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Brandão-Teles C, Antunes ASLM, de Moraes Vrechi TA, Martins-de-Souza D. The Roles of hnRNP Family in the Brain and Brain-Related Disorders. Mol Neurobiol 2024; 61:3578-3595. [PMID: 37999871 DOI: 10.1007/s12035-023-03747-4] [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: 08/31/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023]
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) belong to a complex family of RNA-binding proteins that are essential to control alternative splicing, mRNA trafficking, synaptic plasticity, stress granule formation, cell cycle regulation, and axonal transport. Over the past decade, hnRNPs have been associated with different brain disorders such as Alzheimer's disease, multiple sclerosis, and schizophrenia. Given their essential role in maintaining cell function and integrity, it is not surprising that dysregulated hnRNP levels lead to neurological implications. This review aims to explore the primary functions of hnRNPs in neurons, oligodendrocytes, microglia, and astrocytes, and their roles in brain disorders. We also discuss proteomics and other technologies and their potential for studying and evaluating hnRNPs in brain disorders, including the discovery of new therapeutic targets and possible pharmacological interventions.
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Affiliation(s)
- Caroline Brandão-Teles
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil.
| | - André S L M Antunes
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Talita Aparecida de Moraes Vrechi
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil.
- D'Or Institute for Research and Education (IDOR), São Paulo, Brazil.
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, SP, 13083-862, Brazil.
- INCT in Modelling Human Complex Diseases with 3D Platforms (Model3D), São Paulo, Brazil.
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, Instituto Nacional de Biomarcadores em Neuropsiquiatria, São Paulo, Brazil.
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2
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Varesi A, Campagnoli LIM, Barbieri A, Rossi L, Ricevuti G, Esposito C, Chirumbolo S, Marchesi N, Pascale A. RNA binding proteins in senescence: A potential common linker for age-related diseases? Ageing Res Rev 2023; 88:101958. [PMID: 37211318 DOI: 10.1016/j.arr.2023.101958] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/09/2023] [Accepted: 05/18/2023] [Indexed: 05/23/2023]
Abstract
Aging represents the major risk factor for the onset and/or progression of various disorders including neurodegenerative diseases, metabolic disorders, and bone-related defects. As the average age of the population is predicted to exponentially increase in the coming years, understanding the molecular mechanisms underlying the development of aging-related diseases and the discovery of new therapeutic approaches remain pivotal. Well-reported hallmarks of aging are cellular senescence, genome instability, autophagy impairment, mitochondria dysfunction, dysbiosis, telomere attrition, metabolic dysregulation, epigenetic alterations, low-grade chronic inflammation, stem cell exhaustion, altered cell-to-cell communication and impaired proteostasis. With few exceptions, however, many of the molecular players implicated within these processes as well as their role in disease development remain largely unknown. RNA binding proteins (RBPs) are known to regulate gene expression by dictating at post-transcriptional level the fate of nascent transcripts. Their activity ranges from directing primary mRNA maturation and trafficking to modulation of transcript stability and/or translation. Accumulating evidence has shown that RBPs are emerging as key regulators of aging and aging-related diseases, with the potential to become new diagnostic and therapeutic tools to prevent or delay aging processes. In this review, we summarize the role of RBPs in promoting cellular senescence and we highlight their dysregulation in the pathogenesis and progression of the main aging-related diseases, with the aim of encouraging further investigations that will help to better disclose this novel and captivating molecular scenario.
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Affiliation(s)
- Angelica Varesi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
| | | | - Annalisa Barbieri
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy
| | - Lorenzo Rossi
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | | | - Ciro Esposito
- Department of Internal Medicine and Therapeutics, University of Pavia, Italy; Nephrology and dialysis unit, ICS S. Maugeri SPA SB Hospital, Pavia, Italy; High School in Geriatrics, University of Pavia, Italy
| | | | - Nicoletta Marchesi
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy
| | - Alessia Pascale
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy.
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3
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Xia T, Yang C, Wang X, Bai L, Ma J, Zhao M, Hua W, Wang H. Heterogeneous nuclear ribonucleoprotein A2/B1 as a novel biomarker in elderly patients for the prediction of postoperative neurocognitive dysfunction: A prospective nested case-control study. Front Aging Neurosci 2022; 14:1034041. [PMID: 36337695 PMCID: PMC9634074 DOI: 10.3389/fnagi.2022.1034041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background and objective Postoperative neurocognitive dysfunction (PND) occurs in up to 54% of older patients, giving rise to the heavy psychological and economic burdens to patients and society. To date, the development of PND biomarkers remains a challenge. Heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNPA2/B1) is an RNA-binding protein whose prion-like structure is prone to mutation and hence leads to neurodegenerative diseases, but its expression changes in PND remains unclear. Here, we detect the preoperative hnRNPA2/B1 level in patients with PND, and to explore its value in the prediction and diagnosis of PND. Methods The study included 161 elderly patients undergoing lumbar decompression and fusion in Nankai University Affinity the Third Central Hospital from September 2021 to July 2022. Neuropsychological and psychometric evaluations were performed before surgery, 1 week and 3 months after surgery to diagnose the occurrence of PND, then the peripheral blood was collected from patients before induction of anesthesia. The concentration in plasma of hnRNPA2/B1 and amyloid-β 42 were determined by enzyme-linked immunosorbent assay. The median fluorescence intensity and mRNA levels of hnRNPA2/B1 in peripheral blood mononuclear cells was detected by indirect intracellular staining flow cytometry and quantitative real-time PCR, respectively. Results The preoperative hnRNPA2/B1 level in patients with PND was higher both in short-time and long-time follow-up. We found significantly higher concentrations of hnRNPA2/B1 in PND at 7 days after surgery (median, 72.26 pg/mL vs. 54.95 pg/mL, p = 0.022) compared with patients without PND, and so as 3 months after surgery (median, 102.93 pg/mL vs. 56.38 pg/mL, p = 0.012). The area under the curve (AUC) was predicted to be 0.686 at 7 days after surgery and 0.735 at 3 months. In addition, when combining several clinical information, the diagnostic efficiency of hnRNPA2/B1 for PND could further increase (AUC, 0.707 at 7 days, 0.808 at 3 months). Conclusion Based on the findings reported here, hnRNPA2/B1 may serve as a new and powerful predictive biomarker to identify elderly patients with PND.
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Affiliation(s)
- Tong Xia
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin, China
| | - Chenyi Yang
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin, China
- Department of Anesthesiology, Nankai University Affinity the Third Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
- Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Xinyi Wang
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin, China
- Department of Anesthesiology, Nankai University Affinity the Third Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
- Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Lili Bai
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin, China
| | - Ji Ma
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin, China
- Department of Anesthesiology, Nankai University Affinity the Third Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
- Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Mingshu Zhao
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin, China
- Department of Anesthesiology, Nankai University Affinity the Third Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
- Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Wei Hua
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin, China
- Department of Anesthesiology, Nankai University Affinity the Third Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
- Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Haiyun Wang
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin, China
- Department of Anesthesiology, Nankai University Affinity the Third Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
- Tianjin Institute of Hepatobiliary Disease, Tianjin, China
- *Correspondence: Haiyun Wang,
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4
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Low YH, Asi Y, Foti SC, Lashley T. Heterogeneous Nuclear Ribonucleoproteins: Implications in Neurological Diseases. Mol Neurobiol 2021; 58:631-646. [PMID: 33000450 PMCID: PMC7843550 DOI: 10.1007/s12035-020-02137-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022]
Abstract
Heterogenous nuclear ribonucleoproteins (hnRNPs) are a complex and functionally diverse family of RNA binding proteins with multifarious roles. They are involved, directly or indirectly, in alternative splicing, transcriptional and translational regulation, stress granule formation, cell cycle regulation, and axonal transport. It is unsurprising, given their heavy involvement in maintaining functional integrity of the cell, that their dysfunction has neurological implications. However, compared to their more established roles in cancer, the evidence of hnRNP implication in neurological diseases is still in its infancy. This review aims to consolidate the evidences for hnRNP involvement in neurological diseases, with a focus on spinal muscular atrophy (SMA), Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), multiple sclerosis (MS), congenital myasthenic syndrome (CMS), and fragile X-associated tremor/ataxia syndrome (FXTAS). Understanding more about hnRNP involvement in neurological diseases can further elucidate the pathomechanisms involved in these diseases and perhaps guide future therapeutic advances.
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Affiliation(s)
- Yi-Hua Low
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- Duke-NUS Medical School, Singapore, Singapore
| | - Yasmine Asi
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Sandrine C Foti
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Tammaryn Lashley
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK.
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Ma Y, Yang L, Li R. HnRNPA2/B1 Is a Novel Prognostic Biomarker for Breast Cancer Patients. Genet Test Mol Biomarkers 2020; 24:701-707. [PMID: 32985904 DOI: 10.1089/gtmb.2020.0086] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aims: Heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNPA2/B1) is highly expressed in multiple types of tumor tissues and could potentially be used as a biomarker for the early detection of lung cancer. However, there is little evidence supporting its clinical significance as a prognostic marker in breast cancer. Materials and Methods: We retrospectively analyzed the protein expression and localization of hnRNPA2/B1 protein in breast cancer tissues and adjacent normal tissues from 50 patients with Stage II and III breast cancer who were treated at Shanxi Provincial People's Hospital from May 2018 to May 2019 using western blot, and immunofluorescent and immunohistochemical staining assays. In addition, bioinformatic analyses using the Affymetrix Human Genome database were performed to examine the mRNA levels of hnRNPA2/B1 in normal and breast cancer tissues, and to determine their correlation with the survival rates of breast cancer patients. Results: Based on the cohort of 50 patients, HnRNPA2/B1 protein was expressed in both the cytoplasm and nucleus of breast cancer cells. The protein levels of hnRNPA2/B1 in breast cancer tissues were significantly higher than those in adjacent normal tissues (p < 0.001). Furthermore, bioinformatic analyses of hnRNPA2/B1 mRNA expression levels demonstrated that they were negatively correlated with overall survival and disease-specific survival rates in breast cancer patients. Conclusion: Our study indicates that hnRNPA2/B1 could serve as a novel prognostic biomarker for breast cancer.
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Affiliation(s)
- Yuehong Ma
- Department of Nephrology, The Affiliated People's Hospital of Shanxi Medical University, Shanxi Precision Medicine Center, Shanxi Provincial People's Hospital, Taiyuan, P.R. China
| | - Lizhu Yang
- Department of Pathology, The Affiliated People's Hospital of Shanxi Medical University, Shanxi Provincial People's Hospital, Taiyuan, P.R. China
| | - Rongshan Li
- Department of Nephrology, The Affiliated People's Hospital of Shanxi Medical University, Shanxi Precision Medicine Center, Shanxi Provincial People's Hospital, Taiyuan, P.R. China
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6
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Liu Y, Shi SL. The roles of hnRNP A2/B1 in RNA biology and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1612. [PMID: 32588964 DOI: 10.1002/wrna.1612] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022]
Abstract
The RNA-binding protein hnRNPA2/B1 is a member of the hnRNPs family and is widely expressed in various tissues. hnRNPA2/B1 recognizes and binds specific RNA substrates and DNA motifs and is involved in the transcription, splicing processing, transport, stability, and translation regulation of a variety of RNA molecules and in regulating the expression of a large number of genes. hnRNPA2/B1 is also involved in telomere maintenance and DNA repair, while its expression changes and mutations are involved in the development of various tumors and neurodegenerative and autoimmune diseases. This paper reviews the role and mechanism of hnRNPA2/B1 in RNA metabolism, tumors, and neurodegenerative and autoimmune diseases. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Yu Liu
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, China.,School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Song-Lin Shi
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, China
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7
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Sackmann C, Hallbeck M. Oligomeric amyloid-β induces early and widespread changes to the proteome in human iPSC-derived neurons. Sci Rep 2020; 10:6538. [PMID: 32300132 PMCID: PMC7162932 DOI: 10.1038/s41598-020-63398-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/23/2020] [Indexed: 01/05/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia globally and is characterized by aberrant accumulations of amyloid-beta (Aβ) and tau proteins. Oligomeric forms of these proteins are believed to be most relevant to disease progression, with oligomeric amyloid-β (oAβ) particularly implicated in AD. oAβ pathology spreads among interconnected brain regions, but how oAβ induces pathology in these previously unaffected neurons requires further study. Here, we use well characterized iPSC-derived human neurons to study the early changes to the proteome and phosphoproteome after 24 h exposure to oAβ 1-42. Using nLC-MS/MS and label-free quantification, we identified several proteins that are differentially regulated in response to acute oAβ challenge. At this early timepoint, oAβ induced the decrease of TDP-43, heterogeneous nuclear ribonucleoproteins (hnRNPs), and coatomer complex I (COPI) proteins. Conversely, increases were observed in 20 S proteasome subunits and vesicle associated proteins VAMP1/2, as well as the differential phosphorylation of tau at serine 208. These changes show that there are widespread alterations to the neuronal proteome within 24 h of oAβ uptake, including proteins previously not shown to be related to neurodegeneration. This study provides new targets for the further study of early mediators of AD pathogenesis.
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Affiliation(s)
- Christopher Sackmann
- Department of Clinical Pathology and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Martin Hallbeck
- Department of Clinical Pathology and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
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8
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Wang J, Yang C, Wang H, Li D, Li T, Sun Y, Zhao M, Ma J, Hua W, Yang Z. A New Rat Model of Chronic Cerebral Hypoperfusion Resulting in Early-Stage Vascular Cognitive Impairment. Front Aging Neurosci 2020; 12:86. [PMID: 32351379 PMCID: PMC7174718 DOI: 10.3389/fnagi.2020.00086] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/12/2020] [Indexed: 12/12/2022] Open
Abstract
Objective Currently, most models of vascular cognitive impairment are established by occluding the carotid arteries uni- or bilaterally to reduce the cerebral blood flow mimicking chronic cerebral hypoxia. Due to the sudden blood flow interruption, a gradual narrowing of the carotid artery cannot be completely imitated. This paper aims to establish a bilateral carotid stenosis model with mild cognitive dysfunction and mild white matter changes to simulate patients with vascular predementia. Methods Aged Wistar rats (18 months old) underwent either bilateral common carotid artery stenosis (BCAS) or occlusion (BCAO) surgery or a sham operation (control group). The cerebral blood flow in the frontal cortex was measured using Doppler flowmetry. Thirty days after surgery, cognitive function impairments were determined with the Morris water maze; cerebral magnetic resonance imaging was performed to detect changes in fractional anisotropy to assess white matter injuries, and histological studies were performed. Results The aged rats in the BCAS group showed a more gradual cerebral blood flow reduction and a lower mortality rate (11%) compared to rats in the BCAO group. The water maze test revealed a more marginal impairment affecting spatial learning and memory in rats with BCAS than in rats with BCAO. Diffusion tensor imaging detected white matter injuries in the hippocampus and cerebral cortex of BCAS rats. Particularly, a small portion of nerve fibers of the lateral somatosensory cortex was significantly different between rats of the BCAO and BCAS groups. In the BCAS group, the microscopic structure of the hippocampal CA1 region changed slightly after 30 days and sustained a slight mitochondrial crista crack. Fluorescence staining indicated that the number of GFAP-positive cells was increased in rat brains of the BCAS group, and this phenomenon was even more pronounced in the BCAO group. The hnRNPA2/B1 and GABAAR-α1 expression levels were significantly decreased in the hippocampus of rats with BCAS compared to those of controls. Conclusion Severe bilateral carotid stenosis induced mild cognitive dysfunction and slight structural changes in the brains of aged rats. Thus, a chronic cerebral hypoperfusion model was successfully established.
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Affiliation(s)
- Jinxin Wang
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin Third Central Hospital, Nankai University Affinity the Third Central Hospital, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
| | - Chenyi Yang
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin Third Central Hospital, Nankai University Affinity the Third Central Hospital, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
| | - Haiyun Wang
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin Third Central Hospital, Nankai University Affinity the Third Central Hospital, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China.,Medical College of Nankai University, Nankai University, Tianjin, China.,Tianjin Research Institute of Anesthesiology, Tianjin, China
| | - Dongxue Li
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin Third Central Hospital, Nankai University Affinity the Third Central Hospital, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
| | - Tang Li
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin Third Central Hospital, Nankai University Affinity the Third Central Hospital, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
| | - Yi Sun
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin Third Central Hospital, Nankai University Affinity the Third Central Hospital, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
| | - Mingshu Zhao
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin Third Central Hospital, Nankai University Affinity the Third Central Hospital, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
| | - Ji Ma
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin Third Central Hospital, Nankai University Affinity the Third Central Hospital, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
| | - Wei Hua
- Department of Anesthesiology, The Third Central Clinical College of Tianjin Medical University, Tianjin Third Central Hospital, Nankai University Affinity the Third Central Hospital, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
| | - Zhuo Yang
- Medical College of Nankai University, Nankai University, Tianjin, China
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9
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Cruz-Rivera YE, Perez-Morales J, Santiago YM, Gonzalez VM, Morales L, Cabrera-Rios M, Isaza CE. A Selection of Important Genes and Their Correlated Behavior in Alzheimer's Disease. J Alzheimers Dis 2019; 65:193-205. [PMID: 30040709 PMCID: PMC6087431 DOI: 10.3233/jad-170799] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In 2017, approximately 5 million Americans were living with Alzheimer’s disease (AD), and it is estimated that by 2050 this number could increase to 16 million. In this study, we apply mathematical optimization to approach microarray analysis to detect differentially expressed genes and determine the most correlated structure among their expression changes. The analysis of GSE4757 microarray dataset, which compares expression between AD neurons without neurofibrillary tangles (controls) and with neurofibrillary tangles (cases), was casted as a multiple criteria optimization (MCO) problem. Through the analysis it was possible to determine a series of Pareto efficient frontiers to find the most differentially expressed genes, which are here proposed as potential AD biomarkers. The Traveling Sales Problem (TSP) model was used to find the cyclical path of maximal correlation between the expression changes among the genes deemed important from the previous stage. This leads to a structure capable of guiding biological exploration with enhanced precision and repeatability. Ten genes were selected (FTL, GFAP, HNRNPA3, COX1, ND2, ND3, ND4, NUCKS1, RPL41, and RPS10) and their most correlated cyclic structure was found in our analyses. The biological functions of their products were found to be linked to inflammation and neurodegenerative diseases and some of them had not been reported for AD before. The TSP path connects genes coding for mitochondrial electron transfer proteins. Some of these proteins are closely related to other electron transport proteins already reported as important for AD.
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Affiliation(s)
- Yazeli E Cruz-Rivera
- The Applied Optimization Group/Department of Industrial Engineering, University of Puerto Rico, Mayagüez Campus, Mayagüez, Puerto Rico
| | - Jaileene Perez-Morales
- Department of Basic Science-Biochemistry Division, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Yaritza M Santiago
- The Applied Optimization Group/Department of Industrial Engineering, University of Puerto Rico, Mayagüez Campus, Mayagüez, Puerto Rico
| | - Valerie M Gonzalez
- The Applied Optimization Group/Department of Industrial Engineering, University of Puerto Rico, Mayagüez Campus, Mayagüez, Puerto Rico
| | - Luisa Morales
- Public Health Program, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Mauricio Cabrera-Rios
- The Applied Optimization Group/Department of Industrial Engineering, University of Puerto Rico, Mayagüez Campus, Mayagüez, Puerto Rico
| | - Clara E Isaza
- The Applied Optimization Group/Department of Industrial Engineering, University of Puerto Rico, Mayagüez Campus, Mayagüez, Puerto Rico.,Public Health Program, Ponce Health Sciences University, Ponce, Puerto Rico
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10
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Barton SK, Gregory JM, Chandran S, Turner BJ. Could an Impairment in Local Translation of mRNAs in Glia be Contributing to Pathogenesis in ALS? Front Mol Neurosci 2019; 12:124. [PMID: 31164803 PMCID: PMC6536688 DOI: 10.3389/fnmol.2019.00124] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/26/2019] [Indexed: 12/13/2022] Open
Abstract
One of the key pathways implicated in amyotrophic lateral sclerosis (ALS) pathogenesis is abnormal RNA processing. Studies to date have focussed on defects in RNA stability, splicing, and translation, but this review article will focus on the largely overlooked RNA processing mechanism of RNA trafficking, with particular emphasis on the importance of glia. In the central nervous system (CNS), oligodendrocytes can extend processes to myelinate and metabolically support up to 50 axons and astrocytes can extend processes to cover up to 100,000 synapses, all with differing local functional requirements. Furthermore, many of the proteins required in these processes are large, aggregation-prone proteins which would be difficult to transport in their fully translated, terminally-folded state. This, therefore, highlights a critical requirement in these cells for local control of protein translation, which is achieved through specific trafficking of mRNAs to each process and local translation therein. Given that a large number of RNA-binding proteins have been implicated in ALS, and RNA-binding proteins are essential for trafficking mRNAs from the nucleus to glial processes for local translation, RNA misprocessing in glial cells is a likely source of cellular dysfunction in ALS. To date, neurons have been the focus of ALS research, but an intrinsic deficit in glia, namely astrocytes and oligodendrocytes, could have an additive effect on declining neuronal function in ALS. This review article aims to highlight the key evidence that supports the contention that RNA trafficking deficits in astrocytes and oligodendrocytes may contribute to in ALS.
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Affiliation(s)
- Samantha K Barton
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jenna M Gregory
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,UK Dementia Research Institute at University of Edinburgh, Edinburgh, United Kingdom
| | - Siddharthan Chandran
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,UK Dementia Research Institute at University of Edinburgh, Edinburgh, United Kingdom
| | - Bradley J Turner
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
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Dong Z, Yang T, Yang Y, Dou H, Chen G. DjhnRNPA2/B1-like gene is required for planarian regeneration and tissue homeostasis. Gene 2017; 633:9-16. [DOI: 10.1016/j.gene.2017.08.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/18/2017] [Accepted: 08/23/2017] [Indexed: 12/25/2022]
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12
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Kim C, Kang D, Lee EK, Lee JS. Long Noncoding RNAs and RNA-Binding Proteins in Oxidative Stress, Cellular Senescence, and Age-Related Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:2062384. [PMID: 28811863 PMCID: PMC5547732 DOI: 10.1155/2017/2062384] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/27/2017] [Accepted: 06/06/2017] [Indexed: 12/12/2022]
Abstract
Cellular senescence is a complex biological process that leads to irreversible cell-cycle arrest. Various extrinsic and intrinsic insults are associated with the onset of cellular senescence and frequently accompany genomic or epigenomic alterations. Cellular senescence is believed to contribute to tumor suppression, immune response, and tissue repair as well as aging and age-related diseases. Long noncoding RNAs (lncRNAs) are >200 nucleotides long, poorly conserved, and transcribed in a manner similar to that of mRNAs. They are tightly regulated during various cellular and physiological processes. Although many lncRNAs and their functional roles are still undescribed, the importance of lncRNAs in a variety of biological processes is widely recognized. RNA-binding proteins (RBPs) have a pivotal role in posttranscriptional regulation as well as in mRNA transport, storage, turnover, and translation. RBPs interact with mRNAs, other RBPs, and noncoding RNAs (ncRNAs) including lncRNAs, and they are involved in the regulation of a broad spectrum of cellular processes. Like other cell fate regulators, lncRNAs and RBPs, separately or cooperatively, are implicated in initiation and maintenance of cellular senescence, aging, and age-related diseases. Here, we review the current understanding of both lncRNAs and RBPs and their association with oxidative stress, senescence, and age-related diseases.
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Affiliation(s)
- Chongtae Kim
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul 06591, Republic of Korea
| | - Donghee Kang
- Department of Molecular Medicine and Hypoxia-Related Disease Research Center, Inha University College of Medicine, Incheon 22212, Republic of Korea
| | - Eun Kyung Lee
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul 06591, Republic of Korea
| | - Jae-Seon Lee
- Department of Molecular Medicine and Hypoxia-Related Disease Research Center, Inha University College of Medicine, Incheon 22212, Republic of Korea
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13
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Moncini S, Lunghi M, Valmadre A, Grasso M, Del Vescovo V, Riva P, Denti MA, Venturin M. The miR-15/107 Family of microRNA Genes Regulates CDK5R1/p35 with Implications for Alzheimer's Disease Pathogenesis. Mol Neurobiol 2016; 54:4329-4342. [PMID: 27343180 DOI: 10.1007/s12035-016-0002-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 06/14/2016] [Indexed: 02/06/2023]
Abstract
Cyclin-dependent kinase 5 regulatory subunit 1 (CDK5R1) encodes p35, the main activatory subunit of cyclin-dependent kinase 5 (CDK5). The p35/CDK5 active complex plays a fundamental role in brain development and functioning, but its deregulated activity has also been implicated in various neurodegenerative disorders, including Alzheimer's disease (AD). CDK5R1 displays a large and highly evolutionarily conserved 3'-untranslated region (3'-UTR), a fact that has suggested a role for this region in the post-transcriptional control of CDK5R1 expression. Our group has recently demonstrated that two miRNAs, miR-103 and miR-107, regulate CDK5R1 expression and affect the levels of p35. MiR-103 and miR-107 belong to the miR-15/107 family, a group of evolutionarily conserved miRNAs highly expressed in human cerebral cortex. In this work, we tested the hypothesis that other members of this group of miRNAs, in addition to miR-103 and miR-107, were able to modulate CDK5R1 expression. We provide evidence that several miRNAs belonging to the miR-15/107 family regulate p35 levels. BACE1 expression levels were also found to be modulated by different members of this family. Furthermore, overexpression of these miRNAs led to reduced APP phosphorylation levels at the CDK5-specific Thr668 residue. We also show that miR-15/107 miRNAs display reduced expression levels in hippocampus and temporal cortex, but not in cerebellum, of AD brains. Moreover, increased CDK5R1 mRNA levels were observed in AD hippocampus tissues. Our results suggest that the downregulation of the miR-15/107 family might have a role in the pathogenesis of AD by increasing the levels of CDK5R1/p35 and consequently enhancing CDK5 activity.
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Affiliation(s)
- Silvia Moncini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Viotti 3/5, 20133, Milan, Italy
| | - Marta Lunghi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Viotti 3/5, 20133, Milan, Italy
| | - Alice Valmadre
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Viotti 3/5, 20133, Milan, Italy
| | - Margherita Grasso
- Centre for Integrative Biology, Università degli Studi di Trento, Via Sommarive 9, 38123, Povo, (TN), Italy
| | - Valerio Del Vescovo
- Centre for Integrative Biology, Università degli Studi di Trento, Via Sommarive 9, 38123, Povo, (TN), Italy
| | - Paola Riva
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Viotti 3/5, 20133, Milan, Italy
| | - Michela Alessandra Denti
- Centre for Integrative Biology, Università degli Studi di Trento, Via Sommarive 9, 38123, Povo, (TN), Italy.,Istituto di Neuroscienze, CNR, Viale Giuseppe Colombo 3, 35121, Padova, Italy
| | - Marco Venturin
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Viotti 3/5, 20133, Milan, Italy.
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14
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Liu XY, Li HL, Su JB, Ding FH, Zhao JJ, Chai F, Li YX, Cui SC, Sun FY, Wu ZY, Xu P, Chen XH. Regulation of RAGE splicing by hnRNP A1 and Tra2β-1 and its potential role in AD pathogenesis. J Neurochem 2015; 133:187-98. [PMID: 25689357 DOI: 10.1111/jnc.13069] [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: 08/29/2014] [Revised: 02/01/2015] [Accepted: 02/09/2015] [Indexed: 11/29/2022]
Abstract
The receptor for advanced glycation end products (RAGE) gene expresses two major alternative splicing isoforms, full-length membrane-bound RAGE (mRAGE) and secretory RAGE (esRAGE). Both isoforms play important roles in Alzheimer's disease (AD) pathogenesis, either via interaction of mRAGE with β-amyloid peptide (Aβ) or inhibition of the mRAGE-activated signaling pathway. In the present study, we showed that heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and Transformer2β-1 (Tra2β-1) were involved in the alternative splicing of mRAGE and esRAGE. Functionally, two factors had an antagonistic effect on the regulation. Glucose deprivation induced an increased ratio of mRAGE/esRAGE via up-regulation of hnRNP A1 and down-regulation of Tra2β-1. Moreover, the ratios of mRAGE/esRAGE and hnRNP A1/Tra2β-1 were increased in peripheral blood mononuclear cells from AD patients. The results provide a molecular basis for altered splicing of mRAGE and esRAGE in AD pathogenesis. The receptor for advanced glycation end products (RAGE) gene expresses two major alternative splicing isoforms, membrane-bound RAGE (mRAGE) and secretory RAGE (esRAGE). Both isoforms play important roles in Alzheimer's disease (AD) pathogenesis. Mechanism for imbalanced expression of these two isoforms in AD brain remains elusive. We proposed here a hypothetic model to illustrate that impaired glucose metabolism in AD brain may increase the expression of splicing protein hnRNP A1 and reduce Tra2β-1, which cause the imbalanced expression of mRAGE and esRAGE.
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Affiliation(s)
- Xiao-Yan Liu
- Department of Neurobiology, Laboratory of Genomic Physiology, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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15
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Zuccotti P, Colombrita C, Moncini S, Barbieri A, Lunghi M, Gelfi C, De Palma S, Nicolin A, Ratti A, Venturin M, Riva P. hnRNPA2/B1 and nELAV proteins bind to a specific U-rich element in CDK5R1 3'-UTR and oppositely regulate its expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:506-16. [PMID: 24792867 DOI: 10.1016/j.bbagrm.2014.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 04/09/2014] [Accepted: 04/23/2014] [Indexed: 01/27/2023]
Abstract
Cyclin-dependent kinase 5 regulatory subunit 1 (CDK5R1) encodes p35, a specific activator of cyclin-dependent kinase 5 (CDK5). CDK5 and p35 have a fundamental role in neuronal migration and differentiation during CNS development. Both the CDK5R1 3'-UTR's remarkable size and its conservation during evolution strongly indicate an important role in post-transcriptional regulation. We previously validated different regulatory elements in the 3'-UTR of CDK5R1, which affect transcript stability, p35 levels and cellular migration through the binding with nELAV proteins and miR-103/7 miRNAs. Interestingly, a 138 bp-long region, named C2.1, was identified as the most mRNA destabilizing portion within CDK5R1 3'-UTR. This feature was maintained by a shorter region of 73 bp, characterized by two poly-U stretches. UV-CL experiments showed that this region interacts with protein factors. UV-CLIP assays and pull-down experiments followed by mass spectrometry analysis demonstrated that nELAV and hnRNPA2/B1 proteins bind to the same U-rich element. These RNA-binding proteins (RBPs) were shown to oppositely control CDK5R1 mRNA stability and p35 protein content at post-trascriptional level. While nELAV proteins have a positive regulatory effect, hnRNPA2/B1 has a negative action that is responsible for the mRNA destabilizing activity both of the C2.1 region and of the full-length 3'-UTR. In co-expression experiments of hnRNPA2/B1 and nELAV RBPs we observed an overall decrease of p35 content. We also demonstrated that hnRNPA2/B1 can downregulate nELAV protein content but not vice versa. This study, by providing new insights on the combined action of different regulatory factors, contributes to clarify the complex post-transcriptional control of CDK5R1 gene expression.
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Affiliation(s)
- Paola Zuccotti
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Claudia Colombrita
- Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, Università degli Studi di Milano, Milan, Italy; IRCCS Istituto Auxologico Italiano, Cusano, Milan, Italy
| | - Silvia Moncini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Andrea Barbieri
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Marta Lunghi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Cecilia Gelfi
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan, Italy; IBFM-CNR, Segrate, Milan, Italy
| | - Sara De Palma
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan, Italy; IBFM-CNR, Segrate, Milan, Italy
| | - Angelo Nicolin
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Antonia Ratti
- Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, Università degli Studi di Milano, Milan, Italy; IRCCS Istituto Auxologico Italiano, Cusano, Milan, Italy
| | - Marco Venturin
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy.
| | - Paola Riva
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy.
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16
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Grabrucker S, Proepper C, Mangus K, Eckert M, Chhabra R, Schmeisser MJ, Boeckers TM, Grabrucker AM. The PSD protein ProSAP2/Shank3 displays synapto-nuclear shuttling which is deregulated in a schizophrenia-associated mutation. Exp Neurol 2013; 253:126-37. [PMID: 24382453 DOI: 10.1016/j.expneurol.2013.12.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 12/12/2013] [Accepted: 12/20/2013] [Indexed: 12/11/2022]
Abstract
Recently, mutations in ProSAP2/Shank3 have been discovered as one of the genetic factors for schizophrenia (SCZ). Here, we show that the postsynaptic density protein ProSAP2/Shank3 undergoes activity dependent synapse-to-nucleus shuttling in hippocampal neurons. Our study shows that the de novo mutation (R1117X) in ProSAP2/Shank3 that was identified in a patient with SCZ leads to an accumulation of mutated ProSAP2/Shank3 within the nucleus independent of synaptic activity. Furthermore, we identified novel nuclear ProSAP2/Shank3 interaction partners. Nuclear localization of mutated ProSAP2/Shank3 alters transcription of several genes, among them already identified genetic risk factors for SCZ such as Synaptotagmin 1 and LRRTM1. Comparing the SCZ mutation of ProSAP2/Shank3 to the knockdown of ProSAP2/Shank3 we found some shared features such as reduced synaptic density in neuronal cultures. However, hippocampal neurons expressing the ProSAP2/Shank3 SCZ mutation furthermore show altered E/I ratio and reduced dendritic branching. Thus, we conclude that the uncoupling of ProSAP2/Shank3 nuclear shuttling from synaptic activity may represent a molecular mechanism that contributes to the pathology of SCZ in patients with mutations in ProSAP2/Shank3.
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Affiliation(s)
- Stefanie Grabrucker
- WG Molecular Analysis of Synaptopathies, Neurology Dept., Neurocenter of Ulm University, Albert-Einstein Allee 11, 89081 Ulm, Germany; Institute for Anatomy and Cell Biology, Ulm University, Albert-Einstein Allee 11, 89081 Ulm, Germany
| | - Christian Proepper
- Institute for Anatomy and Cell Biology, Ulm University, Albert-Einstein Allee 11, 89081 Ulm, Germany
| | - Katharina Mangus
- WG Molecular Analysis of Synaptopathies, Neurology Dept., Neurocenter of Ulm University, Albert-Einstein Allee 11, 89081 Ulm, Germany
| | - Matti Eckert
- WG Molecular Analysis of Synaptopathies, Neurology Dept., Neurocenter of Ulm University, Albert-Einstein Allee 11, 89081 Ulm, Germany
| | - Resham Chhabra
- WG Molecular Analysis of Synaptopathies, Neurology Dept., Neurocenter of Ulm University, Albert-Einstein Allee 11, 89081 Ulm, Germany
| | - Michael J Schmeisser
- Institute for Anatomy and Cell Biology, Ulm University, Albert-Einstein Allee 11, 89081 Ulm, Germany
| | - Tobias M Boeckers
- Institute for Anatomy and Cell Biology, Ulm University, Albert-Einstein Allee 11, 89081 Ulm, Germany
| | - Andreas M Grabrucker
- WG Molecular Analysis of Synaptopathies, Neurology Dept., Neurocenter of Ulm University, Albert-Einstein Allee 11, 89081 Ulm, Germany; Institute for Anatomy and Cell Biology, Ulm University, Albert-Einstein Allee 11, 89081 Ulm, Germany.
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17
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Barthéléry M, Jaishankar A, Salli U, Freeman WM, Vrana KE. 2-D DIGE identification of differentially expressed heterogeneous nuclear ribonucleoproteins and transcription factors during neural differentiation of human embryonic stem cells. Proteomics Clin Appl 2012; 3:505-14. [PMID: 21136975 DOI: 10.1002/prca.200800109] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Neural stem cells (NSC) are progenitors that can give rise to all neural lineages. They are found in specific niches of fetal and adult brains and grow in vitro as non-adherent colonies, the neurospheres. These cells express the intermediate filament nestin, commonly considered an NSC marker. NSC can be derived as neurospheres from human embryonic stem cells (hESC). The mechanisms of cellular programming that hESC undergo during differentiation remain obscure. To investigate the commitment process of hESC during directed neural differentiation, we compared the nuclear proteomes of hESC and hESC-derived neurospheres. We used 2-D DIGE to conduct a quantitative comparison of hESC and NSC nuclear proteins and detected 1521 protein spots matched across three gels. Statistical analysis (ANOVA n = 3 with false discovery correction) revealed that only 2.1% of the densitometric signal was significantly changed. The ranges of average ratios varied from 1.2- to 11-fold at a statistically significant p-value <0.05. MS/MS identified 15 regulated proteins previously shown to be involved in chromatin remodeling, mRNA processing and gene expression regulation. Notably, three members of the heterogeneous nuclear ribonucleoprotein family (AUF-1, and FBP-1 and FBP-2) register a 54, 70 and 99% increased expression, highlighting them as potential markers for NSC in vitro derivation. By contrast, Cpsf-6 virtually disappears with differentiation with an 11-fold drop in NSC, highlighting this protein as a novel marker for undifferentiated ESC.
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Affiliation(s)
- Miguel Barthéléry
- Pennsylvania State University College of Medicine, Department of Pharmacology, Hummelstown, PA, USA
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18
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Brazão TF, Demmers J, van IJcken W, Strouboulis J, Fornerod M, Romão L, Grosveld FG. A new function of ROD1 in nonsense-mediated mRNA decay. FEBS Lett 2012; 586:1101-10. [PMID: 22575643 DOI: 10.1016/j.febslet.2012.03.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 03/06/2012] [Accepted: 03/06/2012] [Indexed: 10/28/2022]
Abstract
RNA-binding proteins play a crucial role in the post-transcriptional regulation of gene expression. Polypyrimidine tract binding protein (PTB in humans) has been extensively characterized as an important splicing factor, and has additional functions in 3' end processing and translation. ROD1 is a PTB paralog containing four RRM (RNA recognition motif) domains. Here, we discover a function of ROD1 in nonsense-mediated mRNA decay (NMD). We show that ROD1 and the core NMD factor UPF1 interact and co-regulate an extensive number of target genes. Using a reporter system, we demonstrate that ROD1, similarly to UPF1 and UPF2, is required for the destabilization of a known NMD substrate. Finally, we show through RIP-seq that ROD1 and UPF1 associate with a significant number of common transcripts.
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Affiliation(s)
- T F Brazão
- Department of Cell Biology & Genetics, Erasmus MC, Rotterdam, The Netherlands.
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19
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Abstract
The hnRNPs (heterogeneous nuclear ribonucleoproteins) are RNA-binding proteins with important roles in multiple aspects of nucleic acid metabolism, including the packaging of nascent transcripts, alternative splicing and translational regulation. Although they share some general characteristics, they vary greatly in terms of their domain composition and functional properties. Although the traditional grouping of the hnRNPs as a collection of proteins provided a practical framework, which has guided much of the research on them, this approach is becoming increasingly incompatible with current knowledge about their structural and functional divergence. Hence, we review the current literature to examine hnRNP diversity, and discuss how this impacts upon approaches to the classification of RNA-binding proteins in general.
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20
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Liu Y, Gao Y, Wu Y, Wu Y, Wang H, Zhang C. Histochemical mapping of hnRNP A2/B1 in rat brain after ischemia-reperfusion insults. J Histochem Cytochem 2010; 58:695-705. [PMID: 20421594 DOI: 10.1369/jhc.2010.955021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Cerebral ischemia-reperfusion (I/R) insults result in neuronal cell death, brain tissue loss, and severe neurological deficits. However, the underlying mechanism is still not fully understood. Heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1 belongs to a family of RNA-binding proteins that plays a central role in pre-mRNA processing. Recent studies have revealed that hnRNP A2/B1 may be involved in the progress of I/R; therefore, the present study aimed to examine expression patterns of hnRNP A2/B1 to better understand posttranscriptional regulations in cerebral I/R insults. Focal cerebral I/R models were induced by right middle cerebral artery occlusion (MCAO) for 120 min followed by 3, 6, 12, 24, 48, and 72 hr of reperfusion in male Sprague-Dawley rats. We employed immunohistochemistry to examine expression of hnRNP A2/B1 in rat cerebral cortex (including cingulate cortex, striate cortex, temporal cortex, and piriform cortex) and hippocampus after I/R insults. Results showed that expression of hnRNP A2/B1 was significantly downregulated in cerebral cortex and hippocampus from 3 to 24 hr of reperfusion after MCAO for 120 min, but significantly upregulated at 48 hr of reperfusion. Unexpectedly, translocation of hnRNP A2/B1 from nucleus to cytoplasm and even to neurites was observed in cerebral cortex at 3 hr of reperfusion, reaching a peak at 24 hr of reperfusion, but not in hippocampus, indicating different posttranscriptional regulation patterns in different brain regions. Interestingly, translocation of hnRNP A2/B1 was only observed in cerebral cortex with MCAO but not in the opposite side, suggesting an I/R-specific expression pattern in the brain. Our data suggest that hnRNP A2/B1 participates in posttranscriptional regulation of neurons in cerebral cortex and hippocampus that suffered I/R insults, although posttranscriptional regulation is more extensive in neuronal cells of cerebral cortex than in hippocampus.
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Affiliation(s)
- Yichen Liu
- Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing, China
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21
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Han SP, Friend LR, Carson JH, Korza G, Barbarese E, Maggipinto M, Hatfield JT, Rothnagel JA, Smith R. Differential subcellular distributions and trafficking functions of hnRNP A2/B1 spliceoforms. Traffic 2010; 11:886-98. [PMID: 20406423 DOI: 10.1111/j.1600-0854.2010.01072.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Trafficking of mRNA molecules from the nucleus to distal processes in neural cells is mediated by heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1 trans-acting factors. Although hnRNP A2/B1 is alternatively spliced to generate four isoforms, most functional studies have not distinguished between these isoforms. Here, we show, using isoform-specific antibodies and isoform-specific green fluorescent protein (GFP)-fusion expression constructs, that A2b is the predominant cytoplasmic isoform in neural cells, suggesting that it may play a key role in mRNA trafficking. The differential subcellular distribution patterns of the individual isoforms are determined by the presence or absence of alternative exons that also affect their dynamic behavior in different cellular compartments, as measured by fluorescence correlation spectroscopy. Expression of A2b is also differentially regulated with age, species and cellular development. Furthermore, coinjection of isoform-specific antibodies and labeled RNA into live oligodendrocytes shows that the assembly of RNA granules is impaired by blockade of A2b function. These findings suggest that neural cells modulate mRNA trafficking by regulating alternative splicing of hnRNP A2/B1 and controlling expression levels of A2b, which may be the predominant mediator of cytoplasmic-trafficking functions. These findings highlight the importance of considering isoform-specific functions for alternatively spliced proteins.
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Affiliation(s)
- Siew Ping Han
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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22
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Woulfe J. Nuclear bodies in neurodegenerative disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1783:2195-206. [PMID: 18539152 DOI: 10.1016/j.bbamcr.2008.05.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Revised: 03/31/2008] [Accepted: 05/08/2008] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases are characterized by a relentlessly progressive loss of the functional and structural integrity of the central nervous system. In many cases, these diseases arise sporadically and the causes are unknown. The abnormal aggregation of protein within the cytoplasm or the nucleus of brain cells represents a unifying pathological feature of these diseases. There is increasing evidence for nuclear dysfunction in neurodegenerative diseases. How this relates to protein aggregation in the context of "cause and effect" remains to be determined in most cases. Co-ordinated nuclear function is predicated on the activity of distinct nuclear subdomains, or nuclear bodies, each responsible for a specific function. If nuclear dysfunction represents an important etiopathological feature in neurodegenerative disease, then this should be reflected by functional and/or morphological alterations in this nuclear compartmentalization. For most neurodegenerative diseases, evidence for nuclear dysfunction, with attendant consequences for nuclear architecture, is only beginning to emerge. In this review, I will discuss neurodegenerative diseases in the context of nuclear dysfunction and, more specifically, alterations in nuclear bodies. Although research in this field is in its infancy, identifying alterations in the nucleus in neurodegenerative disease has potentially profound implications for elucidating the pathogenesis of these disorders.
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Affiliation(s)
- John Woulfe
- Department of Pathology, The Ottawa Hospital, Civic Campus, 1053 Carling Avenue, Ottawa, Ontario, Canada K1Y 4E9.
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23
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Woulfe JM. Abnormalities of the nucleus and nuclear inclusions in neurodegenerative disease: a work in progress. Neuropathol Appl Neurobiol 2007; 33:2-42. [PMID: 17239006 DOI: 10.1111/j.1365-2990.2006.00819.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases are characterized pathologically by the abnormal accumulation of pathogenic protein species within the cell. Several neurodegenerative diseases feature intranuclear protein aggregation in the form of intranuclear inclusion bodies. Studies of these intranuclear inclusions are providing important clues regarding the cellular pathophysiology of these diseases, as exemplified by recent progress in defining the genetic basis of a subset of frontotemporal dementia cases. The precise role of intranuclear inclusion bodies in disease pathogenesis is currently a focus of debate. The present review provides an overview of the diverse family of neurodegenerative diseases in which nuclear inclusions form part of the neuropathological spectrum. In addition, current pathogenetic concepts relevant to these diseases will be reviewed and arguments for and against a protective role for intranuclear inclusions will be presented. The relationship of pathological intranuclear inclusions to functional intranuclear bodies will also be discussed. Finally, by analogy with pathological intranuclear inclusions, I will speculate on the possibility that intranuclear protein aggregation may represent a constitutive cellular protective mechanism occurring in neurons under physiological conditions.
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Affiliation(s)
- J M Woulfe
- Department of Pathology, The Ottawa Hospital, University of Ottawa, and Cancer Research Program, The Ottawa Health Research Institute, Ottawa, Canada.
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