroup. The top biological pathways involved changes in the immune system, metal ion transport, and reactive oxygen species. A 4-protein model showed high accuracy in discriminating control individuals from dystonia cases [average area under the curve (AUC) = 0.89]. INTERPRETATION These studies provide novel insights into the etiopathogenesis of dystonia, as well as novel potential biomarkers. ANN NEUROL 2024.
Collapse
Affiliation(s)
- Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Ashok Dinasarapu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Gamze Kilic-Berkmen
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Adam M Klein
- Department of Otolaryngology, Emory University School of Medicine, Atlanta, GA, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO, USA
| | - H A Jinnah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| |
Collapse
|
3
|
Zhong H, Zhou X, Uhm H, Jiang Y, Cao H, Chen Y, Mak TTW, Lo RMN, Wong BWY, Cheng EYL, Mok KY, Chan ALT, Kwok TCY, Mok VCT, Ip FCF, Hardy J, Fu AKY, Ip NY. Using blood transcriptome analysis for Alzheimer's disease diagnosis and patient stratification. Alzheimers Dement 2024; 20:2469-2484. [PMID: 38323937 PMCID: PMC11032555 DOI: 10.1002/alz.13691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 02/08/2024]
Abstract
INTRODUCTION Blood protein biomarkers demonstrate potential for Alzheimer's disease (AD) diagnosis. Limited studies examine the molecular changes in AD blood cells. METHODS Bulk RNA-sequencing of blood cells was performed on AD patients of Chinese descent (n = 214 and 26 in the discovery and validation cohorts, respectively) with normal controls (n = 208 and 38 in the discovery and validation cohorts, respectively). Weighted gene co-expression network analysis (WGCNA) and deconvolution analysis identified AD-associated gene modules and blood cell types. Regression and unsupervised clustering analysis identified AD-associated genes, gene modules, cell types, and established AD classification models. RESULTS WGCNA on differentially expressed genes revealed 15 gene modules, with 6 accurately classifying AD (areas under the receiver operating characteristics curve [auROCs] > 0.90). These modules stratified AD patients into subgroups with distinct disease states. Cell-type deconvolution analysis identified specific blood cell types potentially associated with AD pathogenesis. DISCUSSION This study highlights the potential of blood transcriptome for AD diagnosis, patient stratification, and mechanistic studies. HIGHLIGHTS We comprehensively analyze the blood transcriptomes of a well-characterized Alzheimer's disease cohort to identify genes, gene modules, pathways, and specific blood cells associated with the disease. Blood transcriptome analysis accurately classifies and stratifies patients with Alzheimer's disease, with some gene modules achieving classification accuracy comparable to that of the plasma ATN biomarkers. Immune-associated pathways and immune cells, such as neutrophils, have potential roles in the pathogenesis and progression of Alzheimer's disease.
Collapse
Affiliation(s)
- Huan Zhong
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
| | - Xiaopu Zhou
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhenGuangdongChina
| | - Hyebin Uhm
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
| | - Yuanbing Jiang
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
| | - Han Cao
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
| | - Yu Chen
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhenGuangdongChina
- The Brain Cognition and Brain Disease InstituteShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen–Hong Kong Institute of Brain Science‐Shenzhen Fundamental Research InstitutionsShenzhenGuangdongChina
| | - Tiffany T. W. Mak
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
| | - Ronnie Ming Nok Lo
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
| | - Bonnie Wing Yan Wong
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
| | - Elaine Yee Ling Cheng
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
| | - Kin Y. Mok
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
| | | | - Timothy C. Y. Kwok
- Therese Pei Fong Chow Research Centre for Prevention of DementiaDivision of GeriatricsDepartment of Medicine and TherapeuticsThe Chinese University of Hong KongHKSARChina
| | - Vincent C. T. Mok
- Lau Tat‐chuen Research Centre of Brain Degenerative Diseases in ChineseTherese Pei Fong Chow Research Centre for Prevention of DementiaGerald Choa Neuroscience InstituteLi Ka Shing Institute of Health SciencesDivision of NeurologyDepartment of Medicine and TherapeuticsThe Chinese University of Hong KongHKSARChina
| | - Fanny C. F. Ip
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhenGuangdongChina
| | - John Hardy
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
- Institute for Advanced StudyThe Hong Kong University of Science and TechnologyHKSARChina
| | - Amy K. Y. Fu
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhenGuangdongChina
| | - Nancy Y. Ip
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyHKSARChina
- Hong Kong Center for Neurodegenerative DiseasesInnoHKHKSARChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhenGuangdongChina
| |
Collapse
|
4
|
Saloner R, Staffaroni A, Dammer E, Johnson ECB, Paolillo E, Wise A, Heuer H, Forsberg L, Lago AL, Webb J, Vogel J, Santillo A, Hansson O, Kramer J, Miller B, Li J, Loureiro J, Sivasankaran R, Worringer K, Seyfried N, Yokoyama J, Seeley W, Spina S, Grinberg L, VandeVrede L, Ljubenkov P, Bayram E, Bozoki A, Brushaber D, Considine C, Day G, Dickerson B, Domoto-Reilly K, Faber K, Galasko D, Geschwind D, Ghoshal N, Graff-Radford N, Hales C, Honig L, Hsiung GY, Huey E, Kornak J, Kremers W, Lapid M, Lee S, Litvan I, McMillan C, Mendez M, Miyagawa T, Pantelyat A, Pascual B, Paulson H, Petrucelli L, Pressman P, Ramos E, Rascovsky K, Roberson E, Savica R, Snyder A, Sullivan AC, Tartaglia C, Vandebergh M, Boeve B, Rosen H, Rojas J, Boxer A, Casaletto K. Large-scale network analysis of the cerebrospinal fluid proteome identifies molecular signatures of frontotemporal lobar degeneration. Res Sq 2024:rs.3.rs-4103685. [PMID: 38585969 PMCID: PMC10996789 DOI: 10.21203/rs.3.rs-4103685/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The pathophysiological mechanisms driving disease progression of frontotemporal lobar degeneration (FTLD) and corresponding biomarkers are not fully understood. We leveraged aptamer-based proteomics (> 4,000 proteins) to identify dysregulated communities of co-expressed cerebrospinal fluid proteins in 116 adults carrying autosomal dominant FTLD mutations (C9orf72, GRN, MAPT) compared to 39 noncarrier controls. Network analysis identified 31 protein co-expression modules. Proteomic signatures of genetic FTLD clinical severity included increased abundance of RNA splicing (particularly in C9orf72 and GRN) and extracellular matrix (particularly in MAPT) modules, as well as decreased abundance of synaptic/neuronal and autophagy modules. The generalizability of genetic FTLD proteomic signatures was tested and confirmed in independent cohorts of 1) sporadic progressive supranuclear palsy-Richardson syndrome and 2) frontotemporal dementia spectrum syndromes. Network-based proteomics hold promise for identifying replicable molecular pathways in adults living with FTLD. 'Hub' proteins driving co-expression of affected modules warrant further attention as candidate biomarkers and therapeutic targets.
Collapse
Affiliation(s)
| | | | | | | | | | - Amy Wise
- University of California, San Francisco
| | | | | | | | | | | | | | | | | | | | - Jingyao Li
- Novartis Institutes for Biomedical Research, Inc
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Suzee Lee
- University of California, San Francisco
| | | | - Corey McMillan
- Department of Neurology, University of Pennsylvania, Philadelphia, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Adam Boxer
- Memory and Aging Center, Department of Neurology, University of California, San Francisco
| | | |
Collapse
|
5
|
Wang Y, Sun Y, Wang Y, Jia S, Qiao Y, Zhou Z, Shao W, Zhang X, Guo J, Song X, Niu X, Peng D. Urine metabolomics phenotyping and urinary biomarker exploratory in mild cognitive impairment and Alzheimer's disease. Front Aging Neurosci 2023; 15:1273807. [PMID: 38187356 PMCID: PMC10768723 DOI: 10.3389/fnagi.2023.1273807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/20/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction Alzheimer's disease is a prevalent disease with a heavy global burden and is suggested to be a metabolic disease in the brain in recent years. The metabolome is considered to be the most promising phenotype which reflects changes in genetic, transcript, and protein profiles as well as environmental effects. Aiming to obtain a comprehensive understanding and convenient diagnosis of MCI and AD from another perspective, researchers are working on AD metabolomics. Urine is more convenient which could reflect the change of disease at an earlier stage. Thus, we conducted a cross-sectional study to investigate novel diagnostic panels. Methods We first enrolled participants from China-Japan Friendship Hospital from April 2022 to November 2022, collected urine samples and conducted an LC-MS/MS analysis. In parallel, clinical data were collected and clinical examinations were performed. After statistical and bioinformatics analyzes, significant risk factors and differential urinary metabolites were determined. We attempt to investigate diagnostic panels based on machine learning including LASSO and SVM. Results Fifty-seven AD patients, 43 MCI patients and 62 CN subjects were enrolled. A total of 2,140 metabolites were identified among which 125 significantly differed between the AD and CN groups, including 46 upregulated ones and 79 downregulated ones. In parallel, there were 93 significant differential metabolites between the MCI and CN groups, including 23 upregulated ones and 70 downregulated ones. AD diagnostic panel (30 metabolites+ age + APOE) achieved an AUC of 0.9575 in the test set while MCI diagnostic panel (45 metabolites+ age + APOE) achieved an AUC of 0.7333 in the test set. Atropine, S-Methyl-L-cysteine-S-oxide, D-Mannose 6-phosphate (M6P), Spiculisporic Acid, N-Acetyl-L-methionine, 13,14-dihydro-15-keto-tetranor Prostaglandin D2, Pyridoxal 5'-Phosphate (PLP) and 17(S)-HpDHA were considered valuable for both AD and MCI diagnosis and defined as hub metabolites. Besides, diagnostic metabolites were weakly correlated with cognitive functions. Discussion In conclusion, the procedure is convenient, non-invasive, and useful for diagnosis, which could assist physicians in differentiating AD and MCI from CN. Atropine, M6P and PLP were evidence-based hub metabolites in AD.
Collapse
Affiliation(s)
- Yuye Wang
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Yu Sun
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Yu Wang
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Shuhong Jia
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Yanan Qiao
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Zhi Zhou
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Wen Shao
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Xiangfei Zhang
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Jing Guo
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Xincheng Song
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Xiaoqian Niu
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Dantao Peng
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| |
Collapse
|
6
|
Wang Y, Sun Y, Wang Y, Jia S, Qiao Y, Zhou Z, Shao W, Zhang X, Guo J, Zhang B, Niu X, Wang Y, Peng D. Identification of novel diagnostic panel for mild cognitive impairment and Alzheimer's disease: findings based on urine proteomics and machine learning. Alzheimers Res Ther 2023; 15:191. [PMID: 37925455 PMCID: PMC10625308 DOI: 10.1186/s13195-023-01324-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/04/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Alzheimer's disease is a prevalent disease with a heavy global burden. Proteomics is the systematic study of proteins and peptides to provide comprehensive descriptions. Aiming to obtain a more accurate and convenient clinical diagnosis, researchers are working for better biomarkers. Urine is more convenient which could reflect the change of disease at an earlier stage. Thus, we conducted a cross-sectional study to investigate novel diagnostic panels. METHODS We firstly enrolled participants from China-Japan Friendship Hospital from April 2022 to November 2022, collected urine samples, and conducted an LC-MS/MS analysis. In parallel, clinical data were collected, and clinical examinations were performed. After statistical and bioinformatics analyses, significant risk factors and differential urinary proteins were determined. We attempt to investigate diagnostic panels based on machine learning including LASSO and SVM. RESULTS Fifty-seven AD patients, 43 MCI patients, and 62 CN subjects were enrolled. A total of 3366 proteins were identified, and 608 urine proteins were finally included in the analysis. There were 33 significantly differential proteins between the AD and CN groups and 15 significantly differential proteins between the MCI and CN groups. AD diagnostic panel included DDC, CTSC, EHD4, GSTA3, SLC44A4, GNS, GSTA1, ANXA4, PLD3, CTSH, HP, RPS3, CPVL, age, and APOE ε4 with an AUC of 0.9989 in the training test and 0.8824 in the test set while MCI diagnostic panel included TUBB, SUCLG2, PROCR, TCP1, ACE, FLOT2, EHD4, PROZ, C9, SERPINA3, age, and APOE ε4 with an AUC of 0.9985 in the training test and 0.8143 in the test set. Besides, diagnostic proteins were weakly correlated with cognitive functions. CONCLUSIONS In conclusion, the procedure is convenient, non-invasive, and useful for diagnosis, which could assist physicians in differentiating AD and MCI from CN.
Collapse
Affiliation(s)
- Yuye Wang
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Yu Sun
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Yu Wang
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Shuhong Jia
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Yanan Qiao
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Zhi Zhou
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Wen Shao
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Xiangfei Zhang
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Jing Guo
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Bin Zhang
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Xiaoqian Niu
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Dantao Peng
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China.
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China.
| |
Collapse
|
7
|
Shi L, Xu J, Green R, Wretlind A, Homann J, Buckley NJ, Tijms BM, Vos SJB, Lill CM, Kate MT, Engelborghs S, Sleegers K, Frisoni GB, Wallin A, Lleó A, Popp J, Martinez-Lage P, Streffer J, Barkhof F, Zetterberg H, Visser PJ, Lovestone S, Bertram L, Nevado-Holgado AJ, Proitsi P, Legido-Quigley C. Multiomics profiling of human plasma and cerebrospinal fluid reveals ATN-derived networks and highlights causal links in Alzheimer's disease. Alzheimers Dement 2023; 19:3350-3364. [PMID: 36790009 DOI: 10.1002/alz.12961] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 02/16/2023]
Abstract
INTRODUCTION This study employed an integrative system and causal inference approach to explore molecular signatures in blood and CSF, the amyloid/tau/neurodegeneration [AT(N)] framework, mild cognitive impairment (MCI) conversion to Alzheimer's disease (AD), and genetic risk for AD. METHODS Using the European Medical Information Framework (EMIF)-AD cohort, we measured 696 proteins in cerebrospinal fluid (n = 371), 4001 proteins in plasma (n = 972), 611 metabolites in plasma (n = 696), and genotyped whole-blood (7,778,465 autosomal single nucleotide epolymorphisms, n = 936). We investigated associations: molecular modules to AT(N), module hubs with AD Polygenic Risk scores and APOE4 genotypes, molecular hubs to MCI conversion and probed for causality with AD using Mendelian randomization (MR). RESULTS AT(N) framework associated with protein and lipid hubs. In plasma, Proprotein Convertase Subtilisin/Kexin Type 7 showed evidence for causal associations with AD. AD was causally associated with Reticulocalbin 2 and sphingomyelins, an association driven by the APOE isoform. DISCUSSION This study reveals multi-omics networks associated with AT(N) and causal AD molecular candidates.
Collapse
Affiliation(s)
- Liu Shi
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Jin Xu
- Institute of Pharmaceutical Science, King's College London, London, UK
| | - Rebecca Green
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- UK National Institute for Health Research (NIHR) Maudsley Biomedical Research Centre, South London and Maudsley Trust, London, UK
- MRC Unit for Lifelong Health & Ageing at UCL, University College London, London, UK
| | | | - Jan Homann
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Noel J Buckley
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Betty M Tijms
- 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
| | - Christina M Lill
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
- Institute of Epidemiology and Social Medicine, University of Muenster, Muenster, Germany
- Ageing Epidemiology Research Unit (AGE), School of Public Health, Imperial College London, London, UK
| | - Mara Ten Kate
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
| | - 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
| | - 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
| | - Anders Wallin
- Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Alberto Lleó
- Neurology Department, Centro de Investigación en Red en enfermedades neurodegenerativas (CIBERNED), Hospital Sant Pau, Barcelona, Spain
| | - Julius Popp
- University Hospital of Lausanne, Lausanne, Switzerland
- Department of Geriatric Psychiatry, University Hospital of Psychiatry and University of Zürich, Zürich, Switzerland
| | | | - Johannes Streffer
- AC Immune SA, formerly Janssen R&D, LLC. Beerse, Belgium at the time of study conduct, Lausanne, Switzerland
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherland
- Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, London, UK
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden
- UK Dementia Research Institute at UCL, London, UK
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
| | - Pieter Jelle Visser
- Alzheimer Center, VU University Medical Center, Amsterdam, the Netherlands
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
| | - Simon Lovestone
- Department of Psychiatry, University of Oxford, Oxford, UK
- Janssen Medical (UK), High Wycombe, UK
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
- Department of Psychology, University of Oslo, Oslo, Norway
| | | | - Petroula Proitsi
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Cristina Legido-Quigley
- Institute of Pharmaceutical Science, King's College London, London, UK
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| |
Collapse
|
8
|
Weiner S, Blennow K, Zetterberg H, Gobom J. Next-generation proteomics technologies in Alzheimer's disease: from clinical research to routine diagnostics. Expert Rev Proteomics 2023; 20:143-150. [PMID: 37701966 DOI: 10.1080/14789450.2023.2255752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/18/2023] [Indexed: 09/14/2023]
Abstract
INTRODUCTION Clinical proteomics studies of Alzheimer's disease (AD) research aim to identify biomarkers useful for clinical research, diagnostics, and improve our understanding of the pathological processes involved in the disease. The rapidly increasing performance of proteomics technologies is likely to have great impact on AD research. AREAS COVERED We review recent proteomics approaches that have advanced the field of clinical AD research. Specifically, we discuss the application of targeted mass spectrometry (MS), labeling-based and label-free MS-based as well as affinity-based proteomics to AD biomarker development, underpinning their importance with the latest impactful clinical studies. We evaluate how proteomics technologies have been adapted to meet current challenges. Finally, we discuss the limitations and potential of proteomics techniques and whether their scope might extend beyond current research-based applications. EXPERT OPINION To date, proteomics technologies in the AD field have been largely limited to AD biomarker discovery. The recent development of the first successful disease-modifying treatments of AD will further increase the need for blood biomarkers for early, accurate diagnosis, and CSF biomarkers that reflect specific pathological processes. Proteomics has the potential to meet these requirements and to progress into clinical routine practice, provided that current limitations are overcome.
Collapse
Affiliation(s)
- Sophia Weiner
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Dementia Research Institute at UCL, London, UK
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
| | - Johan Gobom
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| |
Collapse
|
9
|
Vorn R, Devoto C, Meier TB, Lai C, Yun S, Broglio SP, Mithani S, McAllister TW, Giza CC, Kim HS, Huber D, Harezlak J, Cameron KL, McGinty G, Jackson J, Guskiewicz KM, Mihalik JP, Brooks A, Duma S, Rowson S, Nelson LD, Pasquina P, McCrea MA, Gill JM. Are EPB41 and alpha-synuclein diagnostic biomarkers of sport-related concussion? Findings from the NCAA and Department of Defense CARE Consortium. J Sport Health Sci 2023; 12:379-387. [PMID: 36403906 DOI: 10.1016/j.jshs.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 07/15/2022] [Accepted: 10/08/2022] [Indexed: 05/17/2023]
Abstract
BACKGROUND Current protein biomarkers are only moderately predictive at identifying individuals with mild traumatic brain injury or concussion. Therefore, more accurate diagnostic markers are needed for sport-related concussion. METHODS This was a multicenter, prospective, case-control study of athletes who provided blood samples and were diagnosed with a concussion or were a matched non-concussed control within the National Collegiate Athletic Association-Department of Defense Concussion Assessment, Research, and Education Consortium conducted between 2015 and 2019. The blood was collected within 48 h of injury to identify protein abnormalities at the acute and subacute timepoints. Athletes with concussion were divided into 6 h post-injury (0-6 h post-injury) and after 6 h post-injury (7-48 h post-injury) groups. We applied a highly multiplexed proteomic technique that used a DNA aptamers assay to target 1305 proteins in plasma samples from athletes with and without sport-related concussion. RESULTS A total of 140 athletes with concussion (79.3% males; aged 18.71 ± 1.10 years, mean ± SD) and 21 non-concussed athletes (76.2% males; 19.14 ± 1.10 years) were included in this study. We identified 338 plasma proteins that significantly differed in abundance (319 upregulated and 19 downregulated) in concussed athletes compared to non-concussed athletes. The top 20 most differentially abundant proteins discriminated concussed athletes from non-concussed athletes with an area under the curve (AUC) of 0.954 (95% confidence interval: 0.922‒0.986). Specifically, after 6 h of injury, the individual AUC of plasma erythrocyte membrane protein band 4.1 (EPB41) and alpha-synuclein (SNCA) were 0.956 and 0.875, respectively. The combination of EPB41 and SNCA provided the best AUC (1.000), which suggests this combination of candidate plasma biomarkers is the best for diagnosing concussion in athletes after 6 h of injury. CONCLUSION Our data suggest that proteomic profiling may provide novel diagnostic protein markers and that a combination of EPB41 and SNCA is the most predictive biomarker of concussion after 6 h of injury.
Collapse
Affiliation(s)
- Rany Vorn
- Johns Hopkins School of Nursing and Medicine, Baltimore, MD 21205, USA; National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Timothy B Meier
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chen Lai
- National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijung Yun
- Predictiv Care, Inc., Mountain View, CA 94086, USA
| | - Steven P Broglio
- Michigan Concussion Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sara Mithani
- National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas W McAllister
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Christopher C Giza
- Departments of Pediatrics and Neurosurgery, University of California at Los Angeles (UCLA), Los Angeles, CA 90024, USA
| | - Hyung-Suk Kim
- National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel Huber
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jaroslaw Harezlak
- Department of Epidemiology and Biostatistics School of Public Health - Bloomington, Indiana University, Bloomington, IN 47405, USA
| | - Kenneth L Cameron
- John A. Feagin Sports Medicine Fellowship, Keller Army Community Hospital, West Point, NY 10996, USA
| | - Gerald McGinty
- United States Air Force Academy, Colorado Springs, CO 80840, USA
| | - Jonathan Jackson
- United States Air Force Academy, Colorado Springs, CO 80840, USA
| | - Kevin M Guskiewicz
- Mathew Gfeller Center, Department of Exercise and Sport Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Jason P Mihalik
- Mathew Gfeller Center, Department of Exercise and Sport Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Alison Brooks
- Department of Orthopedics, Division of Sports Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA
| | - Stefan Duma
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Steven Rowson
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Lindsay D Nelson
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Paul Pasquina
- Center for Neuroscience & Regenerative Medicine, Uniformed Services University, Bethesda, MD 20814, USA
| | - Michael A McCrea
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jessica M Gill
- Johns Hopkins School of Nursing and Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
10
|
Shami-Shah A, Norman M, Walt DR. Ultrasensitive protein detection technologies for extracellular vesicle measurements. Mol Cell Proteomics 2023; 22:100557. [PMID: 37088150 DOI: 10.1016/j.mcpro.2023.100557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 04/25/2023] Open
Abstract
Extracellular Vesicles (EVs) are nanoscopic, heterogenous, lipid-rich particles that carry a multitude of cargo biomolecules including proteins, nucleic acids, and metabolites. Although historically, EVs were regarded as cellular debris with no intrinsic value, growing understanding of EV biogenesis has led to the realization that EVs facilitate intercellular communication and are sources of liquid biomarkers. EVs can be isolated and analyzed from a wide variety of accessible biofluids for biomarker discovery and diagnostic applications. There is a diversity of EVs from different biological compartments (e.g., cells, tissues) and some of these EVs are present at extremely low concentrations. Consequently, a challenge in the field is to find appropriate markers that enable selective isolation of these rare EVs. Many conventional protein detection technologies have limited sensitivity to detect low abundance biomarkers in EVs, limiting their use in EV research. Advances in ultrasensitive detection technologies are needed to harness the potential of EVs for clinical application. This Perspective highlights current EV research focusing on ultrasensitive detection technologies, their limitations, and areas of potential growth in the future.
Collapse
Affiliation(s)
- Adnan Shami-Shah
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Maia Norman
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA; Tufts University School of Medicine, Boston, MA
| | - David R Walt
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA.
| |
Collapse
|
11
|
Wiredu K, Aduse-Poku E, Shaefi S, Gerber SA. Proteomics for the Discovery of Clinical Delirium Biomarkers: A Systematic Review of Major Studies. Anesth Analg 2023; 136:422-432. [PMID: 36580411 DOI: 10.1213/ane.0000000000006246] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Delirium represents a significant health care burden, diagnosed in more than 2 million elderly Americans each year. In the surgical population, delirium remains the most common complication among elderly patients, and is associated with longer hospital stays, higher costs of care, increased mortality, and functional impairment. The pathomechanism of disease is poorly understood, with current diagnostic approaches somewhat subjective and arbitrary, and definitive diagnostic biomarkers are currently lacking. Despite the recent interest in delirium research, biomarker discovery for it remains new. Most attempts to discover biomarkers are targeted studies that seek to assess the involvement of one or more members of a focused panel of candidates in delirium. For a more unbiased, system-biology view, we searched literature from Medical Literature Analysis and Retrieval System Online (MEDLINE), Cochrane Central, Web of Science, SCOPUS, and Dimensions between 2016 and 2021 for untargeted proteomic discovery studies for biomarkers of delirium conducted on human geriatric subjects. Two reviewers conducted an independent review of all search results and resolved discordance by consensus. From an overall search of 1172 publications, 8 peer-reviewed studies met our defined inclusion criteria. The 370 unique perioperative biomarkers identified in these reports are enriched in pathways involving activation of the immune system, inflammatory response, and the coagulation cascade. The most frequently identified biomarker was interleukin-6 (IL-6). By reviewing the distribution of protein biomarker candidates from these studies, we conclude that a panel of proteins, rather than a single biomarker, would allow for discriminating delirium cases from noncases. The paucity of hypothesis-generating studies in the peer-reviewed literature also suggests that a system-biology view of delirium pathomechanisms has yet to fully emerge.
Collapse
Affiliation(s)
- Kwame Wiredu
- From the Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.,Program in Quantitative Biomedical Science, Dartmouth College, Hanover, New Hampshire
| | | | - Shahzad Shaefi
- Department of Anesthesiology, Critical Care and Pain Medicine, Harvard Medical School/Critical Care and Pain Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Scott A Gerber
- From the Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.,Program in Quantitative Biomedical Science, Dartmouth College, Hanover, New Hampshire.,Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| |
Collapse
|
12
|
Short MI, Fohner AE, Skjellegrind HK, Beiser A, Gonzales MM, Satizabal CL, Austin TR, Longstreth W, Bis JC, Lopez O, Hveem K, Selbæk G, Larson MG, Yang Q, Aparicio HJ, McGrath ER, Gerszten RE, DeCarli CS, Psaty BM, Vasan RS, Zare H, Seshadri S. Proteome Network Analysis Identifies Potential Biomarkers for Brain Aging. J Alzheimers Dis 2023; 96:1767-1780. [PMID: 38007645 PMCID: PMC10741337 DOI: 10.3233/jad-230145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND Alzheimer's disease and related dementias (ADRD) involve biological processes that begin years to decades before onset of clinical symptoms. The plasma proteome can offer insight into brain aging and risk of incident dementia among cognitively healthy adults. OBJECTIVE To identify biomarkers and biological pathways associated with neuroimaging measures and incident dementia in two large community-based cohorts by applying a correlation-based network analysis to the plasma proteome. METHODS Weighted co-expression network analysis of 1,305 plasma proteins identified four modules of co-expressed proteins, which were related to MRI brain volumes and risk of incident dementia over a median 20-year follow-up in Framingham Heart Study (FHS) Offspring cohort participants (n = 1,861). Analyses were replicated in the Cardiovascular Health Study (CHS) (n = 2,117, mean 6-year follow-up). RESULTS Two proteomic modules, one related to protein clearance and synaptic maintenance (M2) and a second to inflammation (M4), were associated with total brain volume in FHS (M2: p = 0.014; M4: p = 4.2×10-5). These modules were not significantly associated with hippocampal volume, white matter hyperintensities, or incident all-cause or AD dementia. Associations with TCBV did not replicate in CHS, an older cohort with a greater burden of comorbidities. CONCLUSIONS Proteome networks implicate an early role for biological pathways involving inflammation and synaptic function in preclinical brain atrophy, with implications for clinical dementia.
Collapse
Affiliation(s)
- Meghan I. Short
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA, USA
- Department of Medicine, Tufts University School of Medicine, Boston, MA, USA
| | - Alison E. Fohner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Håvard K. Skjellegrind
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Levanger, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Alexa Beiser
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Mitzi M. Gonzales
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Neurology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Claudia L. Satizabal
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA
| | - Thomas R. Austin
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - W.T. Longstreth
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Neurology, University of Washington, Seattle, WA, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Oscar Lopez
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Levanger, Norway
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Geir Selbæk
- Norwegian National Centre for Ageing and Health, Vestfold Hospital Trust, Tønsberg, Norway
- Department of Geriatric Medicine, Oslo University Hospital, Oslo, Norway
| | - Martin G. Larson
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Hugo J. Aparicio
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Emer R. McGrath
- Framingham Heart Study, Framingham, MA, USA
- School of Medicine, National University of Ireland Galway, Galway, Ireland
- HRB Clinical Research Facility, National University of Ireland Galway, Galway, Ireland
| | - Robert E. Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Charles S. DeCarli
- Department of Neurology, School of Medicine and Imaging of Dementia and Aging Laboratory, Center for Neuroscience, University of California, Davis, Sacramento, CA, USA
| | - Bruce M. Psaty
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Ramachandran S. Vasan
- Framingham Heart Study, Framingham, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Boston University Center for Computing and Data Science, Boston, MA, USA
| | - Habil Zare
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Cell Systems and Anatomy, University of Texas Health Science Center, San Antonio, TX, USA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| |
Collapse
|
13
|
Winchester L, Barber I, Lawton M, Ash J, Liu B, Evetts S, Hopkins-Jones L, Lewis S, Bresner C, Malpartida AB, Williams N, Gentlemen S, Wade-Martins R, Ryan B, Holgado-Nevado A, Hu M, Ben-Shlomo Y, Grosset D, Lovestone S. Identification of a possible proteomic biomarker in Parkinson's disease: discovery and replication in blood, brain and cerebrospinal fluid. Brain Commun 2023; 5:fcac343. [PMID: 36694577 PMCID: PMC9856276 DOI: 10.1093/braincomms/fcac343] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/27/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022] Open
Abstract
Biomarkers to aid diagnosis and delineate the progression of Parkinson's disease are vital for targeting treatment in the early phases of the disease. Here, we aim to discover a multi-protein panel representative of Parkinson's and make mechanistic inferences from protein expression profiles within the broader objective of finding novel biomarkers. We used aptamer-based technology (SomaLogic®) to measure proteins in 1599 serum samples, 85 cerebrospinal fluid samples and 37 brain tissue samples collected from two observational longitudinal cohorts (the Oxford Parkinson's Disease Centre and Tracking Parkinson's) and the Parkinson's Disease Brain Bank, respectively. Random forest machine learning was performed to discover new proteins related to disease status and generate multi-protein expression signatures with potential novel biomarkers. Differential regulation analysis and pathway analysis were performed to identify functional and mechanistic disease associations. The most consistent diagnostic classifier signature was tested across modalities [cerebrospinal fluid (area under curve) = 0.74, P = 0.0009; brain area under curve = 0.75, P = 0.006; serum area under curve = 0.66, P = 0.0002]. Focusing on serum samples and using only those with severe disease compared with controls increased the area under curve to 0.72 (P = 1.0 × 10-4). In the validation data set, we showed that the same classifiers were significantly related to disease status (P < 0.001). Differential expression analysis and weighted gene correlation network analysis highlighted key proteins and pathways with known relationships to Parkinson's. Proteins from the complement and coagulation cascades suggest a disease relationship to immune response. The combined analytical approaches in a relatively large number of samples, across tissue types, with replication and validation, provide mechanistic insights into the disease as well as nominate a protein signature classifier that deserves further biomarker evaluation.
Collapse
Affiliation(s)
- Laura Winchester
- Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
| | - Imelda Barber
- Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
| | - Michael Lawton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jessica Ash
- Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
| | - Benjamine Liu
- Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
| | - Samuel Evetts
- Oxford Parkinson's Disease Centre and Division of Neurology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Lucinda Hopkins-Jones
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, Wales, UK
| | - Suppalak Lewis
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, Wales, UK
| | - Catherine Bresner
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, Wales, UK
| | - Ana Belen Malpartida
- Oxford Parkinson's Disease Centre, Kavli Institute for Nanoscience Discovery, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Nigel Williams
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, Wales, UK
| | - Steve Gentlemen
- Department of Brain Sciences, Imperial College London, London, UK
| | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre, Kavli Institute for Nanoscience Discovery, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Brent Ryan
- Oxford Parkinson's Disease Centre, Kavli Institute for Nanoscience Discovery, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | | | - Michele Hu
- Oxford Parkinson's Disease Centre and Division of Neurology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Yoav Ben-Shlomo
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Donald Grosset
- Institute of Neuroscience and Psychology, University of Glasgow, Glasgow, UK
| | - Simon Lovestone
- Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
| |
Collapse
|
14
|
Zhang Y, Ghose U, Buckley NJ, Engelborghs S, Sleegers K, Frisoni GB, Wallin A, Lleó A, Popp J, Martinez-Lage P, Legido-Quigley C, Barkhof F, Zetterberg H, Visser PJ, Bertram L, Lovestone S, Nevado-Holgado AJ, Shi L. Predicting AT(N) pathologies in Alzheimer's disease from blood-based proteomic data using neural networks. Front Aging Neurosci 2022; 14:1040001. [PMID: 36523958 PMCID: PMC9746615 DOI: 10.3389/fnagi.2022.1040001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/04/2022] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND AND OBJECTIVE Blood-based biomarkers represent a promising approach to help identify early Alzheimer's disease (AD). Previous research has applied traditional machine learning (ML) to analyze plasma omics data and search for potential biomarkers, but the most modern ML methods based on deep learning has however been scarcely explored. In the current study, we aim to harness the power of state-of-the-art deep learning neural networks (NNs) to identify plasma proteins that predict amyloid, tau, and neurodegeneration (AT[N]) pathologies in AD. METHODS We measured 3,635 proteins using SOMAscan in 881 participants from the European Medical Information Framework for AD Multimodal Biomarker Discovery study (EMIF-AD MBD). Participants underwent measurements of brain amyloid β (Aβ) burden, phosphorylated tau (p-tau) burden, and total tau (t-tau) burden to determine their AT(N) statuses. We ranked proteins by their association with Aβ, p-tau, t-tau, and AT(N), and fed the top 100 proteins along with age and apolipoprotein E (APOE) status into NN classifiers as input features to predict these four outcomes relevant to AD. We compared NN performance of using proteins, age, and APOE genotype with performance of using age and APOE status alone to identify protein panels that optimally improved the prediction over these main risk factors. Proteins that improved the prediction for each outcome were aggregated and nominated for pathway enrichment and protein-protein interaction enrichment analysis. RESULTS Age and APOE alone predicted Aβ, p-tau, t-tau, and AT(N) burden with area under the curve (AUC) scores of 0.748, 0.662, 0.710, and 0.795. The addition of proteins significantly improved AUCs to 0.782, 0.674, 0.734, and 0.831, respectively. The identified proteins were enriched in five clusters of AD-associated pathways including human immunodeficiency virus 1 infection, p53 signaling pathway, and phosphoinositide-3-kinase-protein kinase B/Akt signaling pathway. CONCLUSION Combined with age and APOE genotype, the proteins identified have the potential to serve as blood-based biomarkers for AD and await validation in future studies. While the NNs did not achieve better scores than the support vector machine model used in our previous study, their performances were likely limited by small sample size.
Collapse
Affiliation(s)
- Yuting Zhang
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Upamanyu Ghose
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Noel J. Buckley
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Sebastiaan Engelborghs
- Department of Biomedical Sciences, Reference Center for Biological Markers of Dementia (BIODEM), Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Department of Neurology, Universitair Ziekenhuis Brussel, Brussels, Belgium
- Center for Neurociences (C4N), Vrije Universiteit Brussel, Brussels, Belgium
| | - Kristel Sleegers
- Complex Genetics Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Anders Wallin
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Alberto Lleó
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Julius Popp
- Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
- Department of Geriatric Psychiatry, University Hospital of Psychiatry and University of Zürich, Zürich, Switzerland
| | | | - Cristina Legido-Quigley
- Kings College London, London, United Kingdom
- The Systems Medicine Group, Steno Diabetes Center, Gentofte, Denmark
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, VU University Medical Center, Amsterdam, Netherlands
- University College London (UCL) Institutes of Neurology and Healthcare Engineering, London, United Kingdom
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, 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, United Kingdom
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Pieter Jelle Visser
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, Netherlands
- Alzheimer Center, VU University Medical Center, Amsterdam, Netherlands
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Simon Lovestone
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
- Janssen R&D, High Wycombe, United Kingdom
| | | | - Liu Shi
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
15
|
Aerqin Q, Wang ZT, Wu KM, He XY, Dong Q, Yu JT. Omics-based biomarkers discovery for Alzheimer's disease. Cell Mol Life Sci 2022; 79:585. [PMID: 36348101 DOI: 10.1007/s00018-022-04614-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorders presenting with the pathological hallmarks of amyloid plaques and tau tangles. Over the past few years, great efforts have been made to explore reliable biomarkers of AD. High-throughput omics are a technology driven by multiple levels of unbiased data to detect the complex etiology of AD, and it provides us with new opportunities to better understand the pathophysiology of AD and thereby identify potential biomarkers. Through revealing the interaction networks between different molecular levels, the ultimate goal of multi-omics is to improve the diagnosis and treatment of AD. In this review, based on the current AD pathology and the current status of AD diagnostic biomarkers, we summarize how genomics, transcriptomics, proteomics and metabolomics are all conducing to the discovery of reliable AD biomarkers that could be developed and used in clinical AD management.
Collapse
Affiliation(s)
- Qiaolifan Aerqin
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Zuo-Teng Wang
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Kai-Min Wu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Xiao-Yu He
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Qiang Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Jin-Tai Yu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China.
| |
Collapse
|
16
|
He B, Huang Z, Huang C, Nice EC. Clinical applications of plasma proteomics and peptidomics: Towards precision medicine. Proteomics Clin Appl 2022; 16:e2100097. [PMID: 35490333 DOI: 10.1002/prca.202100097] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023]
Abstract
In the context of precision medicine, disease treatment requires individualized strategies based on the underlying molecular characteristics to overcome therapeutic challenges posed by heterogeneity. For this purpose, it is essential to develop new biomarkers to diagnose, stratify, or possibly prevent diseases. Plasma is an available source of biomarkers that greatly reflects the physiological and pathological conditions of the body. An increasing number of studies are focusing on proteins and peptides, including many involving the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), and proteomics and peptidomics techniques are emerging as critical tools for developing novel precision medicine preventative measures. Excitingly, the emerging plasma proteomics and peptidomics toolbox exhibits a huge potential for studying pathogenesis of diseases (e.g., COVID-19 and cancer), identifying valuable biomarkers and improving clinical management. However, the enormous complexity and wide dynamic range of plasma proteins makes plasma proteome profiling challenging. Herein, we summarize the recent advances in plasma proteomics and peptidomics with a focus on their emerging roles in COVID-19 and cancer research, aiming to emphasize the significance of plasma proteomics and peptidomics in clinical applications and precision medicine.
Collapse
Affiliation(s)
- Bo He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China.,Department of Pharmacology, and Provincial Key Laboratory of Pathophysiology in Ningbo University School of Medicine, Ningbo, Zhejiang, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| |
Collapse
|
17
|
Botella Lucena P, Vanherle S, Lodder C, Gutiérrez de Ravé M, Stancu IC, Lambrichts I, Vangheluwe R, Bruffaerts R, Dewachter I. Blood-based Aβ42 increases in the earliest pre-pathological stage before decreasing with progressive amyloid pathology in preclinical models and human subjects: opening new avenues for prevention. Acta Neuropathol 2022; 144:489-508. [PMID: 35796870 PMCID: PMC9381631 DOI: 10.1007/s00401-022-02458-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 11/27/2022]
Abstract
Blood-based (BB) biomarkers for Aβ and tau can indicate pathological processes in the brain, in the early pathological, even pre-symptomatic stages in Alzheimer’s disease. However, the relation between BB biomarkers and AD-related processes in the brain in the earliest pre-pathology stage before amyloid pathology develops, and their relation with total brain concentrations of Aβ and tau, is poorly understood. This stage presents a critical window for the earliest prevention of AD. Preclinical models with well-defined temporal progression to robust amyloid and tau pathology provide a unique opportunity to study this relation and were used here to study the link between BB biomarkers with AD-related processes in pre- and pathological stages. We performed a cross-sectional study at different ages assessing the link between BB concentrations and AD-related processes in the brain. This was complemented with a longitudinal analysis and with analysis of age-related changes in a small cohort of human subjects. We found that BB-tau concentrations increased in serum, correlating with progressive development of tau pathology and with increasing tau aggregates and p-tau concentrations in brain in TauP301S mice (PS19) developing tauopathy. BB-Aβ42 concentrations in serum decreased between 4.5 and 9 months of age, correlating with the progressive development of robust amyloid pathology in APP/PS1 (5xFAD) mice, in line with previous findings. Most importantly, BB-Aβ42 concentrations significantly increased between 1.5 and 4.5 months, i.e., in the earliest pre-pathological stage, before robust amyloid pathology develops in the brain, indicating biphasic BB-Aβ42 dynamics. Furthermore, increasing BB-Aβ42 in the pre-pathological phase, strongly correlated with increasing Aβ42 concentrations in brain. Our subsequent longitudinal analysis of BB-Aβ42 in 5xFAD mice, confirmed biphasic BB-Aβ42, with an initial increase, before decreasing with progressive robust pathology. Furthermore, in human samples, BB-Aβ42 concentrations were significantly higher in old (> 60 years) compared to young (< 50 years) subjects, as well as to age-matched AD patients, further supporting age-dependent increase of Aβ42 concentrations in the earliest pre-pathological phase, before amyloid pathology. Also BB-Aβ40 concentrations were found to increase in the earliest pre-pathological phase both in preclinical models and human subjects, while subsequent significantly decreasing concentrations in the pathological phase were characteristic for BB-Aβ42. Together our data indicate that BB biomarkers reflect pathological processes in brain of preclinical models with amyloid and tau pathology, both in the pathological and pre-pathological phase. Our data indicate a biphasic pattern of BB-Aβ42 in preclinical models and a human cohort. And most importantly, we here show that BB-Aβ increased and correlated with increasing concentrations of Aβ in the brain, in the earliest pre-pathological stage in a preclinical model. Our data thereby identify a novel critical window for prevention, using BB-Aβ as marker for accumulating Aβ in the brain, in the earliest pre-pathological stage, opening new avenues for personalized early preventive strategies against AD, even before amyloid pathology develops.
Collapse
Affiliation(s)
- Pablo Botella Lucena
- Biomedical Research Institute, BIOMED, Hasselt University, 3590, Diepenbeek, Belgium
| | - Sarah Vanherle
- Biomedical Research Institute, BIOMED, Hasselt University, 3590, Diepenbeek, Belgium
| | - Chritica Lodder
- Biomedical Research Institute, BIOMED, Hasselt University, 3590, Diepenbeek, Belgium
| | | | - Ilie-Cosmin Stancu
- Biomedical Research Institute, BIOMED, Hasselt University, 3590, Diepenbeek, Belgium
| | - Ivo Lambrichts
- Biomedical Research Institute, BIOMED, Hasselt University, 3590, Diepenbeek, Belgium
| | - Riet Vangheluwe
- Neurology Department, ZOL Genk General Hospital, Genk, Belgium
| | - Rose Bruffaerts
- Biomedical Research Institute, BIOMED, Hasselt University, 3590, Diepenbeek, Belgium.,Laboratory for Cognitive Neurology, Department of Neurosciences, Leuven Brain Institute (LBI), KU, 3000, Leuven, Belgium.,Department of Neurology, University Hospitals, 3000, Leuven, Belgium.,Computational Neurology, Experimental Neurobiology Unit, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Ilse Dewachter
- Biomedical Research Institute, BIOMED, Hasselt University, 3590, Diepenbeek, Belgium.
| |
Collapse
|
18
|
Hawksworth J, Fernández E, Gevaert K. A new generation of AD biomarkers: 2019 to 2021. Ageing Res Rev 2022; 79:101654. [PMID: 35636691 DOI: 10.1016/j.arr.2022.101654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) is the most common form of dementia and cases are rising worldwide. The effort to fight this disease is hampered by a lack of disease-modifying treatments and the absence of an early, accurate diagnostic tool. Neuropathology begins years or decades before symptoms occur and, upon onset of symptoms, diagnosis can take a year or more. Such delays postpone treatment and make research into the early stages of the disease difficult. Ideally, clinicians require a minimally invasive test that can detect AD in its early stages, before cognitive symptoms occur. Advances in proteomic technologies have facilitated the study of promising biomarkers of AD. Over the last two years (2019-2021) studies have identified and validated many species which can be measured in cerebrospinal fluid (CSF), plasma, or in both fluids, and which have a high predictive value for AD. We herein discuss proteins which have been highlighted as promising biomarkers of AD in the last two years, and consider implications for future research within the research framework of the amyloid (A), tau (T), neurodegeneration (N) scoring system. We review recently identified species of amyloid and tau which may improve diagnosis when used in combination with current measures such as amyloid-beta-42 (Aβ42), total tau (t-tau) and phosphorylated tau (p-tau). In addition, several proteins have been identified as likely proxies for neurodegeneration, including neurofilament light (NfL), synaptosomal-associated protein 25 (SNAP-25) and neurogranin (NRGN). Finally, proteins originating from diverse processes such as neuroinflammation, lipid transport and mitochondrial dysfunction could aid in both AD diagnosis and patient stratification.
Collapse
|
19
|
Salimi Y, Domingo-Fernández D, Bobis-Álvarez C, Hofmann-Apitius M, Birkenbihl C. ADataViewer: exploring semantically harmonized Alzheimer's disease cohort datasets. Alzheimers Res Ther 2022; 14:69. [PMID: 35598021 PMCID: PMC9123725 DOI: 10.1186/s13195-022-01009-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/27/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Currently, Alzheimer's disease (AD) cohort datasets are difficult to find and lack across-cohort interoperability, and the actual content of publicly available datasets often only becomes clear to third-party researchers once data access has been granted. These aspects severely hinder the advancement of AD research through emerging data-driven approaches such as machine learning and artificial intelligence and bias current data-driven findings towards the few commonly used, well-explored AD cohorts. To achieve robust and generalizable results, validation across multiple datasets is crucial. METHODS We accessed and systematically investigated the content of 20 major AD cohort datasets at the data level. Both, a medical professional and a data specialist, manually curated and semantically harmonized the acquired datasets. Finally, we developed a platform that displays vital information about the available datasets. RESULTS Here, we present ADataViewer, an interactive platform that facilitates the exploration of 20 cohort datasets with respect to longitudinal follow-up, demographics, ethnoracial diversity, measured modalities, and statistical properties of individual variables. It allows researchers to quickly identify AD cohorts that meet user-specified requirements for discovery and validation studies regarding available variables, sample sizes, and longitudinal follow-up. Additionally, we publish the underlying variable mapping catalog that harmonizes 1196 unique variables across the 20 cohorts and paves the way for interoperable AD datasets. CONCLUSIONS In conclusion, ADataViewer facilitates fast, robust data-driven research by transparently displaying cohort dataset content and supporting researchers in selecting datasets that are suited for their envisioned study. The platform is available at https://adata.scai.fraunhofer.de/ .
Collapse
Affiliation(s)
- Yasamin Salimi
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754, Sankt Augustin, Germany.
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115, Bonn, Germany.
| | - Daniel Domingo-Fernández
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754, Sankt Augustin, Germany
| | - Carlos Bobis-Álvarez
- University Hospital Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, 38010, Spain
| | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754, Sankt Augustin, Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115, Bonn, Germany
| | - Colin Birkenbihl
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754, Sankt Augustin, Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115, Bonn, Germany
| |
Collapse
|
20
|
Hillary RF, Gadd DA, McCartney DL, Shi L, Campbell A, Walker RM, Ritchie CW, Deary IJ, Evans KL, Nevado‐Holgado AJ, Hayward C, Porteous DJ, McIntosh AM, Lovestone S, Robinson MR, Marioni RE. Genome- and epigenome-wide studies of plasma protein biomarkers for Alzheimer's disease implicate TBCA and TREM2 in disease risk. Alzheimers Dement (Amst) 2022; 14:e12280. [PMID: 35475137 PMCID: PMC9019629 DOI: 10.1002/dad2.12280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/24/2022]
Abstract
Introduction The levels of many blood proteins are associated with Alzheimer's disease (AD) or its pathological hallmarks. Elucidating the molecular factors that control circulating levels of these proteins may help to identify proteins associated with disease risk mechanisms. Methods Genome-wide and epigenome-wide studies (nindividuals ≤1064) were performed on plasma levels of 282 AD-associated proteins, identified by a structured literature review. Bayesian penalized regression estimated contributions of genetic and epigenetic variation toward inter-individual differences in plasma protein levels. Mendelian randomization (MR) and co-localization tested associations between proteins and disease-related phenotypes. Results Sixty-four independent genetic and 26 epigenetic loci were associated with 45 proteins. Novel findings included an association between plasma triggering receptor expressed on myeloid cells 2 (TREM2) levels and a polymorphism and cytosine-phosphate-guanine (CpG) site within the MS4A4A locus. Higher plasma tubulin-specific chaperone A (TBCA) and TREM2 levels were significantly associated with lower AD risk. Discussion Our data inform the regulation of biomarker levels and their relationships with AD.
Collapse
Affiliation(s)
- Robert F. Hillary
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
| | - Danni A. Gadd
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
| | - Daniel L. McCartney
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
| | - Liu Shi
- Department of PsychiatryUniversity of OxfordOxfordUK
| | - Archie Campbell
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
| | - Rosie M. Walker
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
- Centre for Clinical Brain Sciences, Chancellor's Building, 49 Little France CrescentUniversity of EdinburghEdinburghUK
| | - Craig W. Ritchie
- Edinburgh Dementia Prevention, Centre for Clinical Brain SciencesUniversity of EdinburghEdinburghUK
| | - Ian J. Deary
- Lothian Birth Cohorts, Department of PsychologyUniversity of EdinburghEdinburghUK
| | - Kathryn L. Evans
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
| | | | - Caroline Hayward
- MRC Human Genetics UnitInstitute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - David J. Porteous
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
| | - Andrew M. McIntosh
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
- Division of Psychiatry, Centre for Clinical Brain SciencesUniversity of EdinburghEdinburghUK
| | - Simon Lovestone
- Department of PsychiatryUniversity of OxfordOxfordUK
- NeurodegenerationJohnson and Johnson Medical LtdWokinghamUK
| | - Matthew R. Robinson
- Medical Genomics GroupInstitute of Science and Technology AustriaKlosterneuburgAustria
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
| |
Collapse
|
21
|
Zelek WM, Morgan BP. Targeting complement in neurodegeneration: challenges, risks, and strategies. Trends Pharmacol Sci 2022; 43:615-628. [DOI: 10.1016/j.tips.2022.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/13/2022]
|
22
|
Abstract
Purpose: Neurodegenerative disorders are a global health burden with costly and invasive diagnoses relying on brain imaging technology or CSF-based biomarkers. Therefore, considerable efforts to identify blood-biomarkers for Alzheimer's (AD) and Parkinson's diseases (PD) are ongoing. Objectives: This review evaluates the blood biomarkers for AD and PD for their diagnostic value. Methods: This study systematically reviewed articles published between July 1984 and February 2021. Among 1266 papers, we selected 42 studies for a systematic review and 23 studies for meta-analysis. Results & conclusion: Our analysis highlights P-tau181, T-tau and Nfl as promising blood biomarkers for AD diagnosis. Nfl levels were consistently raised in 16 AD and three PD cohorts. P-tau181 and T-tau were also significantly increased in 12 and eight AD cohorts, respectively.
Collapse
Affiliation(s)
- Kailash Singh
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong, China
| | - Bernard My Cheung
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong, China.,Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Aimin Xu
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong, China.,Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China.,Department of Pharmacy & Pharmacology, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
23
|
Ren AH, Diamandis EP, Kulasingam V. Uncovering the Depths of the Human Proteome: Antibody-based Technologies for Ultrasensitive Multiplexed Protein Detection and Quantification. Mol Cell Proteomics 2021; 20:100155. [PMID: 34597790 PMCID: PMC9357438 DOI: 10.1016/j.mcpro.2021.100155] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/01/2021] [Accepted: 09/25/2021] [Indexed: 12/20/2022] Open
Abstract
Probing the human proteome in tissues and biofluids such as plasma is attractive for biomarker and drug target discovery. Recent breakthroughs in multiplex, antibody-based, proteomics technologies now enable the simultaneous quantification of thousands of proteins at as low as sub fg/ml concentrations with remarkable dynamic ranges of up to 10-log. We herein provide a comprehensive guide to the methodologies, performance, technical comparisons, advantages, and disadvantages of established and emerging technologies for the multiplexed ultrasensitive measurement of proteins. Gaining holistic knowledge on these innovations is crucial for choosing the right multiplexed proteomics tool for applications at hand to critically complement traditional proteomics methods. This can bring researchers closer than ever before to elucidating the intricate inner workings and cross talk that spans multitude of proteins in disease mechanisms.
Collapse
Affiliation(s)
- Annie H Ren
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada.
| |
Collapse
|
24
|
Thanasupawat T, Glogowska A, Pascoe C, Krishnan SN, Munir M, Begum F, Beiko J, Krcek J, Del Bigio MR, Pitz M, Shen Y, Spicer V, Coombs KM, Wilkins J, Hombach-Klonisch S, Klonisch T. Slow Off-Rate Modified Aptamer (SOMAmer) Proteomic Analysis of Patient-Derived Malignant Glioma Identifies Distinct Cellular Proteomes. Int J Mol Sci 2021; 22:9566. [PMID: 34502484 DOI: 10.3390/ijms22179566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 02/04/2023] Open
Abstract
Malignant gliomas derive from brain glial cells and represent >75% of primary brain tumors. This includes anaplastic astrocytoma (grade III; AS), the most common and fatal glioblastoma multiforme (grade IV; GBM), and oligodendroglioma (ODG). We have generated patient-derived AS, GBM, and ODG cell models to study disease mechanisms and test patient-centered therapeutic strategies. We have used an aptamer-based high-throughput SOMAscan® 1.3K assay to determine the proteomic profiles of 1307 different analytes. SOMAscan® proteomes of AS and GBM self-organized into closely adjacent proteomes which were clearly distinct from ODG proteomes. GBM self-organized into four proteomic clusters of which SOMAscan® cluster 4 proteome predicted a highly inter-connected proteomic network. Several up- and down-regulated proteins relevant to glioma were successfully validated in GBM cell isolates across different SOMAscan® clusters and in corresponding GBM tissues. Slow off-rate modified aptamer proteomics is an attractive analytical tool for rapid proteomic stratification of different malignant gliomas and identified cluster-specific SOMAscan® signatures and functionalities in patient GBM cells.
Collapse
|
25
|
Kawashima Y, Nishikomori R, Ohara O. Multiomic technologies for analyses of inborn errors of immunity: from snapshot of the average cell to dynamic temporal picture at single-cell resolution. Inflamm Regen 2021; 41:19. [PMID: 34193319 PMCID: PMC8247241 DOI: 10.1186/s41232-021-00169-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/02/2021] [Indexed: 11/29/2022] Open
Abstract
Advances in DNA sequencing technology have significantly impacted human genetics; they have enabled the analysis of genetic causes of rare diseases, which are usually pathogenic variants in a single gene at the nucleotide sequence level. However, since the quantity of data regarding the relationship between genotype and phenotype is insufficient to diagnose some rare immune diseases definitively, genetic information alone cannot help obtain a mechanistic understanding of the disease etiology. For such cases, exploring the molecular phenotype using multiomic analyses could be the approach of choice. In this review, we first overview current technologies for multiomic analysis, particularly focusing on RNA and protein profiling of bulk cell ensembles. We then discuss the measurement modality and granularity issue because it is critical to design multiomic experiments properly. Next, we illustrate the importance of bioimaging by describing our experience with the analysis of an autoinflammatory disease, cryopyrin-associated periodic fever syndrome, which could be caused by low-frequency somatic mosaicism and cannot be well characterized only by multiomic snapshot analyses of an ensemble of many immune cells. We found it powerful to complement the multiomic data with bioimaging data that can provide us with indispensable time-specific dynamic information of every single cell in the "immune cell society." Because we now have many measurement tools in different modalities and granularity to tackle the etiology of rare hereditary immune diseases, we might gain a deeper understanding of the pathogenic mechanisms of these diseases by taking full advantage of these tools in an integrated manner.
Collapse
Affiliation(s)
- Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Ryuta Nishikomori
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, 830-0011, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan.
- Future Medicine Education and Research Organization, Chiba University, Chiba, 260-8670, Japan.
| |
Collapse
|
26
|
Florentinus-Mefailoski A, Bowden P, Scheltens P, Killestein J, Teunissen C, Marshall JG. The plasma peptides of Alzheimer's disease. Clin Proteomics 2021; 18:17. [PMID: 34182925 PMCID: PMC8240224 DOI: 10.1186/s12014-021-09320-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/20/2021] [Indexed: 02/06/2023] Open
Abstract
Background A practical strategy to discover proteins specific to Alzheimer’s dementia (AD) may be to compare the plasma peptides and proteins from patients with dementia to normal controls and patients with neurological conditions like multiple sclerosis or other diseases. The aim was a proof of principle for a method to discover proteins and/or peptides of plasma that show greater observation frequency and/or precursor intensity in AD. The endogenous tryptic peptides of Alzheimer’s were compared to normals, multiple sclerosis, ovarian cancer, breast cancer, female normal, sepsis, ICU Control, heart attack, along with their institution-matched controls, and normal samples collected directly onto ice. Methods Endogenous tryptic peptides were extracted from blinded, individual AD and control EDTA plasma samples in a step gradient of acetonitrile for random and independent sampling by LC–ESI–MS/MS with a set of robust and sensitive linear quadrupole ion traps. The MS/MS spectra were fit to fully tryptic peptides within proteins identified using the X!TANDEM algorithm. Observation frequency of the identified proteins was counted using SEQUEST algorithm. The proteins with apparently increased observation frequency in AD versus AD Control were revealed graphically and subsequently tested by Chi Square analysis. The proteins specific to AD plasma by Chi Square with FDR correction were analyzed by the STRING algorithm. The average protein or peptide log10 precursor intensity was compared across disease and control treatments by ANOVA in the R statistical system. Results Peptides and/or phosphopeptides of common plasma proteins such as complement C2, C7, and C1QBP among others showed increased observation frequency by Chi Square and/or precursor intensity in AD. Cellular gene symbols with large Chi Square values (χ2 ≥ 25, p ≤ 0.001) from tryptic peptides included KIF12, DISC1, OR8B12, ZC3H12A, TNF, TBC1D8B, GALNT3, EME2, CD1B, BAG1, CPSF2, MMP15, DNAJC2, PHACTR4, OR8B3, GCK, EXOSC7, HMGA1 and NT5C3A among others. Similarly, increased frequency of tryptic phosphopeptides were observed from MOK, SMIM19, NXNL1, SLC24A2, Nbla10317, AHRR, C10orf90, MAEA, SRSF8, TBATA, TNIK, UBE2G1, PDE4C, PCGF2, KIR3DP1, TJP2, CPNE8, and NGF amongst others. STRING analysis showed an increase in cytoplasmic proteins and proteins associated with alternate splicing, exocytosis of luminal proteins, and proteins involved in the regulation of the cell cycle, mitochondrial functions or metabolism and apoptosis. Increases in mean precursor intensity of peptides from common plasma proteins such as DISC1, EXOSC5, UBE2G1, SMIM19, NXNL1, PANO, EIF4G1, KIR3DP1, MED25, MGRN1, OR8B3, MGC24039, POLR1A, SYTL4, RNF111, IREB2, ANKMY2, SGKL, SLC25A5, CHMP3 among others were associated with AD. Tryptic peptides from the highly conserved C-terminus of DISC1 within the sequence MPGGGPQGAPAAAGGGGVSHRAGSRDCLPPAACFR and ARQCGLDSR showed a higher frequency and highest intensity in AD compared to all other disease and controls. Conclusion Proteins apparently expressed in the brain that were directly related to Alzheimer’s including Nerve Growth Factor (NFG), Sphingomyelin Phosphodiesterase, Disrupted in Schizophrenia 1 (DISC1), the cell death regulator retinitis pigmentosa (NXNl1) that governs the loss of nerve cells in the retina and the cell death regulator ZC3H12A showed much higher observation frequency in AD plasma vs the matched control. There was a striking agreement between the proteins known to be mutated or dis-regulated in the brains of AD patients with the proteins observed in the plasma of AD patients from endogenous peptides including NBN, BAG1, NOX1, PDCD5, SGK3, UBE2G1, SMPD3 neuronal proteins associated with synapse function such as KSYTL4, VTI1B and brain specific proteins such as TBATA. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-021-09320-2.
Collapse
Affiliation(s)
- Angelique Florentinus-Mefailoski
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada
| | - Peter Bowden
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada
| | - Philip Scheltens
- Alzheimer Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Joep Killestein
- MS Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Charlotte Teunissen
- Neurochemistry Lab and Biobank, Dept of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - John G Marshall
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada. .,International Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (Formerly CRP Sante Luxembourg), Strassen, Luxembourg.
| |
Collapse
|
27
|
Abstract
Introduction: Atopic dermatitis (AD) is a chronic inflammatory skin condition characterized by cutaneous and systemic inflammation and barrier abnormalities. Over the past few decades, proteomic studies have been increasingly applied to AD research to compliment transcriptomic evaluations. Proteomic analyses helped identify new biomarkers of AD, allowing investigation of both the cutaneous AD profile and the systemic inflammation associated with the disease.Areas covered: This review discusses key studies that utilized various proteomic technologies to analyze AD skin and/or blood, which facilitated discovery of biomarkers related to pathogenesis, disease severity, systemic inflammation, and therapeutic response. Moreover, this review summarizes proteomic studies that helped define various AD endotypes/phenotypes. A literature search was conducted by querying Scopus, Google Scholar, PubMed/Medline, and Clinicaltrials.gov up to January 2021.Expert opinion: Use of proteomics in AD has allowed for identification of novel AD-related protein biomarkers. This approach continues to evolve and is becoming increasingly common for the study of AD, in conjunction with other -omics platforms, as proteomics shifts to quicker and more sensitive methods for detection of potential protein biomarkers. Although many biomarkers have been identified thus far, future larger studies are necessary to further correlate these markers with clinical parameters.
Collapse
Affiliation(s)
- Daniela Mikhaylov
- Department of Dermatology, and Laboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ester Del Duca
- Department of Dermatology, and Laboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Dermatology, University of Magna Graecia, Catanzaro, Italy
| | - Emma Guttman-Yassky
- Department of Dermatology, and Laboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
28
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| | | |
Collapse
|
29
|
Ashford MT, Veitch DP, Neuhaus J, Nosheny RL, Tosun D, Weiner MW. The search for a convenient procedure to detect one of the earliest signs of Alzheimer's disease: A systematic review of the prediction of brain amyloid status. Alzheimers Dement 2021; 17:866-887. [PMID: 33583100 DOI: 10.1002/alz.12253] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/10/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Convenient, cost-effective tests for amyloid beta (Aβ) are needed to identify those at higher risk for developing Alzheimer's disease (AD). This systematic review evaluates recent models that predict dichotomous Aβ. (PROSPERO: CRD42020144734). METHODS We searched Embase and identified 73 studies from 29,581 for review. We assessed study quality using established tools, extracted information, and reported results narratively. RESULTS We identified few high-quality studies due to concerns about Aβ determination and analytical issues. The most promising convenient, inexpensive classifiers consist of age, apolipoprotein E genotype, cognitive measures, and/or plasma Aβ. Plasma Aβ may be sufficient if pre-analytical variables are standardized and scalable assays developed. Some models lowered costs associated with clinical trial recruitment or clinical screening. DISCUSSION Conclusions about models are difficult due to study heterogeneity and quality. Promising prediction models used demographic, cognitive/neuropsychological, imaging, and plasma Aβ measures. Further studies using standardized Aβ determination, and improved model validation are required.
Collapse
Affiliation(s)
- Miriam T Ashford
- Department of Veterans Affairs Medical Center, Northern California Institute for Research and Education, San Francisco, California, USA.,Department of Veterans Affairs Medical Center, Center for Imaging and Neurodegenerative Diseases, San Francisco, California, USA
| | - Dallas P Veitch
- Department of Veterans Affairs Medical Center, Northern California Institute for Research and Education, San Francisco, California, USA
| | - John Neuhaus
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Rachel L Nosheny
- Department of Veterans Affairs Medical Center, Center for Imaging and Neurodegenerative Diseases, San Francisco, California, USA.,Department of Psychiatry, University of California San Francisco, San Francisco, California, USA
| | - Duygu Tosun
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Michael W Weiner
- Department of Veterans Affairs Medical Center, Northern California Institute for Research and Education, San Francisco, California, USA.,Department of Veterans Affairs Medical Center, Center for Imaging and Neurodegenerative Diseases, San Francisco, California, USA.,Department of Psychiatry, University of California San Francisco, San Francisco, California, USA.,Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA.,Department of Medicine, University of California San Francisco, San Francisco, California, USA.,Department of Neurology, University of California San Francisco, San Francisco, California, USA
| |
Collapse
|
30
|
Khan MJ, Desaire H, Lopez OL, Kamboh MI, Robinson RA. Why Inclusion Matters for Alzheimer’s Disease Biomarker Discovery in Plasma. J Alzheimers Dis 2021; 79:1327-1344. [DOI: 10.3233/jad-201318] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Background: African American/Black adults have a disproportionate incidence of Alzheimer’s disease (AD) and are underrepresented in biomarker discovery efforts. Objective: This study aimed to identify potential diagnostic biomarkers for AD using a combination of proteomics and machine learning approaches in a cohort that included African American/Black adults. Methods: We conducted a discovery-based plasma proteomics study on plasma samples (N = 113) obtained from clinically diagnosed AD and cognitively normal adults that were self-reported African American/Black or non-Hispanic White. Sets of differentially-expressed proteins were then classified using a support vector machine (SVM) to identify biomarker candidates. Results: In total, 740 proteins were identified of which, 25 differentially-expressed proteins in AD came from comparisons within a single racial and ethnic background group. Six proteins were differentially-expressed in AD regardless of racial and ethnic background. Supervised classification by SVM yielded an area under the curve (AUC) of 0.91 and accuracy of 86%for differentiating AD in samples from non-Hispanic White adults when trained with differentially-expressed proteins unique to that group. However, the same model yielded an AUC of 0.49 and accuracy of 47%for differentiating AD in samples from African American/Black adults. Other covariates such as age, APOE4 status, sex, and years of education were found to improve the model mostly in the samples from non-Hispanic White adults for classifying AD. Conclusion: These results demonstrate the importance of study designs in AD biomarker discovery, which must include diverse racial and ethnic groups such as African American/Black adults to develop effective biomarkers.
Collapse
Affiliation(s)
- Mostafa J. Khan
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS, USA
| | - Oscar L. Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - M. Ilyas Kamboh
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Renã A.S. Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| |
Collapse
|
31
|
Xu J, Bankov G, Kim M, Wretlind A, Lord J, Green R, Hodges A, Hye A, Aarsland D, Velayudhan L, Dobson RJB, Proitsi P, Legido-Quigley C. Integrated lipidomics and proteomics network analysis highlights lipid and immunity pathways associated with Alzheimer's disease. Transl Neurodegener 2020; 9:36. [PMID: 32951606 PMCID: PMC7504646 DOI: 10.1186/s40035-020-00215-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/18/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND There is an urgent need to understand the pathways and processes underlying Alzheimer's disease (AD) for early diagnosis and development of effective treatments. This study was aimed to investigate Alzheimer's dementia using an unsupervised lipid, protein and gene multi-omics integrative approach. METHODS A lipidomics dataset comprising 185 AD patients, 40 mild cognitive impairment (MCI) individuals and 185 controls, and two proteomics datasets (295 AD, 159 MCI and 197 controls) were used for weighted gene co-expression network analyses (WGCNA). Correlations of modules created within each modality with clinical AD diagnosis, brain atrophy measures and disease progression, as well as their correlations with each other, were analyzed. Gene ontology enrichment analysis was employed to examine the biological processes and molecular and cellular functions of protein modules associated with AD phenotypes. Lipid species were annotated in the lipid modules associated with AD phenotypes. The associations between established AD risk loci and the lipid/protein modules that showed high correlation with AD phenotypes were also explored. RESULTS Five of the 20 identified lipid modules and five of the 17 identified protein modules were correlated with clinical AD diagnosis, brain atrophy measures and disease progression. The lipid modules comprising phospholipids, triglycerides, sphingolipids and cholesterol esters were correlated with AD risk loci involved in immune response and lipid metabolism. The five protein modules involved in positive regulation of cytokine production, neutrophil-mediated immunity, and humoral immune responses were correlated with AD risk loci involved in immune and complement systems and in lipid metabolism (the APOE ε4 genotype). CONCLUSIONS Modules of tightly regulated lipids and proteins, drivers in lipid homeostasis and innate immunity, are strongly associated with AD phenotypes.
Collapse
Affiliation(s)
- Jin Xu
- Institute of Pharmaceutical Science, King's College London, London, UK
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Giulia Bankov
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Min Kim
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | | | - Jodie Lord
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Rebecca Green
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Angela Hodges
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Abdul Hye
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Dag Aarsland
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Center for Age-Related Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Latha Velayudhan
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Richard J B Dobson
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
| | - Petroula Proitsi
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
| | - Cristina Legido-Quigley
- Institute of Pharmaceutical Science, King's College London, London, UK.
- Steno Diabetes Center Copenhagen, Gentofte, Denmark.
| |
Collapse
|
32
|
Peña-Bautista C, Álvarez L, Durand T, Vigor C, Cuevas A, Baquero M, Vento M, Hervás D, Cháfer-Pericás C. Clinical Utility of Plasma Lipid Peroxidation Biomarkers in Alzheimer's Disease Differential Diagnosis. Antioxidants (Basel) 2020; 9:antiox9080649. [PMID: 32707935 PMCID: PMC7464465 DOI: 10.3390/antiox9080649] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Differential diagnosis of Alzheimer's disease (AD) is a complex task due to the clinical similarity among neurodegenerative diseases. Previous studies showed the role of lipid peroxidation in early AD development. However, the clinical validation of potential specific biomarkers in minimally invasive samples constitutes a great challenge in early AD diagnosis. METHODS Plasma samples from participants classified into AD (n = 138), non-AD (including MCI and other dementias not due to AD) (n = 70) and healthy (n = 50) were analysed. Lipid peroxidation compounds (isoprostanes, isofurans, neuroprostanes, neurofurans) were determined by ultra-performance liquid chromatography coupled with tandem mass spectrometry. Statistical analysis for biomarkers' clinical validation was based on Elastic Net. RESULTS A two-step diagnosis model was developed from plasma lipid peroxidation products to diagnose early AD specifically, and a bootstrap validated AUC of 0.74 was obtained. CONCLUSION A promising AD differential diagnosis model was developed. It was clinically validated as a screening test. However, further external validation is required before clinical application.
Collapse
Affiliation(s)
- Carmen Peña-Bautista
- Neonatal Research Unit, Health Research Institute La Fe, 46026 Valencia, Spain; (C.P.-B.); (M.V.)
| | - Lourdes Álvarez
- Neurology Unit, University and Polytechnic Hospital La Fe, 46026 Valencia, Spain; (L.A.); (A.C.); (M.B.)
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, CNRS ENSCM, 34093 Montpellier, France; (T.D.); (C.V.)
| | - Claire Vigor
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, CNRS ENSCM, 34093 Montpellier, France; (T.D.); (C.V.)
| | - Ana Cuevas
- Neurology Unit, University and Polytechnic Hospital La Fe, 46026 Valencia, Spain; (L.A.); (A.C.); (M.B.)
| | - Miguel Baquero
- Neurology Unit, University and Polytechnic Hospital La Fe, 46026 Valencia, Spain; (L.A.); (A.C.); (M.B.)
| | - Máximo Vento
- Neonatal Research Unit, Health Research Institute La Fe, 46026 Valencia, Spain; (C.P.-B.); (M.V.)
| | - David Hervás
- Biostatistical Unit, Health Research Institute La Fe, 46026 Valencia, Spain;
| | - Consuelo Cháfer-Pericás
- Neonatal Research Unit, Health Research Institute La Fe, 46026 Valencia, Spain; (C.P.-B.); (M.V.)
- Correspondence: ; Tel.: +34-961-246-721; Fax: +34-961-246-620
| |
Collapse
|
33
|
Ellegaard Nielsen J, Sofie Pedersen K, Vestergård K, Georgiana Maltesen R, Christiansen G, Lundbye-Christensen S, Moos T, Risom Kristensen S, Pedersen S. Novel Blood-Derived Extracellular Vesicle-Based Biomarkers in Alzheimer's Disease Identified by Proximity Extension Assay. Biomedicines 2020; 8:E199. [PMID: 32645971 PMCID: PMC7400538 DOI: 10.3390/biomedicines8070199] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 12/14/2022] Open
Abstract
Easily accessible biomarkers for Alzheimer's dementia (AD) are lacking and established clinical markers are limited in applicability. Blood is a common biofluid for biomarker discoveries, and extracellular vesicles (EVs) may provide a matrix for exploring AD related biomarkers. Thus, we investigated proteins related to neurological and inflammatory processes in plasma and EVs. By proximity extension assay (PEA), 182 proteins were measured in plasma and EVs from patients with AD (n = 10), Mild Cognitive Impairment (MCI, n = 10), and healthy controls (n = 10). Plasma-derived EVs were enriched by 20,000× g, 1 h, 4 °C, and confirmed using nanoparticle tracking analysis (NTA), western blotting, and transmission electron microscopy with immunolabelling (IEM). Presence of CD9+ EVs was confirmed by western blotting and IEM. No group differences in particle concentration or size were detected by NTA. However, significant protein profiles were observed among subjects, particularly for EVs. Several proteins and their ratios could distinguish cognitively affected from healthy individuals. For plasma TGF-α│CCL20 (AUC = 0.96, 95% CI = 0.88-1.00, p = 0.001) and EVs CLEC1B│CCL11 (AUC = 0.95, 95% CI = 0.86-1.00, p = 0.001) showed diagnostic capabilities. Using PEA, we identified protein profiles capable of distinguishing healthy controls from AD patients. EVs provided additional biological information related to AD not observed in plasma alone.
Collapse
Affiliation(s)
- Jonas Ellegaard Nielsen
- Department of Clinical Medicine, Aalborg University, DK-9000 Aalborg, Denmark; (S.L.-C.); (S.R.K.)
- Department of Clinical Biochemistry, Aalborg University Hospital, DK-9000 Aalborg, Denmark
| | | | - Karsten Vestergård
- Department of Neurology, Aalborg University Hospital, DK-9000 Aalborg, Denmark;
| | - Raluca Georgiana Maltesen
- Department of Anaesthesia and Intensive Care, Aalborg University Hospital, DK-9000 Aalborg, Denmark;
| | - Gunna Christiansen
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus, Denmark;
- Department of Health Science and Technology, Aalborg University, DK-9220 Aalborg, Denmark;
| | - Søren Lundbye-Christensen
- Department of Clinical Medicine, Aalborg University, DK-9000 Aalborg, Denmark; (S.L.-C.); (S.R.K.)
- Unit of Clinical Biostatistics, Aalborg University Hospital, DK-9000 Aalborg, Denmark
| | - Torben Moos
- Department of Health Science and Technology, Aalborg University, DK-9220 Aalborg, Denmark;
| | - Søren Risom Kristensen
- Department of Clinical Medicine, Aalborg University, DK-9000 Aalborg, Denmark; (S.L.-C.); (S.R.K.)
- Department of Clinical Biochemistry, Aalborg University Hospital, DK-9000 Aalborg, Denmark
| | - Shona Pedersen
- Department of Clinical Medicine, Aalborg University, DK-9000 Aalborg, Denmark; (S.L.-C.); (S.R.K.)
- Department of Clinical Biochemistry, Aalborg University Hospital, DK-9000 Aalborg, Denmark
| |
Collapse
|
34
|
Tanaka T, Lavery R, Varma V, Fantoni G, Colpo M, Thambisetty M, Candia J, Resnick SM, Bennett DA, Biancotto A, Bandinelli S, Ferrucci L. Plasma proteomic signatures predict dementia and cognitive impairment. Alzheimers Dement (N Y) 2020; 6:e12018. [PMID: 32607407 PMCID: PMC7210784 DOI: 10.1002/trc2.12018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 02/27/2020] [Indexed: 12/03/2022]
Abstract
INTRODUCTION Biomarker discovery of dementia and cognitive impairment is important to gather insight into mechanisms underlying the pathogenesis of these conditions. METHODS In 997 adults from the InCHIANTI study, we assessed the association of 1301 plasma proteins with dementia and cognitive impairment. Validation was conducted in two Alzheimer's disease (AD) case-control studies as well as endophenotypes of AD including cognitive decline, brain amyloid burden, and brain volume. RESULTS We identified four risk proteins that were significantly associated with increased odds (peptidase inhibitor 3 (PI3), trefoil factor 3 (TFF3), pregnancy associated plasma protein A (PAPPA), agouti-related peptide (AGRP)) and two protective proteins (myostatin (MSTN), integrin aVb5 (ITGAV/ITGB5)) with decreased odds of baseline cognitive impairment or dementia. Of these, four proteins (MSTN, PI3, TFF3, PAPPA) were associated cognitive decline in subjects that were cognitively normal at baseline. ITGAV/ITGB5 was associated with lower brain amyloid burden, MSTN and ITGAV/ITGB5 were associated with larger brain volume and slower brain atrophy, and PI3, PAPPA, and AGRP were associated with smaller brain volume and/or faster brain atrophy. DISCUSSION These proteins may be useful as non-invasive biomarkers of dementia and cognitive impairment.
Collapse
Affiliation(s)
- Toshiko Tanaka
- Translational Gerontology BranchNational Institute on AgingNIHBaltimoreMaryland
| | - Robert Lavery
- Translational Gerontology BranchNational Institute on AgingNIHBaltimoreMaryland
| | - Vijay Varma
- Laboratory of Behavioral NeuroscienceNational Institute on AgingNIHBaltimoreMaryland
| | - Giovanna Fantoni
- National Institute on Aging (NIA)Intramural Research Program (IRP)Clinical Research Core (CRC)
| | - Marco Colpo
- Geriatric UnitAzienda Sanitaria di FirenzeFlorenceItaly
| | - Madhav Thambisetty
- Laboratory of Behavioral NeuroscienceNational Institute on AgingNIHBaltimoreMaryland
| | - Julian Candia
- Laboratory of Human CarcinogenesisCenter for Cancer ResearchNational Cancer InstituteNIHBethesdaMaryland
| | - Susan M. Resnick
- Laboratory of Behavioral NeuroscienceNational Institute of AgingBaltimoreMaryland
| | - David A. Bennett
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinois
| | - Angelique Biancotto
- Precision Immunology, Immunology and Inflammation Research Therapeutic AreaSanofiCambridgeMAUSA
| | | | - Luigi Ferrucci
- Translational Gerontology BranchNational Institute on AgingNIHBaltimoreMaryland
| |
Collapse
|
35
|
Su C, Zhao N, Zou J, Yan X. TDZD-8 alleviates delayed neurological sequelae following acute carbon monoxide poisoning involving tau protein phosphorylation. Inhal Toxicol 2020; 32:79-85. [PMID: 32188325 DOI: 10.1080/08958378.2020.1741739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Objective: Acute carbon monoxide (CO)poisoning can cause delayed neurological sequelae (DNS). Glycogen synthase kinase 3β (GSK-3β) /Tau protein pathway is reported to play a key role in neurological abnormalities. In the present study, we aimed to determine the role of GSK-3β/Tau in DNS following acute CO poisoning.Methods: 4-benzyl-2-methyl-1,2,4-thiadiazolidine-3,5-dione (TDZD-8), a specific non-competitive inhibitor of GSK-3β, was used to inhibit GSK-3β. Twenty-four male Sprague-Dawley rats were randomly assigned to the three groups: Control group, CO group and CO-TDZD-8 group. Rats breathed 1000 ppm CO for 40 minutes and then 3000 ppm for up to 20 minutes until they lost consciousness. TDZD-8 (1 mg/kg) was administered intravenously three times after the end of CO exposure at 0, 24, 48 hours late. Learning and memory abilities were observed using the Morris Water Maze (MWM). Brain histological changes were evaluated by hematoxylin-eosin staining. Moreover, the expression levels of Tau and GSK-3β were detected after acute carbon monoxide poisoning.Results: TDZD-8 significantly attenuated the learning and memory dysfunction induced by acute CO poisoning, ameliorated the histology structure of damaged neural cells in cortex and hippocampus CA1 area. TDZD-8 clearly decreased p-Tau expression, reversed the reduction of p-GSK-3β induced by acute CO poisoning.Conclusions: The therapeutic effect of TDZD-8 in alleviating DNS caused by acute CO poisoning is related to the inactivation of Tau by intensifying the level of GSK-3β phosphorylation.
Collapse
Affiliation(s)
- Chenglei Su
- Department of Emergency Medicine Center, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ningjun Zhao
- Department of Emergency Medicine Center, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jianjiao Zou
- Department of Emergency Medicine Center, Lanling Hospital, Linyi, Shandong, China
| | - Xianliang Yan
- Department of Emergency Medicine Center, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| |
Collapse
|
36
|
Kudryashova KS, Burka K, Kulaga AY, Vorobyeva NS, Kennedy BK. Aging Biomarkers: From Functional Tests to Multi‐Omics Approaches. Proteomics 2020; 20:e1900408. [DOI: 10.1002/pmic.201900408] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/07/2020] [Indexed: 12/15/2022]
Affiliation(s)
| | - Ksenia Burka
- Centaura AG Bleicherweg 10 Zurich 8002 Switzerland
| | - Anton Y. Kulaga
- Centaura AG Bleicherweg 10 Zurich 8002 Switzerland
- Systems Biology of Aging GroupInstitute of Biochemistry of the Romanian Academy Splaiul Independentei 296 Bucharest 060031 Romania
| | | | - Brian K. Kennedy
- Departments of Biochemistry and Physiology Yong Loo Lin School of MedicineNational University of Singapore 8 Medical Drive, MD7, 117596 Singapore
- Singapore Institute for Clinical Sciences (SICS)Agency for Science and Technology (A*STAR)Brenner Centre for Molecular Medicine 30 Medical Drive Singapore 117609 Singapore
- Buck Institute for Research on Aging 8001 Redwood Blvd. Novato CA 94945‐1400 USA
| |
Collapse
|