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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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2
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Xing M, Yang X, Jin S, Xu X. Inhibition of neuronal pentraxin 2 relieved epileptic seizure via reducing GluA1 phosphorylation. Cell Biochem Funct 2024; 42:e4003. [PMID: 38597235 DOI: 10.1002/cbf.4003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024]
Abstract
Neuronal pentraxin 2 (Nptx2), a member of the synaptic protein family linked to excitatory synaptic formation, is found to be upregulated in epileptic mice, yet its role in epilepsy has been unclear. In vivo, we constructed a mouse model of epilepsy by using kainic acid induction. In vitro experiments, a Mg2+-free medium was used to induce epileptiform discharges in neurons. The results showed that the Nptx2 was upregulated in epileptic mice. Moreover, Nptx2 knockdown reduced the number of seizures and seizure duration. Knocking down Nptx2 not only reduced the number and duration of seizures but also showed a decrease in electroencephalogram amplitude. Behavioral tests indicated improvements in learning and memory abilities after Nptx2 knockdown. The Nissl staining and Timms staining revealed that Nptx2 silencing mitigated epilepsy-induced brain damage. The immunofluorescence staining revealed that Nptx2 absence resulted in a reduction of apoptosis. Nptx2 knockdown reduced Bax, cleaved caspase3, and cleaved caspase9 expression, while increased Bcl-2 expression. Notably, Nptx2 knockdown inhibited GluA1 phosphorylation at the S831 site and reduced the GluA1 membrane expression. The PSD95 expression declined in the epilepsy model, while the Nptx2 knockdown reversed it. Collectively, our study indicated that Nptx2 silencing not only alleviated brain damage and neuron apoptosis but also improved learning and memory ability in epileptic mice, suggesting Nptx2 as a promising target for epilepsy treatment.
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Affiliation(s)
- Mengnan Xing
- Department of Pediatrics, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinlei Yang
- Animal Laboratory Center, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Sinan Jin
- Department of Pathology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiangping Xu
- Department of Pediatrics, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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3
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Kondo K, Muguruma K, Soejima S, Takai C, Kenzaki K, Kawakita N, Toba H, Takizawa H. Aberrant DNA Methylation of NPTX2 as an Indicator of Malignant Behavior in Thymic Epithelial Tumors. Cancers (Basel) 2024; 16:329. [PMID: 38254821 PMCID: PMC10813937 DOI: 10.3390/cancers16020329] [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: 11/22/2023] [Revised: 12/28/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Thymic epithelial tumors (TET) consist of thymomas, thymic carcinoma (TC), and neuroendocrine tumors of the thymus (NECTT). Genetic and epigenetic alterations in TET have been the focus of recent research. In the present study, genome-wide screening was performed on aberrantly methylated CpG islands in TET, and this identified neuronal pentraxin 2 (NTPX2) as a significantly hypermethylated CpG island in TC relative to thymomas. NPTX2 is released from pre-synaptic cells in response to neuronal activity/seizure, and plays a role in host immunity and acute inflammation. TET samples were obtained from 38 thymomas, 25 TC, and 6 NECTT. The DNA methylation, mRNA, and protein expression levels of NPTX2 were examined. The DNA methylation rate of the NPTX2 gene was significantly higher in TC than in the normal thymus and thymomas, except B3. The mRNA expression level of NPTX2 was lower in TC than in the normal thymus. An inverse relationship was observed between mRNA expression levels and methylation levels. Relapse-free survival was shorter in patients with high NPTX2 DNA methylation levels than in those with low DNA methylation levels. NECTT showed very high mRNA and protein expression levels and low DNA methylation levels of NPTX2. NPTX2 may function as a tumor suppressor in TC, and have an oncogenic function in NECTT.
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Affiliation(s)
- Kazuya Kondo
- Department of Oncological Medical Services, Graduate School of Biomedical Sciences, Tokushima University, Tokushima 770-8509, Japan; (K.M.); (S.S.); (C.T.)
| | - Kyoka Muguruma
- Department of Oncological Medical Services, Graduate School of Biomedical Sciences, Tokushima University, Tokushima 770-8509, Japan; (K.M.); (S.S.); (C.T.)
| | - Shiho Soejima
- Department of Oncological Medical Services, Graduate School of Biomedical Sciences, Tokushima University, Tokushima 770-8509, Japan; (K.M.); (S.S.); (C.T.)
| | - Chikako Takai
- Department of Oncological Medical Services, Graduate School of Biomedical Sciences, Tokushima University, Tokushima 770-8509, Japan; (K.M.); (S.S.); (C.T.)
| | - Koichiro Kenzaki
- Department of Chest and Breast Surgical Oncology, Takamatsu Red Cross Hospital, Takamatsu 760-0017, Japan;
| | - Naoya Kawakita
- Department of Thoracic, Endocrine Surgery and Oncology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima 770-8503, Japan; (N.K.); (H.T.); (H.T.)
| | - Hiroaki Toba
- Department of Thoracic, Endocrine Surgery and Oncology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima 770-8503, Japan; (N.K.); (H.T.); (H.T.)
| | - Hiromitsu Takizawa
- Department of Thoracic, Endocrine Surgery and Oncology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima 770-8503, Japan; (N.K.); (H.T.); (H.T.)
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Zamanian MY, Ivraghi MS, Gupta R, Prasad KDV, Alsaab HO, Hussien BM, Ahmed H, Ramadan MF, Golmohammadi M, Nikbakht N, Oz T, Kujawska M. miR-221 and Parkinson's disease: A biomarker with therapeutic potential. Eur J Neurosci 2024; 59:283-297. [PMID: 38043936 DOI: 10.1111/ejn.16207] [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: 07/11/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 12/05/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder characterized by the loss of dopaminergic neurons in the substantia nigra, leading to various motor and non-motor symptoms. Several cellular and molecular mechanisms such as alpha-synuclein (α-syn) accumulation, mitochondrial dysfunction, oxidative stress and neuroinflammation are involved in the pathogenesis of this disease. MicroRNAs (miRNAs) play important roles in post-transcriptional gene regulation. They are typically about 21-25 nucleotides in length and are involved in the regulation of gene expression by binding to the messenger RNA (mRNA) molecules. miRNAs like miR-221 play important roles in various biological processes, including development, cell proliferation, differentiation and apoptosis. miR-221 promotes neuronal survival against oxidative stress and neurite outgrowth and neuronal differentiation. Additionally, the role of miR-221 in PD has been investigated in several studies. According to the results of these studies, (1) miR-221 protects PC12 cells against oxidative stress induced by 6-hydroxydopamine; (2) miR-221 prevents Bax/caspase-3 signalling activation by stopping Bim; (3) miR-221 has moderate predictive power for PD; (4) miR-221 directly targets PTEN, and PTEN over-expression eliminates the protective action of miR-221 on p-AKT expression in PC12 cells; and (5) miRNA-221 controls cell viability and apoptosis by manipulating the Akt signalling pathway in PD. This review study suggested that miR-221 has the potential to be used as a clinical biomarker for PD diagnosis and stage assignment.
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Affiliation(s)
- Mohammad Yasin Zamanian
- Neurophysiology Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
- Department of Physiology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Reena Gupta
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India
| | - K D V Prasad
- Symbiosis Institute of Business Management (SIBM), Hyderabad, India
- Symbiosis International (Deemed University) (SIU), Hyderabad, Telangana, India
| | - Hashem O Alsaab
- Pharmaceutics and Pharmaceutical Technology, Taif University, Taif, Saudi Arabia
| | - Beneen M Hussien
- Medical Laboratory Technology Department, College of Medical Technology, Islamic University, Najaf, Iraq
| | - Hazem Ahmed
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
| | | | - Maryam Golmohammadi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nikta Nikbakht
- Department of Physical Medicine and Rehabilitation, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Tuba Oz
- Department of Toxicology, Poznan University of Medical Sciences, Poznań, Poland
| | - Małgorzata Kujawska
- Department of Toxicology, Poznan University of Medical Sciences, Poznań, Poland
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5
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Huang XF, Xu MX, Chen YF, Lin YQ, Lin YX, Wang F. Serum neuronal pentraxin 2 is related to cognitive dysfunction and electroencephalogram slow wave/fast wave frequency ratio in epilepsy. World J Psychiatry 2023; 13:714-723. [PMID: 38058685 PMCID: PMC10696288 DOI: 10.5498/wjp.v13.i10.714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/08/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023] Open
Abstract
BACKGROUND Cognitive dysfunction in epileptic patients is a high-incidence complication. Its mechanism is related to nervous system damage during seizures, but there is no effective diagnostic biomarker. Neuronal pentraxin 2 (NPTX2) is thought to play a vital role in neurotransmission and the maintenance of synaptic plasticity. This study explored how serum NPTX2 and electroencephalogram (EEG) slow wave/fast wave frequency ratio relate to cognitive dysfunction in patients with epilepsy. AIM To determine if serum NPTX2 could serve as a potential biomarker for diagnosing cognitive impairment in epilepsy patients. METHODS The participants of this study, conducted from January 2020 to December 2021, comprised 74 epilepsy patients with normal cognitive function (normal group), 37 epilepsy patients with cognitive dysfunction [epilepsy patients with cognitive dysfunction (ECD) group] and 30 healthy people (control group). The mini-mental state examination (MMSE) scale was used to evaluate cognitive function. We determined serum NPTX2 levels using an enzyme-linked immunosorbent kit and calculated the signal value of EEG regions according to the EEG recording. Pearson correlation coefficient was used to analyze the correlation between serum NPTX2 and the MMSE score. RESULTS The serum NPTX2 level in the control group, normal group and ECD group were 240.00 ± 35.06 pg/mL, 235.80 ± 38.01 pg/mL and 193.80 ± 42.72 pg/mL, respectively. The MMSE score was lowest in the ECD group among the three, while no significant difference was observed between the control and normal groups. In epilepsy patients with cognitive dysfunction, NPTX2 level had a positive correlation with the MMSE score (r = 0.367, P = 0.0253) and a negative correlation with epilepsy duration (r = -0.443, P = 0.0061) and the EEG slow wave/fast wave frequency ratio value in the temporal region (r = -0.339, P = 0.039). CONCLUSION Serum NPTX2 was found to be related to cognitive dysfunction and the EEG slow wave/fast wave frequency ratio in patients with epilepsy. It is thus a potential biomarker for the diagnosis of cognitive impairment in patients with epilepsy.
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Affiliation(s)
- Xiao-Fen Huang
- Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, Fujian Province, China
| | - Ming-Xia Xu
- Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, Fujian Province, China
| | - Yue-Fan Chen
- Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, Fujian Province, China
| | - Yun-Qing Lin
- Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, Fujian Province, China
| | - Yuan-Xiang Lin
- Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, Fujian Province, China
| | - Feng Wang
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, Fujian Province, China
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6
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Nilsson J, Constantinescu J, Nellgård B, Jakobsson P, Brum WS, Gobom J, Forsgren L, Dalla K, Constantinescu R, Zetterberg H, Hansson O, Blennow K, Bäckström D, Brinkmalm A. Cerebrospinal Fluid Biomarkers of Synaptic Dysfunction are Altered in Parkinson's Disease and Related Disorders. Mov Disord 2023; 38:267-277. [PMID: 36504237 DOI: 10.1002/mds.29287] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Synaptic dysfunction and degeneration are central contributors to the pathogenesis and progression of parkinsonian disorders. Therefore, identification and validation of biomarkers reflecting pathological synaptic alterations are greatly needed and could be used in prognostic assessment and to monitor treatment effects. OBJECTIVE To explore candidate biomarkers of synaptic dysfunction in Parkinson's disease (PD) and related disorders. METHODS Mass spectrometry was used to quantify 15 synaptic proteins in two clinical cerebrospinal fluid (CSF) cohorts, including PD (n1 = 51, n2 = 101), corticobasal degeneration (CBD) (n1 = 11, n2 = 3), progressive supranuclear palsy (PSP) (n1 = 22, n2 = 21), multiple system atrophy (MSA) (n1 = 31, n2 = 26), and healthy control (HC) (n1 = 48, n2 = 30) participants, as well as Alzheimer's disease (AD) (n2 = 23) patients in the second cohort. RESULTS Across both cohorts, lower levels of the neuronal pentraxins (NPTX; 1, 2, and receptor) were found in PD, MSA, and PSP, compared with HC. In MSA and PSP, lower neurogranin, AP2B1, and complexin-2 levels compared with HC were observed. In AD, levels of 14-3-3 zeta/delta, beta- and gamma-synuclein were higher compared with the parkinsonian disorders. Lower pentraxin levels in PD correlated with Mini-Mental State Exam scores and specific cognitive deficits (NPTX2; rho = 0.25-0.32, P < 0.05) and reduced dopaminergic pre-synaptic integrity as measured by DaTSCAN (NPTX2; rho = 0.29, P = 0.023). Additionally, lower levels were associated with the progression of postural imbalance and gait difficulty symptoms (All NPTX; β-estimate = -0.025 to -0.038, P < 0.05) and cognitive decline (NPTX2; β-estimate = 0.32, P = 0.021). CONCLUSIONS These novel findings show different alterations of synaptic proteins in parkinsonian disorders compared with AD and HC. The neuronal pentraxins may serve as prognostic CSF biomarkers for both cognitive and motor symptom progression in PD. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Johanna Nilsson
- Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Julius Constantinescu
- Department of Neurology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Bengt Nellgård
- Department of Anesthesiology and Intensive Care, Institute of Clinical Sciences, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Protik Jakobsson
- Department of Clinical Science, Neurosciences, Umeå University, Umeå, Sweden
| | - Wagner S Brum
- Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Graduate Program in Biological Sciences: Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Johan Gobom
- Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Lars Forsgren
- Department of Clinical Science, Neurosciences, Umeå University, Umeå, Sweden
| | - Keti Dalla
- Department of Anesthesiology and Intensive Care, Institute of Clinical Sciences, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Radu Constantinescu
- Department of Neurology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,UK Dementia Research Institute at UCL, London, United Kingdom.,Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom.,Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Oskar Hansson
- Clinical Memory Research Unit, Department of Clinical Sciences, Malmö, Lund University, Lund, Sweden.,Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - David Bäckström
- Department of Clinical Science, Neurosciences, Umeå University, Umeå, Sweden
| | - Ann Brinkmalm
- Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
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Alamro H, Bajic V, Macvanin MT, Isenovic ER, Gojobori T, Essack M, Gao X. Type 2 Diabetes Mellitus and its comorbidity, Alzheimer's disease: Identifying critical microRNA using machine learning. Front Endocrinol (Lausanne) 2023; 13:1084656. [PMID: 36743910 PMCID: PMC9893111 DOI: 10.3389/fendo.2022.1084656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/23/2022] [Indexed: 01/21/2023] Open
Abstract
MicroRNAs (miRNAs) are critical regulators of gene expression in healthy and diseased states, and numerous studies have established their tremendous potential as a tool for improving the diagnosis of Type 2 Diabetes Mellitus (T2D) and its comorbidities. In this regard, we computationally identify novel top-ranked hub miRNAs that might be involved in T2D. We accomplish this via two strategies: 1) by ranking miRNAs based on the number of T2D differentially expressed genes (DEGs) they target, and 2) using only the common DEGs between T2D and its comorbidity, Alzheimer's disease (AD) to predict and rank miRNA. Then classifier models are built using the DEGs targeted by each miRNA as features. Here, we show the T2D DEGs targeted by hsa-mir-1-3p, hsa-mir-16-5p, hsa-mir-124-3p, hsa-mir-34a-5p, hsa-let-7b-5p, hsa-mir-155-5p, hsa-mir-107, hsa-mir-27a-3p, hsa-mir-129-2-3p, and hsa-mir-146a-5p are capable of distinguishing T2D samples from the controls, which serves as a measure of confidence in the miRNAs' potential role in T2D progression. Moreover, for the second strategy, we show other critical miRNAs can be made apparent through the disease's comorbidities, and in this case, overall, the hsa-mir-103a-3p models work well for all the datasets, especially in T2D, while the hsa-mir-124-3p models achieved the best scores for the AD datasets. To the best of our knowledge, this is the first study that used predicted miRNAs to determine the features that can separate the diseased samples (T2D or AD) from the normal ones, instead of using conventional non-biology-based feature selection methods.
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Affiliation(s)
- Hind Alamro
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- College of Computer and Information Systems, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Vladan Bajic
- Department of Radiology and Molecular Genetics, VINCA Institute of Nuclear Science - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Mirjana T. Macvanin
- Department of Radiology and Molecular Genetics, VINCA Institute of Nuclear Science - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Esma R. Isenovic
- Department of Radiology and Molecular Genetics, VINCA Institute of Nuclear Science - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Takashi Gojobori
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Magbubah Essack
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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8
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Peng W, Kobeissy F, Mondello S, Barsa C, Mechref Y. MS-based glycomics: An analytical tool to assess nervous system diseases. Front Neurosci 2022; 16:1000179. [PMID: 36408389 PMCID: PMC9671362 DOI: 10.3389/fnins.2022.1000179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/05/2022] [Indexed: 08/27/2023] Open
Abstract
Neurological diseases affect millions of peopleochemistryorldwide and are continuously increasing due to the globe's aging population. Such diseases affect the nervous system and are characterized by a progressive decline in brain function and progressive cognitive impairment, decreasing the quality of life for those with the disease as well as for their families and loved ones. The increased burden of nervous system diseases demands a deeper insight into the biomolecular mechanisms at work during disease development in order to improve clinical diagnosis and drug design. Recently, evidence has related glycosylation to nervous system diseases. Glycosylation is a vital post-translational modification that mediates many biological functions, and aberrant glycosylation has been associated with a variety of diseases. Thus, the investigation of glycosylation in neurological diseases could provide novel biomarkers and information for disease pathology. During the last decades, many techniques have been developed for facilitation of reliable and efficient glycomic analysis. Among these, mass spectrometry (MS) is considered the most powerful tool for glycan analysis due to its high resolution, high sensitivity, and the ability to acquire adequate structural information for glycan identification. Along with MS, a variety of approaches and strategies are employed to enhance the MS-based identification and quantitation of glycans in neurological samples. Here, we review the advanced glycomic tools used in nervous system disease studies, including separation techniques prior to MS, fragmentation techniques in MS, and corresponding strategies. The glycan markers in common clinical nervous system diseases discovered by utilizing such MS-based glycomic tools are also summarized and discussed.
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Affiliation(s)
- Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Firas Kobeissy
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL, United States
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Chloe Barsa
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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Bolsewig K, Hok-A-Hin Y, Sepe F, Boonkamp L, Jacobs D, Bellomo G, Paoletti FP, Vanmechelen E, Teunissen C, Parnetti L, Willemse E. A Combination of Neurofilament Light, Glial Fibrillary Acidic Protein, and Neuronal Pentraxin-2 Discriminates Between Frontotemporal Dementia and Other Dementias. J Alzheimers Dis 2022; 90:363-380. [DOI: 10.3233/jad-220318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: The differential diagnosis of frontotemporal dementia (FTD) is still a challenging task due to its symptomatic overlap with other neurological diseases and the lack of biofluid-based biomarkers. Objective: To investigate the diagnostic potential of a combination of novel biomarkers in cerebrospinal fluid (CSF) and blood. Methods: We included 135 patients from the Centre for Memory Disturbances, University of Perugia, with the diagnoses FTD (n = 37), mild cognitive impairment due to Alzheimer’s disease (MCI-AD, n = 47), Lewy body dementia (PDD/DLB, n = 22), and cognitively unimpaired patients as controls (OND, n = 29). Biomarker levels of neuronal pentraxin-2 (NPTX2), neuronal pentraxin receptor, neurofilament light (NfL) and glial fibrillary acidic protein (GFAP) were measured in CSF, as well as NfL and GFAP in serum. We assessed biomarker differences by analysis of covariance and generalized linear models (GLM). We performed receiver operating characteristics analyses and Spearman correlation to determine biomarker associations. Results: CSF NPTX2 and serum GFAP levels varied most between diagnostic groups. The combination of CSF NPTX2, serum NfL and serum GFAP differentiated FTD from the other groups with good accuracy FTD versus MCI-AD: area under the curve (AUC [95% CI] = 0.89 [0.81–0.96]; FTD versus PDD/DLB: AUC = 0.82 [0.71–0.93]; FTD versus OND: AUC = 0.80 [0.70–0.91]). CSF NPTX2 and serum GFAP correlated positively only in PDD/DLB (ρ= 0.56, p < 0.05). NPTX2 and serum NfL did not correlate in any of the diagnostic groups. Serum GFAP and serum NfL correlated positively in all groups (ρ= 0.47–0.74, p < 0.05). Conclusion: We show the combined potential of CSF NPTX2, serum NfL, and serum GFAP to differentiate FTD from other neurodegenerative disorders.
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Affiliation(s)
- Katharina Bolsewig
- Department of Clinical Chemistry, Neuro chemistry Laboratory and Biobank, Amsterdam Neuroscience, Amsterdam UMC, VU University, The Netherlands
| | - Yanaika Hok-A-Hin
- Department of Clinical Chemistry, Neuro chemistry Laboratory and Biobank, Amsterdam Neuroscience, Amsterdam UMC, VU University, The Netherlands
| | - Federica Sepe
- Department of Clinical Chemistry, Neuro chemistry Laboratory and Biobank, Amsterdam Neuroscience, Amsterdam UMC, VU University, The Netherlands
- Department of Medicine and Surgery, Laboratory of Clinical Neuro chemistry, University of Perugia, Perugia, Italy
| | - Lynn Boonkamp
- Department of Clinical Chemistry, Neuro chemistry Laboratory and Biobank, Amsterdam Neuroscience, Amsterdam UMC, VU University, The Netherlands
| | | | - Giovanni Bellomo
- Department of Medicine and Surgery, Laboratory of Clinical Neuro chemistry, University of Perugia, Perugia, Italy
| | - Federico Paolini Paoletti
- Department of Medicine and Surgery, Laboratory of Clinical Neuro chemistry, University of Perugia, Perugia, Italy
| | | | - Charlotte Teunissen
- Department of Clinical Chemistry, Neuro chemistry Laboratory and Biobank, Amsterdam Neuroscience, Amsterdam UMC, VU University, The Netherlands
| | - Lucilla Parnetti
- Department of Medicine and Surgery, Laboratory of Clinical Neuro chemistry, University of Perugia, Perugia, Italy
| | - Eline Willemse
- Department of Clinical Chemistry, Neuro chemistry Laboratory and Biobank, Amsterdam Neuroscience, Amsterdam UMC, VU University, The Netherlands
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10
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Göverti D, Büyüklüoğlu N, Kaya H, Yüksel RN, Yücel Ç, Göka E. Neuronal pentraxin-2 (NPTX2) serum levels during an acute psychotic episode in patients with schizophrenia. Psychopharmacology (Berl) 2022; 239:2585-2591. [PMID: 35482070 DOI: 10.1007/s00213-022-06147-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 04/14/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Neuronal pentraxin-2 (NPTX2, an immediate-early gene), which regulates synapse activity and neuroplasticity, plays an essential role in the neurodevelopmental process. NPTX2 possibly enhances the accumulation of amino-3-hydroxy-5-methyl-4-isoxazolepropionic receptors (AMPAR) on the postsynaptic membranes and stimulates excitatory synaptogenesis. We aimed to evaluate the plasma concentrations of NPTX2 of patients with schizophrenia in acute psychotic episodes compared with matched community-based controls. METHODS Ninety-three (93) patients diagnosed with schizophrenia according to DSM-5 and 83 healthy controls were included. The patients, all of which were in acute psychotic episodes, were recruited from the inpatient clinic. The patients were assessed by the Positive and Negative Syndrome Scale (PANSS) and Clinical Global Impression- Severity (CGIS) scale, whereas the healthy subjects were evaluated with Structured Clinical Interview for DSM-5 (SCID-5) to exclude any major psychiatric diagnoses. RESULTS NPTX2 serum concentrations were significantly higher in the schizophrenia group (p < 0.001). NPTX2 levels negatively correlated with age (p = 0.004) and PANSS-positive symptom scores (p < 0.001). The most determinant factors in predicting the change in NPTX2 levels were PANSS-positive symptom and general psychopathology scores. CONCLUSIONS We conclude that NPTX2 could be involved in schizophrenia pathophysiology and valuable as a synapse-derived and glutamate-related biomarker. Further studies in larger samples assessing NPTX2 levels in remitted schizophrenia patients and combining neuroimaging techniques and cognitive evaluations with blood samples are needed.
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Affiliation(s)
- Diğdem Göverti
- Department of Psychiatry, University of Health Sciences, Erenkoy Mental Health and Neurologic Disorders Training and Research Hospital, Istanbul, Turkey.
| | - Nihan Büyüklüoğlu
- Department of Psychiatry, University of Health Sciences, Ankara City Hospital, Ankara, Turkey
| | - Hasan Kaya
- Department of Psychiatry, University of Health Sciences, Ankara City Hospital, Ankara, Turkey
| | - Rabia Nazik Yüksel
- Department of Psychiatry, University of Health Sciences, Ankara City Hospital, Ankara, Turkey
| | - Çiğdem Yücel
- Department of Biochemistry, University of Health Sciences, Gulhane Training and Research Hospital, Ankara, Turkey
| | - Erol Göka
- Department of Psychiatry, University of Health Sciences, Ankara City Hospital, Ankara, Turkey
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11
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Zhai F, Li J, Ye M, Jin X. The functions and effects of CUL3-E3 ligases mediated non-degradative ubiquitination. Gene X 2022; 832:146562. [PMID: 35580799 DOI: 10.1016/j.gene.2022.146562] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/30/2022] [Accepted: 05/06/2022] [Indexed: 02/09/2023] Open
Abstract
Ubiquitination of substrates usually have two fates: one is degraded by 26S proteasome, and the other is non-degradative ubiquitination modification which is associated with cell cycle regulation, chromosome inactivation, protein transportation, tumorigenesis, achondroplasia, and neurological diseases. Cullin3 (CUL3), a scaffold protein, binding with the Bric-a-Brac-Tramtrack-Broad-complex (BTB) domain of substrates recognition adaptor and RING-finger protein 1 (RBX1) form ubiquitin ligases (E3). Based on the current researches, this review has summarized the functions and effects of CUL3-E3 ligases mediated non-degradative ubiquitination.
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Affiliation(s)
- Fengguang Zhai
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Jingyun Li
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Meng Ye
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China.
| | - Xiaofeng Jin
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China.
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12
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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: 4] [Impact Index Per Article: 2.0] [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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13
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Song H, Yang J, Yu W. Promoter Hypomethylation of TGFBR3 as a Risk Factor of Alzheimer’s Disease: An Integrated Epigenomic-Transcriptomic Analysis. Front Cell Dev Biol 2022; 9:825729. [PMID: 35310542 PMCID: PMC8924075 DOI: 10.3389/fcell.2021.825729] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
Alzheimer’s disease (AD) is characterized by the abnormal deposition of amyloid-β (Aβ) plaques and tau tangles in the brain and accompanied with cognitive impairment. However, the fundamental cause of this disease remains elusive. To elucidate the molecular processes related to AD, we carried out an integrated analysis utilizing gene expression microarrays (GSE36980 and GSE5281) and DNA methylation microarray (GSE66351) in temporal cortex of AD patients from the Gene Expression Omnibus (GEO) database. We totally discovered 409 aberrantly methylated and differentially expressed genes. These dysregulated genes were significantly enriched in biological processes including cell part morphogenesis, chemical synaptic transmission and regulation of Aβ formation. Through convergent functional genomic (CFG) analysis, expression cross-validation and clinicopathological correlation analysis, higher TGFBR3 level was observed in AD and positively correlated with Aβ accumulation. Meanwhile, the promoter methylation level of TGFBR3 was reduced in AD and negatively associated with Aβ level and advanced Braak stage. Mechanically, TGFBR3 might promote Aβ production by enhancing β- and γ-secretase activities. Further investigation revealed that TGFBR3 may exert its functions via Synaptic vesicle cycle, Calcium signaling pathway and MAPK signal pathway by regulating hub genes GNB1, GNG3, CDC5L, DYNC1H1 and FBXW7. Overall, our findings highlighted TGFBR3 as an AD risk gene and might be used as a diagnostic biomarker and therapeutic target for AD treatment.
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Affiliation(s)
- Hui Song
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Jue Yang
- The State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, China
| | - Wenfeng Yu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- *Correspondence: Wenfeng Yu,
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14
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Cervantes González A, Belbin O. Fluid markers of synapse degeneration in synucleinopathies. J Neural Transm (Vienna) 2022; 129:187-206. [PMID: 35147800 DOI: 10.1007/s00702-022-02467-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/20/2022] [Indexed: 01/06/2023]
Abstract
The abnormal accumulation of α-synuclein in the brain is a common feature of Parkinson's disease (PD), PD dementia (PDD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA), and synucleinopathies that present with overlapping but distinct clinical symptoms that include motor and cognitive deficits. Synapse degeneration is the crucial neuropathological event in these synucleinopathies and the neuropathological correlate of connectome dysfunction. The cognitive and motor deficits resulting from the connectome dysfunction are currently measured by scalar systems that are limited in their sensitivity and largely subjective. Ideally, a marker of synapse degeneration would correlate with measures of cognitive or motor impairment, and could therefore be used as a more objective, surrogate biomarker of the core clinical features of these diseases. Furthermore, an objective surrogate biomarker that can detect and monitor the progression of synapse degeneration would improve patient management and clinical trial design, and could provide a measure of therapeutic response. Here, we review the published findings relating to candidate biomarkers of synapse degeneration in PD, PDD, DLB, and MSA patient-derived biofluids and discuss the findings in the context of the mechanisms associated with α-synuclein-mediated synapse degeneration. Understanding these mechanisms is essential not only for discovery of biomarkers, but also to improve our understanding of the earliest changes in disease pathogenesis of synucleinopathies.
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Affiliation(s)
- Alba Cervantes González
- Neurology Department, Biomedical Research Institute Sant Pau (IIB Sant Pau) and Sant Pau Memory Unit, Hospital de la Santa Creu i Sant Pau, 08025, Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain
| | - Olivia Belbin
- Neurology Department, Biomedical Research Institute Sant Pau (IIB Sant Pau) and Sant Pau Memory Unit, Hospital de la Santa Creu i Sant Pau, 08025, Barcelona, Spain.
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain.
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15
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Gómez de San José N, Massa F, Halbgebauer S, Oeckl P, Steinacker P, Otto M. Neuronal pentraxins as biomarkers of synaptic activity: from physiological functions to pathological changes in neurodegeneration. J Neural Transm (Vienna) 2022; 129:207-230. [PMID: 34460014 PMCID: PMC8866268 DOI: 10.1007/s00702-021-02411-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/17/2021] [Indexed: 12/22/2022]
Abstract
The diagnosis of neurodegenerative disorders is often challenging due to the lack of diagnostic tools, comorbidities and shared pathological manifestations. Synaptic dysfunction is an early pathological event in many neurodegenerative disorders, but the underpinning mechanisms are still poorly characterised. Reliable quantification of synaptic damage is crucial to understand the pathophysiology of neurodegeneration, to track disease status and to obtain prognostic information. Neuronal pentraxins (NPTXs) are extracellular scaffolding proteins emerging as potential biomarkers of synaptic dysfunction in neurodegeneration. They are a family of proteins involved in homeostatic synaptic plasticity by recruiting post-synaptic receptors into synapses. Recent research investigates the dynamic changes of NPTXs in the cerebrospinal fluid (CSF) as an expression of synaptic damage, possibly related to cognitive impairment. In this review, we summarise the available data on NPTXs structure and expression patterns as well as on their contribution in synaptic function and plasticity and other less well-characterised roles. Moreover, we propose a mechanism for their involvement in synaptic damage and neurodegeneration and assess their potential as CSF biomarkers for neurodegenerative diseases.
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Affiliation(s)
| | - Federico Massa
- Department of Neurology, University of Ulm, Ulm, Germany
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | | | - Patrick Oeckl
- Department of Neurology, University of Ulm, Ulm, Germany
- German Center for Neurodegenerative Diseases (DZNE E.V.), Ulm, Germany
| | | | - Markus Otto
- Department of Neurology, University of Ulm, Ulm, Germany.
- Department of Neurology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany.
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16
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Antunes ASLM. Post-translational Modifications in Parkinson’s Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1382:85-94. [DOI: 10.1007/978-3-031-05460-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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17
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Tiklová K, Gillberg L, Volakakis N, Lundén-Miguel H, Dahl L, Serrano GE, Adler CH, Beach TG, Perlmann T. Disease Duration Influences Gene Expression in Neuromelanin-Positive Cells From Parkinson's Disease Patients. Front Mol Neurosci 2021; 14:763777. [PMID: 34867188 PMCID: PMC8632647 DOI: 10.3389/fnmol.2021.763777] [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: 08/24/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Analyses of gene expression in cells affected by neurodegenerative disease can provide important insights into disease mechanisms and relevant stress response pathways. Major symptoms in Parkinson’s disease (PD) are caused by the degeneration of midbrain dopamine (mDA) neurons within the substantia nigra. Here we isolated neuromelanin-positive dopamine neurons by laser capture microdissection from post-mortem human substantia nigra samples recovered at both early and advanced stages of PD. Neuromelanin-positive cells were also isolated from individuals with incidental Lewy body disease (ILBD) and from aged-matched controls. Isolated mDA neurons were subjected to genome-wide gene expression analysis by mRNA sequencing. The analysis identified hundreds of dysregulated genes in PD. Results showed that mostly non-overlapping genes were differentially expressed in ILBD, subjects who were early after diagnosis (less than five years) and those autopsied at more advanced stages of disease (over five years since diagnosis). The identity of differentially expressed genes suggested that more resilient, stably surviving DA neurons were enriched in samples from advanced stages of disease, either as a consequence of positive selection of a less vulnerable long-term surviving mDA neuron subtype or due to up-regulation of neuroprotective gene products.
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Affiliation(s)
- Katarína Tiklová
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.,Ludwig Institute for Cancer Research, Stockholm, Sweden
| | - Linda Gillberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.,Ludwig Institute for Cancer Research, Stockholm, Sweden
| | | | | | - Lina Dahl
- Ludwig Institute for Cancer Research, Stockholm, Sweden
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, AZ, United States
| | - Charles H Adler
- Department of Neurology, Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, AZ, United States
| | - Thomas Perlmann
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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18
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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: 15] [Impact Index Per Article: 5.0] [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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19
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Identifying Methylation Patterns in Dental Pulp Aging: Application to Age-at-Death Estimation in Forensic Anthropology. Int J Mol Sci 2021; 22:ijms22073717. [PMID: 33918302 PMCID: PMC8038189 DOI: 10.3390/ijms22073717] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/19/2022] Open
Abstract
Age-at-death estimation constitutes one of the key parameters for identification of human remains in forensic investigations. However, for applications in forensic anthropology, many current methods are not sufficiently accurate for adult individuals, leading to chronological age estimates erring by ±10 years. Based on recent trends in aging studies, DNA methylation has great potential as a solution to this problem. However, there are only a few studies that have been published utilizing DNA methylation to determine age from human remains. The aim of the present study was to expand the range of this work by analyzing DNA methylation in dental pulp from adult individuals. Healthy erupted third molars were extracted from individuals aged 22–70. DNA from pulp was isolated and bisulfite converted. Pyrosequencing was the chosen technique to assess DNA methylation. As noted in previous studies, we found that ELOVL2 and FHL2 CpGs played a role in age estimation. In addition, three new markers were evaluated—NPTX2, KLF14, and SCGN. A set of CpGs from these five loci was used in four different multivariate regression models, providing a Mean Absolute Error (MAE) between predicted and chronological age of 1.5–2.13 years. The findings from this research can improve age estimation, increasing the accuracy of identification in forensic anthropology.
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20
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Han X, Lu Y, Li X, Xia L, Wen H, Feng Z, Ju X, Chen X, Wu X. Overexpression of NPTX2 Promotes Malignant Phenotype of Epithelial Ovarian Carcinoma via IL6-JAK2/STAT3 Signaling Pathway Under Hypoxia. Front Oncol 2021; 11:643986. [PMID: 33768003 PMCID: PMC7985451 DOI: 10.3389/fonc.2021.643986] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 01/25/2021] [Indexed: 01/14/2023] Open
Abstract
Background Epithelial ovarian cancer (EOC) is the main subtype of ovarian cancer and shows an aggressive phenotype and poor prognosis. Neuronal pentraxin II (NPTX2) is a member of the neuronal pentraxin family and plays a contradictory role in different tumors. However, there has been no report about the possible role and effect of NPTX2 in EOC. Methods Bioinformatics analysis, qPCR, western blotting and immunohistochemistry were used to detect the expression of NPTX2 in EOC. Lentivirus-based transfection for NPTX2 overexpression or knockdown was performed on the EOC cell lines A2780, HEY, SKOV3 and OVCAR-3. The effect of NPTX2 on the malignant phenotype of EOC was examined through methods of MTS assay, Edu assay, transwell assay, western blotting analysis, qPCR analysis, luciferase reporter assay and xenograft experiment. Results EOC tissues showed higher NPTX2 expression than the normal tissues with poor prognosis. NPTX2 overexpression can promote the proliferation, invasion, migration and tumorigenesis of EOC via IL6-JAK2/STAT3 signaling pathway. Moreover, hypoxia-inducible factor-1(HIF-1) can promote the transcription and expression of NPTX2 under the hypoxic environment. NPTX2 knockdown abolished the hypoxia-induced malignant phenotypes in ECO. Conclusions The above results suggest that NPTX2 may play a novel role in ovarian cancer's malignant phenotype and act as a promising treatment target for EOC molecular therapy.
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Affiliation(s)
- Xiaotian Han
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yechen Lu
- Wound Repair Center, Ruijin Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Xiaoqi Li
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lingfang Xia
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hao Wen
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zheng Feng
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xingzhu Ju
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaojun Chen
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaohua Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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21
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Simmnacher K, Krach F, Schneider Y, Alecu JE, Mautner L, Klein P, Roybon L, Prots I, Xiang W, Winner B. Unique signatures of stress-induced senescent human astrocytes. Exp Neurol 2020; 334:113466. [PMID: 32949572 DOI: 10.1016/j.expneurol.2020.113466] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022]
Abstract
Senescence was recently linked to neurodegeneration and astrocytes are one of the major cell types to turn senescent under neurodegenerative conditions. Senescent astrocytes were detected in Parkinson's disease (PD) patients' brains besides reactive astrocytes, yet the difference between senescent and reactive astrocytes is unclear. We aimed to characterize senescent astrocytes in comparison to reactive astrocytes and investigate differences and similarities. In a cell culture model of human fetal astrocytes, we determined a unique senescent transcriptome distinct from reactive astrocytes, which comprises dysregulated pathways. Both, senescent and reactive human astrocytes activated a proinflammatory pattern. Astrocyte senescence was at least partially depending on active mechanistic-target-of-rapamycin (mTOR) and DNA-damage response signaling, both drivers of senescence. To further investigate how PD and senescence connect to each other, we asked if a PD-linked environmental factor induces senescence and if senescence impairs midbrain neurons. We could show that the PD-linked pesticide rotenone causes astrocyte senescence. We further delineate, that the senescent secretome exaggerates rotenone-induced neurodegeneration in midbrain neurons differentiated from human induced pluripotent stem cells (hiPSC) of PD patients with alpha-synuclein gene (SNCA) locus duplication.
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Affiliation(s)
- Katrin Simmnacher
- Department of Stem Cell Biology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Florian Krach
- Department of Stem Cell Biology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yanni Schneider
- Department of Molecular Neurology, FAU Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Julian E Alecu
- Department of Stem Cell Biology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Lena Mautner
- Department of Stem Cell Biology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Paulina Klein
- Department of Stem Cell Biology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Laurent Roybon
- Stem Cell Laboratory for CNS Disease Modeling, MultiPark and Lund Stem Cell Center, Department of Experimental Medical Science, Faculty of Medicine, Lund University, 22184 Lund, Sweden
| | - Iryna Prots
- Department of Stem Cell Biology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Wei Xiang
- Department of Molecular Neurology, FAU Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Beate Winner
- Department of Stem Cell Biology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany.
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22
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Dyavar SR, Potts LF, Beck G, Dyavar Shetty BL, Lawson B, Podany AT, Fletcher CV, Amara RR, Papa SM. Transcriptomic approach predicts a major role for transforming growth factor beta type 1 pathway in L-Dopa-induced dyskinesia in parkinsonian rats. GENES BRAIN AND BEHAVIOR 2020; 19:e12690. [PMID: 32741046 DOI: 10.1111/gbb.12690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/24/2020] [Accepted: 07/29/2020] [Indexed: 01/21/2023]
Abstract
Dyskinesia induced by long-term L-Dopa (LID) therapy in Parkinson disease is associated with altered striatal function whose molecular bases remain unclear. Here, a transcriptomic approach was applied for comprehensive analysis of distinctively regulated genes in striatal tissue, their specific pathways, and functional- and disease-associated networks in a rodent model of LID. This approach has identified transforming growth factor beta type 1 (TGFβ1) as a highly upregulated gene in dyskinetic animals. TGFβ1 pathway is a top aberrantly regulated pathway in the striatum following LID development based on differentially expressed genes (> 1.5 fold change and P < 0.05). The induction of TGFβ1 pathway specific genes, TGFβ1, INHBA, AMHR2 and PMEPA1 was also associated with regulation of NPTX2, PDP1, SCG2, SYNPR, TAC1, TH, TNNT1 genes. Transcriptional network and upstream regulator analyses have identified AKT-centered functional and ERK-centered disease networks revealing the association of TGFβ1, IL-1β and TNFα with LID development. Therefore, results support that TGFβ1 pathway is a major contributor to the pathogenic mechanisms of LID.
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Affiliation(s)
- Shetty Ravi Dyavar
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Lisa F Potts
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Goichi Beck
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | | | - Benton Lawson
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Anthony T Podany
- Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Courtney V Fletcher
- Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Rama Rao Amara
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Stella M Papa
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
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23
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Kumar R, Donakonda S, Müller SA, Lichtenthaler SF, Bötzel K, Höglinger GU, Koeglsperger T. Basic Fibroblast Growth Factor 2-Induced Proteome Changes Endorse Lewy Body Pathology in Hippocampal Neurons. iScience 2020; 23:101349. [PMID: 32707433 PMCID: PMC7381695 DOI: 10.1016/j.isci.2020.101349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/11/2020] [Accepted: 07/03/2020] [Indexed: 12/15/2022] Open
Abstract
Hippocampal Lewy body pathology (LBP) is associated with changes in neurotrophic factor signaling and neuronal energy metabolism. LBP progression is attributed to the aggregation of α-synuclein (α-Syn) and its cell-to-cell transmission via extracellular vehicles (EVs). We recently discovered an enhanced EV release in basic fibroblast growth factor (bFGF)-treated hippocampal neurons. Here, we examined the EV and cell lysate proteome changes in bFGF-treated hippocampal neurons. We identified n = 2,310 differentially expressed proteins (DEPs) induced by bFGF. We applied weighted protein co-expression network analysis (WPCNA) to generate protein modules from DEPs and mapped them to published LBP datasets. This approach revealed n = 532 LBP-linked DEPs comprising key α-Syn-interacting proteins, LBP-associated RNA-binding proteins (RBPs), and neuronal ion channels and receptors that can impact LBP onset and progression. In summary, our deep proteomic analysis affirms the potential influence of bFGF signaling on LBP-related proteome changes and associated molecular interactions.
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Affiliation(s)
- Rohit Kumar
- German Center for Neurodegenerative Diseases (DZNE), 81337 Munich, Germany; Faculty of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; Department of Neurology, Ludwig Maximilian University, 81377 Munich, Germany.
| | - Sainitin Donakonda
- Institute of Immunology and Experimental Oncology, Technical University of Munich, 81675 Munich, Germany
| | - Stephan A Müller
- German Center for Neurodegenerative Diseases (DZNE), 81337 Munich, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), 81337 Munich, Germany; Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | - Kai Bötzel
- Department of Neurology, Ludwig Maximilian University, 81377 Munich, Germany
| | - Günter U Höglinger
- German Center for Neurodegenerative Diseases (DZNE), 81337 Munich, Germany; Faculty of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; Department of Neurology, Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Thomas Koeglsperger
- German Center for Neurodegenerative Diseases (DZNE), 81337 Munich, Germany; Department of Neurology, Ludwig Maximilian University, 81377 Munich, Germany.
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24
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van Steenoven I, Koel-Simmelink MJA, Vergouw LJM, Tijms BM, Piersma SR, Pham TV, Bridel C, Ferri GL, Cocco C, Noli B, Worley PF, Xiao MF, Xu D, Oeckl P, Otto M, van der Flier WM, de Jong FJ, Jimenez CR, Lemstra AW, Teunissen CE. Identification of novel cerebrospinal fluid biomarker candidates for dementia with Lewy bodies: a proteomic approach. Mol Neurodegener 2020; 15:36. [PMID: 32552841 PMCID: PMC7301448 DOI: 10.1186/s13024-020-00388-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Diagnosis of dementia with Lewy bodies (DLB) is challenging, largely due to a lack of diagnostic tools. Cerebrospinal fluid (CSF) biomarkers have been proven useful in Alzheimer's disease (AD) diagnosis. Here, we aimed to identify novel CSF biomarkers for DLB using a high-throughput proteomic approach. METHODS We applied liquid chromatography/tandem mass spectrometry with label-free quantification to identify biomarker candidates to individual CSF samples from a well-characterized cohort comprising patients with DLB (n = 20) and controls (n = 20). Validation was performed using (1) the identical proteomic workflow in an independent cohort (n = 30), (2) proteomic data from patients with related neurodegenerative diseases (n = 149) and (3) orthogonal techniques in an extended cohort consisting of DLB patients and controls (n = 76). Additionally, we utilized random forest analysis to identify the subset of candidate markers that best distinguished DLB from all other groups. RESULTS In total, we identified 1995 proteins. In the discovery cohort, 69 proteins were differentially expressed in DLB compared to controls (p < 0.05). Independent cohort replication confirmed VGF, SCG2, NPTX2, NPTXR, PDYN and PCSK1N as candidate biomarkers for DLB. The downregulation of the candidate biomarkers was somewhat more pronounced in DLB in comparison with related neurodegenerative diseases. Using random forest analysis, we identified a panel of VGF, SCG2 and PDYN to best differentiate between DLB and other clinical groups (accuracy: 0.82 (95%CI: 0.75-0.89)). Moreover, we confirmed the decrease of VGF and NPTX2 in DLB by ELISA and SRM methods. Low CSF levels of all biomarker candidates, except PCSK1N, were associated with more pronounced cognitive decline (0.37 < r < 0.56, all p < 0.01). CONCLUSION We identified and validated six novel CSF biomarkers for DLB. These biomarkers, particularly when used as a panel, show promise to improve diagnostic accuracy and strengthen the importance of synaptic dysfunction in the pathophysiology of DLB.
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Affiliation(s)
- Inger van Steenoven
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Marleen J. A. Koel-Simmelink
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Leonie J. M. Vergouw
- Alzheimer Center Erasmus MC, Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Betty M. Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Sander R. Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Thang V. Pham
- OncoProteomics Laboratory, Department of Medical Oncology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Claire Bridel
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Gian-Luca Ferri
- NEF-laboratory, Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Cristina Cocco
- NEF-laboratory, Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Barbara Noli
- NEF-laboratory, Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Paul F. Worley
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Mei-Fang Xiao
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Desheng Xu
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Patrick Oeckl
- Department of Neurology, Ulm University Hospital, Ulm, Germany
| | - Markus Otto
- Department of Neurology, Ulm University Hospital, Ulm, Germany
| | - Wiesje M. van der Flier
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
- Department of Epidemiology and Biostatistics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Frank Jan de Jong
- Alzheimer Center Erasmus MC, Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Connie R. Jimenez
- OncoProteomics Laboratory, Department of Medical Oncology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Afina W. Lemstra
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Charlotte E. Teunissen
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
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25
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van der Ende EL, Xiao M, Xu D, Poos JM, Panman JL, Jiskoot LC, Meeter LH, Dopper EG, Papma JM, Heller C, Convery R, Moore K, Bocchetta M, Neason M, Peakman G, Cash DM, Teunissen CE, Graff C, Synofzik M, Moreno F, Finger E, Sánchez-Valle R, Vandenberghe R, Laforce R, Masellis M, Tartaglia MC, Rowe JB, Butler CR, Ducharme S, Gerhard A, Danek A, Levin J, Pijnenburg YA, Otto M, Borroni B, Tagliavini F, de Mendonca A, Santana I, Galimberti D, Seelaar H, Rohrer JD, Worley PF, van Swieten JC. Neuronal pentraxin 2: a synapse-derived CSF biomarker in genetic frontotemporal dementia. J Neurol Neurosurg Psychiatry 2020; 91:612-621. [PMID: 32273328 PMCID: PMC7279197 DOI: 10.1136/jnnp-2019-322493] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Synapse dysfunction is emerging as an early pathological event in frontotemporal dementia (FTD), however biomarkers are lacking. We aimed to investigate the value of cerebrospinal fluid (CSF) neuronal pentraxins (NPTXs), a family of proteins involved in homeostatic synapse plasticity, as novel biomarkers in genetic FTD. METHODS We included 106 presymptomatic and 54 symptomatic carriers of a pathogenic mutation in GRN, C9orf72 or MAPT, and 70 healthy non-carriers participating in the Genetic Frontotemporal dementia Initiative (GENFI), all of whom had at least one CSF sample. We measured CSF concentrations of NPTX2 using an in-house ELISA, and NPTX1 and NPTX receptor (NPTXR) by Western blot. We correlated NPTX2 with corresponding clinical and neuroimaging datasets as well as with CSF neurofilament light chain (NfL) using linear regression analyses. RESULTS Symptomatic mutation carriers had lower NPTX2 concentrations (median 643 pg/mL, IQR (301-872)) than presymptomatic carriers (1003 pg/mL (624-1358), p<0.001) and non-carriers (990 pg/mL (597-1373), p<0.001) (corrected for age). Similar results were found for NPTX1 and NPTXR. Among mutation carriers, NPTX2 concentration correlated with several clinical disease severity measures, NfL and grey matter volume of the frontal, temporal and parietal lobes, insula and whole brain. NPTX2 predicted subsequent decline in phonemic verbal fluency and Clinical Dementia Rating scale plus FTD modules. In longitudinal CSF samples, available in 13 subjects, NPTX2 decreased around symptom onset and in the symptomatic stage. DISCUSSION We conclude that NPTX2 is a promising synapse-derived disease progression biomarker in genetic FTD.
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Affiliation(s)
- Emma L van der Ende
- Department of Neurology and Alzheimer Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Meifang Xiao
- Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Desheng Xu
- Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Jackie M Poos
- Department of Neurology and Alzheimer Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jessica L Panman
- Department of Neurology and Alzheimer Center, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Lize C Jiskoot
- Department of Neurology and Alzheimer Center, Erasmus University Medical Center, Rotterdam, Netherlands
- Dementia Research Centre, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Lieke H Meeter
- Department of Neurology and Alzheimer Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Elise Gp Dopper
- Department of Neurology and Alzheimer Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Janne M Papma
- Department of Neurology and Alzheimer Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Carolin Heller
- Dementia Research Institute, Department of Neurodegenerative Disease, University College London, London, United Kingdom
| | - Rhian Convery
- Dementia Research Centre, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Katrina Moore
- Dementia Research Centre, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Martina Bocchetta
- Dementia Research Centre, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Mollie Neason
- Dementia Research Centre, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Georgia Peakman
- Dementia Research Centre, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - David M Cash
- Dementia Research Centre, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Caroline Graff
- Karolinska Institutet, Dept NVS, Division of Neurogeriatrics, Bioclinicum, Stockholm, Sweden
- Unit of Hereditary Dementia, Theme Aging, Karolinska University Hospital-Solna, Stockholm, Sweden
| | - Matthis Synofzik
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, Tübingen, Germany
| | - Fermin Moreno
- Department of Neurology, Donostia University Hospital, San Sebastian, Gipuzkoa, Spain
| | - Elizabeth Finger
- Department of Clinical Neurological Sciences, University of Western Ontario, London, Ontario, Canada
| | - Raquel Sánchez-Valle
- Alzheimer's Disease and Other Cognitive Disorders Unit, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Rik Vandenberghe
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Robert Laforce
- Clinique Interdisciplinaire de Mémoire du CHU de Québec, Département des Sciences Neurologiques, Université Laval, Québec, Quebec City, Canada
| | - Mario Masellis
- Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Maria Carmela Tartaglia
- Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, Toronto, Ontario, Canada
| | - James B Rowe
- Cambridge University Centre for Frontotemporal Dementia, University of Cambridge, Cambridge, United Kingdom
| | | | - Simon Ducharme
- Montreal Neurological Institute and McGill University Health Centre, McGill University, Montreal, Québec, Canada
| | - Alex Gerhard
- Department of Nuclear Medicine and Geriatric Medicine, University Hospital Essen, Essen, Germany
- Divison of Neuroscience and Experimental Psychology, University of Manchester, Manchester, United Kingdom
| | - Adrian Danek
- Neurologische Klinik und Poliklinik, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Johannes Levin
- Neurologische Klinik und Poliklinik, Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Neurodegenerative Diseases, (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology, (SyNergy), Munich, Germany
| | - Yolande Al Pijnenburg
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, Netherlands
| | - Markus Otto
- Department of Neurology, Universität Ulm, Ulm, Germany
| | - Barbara Borroni
- Centre for Neurodegenerative Disorders, Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | | | | | - Isabel Santana
- Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Daniela Galimberti
- Department of Neurological Sciences, Dino Ferrari Center, University of Milan, Milan, Italy
- Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Harro Seelaar
- Department of Neurology and Alzheimer Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jonathan D Rohrer
- Dementia Research Centre, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Paul F Worley
- Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - John C van Swieten
- Department of Neurology and Alzheimer Center, Erasmus University Medical Center, Rotterdam, Netherlands
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26
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Chew S, Lampinen R, Saveleva L, Korhonen P, Mikhailov N, Grubman A, Polo JM, Wilson T, Komppula M, Rönkkö T, Gu C, Mackay-Sim A, Malm T, White AR, Jalava P, Kanninen KM. Urban air particulate matter induces mitochondrial dysfunction in human olfactory mucosal cells. Part Fibre Toxicol 2020; 17:18. [PMID: 32487172 PMCID: PMC7268298 DOI: 10.1186/s12989-020-00352-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/20/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The adverse effects of air pollutants including particulate matter (PM) on the central nervous system is increasingly reported by epidemiological, animal and post-mortem studies in the last decade. Oxidative stress and inflammation are key consequences of exposure to PM although little is known of the exact mechanism. The association of PM exposure with deteriorating brain health is speculated to be driven by PM entry via the olfactory system. How air pollutants affect this key entry site remains elusive. In this study, we investigated effects of urban size-segregated PM on a novel cellular model: primary human olfactory mucosal (hOM) cells. RESULTS Metabolic activity was reduced following 24-h exposure to PM without evident signs of toxicity. Results from cytometric bead array suggested a mild inflammatory response to PM exposure. We observed increased oxidative stress and caspase-3/7 activity as well as perturbed mitochondrial membrane potential in PM-exposed cells. Mitochondrial dysfunction was further verified by a decrease in mitochondria-dependent respiration. Transient suppression of the mitochondria-targeted gene, neuronal pentraxin 1 (NPTX1), was carried out, after being identified to be up-regulated in PM2.5-1 treated cells via RNA sequencing. Suppression of NPTX1 in cells exposed to PM did not restore mitochondrial defects resulting from PM exposure. In contrast, PM-induced adverse effects were magnified in the absence of NPTX1, indicating a critical role of this protein in protection against PM effects in hOM cells. CONCLUSION Key mitochondrial functions were perturbed by urban PM exposure in a physiologically relevant cellular model via a mechanism involving NPTX1. In addition, inflammatory response and early signs of apoptosis accompanied mitochondrial dysfunction during exposure to PM. Findings from this study contribute to increased understanding of harmful PM effects on human health and may provide information to support mitigation strategies targeted at air pollution.
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Affiliation(s)
- Sweelin Chew
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Riikka Lampinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Liudmila Saveleva
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Paula Korhonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nikita Mikhailov
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Alexandra Grubman
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
| | - Trevor Wilson
- Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
| | | | - Teemu Rönkkö
- Inhalation Toxicology Laboratory, Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Cheng Gu
- School of the Environment, Nanjing University, Nanjing, China
| | - Alan Mackay-Sim
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, 4111, Australia
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Anthony R White
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Pasi Jalava
- Inhalation Toxicology Laboratory, Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Katja M Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
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HOTAIR drives autophagy in midbrain dopaminergic neurons in the substantia nigra compacta in a mouse model of Parkinson's disease by elevating NPTX2 via miR-221-3p binding. Aging (Albany NY) 2020; 12:7660-7678. [PMID: 32396526 PMCID: PMC7244061 DOI: 10.18632/aging.103028] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 02/05/2020] [Indexed: 01/17/2023]
Abstract
Parkinson’s disease (PD) is a neurodegenerative disorder characterized by progressive cell loss, largely confined to mesencephalic dopamine neurons of the substantia nigra. This study investigated the functional relevance of the HOX transcript antisense intergenic RNA (HOTAIR)/microRNA-221-3 (miR-221-3p)/neuronal pentraxin II (NPTX2) axis in the process of dopaminergic neuron autophagy using PD mouse models. The PD mouse models were established by intraperitoneal injection of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyrindine (MPTP), while PD cell model was constructed by pretreatment with 1-methyl-4-phenylpyridinium (MPP+). The expression of HOTAIR was then examined using RT-qPCR. In addition, the interactions between HOTAIR, miR-221-3p, and NPTX2 were detected through RIP and dual-luciferase reporter gene assays. CCK-8 assay was performed to measure cell viability, and the expression of autophagy-related genes was determined using Western blot analysis. HOTAIR was found to be significantly expressed in the substantia nigra compact tissues and MN9D cells following PD modeling. HOTAIR could bind to miR-221-3p and elevate the NPTX2 expression, which resulted in diminished cell viability and enhanced autophagy of dopaminergic neurons both in vitro and in vivo. In summary, down-regulation of HOTAIR could potentially inhibit the autophagy of dopaminergic neurons in the substantia nigra compacta in a mouse model of PD, thus saving the demise of dopaminergic neurons.
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Chapman G, Shanmugalingam U, Smith PD. The Role of Neuronal Pentraxin 2 (NP2) in Regulating Glutamatergic Signaling and Neuropathology. Front Cell Neurosci 2020; 13:575. [PMID: 31969807 PMCID: PMC6960182 DOI: 10.3389/fncel.2019.00575] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 12/12/2019] [Indexed: 01/30/2023] Open
Abstract
Pentraxins are a superfamily of evolutionarily conserved proteins that are characterized by their multimeric architecture and their calcium-dependent binding. They can be broadly grouped into two subfamilies: short pentraxins and long pentraxins. Pentraxins regulate many processes in the brain as well as the periphery. Neuronal pentraxin 2 (NP2/NPTX2), also known as neuronal activity-regulated pentraxin (Narp), is an immediate-early gene that has been shown to play a critical role in guiding synaptic plasticity. NP2 has been previously linked to excitatory neurotransmission, based on its ability to aggregate excitatory receptors in the central nervous system. The mechanisms mediating the effects of NP2 on excitatory neurotransmission remain unclear and warrants further investigation. This review article focuses on the biological features of NP2 and discusses the literature supporting a role for NP2 and other pentraxins in glutamatergic signaling. An analysis of evidence around the role of pentraxins in neuropathology is also reviewed.
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Affiliation(s)
- Georgina Chapman
- Department of Neuroscience, Carleton University, Ottawa, ON, Canada
| | | | - Patrice D Smith
- Department of Neuroscience, Carleton University, Ottawa, ON, Canada
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Sathe G, Na CH, Renuse S, Madugundu AK, Albert M, Moghekar A, Pandey A. Quantitative Proteomic Profiling of Cerebrospinal Fluid to Identify Candidate Biomarkers for Alzheimer's Disease. Proteomics Clin Appl 2019; 13:e1800105. [PMID: 30578620 PMCID: PMC6639119 DOI: 10.1002/prca.201800105] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 12/17/2018] [Indexed: 12/13/2022]
Abstract
PURPOSE The aim of this study is to identify the potential cerebrospinal fluid (CSF) biomarkers for Alzheimer's disease and to evaluate these markers on independent CSF samples using parallel reaction monitoring (PRM) assays. EXPERIMENTAL DESIGN High-Resolution mass spectrometry and tandem mass tag (TMT) multiplexing technology are employed to identify potential biomarkers for Alzheimer's disease. Some of the identified potential biomarkers are validated using PRM assays. RESULTS A total of 2327 proteins are identified in the CSF of which 139 are observed to be significantly altered in the CSF of AD patients. The proteins altered in AD includes a number of known AD marker such as MAPT, NPTX2, VGF, GFAP, and NCAM1 as well as novel biomarkers such as PKM and YWHAG. These findings are validated in a separate set of CSF specimens from AD dementia patients and controls. NPTX2, in combination with PKM or YWHAG, leads to the best results with AUCs of 0.935 and 0.933, respectively. CONCLUSIONS AND CLINICAL RELEVANCE The proteins that are found to be altered in the CSF of patients with AD could be used for monitoring disease progression and therapeutic response and perhaps also for early detection once they are validated in larger studies.
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Affiliation(s)
- Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Chan Hyun Na
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Santosh Renuse
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Anil K. Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Marilyn Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
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Tang CZ, Zhang DF, Yang JT, Liu QH, Wang YR, Wang WS. Overexpression of microRNA-301b accelerates hippocampal microglia activation and cognitive impairment in mice with depressive-like behavior through the NF-κB signaling pathway. Cell Death Dis 2019; 10:316. [PMID: 30962417 PMCID: PMC6453902 DOI: 10.1038/s41419-019-1522-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 02/19/2019] [Accepted: 03/13/2019] [Indexed: 12/30/2022]
Abstract
Depression is a condition with a complex etiological pattern, whose effective treatments are highly limited. MicroRNAs (miRNAs) have been investigated in intensive studies owing to their involvement in pathophysiology of mood disorders. The current study aimed to elucidate the role of miR-301b in hippocampus in mouse models of depressive-like behavior. Microarray-based prediction identified the differentially expressed gene neuronal pentraxin II (NPTX2) related to mental depression. Next, the putative miR-301b binding sites on the 3'UTR of NPTX2 were verified. Then the effect of miR-301b on cognitive function of mice with depressive-like behavior was analyzed using the Morris water maze test. In addition, the regulation of miR-301b to NPTX2 and activation of NF-κB signaling pathway was assessed. Following that, the microglia activation and inflammation in hippocampus were evaluated, with the expressions of inflammatory factors being examined. At last, microglia were flow cytometrically sorted and the inflammatory reaction was also assessed in vitro. The obtained findings revealed that miR-301b targeted and negatively regulated NPTX2. Moreover, overexpressed miR-301b activated the NF-κB signaling pathway, as reflected by increasing protein expressions of p-NF-κB. Upregulated miR-301b accelerated cognitive impairment in mice with depressive-like behavior. In addition, overexpression of miR-301b activated microglia and stimulated inflammation in hippocampus, accompanied by enhanced release of tumor necrosis factor-α (TNF-α), interleukin-Iβ (IL-Iβ) and cyclooxygenase-2(COX-2). Taken together, the evidence provided by the current study indicated that overexpression of miR-301b augmented hippocampal microglia activation, thus exacerbating cognitive impairment and inflammation in mice with depressive-like behavior by activating the NF-κB signaling pathway.
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Affiliation(s)
- Chao-Zhi Tang
- Laboratory of Molecular Medicine, College of Life Science, Henan Normal University, 453007, Xinxiang, People's Republic of China
| | - Dong-Fang Zhang
- Laboratory of Molecular Medicine, College of Life Science, Henan Normal University, 453007, Xinxiang, People's Republic of China
| | - Jun-Tang Yang
- Laboratory of Molecular Medicine, College of Life Science, Henan Normal University, 453007, Xinxiang, People's Republic of China
| | - Qing-Hui Liu
- Laboratory of Molecular Medicine, College of Life Science, Henan Normal University, 453007, Xinxiang, People's Republic of China
| | - Ya-Ru Wang
- Laboratory of Molecular Medicine, College of Life Science, Henan Normal University, 453007, Xinxiang, People's Republic of China
| | - Wen-Sheng Wang
- Laboratory of Molecular Medicine, College of Life Science, Henan Normal University, 453007, Xinxiang, People's Republic of China.
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Xu C, Tian G, Jiang C, Xue H, Kuerbanjiang M, Sun L, Gu L, Zhou H, Liu Y, Zhang Z, Xu Q. NPTX2 promotes colorectal cancer growth and liver metastasis by the activation of the canonical Wnt/β-catenin pathway via FZD6. Cell Death Dis 2019; 10:217. [PMID: 30833544 PMCID: PMC6399240 DOI: 10.1038/s41419-019-1467-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/04/2019] [Accepted: 02/12/2019] [Indexed: 12/21/2022]
Abstract
Accumulating evidence from clinical and epidemiological studies has highlighted the close correlation between the individual risk of cancer and nervous system diseases. The expression of neuronal pentraxin 2 (NPTX2) is absent in Alzheimer's disease, anxiety, and depression. Herein, we found that NPTX2 mRNA and protein expression was significantly upregulated in colorectal carcinoma (CRC). NPTX2 expression level gradually increased with CRC progression and was closely associated with poor prognosis. In vitro and in vivo studies demonstrated that NPTX2 promoted CRC proliferation and metastasis through the activation of the Wnt/β-catenin signaling pathway. As NPTX2 receptors are absent on CRC cells, NPTX2 was shown to physically interact with frizzled class receptor 6 (FZD6) to promote β-catenin translocation into the cell nucleus, resulting in an increase in the expression of MYC, cyclin D1, snail, and N-cadherin along with a decrease in the expression of E-cadherin. Knockdown of FZD6 expression with a small-interfering RNA almost completely reversed the proliferative effects of NPTX2 on CRC development. In conclusion, NPTX2, a molecule related to nervous system diseases, promotes CRC cell proliferation and metastasis through the activation of the Wnt/β-catenin pathway via direct interaction with FZD6.
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Affiliation(s)
- Chunjie Xu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P.R. China
| | - Guangang Tian
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, P.R. China
| | - Chunhui Jiang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P.R. China
| | - Hanbing Xue
- Division of Gastroenterology and Hepatology; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001, P.R. China
| | - Manzila Kuerbanjiang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P.R. China
| | - Longci Sun
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P.R. China
| | - Lei Gu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P.R. China
| | - Hong Zhou
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P.R. China
| | - Ye Liu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P.R. China
| | - Zhigang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, P.R. China.
| | - Qing Xu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P.R. China.
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Li J, Sun Y, Chen J. Transcriptome sequencing in a 6-hydroxydopamine rat model of Parkinson's disease. Genes Genet Syst 2019; 94:61-69. [PMID: 30713215 DOI: 10.1266/ggs.18-00036] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The neurotoxin 6-hydroxydopamine (6-OHDA) has been widely exploited as a tool for modeling Parkinson's disease (PD) in the rat. This study aimed to provide a comprehensive profile of the mRNAs and long noncoding RNAs (lncRNAs) in rats treated with 6-OHDA as a model of PD. Female SPF Wistar rats were randomly divided into two groups: a PD model group and a control group. The PD model was induced by 6-OHDA injection. RNA-seq analysis was performed on 6-OHDA-treated rats and corresponding controls. Novel lncRNAs were identified. Differentially expressed genes (DEGs) and differentially expressed lncRNAs were identified in the PD group compared with controls. Gene Ontology function and pathway enrichment analyses were conducted on the DEGs, followed by construction of a protein-protein interaction (PPI) network. In addition, prediction of lncRNA target genes and function prediction of lncRNAs were performed. Moreover, microRNAs (miRNAs) that interacted with the DEGs and differentially expressed lncRNAs were predicted to construct a miRNA-lncRNA-mRNA regulatory network. A total of 536 DEGs and 512 differentially expressed lncRNAs (44 up-regulated and 10 down-regulated known lncRNAs; 407 up-regulated and 51 down-regulated novel lncRNAs) were identified in the PD rat model compared with controls. The DEGs and target genes of lncRNAs were mainly associated with the innate immune response, 2'-5'-oligoadenylate synthetase activity, GTPase activity, GTP binding and the RIG-I-like receptor signaling pathway. IRF7 and ISG15 were hub proteins in the PPI network. Many mRNAs and lncRNAs interacted with other molecules in a competing endogenous RNA network, such as MAS1, TMPRSS2, NPTX1, XLOC_016191, XLOC_026924 and XLOC_005439. We conclude that IRF7, ISG15, MAS1, TMPRSS2, NPTX1, XLOC_016191, XLOC_026924 and XLOC_005439 may contribute critical roles in the pathogenesis of PD.
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Affiliation(s)
- Jia Li
- Department of Neurology, China-Japan Union Hospital of Jilin University
| | - Yajuan Sun
- Department of Neurology, China-Japan Union Hospital of Jilin University
| | - Jiajun Chen
- Department of Neurology, China-Japan Union Hospital of Jilin University
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Abstract
Obesity is a medical condition that impacts on all levels of society and causes numerous comorbidities, such as diabetes, cardiovascular disease, and cancer. We assessed the suitability of targeting enolase, a glycolysis pathway enzyme with multiple, secondary functions in cells, to treat obesity. Treating adipocytes with ENOblock, a novel modulator of these secondary ‘moonlighting’ functions of enolase, suppressed the adipogenic program and induced mitochondrial uncoupling. Obese animals treated with ENOblock showed a reduction in body weight and increased core body temperature. Metabolic and inflammatory parameters were improved in the liver, adipose tissue and hippocampus. The mechanism of ENOblock was identified as transcriptional repression of master regulators of lipid homeostasis (Srebp-1a and Srebp-1c), gluconeogenesis (Pck-1) and inflammation (Tnf-α and Il-6). ENOblock treatment also reduced body weight gain, lowered cumulative food intake and increased fecal lipid content in mice fed a high fat diet. Our results support the further drug development of ENOblock as a therapeutic for obesity and suggest enolase as a new target for this disorder.
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Pascovici D, Wu JX, McKay MJ, Joseph C, Noor Z, Kamath K, Wu Y, Ranganathan S, Gupta V, Mirzaei M. Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools. Int J Mol Sci 2018; 20:E16. [PMID: 30577541 PMCID: PMC6337699 DOI: 10.3390/ijms20010016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/09/2018] [Accepted: 12/17/2018] [Indexed: 01/04/2023] Open
Abstract
Post-translational modifications (PTMs) can occur soon after translation or at any stage in the lifecycle of a given protein, and they may help regulate protein folding, stability, cellular localisation, activity, or the interactions proteins have with other proteins or biomolecular species. PTMs are crucial to our functional understanding of biology, and new quantitative mass spectrometry (MS) and bioinformatics workflows are maturing both in labelled multiplexed and label-free techniques, offering increasing coverage and new opportunities to study human health and disease. Techniques such as Data Independent Acquisition (DIA) are emerging as promising approaches due to their re-mining capability. Many bioinformatics tools have been developed to support the analysis of PTMs by mass spectrometry, from prediction and identifying PTM site assignment, open searches enabling better mining of unassigned mass spectra-many of which likely harbour PTMs-through to understanding PTM associations and interactions. The remaining challenge lies in extracting functional information from clinically relevant PTM studies. This review focuses on canvassing the options and progress of PTM analysis for large quantitative studies, from choosing the platform, through to data analysis, with an emphasis on clinically relevant samples such as plasma and other body fluids, and well-established tools and options for data interpretation.
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Affiliation(s)
- Dana Pascovici
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Jemma X Wu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Matthew J McKay
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Chitra Joseph
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
| | - Zainab Noor
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Karthik Kamath
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Yunqi Wu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Vivek Gupta
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
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35
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Swanson A, Wolf T, Sitzmann A, Willette AA. Neuroinflammation in Alzheimer's disease: Pleiotropic roles for cytokines and neuronal pentraxins. Behav Brain Res 2018; 347:49-56. [PMID: 29462653 PMCID: PMC5988985 DOI: 10.1016/j.bbr.2018.02.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/30/2018] [Accepted: 02/13/2018] [Indexed: 12/14/2022]
Abstract
Neuroinflammation is a potential factor speculated to underlie Alzheimer's disease (AD) etiopathogenesis and progression. The overwhelming focus in this area of research to date has been on the chronic upregulation of pro-inflammatory cytokines to understand how neuroinflammatory mechanisms contribute to neurodegeneration. Yet, it is important to understand the pleiotropic roles of these cytokines in modulating neuroinflammation in which they cannot be labeled as a strictly "good" or "bad" biomarker phenotype. As such, biomarkers with more precise functions are needed to better understand how neuroinflammation impacts the brain in AD. Neuronal pentraxins are a concentration- dependent group of pro- or anti- inflammatory cytokines. There is contradictory evidence of these pentraxins as being both neuroprotective and potentially detrimental in AD. Potential neuroprotective examples include their ability to predict AD-related outcomes such as cognition, memory function and synaptic refinement. This review will briefly outline the basis of AD and subsequently summarize findings for neuropathological mechanisms of neuroinflammation, roles for traditional pro-and anti-inflammatory cytokines, and data found thus far on the neuronal pentraxins.
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Affiliation(s)
- Ashley Swanson
- Department of Food Science and Human Nutrition, Iowa State University, 2312 Food Sciences Building, 536 Farm House Lane, Ames, IA 50011, United States.
| | - Tovah Wolf
- Department of Food Science and Human Nutrition, Iowa State University, 2312 Food Sciences Building, 536 Farm House Lane, Ames, IA 50011, United States.
| | - Alli Sitzmann
- Department of Psychology, Iowa State University, W112 Lagomarcino Hall, 901 Stange Road, Ames, IA 50011, United States.
| | - Auriel A Willette
- Department of Food Science and Human Nutrition, Iowa State University, 2312 Food Sciences Building, 536 Farm House Lane, Ames, IA 50011, United States; Department of Psychology, Iowa State University, W112 Lagomarcino Hall, 901 Stange Road, Ames, IA 50011, United States; Department of Biomedical Sciences, Iowa State University, 2008 Veterinary Medicine, Ames, IA 50011, United States; Department of Neurology, University of Iowa, 2007 Roy Carver Pavilion, 200 Hawkins Drive, Iowa City, IA 52242, United States.
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Wassouf Z, Hentrich T, Samer S, Rotermund C, Kahle PJ, Ehrlich I, Riess O, Casadei N, Schulze-Hentrich JM. Environmental Enrichment Prevents Transcriptional Disturbances Induced by Alpha-Synuclein Overexpression. Front Cell Neurosci 2018; 12:112. [PMID: 29755323 PMCID: PMC5932345 DOI: 10.3389/fncel.2018.00112] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/06/2018] [Indexed: 12/13/2022] Open
Abstract
Onset and progression of neurodegenerative disorders, including synucleinopathies such as Parkinson's disease, have been associated with various environmental factors. A highly compelling association from a therapeutic point of view has been found between a physically active lifestyle and a significantly reduced risk for Parkinson's disease. Mimicking such conditions in animal models by promoting physical activity, social interactions, and novel surroundings yields in a so-called enriched environment known to enhance adult neurogenesis, increase synaptic plasticity, and decelerate neuronal loss. Yet, the genes that connect beneficial environmental cues to the genome and delay disease-related symptoms have remained largely unclear. To identify such mediator genes, we used a 2 × 2 factorial design opposing genotype and environment. Specifically, we compared wildtype to transgenic mice overexpressing human SNCA, a key gene in synucleinopathies encoding alpha-synuclein, and housed them in a standard and enriched environment from weaning to 12 months of age before profiling their hippocampal transcriptome using RNA-sequencing. Under standard environmental conditions, differentially expressed genes were overrepresented for calcium ion binding, membrane, synapse, and other Gene Ontology terms previously linked to alpha-synuclein biology. Upregulated genes were significantly enriched for genes attributed to astrocytes, microglia, and oligodendrocytes. These disturbances in gene activity were accompanied by reduced levels of several presynaptic proteins and the immediate early genes EGR1 and NURR1. Intriguingly, housing transgenic animals in the enriched environment prevented most of these perturbations in gene activity. In addition, a sustained activation specifically in transgenic animals housed in enriched conditions was observed for several immediate early genes including Egr1, Nr4a2/Nurr1, Arc, and Homer1a. These findings suggest a compensatory mechanism through an enriched environment-activated immediate early gene network that prevented most disturbances induced by alpha-synuclein overexpression. This regulatory framework might harbor attractive targets for novel therapeutic approaches that mimic beneficial environmental stimuli.
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Affiliation(s)
- Zinah Wassouf
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Thomas Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Sebastian Samer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Centre for Integrative Neuroscience, University of Tübingen, Tübingen, Germany
| | | | - Philipp J Kahle
- German Center for Neurodegenerative Diseases, Tübingen, Germany.,Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Ingrid Ehrlich
- Centre for Integrative Neuroscience, University of Tübingen, Tübingen, Germany.,Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,Department of Neurobiology, IBBS, University of Stuttgart, Stuttgart, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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Schwamborn JC. Is Parkinson's Disease a Neurodevelopmental Disorder and Will Brain Organoids Help Us to Understand It? Stem Cells Dev 2018; 27:968-975. [PMID: 29415619 DOI: 10.1089/scd.2017.0289] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder after Alzheimer's disease. The incidence of PD cases increases with age, accordingly classically PD is considered to be an age-associated neurodegenerative disease. In this review, the hypothesis that PD is actually a neurodevelopmental disorder that is compensated for a long time will be discussed. However, patients who suffer from PD typically do not show symptoms early in their lives. This implies that, if the hypothesis that PD has a significant neurodevelopmental component is correct, the developmental defects are compensated for a long time. Furthermore, these developmental defects might not causally lead to the disease but increase the susceptibility for disease onset after a "second hit." In this logic, deregulated developmental processes might represent the "first hit." Even a minor developmental defect could lead to a reduced compensatory capacity or reduced fault tolerance of the entire system. In such a case of an already imbalanced system one or more additional hits could perturb the entire system sufficiently to bring it out of balance and lead to the pathology and symptoms which we classify as PD. However, if the developmental hypothesis and the "multiple hit" hypothesis are correct, an early diagnosis of these developmental defects might allow the start of a therapy for at-risk individuals before disease pathology becomes severe and before symptoms occur. Modern stem cell technologies, including the generation of personalized brain organoids, might play an important role in these strategies.
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Affiliation(s)
- Jens C Schwamborn
- Luxembourg Centre for Systems Biomedicine, Developmental and Cellular Biology, University of Luxembourg , Belvaux, Luxembourg
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38
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The integration of epigenetics and genetics in nutrition research for CVD risk factors. Proc Nutr Soc 2016; 76:333-346. [DOI: 10.1017/s0029665116000823] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is increasing evidence documenting gene-by-environment (G × E) interactions for CVD related traits. However, the underlying mechanisms are still unclear. DNA methylation may represent one of such potential mechanisms. The objective of this review paper is to summarise the current evidence supporting the interplay among DNA methylation, genetic variants, and environmental factors, specifically (1) the association between SNP and DNA methylation; (2) the role that DNA methylation plays in G × E interactions. The current evidence supports the notion that genotype-dependent methylation may account, in part, for the mechanisms underlying observed G × E interactions in loci such asAPOE, IL6and ATP-binding cassette A1. However, these findings should be validated using intervention studies with high level of scientific evidence. The ultimate goal is to apply the knowledge and the technology generated by this research towards genetically based strategies for the development of personalised nutrition and medicine.
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Mariani E, Frabetti F, Tarozzi A, Pelleri MC, Pizzetti F, Casadei R. Meta-Analysis of Parkinson's Disease Transcriptome Data Using TRAM Software: Whole Substantia Nigra Tissue and Single Dopamine Neuron Differential Gene Expression. PLoS One 2016; 11:e0161567. [PMID: 27611585 PMCID: PMC5017670 DOI: 10.1371/journal.pone.0161567] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 08/08/2016] [Indexed: 01/21/2023] Open
Abstract
The understanding of the genetic basis of the Parkinson's disease (PD) and the correlation between genotype and phenotype has revolutionized our knowledge about the pathogenetic mechanisms of neurodegeneration, opening up exciting new therapeutic and neuroprotective perspectives. Genomic knowledge of PD is still in its early stages and can provide a good start for studies of the molecular mechanisms that underlie the gene expression variations and the epigenetic mechanisms that may contribute to the complex and characteristic phenotype of PD. In this study we used the software TRAM (Transcriptome Mapper) to analyse publicly available microarray data of a total of 151 PD patients and 130 healthy controls substantia nigra (SN) samples, to identify chromosomal segments and gene loci differential expression. In particular, we separately analyzed PD patients and controls data from post-mortem snap-frozen SN whole tissue and from laser microdissected midbrain dopamine (DA) neurons, to better characterize the specific DA neuronal expression profile associated with the late-stage Parkinson's condition. The default "Map" mode analysis resulted in 10 significantly over/under-expressed segments, mapping on 8 different chromosomes for SN whole tissue and in 4 segments mapping on 4 different chromosomes for DA neurons. In conclusion, TRAM software allowed us to confirm the deregulation of some genomic regions and loci involved in key molecular pathways related to neurodegeneration, as well as to provide new insights about genes and non-coding RNA transcripts not yet associated with the disease.
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Affiliation(s)
- Elisa Mariani
- Department for Life Quality Studies, University of Bologna, Rimini, Italy
| | - Flavia Frabetti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Andrea Tarozzi
- Department for Life Quality Studies, University of Bologna, Rimini, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Fabrizio Pizzetti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Raffaella Casadei
- Department for Life Quality Studies, University of Bologna, Rimini, Italy
- * E-mail:
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Abou-Abbass H, Abou-El-Hassan H, Bahmad H, Zibara K, Zebian A, Youssef R, Ismail J, Zhu R, Zhou S, Dong X, Nasser M, Bahmad M, Darwish H, Mechref Y, Kobeissy F. Glycosylation and other PTMs alterations in neurodegenerative diseases: Current status and future role in neurotrauma. Electrophoresis 2016; 37:1549-61. [PMID: 26957254 PMCID: PMC4962686 DOI: 10.1002/elps.201500585] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 02/28/2016] [Accepted: 02/29/2016] [Indexed: 12/12/2022]
Abstract
Traumatic brain injuries (TBIs) present a chief public health threat affecting nations worldwide. As numbers of patients afflicted by TBI are expected to rise, the necessity to increase our understanding of the pathophysiological mechanism(s) as a result of TBI mounts. TBI is known to augment the risk of developing a number of neurodegenerative diseases (NDs) such as Alzheimer's disease (AD) and Parkinson's disease (PD). Hence, it is rational to assume that a common mechanistic ground links the pathophysiology of NDs to that of TBIs. Through this review, we aim to identify the protein-protein interactions, differential proteins expression, and PTMs, mainly glycosylation, that are involved in the pathogenesis of both ND and TBI. OVID and PubMed have been rigorously searched to identify studies that utilized advanced proteomic platforms (MS based) and systems biology tools to unfold the mechanism(s) behind ND in an attempt to unveil the mysterious biological processes that occur postinjury. Various PTMs have been found to be common between TBI and AD, whereas no similarities have been found between TBI and PD. Phosphorylated tau protein, glycosylated amyloid precursor protein, and many other modifications appear to be common in both TBI and AD. PTMs, differential protein profiles, and altered biological pathways appear to have critical roles in ND processes by interfering with their pathological condition in a manner similar to TBI. Advancement in glycoproteomic studies pertaining to ND and TBI is urgently needed in order to develop better diagnostic tools, therapies, and more favorable prognoses.
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Affiliation(s)
- Hussein Abou-Abbass
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Faculty of Medicine, Beirut Arab University, Beirut, Lebanon
| | | | - Hisham Bahmad
- Faculty of Medicine, Beirut Arab University, Beirut, Lebanon
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Kazem Zibara
- ER045 - Laboratory of Stem Cells, DSST, Lebanese University, Beirut, Lebanon
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Abir Zebian
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Rabab Youssef
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Joy Ismail
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Rui Zhu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Shiyue Zhou
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Xue Dong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Mayse Nasser
- Faculty of Medicine, Beirut Arab University, Beirut, Lebanon
| | - Marwan Bahmad
- Faculty of Medicine, Beirut Arab University, Beirut, Lebanon
| | - Hala Darwish
- Faculty of Medicine-School of Nursing, American University of Beirut, New York, NY, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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Dumitriu A, Golji J, Labadorf AT, Gao B, Beach TG, Myers RH, Longo KA, Latourelle JC. Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease. BMC Med Genomics 2016; 9:5. [PMID: 26793951 PMCID: PMC4722694 DOI: 10.1186/s12920-016-0164-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/30/2015] [Indexed: 12/20/2022] Open
Abstract
Background Parkinson disease (PD) is a neurodegenerative disease characterized by the accumulation of alpha-synuclein (SNCA) and other proteins in aggregates termed “Lewy Bodies” within neurons. PD has both genetic and environmental risk factors, and while processes leading to aberrant protein aggregation are unknown, past work points to abnormal levels of SNCA and other proteins. Although several genome-wide studies have been performed for PD, these have focused on DNA sequence variants by genome-wide association studies (GWAS) and on RNA levels (microarray transcriptomics), while genome-wide proteomics analysis has been lacking. Methods This study employed two state-of-the-art technologies, three-stage Mass Spectrometry Tandem Mass Tag Proteomics (12 PD, 12 controls) and RNA-sequencing transcriptomics (29 PD, 44 controls), evaluated in the context of PD GWAS implicated loci and microarray transcriptomics (19 PD, 24 controls). The technologies applied for this study were performed in a set of overlapping prefrontal cortex (Brodmann area 9) samples obtained from PD patients and sex and age similar neurologically healthy controls. Results After appropriate filters, proteomics robustly identified 3558 unique proteins, with 283 of these (7.9 %) significantly different between PD and controls (q-value < 0.05). RNA-sequencing identified 17,580 protein-coding genes, with 1095 of these (6.2 %) significantly different (FDR p-value < 0.05); only 166 of the FDR significant protein-coding genes (0.94 %) were present among the 3558 proteins characterized. Of these 166, eight genes (4.8 %) were significant in both studies, with the same direction of effect. Functional enrichment analysis of the proteomics results strongly supports mitochondrial-related pathways, while comparable analysis of the RNA-sequencing results implicates protein folding pathways and metallothioneins. Ten of the implicated genes or proteins co-localized to GWAS loci. Evidence implicating SNCA was stronger in proteomics than in RNA-sequencing analyses. Conclusions We report the largest analysis of proteomics in PD to date, and the first to combine this technology with RNA-sequencing to investigate GWAS implicated loci. Notably, differentially expressed protein-coding genes were more likely to not be characterized in the proteomics analysis, which lessens the ability to compare across platforms. Combining multiple genome-wide platforms offers novel insights into the pathological processes responsible for this disease by identifying pathways implicated across methodologies. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0164-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandra Dumitriu
- Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - Javad Golji
- Proteostasis Therapeutics Inc., Cambridge, MA, 02139, USA.
| | - Adam T Labadorf
- Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - Benbo Gao
- Proteostasis Therapeutics Inc., Cambridge, MA, 02139, USA.
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, AZ, 85351, USA.
| | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA. .,Genome Science Institute, Boston University School of Medicine, Boston, MA, 02118, USA.
| | | | - Jeanne C Latourelle
- Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA.
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Jamil A, Mahboob A, Ahmed T. Ibuprofen targets neuronal pentraxins expresion and improves cognitive function in mouse model of AlCl 3-induced neurotoxicity. Exp Ther Med 2015; 11:601-606. [PMID: 26893653 DOI: 10.3892/etm.2015.2928] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 09/01/2015] [Indexed: 11/06/2022] Open
Abstract
Aluminum is known to exert neurotoxic effects associated with various neurodegenerative disorders, including Alzheimer's disease (AD). Ibuprofen is a well-known non-steroidal anti-inflammatory drug, which has demonstrated potential efficacy in the treatment of numerous inflammatory and neurodegenerative disorders, including AD. The present study aimed to investigate the protective effects of ibuprofen on cognitive function, and the expression levels of neuronal pentraxins (NPs) and interleukin (IL)-1β in an aluminum chloride (AlCl3)-induced mouse model of neurotoxicity. The effects of ibuprofen (100 mg/kg/day for 12 days) on learning and memory were evaluated in the AlCl3-induced neurotoxic mice using a Morris water maze and open field tests. In addition, ibuprofen was assessed for its effects on the expression levels of NPs and IL-1β in the hippocampus, cortex and amygdala of the brain. Treatment of the AlCl3-treated mice with ibuprofen decreased anxiety levels (6.90±0.34 min) compared with the AlCl3-treated group (1.80±0.29 min), as indicated by the time spent in the central area in an open field test. Furthermore, the expression levels of NP1 (1.32±0.47) and IL-1β (0.99±0.21) were significantly decreased in the hippocampus of mice following ibuprofen treatment, as compared with the AlCl3-treated mice (8.62±1.54 and 7.47±0.53, respectively). In the present study, ibuprofen was able to target novel structures in order to attenuate the inflammation associated with an AlCl3-induced mouse model of neurotoxicity; thus suggesting that ibuprofen may be considered a potential therapeutic option for the treatment of neurodegenerative diseases, including AD.
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Affiliation(s)
- Anum Jamil
- Neurobiology Laboratory, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Sector H-12, Islamabad 44000, Pakistan
| | - Aamra Mahboob
- Neurobiology Laboratory, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Sector H-12, Islamabad 44000, Pakistan
| | - Touqeer Ahmed
- Neurobiology Laboratory, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Sector H-12, Islamabad 44000, Pakistan
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Soares Bispo Santos Silva D, Antunes J, Balamurugan K, Duncan G, Sampaio Alho C, McCord B. Evaluation of DNA methylation markers and their potential to predict human aging. Electrophoresis 2015; 36:1775-80. [PMID: 26010003 DOI: 10.1002/elps.201500137] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/14/2015] [Accepted: 04/15/2015] [Indexed: 11/11/2022]
Abstract
We present epigenetic methylation data for two genetic loci, GRIA2, and NPTX2, which were tested for prediction of age from different donors of biofluids. We analyzed 44 saliva samples and 23 blood samples from volunteers with ages ranging from 5 to 72 years. DNA was extracted and bisulfite modified using commercial kits. Specific primers were used for amplification and methylation profiles were determined by pyrosequencing. Methylation data from both markers and their relationship with age were determined using linear regression analysis, which indicates a positive correlation between methylation and age. Older individuals tend to have increased methylation in both markers compared to younger individuals and this trend was more pronounced in the GRIA2 locus when compared to NPTX2. The epigenetic predicted age, calculated using a GRIA2 regression analysis model, was strongly correlated to chronological age (R(2) = 0.801), with an average difference of 6.9 years between estimated and observed ages. When using a NPTX2 regression model, we observed a lower correlation between predicted and chronological age (R(2) = 0.654), with an average difference of 9.2 years. These data indicate these loci can be used as a novel tool for age prediction with potential applications in many areas, including clinical and forensic investigations.
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Affiliation(s)
- Deborah Soares Bispo Santos Silva
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA.,Faculty of Biosciences, Laboratory of Human and Molecular Genetics, PUCRS, Porto Alegre, Brazil
| | - Joana Antunes
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | | | - George Duncan
- DNA Laboratory, Broward County Sheriff's Office, Fort Lauderdale, FL, USA
| | - Clarice Sampaio Alho
- Faculty of Biosciences, Laboratory of Human and Molecular Genetics, PUCRS, Porto Alegre, Brazil
| | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
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Gene expression analyses identify Narp contribution in the development of L-DOPA-induced dyskinesia. J Neurosci 2015; 35:96-111. [PMID: 25568106 DOI: 10.1523/jneurosci.5231-13.2015] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
In Parkinson's disease, long-term dopamine replacement therapy is complicated by the appearance of L-DOPA-induced dyskinesia (LID). One major hypothesis is that LID results from an aberrant transcriptional program in striatal neurons induced by L-DOPA and triggered by the activation of ERK. To identify these genes, we performed transcriptome analyses in the striatum in 6-hydroxydopamine-lesioned mice. A time course analysis (0-6 h after treatment with L-DOPA) identified an acute signature of 709 genes, among which genes involved in protein phosphatase activity were overrepresented, suggesting a negative feedback on ERK activation by l-DOPA. l-DOPA-dependent deregulation of 28 genes was blocked by pretreatment with SL327, an inhibitor of ERK activation, and 26 genes were found differentially expressed between highly and weakly dyskinetic animals after treatment with L-DOPA. The intersection list identified five genes: FosB, Th, Nptx2, Nedd4l, and Ccrn4l. Nptx2 encodes neuronal pentraxin II (or neuronal activity-regulated pentraxin, Narp), which is involved in the clustering of glutamate receptors. We confirmed increased Nptx2 expression after L-DOPA and its blockade by SL327 using quantitative RT-PCR in independent experiments. Using an escalating L-DOPA dose protocol, LID severity was decreased in Narp knock-out mice compared with their wild-type littermates or after overexpression of a dominant-negative form of Narp in the striatum. In conclusion, we have identified a molecular signature induced by L-DOPA in the dopamine-denervated striatum that is dependent on ERK and associated with LID. Here, we demonstrate the implication of one of these genes, Nptx2, in the development of LID.
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Filiou MD, Arefin AS, Moscato P, Graeber MB. 'Neuroinflammation' differs categorically from inflammation: transcriptomes of Alzheimer's disease, Parkinson's disease, schizophrenia and inflammatory diseases compared. Neurogenetics 2014; 15:201-12. [PMID: 24928144 DOI: 10.1007/s10048-014-0409-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/02/2014] [Indexed: 12/30/2022]
Abstract
'Neuroinflammation' has become a widely applied term in the basic and clinical neurosciences but there is no generally accepted neuropathological tissue correlate. Inflammation, which is characterized by the presence of perivascular infiltrates of cells of the adaptive immune system, is indeed seen in the central nervous system (CNS) under certain conditions. Authors who refer to microglial activation as neuroinflammation confuse this issue because autoimmune neuroinflammation serves as a synonym for multiple sclerosis, the prototypical inflammatory disease of the CNS. We have asked the question whether a data-driven, unbiased in silico approach may help to clarify the nomenclatorial confusion. Specifically, we have examined whether unsupervised analysis of microarray data obtained from human cerebral cortex of Alzheimer's, Parkinson's and schizophrenia patients would reveal a degree of relatedness between these diseases and recognized inflammatory conditions including multiple sclerosis. Our results using two different data analysis methods provide strong evidence against this hypothesis demonstrating that very different sets of genes are involved. Consequently, the designations inflammation and neuroinflammation are not interchangeable. They represent different categories not only at the histophenotypic but also at the transcriptomic level. Therefore, non-autoimmune neuroinflammation remains a term in need of definition.
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Affiliation(s)
- Michaela D Filiou
- Max Planck Institute of Psychiatry, Kraepelinstraße 2, 80804, Munich, Germany
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Sajjan S, Holsinger RMD, Fok S, Ebrahimkhani S, Rollo JL, Banati RB, Graeber MB. Up-regulation of matrix metallopeptidase 12 in motor neurons undergoing synaptic stripping. Neuroscience 2014; 274:331-40. [PMID: 24907602 DOI: 10.1016/j.neuroscience.2014.05.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 01/07/2023]
Abstract
Axotomy of the rodent facial nerve represents a well-established model of synaptic plasticity. Post-traumatic "synaptic stripping" was originally discovered in this system. We report upregulation of matrix metalloproteinase MMP12 in regenerating motor neurons of the mouse and rat facial nucleus. Matrix metalloproteinases (matrix metallopeptidases, MMPs) are zinc-binding proteases capable of degrading components of the extracellular matrix and of regulating extracellular signaling networks including within synapses. MMP12 protein expression in facial motor neurons was enhanced following axotomy and peaked at day 3 after the operation. The peak of neuronal MMP12 expression preceded the peak of experimentally induced synaptic plasticity. At the same time, MMP12 redistributed intracellularly and became predominantly localized beneath the neuronal somatic cytoplasmic membrane. Both findings point to a role of MMP12 in the neuronal initiation of the synaptic stripping process. MMP12 is the first candidate molecule for such a trigger function and has potential as a therapeutic target. Moreover, since statins have been shown to increase the expression of MMP12, interference with synaptic stability may represent one mechanism by which these widely used drugs exert their side effects on higher CNS functions.
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Affiliation(s)
- S Sajjan
- Brain Tumor Research and Molecular Neuroscience & Neuropathology Laboratories, Brain and Mind Research Institute, Faculty of Medicine and Faculty of Health Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - R M D Holsinger
- Brain Tumor Research and Molecular Neuroscience & Neuropathology Laboratories, Brain and Mind Research Institute, Faculty of Medicine and Faculty of Health Sciences, The University of Sydney, Camperdown, NSW, Australia; Discipline of Biomedical Science, School of Medical Sciences, Sydney Medical School, The University of Sydney, Lidcombe, NSW, Australia
| | - S Fok
- Brain Tumor Research and Molecular Neuroscience & Neuropathology Laboratories, Brain and Mind Research Institute, Faculty of Medicine and Faculty of Health Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - S Ebrahimkhani
- Brain Tumor Research and Molecular Neuroscience & Neuropathology Laboratories, Brain and Mind Research Institute, Faculty of Medicine and Faculty of Health Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - J L Rollo
- Brain Tumor Research and Molecular Neuroscience & Neuropathology Laboratories, Brain and Mind Research Institute, Faculty of Medicine and Faculty of Health Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - R B Banati
- Discipline of Medical Radiation Sciences, Faculty of Health Sciences, The University of Sydney, Cumberland, NSW, Australia; Ramaciotti Imaging Center, Brain and Mind Research Institute, The University of Sydney, Camperdown, NSW, Australia; Australian Nuclear Science and Technology Organization, Lucas Heights, NSW, Australia
| | - M B Graeber
- Brain Tumor Research and Molecular Neuroscience & Neuropathology Laboratories, Brain and Mind Research Institute, Faculty of Medicine and Faculty of Health Sciences, The University of Sydney, Camperdown, NSW, Australia.
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Shukla S, Pia Patric IR, Thinagararjan S, Srinivasan S, Mondal B, Hegde AS, Chandramouli BA, Santosh V, Arivazhagan A, Somasundaram K. A DNA methylation prognostic signature of glioblastoma: identification of NPTX2-PTEN-NF-κB nexus. Cancer Res 2013; 73:6563-73. [PMID: 24078801 DOI: 10.1158/0008-5472.can-13-0298] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Glioblastoma (GBM) is the most common, malignant adult primary tumor with dismal patient survival, yet the molecular determinants of patient survival are poorly characterized. Global methylation profile of GBM samples (our cohort; n = 44) using high-resolution methylation microarrays was carried out. Cox regression analysis identified a 9-gene methylation signature that predicted survival in GBM patients. A risk-score derived from methylation signature predicted survival in univariate analysis in our and The Cancer Genome Atlas (TCGA) cohort. Multivariate analysis identified methylation risk score as an independent survival predictor in TCGA cohort. Methylation risk score stratified the patients into low-risk and high-risk groups with significant survival difference. Network analysis revealed an activated NF-κB pathway association with high-risk group. NF-κB inhibition reversed glioma chemoresistance, and RNA interference studies identified interleukin-6 and intercellular adhesion molecule-1 as key NF-κB targets in imparting chemoresistance. Promoter hypermethylation of neuronal pentraxin II (NPTX2), a risky methylated gene, was confirmed by bisulfite sequencing in GBMs. GBMs and glioma cell lines had low levels of NPTX2 transcripts, which could be reversed upon methylation inhibitor treatment. NPTX2 overexpression induced apoptosis, inhibited proliferation and anchorage-independent growth, and rendered glioma cells chemosensitive. Furthermore, NPTX2 repressed NF-κB activity by inhibiting AKT through a p53-PTEN-dependent pathway, thus explaining the hypermethylation and downregulation of NPTX2 in NF-κB-activated high-risk GBMs. Taken together, a 9-gene methylation signature was identified as an independent GBM prognosticator and could be used for GBM risk stratification. Prosurvival NF-κB pathway activation characterized high-risk patients with poor prognosis, indicating it to be a therapeutic target.
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Affiliation(s)
- Sudhanshu Shukla
- Authors' Affiliations: Department of Microbiology and Cell Biology, Indian Institute of Science; Sri SatyaSai Institute of Higher Medical Sciences; Departments of Neurosurgery and Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India
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Johnson AA, Akman K, Calimport SRG, Wuttke D, Stolzing A, de Magalhães JP. The role of DNA methylation in aging, rejuvenation, and age-related disease. Rejuvenation Res 2013; 15:483-94. [PMID: 23098078 DOI: 10.1089/rej.2012.1324] [Citation(s) in RCA: 232] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
DNA methylation is a major control program that modulates gene expression in a plethora of organisms. Gene silencing through methylation occurs through the activity of DNA methyltransferases, enzymes that transfer a methyl group from S-adenosyl-L-methionine to the carbon 5 position of cytosine. DNA methylation patterns are established by the de novo DNA methyltransferases (DNMTs) DNMT3A and DNMT3B and are subsequently maintained by DNMT1. Aging and age-related diseases include defined changes in 5-methylcytosine content and are generally characterized by genome-wide hypomethylation and promoter-specific hypermethylation. These changes in the epigenetic landscape represent potential disease biomarkers and are thought to contribute to age-related pathologies, such as cancer, osteoarthritis, and neurodegeneration. Some diseases, such as a hereditary form of sensory neuropathy accompanied by dementia, are directly caused by methylomic changes. Epigenetic modifications, however, are reversible and are therefore a prime target for therapeutic intervention. Numerous drugs that specifically target DNMTs are being tested in ongoing clinical trials for a variety of cancers, and data from finished trials demonstrate that some, such as 5-azacytidine, may even be superior to standard care. DNMTs, demethylases, and associated partners are dynamically shaping the methylome and demonstrate great promise with regard to rejuvenation.
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Affiliation(s)
- Adiv A Johnson
- Department of Physiological Sciences, University of Arizona, Tucson, AZ, USA
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Twine NA, Janitz C, Wilkins MR, Janitz M. Sequencing of hippocampal and cerebellar transcriptomes provides new insights into the complexity of gene regulation in the human brain. Neurosci Lett 2013; 541:263-8. [PMID: 23454452 DOI: 10.1016/j.neulet.2013.02.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/13/2013] [Accepted: 02/17/2013] [Indexed: 11/28/2022]
Abstract
The hippocampus and cerebellum represent anatomically and functionally distinct parts of the human brain. The RNA-Seq technique makes it possible to investigate the human transcriptome with unprecedented resolution, allowing identification of differential mRNA splicing and promoter usage on a genome-wide scale. We undertook whole-mRNA sequencing of samples from the human hippocampus and cerebellum. A bioinformatic analysis revealed distinct expression patterns of genes related to the molecular physiology of neurons and glial cells. Upregulated genes in hippocampal tissue included serpin peptidase inhibitor, clade A (SERPINA3), lymphocyte antigen 6 complex, locus H (LY6H) and transthyretin (TTR). In cerebellum, the cerebellin 3 precursor (CLBN3) and Zic family member 4 (ZIC4) genes were significantly upregulated. These changes were validated in independent donor samples by qRT-PCR. The hippocampus and the cerebellum showed striking differences in splicing patterns and promoter usage. A notable example of this was the gene for NGFI-A binding protein 2 (NAB2), which displayed tissue-specific isoforms which may affect its function as a transcriptional repressor.
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Affiliation(s)
- Natalie A Twine
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Postmortem Interval Influences α-Synuclein Expression in Parkinson Disease Brain. PARKINSONS DISEASE 2012; 2012:614212. [PMID: 22530163 PMCID: PMC3317023 DOI: 10.1155/2012/614212] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 12/19/2011] [Indexed: 12/20/2022]
Abstract
Duplications and triplications of the α-synuclein (SNCA) gene increase risk for PD, suggesting increased expression levels of the gene to be associated with increased PD risk. However, past SNCA expression studies in brain tissue report inconsistent results. We examined expression of the full-length SNCA transcript (140 amino acid protein isoform), as well as total SNCA mRNA levels in 165 frontal cortex samples (101 PD, 64 control) using quantitative real-time polymerase chain reaction. Additionally, we evaluated the relationship of eight SNPs in both 5′ and 3′ regions of SNCA with the gene expression levels. The association between postmortem interval (PMI) and SNCA expression was different for PD and control samples: SNCA expression decreased with increasing PMI in cases, while staying relatively constant in controls. For short PMI, SNCA expression was increased in PD relative to control samples, whereas for long PMI, SNCA expression in PD was decreased relative to control samples.
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