1
|
Mol P, Gopalakrishnan L, Chatterjee O, Mangalaparthi KK, Kumar M, Durgad SS, Nair B, Shankar SK, Mahadevan A, Prasad TSK. Proteomic Analysis of Adult Human Hippocampal Subfields Demonstrates Regional Heterogeneity in the Protein Expression. J Proteome Res 2022; 21:2293-2310. [PMID: 36039803 DOI: 10.1021/acs.jproteome.2c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Background: Distinct hippocampal subfields are known to get affected during aging, psychiatric disorders, and various neurological and neurodegenerative conditions. To understand the biological processes associated with each subfield, it is important to understand its heterogeneity at the molecular level. To address this lacuna, we investigated the proteomic analysis of hippocampal subfields─the cornu ammonis sectors (CA1, CA2, CA3, CA4) and dentate gyrus (DG) from healthy adult human cohorts. Findings: Microdissection of hippocampal subfields from archived formalin-fixed paraffin-embedded tissue sections followed by TMT-based multiplexed proteomic analysis resulted in the identification of 5,593 proteins. Out of these, 890 proteins were found to be differentially abundant among the subfields. Further bioinformatics analysis suggested proteins related to gene splicing, transportation, myelination, structural activity, and learning processes to be differentially abundant in DG, CA4, CA3, CA2, and CA1, respectively. A subset of proteins was selected for immunohistochemistry-based validation in an independent set of hippocampal samples. Conclusions: We believe that our findings will effectively pave the way for further analysis of the hippocampal subdivisions and provide awareness of its subfield-specific association to various neurofunctional anomalies in the future. The current mass spectrometry data is deposited and publicly made available through ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD029697.
Collapse
Affiliation(s)
- Praseeda Mol
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore 560066,India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Lathika Gopalakrishnan
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore 560066,India.,Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Oishi Chatterjee
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore 560066,India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India.,Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Kiran K Mangalaparthi
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore 560066,India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore 560066,India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Shwetha S Durgad
- Human Brain Tissue Repository, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Susarla K Shankar
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India.,Human Brain Tissue Repository, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India.,Human Brain Tissue Repository, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | | |
Collapse
|
2
|
Liu JYW, Dzurova N, Al-Kaaby B, Mills K, Sisodiya SM, Thom M. Granule Cell Dispersion in Human Temporal Lobe Epilepsy: Proteomics Investigation of Neurodevelopmental Migratory Pathways. Front Cell Neurosci 2020; 14:53. [PMID: 32256318 PMCID: PMC7090224 DOI: 10.3389/fncel.2020.00053] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/21/2020] [Indexed: 12/23/2022] Open
Abstract
Granule cell dispersion (GCD) is a common pathological feature observed in the hippocampus of patients with Mesial Temporal Lobe Epilepsy (MTLE). Pathomechanisms underlying GCD remain to be elucidated, but one hypothesis proposes aberrant reactivation of neurodevelopmental migratory pathways, possibly triggered by febrile seizures. This study aims to compare the proteomes of basal and dispersed granule cells in the hippocampus of eight MTLE patients with GCD to identify proteins that may mediate GCD in MTLE. Quantitative proteomics identified 1,882 proteins, of which 29% were found in basal granule cells only, 17% in dispersed only and 54% in both samples. Bioinformatics analyses revealed upregulated proteins in dispersed samples were involved in developmental cellular migratory processes, including cytoskeletal remodeling, axon guidance and signaling by Ras homologous (Rho) family of GTPases (P < 0.01). The expression of two Rho GTPases, RhoA and Rac1, was subsequently explored in immunohistochemical and in situ hybridization studies involving eighteen MTLE cases with or without GCD, and three normal post mortem cases. In cases with GCD, most dispersed granule cells in the outer-granular and molecular layers have an elongated soma and bipolar processes, with intense RhoA immunolabeling at opposite poles of the cell soma, while most granule cells in the basal granule cell layer were devoid of RhoA. A higher percentage of cells expressing RhoA was observed in cases with GCD than without GCD (P < 0.004). In GCD cases, the percentage of cells expressing RhoA was significantly higher in the inner molecular layer than the granule cell layer (P < 0.026), supporting proteomic findings. In situ hybridization studies using probes against RHOA and RAC1 mRNAs revealed fine peri- and nuclear puncta in granule cells of all cases. The density of cells expressing RHOA mRNAs was significantly higher in the inner molecular layer of cases with GCD than without GCD (P = 0.05). In summary, our study has found limited evidence for ongoing adult neurogenesis in the hippocampus of patients with MTLE, but evidence of differential dysmaturation between dispersed and basal granule cells has been demonstrated, and elevated expression of Rho GTPases in dispersed granule cells may contribute to the pathomechanisms underpinning GCD in MTLE.
Collapse
Affiliation(s)
- Joan Y W Liu
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, London, United Kingdom.,Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, United Kingdom.,School of Life Sciences, University of Westminster, London, United Kingdom
| | - Natasha Dzurova
- School of Life Sciences, University of Westminster, London, United Kingdom
| | - Batoul Al-Kaaby
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Kevin Mills
- Biological Mass Spectrometry Centre, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, United Kingdom.,Chalfont Centre for Epilepsy, Chalfont St Peter, United Kingdom
| | - Maria Thom
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, London, United Kingdom.,Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, United Kingdom
| |
Collapse
|
3
|
Schubert KO, Stacey D, Arentz G, Clark SR, Air T, Hoffmann P, Baune BT. Targeted proteomic analysis of cognitive dysfunction in remitted major depressive disorder: Opportunities of multi-omics approaches towards predictive, preventive, and personalized psychiatry. J Proteomics 2018; 188:63-70. [PMID: 29474866 DOI: 10.1016/j.jprot.2018.02.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 01/29/2018] [Accepted: 02/16/2018] [Indexed: 12/19/2022]
Abstract
In order to accelerate the understanding of pathophysiological mechanisms and clinical biomarker discovery and in psychiatry, approaches that integrate multiple -omics platforms are needed. We introduce a workflow that investigates a narrowly defined psychiatric phenotype, makes use of the potent and cost-effective discovery technology of gene expression microarrays, applies Weighted Gene Co-Expression Network Analysis (WGCNA) to better capture complex and polygenic traits, and finally explores gene expression findings on the proteomic level using targeted mass-spectrometry (MS) technologies. To illustrate the effectiveness of the workflow, we present a proteomic analysis of peripheral blood plasma from patient's remitted major depressive disorder (MDD) who experience ongoing cognitive deficits. We show that co-expression patterns previous detected on the transcript level could be replicated for plasma proteins, as could the module eigengene correlation with cognitive performance. Further, we demonstrate that functional analysis of multi-omics data has the potential to point to cellular mechanisms and candidate biomarkers for cognitive dysfunction in MDD, implicating cell cycle regulation by cyclin D3 (CCND3), regulation of protein processing in the endoplasmatic reticulum by Thioredoxin domain-containing protein 5 (TXND5), and modulation of inflammatory cytokines by Tripartite Motif Containing 26 (TRI26). SIGNIFICANCE This paper discusses how data from multiple -omics platforms can be integrated to accelerate biomarker discovery in psychiatry. Using the phenotype of cognitive impairment in remitted major depressive disorder (MDD) as an example, we show that the application of a systems biology approach - weighted gene co-expression network analysis (WGCNA) - in the discovery phase, and targeted proteomic follow-up of results, provides a structured avenue towards uncovering novel candidate markers and pathways for personalized clinical psychiatry.
Collapse
Affiliation(s)
- K Oliver Schubert
- Discipline of Psychiatry, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia; Mental Health Services, Northern Adelaide Local Health Network, Lyell McEwin Hospital, Elizabeth Vale, Australia.
| | - David Stacey
- Discipline of Psychiatry, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia; MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Georgia Arentz
- Biomaterials Engineering and Nanomedicine, Future Industries Institute, University of South Australia, Adelaide, Australia
| | - Scott R Clark
- Discipline of Psychiatry, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Tracy Air
- Discipline of Psychiatry, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Peter Hoffmann
- Biomaterials Engineering and Nanomedicine, Future Industries Institute, University of South Australia, Adelaide, Australia
| | - Bernhard T Baune
- Discipline of Psychiatry, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| |
Collapse
|
4
|
Schubert KO, Weiland F, Baune BT, Hoffmann P. The use of MALDI-MSI in the investigation of psychiatric and neurodegenerative disorders: A review. Proteomics 2016; 16:1747-58. [DOI: 10.1002/pmic.201500460] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/08/2016] [Accepted: 02/24/2016] [Indexed: 11/11/2022]
Affiliation(s)
| | - Florian Weiland
- Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
- Institute for Photonics and Advanced Sensing (IPAS); The University of Adelaide; Adelaide Australia
| | - Bernhard T. Baune
- Discipline of Psychiatry; The University of Adelaide; Adelaide Australia
| | - Peter Hoffmann
- Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
- Institute for Photonics and Advanced Sensing (IPAS); The University of Adelaide; Adelaide Australia
| |
Collapse
|
5
|
Kang MG, Byun K, Kim JH, Park NH, Heinsen H, Ravid R, Steinbusch HW, Lee B, Park YM. Proteogenomics of the human hippocampus: The road ahead. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:788-97. [PMID: 25770686 DOI: 10.1016/j.bbapap.2015.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 02/10/2015] [Accepted: 02/15/2015] [Indexed: 12/26/2022]
Abstract
The hippocampus is one of the most essential components of the human brain and plays an important role in learning and memory. The hippocampus has drawn great attention from scientists and clinicians due to its clinical importance in diseases such as Alzheimer's disease (AD), non-AD dementia, and epilepsy. Understanding the function of the hippocampus and related disease mechanisms requires comprehensive knowledge of the orchestration of the genome, epigenome, transcriptome, proteome, and post-translational modifications (PTMs) of proteins. The past decade has seen remarkable advances in the high-throughput sequencing techniques that are collectively called next generation sequencing (NGS). NGS enables the precise analysis of gene expression profiles in cells and tissues, allowing powerful and more feasible integration of expression data from the gene level to the protein level, even allowing "-omic" level assessment of PTMs. In addition, improved bioinformatics algorithms coupled with NGS technology are finally opening a new era for scientists to discover previously unidentified and elusive proteins. In the present review, we will focus mainly on the proteomics of the human hippocampus with an emphasis on the integrated analysis of genomics, epigenomics, transcriptomics, and proteomics. Finally, we will discuss our perspectives on the potential and future of proteomics in the field of hippocampal biology. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
Collapse
Affiliation(s)
- Myoung-Goo Kang
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - Kyunghee Byun
- Center for Genomics and Proteomics, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 406-840, Republic of Korea
| | - Jae Ho Kim
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea
| | - Nam Hyun Park
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Helmut Heinsen
- Morphological Brain Research Unit, Department of Psychiatry, Universität of Würzburg, Würzburg, Germany
| | - Rivka Ravid
- Brain Bank Consultant, Amsterdam, The Netherlands
| | - Harry W Steinbusch
- School for Mental Health and Neuroscience, Department of Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Bonghee Lee
- Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea.
| | - Young Mok Park
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Republic of Korea.
| |
Collapse
|
6
|
Severino G, Squassina A, Costa M, Pisanu C, Calza S, Alda M, Del Zompo M, Manchia M. Pharmacogenomics of bipolar disorder. Pharmacogenomics 2014; 14:655-74. [PMID: 23570469 DOI: 10.2217/pgs.13.51] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bipolar disorder (BD) is a lifelong severe psychiatric condition with high morbidity, disability and excess mortality. The longitudinal clinical trajectory of BD is significantly modified by pharmacological treatment(s), both in acute and in long-term stages. However, a large proportion of BD patients have inadequate response to pharmacological treatments. Pharmacogenomic research may lead to the identification of molecular predictors of treatment response. When integrated with clinical information, pharmacogenomic findings may be used in the future to determine the probability of response/nonresponse to treatment on an individual basis. Here we present a selective review of pharmacogenomic findings in BD. In light of the evidence suggesting a genetic effect of lithium reponse in BD, we focused particularly on the pharmacogenomic literature relevant to this trait. The article contributes a detailed overview of the current status of pharmacogenomics in BD and offers a perspective on the challenges that can hinder its transition to personalized healthcare.
Collapse
Affiliation(s)
- Giovanni Severino
- Laboratory of Molecular Genetics, Section of Neuroscience & Clinical Pharmacology, Department of Biomedical Sciences, Sp 8, Sestu-Monserrato, Km 0.700 CA, University of Cagliari, Cagliari, Italy
| | | | | | | | | | | | | | | |
Collapse
|
7
|
Lubec G. Focus on brain proteins and proteomics. Proteomics 2012; 12:2402-3. [PMID: 22903839 DOI: 10.1002/pmic.201270105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|