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Mathew D, Purohit P, Gadwal A, Anil A, Sharma RK, Meshram VP, Setia P. Integrated Assessment of GFAP and UCH-L1 for their utility in severity assessment and outcome prediction in Traumatic Brain Injury. Int J Legal Med 2024:10.1007/s00414-024-03287-z. [PMID: 38977505 DOI: 10.1007/s00414-024-03287-z] [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: 09/12/2023] [Accepted: 07/01/2024] [Indexed: 07/10/2024]
Abstract
OBJECTIVES This study aimed to explore the potential of glial fibrillary acidic protein (GFAP) and ubiquitin C-terminal hydrolase-L1 (UCH-L1) as biomarkers for diagnosis and prognosis in mild and severe TBI cases, including TBI-related deaths. METHODS This prospective cohort study includes 40 cases each of mild, severe, fatal TBI cases, and 40 healthy controls. Serum samples were collected from live patients at 8 and 20 h post injury for UCH-L1 and GFAP respectively, and from deceased patients within 6 h of death. RESULTS Elevated levels of both GFAP and UCH-L1 were observed in patients with severe and fatal TBI cases. These biomarkers exhibited promising potential for predicting various Glasgow Outcome Scale Extended (GOSE) categories. Combining GFAP and UCH-L1 yielded higher predictive accuracy both for diagnosis and prognosis in TBI cases. The study additionally established specific cut-off levels for GFAP and UCH-L1 stratified according to the severity and prognosis. CONCLUSION GFAP and UCH-L1 individually demonstrated moderate to good discrimination capacity in predicting TBI severity and functional outcomes. However, combining these biomarkers is recommended for improved diagnostic and prognostic utility. This precision tool can enhance patient care, enabling tailored treatment plans, ultimately reducing morbidity and mortality rates in TBI cases.
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Affiliation(s)
- Deepu Mathew
- Department of Forensic Medicine and Toxicology, All India Institute of Medical Sciences, Jodhpur, Rajasthan, 342005, India
| | - Purvi Purohit
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan, 342005, India
| | - Ashita Gadwal
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan, 342005, India
| | - Abhishek Anil
- Department of Pharmacology, All India Institute of Medical Sciences, Jodhpur, Rajasthan, 342005, India
| | - Raghavendra Kumar Sharma
- Department of Neurosurgery, All India Institute of Medical Sciences, Jodhpur, Rajasthan, 342005, India
| | - Vikas P Meshram
- Department of Forensic Medicine and Toxicology, All India Institute of Medical Sciences, Jodhpur, Rajasthan, 342005, India
| | - Puneet Setia
- Department of Forensic Medicine and Toxicology, All India Institute of Medical Sciences, Jodhpur, Rajasthan, 342005, India.
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2
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Kumari A, Rahaman A, Zeng XA, Farooq MA, Huang Y, Yao R, Ali M, Ishrat R, Ali R. Temporal Cortex Microarray Analysis Revealed Impaired Ribosomal Biogenesis and Hyperactivity of the Glutamatergic System: An Early Signature of Asymptomatic Alzheimer's Disease. Front Neurosci 2022; 16:966877. [PMID: 35958988 PMCID: PMC9359077 DOI: 10.3389/fnins.2022.966877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 06/23/2022] [Indexed: 11/21/2022] Open
Abstract
Pathogenic aging is regarded as asymptomatic AD when there is no cognitive deficit except for neuropathology consistent with Alzheimer's disease. These individuals are highly susceptible to developing AD. Braak and Braak's theory specific to tau pathology illustrates that the brain's temporal cortex region is an initiation site for early AD progression. So, the hub gene analysis of this region may reveal early altered biological cascades that may be helpful to alleviate AD in an early stage. Meanwhile, cognitive processing also drags its attention because cognitive impairment is the ultimate result of AD. Therefore, this study aimed to explore changes in gene expression of aged control, asymptomatic AD (AsymAD), and symptomatic AD (symAD) in the temporal cortex region. We used microarray data sets to identify differentially expressed genes (DEGs) with the help of the R programming interface. Further, we constructed the protein-protein interaction (PPI) network by performing the STRING plugin in Cytoscape and determined the hub genes via the CytoHubba plugin. Furthermore, we conducted Gene Ontology (GO) enrichment analysis via Bioconductor's cluster profile package. Resultant, the AsymAD transcriptome revealed the early-stage changes of glutamatergic hyperexcitability. Whereas the connectivity of major hub genes in this network indicates a shift from initially reduced rRNA biosynthesis in the AsymAD group to impaired protein synthesis in the symAD group. Both share the phenomenon of breaking tight junctions and others. In conclusion, this study offers new understandings of the early biological vicissitudes that occur in the brain before the manifestation of symAD and gives new promising therapeutic targets for early AD intervention.
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Affiliation(s)
- Ankita Kumari
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
| | - Abdul Rahaman
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
- Abdul Rahaman
| | - Xin-An Zeng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
- *Correspondence: Xin-An Zeng
| | - Muhammad Adil Farooq
- Institute of Food Science and Technology, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Yanyan Huang
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
| | - Runyu Yao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
| | - Murtaza Ali
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
| | - Romana Ishrat
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Romana Ishrat
| | - Rafat Ali
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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3
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Wang Q, Wang Q, Melak S, Lin X, Wei W, Zhang L, Chen J. A novel c.-652C>T mutation in UCHL1 gene is associated with the growth performance in Yangzhou goose. Poult Sci 2021; 100:101089. [PMID: 34051408 PMCID: PMC8165569 DOI: 10.1016/j.psj.2021.101089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 12/22/2020] [Accepted: 03/01/2021] [Indexed: 12/17/2022] Open
Abstract
As a member of the ubiquitin-dependent proteasome degradation pathway, Ubiquitin carboxyl-terminal hydrolase-L1 (UCHL1) plays a key role in post-translational modification and protein degradation, and it is extensive and important for the regulation of various biological functions of the organism. However, its function remains unclear in goose growth performance. In this study, the full-length genomic DNA and coding region of UCHL1 gene was firstly cloned and characterized in Yangzhou goose. Tissue expression profile revealed that UCHL1 was exclusively expressed in brain and gonads. A novel single nucleotide polymorphisms c.-652C>T which is significantly related to 64-d body weight of Yangzhou goose was found in UCHL1 promoter region by comparative sequencing. Correlation analysis in a population of 405 geese showed that TT genotype individuals had higher body weight than CC individuals in male, but not in female geese. Dual-luciferase reporter assay indicated that the single nucleotide polymorphisms c.-652C>T is located at the core promoter region of UCHL1, and the promoter transcription activity was significantly increased (P < 0.01) when allele C changed to T. Geese with TT genotype had higher mRNA level of UCHL1 in brain tissue than those of CC genotype (P < 0.01). Compared with CC individuals, neuropeptide Y and AdipoR1 mRNA level was significantly higher in TT individuals (P < 0.05), while FAS mRNA level was lower in the TT individuals (P < 0.05). In summary, we identify a novel mutation in the promoter of UCHL1 gene, which can alter transcriptional activity of UCHL1 gene, and affect the growth performance of male goose.
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Affiliation(s)
- Qin Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Qiushi Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Sherif Melak
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiangsheng Lin
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wei Wei
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jie Chen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China.
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4
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Tangri A, Lighty K, Loganathan J, Mesmar F, Podicheti R, Zhang C, Iwanicki M, Drapkin R, Nakshatri H, Mitra S. Deubiquitinase UCHL1 Maintains Protein Homeostasis through the PSMA7-APEH-Proteasome Axis in High-grade Serous Ovarian Carcinoma. Mol Cancer Res 2021; 19:1168-1181. [PMID: 33753553 DOI: 10.1158/1541-7786.mcr-20-0883] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/10/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022]
Abstract
High-grade serous ovarian cancer (HGSOC) is characterized by chromosomal instability, DNA damage, oxidative stress, and high metabolic demand that exacerbate misfolded, unfolded, and damaged protein burden resulting in increased proteotoxicity. However, the underlying mechanisms that maintain protein homeostasis to promote HGSOC growth remain poorly understood. This study reports that the neuronal deubiquitinating enzyme, ubiquitin carboxyl-terminal hydrolase L1 (UCHL1), is overexpressed in HGSOC and maintains protein homeostasis. UCHL1 expression was markedly increased in HGSOC patient tumors and serous tubal intraepithelial carcinoma (HGSOC precursor lesions). High UCHL1 levels correlated with higher tumor grade and poor patient survival. UCHL1 inhibition reduced HGSOC cell proliferation and invasion, as well as significantly decreased the in vivo metastatic growth of ovarian cancer xenografts. Transcriptional profiling of UCHL1-silenced HGSOC cells revealed downregulation of genes implicated with proteasome activity along with upregulation of endoplasmic reticulum stress-induced genes. Reduced expression of proteasome subunit alpha 7 (PSMA7) and acylaminoacyl peptide hydrolase (APEH), upon silencing of UCHL1, resulted in a significant decrease in proteasome activity, impaired protein degradation, and abrogated HGSOC growth. Furthermore, the accumulation of polyubiquitinated proteins in the UCHL1-silenced cells led to attenuation of mTORC1 activity and protein synthesis, and induction of terminal unfolded protein response. Collectively, these results indicate that UCHL1 promotes HGSOC growth by mediating protein homeostasis through the PSMA7-APEH-proteasome axis. IMPLICATIONS: This study identifies the novel links in the proteostasis network to target protein homeostasis in HGSOC and recognizes the potential of inhibiting UCHL1 and APEH to sensitize cancer cells to proteotoxic stress in solid tumors.
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Affiliation(s)
- Apoorva Tangri
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kinzie Lighty
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jagadish Loganathan
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Fahmi Mesmar
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana
| | - Ram Podicheti
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana
| | - Chi Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Marcin Iwanicki
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey
| | - Ronny Drapkin
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, Indiana
| | - Sumegha Mitra
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana.
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, Indiana
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5
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Colquitt BM, Merullo DP, Konopka G, Roberts TF, Brainard MS. Cellular transcriptomics reveals evolutionary identities of songbird vocal circuits. Science 2021; 371:371/6530/eabd9704. [PMID: 33574185 DOI: 10.1126/science.abd9704] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022]
Abstract
Birds display advanced behaviors, including vocal learning and problem-solving, yet lack a layered neocortex, a structure associated with complex behavior in mammals. To determine whether these behavioral similarities result from shared or distinct neural circuits, we used single-cell RNA sequencing to characterize the neuronal repertoire of the songbird song motor pathway. Glutamatergic vocal neurons had considerable transcriptional similarity to neocortical projection neurons; however, they displayed regulatory gene expression patterns more closely related to neurons in the ventral pallium. Moreover, while γ-aminobutyric acid-releasing neurons in this pathway appeared homologous to those in mammals and other amniotes, the most abundant avian class is largely absent in the neocortex. These data suggest that songbird vocal circuits and the mammalian neocortex have distinct developmental origins yet contain transcriptionally similar neurons.
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Affiliation(s)
- Bradley M Colquitt
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Departments of Physiology and Psychiatry, University of California-San Francisco, San Francisco, CA 94158, USA
| | - Devin P Merullo
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Todd F Roberts
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Michael S Brainard
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. .,Departments of Physiology and Psychiatry, University of California-San Francisco, San Francisco, CA 94158, USA
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6
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Zolochevska O, Bjorklund N, Woltjer R, Wiktorowicz JE, Taglialatela G. Postsynaptic Proteome of Non-Demented Individuals with Alzheimer's Disease Neuropathology. J Alzheimers Dis 2019; 65:659-682. [PMID: 30103319 PMCID: PMC6130411 DOI: 10.3233/jad-180179] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Some individuals, here referred to as Non-Demented with Alzheimer’s Neuropathology (NDAN), retain their cognitive function despite the presence of amyloid plaques and tau tangles typical of symptomatic Alzheimer’s disease (AD). In NDAN, unlike AD, toxic amyloid-β oligomers do not localize to the postsynaptic densities (PSDs). Synaptic resistance to amyloid-β in NDAN may thus enable these individuals to remain cognitively intact despite the AD-like pathology. The mechanism(s) responsible for this resistance remains unresolved and understanding such protective biological processes could reveal novel targets for the development of effective treatments for AD. The present study uses a proteomic approach to compare the hippocampal postsynaptic densities of NDAN, AD, and healthy age-matched persons to identify protein signatures characteristic for these groups. Subcellular fractionation followed by 2D gel electrophoresis and mass spectrometry were used to analyze the PSDs. We describe fifteen proteins which comprise the unique proteomic signature of NDAN PSDs, thus setting them apart from control subjects and AD patients.
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Affiliation(s)
- Olga Zolochevska
- Department of Neurology, University of Texas Medical Branch, Galveston, TX, USA
| | - Nicole Bjorklund
- Department of Neurology, University of Texas Medical Branch, Galveston, TX, USA
| | - Randall Woltjer
- Department of Pathology, Oregon Health and Science University, Portland, OR, USA
| | - John E Wiktorowicz
- Department of Biochemistry and Molecular Biology, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Giulio Taglialatela
- Department of Neurology, University of Texas Medical Branch, Galveston, TX, USA
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7
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Zlatic SA, Vrailas-Mortimer A, Gokhale A, Carey LJ, Scott E, Burch R, McCall MM, Rudin-Rush S, Davis JB, Hartwig C, Werner E, Li L, Petris M, Faundez V. Rare Disease Mechanisms Identified by Genealogical Proteomics of Copper Homeostasis Mutant Pedigrees. Cell Syst 2018; 6:368-380.e6. [PMID: 29397366 DOI: 10.1016/j.cels.2018.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/28/2017] [Accepted: 01/05/2018] [Indexed: 12/22/2022]
Abstract
Rare neurological diseases shed light onto universal neurobiological processes. However, molecular mechanisms connecting genetic defects to their disease phenotypes are elusive. Here, we obtain mechanistic information by comparing proteomes of cells from individuals with rare disorders with proteomes from their disease-free consanguineous relatives. We use triple-SILAC mass spectrometry to quantify proteomes from human pedigrees affected by mutations in ATP7A, which cause Menkes disease, a rare neurodegenerative and neurodevelopmental disorder stemming from systemic copper depletion. We identified 214 proteins whose expression was altered in ATP7A-/y fibroblasts. Bioinformatic analysis of ATP7A-mutant proteomes identified known phenotypes and processes affected in rare genetic diseases causing copper dyshomeostasis, including altered mitochondrial function. We found connections between copper dyshomeostasis and the UCHL1/PARK5 pathway of Parkinson disease, which we validated with mitochondrial respiration and Drosophila genetics assays. We propose that our genealogical "omics" strategy can be broadly applied to identify mechanisms linking a genomic locus to its phenotypes.
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Affiliation(s)
| | - Alysia Vrailas-Mortimer
- School of Biological Sciences Illinois State University, Normal, IL 617901, USA; University of Denver, Department of Biological Sciences, Denver, CO 80208, USA
| | - Avanti Gokhale
- Department of Cell Biology, Emory University, Atlanta, GA 30322, USA
| | - Lucas J Carey
- School of Biological Sciences Illinois State University, Normal, IL 617901, USA
| | - Elizabeth Scott
- School of Biological Sciences Illinois State University, Normal, IL 617901, USA
| | - Reid Burch
- School of Biological Sciences Illinois State University, Normal, IL 617901, USA; University of Denver, Department of Biological Sciences, Denver, CO 80208, USA
| | - Morgan M McCall
- School of Biological Sciences Illinois State University, Normal, IL 617901, USA
| | | | | | - Cortnie Hartwig
- Department of Cell Biology, Emory University, Atlanta, GA 30322, USA; Department of Chemistry, Agnes Scott College, Decatur, GA 30030, USA
| | - Erica Werner
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Lian Li
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA
| | - Michael Petris
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Victor Faundez
- Department of Cell Biology, Emory University, Atlanta, GA 30322, USA.
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8
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Shahjouei S, Sadeghi-Naini M, Yang Z, Kobeissy F, Rathore D, Shokraneh F, Blackburn S, Manley GT, Wang KK. The diagnostic values of UCH-L1 in traumatic brain injury: A meta-analysis. Brain Inj 2017; 32:1-17. [DOI: 10.1080/02699052.2017.1382717] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Shima Shahjouei
- Department of Neurosurgery, Children’s Hospital Medical Centre, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohsen Sadeghi-Naini
- Department of Neurosurgery, Imam Hossein hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Sina Trauma and Surgery Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Zhihui Yang
- Program for Neurotrauma, Neuroproteomics and Biomarker Research, Departments of Emergency Medicine and Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Firas Kobeissy
- Program for Neurotrauma, Neuroproteomics and Biomarker Research, Departments of Emergency Medicine and Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
- American University of Beirut, Department of Biochemistry and Molecular Genetics, Beirut, Lebanon
| | - Disa Rathore
- Program for Neurotrauma, Neuroproteomics and Biomarker Research, Departments of Emergency Medicine and Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Farhad Shokraneh
- Research Center for Modeling in Health, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
- Cochrane Schizophrenia Group, The Institute of Mental Health, A Partnership Between the University of Nottingham and Nottinghamshire Healthcare NHS Trust, Nottingham, UK
| | - Spiros Blackburn
- University of Texas, Health Sciences Center, Houston, Texas, USA
| | - Geoff T Manley
- Department of Neurological surgery, San Francisco General Hospital, University of California, San Francisco, USA
| | - Kevin K.W. Wang
- Program for Neurotrauma, Neuroproteomics and Biomarker Research, Departments of Emergency Medicine and Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
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9
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In vivo transduction of neurons with TAT-UCH-L1 protects brain against controlled cortical impact injury. PLoS One 2017; 12:e0178049. [PMID: 28542502 PMCID: PMC5443532 DOI: 10.1371/journal.pone.0178049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 05/07/2017] [Indexed: 12/17/2022] Open
Abstract
Many mechanisms or pathways are involved in secondary post-traumatic brain injury, such as the ubiquitin-proteasome pathway (UPP), axonal degeneration and neuronal cell apoptosis. UCH-L1 is a protein that is expressed in high levels in neurons and may have important roles in the UPP, autophagy and axonal integrity. The current study aims to evaluate the role of UCH-L1 in post-traumatic brain injury (TBI) and its potential therapeutic effects. A novel protein was constructed that fused the protein transduction domain (PTD) of trans-activating transduction (TAT) protein with UCH-L1 (TAT-UCH-L1) in order to promote neuronal transduction. The TAT-UCH-L1 protein was readily detected in brain by immunoblotting and immunohistochemistry after i.p. administration in mice. TBI was induced in mice using the controlled cortical impact (CCI) model. TAT-UCH-L1 treatment significantly attenuated K48-linkage polyubiquitin (polyUb)-protein accumulation in hippocampus after CCI compared to vehicle controls, but had no effects on K65-linkage polyUb-protein. TAT-UCH-L1 treatment also attenuated expression of Beclin-1 and LC3BII after CCI. TAT-UCH-L1-treated mice had significantly increased spared tissue volumes and increased survival of CA3 neurons 21 d after CCI compared to control vehicle-treated mice. Axonal injury, detected by APP immunohistochemistry, was reduced in thalamus 24 h and 21 d after CCI in TAT-UCH-L1-treated mice. These results suggest that TAT-UCH-L1 treatment improves function of the UPP and decreases activation of autophagy after CCI. Furthermore, TAT-UCH-L1 treatment also attenuates axonal injury and increases hippocampal neuronal survival after CCI. Taken together these results suggest that UCH-L1 may play an important role in the pathogenesis of cell death and axonal injury after TBI.
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10
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Graham SH, Liu H. Life and death in the trash heap: The ubiquitin proteasome pathway and UCHL1 in brain aging, neurodegenerative disease and cerebral Ischemia. Ageing Res Rev 2017; 34:30-38. [PMID: 27702698 DOI: 10.1016/j.arr.2016.09.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/08/2016] [Accepted: 09/29/2016] [Indexed: 12/11/2022]
Abstract
The ubiquitin proteasome pathway (UPP) is essential for removing abnormal proteins and preventing accumulation of potentially toxic proteins within the neuron. UPP dysfunction occurs with normal aging and is associated with abnormal accumulation of protein aggregates within neurons in neurodegenerative diseases. Ischemia disrupts UPP function and thus may contribute to UPP dysfunction seen in the aging brain and in neurodegenerative diseases. Ubiquitin carboxy-terminal hydrolase L1 (UCHL1), an important component of the UPP in the neuron, is covalently modified and its activity inhibited by reactive lipids produced after ischemia. As a result, degradation of toxic proteins is impaired which may exacerbate neuronal function and cell death in stroke and neurodegenerative diseases. Preserving or restoring UCHL1 activity may be an effective therapeutic strategy in stroke and neurodegenerative diseases.
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11
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Bramley JC, Collins SVA, Clark KB, Buchser WJ. Avian axons undergo Wallerian degeneration after injury and stress. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2016; 202:813-822. [PMID: 27614771 DOI: 10.1007/s00359-016-1123-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 06/20/2016] [Accepted: 08/31/2016] [Indexed: 12/22/2022]
Abstract
The integrity of long axons is essential for neural communication. Unfortunately, relatively minor stress to a neuron can cause extensive loss of this integrity. Axon degeneration is the cell-intrinsic program that actively deconstructs an axon after injury or damage. Although ultrastructural examination has revealed signs of axon degeneration in vivo, the occurrence and progression of axon degeneration in avian species have not yet been documented in vitro. Here, we use a novel cell culture system with primary embryonic zebra finch retinal ganglion cells to interrogate the properties of avian axon degeneration. First, we establish that both axotomy and a chemically induced injury (taxol and vincristine) are sufficient to initiate degeneration. These events are dependent on a late influx of calcium. In addition, as in mammals, the NAD pathway is involved, since a decrease in NMN with FK866 can reduce degeneration. Importantly, these retinal ganglion cell axons were sensitive to a pressure-induced injury, which may mimic the effect of high intraocular pressure associated with glaucoma. We have demonstrated that avian neurons undergo Wallerian degeneration in response to both physical and chemical injury. Subsequent avian studies will investigate whether blocking the degeneration pathway can protect individuals from neurodegenerative disease.
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Affiliation(s)
- John C Bramley
- Department of Biology, College of William & Mary, 540 Landrum Dr., Williamsburg, VA, USA
| | - Samantha V A Collins
- Department of Biology, College of William & Mary, 540 Landrum Dr., Williamsburg, VA, USA
| | - Karen B Clark
- Department of Biology, College of William & Mary, 540 Landrum Dr., Williamsburg, VA, USA
| | - William J Buchser
- Department of Biology, College of William & Mary, 540 Landrum Dr., Williamsburg, VA, USA.
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12
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Chikin VV, Smolyannikova VA, Proshutinskaya DV, Nefedova MA. Assessing the itching intensity using visual analogue scales in atopic dermatitis patients against the background of a therapy with calcineurin inhibitors. VESTNIK DERMATOLOGII I VENEROLOGII 2016. [DOI: 10.25208/0042-4609-2016-92-3-46-55] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Goal. To assess the effect of topical treatment of atopic dermatitis patients with the 0.1% tacrolimus ointment on the itching intensity and skin expression level of growth factor proteins affecting the intensity of cutaneous innervation. Materials and methods. Fifteen patients suffering from atopic dermatitis underwent treatment with the 0.1% tacrolimus ointment. The SCORAD index was calculated to assess the severity of clinical manifestations. The itching intensity was assessed using a visual analogue scale. The skin expression of nerve growth factors, amphiregulin, semaphorin 3A and PGP9.5 protein (a nerve fiber marker) was assessed by the indirect immunofluorescence method. Results. An increased expression of the nerve growth factor and reduced semaphorin 3A expression levels were noted in the patients’ epidermis; there was an increase in the quantity, mean length and fluorescence intensity of PGP9.5+ nerve fibers. As a result of the treatment, the disease severity and itching intensity were reduced, the nerve growth factor expression level was reduced while semaphorin 3A expression level increased in the epidermis, and the mean length and fluorescence intensity of PGP9.5+ nerve fibers was also reduced. A positive correlation among the itching intensity and nerve growth factor expression level, quantity and mean length of PGP9.5+ nerve fibers in the epidermis was revealed, and negative correlation between the itching intensity and semaphorin 3A expression level in the epidermis was established. Conclusion. Topical treatment with the 0.1% Tacrolimus ointment reduces the itching intensity in atopic dermatitis patients, which is related to the therapy-mediated reduction in the epidermis innervation level, decreased expression of epidermal nerve growth factor and increased semaphorin 3A expression level.
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Jara JH, Genç B, Cox GA, Bohn MC, Roos RP, Macklis JD, Ulupınar E, Özdinler PH. Corticospinal Motor Neurons Are Susceptible to Increased ER Stress and Display Profound Degeneration in the Absence of UCHL1 Function. Cereb Cortex 2015; 25:4259-72. [PMID: 25596590 PMCID: PMC4626833 DOI: 10.1093/cercor/bhu318] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Corticospinal motor neurons (CSMN) receive, integrate, and relay cerebral cortex's input toward spinal targets to initiate and modulate voluntary movement. CSMN degeneration is central for numerous motor neuron disorders and neurodegenerative diseases. Previously, 5 patients with mutations in the ubiquitin carboxy-terminal hydrolase-L1 (UCHL1) gene were reported to have neurodegeneration and motor neuron dysfunction with upper motor neuron involvement. To investigate the role of UCHL1 on CSMN health and stability, we used both in vivo and in vitro approaches, and took advantage of the Uchl1nm3419 (UCHL1−/−) mice, which lack all UCHL1 function. We report a unique role of UCHL1 in maintaining CSMN viability and cellular integrity. CSMN show early, selective, progressive, and profound cell loss in the absence of UCHL1. CSMN degeneration, evident even at pre-symptomatic stages by disintegration of the apical dendrite and spine loss, is mediated via increased ER stress. These findings bring a novel understanding to the basis of CSMN vulnerability, and suggest UCHL1−/− mice as a tool to study CSMN pathology.
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Affiliation(s)
- Javier H Jara
- Davee Department of Neurology and Clinical Neurological Sciences
| | - Barış Genç
- Davee Department of Neurology and Clinical Neurological Sciences
| | | | - Martha C Bohn
- Neurobiology Program, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago Research Center, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Raymond P Roos
- Department of Neurology, University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Jeffrey D Macklis
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, UK
| | - Emel Ulupınar
- Department of Anatomy, Eskişehir Osmangazi University Medical School, Eskişehir, Turkey
| | - P Hande Özdinler
- Davee Department of Neurology and Clinical Neurological Sciences Robert H. Lurie Cancer Center Cognitive Neurology and Alzheimer's Disease Center, Northwestern University, Chicago, IL 60611, USA
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14
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Whitney O, Pfenning AR, Howard JT, Blatti CA, Liu F, Ward JM, Wang R, Audet JN, Kellis M, Mukherjee S, Sinha S, Hartemink AJ, West AE, Jarvis ED. Core and region-enriched networks of behaviorally regulated genes and the singing genome. Science 2014; 346:1256780. [PMID: 25504732 DOI: 10.1126/science.1256780] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Songbirds represent an important model organism for elucidating molecular mechanisms that link genes with complex behaviors, in part because they have discrete vocal learning circuits that have parallels with those that mediate human speech. We found that ~10% of the genes in the avian genome were regulated by singing, and we found a striking regional diversity of both basal and singing-induced programs in the four key song nuclei of the zebra finch, a vocal learning songbird. The region-enriched patterns were a result of distinct combinations of region-enriched transcription factors (TFs), their binding motifs, and presinging acetylation of histone 3 at lysine 27 (H3K27ac) enhancer activity in the regulatory regions of the associated genes. RNA interference manipulations validated the role of the calcium-response transcription factor (CaRF) in regulating genes preferentially expressed in specific song nuclei in response to singing. Thus, differential combinatorial binding of a small group of activity-regulated TFs and predefined epigenetic enhancer activity influences the anatomical diversity of behaviorally regulated gene networks.
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Affiliation(s)
- Osceola Whitney
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA.
| | - Andreas R Pfenning
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA. Computer Science and Artificial Intelligence Laboratory and the Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Jason T Howard
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Charles A Blatti
- Department of Computer Science, University of Illinois, Urbana-Champaign, IL, USA
| | - Fang Liu
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - James M Ward
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Rui Wang
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Jean-Nicoles Audet
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory and the Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Saurabh Sinha
- Department of Computer Science, University of Illinois, Urbana-Champaign, IL, USA
| | | | - Anne E West
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Erich D Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA.
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15
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Phosphoproteomic profiling of selenate-treated Alzheimer's disease model cells. PLoS One 2014; 9:e113307. [PMID: 25485856 PMCID: PMC4259334 DOI: 10.1371/journal.pone.0113307] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/21/2014] [Indexed: 11/19/2022] Open
Abstract
The reversible phosphorylation of proteins regulates most biological processes, while abnormal phosphorylation is a cause or consequence of many diseases including Alzheimer's disease (AD). One of the hallmarks of AD is the formation of neurofibrillary tangles (NFTs), which is composed of hyperphosphorylated tau proteins. Sodium selenate has been recently found to reduce tau hyperphosphorylation and NFTs formation, and to improve spatial learning and motor performance in AD mice. In the current study, the phosphoproteomics of N2aSW cells treated with selenate were investigated. To avoid missing low-abundance phosphoproteins, both the total proteins of cells and the phosphor-enriched proteins were extracted and subjected to the two-dimensional gel electrophoresis with Pro-Q diamond staining and then LC-MS/MS analysis. A total of 65 proteins were altered in phosphorylation level, of which 39 were up-regulated and 26 were down-regulated. All identified phosphoproteins were bioinformatically annotated according to their physiochemical features, subcellular location, and biological function. Most of these significantly changed phosphoproteins are involved in crucial neural processes such as protesome activity, oxidative stress, cysteine and methionine metabolism, and energy metabolism. Furthermore, decreases were found in homocysteine, phosphor-tau and amyloid β upon selenate treatment. Our results suggest that selenate may intervene in the pathological process of AD by altering the phosphorylation of some key proteins involved in oxidative stress, energy metabolism and protein degradation, thus play important roles in maintaining redox homeostasis, generating ATP, and clearing misfolded proteins and aggregates. The present paper provides some new clues to the mechanism of selenate in AD prevention.
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16
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Coulombe J, Gamage P, Gray MT, Zhang M, Tang MY, Woulfe J, Saffrey MJ, Gray DA. Loss of UCHL1 promotes age-related degenerative changes in the enteric nervous system. Front Aging Neurosci 2014; 6:129. [PMID: 24994982 PMCID: PMC4063237 DOI: 10.3389/fnagi.2014.00129] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 05/31/2014] [Indexed: 12/31/2022] Open
Abstract
UCHL1 (ubiquitin carboxyterminal hydrolase 1) is a deubiquitinating enzyme that is particularly abundant in neurons. From studies of a spontaneous mutation arising in a mouse line it is clear that loss of function of UCHL1 generates profound degenerative changes in the central nervous system, and it is likely that a proteolytic deficit contributes to the pathology. Here these effects were found to be recapitulated in mice in which the Uchl1 gene had been inactivated by homologous recombination. In addition to the previously documented neuropathology associated with loss of UCHL1 function, axonal swellings were detected in the striatum. In agreement with previously reported findings the loss of UCHL1 function was accompanied by perturbations in ubiquitin pools, but glutathione levels were also significantly depleted in the brains of the knockout mice, suggesting that oxidative defense mechanisms may be doubly compromised. To determine if, in addition to its role in the central nervous system, UCHL1 function is also required for homeostasis of the enteric nervous system the gastrointestinal tract was analyzed in UCHL1 knockout mice. The mice displayed functional changes and morphological changes in gut neurons that preceded degenerative changes in the brain. The changes were qualitatively and quantitatively similar to those observed in wild type mice of much greater age, and strongly resemble changes reported for elderly humans. UCHL1 knockout mice should therefore serve as a useful model of gut aging.
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Affiliation(s)
- Josée Coulombe
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute Ottawa, ON, Canada
| | - Prasanna Gamage
- Biomedical Research Network, Department of Life, Health and Chemical Sciences, Open University Milton Keynes, UK
| | - Madison T Gray
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute Ottawa, ON, Canada
| | - Mei Zhang
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute Ottawa, ON, Canada
| | - Matthew Y Tang
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute Ottawa, ON, Canada
| | - John Woulfe
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute Ottawa, ON, Canada
| | - M Jill Saffrey
- Biomedical Research Network, Department of Life, Health and Chemical Sciences, Open University Milton Keynes, UK
| | - Douglas A Gray
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute Ottawa, ON, Canada ; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa Ottawa, ON, Canada
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17
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Schlaudraff F, Gründemann J, Fauler M, Dragicevic E, Hardy J, Liss B. Orchestrated increase of dopamine and PARK mRNAs but not miR-133b in dopamine neurons in Parkinson's disease. Neurobiol Aging 2014; 35:2302-15. [PMID: 24742361 PMCID: PMC4099518 DOI: 10.1016/j.neurobiolaging.2014.03.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 02/27/2014] [Accepted: 03/14/2014] [Indexed: 01/25/2023]
Abstract
Progressive loss of substantia nigra dopamine neurons (SN DA) is a hallmark of aging and of Parkinson's disease (PD). Mutations in PARK genes cause familial PD forms. Increased expression of alpha-synuclein (PARK4) is a disease-triggering event in familial PD and also observed in SN DA neurons in sporadic PD but related transcriptional changes are unknown. With optimized single-cell quantitative real-time polymerase chain reaction analysis, we compared messenger RNA and microRNA levels in SN DA neurons from sporadic PD patients and controls. Non-optimally matched donor ages and RNA integrities are common problems when analyzing human samples. We dissected the influence of distinct ages and RNA integrities of our samples by applying a specifically-optimized, linear-mixed-effects model to quantitative real-time polymerase chain reaction-data. We identified that elevated alpha-synuclein messenger RNA levels in SN DA neurons of human PD brains were positively correlated with corresponding elevated levels of mRNAs for functional compensation of progressive SN DA loss and for enhanced proteasomal (PARK5/UCHL1) and lysosomal (PARK9/ATPase13A2) function, possibly counteracting alpha-synuclein toxicity. In contrast, microRNA miR-133b levels, previously implicated in transcriptional dysregulation in PD, were not altered in SN DA neurons in PD.
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Affiliation(s)
- Falk Schlaudraff
- Department of Applied Physiology, Institute of Applied Physiology, University of Ulm, Ulm, Germany
| | - Jan Gründemann
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Michael Fauler
- Department of Applied Physiology, Institute of Applied Physiology, University of Ulm, Ulm, Germany
| | - Elena Dragicevic
- Department of Applied Physiology, Institute of Applied Physiology, University of Ulm, Ulm, Germany
| | - John Hardy
- Department of Molecular Neuroscience and Reta Lila Weston Laboratories, Institute of Neurology, London, UK
| | - Birgit Liss
- Department of Applied Physiology, Institute of Applied Physiology, University of Ulm, Ulm, Germany.
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18
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Toyama T, Shinkai Y, Yazawa A, Kakehashi H, Kaji T, Kumagai Y. Glutathione-mediated reversibility of covalent modification of ubiquitin carboxyl-terminal hydrolase L1 by 1,2-naphthoquinone through Cys152, but not Lys4. Chem Biol Interact 2014; 214:41-8. [PMID: 24582816 DOI: 10.1016/j.cbi.2014.02.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/31/2013] [Accepted: 02/19/2014] [Indexed: 12/13/2022]
Abstract
Covalent modification of cellular proteins by electrophiles affects electrophilic signal transduction and the dysfunction of enzymes that is involved in cytotoxicity. We have recently found a unique reaction which restores glyceraldehyde-3-phosphate dehydrogenase (GAPDH) that has been modified by 1,2-naphthoquinone (1,2-NQ) through a glutathione (GSH)-dependent S-transarylation reaction. We report here that ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1) undergoes the same reaction. Exposure of human neuroblastoma SH-SY5Y cells to 1,2-NQ after pretreatment with buthionine sulfoximine (BSO) to deplete GSH resulted in an enhancement of covalent modification of UCH-L1 by 1,2-NQ. With recombinant human UCH-L1, we demonstrated that UCH-L1 underwent arylation by 1,2-NQ through Cys152 and Lys4, thereby decreasing its catalytic activity. Addition of GSH to an incubation mixture of 1,2-NQ-UCH-L1 adduct partially restored this decline in enzyme activity which was accompanied by decreased covalent attachment of 1,2-NQ, together with production of 1,2-NQ-GSH adduct. UCH-L1 in which Lys4 was mutated exhibited a lower level of covalent modification and enzyme inhibition, but completely recovered after addition of GSH. Taken together, these results suggest that Cys152 modification in UCH-L1 by 1,2-NQ is reversible via GSH-mediated S-transarylation reaction whereas Lys4 modification by 1,2-NQ is irreversible by GSH. Because UCH-L1 dysfunction has been associated with neurodegeneration, the electrophilic modification of Lys rather than Cys in UCH-L1 may be implicated in such neurodegenerative diseases.
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Affiliation(s)
- Takashi Toyama
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Research Fellow of the Japan Society for the Promotion of Science, 1-8 Chiyoda, Tokyo 102-8472, Japan
| | - Yasuhiro Shinkai
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Master's Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Aki Yazawa
- College of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Hidenao Kakehashi
- Master's Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Toshiyuki Kaji
- Department of Environmental Health, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Yoshito Kumagai
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Master's Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.
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19
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Liu H, Li W, Ahmad M, Rose ME, Miller TM, Yu M, Chen J, Pascoe JL, Poloyac SM, Hickey RW, Graham SH. Increased generation of cyclopentenone prostaglandins after brain ischemia and their role in aggregation of ubiquitinated proteins in neurons. Neurotox Res 2013; 24:191-204. [PMID: 23355003 DOI: 10.1007/s12640-013-9377-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/04/2013] [Accepted: 01/08/2013] [Indexed: 11/26/2022]
Abstract
The cyclopentenone prostaglandin (CyPG) J₂ series, including prostaglandin J₂ (PGJ₂), Δ¹²-PGJ₂, and 15-deoxy-∆¹²,¹⁴-prostaglandin J₂ (15d-PGJ₂), are active metabolites of PGD₂, exerting multiple effects on neuronal function. However, the physiologic relevance of these effects remains uncertain as brain concentrations of CyPGs have not been precisely determined. In this study, we found that free PGD₂ and the J₂ series CyPGs (PGJ₂, Δ¹²-PGJ₂, and 15d-PGJ₂) were increased in post-ischemic rat brain as detected by UPLC-MS/MS with 15d-PGJ₂ being the most abundant CyPG. These increases were attenuated by pre-treating with the cyclooxygenase (COX) inhibitor piroxicam. Next, effects of chronic exposure to 15d-PGJ₂ were examined by treating primary neurons with 15d-PGJ₂, CAY10410 (a 15d-PGJ₂ analog lacking the cyclopentenone ring structure), or vehicle for 24 to 96 h. Because we found that the concentration of free 15d-PGJ₂ decreased rapidly in cell culture medium, freshly prepared medium containing 15d-PGJ₂, CAY10410, or vehicle was changed twice daily to maintain steady extracellular concentrations. Incubation with 2.5 μM 15d-PGJ₂, but not CAY10410, increased the neuronal cell death without the induction of caspase-3 or PARP cleavage, consistent with a primarily necrotic mechanism for 15d-PGJ₂-induced cell death which was further supported by TUNEL assay results. Ubiquitinated protein accumulation and aggregation was observed after 96 h 15d-PGJ₂ incubation, accompanied by compromised 20S proteasome activity. Unlike another proteasome inhibitor, MG132, 15d-PGJ₂ treatment did not activate autophagy or induce aggresome formation. Therefore, the cumulative cytotoxic effects of increased generation of CyPGs after stroke may contribute to delayed post-ischemic neuronal injury.
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Affiliation(s)
- Hao Liu
- Geriatric Research Education and Clinical Center 00-GR-H, V.A. Pittsburgh Healthcare, 7180 Highland Drive, Pittsburgh, PA 15206, USA
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20
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McGinn MJ, Colello RJ, Sun D. Age-related proteomic changes in the subventricular zone and their association with neural stem/progenitor cell proliferation. J Neurosci Res 2012; 90:1159-68. [PMID: 22344963 DOI: 10.1002/jnr.23012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 11/23/2011] [Accepted: 11/26/2011] [Indexed: 01/26/2023]
Abstract
In the mammalian central nervous system, generation of new neurons persists in the subventricular zone (SVZ) throughout life. However, the capacity for neurogenesis in this region declines with aging. Recent studies have examined the degree of these age-related neurogenic declines and the changes of cytoarchitecture of the SVZ with aging. However, little is known about the molecular changes in the SVZ with aging. In this study, we dissected the SVZs from rats aged postnatal day 28, 3 months, and 24 months. The SVZ tissues were processed for 2-D gel electrophoresis to identify protein changes following aging. Protein spots were subsequently subjected to mass spectrometry analysis to compare age-related alterations in the SVZ proteome. We also examined the level of cell proliferation in the SVZ in animals of these three age groups by using bromodeoxyuridine labeling. We found significant age-related changes in the expression of several proteins that play critical roles in the proliferation and survival of neural stem/progenitor cells in the SVZ. Among these proteins, glial fibrillary acidic protein, ubiquitin carboxy terminal hydrolase 1, glutathione S-transferase omega, and preproalbumin were increased with aging, whereas collapsin response-mediated protein 4 (CRMP-4), CRMP-5, and microsomal protease ER60 exhibited declines with aging. We have also observed a significant decline of neural stem/progenitor cell proliferation in the SVZ with aging. These alterations in protein expression in the SVZ with aging likely underlie the diminishing proliferative capacity of stem/progenitor cells in the aging brain.
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Affiliation(s)
- Melissa J McGinn
- Department of Anatomy and Neurobiology, Medical College of Virginia, Virginia Commonwealth University, Richmond, Virginia 23298, USA
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21
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Gasperini L, Piubelli C, Carboni L. Proteomics of rat hypothalamus, hippocampus and pre-frontal/frontal cortex after central administration of the neuropeptide PACAP. Mol Biol Rep 2011; 39:2921-35. [PMID: 21687973 DOI: 10.1007/s11033-011-1054-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2010] [Accepted: 06/08/2011] [Indexed: 11/25/2022]
Abstract
Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuropeptide that exerts pleiotropic functions, acting as a hypophysiotropic factor, a neurotrophic and a neuroprotective agent. The molecular pathways activated by PACAP to exert its physiological roles in brain are incompletely understood. In this study, adrenocorticotropic hormone (ACTH), prolactin, luteinising hormone (LH), follicle-stimulating hormone (FSH), thyroid-stimulating hormone (TSH), brain-derived neurotrophic factor and corticosterone blood levels were determined before and 20, 40, 60, and 120 min after PACAP intracerebroventricular administration. PACAP treatment increased ACTH, corticosterone, LH and FSH blood concentrations, while it decreased TSH levels. A proteomics investigation was carried out in hypothalamus, hippocampus and pre-frontal/frontal cortex (P/FC) using 2-dimensional gel electrophoresis at 120 min, the end-point suggested by studies on PACAP hypophysiotropic activities. Spots showing statistically significant alterations after PACAP treatment were identified by Matrix-assisted laser desorption/ionization-Time of flight mass spectrometry. Identified proteins were consistent with PACAP involvement in different molecular processes in brain. Altered expression levels were observed for proteins involved in cytoskeleton modulation and synaptic plasticity: actin in the hypothalamus; stathmin, dynamin, profilin and cofilin in hippocampus; synapsin in P/FC. Proteins involved in cellular differentiation were also modulated: glutathione-S-transferase α and peroxiredoxin in hippocampus; nucleoside diphosphate kinase in P/FC. Alterations were detected in proteins involved in neuroprotection, neurodegeneration and apoptosis: ubiquitin carboxyl-terminal hydrolase isozyme L1 and heat shock protein 90-β in hypothalamus; α-synuclein in hippocampus; glyceraldehyde-3-phosphate dehydrogenase and prohibitin in P/FC. This proteomics study identified new proteins involved in molecular mechanisms mediating PACAP functions in the central nervous system.
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Affiliation(s)
- Lisa Gasperini
- Neurosciences CEDD, GlaxoSmithKline Medicines Research Centre, Via A Fleming 4, 37135 Verona, Italy
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22
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Matsunaga E, Okanoya K. Comparative gene expression analysis among vocal learners (bengalese finch and budgerigar) and non-learners (quail and ring dove) reveals variable cadherin expressions in the vocal system. Front Neuroanat 2011; 5:28. [PMID: 21541260 PMCID: PMC3083831 DOI: 10.3389/fnana.2011.00028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2010] [Accepted: 04/07/2011] [Indexed: 11/13/2022] Open
Abstract
Birds use various vocalizations to communicate with one another, and some are acquired through learning. So far, three families of birds (songbirds, parrots, and hummingbirds) have been identified as having vocal learning ability. Previously, we found that cadherins, a large family of cell-adhesion molecules, show vocal control-area-related expression in a songbird, the Bengalese finch. To investigate the molecular basis of evolution in avian species, we conducted comparative analysis of cadherin expressions in the vocal and other neural systems among vocal learners (Bengalese finch and budgerigar) and a non-learner (quail and ring dove). The gene expression analysis revealed that cadherin expressions were more variable in vocal and auditory areas compared to vocally unrelated areas such as the visual areas among these species. Thus, it appears that such diverse cadherin expressions might have been related to generating species diversity in vocal behavior during the evolution of avian vocal learning.
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Affiliation(s)
- Eiji Matsunaga
- Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute, Wako Saitama, Japan
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23
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Abstract
The ubiquitin/proteasome pathway is the major proteolytic quality control system in cells. In this review we discuss the impact of a deregulation of this pathway on neuronal function and its causal relationship to the intracellular deposition of ubiquitin protein conjugates in pathological inclusion bodies in all the major chronic neurodegenerative disorders, such as Alzheimer's, Parkinson's and Huntington's diseases as well as amyotrophic lateral sclerosis. We describe the intricate nature of the ubiquitin/proteasome pathway and discuss the paradox of protein aggregation, i.e. its potential toxic/protective effect in neurodegeneration. The relations between some of the dysfunctional components of the pathway and neurodegeneration are presented. We highlight possible ubiquitin/proteasome pathway-targeting therapeutic approaches, such as activating the proteasome, enhancing ubiquitination and promoting SUMOylation that might be important to slow/treat the progression of neurodegeneration. Finally, a model time line is presented for neurodegeneration starting at the initial injurious events up to protein aggregation and cell death, with potential time points for therapeutic intervention.
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Wang R, Zhang M, Zhou W, Ly PTT, Cai F, Song W. NF-κB signaling inhibits ubiquitin carboxyl-terminal hydrolase L1 gene expression. J Neurochem 2011; 116:1160-70. [PMID: 21210816 DOI: 10.1111/j.1471-4159.2011.07172.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1) is a deubiquitinating enzyme that plays a regulatory role in targeting proteins for proteasomal degradation. UCH-L1 is highly expressed in neurons and has been demonstrated to promote cell viability and maintain neuronal integrity. Reduced UCH-L1 levels have been observed in various neurodegenerative diseases, and expression of UCH-L1 can rescue synaptic dysfunction and memory deficits in Alzheimer's Disease model mice. However, the mechanisms regulating UCH-L1 expression have not been determined. In this study, we cloned a 1782 bp of the 5' flanking region of the human UCH-L1 gene and identified a 43 bp fragment containing the transcription start site as the minimal region necessary for promoter activity. Sequence analysis revealed several putative regulatory elements including NF-κB, NFAT, CREB, NRSF, YY1, AP1, and STAT in the UCH-L1 promoter. A functional NF-κB response element was identified in the UCH-L1 promoter region. Expression of NF-κB suppressed UCH-L1 gene transcription. In the RelA knockout system where NF-κB activity is ablated, UCH-L1 expression was significantly increased. Furthermore, activation of NF-κB signaling by the inflammatory stimulator lipopolysaccharide and TNFα resulted in a decrease of UCH-L1 gene expression by inhibiting its transcription. As NF-κB is an important signaling module in inflammatory response, our study suggests a possibility that inflammation might compromise neuronal functions via the interaction of NF-κB and UCH-L1. A better understanding of the NF-κB-regulated UCH-L1 transcription will provide insights to the role of inflammatory responses in Alzheimer's disease and Parkinson's disease.
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Affiliation(s)
- Ruitao Wang
- Department of Psychiatry, Brain Research Center, The University of British Columbia, Vancouver, British Columbia, Canada
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25
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Grillari J, Grillari-Voglauer R, Jansen-Dürr P. Post-translational modification of cellular proteins by ubiquitin and ubiquitin-like molecules: role in cellular senescence and aging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 694:172-96. [PMID: 20886764 DOI: 10.1007/978-1-4419-7002-2_13] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ubiquitination ofendogenous proteins is one of the key regulatory steps that guides protein degradation through regulation of proteasome activity. During the last years evidence has accumulated that proteasome activity is decreased during the aging process in various model systems and that these changes might be causally related to aging and age-associated diseases. Since in most instances ubiquitination is the primary event in target selection, the system ofubiquitination and deubiquitination might be of similar importance. Furthermore, ubiquitination and proteasomal degradation are not completely congruent, since ubiquitination confers also functions different from targeting proteins for degradation. Depending on mono- and polyubiquitination and on how ubiquitin chains are linked together, post-translational modifications of cellular proteins by covalent attachment of ubiquitin and ubiquitin-like proteins are involved in transcriptional regulation, receptor internalization, DNA repair, stabilization of protein complexes and autophagy. Here, we summarize the current knowledge regarding the ubiquitinome and the underlying ubiquitin ligases and deubiquitinating enzymes in replicative senescence, tissue aging as well as in segmental progeroid syndromes and discuss potential causes and consequences for aging.
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Affiliation(s)
- Johannes Grillari
- Institute of Applied Microbiology, Department of Biotechnology, University for Natural Resources and Applied Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria.
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26
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Day IN, Thompson RJ. UCHL1 (PGP 9.5): Neuronal biomarker and ubiquitin system protein. Prog Neurobiol 2010; 90:327-62. [DOI: 10.1016/j.pneurobio.2009.10.020] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 10/18/2009] [Accepted: 10/21/2009] [Indexed: 12/16/2022]
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Transgenic songbirds offer an opportunity to develop a genetic model for vocal learning. Proc Natl Acad Sci U S A 2009; 106:17963-7. [PMID: 19815496 DOI: 10.1073/pnas.0909139106] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Zebra finches are widely used for studying the basic biology of vocal learning. The inability to introduce genetic modifications in these animals has substantially limited studies on the molecular biology of this behavior, however. We used an HIV-based lentivirus to produce germline transgenic zebra finches. The lentivirus encoded the GFP regulated by the human ubiquitin-C promoter [Lois C, Hong EJ, Pease S, Brown EJ, Baltimore D (2002) Science 295:868-872], which is active in a wide variety of cells. The virus was injected into the very early embryo (blastodisc stage) to target the primordial germline cells that later give rise to sperm and eggs. A total of 265 fertile eggs were injected with virus, and 35 hatched (13%); 23 of these potential founders (F0) were bred, and three (13%) produced germline transgenic hatchlings that expressed the GFP protein (F1). Two of these three founders (F0) have produced transgenic young at a rate of 12% and the third at a rate of 6%. Furthermore, two of the F1 generation transgenics have since reproduced, one having five offspring (all GFP positive) and the other four offsping (one GFP positive).
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28
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Matsunaga E, Okanoya K. Evolution and diversity in avian vocal system: An Evo-Devo model from the morphological and behavioral perspectives. Dev Growth Differ 2009; 51:355-67. [DOI: 10.1111/j.1440-169x.2009.01091.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Yasuda T, Nihira T, Ren YR, Cao XQ, Wada K, Setsuie R, Kabuta T, Wada K, Hattori N, Mizuno Y, Mochizuki H. Effects of UCH-L1 on α-synuclein over-expression mouse model of Parkinson’s disease. J Neurochem 2009; 108:932-44. [DOI: 10.1111/j.1471-4159.2008.05827.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Allain H, Bentué-Ferrer D, Akwa Y. Disease-modifying drugs and Parkinson's disease. Prog Neurobiol 2007; 84:25-39. [PMID: 18037225 DOI: 10.1016/j.pneurobio.2007.10.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Accepted: 10/11/2007] [Indexed: 12/21/2022]
Abstract
Symptomatic medications, l-Dopa and dopaminergic agents, remain the only clinically pertinent pharmacological treatment proven effective and available for the large population of patients with Parkinson's disease. The challenge for the pharmaceutical industry is to develop disease-modifying drugs which could arrest, delay or at least oppose the progression of the specific pathogenic processes underlying Parkinson's disease. The purpose of this review, based on recent biological and genetic data to be validated with appropriate animal models, was to re-examine the putative neuroprotective agents in Parkinson's disease and discuss the development of new strategies with the ultimate goal of demonstrating neurocytoprotective activity in this neurodegenerative disease. Since guidelines for research on neurocytoprotective drugs remain to be written, innovation will be the key to success of future clinical trials. It is reasonable to expect that future advances in our understanding of the pathogenic processes of Parkinson's disease will open the way to new perspectives for the treatment of other neurodegenerative diseases.
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Affiliation(s)
- Hervé Allain
- Laboratoire de Pharmacologie Expérimentale et Clinique, Faculté de Médecine, 2 av. du Pr Léon Bernard, F-35043 Rennes, France
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31
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Yang P, Smalle J, Lee S, Yan N, Emborg TJ, Vierstra RD. Ubiquitin C-terminal hydrolases 1 and 2 affect shoot architecture in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 51:441-57. [PMID: 17559514 DOI: 10.1111/j.1365-313x.2007.03154.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Ubiquitin C-terminal hydrolases (UCHs) are a subset of de-ubiquitinating proteases that release covalently linked ubiquitin (Ub), and as such play essential roles in recycling Ub and reversing the action of Ub conjugation. We show here that two related Arabidopsis UCHs, UCH1, and UCH2, are important for shoot development. The UCH1 and 2 genes are ubiquitously expressed, with the corresponding proteins present in both the cytoplasm and nucleus. Unlike their animal and fungal counterparts, we found no evidence that the Arabidopsis UCH1 and 2 proteins stably associate with the 26S proteasome. Altering the levels of UCH1 and 2 has substantial effects on Arabidopsis shoot development, especially with respect to inflorescence architecture, with over-expression and double mutants enhancing and suppressing the outgrowth of cauline branches, respectively. Neither UCH1-over-expressing nor uch1-1 uch2-1 plants have detectably altered sensitivity to cytokinins or auxins individually, but exhibit an altered sensitivity to the ratio of the two hormones. UCH1-over-expressing plants show dramatically enhanced phenotypes when combined with auxin-insensitive mutants axr1-3 and axr2-1, suggesting that one or more aspects of auxin signaling are affected by this enzyme pair. Previous studies revealed that the ubiquitination and degradation of the AUX/IAA family of repressors is a key step in auxin signaling. Here, we show that turnover of a reporter fused to a representative AUX/IAA protein AXR3 is faster in the uch1-1 uch2-1 double mutant but slower in the UCH1 over-expression backgrounds. Taken together, our results indicate that de-ubiquitination helps to modify plant shoot architecture, possibly via its ability to directly or indirectly protect upstream target proteins involved in auxin/cytokinin signaling from Ub-mediated degradation.
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Affiliation(s)
- Peizhen Yang
- Department of Genetics, University of Wisconsin-Madison, Madison, WI 53706-1574, USA
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32
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Grillari J, Katinger H, Voglauer R. Aging and the ubiquitinome: traditional and non-traditional functions of ubiquitin in aging cells and tissues. Exp Gerontol 2006; 41:1067-79. [PMID: 17052881 DOI: 10.1016/j.exger.2006.07.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 07/13/2006] [Accepted: 07/18/2006] [Indexed: 01/01/2023]
Abstract
Ubiquitination of endogenous proteins is one of the key regulatory steps of protein degradation followed by regulation of proteasome activity. During the last years evidence has increased that proteasome activity is decreased during the aging process in various model systems and that these changes might be causally related to aging and aging associated diseases. Since in most instances ubiquitination is the primary event in target selection, the system of ubiquitination and deubiquitination might be of similar importance. Furthermore, ubiquitination and proteasomal degradation are not completely congruent, since ubiquitination also confers functions different from giving "the kiss of death" to proteins. Depending on mono- and polyubiquitination and on how ubiquitin chains are linked together, ubiquitination is involved in transcriptional regulation, receptor internalization, DNA repair, and stabilization of protein complexes. This review is therefore the first to summarize the current knowledge regarding the ubiquitinome and the underlying ubiquitin ligases and deubiquitinating enzymes in replicative senescence, tissue aging as well as in segmental progeroid syndromes and to discuss potential causes and consequences for aging.
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Affiliation(s)
- Johannes Grillari
- Department of Biotechnology, Institute of Applied Microbiology, University of Natural Resources and Applied Life Sciences, Vienna Muthgasse 18, A-1190 Vienna, Austria.
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33
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Wada K, Howard JT, McConnell P, Whitney O, Lints T, Rivas MV, Horita H, Patterson MA, White SA, Scharff C, Haesler S, Zhao S, Sakaguchi H, Hagiwara M, Shiraki T, Hirozane-Kishikawa T, Skene P, Hayashizaki Y, Carninci P, Jarvis ED. A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes. Proc Natl Acad Sci U S A 2006; 103:15212-7. [PMID: 17018643 PMCID: PMC1622802 DOI: 10.1073/pnas.0607098103] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2006] [Indexed: 11/18/2022] Open
Abstract
Songbirds have one of the most accessible neural systems for the study of brain mechanisms of behavior. However, neuroethological studies in songbirds have been limited by the lack of high-throughput molecular resources and gene-manipulation tools. To overcome these limitations, we constructed 21 regular, normalized, and subtracted full-length cDNA libraries from brains of zebra finches in 57 developmental and behavioral conditions in an attempt to clone as much of the brain transcriptome as possible. From these libraries, approximately 14,000 transcripts were isolated, representing an estimated 4,738 genes. With the cDNAs, we created a hierarchically organized transcriptome database and a large-scale songbird brain cDNA microarray. We used the arrays to reveal a set of 33 genes that are regulated in forebrain vocal nuclei by singing behavior. These genes clustered into four anatomical and six temporal expression patterns. Their functions spanned a large range of cellular and molecular categories, from signal transduction, trafficking, and structural, to synaptically released molecules. With the full-length cDNAs and a lentiviral vector system, we were able to overexpress, in vocal nuclei, proteins of representative singing-regulated genes in the absence of singing. This publicly accessible resource http://songbirdtranscriptome.net can now be used to study molecular neuroethological mechanisms of behavior.
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Affiliation(s)
| | | | - Patrick McConnell
- Duke Bioinformatics Shared Resource, Duke University Medical Center, Durham, NC 27710
| | | | - Thierry Lints
- Department of Biology, City College of New York, New York, NY 10031
| | | | | | | | - Stephanie A. White
- Department of Physiological Science, University of California, Los Angeles, CA 90095
| | - Constance Scharff
- Neurobiology Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Sebastian Haesler
- Neurobiology Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | | | - Hironobu Sakaguchi
- **Department of Physiology and Biological Information, Dokkyo Medical University, Tochigi 321-0293, Japan
| | - Masatoshi Hagiwara
- Department of Functional Genomics, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Toshiyuki Shiraki
- Genome Science Laboratory, RIKEN, Wako Main Campus, Saitama 351-0198, Japan; and
- Laboratory for Genome Exploration Research Group, RIKEN Yokohama Institute, Yokohama 230-0045, Japan
| | - Tomoko Hirozane-Kishikawa
- Genome Science Laboratory, RIKEN, Wako Main Campus, Saitama 351-0198, Japan; and
- Laboratory for Genome Exploration Research Group, RIKEN Yokohama Institute, Yokohama 230-0045, Japan
| | | | - Yoshihide Hayashizaki
- Genome Science Laboratory, RIKEN, Wako Main Campus, Saitama 351-0198, Japan; and
- Laboratory for Genome Exploration Research Group, RIKEN Yokohama Institute, Yokohama 230-0045, Japan
| | - Piero Carninci
- Genome Science Laboratory, RIKEN, Wako Main Campus, Saitama 351-0198, Japan; and
- Laboratory for Genome Exploration Research Group, RIKEN Yokohama Institute, Yokohama 230-0045, Japan
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34
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Weiler E, Benali A. Olfactory epithelia differentially express neuronal markers. ACTA ACUST UNITED AC 2006; 34:217-40. [PMID: 16841165 DOI: 10.1007/s11068-005-8355-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Revised: 02/17/2006] [Accepted: 03/02/2006] [Indexed: 01/09/2023]
Abstract
All three olfactory epithelia, the olfactory epithelium proper (OE), the septal organ of Masera (SO), and the vomeronasal organ of Jacobson (VNO) originate from the olfactory placode. Here, their diverse neurochemical phenotypes were analyzed using the immunohistochemical expression pattern of different neuronal markers. The olfactory bulb (OB) served as neuronal control. Neuronal Nuclei Marker (NeuN) is neither expressed in sensory neurons in any of the three olfactory epithelia, nor in relay neurons (mitral/tufted cells) of the OB. However, OB interneurons (periglomerular/granule cells) labeled, as did supranuclear structures of VNO supporting cells and VNO glands. Protein Gene Product 9.5 (PGP9.5 = C-terminal ubiquitin hydrolase L1 = UCHL1) expression is exactly the opposite: all olfactory sensory neurons express PGP9.5 as do OB mitral/tufted cells but not interneurons. Neuron Specific Enolase (NSE) expression is highest in the most apically located OE and SO sensory neurons and patchy in VNO. In contrast, the cytoplasm of the most basally located neurons of OE and SO immunoreacted for Growth Associated Protein 43 (GAP-43/B50). In VNO neurons GAP-43 labeling is also nuclear. In the cytoplasm, Olfactory Marker Protein (OMP) is most intensely expressed in SO, followed by OE and least in VNO neurons; further, OMP is also expressed in the nucleus of basally located VNO neurons. OB mitral/tufted cells express OMP at low levels. Neurons closer to respiratory epithelium often expressed a higher level of neuronal markers, suggesting a role of those markers for neuronal protection against take-over. Within the VNO the neurons show clear apical-basal expression diversity, as they do for factors of the signal transduction cascade. Overall, expression patterns of the investigated neuronal markers suggest that OE and SO are more similar to each other than to VNO.
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Affiliation(s)
- Elke Weiler
- Department of Neurophysiology, Ruhr-University Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
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35
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Abstract
The cellular complexity of the brain is a major issue in the planning, execution and interpretation of microarray studies. Recent technical advances allow for high-throughput study of specific cell populations and circuits. Here we review representative examples of currently available methods that allow high resolution and specificity in brain microarray studies, while maintaining the goal of comprehensive, high-throughput analysis.
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Affiliation(s)
- Giovanni Coppola
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
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Lombardino AJ, Hertel M, Li XC, Haripal B, Martin-Harris L, Pariser E, Nottebohm F. Expression profiling of intermingled long-range projection neurons harvested by laser capture microdissection. J Neurosci Methods 2006; 157:195-207. [PMID: 16750569 DOI: 10.1016/j.jneumeth.2006.04.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Revised: 04/10/2006] [Accepted: 04/10/2006] [Indexed: 01/26/2023]
Abstract
Gene expression data are most useful if they can be associated with specific cell types. This is particularly so in an organ such as the brain, where many different cell types lie in close proximity to each other. We used zebra finches (Taeniopygia guttata), fluorescent tracers and laser capture microdissection (LCM) to collect projection neurons and their RNAs from two interspersed populations from the same animal. RNA amplified from each cell class was reverse transcribed, fluorescently labeled, and hybridized to cDNA microarrays of genes expressed in the zebra finch brain. We applied strict fold-expression criteria, supplemented by statistical analysis, to single out genes that showed the most extreme and consistent differential expression between the two cell classes. Confirmation of the true expression pattern of these genes was made by in situ hybridization and Taqman quantitative PCR (qPCR). High quality RNA was obtained, too, from backfilled neurons birth-dated with bromodeoxyuridine (BrdU). We also quantified changes in the levels of three genes after singing behavior using qPCR. Thus, we have brought together a combination of techniques allowing for the molecular profiling of intermingled populations of projection neurons of known connectivity, age and experience, which should constitute a powerful tool for CNS research.
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Affiliation(s)
- Anthony J Lombardino
- Laboratory of Animal Behavior, The Rockefeller University, New York, NY 10021, USA.
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Forero DA, Benítez B, Arboleda G, Yunis JJ, Pardo R, Arboleda H. Analysis of functional polymorphisms in three synaptic plasticity-related genes (BDNF, COMT AND UCHL1) in Alzheimer's disease in Colombia. Neurosci Res 2006; 55:334-41. [PMID: 16698101 DOI: 10.1016/j.neures.2006.04.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Revised: 04/03/2006] [Accepted: 04/05/2006] [Indexed: 12/14/2022]
Abstract
In recent years, it has been proposed that synaptic dysfunction may be an important etiological factor for Alzheimer's disease (AD). This hypothesis has important implications for the analysis of AD genetic risk in case-control studies. In the present work, we analyzed common functional polymorphisms in three synaptic plasticity-related genes (brain-derived neurotrophic factor, BDNF Val66Met; catechol-O-methyl transferase, COMT Val158; ubiquitin carboxyl-terminal hydroxylase, UCHL1 S18Y) in a sample of 102 AD cases and 168 age and sex matched controls living in Bogotá, Colombia. There was not association between UCHL1 polymorphism and AD in our sample. We have found an initial association with BDNF polymorphism in familial cases and with COMT polymorphism in male and sporadic patients. These initial associations were lost after Bonferroni correction for multiple testing. Unadjusted results may be compatible with the expected functional effect of variations in these genes on pathological memory and cognitive dysfunction, as has been implicated in animal and cell models and also from neuropsychological analysis of normal subjects carriers of the AD associated genotypes. An exploration of functional variants in these and in other synaptic plasticity-related genes (a synaptogenomics approach) in independent larger samples will be important to discover new genes associated with AD.
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Affiliation(s)
- Diego A Forero
- Grupo de Neurociencias, Facultad de Medicina e Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
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Abstract
During the past several years, evidence has accumulated suggesting a relationship between newly born cells in the hippocampus and various types of learning and memory. However, most of the evidence is correlational and some of it does not agree. This review discusses both sides of this issue, considering the effects of learning on the production of new neurons in the dentate gyrus and the question of whether newly born cells participate in learning and memory.
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Affiliation(s)
- Benedetta Leuner
- Department of Psychology, Princeton University, Princeton, New Jersey 08544, USA
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39
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Neuronal gene expression profiling: uncovering the molecular biology of neurodegenerative disease. PROGRESS IN BRAIN RESEARCH 2006; 158:197-222. [PMID: 17027698 DOI: 10.1016/s0079-6123(06)58010-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The development of gene array techniques to quantify expression levels of dozens to thousands of genes simultaneously within selected tissue samples from control and diseased brain has enabled researchers to generate expression profiles of vulnerable neuronal populations in several neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, schizophrenia, multiple sclerosis, and Creutzfeld-Jakob disease. Intriguingly, gene expression analysis reveals that vulnerable brain regions in many of these diseases share putative pathogenetic alterations in common classes of genes, including decrements in synaptic transcript levels and increments in immune response transcripts. Thus, gene expression profiles of diseased neuronal populations may reveal mechanistic clues to the molecular pathogenesis underlying various neurological diseases and aid in identifying potential therapeutic targets. This chapter will review how regional and single cell gene array technologies have advanced our understanding of the genetics of human neurological disease.
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Shors TJ, Townsend DA, Zhao M, Kozorovitskiy Y, Gould E. Neurogenesis may relate to some but not all types of hippocampal-dependent learning. Hippocampus 2002; 12:578-84. [PMID: 12440573 PMCID: PMC3289536 DOI: 10.1002/hipo.10103] [Citation(s) in RCA: 679] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The hippocampal formation generates new neurons throughout adulthood. Recent studies indicate that these cells possess the morphology and physiological properties of more established neurons. However, the function of adult generated neurons is still a matter of debate. We previously demonstrated that certain forms of associative learning can enhance the survival of new neurons and a reduction in neurogenesis coincides with impaired learning of the hippocampal-dependent task of trace eyeblink conditioning. Using the toxin methylazoxymethanol acetate (MAM) for proliferating cells, we tested whether reduction of neurogenesis affected learning and performance associated with different hippocampal dependent tasks: spatial navigation learning in a Morris water maze, fear responses to context and an explicit cue after training with a trace fear paradigm. We also examined exploratory behavior in an elevated plus maze. Rats were injected with MAM (7 mg/kg) or saline for 14 days, concurrent with BrdU, to label new neurons on days 10, 12, and 14. After treatment, groups of rats were tested in the various tasks. A significant reduction in new neurons in the adult hippocampus was associated with impaired performance in some tasks, but not with others. Specifically, treatment with the antimitotic agent reduced the amount of fear acquired after exposure to a trace fear conditioning paradigm but did not affect contextual fear conditioning or spatial navigation learning in the Morris water maze. Nor did MAM treatment affect exploration in the elevated plus maze. These results combined with previous ones suggest that neurogenesis may be associated with the formation of some but not all types of hippocampal-dependent memories.
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Affiliation(s)
- Tracey J Shors
- Department of Psychology and Center for Collaborative Neuroscience, Rutgers University, Piscataway, New Jersey 08854-8020, USA.
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