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Barba L, Bellomo G, Oeckl P, Chiasserini D, Gaetani L, Torrigiani EG, Paoletti FP, Steinacker P, Abu-Rumeileh S, Parnetti L, Otto M. CSF neurosecretory proteins VGF and neuroserpin in patients with Alzheimer's and Lewy body diseases. J Neurol Sci 2024; 462:123059. [PMID: 38850771 DOI: 10.1016/j.jns.2024.123059] [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: 03/05/2024] [Revised: 05/19/2024] [Accepted: 05/21/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND VGF and neuroserpin are neurosecretory proteins involved in the pathophysiology of neurodegenerative diseases. We aimed to evaluate their cerebrospinal fluid (CSF) concentrations in patients with Alzheimer's disease (AD) and Lewy body disease (LBD). METHODS We measured CSF VGF [AQEE] peptide and neuroserpin levels in 108 LBD patients, 76 AD patients and 37 controls, and tested their associations with clinical scores and CSF AD markers. RESULTS We found decreased CSF levels of VGF [AQEE] in patients with LBD and dementia compared to controls (p = 0.016) and patients with AD-dementia (p = 0.011), but with significant influence of age and sex distribution. Moreover, we observed, on the one hand, a significant associations between lower VGF [AQEE] and neuroserpin levels and poorer cognitive performance (i.e., lower Mini-Mental State Examination scores). On the other hand, higher levels of CSF tau proteins, especially pTau181, were significantly associated with higher concentrations of VGF [AQEE] and neuroserpin. Indeed, LBD patients with AD-like CSF profiles, especially T+ profiles, had higher levels of VGF [AQEE] and neuroserpin compared to controls and LBD/T- cases. DISCUSSION CSF VGF [AQEE] and neuroserpin may show a complex relationship with cognitive decline when the levels are reduced, and with AD pathology when levels are increased. They may represent novel markers of neurosecretory impairment in neurodegenerative disorders.
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Affiliation(s)
- Lorenzo Barba
- Department of Neurology, Martin-Luther-University of Halle-Wittenberg, Ernst-Grube-Strasse 40, 06120 Halle (Saale), Germany
| | - Giovanni Bellomo
- Section of Neurology, Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06129 Perugia, Italy
| | - Patrick Oeckl
- Department of Neurology, Ulm University, Helmholzstrasse 8/1, 89081 Ulm, Germany; German Center for Neurodegenerative Diseases (DZNE e.V.), Helmholzstrasse 8/1, 89081 Ulm, Germany
| | - Davide Chiasserini
- Section of Biochemistry, Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06129 Perugia, Italy
| | - Lorenzo Gaetani
- Section of Neurology, Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06129 Perugia, Italy
| | - Edoardo Guido Torrigiani
- Section of Neurology, Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06129 Perugia, Italy
| | - Federico Paolini Paoletti
- Section of Neurology, Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06129 Perugia, Italy
| | - Petra Steinacker
- Department of Neurology, Martin-Luther-University of Halle-Wittenberg, Ernst-Grube-Strasse 40, 06120 Halle (Saale), Germany
| | - Samir Abu-Rumeileh
- Department of Neurology, Martin-Luther-University of Halle-Wittenberg, Ernst-Grube-Strasse 40, 06120 Halle (Saale), Germany
| | - Lucilla Parnetti
- Section of Neurology, Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06129 Perugia, Italy
| | - Markus Otto
- Department of Neurology, Martin-Luther-University of Halle-Wittenberg, Ernst-Grube-Strasse 40, 06120 Halle (Saale), Germany.
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Stezin A, Sathe GJ, Gajbhiye A, Bharadwaj S, Ghose V, Bellad A, Malo PK, Holla V, Hegde S, Bharath RD, Saini J, Jain S, Yadav R, Pandey A, Pal PK. Dysregulated Cerebrospinal Fluid Proteome of Spinocerebellar Ataxia Type 2 and its Clinical Implications. Mov Disord 2024. [PMID: 38769639 DOI: 10.1002/mds.29834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/07/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Abnormalities in ataxin-2 associated with spinocerebellar ataxia type 2 (SCA2) may lead to widespread disruptions in the proteome. This study was performed to identify dysregulated proteome in SCA2 and to explore its clinical-radiological correlations. METHODS Cerebrospinal fluid (CSF) samples from 21 genetically confirmed SCA2 were subjected to shotgun proteome analysis using mass spectrometry (MS) and tandem mass tag (TMT)-based multiplexing. Proteins with at least 1.5-fold change in abundance were identified. Their relative abundance was measured using parallel reaction monitoring (PRM) and correlated against disease-related factors. RESULTS Eleven proteins were significantly upregulated in SCA2. They belonged to the family of cell adhesion molecules and granins. Their fold changes showed significant clinical, genetic, and radiological correlations. CONCLUSIONS Significant dysregulation of CSF proteome is seen in SCA2. The dysregulated protein may have potential use in clinical evaluation of patients with SCA2. © 2024 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Albert Stezin
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
- Clinical Neurosciences, Centre for Brain Research (CBR), Indian Institute of Science (IISc), Bangalore, India
| | | | | | - Sujas Bharadwaj
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Vivek Ghose
- Institute of Bioinformatics (IOB), Bangalore, India
| | | | - Palash Kumar Malo
- Clinical Neurosciences, Centre for Brain Research (CBR), Indian Institute of Science (IISc), Bangalore, India
| | - Vikram Holla
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Shantala Hegde
- Department of Clinical Psychology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Rose Dawn Bharath
- Department of Neuroimaging and Interventional Neuroimaging, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Jitender Saini
- Department of Neuroimaging and Interventional Neuroimaging, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Sanjeev Jain
- Molecular Genetics Laboratory, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
- Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Ravi Yadav
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Akhilesh Pandey
- Institute of Bioinformatics (IOB), Bangalore, India
- Center for Individualized Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
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Bartl M, Nilsson J, Dakna M, Weber S, Schade S, Xylaki M, Fernandes Gomes B, Ernst M, Muntean ML, Sixel-Döring F, Trenkwalder C, Zetterberg H, Brinkmalm A, Mollenhauer B. Lysosomal and synaptic dysfunction markers in longitudinal cerebrospinal fluid of de novo Parkinson's disease. NPJ Parkinsons Dis 2024; 10:102. [PMID: 38760408 PMCID: PMC11101466 DOI: 10.1038/s41531-024-00714-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/19/2024] [Indexed: 05/19/2024] Open
Abstract
Lysosomal and synaptic dysfunctions are hallmarks in neurodegeneration and potentially relevant as biomarkers, but data on early Parkinson's disease (PD) is lacking. We performed targeted mass spectrometry with an established protein panel, assessing autophagy and synaptic function in cerebrospinal fluid (CSF) of drug-naïve de novo PD, and sex-/age-matched healthy controls (HC) cross-sectionally (88 PD, 46 HC) and longitudinally (104 PD, 58 HC) over 10 years. Multiple markers of autophagy, synaptic plasticity, and secretory pathways were reduced in PD. We added samples from prodromal subjects (9 cross-sectional, 12 longitudinal) with isolated REM sleep behavior disorder, revealing secretogranin-2 already decreased compared to controls. Machine learning identified neuronal pentraxin receptor and neurosecretory protein VGF as most relevant for discriminating between groups. CSF levels of LAMP2, neuronal pentraxins, and syntaxins in PD correlated with clinical progression, showing predictive potential for motor- and non-motor symptoms as a valid basis for future drug trials.
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Affiliation(s)
- Michael Bartl
- Department of Neurology, University Medical Center Goettingen, Goettingen, Germany.
- Institute for Neuroimmunology and Multiple Sclerosis Research, University Medical Center Goettingen, Goettingen, Germany.
| | - Johanna Nilsson
- Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Mohammed Dakna
- Department of Neurology, University Medical Center Goettingen, Goettingen, Germany
| | - Sandrina Weber
- Department of Neurology, University Medical Center Goettingen, Goettingen, Germany
| | | | - Mary Xylaki
- Department of Neurology, University Medical Center Goettingen, Goettingen, Germany
| | - Bárbara Fernandes Gomes
- Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Marielle Ernst
- Institute of Diagnostic and Interventional Neuroradiology, University Medical Center Goettingen, Goettingen, Germany
| | | | - Friederike Sixel-Döring
- Paracelsus-Elena-Klinik, Kassel, Germany
- Department of Neurology, Philipps-University, Marburg, Germany
| | - Claudia Trenkwalder
- Paracelsus-Elena-Klinik, Kassel, Germany
- Department of Neurosurgery, University Medical Center Goettingen, Goettingen, Germany
| | - Henrik Zetterberg
- 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
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Ann Brinkmalm
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Brit Mollenhauer
- Department of Neurology, University Medical Center Goettingen, Goettingen, Germany
- Paracelsus-Elena-Klinik, Kassel, Germany
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Krauskopf J, Eggermont K, Caiment F, Verfaillie C, de Kok TM. Molecular insights into PCB neurotoxicity: Comparing transcriptomic responses across dopaminergic neurons, population blood cells, and Parkinson's disease pathology. ENVIRONMENT INTERNATIONAL 2024; 186:108642. [PMID: 38608384 DOI: 10.1016/j.envint.2024.108642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
Parkinson's disease (PD) is a complex neurodegenerative disorder influenced by genetic factors and environmental exposures. Polychlorinated biphenyls (PCBs), a group of synthetic organic compounds, have been identified as potential environmental risk factors for neurodegenerative diseases, including PD. We explored PCB-induced neurotoxicity mechanisms using iPSC-derived dopaminergic neurons and assessed their transcriptomic responses to varying PCB concentrations (0.01 μM, 0.5 μM, and 10 μM). Specifically, we focused on PCB-180, a congener known for its accumulation in human brains. The exposure durations were 24 h and 74 h, allowing us to capture both short-term and more prolonged effects on gene expression patterns. We observed that PCB exposure led to the suppression of oxidative phosphorylation, synaptic function, and neurotransmitter release, implicating these pathways in PCB-induced neurotoxicity. In our comparative analysis, we noted similarities in PCB-induced changes with other PD-related compounds like MPP+ and rotenone. Our findings also aligned with gene expression changes in human blood derived from a population exposed to PCBs, highlighting broader inflammatory responses. Additionally, molecular patterns seen in iPSC-derived neurons were confirmed in postmortem PD brain tissues, validating our in vitro results. In conclusion, our study offers novel insights into the multifaceted impacts of PCB-induced perturbations on various cellular contexts relevant to PD. The use of iPSC-derived dopaminergic neurons allowed us to decipher intricate transcriptomic alterations, bridging the gap between in vitro and in vivo findings. This work underscores the potential role of PCB exposure in neurodegenerative diseases like PD, emphasizing the need to consider both systemic and cell specific effects.
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Affiliation(s)
- Julian Krauskopf
- Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands; MHeNS, School for Mental Health and Neuroscience, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands. %
| | - Kristel Eggermont
- Stem Cell Institute, Department of Development and Regeneration, Katholieke Universiteit Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Florian Caiment
- Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Catherine Verfaillie
- Stem Cell Institute, Department of Development and Regeneration, Katholieke Universiteit Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Theo M de Kok
- Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands; MHeNS, School for Mental Health and Neuroscience, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
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Faizan M, Sachan N, Verma O, Sarkar A, Rawat N, Pratap Singh M. Cerebrospinal fluid protein biomarkers in Parkinson's disease. Clin Chim Acta 2024; 556:117848. [PMID: 38417781 DOI: 10.1016/j.cca.2024.117848] [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: 01/10/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Proteomic profiling is an effective way to identify biomarkers for Parkinson's disease (PD). Cerebrospinal fluid (CSF) has direct connectivity with the brain and could be a source of finding biomarkers and their clinical implications. Comparative proteomic profiling has shown that a group of differentially displayed proteins exist. The studies performed using conventional and classical tools also supported the occurrence of these proteins. Many studies have highlighted the potential of CSF proteomic profiling for biomarker identification and their clinical applications. Some of these proteins are useful for disease diagnosis and prediction. Proteomic profiling of CSF also has immense potential to distinguish PD from similar neurodegenerative disorders. A few protein biomarkers help in fundamental knowledge generation and clinical interpretation. However, the specific biomarker of PD is not yet known. The use of proteomic approaches in clinical settings is also rare. A large-scale, multi-centric, multi-population and multi-continental study using multiple proteomic tools is warranted. Such a study can provide valuable, comprehensive and reliable information for a better understanding of PD and the development of specific biomarkers. The current article sheds light on the role of CSF proteomic profiling in identifying biomarkers of PD and their clinical implications. The article also explains the achievements, obstacles and hopes for future directions of this approach.
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Affiliation(s)
- Mohd Faizan
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Nidhi Sachan
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Oyashvi Verma
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Alika Sarkar
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Neeraj Rawat
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Mahendra Pratap Singh
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India; Capacity Building and Knowledge Services, ASSIST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India.
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Manca E, Noli B, Corda G, El-Hassani M, Manai A, Sanna F, Argiolas A, Melis MR, Manconi B, Contini C, Cocco C. VGF modifications related to nigrostriatal dopaminergic neurodegeneration induced by the pesticide fipronil in adult male rats. Ann Anat 2024; 252:152194. [PMID: 38056781 DOI: 10.1016/j.aanat.2023.152194] [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: 08/11/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Dopamine is reduced in the brain of rats treated with fipronil, a broad-spectrum insecticide. VGF (no acronym) is a neurotrophin-inducible protein expressed as the 75 kDa form (precursor or pro-VGF) or its truncated peptides. VGF immunostaining has been revealed using an antibody against the C-terminal nonapeptide of the rat pro-VGF in the nerve terminals of the rat substantia nigra, where it was reduced after 6-hydroxydopamine treatment. It is unknown whether pro-VGF and/or its shortened peptides are present in these neurons. Therefore, the aim of this study was first to determine which types of VGF are expressed in the normal substantia nigra (and striatum) and then to determine VGF modulations and whether they occur in parallel with locomotor changes after fipronil injection. METHODS Rats were divided into two groups that received a unilateral intranigral infusion of either fipronil (25 µg) diluted in dimethyl sulfoxide (DMSO) or DMSO alone, and then were tested for locomotor activity. An untreated group of rats (n=4) was used for identification of the VGF fragments using high performance liquid chromatography-mass spectrometry and western blot, while changes in treated groups (fipronil vs DMSO, each n=6) were investigated by immunohistochemistry using an antibody against the rat pro-VGF C-terminal nonapeptide in parallel with the anti-tyrosine hydroxylase antibody. RESULTS In untreated rats, the VGF C-terminal antibody identified mostly a 75 kDa band in the substantia nigra and striatum, supporting the finding of high-resolution mass spectrometry, which revealed fragments covering the majority of the pro-VGF sequence. Furthermore, several shortened VGF C-terminal forms (varying from 10 to 55 kDa) were also found by western blot, while high-resolution mass spectrometry revealed a C-terminal peptide overlapping the immunogen used to create the VGF antibody in both substantia nigra and striatum. In the substantia nigra of fipronil-treated rats, immunostaining for tyrosine hydroxylase and VGF was reduced compared to DMSO-treated rat group, and this was related with significant changes in locomotor activity. CONCLUSION Fipronil has the ability to modulate the production of pro-VGF and/or its C-terminal truncated peptides in the nigrostriatal system indicating its intimate interaction with the dopaminergic neurotransmission and implying a potential function in modulating locomotor activity.
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Affiliation(s)
- Elias Manca
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Barbara Noli
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Giulia Corda
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Majda El-Hassani
- Department of Internal Medicine III, University Hospital RWTH Aachen, Germany
| | - Antonio Manai
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Fabrizio Sanna
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Antonio Argiolas
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | | | - Barbara Manconi
- Department of Life Sciences and Environment, University of Cagliari, Italy
| | - Cristina Contini
- Department of Life Sciences and Environment, University of Cagliari, Italy
| | - Cristina Cocco
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy.
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Tsukita K, Sakamaki-Tsukita H, Kaiser S, Zhang L, Messa M, Serrano-Fernandez P, Takahashi R. High-Throughput CSF Proteomics and Machine Learning to Identify Proteomic Signatures for Parkinson Disease Development and Progression. Neurology 2023; 101:e1434-e1447. [PMID: 37586882 PMCID: PMC10573147 DOI: 10.1212/wnl.0000000000207725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 05/30/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND AND OBJECTIVES This study aimed to identify CSF proteomic signatures characteristic of Parkinson disease (PD) and evaluate their clinical utility. METHODS This observational study used data from the Parkinson's Progression Markers Initiative (PPMI), which enrolled patients with PD, healthy controls (HCs), and non-PD participants carrying GBA1, LRRK2, and/or SNCA pathogenic variants (genetic prodromals) at international sites. Study participants were chosen from PPMI enrollees based on the availability of aptamer-based CSF proteomic data, quantifying 4,071 proteins, and classified as patients with PD without GBA1, LRRK2, and/or SNCA pathogenic variants (nongenetic PD), HCs, patients with PD carrying the aforementioned pathogenic variants (genetic PD), or genetic prodromals. Differentially expressed protein (DEP) analysis and the least absolute shrinkage and selection operator (LASSO) were applied to the data from nongenetic PD and HCs. Signatures characteristics of nongenetic PD were quantified as a PD proteomic score (PD-ProS), validated internally and then externally using data of 1,556 CSF proteins from the LRRK2 Cohort Consortium (LCC). We further tested the PD-ProS in genetic PD and genetic prodromals and examined associations with clinical progression. RESULTS Data from 279 patients with nongenetic PD (mean ± SD, age 62.0 ± 9.6 years; male 67.7%) and 141 HCs (age 60.5 ± 11.9 years; male 64.5%) were used for PD-ProS derivation. From 23 DEPs, LASSO determined weights of 14 DEPs for the PD-ProS (area under the curve [AUC] 0.83, 95% CI 0.78-0.87), validated in an independent internal validation cohort of 71 patients with nongenetic PD and 35 HCs (AUC 0.81, 95% CI 0.73-0.90). In the LCC, only 5 of the 14 DEPs were also measured. Notably, these 5 DEPs still distinguished 34 patients with nongenetic PD from 31 HCs with the same weights (AUC 0.75, 95% CI 0.63-0.87). Furthermore, the PD-ProS distinguished 258 patients with genetic PD from 365 genetic prodromals. Finally, regardless of genetic status, the PD-ProS independently predicted both cognitive and motor decline in PD (dementia, adjusted hazard ratio in the highest quintile [aHR-Q5] 2.8 [95% CI 1.6-5.0]; Hoehn and Yahr stage IV, aHR-Q5 2.1 [95% CI 1.1-4.0]). DISCUSSION By integrating high-throughput proteomics with machine learning, we identified PD-associated CSF proteomic signatures crucial for PD development and progression. TRIAL REGISTRATION INFORMATION ClinicalTrials.gov (NCT01176565). A link to the trial registry page is clinicaltrials.gov/ct2/show/NCT01141023. CLASSIFICATION OF EVIDENCE This study provides Class II evidence that the CSF proteome contains clinically important information regarding the development and progression of Parkinson disease that can be deciphered by a combination of high-throughput proteomics and machine learning.
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Affiliation(s)
- Kazuto Tsukita
- From the Department of Neurology (K.T., H.S.-T., R.T.), Graduate School of Medicine, Kyoto University; Advanced Comprehensive Research Organization (K.T.), Teikyo University, Itabashi; Division of Sleep Medicine (K.T.), Kansai Electric Power Medical Research Institute, Osaka, Japan; Translational Medicine Department (S.K., P.S.-F.), Novartis Institutes for Biomedical Research, Basel, Switzerland; and Cardiovascular and Metabolism Department (L.Z.), and Neuroscience Department (M.M.), Novartis Institutes for Biomedical Research, Cambridge, MA.
| | - Haruhi Sakamaki-Tsukita
- From the Department of Neurology (K.T., H.S.-T., R.T.), Graduate School of Medicine, Kyoto University; Advanced Comprehensive Research Organization (K.T.), Teikyo University, Itabashi; Division of Sleep Medicine (K.T.), Kansai Electric Power Medical Research Institute, Osaka, Japan; Translational Medicine Department (S.K., P.S.-F.), Novartis Institutes for Biomedical Research, Basel, Switzerland; and Cardiovascular and Metabolism Department (L.Z.), and Neuroscience Department (M.M.), Novartis Institutes for Biomedical Research, Cambridge, MA
| | - Sergio Kaiser
- From the Department of Neurology (K.T., H.S.-T., R.T.), Graduate School of Medicine, Kyoto University; Advanced Comprehensive Research Organization (K.T.), Teikyo University, Itabashi; Division of Sleep Medicine (K.T.), Kansai Electric Power Medical Research Institute, Osaka, Japan; Translational Medicine Department (S.K., P.S.-F.), Novartis Institutes for Biomedical Research, Basel, Switzerland; and Cardiovascular and Metabolism Department (L.Z.), and Neuroscience Department (M.M.), Novartis Institutes for Biomedical Research, Cambridge, MA
| | - Luqing Zhang
- From the Department of Neurology (K.T., H.S.-T., R.T.), Graduate School of Medicine, Kyoto University; Advanced Comprehensive Research Organization (K.T.), Teikyo University, Itabashi; Division of Sleep Medicine (K.T.), Kansai Electric Power Medical Research Institute, Osaka, Japan; Translational Medicine Department (S.K., P.S.-F.), Novartis Institutes for Biomedical Research, Basel, Switzerland; and Cardiovascular and Metabolism Department (L.Z.), and Neuroscience Department (M.M.), Novartis Institutes for Biomedical Research, Cambridge, MA
| | - Mirko Messa
- From the Department of Neurology (K.T., H.S.-T., R.T.), Graduate School of Medicine, Kyoto University; Advanced Comprehensive Research Organization (K.T.), Teikyo University, Itabashi; Division of Sleep Medicine (K.T.), Kansai Electric Power Medical Research Institute, Osaka, Japan; Translational Medicine Department (S.K., P.S.-F.), Novartis Institutes for Biomedical Research, Basel, Switzerland; and Cardiovascular and Metabolism Department (L.Z.), and Neuroscience Department (M.M.), Novartis Institutes for Biomedical Research, Cambridge, MA
| | - Pablo Serrano-Fernandez
- From the Department of Neurology (K.T., H.S.-T., R.T.), Graduate School of Medicine, Kyoto University; Advanced Comprehensive Research Organization (K.T.), Teikyo University, Itabashi; Division of Sleep Medicine (K.T.), Kansai Electric Power Medical Research Institute, Osaka, Japan; Translational Medicine Department (S.K., P.S.-F.), Novartis Institutes for Biomedical Research, Basel, Switzerland; and Cardiovascular and Metabolism Department (L.Z.), and Neuroscience Department (M.M.), Novartis Institutes for Biomedical Research, Cambridge, MA
| | - Ryosuke Takahashi
- From the Department of Neurology (K.T., H.S.-T., R.T.), Graduate School of Medicine, Kyoto University; Advanced Comprehensive Research Organization (K.T.), Teikyo University, Itabashi; Division of Sleep Medicine (K.T.), Kansai Electric Power Medical Research Institute, Osaka, Japan; Translational Medicine Department (S.K., P.S.-F.), Novartis Institutes for Biomedical Research, Basel, Switzerland; and Cardiovascular and Metabolism Department (L.Z.), and Neuroscience Department (M.M.), Novartis Institutes for Biomedical Research, Cambridge, MA
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Paslawski W, Khosousi S, Hertz E, Markaki I, Boxer A, Svenningsson P. Large-scale proximity extension assay reveals CSF midkine and DOPA decarboxylase as supportive diagnostic biomarkers for Parkinson's disease. Transl Neurodegener 2023; 12:42. [PMID: 37667404 PMCID: PMC10476347 DOI: 10.1186/s40035-023-00374-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND There is a need for biomarkers to support an accurate diagnosis of Parkinson's disease (PD). Cerebrospinal fluid (CSF) has been a successful biofluid for finding neurodegenerative biomarkers, and modern highly sensitive multiplexing methods offer the possibility to perform discovery studies. Using a large-scale multiplex proximity extension assay (PEA) approach, we aimed to discover novel diagnostic protein biomarkers allowing accurate discrimination of PD from both controls and atypical Parkinsonian disorders (APD). METHODS CSF from patients with PD, corticobasal syndrome (CBS), progressive supranuclear palsy (PSP), multiple system atrophy and controls, were analysed with Olink PEA panels. Three cohorts were used in this study, comprising 192, 88 and 36 cases, respectively. All samples were run on the Cardiovascular II, Oncology II and Metabolism PEA panels. RESULTS Our analysis revealed that 26 and 39 proteins were differentially expressed in the CSF of test and validation PD cohorts, respectively, compared to controls. Among them, 6 proteins were changed in both cohorts. Midkine (MK) was increased in PD with the strongest effect size and results were validated with ELISA. Another most increased protein in PD, DOPA decarboxylase (DDC), which catalyses the decarboxylation of DOPA (L-3,4-dihydroxyphenylalanine) to dopamine, was strongly correlated with dopaminergic treatment. Moreover, Kallikrein 10 was specifically changed in APD compared with both PD and controls, but unchanged between PD and controls. Wnt inhibitory factor 1 was consistently downregulated in CBS and PSP patients in two independent cohorts. CONCLUSIONS Using the large-scale PEA approach, we have identified potential novel PD diagnostic biomarkers, most notably MK and DDC, in the CSF of PD patients.
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Affiliation(s)
- Wojciech Paslawski
- Laboratory of Translational Neuropharmacology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Shervin Khosousi
- Laboratory of Translational Neuropharmacology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Old Age Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Ellen Hertz
- Laboratory of Translational Neuropharmacology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ioanna Markaki
- Laboratory of Translational Neuropharmacology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Adam Boxer
- Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
| | - Per Svenningsson
- Laboratory of Translational Neuropharmacology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
- Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
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9
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Downs M, Zaia J, Sethi MK. Mass spectrometry methods for analysis of extracellular matrix components in neurological diseases. MASS SPECTROMETRY REVIEWS 2023; 42:1848-1875. [PMID: 35719114 PMCID: PMC9763553 DOI: 10.1002/mas.21792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/12/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The brain extracellular matrix (ECM) is a highly glycosylated environment and plays important roles in many processes including cell communication, growth factor binding, and scaffolding. The formation of structures such as perineuronal nets (PNNs) is critical in neuroprotection and neural plasticity, and the formation of molecular networks is dependent in part on glycans. The ECM is also implicated in the neuropathophysiology of disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), and Schizophrenia (SZ). As such, it is of interest to understand both the proteomic and glycomic makeup of healthy and diseased brain ECM. Further, there is a growing need for site-specific glycoproteomic information. Over the past decade, sample preparation, mass spectrometry, and bioinformatic methods have been developed and refined to provide comprehensive information about the glycoproteome. Core ECM molecules including versican, hyaluronan and proteoglycan link proteins, and tenascin are dysregulated in AD, PD, and SZ. Glycomic changes such as differential sialylation, sulfation, and branching are also associated with neurodegeneration. A more thorough understanding of the ECM and its proteomic, glycomic, and glycoproteomic changes in brain diseases may provide pathways to new therapeutic options.
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Affiliation(s)
- Margaret Downs
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Manveen K Sethi
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
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10
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Zafarullah M, Li J, Salemi MR, Phinney BS, Durbin-Johnson BP, Hagerman R, Hessl D, Rivera SM, Tassone F. Blood Proteome Profiling Reveals Biomarkers and Pathway Alterations in Fragile X PM at Risk for Developing FXTAS. Int J Mol Sci 2023; 24:13477. [PMID: 37686279 PMCID: PMC10488017 DOI: 10.3390/ijms241713477] [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: 07/15/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) is a neurodegenerative disorder associated with the FMR1 premutation. Currently, it is not possible to determine when and if individual premutation carriers will develop FXTAS. Thus, with the aim to identify biomarkers for early diagnosis, development, and progression of FXTAS, along with associated dysregulated pathways, we performed blood proteomic profiling of premutation carriers (PM) who, as part of an ongoing longitudinal study, emerged into two distinct groups: those who developed symptoms of FXTAS (converters, CON) over time (at subsequent visits) and those who did not (non-converters, NCON). We compared these groups to age-matched healthy controls (HC). We assessed CGG repeat allele size by Southern blot and PCR analysis. The proteomic profile was obtained by liquid chromatography mass spectrometry (LC-MS/MS). We identified several significantly differentiated proteins between HC and the PM groups at Visit 1 (V1), Visit 2 (V2), and between the visits. We further reported the dysregulated protein pathways, including sphingolipid and amino acid metabolism. Our findings are in agreement with previous studies showing that pathways involved in mitochondrial bioenergetics, as observed in other neurodegenerative disorders, are significantly altered and appear to contribute to the development of FXTAS. Lastly, we compared the blood proteome of the PM who developed FXTAS over time with the CSF proteome of the FXTAS patients recently reported and found eight significantly differentially expressed proteins in common. To our knowledge, this is the first report of longitudinal proteomic profiling and the identification of unique biomarkers and dysregulated protein pathways in FXTAS.
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Affiliation(s)
- Marwa Zafarullah
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, CA 95817, USA;
| | - Jie Li
- Genome Center, Bioinformatics Core, University of California Davis, Davis, CA 95616, USA;
| | - Michelle R. Salemi
- Genome Center, Proteomics Core, Genome and Biomedical Sciences Facility, University of California Davis, Davis, CA 95616, USA; (M.R.S.); (B.S.P.)
| | - Brett S. Phinney
- Genome Center, Proteomics Core, Genome and Biomedical Sciences Facility, University of California Davis, Davis, CA 95616, USA; (M.R.S.); (B.S.P.)
| | - Blythe P. Durbin-Johnson
- Division of Biostatistics, School of Medicine, University of California Davis, Davis, CA 95616, USA;
| | - Randi Hagerman
- MIND Institute, University of California Davis Medical Center, Sacramento, CA 95817, USA; (R.H.); (D.H.); (S.M.R.)
- Department of Pediatrics, University of California Davis Medical Center, Sacramento, CA 95817, USA
| | - David Hessl
- MIND Institute, University of California Davis Medical Center, Sacramento, CA 95817, USA; (R.H.); (D.H.); (S.M.R.)
- Department of Psychiatry and Behavioral Sciences, University of California Davis Medical Center, Sacramento, CA 95817, USA
| | - Susan M. Rivera
- MIND Institute, University of California Davis Medical Center, Sacramento, CA 95817, USA; (R.H.); (D.H.); (S.M.R.)
- Department of Psychology, University of California Davis, Davis, CA 95616, USA
- Department of Psychology, University of Maryland, College Park, MD 20742, USA
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, CA 95817, USA;
- MIND Institute, University of California Davis Medical Center, Sacramento, CA 95817, USA; (R.H.); (D.H.); (S.M.R.)
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11
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Allen C, Meinl R, Paez JS, Searle BC, Just S, Pino LK, Fondrie WE. nf-encyclopedia: A Cloud-Ready Pipeline for Chromatogram Library Data-Independent Acquisition Proteomics Workflows. J Proteome Res 2023; 22:2743-2749. [PMID: 37417926 DOI: 10.1021/acs.jproteome.2c00613] [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] [Indexed: 07/08/2023]
Abstract
Data-independent acquisition (DIA) mass spectrometry methods provide systematic and comprehensive quantification of the proteome; yet, relatively few open-source tools are available to analyze DIA proteomics experiments. Fewer still are tools that can leverage gas phase fractionated (GPF) chromatogram libraries to enhance the detection and quantification of peptides in these experiments. Here, we present nf-encyclopedia, an open-source NextFlow pipeline that connects three open-source tools, MSConvert, EncyclopeDIA, and MSstats, to analyze DIA proteomics experiments with or without chromatogram libraries. We demonstrate that nf-encyclopedia is reproducible when run on either a cloud platform or a local workstation and provides robust peptide and protein quantification. Additionally, we found that MSstats enhances protein-level quantitative performance over EncyclopeDIA alone. Finally, we benchmarked the ability of nf-encyclopedia to scale to large experiments in the cloud by leveraging the parallelization of compute resources. The nf-encyclopedia pipeline is available under a permissive Apache 2.0 license; run it on your desktop, cluster, or in the cloud: https://github.com/TalusBio/nf-encyclopedia.
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Affiliation(s)
- Carolyn Allen
- Talus Bioscience, Seattle, Washington 98122, United States
| | - Rico Meinl
- Talus Bioscience, Seattle, Washington 98122, United States
| | | | - Brian C Searle
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, United States
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, United States
- Proteome Software, Inc., Portland, Oregon 97219, United States
| | - Seth Just
- Proteome Software, Inc., Portland, Oregon 97219, United States
| | - Lindsay K Pino
- Talus Bioscience, Seattle, Washington 98122, United States
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12
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Cocco C, Manai AL, Manca E, Noli B. Brain-Biomarker Changes in Body Fluids of Patients with Parkinson's Disease. Int J Mol Sci 2023; 24:10932. [PMID: 37446110 DOI: 10.3390/ijms241310932] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Parkinson's disease (PD) is an incurable neurodegenerative disease that is rarely diagnosed at an early stage. Although the understanding of PD-related mechanisms has greatly improved over the last decade, the diagnosis of PD is still based on neurological examination through the identification of motor symptoms, including bradykinesia, rigidity, postural instability, and resting tremor. The early phase of PD is characterized by subtle symptoms with a misdiagnosis rate of approximately 16-20%. The difficulty in recognizing early PD has implications for the potential use of novel therapeutic approaches. For this reason, it is important to discover PD brain biomarkers that can indicate early dopaminergic dysfunction through their changes in body fluids, such as saliva, urine, blood, or cerebrospinal fluid (CSF). For the CFS-based test, the invasiveness of sampling is a major limitation, whereas the other body fluids are easier to obtain and could also allow population screening. Following the identification of the crucial role of alpha-synuclein (α-syn) in the pathology of PD, a very large number of studies have summarized its changes in body fluids. However, methodological problems have led to the poor diagnostic/prognostic value of this protein and alternative biomarkers are currently being investigated. The aim of this paper is therefore to summarize studies on protein biomarkers that are alternatives to α-syn, particularly those that change in nigrostriatal areas and in biofluids, with a focus on blood, and, eventually, saliva and urine.
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Affiliation(s)
- Cristina Cocco
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Antonio Luigi Manai
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Elias Manca
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Barbara Noli
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy
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13
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Maity S, Mayer MG, Shu Q, Linh H, Bao D, Blair RV, He Y, Lyon CJ, Hu TY, Fischer T, Fan J. Cerebrospinal Fluid Protein Markers Indicate Neuro-Damage in SARS-CoV-2-Infected Nonhuman Primates. Mol Cell Proteomics 2023; 22:100523. [PMID: 36870567 PMCID: PMC9981268 DOI: 10.1016/j.mcpro.2023.100523] [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: 07/13/2022] [Revised: 02/18/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Neurologic manifestations are among the most frequently reported complications of COVID-19. However, given the paucity of tissue samples and the highly infectious nature of the etiologic agent of COVID-19, we have limited information to understand the neuropathogenesis of COVID-19. Therefore, to better understand the impact of COVID-19 on the brain, we used mass-spectrometry-based proteomics with a data-independent acquisition mode to investigate cerebrospinal fluid (CSF) proteins collected from two different nonhuman primates, Rhesus Macaque and African Green Monkeys, for the neurologic effects of the infection. These monkeys exhibited minimal to mild pulmonary pathology but moderate to severe central nervous system (CNS) pathology. Our results indicated that CSF proteome changes after infection resolution corresponded with bronchial virus abundance during early infection and revealed substantial differences between the infected nonhuman primates and their age-matched uninfected controls, suggesting these differences could reflect altered secretion of CNS factors in response to SARS-CoV-2-induced neuropathology. We also observed the infected animals exhibited highly scattered data distributions compared to their corresponding controls indicating the heterogeneity of the CSF proteome change and the host response to the viral infection. Dysregulated CSF proteins were preferentially enriched in functional pathways associated with progressive neurodegenerative disorders, hemostasis, and innate immune responses that could influence neuroinflammatory responses following COVID-19. Mapping these dysregulated proteins to the Human Brain Protein Atlas found that they tended to be enriched in brain regions that exhibit more frequent injury following COVID-19. It, therefore, appears reasonable to speculate that such CSF protein changes could serve as signatures for neurologic injury, identify important regulatory pathways in this process, and potentially reveal therapeutic targets to prevent or attenuate the development of neurologic injuries following COVID-19.
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Affiliation(s)
- Sudipa Maity
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Meredith G Mayer
- Division of Comparative Pathology, National Primate Research Center, Covington, Louisiana, USA
| | - Qingbo Shu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Hellmers Linh
- Division of Comparative Pathology, National Primate Research Center, Covington, Louisiana, USA
| | - Duran Bao
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Robert V Blair
- Division of Comparative Pathology, National Primate Research Center, Covington, Louisiana, USA
| | - Yanlin He
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Christopher J Lyon
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Tony Y Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Tracy Fischer
- Division of Comparative Pathology, National Primate Research Center, Covington, Louisiana, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Jia Fan
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA.
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14
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A proteogenomic view of Parkinson's disease causality and heterogeneity. NPJ Parkinsons Dis 2023; 9:24. [PMID: 36774388 PMCID: PMC9922273 DOI: 10.1038/s41531-023-00461-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/19/2023] [Indexed: 02/13/2023] Open
Abstract
The pathogenesis and clinical heterogeneity of Parkinson's disease (PD) have been evaluated from molecular, pathophysiological, and clinical perspectives. High-throughput proteomic analysis of cerebrospinal fluid (CSF) opened new opportunities for scrutinizing this heterogeneity. To date, this is the most comprehensive CSF-based proteomics profiling study in PD with 569 patients (350 idiopathic patients, 65 GBA + mutation carriers and 154 LRRK2 + mutation carriers), 534 controls, and 4135 proteins analyzed. Combining CSF aptamer-based proteomics with genetics we determined protein quantitative trait loci (pQTLs). Analyses of pQTLs together with summary statistics from the largest PD genome wide association study (GWAS) identified 68 potential causal proteins by Mendelian randomization. The top causal protein, GPNMB, was previously reported to be upregulated in the substantia nigra of PD patients. We also compared the CSF proteomes of patients and controls. Proteome differences between GBA + patients and unaffected GBA + controls suggest degeneration of dopaminergic neurons, altered dopamine metabolism and increased brain inflammation. In the LRRK2 + subcohort we found dysregulated lysosomal degradation, altered alpha-synuclein processing, and neurotransmission. Proteome differences between idiopathic patients and controls suggest increased neuroinflammation, mitochondrial dysfunction/oxidative stress, altered iron metabolism and potential neuroprotection mediated by vasoactive substances. Finally, we used proteomic data to stratify idiopathic patients into "endotypes". The identified endotypes show differences in cognitive and motor disease progression based on previously reported protein-based risk scores.Our findings not only contribute to the identification of new therapeutic targets but also to shape personalized medicine in CNS neurodegeneration.
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15
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Isik FI, Katzeff JS, Fu Y, Kim WS. Understanding the Role of CDH4 in Multiple System Atrophy Brain. JOURNAL OF PARKINSON'S DISEASE 2023; 13:1303-1311. [PMID: 38143373 PMCID: PMC10741323 DOI: 10.3233/jpd-230298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2023] [Indexed: 12/26/2023]
Abstract
BACKGROUND Multiple system atrophy (MSA) is a rapidly progressive neurodegenerative disease clinically characterized by parkinsonism, cerebellar ataxia, and autonomic dysfunction. A major pathological feature of MSA is the presence of α-synuclein aggregates in oligodendrocytes, the myelinating cells of the central nervous system. A genome-wide association study revealed that the CDH4 gene is associated with MSA. However, virtually nothing is known about the role of CDH4 in the context of MSA. OBJECTIVE Our aim was to compare the expression of CDH4 between MSA and control brains, and to investigate its relationship with α-synuclein in oligodendrocytes. METHODS RNA and protein were prepared from putamen, motor cortex white matter, cerebellum, and superior occipital cortex tissues collected from MSA (N = 11) and control (N = 13) brains. The expression of CDH4 was measured at mRNA and protein levels by qPCR and western blotting. Oligodendrocyte cells were cultured on plates and transfected with CDH4 cDNA and its impact on α-synuclein was analyzed. RESULTS Firstly, we found that CDH4 in MSA brain was significantly elevated in the disease-affected motor cortex white matter in MSA (N = 11) compared to controls (N = 13) and unaltered in the disease-unaffected superior occipital cortex. Secondly, we determined that increases in CDH4 expression caused changes in the cellular levels of α-synuclein in oligodendrocytes. CONCLUSIONS When put together, these results provide evidence that support the GWAS association of CDH4 with MSA.
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Affiliation(s)
- Finula I. Isik
- Brain and Mind Centre & School of Medical Sciences, The University of Sydney, Sydney NSW, Australia
| | - Jared S. Katzeff
- Brain and Mind Centre & School of Medical Sciences, The University of Sydney, Sydney NSW, Australia
| | - YuHong Fu
- Brain and Mind Centre & School of Medical Sciences, The University of Sydney, Sydney NSW, Australia
| | - Woojin Scott Kim
- Brain and Mind Centre & School of Medical Sciences, The University of Sydney, Sydney NSW, Australia
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López-Cerdán A, Andreu Z, Hidalgo MR, Grillo-Risco R, Català-Senent JF, Soler-Sáez I, Neva-Alejo A, Gordillo F, de la Iglesia-Vayá M, García-García F. Unveiling sex-based differences in Parkinson's disease: a comprehensive meta-analysis of transcriptomic studies. Biol Sex Differ 2022; 13:68. [PMID: 36414996 PMCID: PMC9682715 DOI: 10.1186/s13293-022-00477-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/01/2022] [Indexed: 11/24/2022] Open
Abstract
Background In recent decades, increasing longevity (among other factors) has fostered a rise in Parkinson's disease incidence. Although not exhaustively studied in this devastating disease, the impact of sex represents a critical variable in Parkinson’s disease as epidemiological and clinical features differ between males and females. Methods To study sex bias in Parkinson’s disease, we conducted a systematic review to select sex-labeled transcriptomic data from three relevant brain tissues: the frontal cortex, the striatum, and the substantia nigra. We performed differential expression analysis on each study chosen. Then we summarized the individual differential expression results with three tissue-specific meta-analyses and a global all-tissues meta-analysis. Finally, results from the meta-analysis were functionally characterized using different functional profiling approaches. Results The tissue-specific meta-analyses linked Parkinson’s disease to the enhanced expression of MED31 in the female frontal cortex and the dysregulation of 237 genes in the substantia nigra. The global meta-analysis detected 15 genes with sex-differential patterns in Parkinson’s disease, which participate in mitochondrial function, oxidative stress, neuronal degeneration, and cell death. Furthermore, functional analyses identified pathways, protein–protein interaction networks, and transcription factors that differed by sex. While male patients exhibited changes in oxidative stress based on metal ions, inflammation, and angiogenesis, female patients exhibited dysfunctions in mitochondrial and lysosomal activity, antigen processing and presentation functions, and glutamic and purine metabolism. All results generated during this study are readily available by accessing an open web resource (http://bioinfo.cipf.es/metafun-pd/) for consultation and reuse in further studies. Conclusions Our in silico approach has highlighted sex-based differential mechanisms in typical Parkinson Disease hallmarks (inflammation, mitochondrial dysfunction, and oxidative stress). Additionally, we have identified specific genes and transcription factors for male and female Parkinson Disease patients that represent potential candidates as biomarkers to diagnosis. Supplementary Information The online version contains supplementary material available at 10.1186/s13293-022-00477-5. Females show a significant increase in the expression of MED31 in the frontal cortex. This gene is involved in lipid metabolism and neural diseases. We found 237 genes having sex-based significantly differential expression in substantia nigra. Functional profiling of these genes reveals a differential sex-related behavior in PD regarding their biological functions, protein-protein interaction networks, and transcription factors activation. There are remarkable sex based differential mechanisms in typical PD hallmarks: inflammation, mitochondrial dysfunction, and oxidative stress. Studies on sex differences in PD are needed to improve more targeted interventions.
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Selvaraj C, Pravin MA, Alhoqail WA, Nayarisseri A, Singh SK. Intrinsically disordered proteins in viral pathogenesis and infections. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:221-242. [PMID: 36088077 DOI: 10.1016/bs.apcsb.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Disordered proteins serve a crucial part in many biological processes that go beyond the capabilities of ordered proteins. A large number of virus-encoded proteins have extremely condensed proteomes and genomes, which results in highly disordered proteins. The presence of these IDPs allows them to rapidly adapt to changes in their biological environment and play a significant role in viral replication and down-regulation of host defense mechanisms. Since viruses undergo rapid evolution and have a high rate of mutation and accumulation in their proteome, IDPs' insights into viruses are critical for understanding how viruses hijack cells and cause disease. There are many conformational changes that IDPs can adopt in order to interact with different protein partners and thus stabilize the particular fold and withstand high mutation rates. This chapter explains the molecular mechanism behind viral IDPs, as well as the significance of recent research in the field of IDPs, with the goal of gaining a deeper comprehension of the essential roles and functions played by viral proteins.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - Muthuraja Arun Pravin
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Wardah A Alhoqail
- Department of Biology, College of Education, Majmaah University, Al Majma'ah, Saudi Arabia
| | - Anuraj Nayarisseri
- In Silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
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Raghunathan R, Turajane K, Wong LC. Biomarkers in Neurodegenerative Diseases: Proteomics Spotlight on ALS and Parkinson’s Disease. Int J Mol Sci 2022; 23:ijms23169299. [PMID: 36012563 PMCID: PMC9409485 DOI: 10.3390/ijms23169299] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/13/2022] [Accepted: 08/14/2022] [Indexed: 11/21/2022] Open
Abstract
Neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD) are both characterized by pathogenic protein aggregates that correlate with the progressive degeneration of neurons and the loss of behavioral functions. Both diseases lack biomarkers for diagnosis and treatment efficacy. Proteomics is an unbiased quantitative tool capable of the high throughput quantitation of thousands of proteins from minimal sample volumes. We review recent proteomic studies in human tissues, plasma, cerebrospinal fluid (CSF), and exosomes in ALS and PD that identify proteins with potential utility as biomarkers. Further, we review disease-related post-translational modifications in key proteins TDP43 in ALS and α-synuclein in PD studies, which may serve as biomarkers. We compare relative and absolute quantitative proteomic approaches in key biomarker studies in ALS and PD and discuss recent technological advancements which may identify suitable biomarkers for the early-diagnosis treatment efficacy of these diseases.
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Wang Y, Qin X, Han Y, Li B. VGF: A prospective biomarker and therapeutic target for neuroendocrine and nervous system disorders. Biomed Pharmacother 2022; 151:113099. [PMID: 35594706 DOI: 10.1016/j.biopha.2022.113099] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 11/28/2022] Open
Abstract
Neuroendocrine regulatory polypeptide VGF (nerve growth factor inducible) was firstly found in the rapid induction of nerve growth factor on PC12 cells. It was selectively distributed in neurons and many neuroendocrine tissues. This paper reviewed the latest literatures on the gene structure, transcriptional regulation, protein processing, distribution and potential receptors of VGF. The neuroendocrine roles of VGF and its derived polypeptides in regulating energy, water electrolyte balance, circadian rhythm and reproductive activities were also summarized. Furthermore, based on the experimental evidence in vivo and in vitro, dysregulation of VGF in different neuroendocrine diseases and the possible mechanism mediated by VGF polypeptides were discussed. We next discussed the potential as the clinical diagnosis and therapy for VGF related diseases in the future.
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Affiliation(s)
- Yibei Wang
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China; Department of Developmental Cell Biology, Key Laboratory of Medical Cell Biology, China Medical University, Shenyang, Liaoning Province, China.
| | - Xiaoxue Qin
- Department of Developmental Cell Biology, Key Laboratory of Medical Cell Biology, China Medical University, Shenyang, Liaoning Province, China.
| | - Yun Han
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China.
| | - Bo Li
- Department of Developmental Cell Biology, Key Laboratory of Medical Cell Biology, China Medical University, Shenyang, Liaoning Province, China.
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20
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Ruffini N, Klingenberg S, Heese R, Schweiger S, Gerber S. The Big Picture of Neurodegeneration: A Meta Study to Extract the Essential Evidence on Neurodegenerative Diseases in a Network-Based Approach. Front Aging Neurosci 2022; 14:866886. [PMID: 35832065 PMCID: PMC9271745 DOI: 10.3389/fnagi.2022.866886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/13/2022] [Indexed: 12/12/2022] Open
Abstract
The common features of all neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis (ALS), and Huntington's disease, are the accumulation of aggregated and misfolded proteins and the progressive loss of neurons, leading to cognitive decline and locomotive dysfunction. Still, they differ in their ultimate manifestation, the affected brain region, and the kind of proteinopathy. In the last decades, a vast number of processes have been described as associated with neurodegenerative diseases, making it increasingly harder to keep an overview of the big picture forming from all those data. In this meta-study, we analyzed genomic, transcriptomic, proteomic, and epigenomic data of the aforementioned diseases using the data of 234 studies in a network-based approach to study significant general coherences but also specific processes in individual diseases or omics levels. In the analysis part, we focus on only some of the emerging findings, but trust that the meta-study provided here will be a valuable resource for various other researchers focusing on specific processes or genes contributing to the development of neurodegeneration.
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Affiliation(s)
- Nicolas Ruffini
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Leibniz Institute for Resilience Research, Leibniz Association, Mainz, Germany
| | - Susanne Klingenberg
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Raoul Heese
- Fraunhofer Institute for Industrial Mathematics (ITWM), Kaiserslautern, Germany
| | - Susann Schweiger
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
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21
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Karayel O, Virreira Winter S, Padmanabhan S, Kuras YI, Vu DT, Tuncali I, Merchant K, Wills AM, Scherzer CR, Mann M. Proteome profiling of cerebrospinal fluid reveals biomarker candidates for Parkinson's disease. Cell Rep Med 2022; 3:100661. [PMID: 35732154 PMCID: PMC9245058 DOI: 10.1016/j.xcrm.2022.100661] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/29/2021] [Accepted: 05/23/2022] [Indexed: 11/16/2022]
Abstract
Parkinson's disease (PD) is a growing burden worldwide, and there is no reliable biomarker used in clinical routines to date. Cerebrospinal fluid (CSF) is routinely collected in patients with neurological symptoms and should closely reflect alterations in PD patients' brains. Here, we describe a scalable and sensitive mass spectrometry (MS)-based proteomics workflow for CSF proteome profiling. From two independent cohorts with over 200 individuals, our workflow reproducibly quantifies over 1,700 proteins from minimal CSF amounts. Machine learning determines OMD, CD44, VGF, PRL, and MAN2B1 to be altered in PD patients or to significantly correlate with clinical scores. We also uncover signatures of enhanced neuroinflammation in LRRK2 G2019S carriers, as indicated by increased levels of CTSS, PLD4, and HLA proteins. A comparison with our previously acquired urinary proteomes reveals a large overlap in PD-associated changes, including lysosomal proteins, opening up new avenues to improve our understanding of PD pathogenesis.
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Affiliation(s)
- Ozge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sebastian Virreira Winter
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | | | - Yuliya I Kuras
- APDA Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA; Precision Neurology Program, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Duc Tung Vu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Idil Tuncali
- APDA Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA; Precision Neurology Program, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Kalpana Merchant
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Anne-Marie Wills
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Clemens R Scherzer
- APDA Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA; Precision Neurology Program, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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22
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Zhu S, Bäckström D, Forsgren L, Trupp M. Alterations in Self-Aggregating Neuropeptides in Cerebrospinal Fluid of Patients with Parkinsonian Disorders. JOURNAL OF PARKINSON'S DISEASE 2022; 12:1169-1189. [PMID: 35253777 PMCID: PMC9198747 DOI: 10.3233/jpd-213031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: Parkinson’s disease (PD), progressive supranuclear palsy (PSP), and multiple system atrophy (MSA) present with similar movement disorder symptoms but distinct protein aggregates upon pathological examination. Objective: Discovery and validation of candidate biomarkers in parkinsonian disorders for differential diagnosis of subgroup molecular etiologies. Methods: Untargeted liquid chromatography (LC)-mass spectrometry (MS) proteomics was used for discovery profiling in cerebral spinal fluid (CSF) followed by LC-MS/MS based multiple reaction monitoring for validation of candidates. We compared clinical variation within the parkinsonian cohort including PD subgroups exhibiting tremor dominance (TD) or postural instability gait disturbance and those with detectable leukocytes in CSF. Results: We have identified candidate peptide biomarkers and validated related proteins with targeted quantitative multiplexed assays. Dopamine-drug naïve patients at first diagnosis exhibit reduced levels of signaling neuropeptides, chaperones, and processing proteases for packaging of self-aggregating peptides into dense core vesicles. Distinct patterns of biomarkers were detected in the parkinsonian disorders but were not robust enough to offer a differential diagnosis. Different biomarker changes were detected in male and female patients with PD. Subgroup specific candidate biomarkers were identified for TD PD and PD patients with leukocytes detected in CSF. Conclusion: PD, MSA, and PSP exhibit overlapping as well as distinct protein biomarkers that suggest specific molecular etiologies. This indicates common sensitivity of certain populations of selectively vulnerable neurons in the brain, and distinct therapeutic targets for PD subgroups. Our report validates a decrease in CSF levels of self-aggregating neuropeptides in parkinsonian disorders and supports the role of native amyloidogenic proteins in etiologies of neurodegenerative diseases.
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Affiliation(s)
- Shaochun Zhu
- Department of Clinical Sciences, Neurosciences, Umeå University, Umeå, Sweden
| | - David Bäckström
- Department of Clinical Sciences, Neurosciences, Umeå University, Umeå, Sweden
| | - Lars Forsgren
- Department of Clinical Sciences, Neurosciences, Umeå University, Umeå, Sweden
| | - Miles Trupp
- Department of Clinical Sciences, Neurosciences, Umeå University, Umeå, Sweden
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23
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Dayon L, Cominetti O, Affolter M. Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications. Expert Rev Proteomics 2022; 19:131-151. [PMID: 35466824 DOI: 10.1080/14789450.2022.2070477] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids. AREAS COVERED We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics. EXPERT OPINION While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.
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Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
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24
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Esfandiary A, Finkelstein DI, Voelcker NH, Rudd D. Clinical Sphingolipids Pathway in Parkinson’s Disease: From GCase to Integrated-Biomarker Discovery. Cells 2022; 11:cells11081353. [PMID: 35456032 PMCID: PMC9028315 DOI: 10.3390/cells11081353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 02/01/2023] Open
Abstract
Alterations in the sphingolipid metabolism of Parkinson’s Disease (PD) could be a potential diagnostic feature. Only around 10–15% of PD cases can be diagnosed through genetic alterations, while the remaining population, idiopathic PD (iPD), manifest without validated and specific biomarkers either before or after motor symptoms appear. Therefore, clinical diagnosis is reliant on the skills of the clinician, which can lead to misdiagnosis. IPD cases present with a spectrum of non-specific symptoms (e.g., constipation and loss of the sense of smell) that can occur up to 20 years before motor function loss (prodromal stage) and formal clinical diagnosis. Prodromal alterations in metabolites and proteins from the pathways underlying these symptoms could act as biomarkers if they could be differentiated from the broad values seen in a healthy age-matched control population. Additionally, these shifts in metabolites could be integrated with other emerging biomarkers/diagnostic tests to give a PD-specific signature. Here we provide an up-to-date review of the diagnostic value of the alterations in sphingolipids pathway in PD by focusing on the changes in definitive PD (postmortem confirmed brain data) and their representation in “probable PD” cerebrospinal fluid (CSF) and blood. We conclude that the trend of holistic changes in the sphingolipid pathway in the PD brain seems partly consistent in CSF and blood, and could be one of the most promising pathways in differentiating PD cases from healthy controls, with the potential to improve early-stage iPD diagnosis and distinguish iPD from other Parkinsonism when combined with other pathological markers.
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Affiliation(s)
- Ali Esfandiary
- Drug Delivery, Disposition and Dynamics, Monash University, Parkville, VIC 3052, Australia; (A.E.); (N.H.V.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
| | | | - Nicolas Hans Voelcker
- Drug Delivery, Disposition and Dynamics, Monash University, Parkville, VIC 3052, Australia; (A.E.); (N.H.V.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Clayton, VIC 3168, Australia
- Materials Science and Engineering, Monash University, Clayton, VIC 3168, Australia
| | - David Rudd
- Drug Delivery, Disposition and Dynamics, Monash University, Parkville, VIC 3052, Australia; (A.E.); (N.H.V.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
- Correspondence: ; Tel.: +61-3-9903-9581
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25
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Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research. Molecules 2022; 27:molecules27082411. [PMID: 35458608 PMCID: PMC9031286 DOI: 10.3390/molecules27082411] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.
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26
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Naskar A, Stezin A, Dharmappa A, Hegde S, Philip M, Kamble N, Saini J, Sandhya K, Tatu U, Yadav R, Pal PK, Alladi PA. Fibrinogen and Complement Factor H Are Promising CSF Protein Biomarkers for Parkinson's Disease with Cognitive Impairment─A Proteomics-ELISA-Based Study. ACS Chem Neurosci 2022; 13:1030-1045. [PMID: 35200010 DOI: 10.1021/acschemneuro.2c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Parkinson's disease (PD) with cognitive impairment (PDCI) is essentially diagnosed through clinical and neuropsychological examinations. There is a need to identify biomarkers to foresee cognitive decline in them. We performed label-free unbiased nontargeted proteomics (Q-TOF LC/MS-MS) on the CSF of non-neurological control; PDCI; PD; and normal pressure hydrocephalus (NPH) patients, followed by targeted ELISA for validation. Of the 281 proteins identified, 42 were differentially altered in PD, PDCI, and NPH. With a certain overlap, 28 proteins were altered in PDCI and 25 proteins were altered in NPH. Five significantly upregulated proteins in PDCI were fibrinogen, gelsolin, complement factor-H, and apolipoproteins A-I and A-IV, whereas carnosine dipeptidase-1, carboxypeptidase-E, dickkopf-3, and secretogranin-3 precursor proteins were downregulated. Those uniquely altered in NPH were the insulin-like growth factor-binding protein, ceruloplasmin, α-1 antitrypsin, VGF nerve growth factor, and neural cell adhesion molecule L1-like protein. The ELISA-derived protein concentrations correlated with neuropsychological scores of certain cognitive domains. In PDCI, the Wisconsin card sorting percentile correlated negatively with fibrinogen. Intraperitoneal injection of native fibrinogen caused motor deficits in C57BL/6J mice as assessed by the pole test. Thus, a battery of proteins such as fibrinogen-α-chain, CFAH, and APOA-I/APOA-IV alongside neuropsychological assessment could be reliable biomarkers to distinguish PDCI and NPH.
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Affiliation(s)
- Aditi Naskar
- Department of Clinical Psychopharmacology & Neurotoxicology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Albert Stezin
- Department of Clinical Neurosciences, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Arpitha Dharmappa
- Department of Clinical Psychology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Shantala Hegde
- Department of Clinical Psychology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Mariamma Philip
- Department of Biostatistics, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Nitish Kamble
- Department of Neurology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Jitender Saini
- Department of Neuroimaging & Interventional Radiology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - K. Sandhya
- Department of Anaesthesiology, Bangalore Medical College and Research Institute, Bengaluru 560002, India
| | - Utpal Tatu
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Ravi Yadav
- Department of Neurology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Phalguni Anand Alladi
- Department of Clinical Psychopharmacology & Neurotoxicology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
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27
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Plubell DL, Käll L, Webb-Robertson BJM, Bramer LM, Ives A, Kelleher NL, Smith LM, Montine TJ, Wu CC, MacCoss MJ. Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics? J Proteome Res 2022; 21:891-898. [PMID: 35220718 PMCID: PMC8976764 DOI: 10.1021/acs.jproteome.1c00894] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Bottom-up proteomics provides peptide measurements and has been invaluable for moving proteomics into large-scale analyses. Commonly, a single quantitative value is reported for each protein-coding gene by aggregating peptide quantities into protein groups following protein inference or parsimony. However, given the complexity of both RNA splicing and post-translational protein modification, it is overly simplistic to assume that all peptides that map to a singular protein-coding gene will demonstrate the same quantitative response. By assuming that all peptides from a protein-coding sequence are representative of the same protein, we may miss the discovery of important biological differences. To capture the contributions of existing proteoforms, we need to reconsider the practice of aggregating protein values to a single quantity per protein-coding gene.
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Affiliation(s)
- Deanna L. Plubell
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
| | - Lukas Käll
- Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 17121, Solna, Sweden
| | | | - Lisa M. Bramer
- Pacific Northwest National Laboratory, Richland, WA 99352
| | - Ashley Ives
- Proteomics Center of Excellence & Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Neil L. Kelleher
- Proteomics Center of Excellence & Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | | | - Christine C. Wu
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
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28
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Kwon DH, Hwang JS, Kim SG, Jang YE, Shin TH, Lee G. Cerebrospinal Fluid Metabolome in Parkinson's Disease and Multiple System Atrophy. Int J Mol Sci 2022; 23:ijms23031879. [PMID: 35163800 PMCID: PMC8836409 DOI: 10.3390/ijms23031879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
Parkinson’s disease (PD) and multiple system atrophy (MSA) belong to the neurodegenerative group of synucleinopathies; differential diagnosis between PD and MSA is difficult, especially at early stages, owing to their clinical and biological similarities. Thus, there is a pressing need to identify metabolic biomarkers for these diseases. The metabolic profile of the cerebrospinal fluid (CSF) is reported to be altered in PD and MSA; however, the altered metabolites remain unclear. We created a single network with altered metabolites in PD and MSA based on the literature and assessed biological functions, including metabolic disorders of the nervous system, inflammation, concentration of ATP, and neurological disorder, through bioinformatics methods. Our in-silico prediction-based metabolic networks are consistent with Parkinsonism events. Although metabolomics approaches provide a more quantitative understanding of biochemical events underlying the symptoms of PD and MSA, limitations persist in covering molecules related to neurodegenerative disease pathways. Thus, omics data, such as proteomics and microRNA, help understand the altered metabolomes mechanism. In particular, integrated omics and machine learning approaches will be helpful to elucidate the pathological mechanisms of PD and MSA. This review discusses the altered metabolites between PD and MSA in the CSF and omics approaches to discover diagnostic biomarkers.
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Affiliation(s)
- Do Hyeon Kwon
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Ji Su Hwang
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Seok Gi Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Yong Eun Jang
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Tae Hwan Shin
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea
- Correspondence: (T.H.S.); (G.L.)
| | - Gwang Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea
- Correspondence: (T.H.S.); (G.L.)
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29
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Schumacher-Schuh A, Bieger A, Borelli WV, Portley MK, Awad PS, Bandres-Ciga S. Advances in Proteomic and Metabolomic Profiling of Neurodegenerative Diseases. Front Neurol 2022; 12:792227. [PMID: 35173667 PMCID: PMC8841717 DOI: 10.3389/fneur.2021.792227] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
Proteomics and metabolomics are two emerging fields that hold promise to shine light on the molecular mechanisms causing neurodegenerative diseases. Research in this area may reveal and quantify specific metabolites and proteins that can be targeted by therapeutic interventions intended at halting or reversing the neurodegenerative process. This review aims at providing a general overview on the current status of proteomic and metabolomic profiling in neurodegenerative diseases. We focus on the most common neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. We discuss the relevance of state-of-the-art metabolomics and proteomics approaches and their potential for biomarker discovery. We critically review advancements made so far, highlighting how metabolomics and proteomics may have a significant impact in future therapeutic and biomarker development. Finally, we further outline technologies used so far as well as challenges and limitations, placing the current information in a future-facing context.
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Affiliation(s)
- Artur Schumacher-Schuh
- Departamento de Farmacologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Serviço de Neurologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Andrei Bieger
- Department of Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Wyllians V. Borelli
- Serviço de Neurologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Makayla K. Portley
- Neurodegenerative Disorders Clinic, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Paula Saffie Awad
- Movement Disorders Clinic, Centro de Trastornos de Movimiento (CETRAM), Santiago, Chile
| | - Sara Bandres-Ciga
- Neurodegenerative Disorders Clinic, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
- Laboratory of Neurogenetics, Molecular Genetics Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Sara Bandres-Ciga
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30
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Agrawal I, Tripathi P, Biswas S. Mass Spectrometry Based Protein Biomarkers and Drug Target Discovery and Clinical Diagnosis in Age-Related Progressing Neurodegenerative Diseases. Drug Metab Rev 2022; 54:22-36. [PMID: 35038284 DOI: 10.1080/03602532.2022.2029475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Neurodegenerative diseases correspond to overly complex health disorders that are driven by intersecting pathophysiology that are often trapped in vicious cycles of degeneration and cognitive decline. The usual diagnostic route of these diseases is based on postmortem examination that involves identifying pathology that is specific to the disease in the brain. However, in such cases, accurate diagnosis of the specific disease is limited because clinical disease presentations are often complex that do not easily allow to discriminate patient's cognitive, behavioral, and functional impairment profiles. Additionally, an early identification and therapeutic intervention of these diseases is pivotal to slow the progression of neurodegeneration and extend healthy life span. Mass spectrometry-based techniques have proven to be hugely promising in biological sample analysis and discovery of biomarkers including protein and peptide biomarkers for potential drug target discovery. Recent studies on these biomarkers have demonstrated their potential for applications in early diagnostics and identifying therapeutic targets to battle against neurodegenerative diseases. In this review, we have presented principles of mass spectrometry (MS) and the associated workflows in analyzing and imaging biological samples for discovery of biomarkers. We have especially focused on age- related progressing neurodegenerative diseases such as Alzheimer's (AD) and Parkinson's disease (PD), Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal dementia (FTD) and the related MS-based biomarkers developments for these diseases. Finally, we present a future perspective discussing the potential research directions ahead.
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Affiliation(s)
- Ishita Agrawal
- Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Pallavi Tripathi
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK
| | - Shyamasri Biswas
- USA Prime Biotech LLC, 1330 NW 6th St., Suite A-2, Gainesville, FL 32601, USA
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Lindberg I, Shu Z, Lam H, Helwig M, Yucer N, Laperle A, Svendsen C, Di Monte DA, Maidment NT. The proSAAS Chaperone Provides Neuroprotection and Attenuates Transsynaptic α-Synuclein Spread in Rodent Models of Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2022; 12:1463-1478. [PMID: 35527562 PMCID: PMC9731515 DOI: 10.3233/jpd-213053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND Parkinson's disease involves aberrant aggregation of the synaptic protein alpha-synuclein (aSyn) in the nigrostriatal tract. We have previously shown that proSAAS, a small neuronal chaperone, blocks aSyn-induced dopaminergic cytotoxicity in primary nigral cultures. OBJECTIVE To determine if proSAAS overexpression is neuroprotective in animal models of Parkinson's disease. METHODS proSAAS- or GFP-encoding lentivirus was injected together with human aSyn-expressing AAV unilaterally into the substantia nigra of rats and motor asymmetry assessed using a battery of motor performance tests. Dopamine neuron survival was assessed by nigral stereology and striatal tyrosine hydroxylase (TH) densitometry. To examine transsynaptic spread of aSyn, aSyn AAV was injected into the vagus of mice in the presence of AAVs encoding either GFP or proSAAS; the spread of aSyn-positive neurites into rostral nuclei was quantified following immunohistochemistry. RESULTS Coinjection of proSAAS-encoding lentivirus profoundly reduced the motor asymmetry caused by unilateral nigral AAV-mediated human aSyn overexpression. This was accompanied by significant amelioration of the human aSyn-induced loss of both nigral TH-positive cells and striatal TH-positive terminals, demonstrating clear proSAAS-mediated protection of the nigrostriatal tract. ProSAAS overexpression reduced human aSyn protein levels in nigra and striatum and reduced the loss of TH protein in both regions. Following vagal administration of human aSyn-encoding AAV, the number of human aSyn-positive neurites in the pons and caudal midbrain was considerably reduced in mice coinjected with proSAAS-, but not GFP-encoding AAV, supporting proSAAS-mediated blockade of transsynaptic aSyn transmission. CONCLUSION The proSAAS chaperone may represent a promising target for therapeutic development in Parkinson's disease.
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Affiliation(s)
- Iris Lindberg
- University of Maryland-Baltimore;,To whom correspondence should be addressed: Iris Lindberg, Ph.D., Department of Anatomy and Neurobiology, University of Maryland Medical School, University of Maryland-Baltimore, Baltimore, MD 21201, Phone: (410) 7064778, and Nigel T. Maidment, Ph.D., Department of Psychiatry and Biobehavioral Sciences, Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, University of California at Los Angeles, Los Angeles CA 90024, Phone: (310) 206-7767,
| | - Zhan Shu
- University of California-Los Angeles
| | - Hoa Lam
- University of California-Los Angeles
| | | | - Nur Yucer
- Cedars-Sinai Medical Center, Los Angeles
| | | | | | | | - Nigel T. Maidment
- University of California-Los Angeles;,To whom correspondence should be addressed: Iris Lindberg, Ph.D., Department of Anatomy and Neurobiology, University of Maryland Medical School, University of Maryland-Baltimore, Baltimore, MD 21201, Phone: (410) 7064778, and Nigel T. Maidment, Ph.D., Department of Psychiatry and Biobehavioral Sciences, Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, University of California at Los Angeles, Los Angeles CA 90024, Phone: (310) 206-7767,
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32
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Ito H, Matsui T, Konno R, Itakura M, Kodera Y. LC-MS peak assignment based on unanimous selection by six machine learning algorithms. Sci Rep 2021; 11:23411. [PMID: 34862414 PMCID: PMC8642397 DOI: 10.1038/s41598-021-02899-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Recent mass spectrometry (MS)-based techniques enable deep proteome coverage with relative quantitative analysis, resulting in increased identification of very weak signals accompanied by increased data size of liquid chromatography (LC)–MS/MS spectra. However, the identification of weak signals using an assignment strategy with poorer performance results in imperfect quantification with misidentification of peaks and ratio distortions. Manually annotating a large number of signals within a very large dataset is not a realistic approach. In this study, therefore, we utilized machine learning algorithms to successfully extract a higher number of peptide peaks with high accuracy and precision. Our strategy evaluated each peak identified using six different algorithms; peptide peaks identified by all six algorithms (i.e., unanimously selected) were subsequently assigned as true peaks, which resulted in a reduction in the false-positive rate. Hence, exact and highly quantitative peptide peaks were obtained, providing better performance than obtained applying the conventional criteria or using a single machine learning algorithm.
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Affiliation(s)
- Hiroaki Ito
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Takashi Matsui
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan.,Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, 252-0373, Japan
| | - Ryo Konno
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Makoto Itakura
- Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, 252-0373, Japan.,Department of Biochemistry, School of Medicine, Kitasato University, 1-15-1 Kitasato, Minami-ku , Sagamihara, 252-0373, Japan
| | - Yoshio Kodera
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan. .,Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, 252-0373, Japan.
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Marques TM, van Rumund A, Kersten I, Bruinsma IB, Wessels HJ, Gloerich J, Kaffa C, Esselink RAJ, Bloem BR, Kuiperij HB, Verbeek MM. Identification of cerebrospinal fluid biomarkers for parkinsonism using a proteomics approach. NPJ Parkinsons Dis 2021; 7:107. [PMID: 34848724 PMCID: PMC8633286 DOI: 10.1038/s41531-021-00249-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 10/27/2021] [Indexed: 01/25/2023] Open
Abstract
The aim of our study was to investigate cerebrospinal fluid (CSF) tryptic peptide profiles as potential diagnostic biomarkers for the discrimination of parkinsonian disorders. CSF samples were collected from individuals with parkinsonism, who had an uncertain diagnosis at the time of inclusion and who were followed for up to 12 years in a longitudinal study. We performed shotgun proteomics to identify tryptic peptides in CSF of Parkinson's disease (PD, n = 10), multiple system atrophy patients (MSA, n = 5) and non-neurological controls (n = 10). We validated tryptic peptides with differential levels between PD and MSA using a newly developed selected reaction monitoring (SRM) assay in CSF of PD (n = 46), atypical parkinsonism patients (AP; MSA, n = 17; Progressive supranuclear palsy; n = 8) and non-neurological controls (n = 39). We identified 191 tryptic peptides that differed significantly between PD and MSA, of which 34 met our criteria for SRM development. For 14/34 peptides we confirmed differences between PD and AP. These tryptic peptides discriminated PD from AP with moderate-to-high accuracy. Random forest modelling including tryptic peptides plus either clinical assessments or other CSF parameters (neurofilament light chain, phosphorylated tau protein) and age improved the discrimination of PD vs. AP. Our results show that the discovery of tryptic peptides by untargeted and subsequent validation by targeted proteomics is a suitable strategy to identify potential CSF biomarkers for PD versus AP. Furthermore, the tryptic peptides, and corresponding proteins, that we identified as differential biomarkers may increase our current knowledge about the disease-specific pathophysiological mechanisms of parkinsonism.
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Affiliation(s)
- Tainá M. Marques
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anouke van Rumund
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands
| | - Iris Kersten
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ilona B. Bruinsma
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hans J.C.T. Wessels
- grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jolein Gloerich
- grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Charlotte Kaffa
- grid.10417.330000 0004 0444 9382Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rianne A. J. Esselink
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands
| | - Bastiaan R. Bloem
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands
| | - H. Bea Kuiperij
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marcel M. Verbeek
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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Brockmann K, Quadalti C, Lerche S, Rossi M, Wurster I, Baiardi S, Roeben B, Mammana A, Zimmermann M, Hauser AK, Deuschle C, Schulte C, Waniek K, Lachmann I, Sjödin S, Brinkmalm A, Blennow K, Zetterberg H, Gasser T, Parchi P. Association between CSF alpha-synuclein seeding activity and genetic status in Parkinson's disease and dementia with Lewy bodies. Acta Neuropathol Commun 2021; 9:175. [PMID: 34717775 PMCID: PMC8556894 DOI: 10.1186/s40478-021-01276-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/13/2021] [Indexed: 12/25/2022] Open
Abstract
The clinicopathological heterogeneity in Lewy-body diseases (LBD) highlights the need for pathology-driven biomarkers in-vivo. Misfolded alpha-synuclein (α-Syn) is a lead candidate based on its crucial role in disease pathophysiology. Real-time quaking-induced conversion (RT-QuIC) analysis of CSF has recently shown high sensitivity and specificity for the detection of misfolded α-Syn in patients with Parkinson's disease (PD) and dementia with Lewy bodies (DLB). In this study we performed the CSF RT-QuIC assay in 236 PD and 49 DLB patients enriched for different genetic forms with mutations in GBA, parkin, PINK1, DJ1, and LRRK2. A subgroup of 100 PD patients was also analysed longitudinally. We correlated kinetic seeding parameters of RT-QuIC with genetic status and CSF protein levels of molecular pathways linked to α-Syn proteostasis. Overall, 85% of PD and 86% of DLB patients showed positive RT-QuIC α-Syn seeding activity. Seeding profiles were significantly associated with mutation status across the spectrum of genetic LBD. In PD patients, we detected positive α-Syn seeding in 93% of patients carrying severe GBA mutations, in 78% with LRRK2 mutations, in 59% carrying heterozygous mutations in recessive genes, and in none of those with bi-allelic mutations in recessive genes. Among PD patients, those with severe GBA mutations showed the highest seeding activity based on RT-QuIC kinetic parameters and the highest proportion of samples with 4 out of 4 positive replicates. In DLB patients, 100% with GBA mutations showed positive α-Syn seeding compared to 79% of wildtype DLB. Moreover, we found an association between α-Syn seeding activity and reduced CSF levels of proteins linked to α-Syn proteostasis, specifically lysosome-associated membrane glycoprotein 2 and neurosecretory protein VGF. These findings highlight the value of α-Syn seeding activity as an in-vivo marker of Lewy-body pathology and support its use for patient stratification in clinical trials targeting α-Syn.
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Quinn JP, Kandigian SE, Trombetta BA, Arnold SE, Carlyle BC. VGF as a biomarker and therapeutic target in neurodegenerative and psychiatric diseases. Brain Commun 2021; 3:fcab261. [PMID: 34778762 PMCID: PMC8578498 DOI: 10.1093/braincomms/fcab261] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/01/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Neurosecretory protein VGF (non-acronymic) belongs to the granin family of neuropeptides. VGF and VGF-derived peptides have been repeatedly identified in well-powered and well-designed multi-omic studies as dysregulated in neurodegenerative and psychiatric diseases. New therapeutics is urgently needed for these devastating and costly diseases, as are new biomarkers to improve disease diagnosis and mechanistic understanding. From a list of 537 genes involved in Alzheimer's disease pathogenesis, VGF was highlighted by the Accelerating Medicines Partnership in Alzheimer's disease as the potential therapeutic target of greatest interest. VGF levels are consistently decreased in brain tissue and CSF samples from patients with Alzheimer's disease compared to controls, and its levels correlate with disease severity and Alzheimer's disease pathology. In the brain, VGF exists as multiple functional VGF-derived peptides. Full-length human VGF1-615 undergoes proteolytic processing by prohormone convertases and other proteases in the regulated secretory pathway to produce at least 12 active VGF-derived peptides. In cell and animal models, these VGF-derived peptides have been linked to energy balance regulation, neurogenesis, synaptogenesis, learning and memory, and depression-related behaviours throughout development and adulthood. The C-terminal VGF-derived peptides, TLQP-62 (VGF554-615) and TLQP-21 (VGF554-574) have differential effects on Alzheimer's disease pathogenesis, neuronal and microglial activity, and learning and memory. TLQP-62 activates neuronal cell-surface receptors and regulates long-term hippocampal memory formation. TLQP-62 also prevents immune-mediated memory impairment, depression-like and anxiety-like behaviours in mice. TLQP-21 binds to microglial cell-surface receptors, triggering microglial chemotaxis and phagocytosis. These actions were reported to reduce amyloid-β plaques and decrease neuritic dystrophy in a transgenic mouse model of familial Alzheimer's disease. Expression differences of VGF-derived peptides have also been associated with frontotemporal lobar dementias, amyotrophic lateral sclerosis, Lewy body diseases, Huntington's disease, pain, schizophrenia, bipolar disorder, depression and antidepressant response. This review summarizes current knowledge and highlights questions for future investigation regarding the roles of VGF and its dysregulation in neurodegenerative and psychiatric disease. Finally, the potential of VGF and VGF-derived peptides as biomarkers and novel therapeutic targets for neurodegenerative and psychiatric diseases is highlighted.
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Affiliation(s)
- James P Quinn
- Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Savannah E Kandigian
- Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Bianca A Trombetta
- Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven E Arnold
- Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Becky C Carlyle
- Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
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Gupta N, Ramakrishnan S, Wajid S. Emerging role of metabolomics in protein conformational disorders. Expert Rev Proteomics 2021; 18:395-410. [PMID: 34227444 DOI: 10.1080/14789450.2021.1948330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Introduction: Metabolomics focuses on interactions among different metabolites associated with various cellular functions in cells, tissues, and organs. In recent years, metabolomics has emerged as a powerful tool to identify perturbed metabolites, pathways influenced by the environment, for protein conformational diseases (PCDs) and also offers wide clinical application.Area Covered: This review provides a brief overview of recent advances in metabolomics as applied to identify metabolic variations in PCDs, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, prion disease, and cardiac amyloidosis. The 'PubMed' and 'Google Scholar' database search methods have been used to screen the published reports with key search terms: metabolomics, biomarkers, and protein conformational disorders.Expert opinion: Metabolomics is the large-scale study of metabolites and is deemed to overwhelm other omics. It plays a crucial role in finding variations in diseases due to protein conformational changes. However, many PCDs are yet to be identified. Metabolomics is still an emerging field; there is a need for new high-resolution analytical techniques and more studies need to be carried out to generate new information.
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Affiliation(s)
- Nimisha Gupta
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, India
| | | | - Saima Wajid
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, India
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Lerche S, Sjödin S, Brinkmalm A, Blennow K, Wurster I, Roeben B, Zimmermann M, Hauser AK, Liepelt-Scarfone I, Waniek K, Lachmann I, Gasser T, Zetterberg H, Brockmann K. CSF Protein Level of Neurotransmitter Secretion, Synaptic Plasticity, and Autophagy in PD and DLB. Mov Disord 2021; 36:2595-2604. [PMID: 34180557 DOI: 10.1002/mds.28704] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/11/2021] [Accepted: 06/08/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Molecular pathways associated with α-synuclein proteostasis have been detected in genetic studies and in cell models and include autophagy, ubiquitin-proteasome system, mitochondrial homeostasis, and synaptic plasticity. However, we lack biomarkers that are representative for these pathways in human biofluids. OBJECTIVE The objective of this study was to evaluate CSF protein profiles of pathways related to α-synuclein proteostasis. METHODS We assessed CSF protein profiles associated with neurotransmitter secretion, synapse plasticity, and autophagy in 2 monocentric cohorts with α-synucleinopathy (385 PD patients and 67 DLB patients). We included 80 PD patients and 17 DLB patients with variants in the glucocerebrosidase gene to serve as proxy for accelerated α-synuclein pathology with pronounced clinical trajectories. RESULTS (1) Proteins associated with neurotransmitter secretion, synaptic plasticity, and endolysosomal autophagy were lower in PD and DLB patients compared with healthy controls. (2) These patterns were more pronounced in DLB than in PD patients, accentuated by GBA variant status in both entities. (3) CSF levels of these proteins were positively associated with CSF levels of total α-synuclein, with lower levels of proteostasis proteins related to lower levels of total α-synuclein. (4) These findings could be confirmed longitudinally. PD patients with low CSF profiles of proteostasis proteins showed lower CSF levels of α-synuclein longitudinally compared with PD patients with a normal proteostasis profile. CONCLUSION CSF proteins associated with neurotransmitter secretion, synaptic plasticity, and endolysosomal autophagy might serve as biomarkers related to α-synuclein proteostasis in PD and DLB. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Stefanie Lerche
- Center of Neurology, Department of Neurodegeneration and Hertie-Institute for Clinical Brain Research, University of Tuebingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | - Simon Sjödin
- 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
| | - Ann Brinkmalm
- 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
| | - Kaj Blennow
- 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
| | - Isabel Wurster
- Center of Neurology, Department of Neurodegeneration and Hertie-Institute for Clinical Brain Research, University of Tuebingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | - Benjamin Roeben
- Center of Neurology, Department of Neurodegeneration and Hertie-Institute for Clinical Brain Research, University of Tuebingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | - Milan Zimmermann
- Center of Neurology, Department of Neurodegeneration and Hertie-Institute for Clinical Brain Research, University of Tuebingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | - Ann-Kathrin Hauser
- Center of Neurology, Department of Neurodegeneration and Hertie-Institute for Clinical Brain Research, University of Tuebingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | - Inga Liepelt-Scarfone
- Center of Neurology, Department of Neurodegeneration and Hertie-Institute for Clinical Brain Research, University of Tuebingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | | | | | - Thomas Gasser
- Center of Neurology, Department of Neurodegeneration and Hertie-Institute for Clinical Brain Research, University of Tuebingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
| | - 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.,Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom.,UK Dementia Research Institute at UCL, London, United Kingdom
| | - Kathrin Brockmann
- Center of Neurology, Department of Neurodegeneration and Hertie-Institute for Clinical Brain Research, University of Tuebingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, University of Tuebingen, Tuebingen, Germany
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Sawangareetrakul P, Ngiwsara L, Champattanachai V, Chokchaichamnankit D, Saharat K, Ketudat Cairns JR, Srisomsap C, Khwanraj K, Dharmasaroja P, Pulkes T, Svasti J. Aberrant proteins expressed in skin fibroblasts of Parkinson's disease patients carrying heterozygous variants of glucocerebrosidase and parkin genes. Biomed Rep 2021; 14:36. [PMID: 33732455 PMCID: PMC7907964 DOI: 10.3892/br.2021.1412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/21/2021] [Indexed: 11/23/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder that affects movement, and its development is associated with environmental and genetic factors. Genetic variants in GBA and PARK2 are important risk factors implicated in the development of PD; however, their precise roles have yet to be elucidated. The present study aimed to identify and analyse proteins from the skin fibroblasts of patients with PD carrying heterozygous GBA and PARK2 variants, and from healthy controls. Liquid chromatography coupled with tandem mass spectrometry and label-free quantitative proteomics were performed to identify and compare differential protein expression levels. Moreover, protein-protein interaction networks were assessed using Search Tool for Retrieval of Interacting Genes analysis. Using these proteomic approaches, 122 and 119 differentially expressed proteins from skin fibroblasts of patients with PD carrying heterozygous GBA and PARK2 variants, respectively, were identified and compared. According to the results of protein-protein interaction and Gene Ontology analyses, 14 proteins involved in the negative regulation of macromolecules and mRNA metabolic processes, and protein targeting to the membrane exhibited the largest degree of differential expression in the fibroblasts of patients with PD with a GBA variant, whereas 20 proteins involved in the regulation of biological quality, NAD metabolic process and cytoskeletal organization exhibited the largest degree of differential expression in the fibroblasts of patients with PD with a PARK2 variant. Among these, the expression levels of annexin A2 and tubulin β chain, were most strongly upregulated in the fibroblasts of patients with GBA-PD and PARK2-PD, respectively. Other predominantly expressed proteins were confirmed by western blotting, and the results were consistent with those of the quantitative proteomic analysis. Collectively, the results of the present study demonstrated that the proteomic patterns of fibroblasts of patients with PD carrying heterozygous GBA and PARK2 variants are different and unique. Aberrant expression of the proteins affected by these variants may reflect physiological changes that also occur in neurons, resulting in PD development and progression.
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Affiliation(s)
| | - Lukana Ngiwsara
- Laboratory of Biochemistry, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
| | | | | | - Kittirat Saharat
- Laboratory of Biochemistry, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
| | - James R. Ketudat Cairns
- Laboratory of Biochemistry, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Chantragan Srisomsap
- Laboratory of Biochemistry, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
| | - Kawinthra Khwanraj
- Faculty of Science, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Permphan Dharmasaroja
- Faculty of Science, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Teeratorn Pulkes
- Division of Neurology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Jisnuson Svasti
- Laboratory of Biochemistry, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
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Cerebrospinal Fluid Levels of Chromogranin A in Parkinson's Disease and Multiple System Atrophy. Brain Sci 2021; 11:brainsci11020141. [PMID: 33499181 PMCID: PMC7912438 DOI: 10.3390/brainsci11020141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/11/2021] [Accepted: 01/19/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Chromogranin A (CgA) and other peptides from the chromogranin–secretogranin family have been recently studied as potential biomarkers of various neurodegenerative diseases, including Parkinson’s disease (PD). Methods: We measured CgA in the cerebrospinal fluid (CSF) of 119 PD patients, 18 multiple system atrophy (MSA) patients, and 31 age-matched controls. We also correlated the values with disease duration and levodopa dose equivalent. Results: In the PD patients, CSF CgA tended to be lower than the control group (median 124.5 vs. 185.2 µg/L; p = 0.057); however, the results did not reach statistical significance. CSF CgA levels in MSA were significantly lower compared to the control group (median 104.4 vs. 185.2; p = 0.014). There was no significant difference in CSF CgA between PD and MSA patients (p = 0.372). There was no association between CSF CgA and disease duration or levodopa dose equivalent in PD or in MSA. Conclusions: We observed a tendency toward lower CSF CgA levels in both PD and MSA compared to the control group; however, the difference reached statistical significance only in MSA. Based on these results, CgA may have potential as a biomarker in PD and MSA, but further studies on larger numbers of patients are needed to draw conclusions.
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Ruffini N, Klingenberg S, Schweiger S, Gerber S. Common Factors in Neurodegeneration: A Meta-Study Revealing Shared Patterns on a Multi-Omics Scale. Cells 2020; 9:E2642. [PMID: 33302607 PMCID: PMC7764447 DOI: 10.3390/cells9122642] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/24/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023] Open
Abstract
Neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS) are heterogeneous, progressive diseases with frequently overlapping symptoms characterized by a loss of neurons. Studies have suggested relations between neurodegenerative diseases for many years (e.g., regarding the aggregation of toxic proteins or triggering endogenous cell death pathways). We gathered publicly available genomic, transcriptomic, and proteomic data from 177 studies and more than one million patients to detect shared genetic patterns between the neurodegenerative diseases on three analyzed omics-layers. The results show a remarkably high number of shared differentially expressed genes between the transcriptomic and proteomic levels for all conditions, while showing a significant relation between genomic and proteomic data between AD and PD and AD and ALS. We identified a set of 139 genes being differentially expressed in several transcriptomic experiments of all four diseases. These 139 genes showed overrepresented gene ontology (GO) Terms involved in the development of neurodegeneration, such as response to heat and hypoxia, positive regulation of cytokines and angiogenesis, and RNA catabolic process. Furthermore, the four analyzed neurodegenerative diseases (NDDs) were clustered by their mean direction of regulation throughout all transcriptomic studies for this set of 139 genes, with the closest relation regarding this common gene set seen between AD and HD. GO-Term and pathway analysis of the proteomic overlap led to biological processes (BPs), related to protein folding and humoral immune response. Taken together, we could confirm the existence of many relations between Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis on transcriptomic and proteomic levels by analyzing the pathways and GO-Terms arising in these intersections. The significance of the connection and the striking relation of the results to processes leading to neurodegeneration between the transcriptomic and proteomic data for all four analyzed neurodegenerative diseases showed that exploring many studies simultaneously, including multiple omics-layers of different neurodegenerative diseases simultaneously, holds new relevant insights that do not emerge from analyzing these data separately. Furthermore, the results shed light on processes like the humoral immune response that have previously been described only for certain diseases. Our data therefore suggest human patients with neurodegenerative diseases should be addressed as complex biological systems by integrating multiple underlying data sources.
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Affiliation(s)
- Nicolas Ruffini
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
- Leibniz Institute for Resilience Research, Leibniz Association, Wallstraße 7, 55122 Mainz, Germany
| | - Susanne Klingenberg
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
| | - Susann Schweiger
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
| | - Susanne Gerber
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
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Chaplot K, Jarvela TS, Lindberg I. Secreted Chaperones in Neurodegeneration. Front Aging Neurosci 2020; 12:268. [PMID: 33192447 PMCID: PMC7481362 DOI: 10.3389/fnagi.2020.00268] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022] Open
Abstract
Protein homeostasis, or proteostasis, is a combination of cellular processes that govern protein quality control, namely, protein translation, folding, processing, and degradation. Disruptions in these processes can lead to protein misfolding and aggregation. Proteostatic disruption can lead to cellular changes such as endoplasmic reticulum or oxidative stress; organelle dysfunction; and, if continued, to cell death. A majority of neurodegenerative diseases involve the pathologic aggregation of proteins that subverts normal neuronal function. While prior reviews of neuronal proteostasis in neurodegenerative processes have focused on cytoplasmic chaperones, there is increasing evidence that chaperones secreted both by neurons and other brain cells in the extracellular – including transsynaptic – space play important roles in neuronal proteostasis. In this review, we will introduce various secreted chaperones involved in neurodegeneration. We begin with clusterin and discuss its identification in various protein aggregates, and the use of increased cerebrospinal fluid (CSF) clusterin as a potential biomarker and as a potential therapeutic. Our next secreted chaperone is progranulin; polymorphisms in this gene represent a known genetic risk factor for frontotemporal lobar degeneration, and progranulin overexpression has been found to be effective in reducing Alzheimer’s- and Parkinson’s-like neurodegenerative phenotypes in mouse models. We move on to BRICHOS domain-containing proteins, a family of proteins containing highly potent anti-amyloidogenic activity; we summarize studies describing the biochemical mechanisms by which recombinant BRICHOS protein might serve as a therapeutic agent. The next section of the review is devoted to the secreted chaperones 7B2 and proSAAS, small neuronal proteins which are packaged together with neuropeptides and released during synaptic activity. Since proteins can be secreted by both classical secretory and non-classical mechanisms, we also review the small heat shock proteins (sHsps) that can be secreted from the cytoplasm to the extracellular environment and provide evidence for their involvement in extracellular proteostasis and neuroprotection. Our goal in this review focusing on extracellular chaperones in neurodegenerative disease is to summarize the most recent literature relating to neurodegeneration for each secreted chaperone; to identify any common mechanisms; and to point out areas of similarity as well as differences between the secreted chaperones identified to date.
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Affiliation(s)
- Kriti Chaplot
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Timothy S Jarvela
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Iris Lindberg
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
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Pellegrini L, Bonfio C, Chadwick J, Begum F, Skehel M, Lancaster MA. Human CNS barrier-forming organoids with cerebrospinal fluid production. Science 2020; 369:eaaz5626. [PMID: 32527923 PMCID: PMC7116154 DOI: 10.1126/science.aaz5626] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 05/22/2020] [Indexed: 12/13/2022]
Abstract
Cerebrospinal fluid (CSF) is a vital liquid, providing nutrients and signaling molecules and clearing out toxic by-products from the brain. The CSF is produced by the choroid plexus (ChP), a protective epithelial barrier that also prevents free entry of toxic molecules or drugs from the blood. Here, we establish human ChP organoids with a selective barrier and CSF-like fluid secretion in self-contained compartments. We show that this in vitro barrier exhibits the same selectivity to small molecules as the ChP in vivo and that ChP-CSF organoids can predict central nervous system (CNS) permeability of new compounds. The transcriptomic and proteomic signatures of ChP-CSF organoids reveal a high degree of similarity to the ChP in vivo. Finally, the intersection of single-cell transcriptomics and proteomic analysis uncovers key human CSF components produced by previously unidentified specialized epithelial subtypes.
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Affiliation(s)
- Laura Pellegrini
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Claudia Bonfio
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jessica Chadwick
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Farida Begum
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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