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Pei J, Palanisamy CP, Jayaraman S, Natarajan PM, Umapathy VR, Roy JR, Thalamati D, Ahalliya RM, Kanniappan GV, Mironescu M. Proteomics profiling of extracellular vesicle for identification of potential biomarkers in Alzheimer's disease: A comprehensive review. Ageing Res Rev 2024; 99:102359. [PMID: 38821418 DOI: 10.1016/j.arr.2024.102359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
The intricate origins and diverse symptoms of Alzheimer's disease (AD) pose significant challenges for both diagnosis and treatment. Exosomes and microvesicles, which carry disease-specific cargo from a variety of central nervous system cell types, have emerged as promising reservoirs of biomarkers for AD. Research on the screening of possible biomarkers in Alzheimer's disease using proteomic profiling of EVs is systematically reviewed in this comprehensive review. We highlight key methodologies employed in EV isolation, characterization, and proteomic analysis, elucidating their advantages and limitations. Furthermore, we summarize the evolving landscape of EV-associated biomarkers implicated in AD pathogenesis, including proteins involved in amyloid-beta metabolism, tau phosphorylation, neuroinflammation, synaptic dysfunction, and neuronal injury. The literature review highlights the necessity for robust validation strategies and standardized protocols to effectively transition EV-based biomarkers into clinical use. In the concluding section, this review delves into potential future avenues and technological advancements pivotal in crafting EV-derived biomarkers applicable to AD diagnostics and prognostics. This review contributes to our comprehension of AD pathology and the advancement of precision medicine in neurodegenerative diseases, hinting at a promising era in AD precision medicine.
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Affiliation(s)
- JinJin Pei
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, 2011 QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C, Shaanxi Province Key Laboratory of Bio-Resources, College of Bioscience and Bioengineering, Shaanxi University of Technology, Hanzhong 723001, China
| | - Chella Perumal Palanisamy
- Department of Chemical Technology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Selvaraj Jayaraman
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospital, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai 600077, India
| | - Prabhu Manickam Natarajan
- Department of Clinical Sciences, Center of Medical and Bio-allied Health Sciences and Research, College of Dentistry, Ajman University, Ajman, United Arab Emirates
| | - Vidhya Rekha Umapathy
- Department of Public Health Dentistry, Thai Moogambigai Dental College and Hospital, Dr. MGR Educational and Research Institute, Chennai 600 107, Tamil Nadu, India
| | - Jeane Rebecca Roy
- Department of Anatomy, Bhaarath Medical College and hospital, Bharath Institute of Higher Education and Research (BIHER), Chennai, Tamil Nadu 600073, India
| | | | - Rathi Muthaiyan Ahalliya
- Department of Biochemistry, FASCM, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu 641021, India
| | | | - Monica Mironescu
- Faculty of Agricultural Sciences, Food Industry and Environmental Protection, Research Center in Biotechnology and Food Engineering, Lucian Blaga University of Sibiu, 7-9 Ioan Ratiu Street, Sibiu 550024, Romania.
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Li X, Chen J, Yang Y, Cai H, Ao Z, Xing Y, Li K, Yang K, Wallace A, Friend J, Lee LP, Wang N, Guo F. Extracellular vesicles-based point-of-care testing for the diagnosis and monitoring of Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.587511. [PMID: 38617279 PMCID: PMC11014472 DOI: 10.1101/2024.03.31.587511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Alzheimer's disease (AD) is a debilitating condition that affects millions of people worldwide. One promising strategy for detecting and monitoring AD early on is using extracellular vesicles (EVs)-based point-of-care testing; however, diagnosing AD using EVs poses a challenge due to the low abundance of EV-biomarkers. Here, we present a fully integrated organic electrochemical transistor (OECT) that enables high accuracy, speed, and convenience in the detection of EVs from AD patients. We incorporated self-aligned acoustoelectric enhancement of EVs on a chip that rapidly propels, enriches, and specifically binds EVs to the OECT detection area. With our enhancement of pre-concentration, we increased the sensitivity to a limit of detection of 500 EV particles/μL and reduced the required detection time to just two minutes. We also tested the sensor on an AD mouse model to monitor AD progression, examined mouse Aβ EVs at different time courses, and compared them with intraneuronal Aβ cumulation using MRI. This innovative technology has the potential to diagnose Alzheimer's and other neurodegenerative diseases accurately and quickly, enabling monitoring of disease progression and treatment response.
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Feng Q, Lu Y, Zhang R, Li Y, Zhao Z, Zhou H. Identification of differentially expressed exosome proteins in serum as potential biomarkers for cognitive impairments in cerebral small vessel disease. Neurosci Lett 2024; 822:137631. [PMID: 38211879 DOI: 10.1016/j.neulet.2024.137631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/25/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND Cognitive impairment arising from cerebral small vessel disease (CSVD) represents a critical subtype of vascular cognitive impairments (VCI) and is the primary cause of vascular dementia. However, identifying reliable clinical and laboratory indicators for this disease remain elusive. We hypothesize that plasma exosome proteins hold the potential to serve as biomarkers for the onset of cognitive dysfunction associated with cerebrovascular diseases. METHODS We employed TMT-based proteomics to discern variations in serum exosome proteomes between individuals with cognitive impairments due to CSVD and healthy volunteers. RESULTS Each group comprised 18 subjects, and through differential expression analysis, we identified 22 down-regulated and 8 up-regulated proteins between the two groups. Our research revealed 30 differentially expressed plasma exosome proteins, including histone, proteasome, clusterin and coagulation factor XIII, in individuals with cognitive impairments caused by CSVD. CONCLUSION The 30 differentially expressed plasma exosome proteins identified in our study are promising as biomarkers for diagnosing cognitive impairments resulting from CSVD. These findings may help us better understand the underlying pathological mechanisms involved in the diseases.
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Affiliation(s)
- Qian Feng
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Yanjing Lu
- Department of Neurology, Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Ruyang Zhang
- Department of Neurology, Suzhou Wuzhong People's Hospital, Suzhou, China
| | - Yifan Li
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Zhong Zhao
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.
| | - Hua Zhou
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.
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Soares Martins T, Pelech S, Ferreira M, Pinho B, Leandro K, de Almeida LP, Breitling B, Hansen N, Esselmann H, Wiltfang J, da Cruz e Silva OAB, Henriques AG. Phosphoproteome Microarray Analysis of Extracellular Particles as a Tool to Explore Novel Biomarker Candidates for Alzheimer's Disease. Int J Mol Sci 2024; 25:1584. [PMID: 38338863 PMCID: PMC10855802 DOI: 10.3390/ijms25031584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Phosphorylation plays a key role in Alzheimer's disease (AD) pathogenesis, impacting distinct processes such as amyloid-beta (Aβ) peptide production and tau phosphorylation. Impaired phosphorylation events contribute to senile plaques and neurofibrillary tangles' formation, two major histopathological hallmarks of AD. Blood-derived extracellular particles (bdEP) can represent a disease-related source of phosphobiomarker candidates, and hence, in this pilot study, bdEP of Control and AD cases were analyzed by a targeted phosphoproteomics approach using a high-density microarray that featured at least 1145 pan-specific and 913 phosphosite-specific antibodies. This approach, innovatively applied to bdEP, allowed the identification of 150 proteins whose expression levels and/or phosphorylation patterns were significantly altered across AD cases. Gene Ontology enrichment and Reactome pathway analysis unraveled potentially relevant molecular targets and disease-associated pathways, and protein-protein interaction networks were constructed to highlight key targets. The discriminatory value of both the total proteome and the phosphoproteome was evaluated by univariate and multivariate approaches. This pilot experiment supports that bdEP are enriched in phosphotargets relevant in an AD context, holding value as peripheral biomarker candidates for disease diagnosis.
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Affiliation(s)
- Tânia Soares Martins
- Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (T.S.M.)
| | - Steven Pelech
- Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
- Kinexus Bioinformatics Corporation, Vancouver, BC V6P 6T3, Canada
| | - Maria Ferreira
- Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (T.S.M.)
| | - Beatriz Pinho
- Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (T.S.M.)
| | - Kevin Leandro
- Center for Neuroscience and Cell Biology, Faculty of Pharmacy, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector–Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Luís Pereira de Almeida
- Center for Neuroscience and Cell Biology, Faculty of Pharmacy, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector–Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Benedict Breitling
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, 37075 Goettingen, Germany
| | - Niels Hansen
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, 37075 Goettingen, Germany
| | - Hermann Esselmann
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, 37075 Goettingen, Germany
| | - Jens Wiltfang
- Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (T.S.M.)
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, 37075 Goettingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), 37075 Goettingen, Germany
| | - Odete A. B. da Cruz e Silva
- Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (T.S.M.)
| | - Ana Gabriela Henriques
- Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (T.S.M.)
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Gómez-Carballa A, Navarro L, Pardo-Seco J, Bello X, Pischedda S, Viz-Lasheras S, Camino-Mera A, Currás MJ, Ferreirós I, Mallah N, Rey-Vázquez S, Redondo L, Dacosta-Urbieta A, Caamaño-Viña F, Rivero-Calle I, Rodriguez-Tenreiro C, Martinón-Torres F, Salas A. Music compensates for altered gene expression in age-related cognitive disorders. Sci Rep 2023; 13:21259. [PMID: 38040763 PMCID: PMC10692168 DOI: 10.1038/s41598-023-48094-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023] Open
Abstract
Extensive literature has explored the beneficial effects of music in age-related cognitive disorders (ACD), but limited knowledge exists regarding its impact on gene expression. We analyzed transcriptomes of ACD patients and healthy controls, pre-post a music session (n = 60), and main genes/pathways were compared to those dysregulated in mild cognitive impairment (MCI) and Alzheimer's disease (AD) as revealed by a multi-cohort study (n = 1269 MCI/AD and controls). Music was associated with 2.3 times more whole-genome gene expression, particularly on neurodegeneration-related genes, in ACD than in controls. Co-expressed gene-modules and pathways analysis demonstrated that music impacted autophagy, vesicle and endosome organization, biological processes commonly dysregulated in MCI/AD. Notably, the data indicated a strong negative correlation between musically-modified genes/pathways in ACD and those dysregulated in MCI/AD. These findings highlight the compensatory effect of music on genes/biological processes affected in MCI/AD, providing insights into the molecular mechanisms underlying the benefits of music on these disorders.
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Affiliation(s)
- Alberto Gómez-Carballa
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela (USC), and Genetica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Laura Navarro
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela (USC), and Genetica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Galicia, Spain
| | - Jacobo Pardo-Seco
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela (USC), and Genetica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Xabier Bello
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela (USC), and Genetica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Sara Pischedda
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela (USC), and Genetica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Sandra Viz-Lasheras
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela (USC), and Genetica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Alba Camino-Mera
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela (USC), and Genetica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - María José Currás
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela (USC), and Genetica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Isabel Ferreirós
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela (USC), and Genetica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Narmeen Mallah
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela (USC), and Genetica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706, Santiago de Compostela, Galicia, Spain
- Department of Preventive Medicine, University of Santiago de Compostela (USC), Santiago de Compostela, Galicia, Spain
| | - Sara Rey-Vázquez
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706, Santiago de Compostela, Galicia, Spain
| | - Lorenzo Redondo
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706, Santiago de Compostela, Galicia, Spain
| | - Ana Dacosta-Urbieta
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706, Santiago de Compostela, Galicia, Spain
| | - Fernando Caamaño-Viña
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706, Santiago de Compostela, Galicia, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706, Santiago de Compostela, Galicia, Spain
| | - Carmen Rodriguez-Tenreiro
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706, Santiago de Compostela, Galicia, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706, Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Genetics, Vaccines and Infections Research Group (GenViP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela (USC), 15706, Santiago de Compostela, Galicia, Spain.
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela (USC), and Genetica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Galicia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain.
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Augustine J, Jereesh AS. Identification of gene-level methylation for disease prediction. Interdiscip Sci 2023; 15:678-695. [PMID: 37603212 DOI: 10.1007/s12539-023-00584-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023]
Abstract
DNA methylation is an epigenetic alteration that plays a fundamental part in governing gene regulatory processes. The DNA methylation mechanism affixes methyl groups to distinct cytosine residues, influencing chromatin architectures. Multiple studies have demonstrated that DNA methylation's regulatory effect on genes is linked to the beginning and progression of several disorders. Researchers have recently uncovered thousands of phenotype-related methylation sites through the epigenome-wide association study (EWAS). However, combining the methylation levels of several sites within a gene and determining the gene-level DNA methylation remains challenging. In this study, we proposed the supervised UMAP Assisted Gene-level Methylation method (sUAGM) for disease prediction based on supervised UMAP (Uniform Manifold Approximation and Projection), a manifold learning-based method for reducing dimensionality. The methylation values at the gene level generated using the proposed method are evaluated by employing various feature selection and classification algorithms on three distinct DNA methylation datasets derived from blood samples. The performance has been assessed employing classification accuracy, F-1 score, Mathews Correlation Coefficient (MCC), Kappa, Classification Success Index (CSI) and Jaccard Index. The Support Vector Machine with the linear kernel (SVML) classifier with Recursive Feature Elimination (RFE) performs best across all three datasets. From comparative analysis, our method outperformed existing gene-level and site-level approaches by achieving 100% accuracy and F1-score with fewer genes. The functional analysis of the top 28 genes selected from the Parkinson's disease dataset revealed a significant association with the disease.
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Affiliation(s)
- Jisha Augustine
- Bioinformatics Lab, Department of Computer Science, Cochin University of Science and Technology, Cochin, Kerala, 682022, India.
| | - A S Jereesh
- Bioinformatics Lab, Department of Computer Science, Cochin University of Science and Technology, Cochin, Kerala, 682022, India
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7
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Liu YK, Wu X, Hadisurya M, Li L, Kaimakliotis H, Iliuk A, Tao WA. One-Pot Analytical Pipeline for Efficient and Sensitive Proteomic Analysis of Extracellular Vesicles. J Proteome Res 2023; 22:3301-3310. [PMID: 37702715 PMCID: PMC10897859 DOI: 10.1021/acs.jproteome.3c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Extracellular vesicle (EV) proteomics emerges as an effective tool for discovering potential biomarkers for disease diagnosis, monitoring, and therapeutics. However, the current workflow of mass spectrometry-based EV proteome analysis is not fully compatible in a clinical setting due to inefficient EV isolation methods and a tedious sample preparation process. To streamline and improve the efficiency of EV proteome analysis, here we introduce a one-pot analytical pipeline integrating a robust EV isolation approach, EV total recovery and purification (EVtrap), with in situ protein sample preparation, to detect urinary EV proteome. By incorporating solvent-driven protein capture and fast on-bead digestion, the one-pot pipeline enabled the whole EV proteome analysis to be completed within one day. In comparison with the existing workflow, the one-pot pipeline was able to obtain better peptide yield and identify the equivalent number of unique EV proteins from 1 mL of urine. Finally, we applied the one-pot pipeline to profile proteomes in urinary EVs of bladder cancer patients. A total of 2774 unique proteins were identified in 53 urine samples using a 15 min gradient library-free data-independent acquisition method. Taken altogether, our novel one-pot analytical pipeline demonstrated its potential for routine and robust EV proteomics in biomedical applications.
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Affiliation(s)
- Yi-Kai Liu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Marco Hadisurya
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Li Li
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
| | - Hristos Kaimakliotis
- Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Anton Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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8
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Wang F, Qin Y, Li Z. Serum retinol-binding protein 4 in stroke patients: correlation with T helper 17/regulatory T cell imbalance and 3-year cognitive function decline. Front Neurol 2023; 14:1217979. [PMID: 37808505 PMCID: PMC10551125 DOI: 10.3389/fneur.2023.1217979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/31/2023] [Indexed: 10/10/2023] Open
Abstract
Objective Retinol-binding protein 4 (RBP4) promotes atherosclerotic progression and neuronal loss, whereas its association with cognitive impairment in stroke is unclear. Hence, this prospective study aimed to explore the association of serum RBP4 with the T helper (Th)17/regulatory T (Treg) cell ratio and its correlation with cognitive impairment in stroke patients. Methods Peripheral blood samples from 265 stroke patients and 50 healthy controls (HCs) were collected at enrollment for serum RBP4 (by enzyme-linked immunosorbent assay) and Th17 and Treg cells (by flow cytometry) determination. Additionally, stroke patients underwent routine follow-ups, and their Mini-Mental State Examination (MMSE) scores were assessed at baseline and in years 1, 2, and 3 after enrollment. Results Serum RBP4 was elevated in stroke patients compared to HCs (p < 0.001), with a good ability to differentiate stroke patients from HCs (area under the curve: 0.815). Serum RBP4 was positively associated with Th17 cells (p < 0.001) and the Th17/Treg cell ratio (p < 0.001) and negatively associated with Treg cells (p = 0.003) in stroke patients, whereas it was only positively associated with the Th17/Treg cell ratio (p = 0.027) but not with Th17 (p = 0.075) or Treg (p = 0.130) cells in HCs. Furthermore, increased serum RBP4 was associated with a lower MMSE score (p < 0.001) and a lower incidence of cognition impairment (p = 0.005) at enrollment in stroke patients, as were Th17 cells and the Th17/Treg cell ratio (all p < 0.050). The 1-, 2-, and 3-year MMSE scores in stroke patients were 25.9 ± 2.0, 25.3 ± 2.3, and 24.9 ± 2.3, respectively. More importantly, serum RBP4 was negatively correlated with 1-, 2-, and 3-year MMSE scores (all p < 0.001) and positively associated with 1-year (p = 0.013), 2-year (p = 0.007), and 3-year (p = 0.001) MMSE score declines in stroke patients. Conclusion Serum RBP4 is positively associated with a Th17/Treg cell imbalance and, more importantly, it is indicative of cognitive function decline within 3 years in stroke patients. Thus, early and timely interventions and physical rehabilitation are more necessary in stroke patients with high serum RBP4.
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Affiliation(s)
| | | | - Zongyou Li
- Department of Neurology, Fuyang People’s Hospital, Fuyang, China
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9
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Dang Do AN, Sleat DE, Campbell K, Johnson NL, Zheng H, Wassif CA, Dale RK, Porter FD. Cerebrospinal Fluid Protein Biomarker Discovery in CLN3. J Proteome Res 2023; 22:2493-2508. [PMID: 37338096 PMCID: PMC11095826 DOI: 10.1021/acs.jproteome.3c00199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Syndromic CLN3-Batten is a fatal, pediatric, neurodegenerative disease caused by variants in CLN3, which encodes the endolysosomal transmembrane CLN3 protein. No approved treatment for CLN3 is currently available. The protracted and asynchronous disease presentation complicates the evaluation of potential therapies using clinical disease progression parameters. Biomarkers as surrogates to measure the progression and effect of potential therapeutics are needed. We performed proteomic discovery studies using cerebrospinal fluid (CSF) samples from 28 CLN3-affected and 32 age-similar non-CLN3 individuals. Proximal extension assay (PEA) of 1467 proteins and untargeted data-dependent mass spectrometry [MS; MassIVE FTP server (ftp://MSV000090147@massive.ucsd.edu)] were used to generate orthogonal lists of protein marker candidates. At an adjusted p-value of <0.1 and threshold CLN3/non-CLN3 fold-change ratio of 1.5, PEA identified 54 and MS identified 233 candidate biomarkers. Some of these (NEFL, CHIT1) have been previously linked with other neurologic conditions. Others (CLPS, FAM217B, QRICH2, KRT16, ZNF333) appear to be novel. Both methods identified 25 candidate biomarkers, including CHIT1, NELL1, and ISLR2 which had absolute fold-change ratios >2. NELL1 and ISLR2 regulate axonal development in neurons and are intriguing new candidates for further investigation in CLN3. In addition to identifying candidate proteins for CLN3 research, this study provides a comparison of two large-scale proteomic discovery methods in CSF.
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Affiliation(s)
- An N. Dang Do
- Unit on Cellular Stress in Development and Diseases, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - David E. Sleat
- Center for Advanced Biotechnology and Medicine, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
- Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
| | - Kiersten Campbell
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Nicholas L. Johnson
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
| | - Christopher A. Wassif
- Section on Molecular Dysmorphology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ryan K. Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Forbes D. Porter
- Section on Molecular Dysmorphology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
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10
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He A, Wang M, Li X, Chen H, Lim K, Lu L, Zhang C. Role of Exosomes in the Pathogenesis and Theranostic of Alzheimer's Disease and Parkinson's Disease. Int J Mol Sci 2023; 24:11054. [PMID: 37446231 DOI: 10.3390/ijms241311054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Alzheimer's disease (AD) and Parkinson's disease (PD) are the most common neurodegenerative diseases (NDDs) threatening the lives of millions of people worldwide, including especially elderly people. Currently, due to the lack of a timely diagnosis and proper intervention strategy, AD and PD largely remain incurable. Innovative diagnosis and therapy are highly desired. Exosomes are small vesicles that are present in various bodily fluids, which contain proteins, nucleic acids, and active biomolecules, and which play a crucial role especially in intercellular communication. In recent years, the role of exosomes in the pathogenesis, early diagnosis, and treatment of diseases has attracted ascending attention. However, the exact role of exosomes in the pathogenesis and theragnostic of AD and PD has not been fully illustrated. In the present review, we first introduce the biogenesis, components, uptake, and function of exosomes. Then we elaborate on the involvement of exosomes in the pathogenesis of AD and PD. Moreover, the application of exosomes in the diagnosis and therapeutics of AD and PD is also summarized and discussed. Additionally, exosomes serving as drug carriers to deliver medications to the central nervous system are specifically addressed. The potential role of exosomes in AD and PD is explored, discussing their applications in diagnosis and treatment, as well as their current limitations. Given the limitation in the application of exosomes, we also propose future perspectives for better utilizing exosomes in NDDs. Hopefully, it would pave ways for expanding the biological applications of exosomes in fundamental research as well as theranostics of NDDs.
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Affiliation(s)
- Aojie He
- School of Basic Medical Sciences, Shanxi Medical University, 56 Xinjiannan Road, Taiyuan 030001, China
| | - Meiling Wang
- School of Basic Medical Sciences, Shanxi Medical University, 56 Xinjiannan Road, Taiyuan 030001, China
| | - Xiaowan Li
- School of Basic Medical Sciences, Shanxi Medical University, 56 Xinjiannan Road, Taiyuan 030001, China
| | - Hong Chen
- School of Basic Medical Sciences, Shanxi Medical University, 56 Xinjiannan Road, Taiyuan 030001, China
| | - Kahleong Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore 308232, Singapore
| | - Li Lu
- School of Basic Medical Sciences, Shanxi Medical University, 56 Xinjiannan Road, Taiyuan 030001, China
| | - Chengwu Zhang
- School of Basic Medical Sciences, Shanxi Medical University, 56 Xinjiannan Road, Taiyuan 030001, China
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11
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Fan S, Poetsch A. Proteomic Research of Extracellular Vesicles in Clinical Biofluid. Proteomes 2023; 11:proteomes11020018. [PMID: 37218923 DOI: 10.3390/proteomes11020018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/14/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Extracellular vesicles (EVs), the lipid bilayer membranous structures of particles, are produced and released from almost all cells, including eukaryotes and prokaryotes. The versatility of EVs has been investigated in various pathologies, including development, coagulation, inflammation, immune response modulation, and cell-cell communication. Proteomics technologies have revolutionized EV studies by enabling high-throughput analysis of their biomolecules to deliver comprehensive identification and quantification with rich structural information (PTMs, proteoforms). Extensive research has highlighted variations in EV cargo depending on vesicle size, origin, disease, and other features. This fact has sparked activities to use EVs for diagnosis and treatment to ultimately achieve clinical translation with recent endeavors summarized and critically reviewed in this publication. Notably, successful application and translation require a constant improvement of methods for sample preparation and analysis and their standardization, both of which are areas of active research. This review summarizes the characteristics, isolation, and identification approaches for EVs and the recent advances in EVs for clinical biofluid analysis to gain novel knowledge by employing proteomics. In addition, the current and predicted future challenges and technical barriers are also reviewed and discussed.
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Affiliation(s)
- Shipan Fan
- School of Basic Medical Sciences, Nanchang University, Nanchang 330021, China
| | - Ansgar Poetsch
- Queen Mary School, Medical College, Nanchang University, Nanchang 330021, China
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12
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Kelty TJ, Dashek RJ, Arnold WD, Rector RS. Emerging Links between Nonalcoholic Fatty Liver Disease and Neurodegeneration. Semin Liver Dis 2023; 43:77-88. [PMID: 36764305 DOI: 10.1055/s-0043-1762585] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The association between liver and brain health has gained attention as biomarkers of liver function have been revealed to predict neurodegeneration. The liver is a central regulator in metabolic homeostasis. However, in nonalcoholic fatty liver disease (NAFLD), homeostasis is disrupted which can result in extrahepatic organ pathologies. Emerging literature provides insight into the mechanisms behind the liver-brain health axis. These include the increased production of liver-derived factors that promote insulin resistance and loss of neuroprotective factors under conditions of NAFLD that increase insulin resistance in the central nervous system. In addition, elevated proinflammatory cytokines linked to NAFLD negatively impact the blood-brain barrier and increase neuroinflammation. Furthermore, exacerbated dyslipidemia associated with NAFLD and hepatic dysfunction can promote altered brain bioenergetics and oxidative stress. In this review, we summarize the current knowledge of the crosstalk between liver and brain as it relates to the pathophysiology between NAFLD and neurodegeneration, with an emphasis on Alzheimer's disease. We also highlight knowledge gaps and future areas for investigation to strengthen the potential link between NAFLD and neurodegeneration.
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Affiliation(s)
- Taylor J Kelty
- Department of Biomedical Sciences, University of Missouri - Columbia, Columbia, Missouri
- Department of Nutrition and Exercise Physiology, University of Missouri - Columbia, Columbia, Missouri
- NextGen Precision Health, University of Missouri - Columbia, Columbia, Missouri
| | - Ryan J Dashek
- Department of Biomedical Sciences, University of Missouri - Columbia, Columbia, Missouri
- NextGen Precision Health, University of Missouri - Columbia, Columbia, Missouri
- Comparative Medicine Program, University of Missouri - Columbia, Columbia, Missouri
| | - W David Arnold
- NextGen Precision Health, University of Missouri - Columbia, Columbia, Missouri
- Physical Medicine and Rehabilitation, University of Missouri - Columbia, Columbia, Missouri
| | - R Scott Rector
- Department of Nutrition and Exercise Physiology, University of Missouri - Columbia, Columbia, Missouri
- NextGen Precision Health, University of Missouri - Columbia, Columbia, Missouri
- Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, Missouri
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri - Columbia, Columbia, Missouri
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13
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Doncheva NT, Morris JH, Holze H, Kirsch R, Nastou KC, Cuesta-Astroz Y, Rattei T, Szklarczyk D, von Mering C, Jensen LJ. Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks. J Proteome Res 2022; 22:637-646. [PMID: 36512705 PMCID: PMC9904289 DOI: 10.1021/acs.jproteome.2c00651] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Biological networks are often used to represent complex biological systems, which can contain several types of entities. Analysis and visualization of such networks is supported by the Cytoscape software tool and its many apps. While earlier versions of stringApp focused on providing intraspecies protein-protein interactions from the STRING database, the new stringApp 2.0 greatly improves the support for heterogeneous networks. Here, we highlight new functionality that makes it possible to create networks that contain proteins and interactions from STRING as well as other biological entities and associations from other sources. We exemplify this by complementing a published SARS-CoV-2 interactome with interactions from STRING. We have also extended stringApp with new data and query functionality for protein-protein interactions between eukaryotic parasites and their hosts. We show how this can be used to retrieve and visualize a cross-species network for a malaria parasite, its host, and its vector. Finally, the latest stringApp version has an improved user interface, allows retrieval of both functional associations and physical interactions, and supports group-wise enrichment analysis of different parts of a network to aid biological interpretation. stringApp is freely available at https://apps.cytoscape.org/apps/stringapp.
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Affiliation(s)
- Nadezhda T. Doncheva
- Novo
Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark,
| | - John H. Morris
- Resource
on Biocomputing, Visualization, and Informatics, University of California, San
Francisco, California 94143, United States
| | - Henrietta Holze
- Novo
Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rebecca Kirsch
- Novo
Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Katerina C. Nastou
- Novo
Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Yesid Cuesta-Astroz
- Instituto
Colombiano de Medicina Tropical, Universidad
CES, 055413 Sabaneta, Colombia
| | - Thomas Rattei
- Centre
for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Damian Szklarczyk
- Department
of Molecular Life Sciences, University of
Zurich, 8057 Zurich, Switzerland,SIB
Swiss
Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Christian von Mering
- Department
of Molecular Life Sciences, University of
Zurich, 8057 Zurich, Switzerland,SIB
Swiss
Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Lars J. Jensen
- Novo
Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark,
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14
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Shaba E, Vantaggiato L, Governini L, Haxhiu A, Sebastiani G, Fignani D, Grieco GE, Bergantini L, Bini L, Landi C. Multi-Omics Integrative Approach of Extracellular Vesicles: A Future Challenging Milestone. Proteomes 2022; 10:proteomes10020012. [PMID: 35645370 PMCID: PMC9149947 DOI: 10.3390/proteomes10020012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 02/01/2023] Open
Abstract
In the era of multi-omic sciences, dogma on singular cause-effect in physio-pathological processes is overcome and system biology approaches have been providing new perspectives to see through. In this context, extracellular vesicles (EVs) are offering a new level of complexity, given their role in cellular communication and their activity as mediators of specific signals to target cells or tissues. Indeed, their heterogeneity in terms of content, function, origin and potentiality contribute to the cross-interaction of almost every molecular process occurring in a complex system. Such features make EVs proper biological systems being, therefore, optimal targets of omic sciences. Currently, most studies focus on dissecting EVs content in order to either characterize it or to explore its role in various pathogenic processes at transcriptomic, proteomic, metabolomic, lipidomic and genomic levels. Despite valuable results being provided by individual omic studies, the categorization of EVs biological data might represent a limit to be overcome. For this reason, a multi-omic integrative approach might contribute to explore EVs function, their tissue-specific origin and their potentiality. This review summarizes the state-of-the-art of EVs omic studies, addressing recent research on the integration of EVs multi-level biological data and challenging developments in EVs origin.
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Affiliation(s)
- Enxhi Shaba
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.); (C.L.)
- Correspondence:
| | - Lorenza Vantaggiato
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.); (C.L.)
| | - Laura Governini
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (L.G.); (A.H.)
| | - Alesandro Haxhiu
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (L.G.); (A.H.)
| | - Guido Sebastiani
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (G.S.); (D.F.); (G.E.G.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Daniela Fignani
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (G.S.); (D.F.); (G.E.G.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Giuseppina Emanuela Grieco
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (G.S.); (D.F.); (G.E.G.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Laura Bergantini
- Respiratory Diseases and Lung Transplant Unit, Department of Medical Sciences, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy;
| | - Luca Bini
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.); (C.L.)
| | - Claudia Landi
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.); (C.L.)
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15
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Nielsen JE, Maltesen RG, Havelund JF, Færgeman NJ, Gotfredsen CH, Vestergård K, Kristensen SR, Pedersen S. Characterising Alzheimer's disease through integrative NMR- and LC-MS-based metabolomics. Metabol Open 2021; 12:100125. [PMID: 34622190 PMCID: PMC8479251 DOI: 10.1016/j.metop.2021.100125] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/10/2021] [Accepted: 09/10/2021] [Indexed: 12/14/2022] Open
Abstract
Background Alzheimer's Disease (AD) is a complex and multifactorial disease and novel approaches are needed to illuminate the underlying pathology. Metabolites comprise the end-product of genes, transcripts, and protein regulations and might reflect disease pathogenesis. Blood is a common biofluid used in metabolomics; however, since extracellular vesicles (EVs) hold cell-specific biological material and can cross the blood-brain barrier, their utilization as biological material warrants further investigation. We aimed to investigate blood- and EV-derived metabolites to add insigts to the pathological mechanisms of AD. Methods Blood samples were collected from 10 AD and 10 Mild Cognitive Impairment (MCI) patients, and 10 healthy controls. EVs were enriched from plasma using 100,000×g, 1 h, 4 °C with a wash. Metabolites from serum and EVs were measured using liquid chromatography-mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR) spectroscopy. Multivariate and univariate analyses were employed to identify altered metabolites in cognitively impaired individuals. Results While no significant EV-derived metabolites were found differentiating patients from healthy individuals, six serum metabolites were found important; valine (p = 0.001, fold change, FC = 0.8), histidine (p = 0.001, FC = 0.9), allopurinol riboside (p = 0.002, FC = 0.2), inosine (p = 0.002, FC = 0.3), 4-pyridoxic acid (p = 0.006, FC = 1.6), and guanosine (p = 0.004, FC = 0.3). Pathway analysis revealed branched-chain amino acids, purine and histidine metabolisms to be downregulated, and vitamin B6 metabolism upregulated in patients compared to controls. Conclusion Using a combination of LC-MS and NMR methodologies we identified several altered mechanisms possibly related to AD pathology. EVs require additional optimization prior to their possible utilization as a biological material for AD-related metabolomics studies.
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Key Words
- ACE, Addenbrooke's cognitive examination
- AD, Alzheimer's Disease
- AUC, Area under the curve
- Alzheimer
- Aβ, Amyloid-β
- BBB, Blood-brain barrier
- BCAA, Branched-chain amino acid
- Blood
- CNS, Central nervous system
- CSF, Cerebrospinal fluid
- CV, Cross-validation
- EVs, Extracellular vesicles
- Extracellular vesicles
- FAQ, Functional activities questionnaire
- FDR, False discovery rate
- MCI, Mild cognitive impairment
- MMSE, Mini-mental state examination
- Mass spectrometry
- Metabolites
- Nuclear magnetic resonance
- PCA, Principal component analysis
- ROC, Receiver operating characteristics
- p-tau, Phospho-tau
- sPLS-DA, Sparse partial least squared discriminant analysis
- t-tau, Total-tau
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Affiliation(s)
- Jonas Ellegaard Nielsen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Raluca Georgiana Maltesen
- Translational Radiation Biology and Oncology Laboratory, Centre for Cancer Research, Westmead Institute of Medical Research, Westmead, Australia.,Department of Anaesthesia and Intensive Care, Aalborg University Hospital, Aalborg, Denmark
| | - Jesper F Havelund
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Nils J Færgeman
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | | | | | - Søren Risom Kristensen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Shona Pedersen
- Department of Basic Medical Sciences, College of Medicine, Qatar University, Qatar Health, Doha, Qatar
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