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Gamboa-Sánchez C, Becerril-Villanueva E, Alvarez-Herrera S, Leyva-Mascareño G, González-López SL, Estudillo E, Fernández-Molina AE, Elizalde-Contreras JM, Ruiz-May E, Segura-Cabrera A, Jiménez-Genchi J, Pavón L, Zamudio SR, Pérez-Sánchez G. Upregulation of S100A8 in peripheral blood mononuclear cells from patients with depression treated with SSRIs: a pilot study. Proteome Sci 2023; 21:23. [PMID: 38049858 PMCID: PMC10694904 DOI: 10.1186/s12953-023-00224-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Major depressive disorder (MDD) affects more than 350 million people worldwide, and there is currently no laboratory test to diagnose it. This pilot study aimed to identify potential biomarkers in peripheral blood mononuclear cells (PBMCs) from MDD patients. METHODS We used tandem mass tagging coupled to synchronous precursor selection (mass spectrometry) to obtain the differential proteomic profile from a pool of PBMCs from MDD patients and healthy subjects, and quantitative PCR to assess gene expression of differentially expressed proteins (DEPs) of our interest. RESULTS We identified 247 proteins, of which 133 had a fold change ≥ 2.0 compared to healthy volunteers. Using pathway enrichment analysis, we found that some processes, such as platelet degranulation, coagulation, and the inflammatory response, are perturbed in MDD patients. The gene-disease association analysis showed that molecular alterations in PBMCs from MDD patients are associated with cerebral ischemia, vascular disease, thrombosis, acute coronary syndrome, and myocardial ischemia, in addition to other conditions such as inflammation and diabetic retinopathy. CONCLUSIONS We confirmed by qRT-PCR that S100A8 is upregulated in PBMCs from MDD patients and thus could be an emerging biomarker of this disorder. This report lays the groundwork for future studies in a broader and more diverse population and contributes to a deeper characterization of MDD.
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Affiliation(s)
- Concepción Gamboa-Sánchez
- Laboratorio de Psicoinmunología, Instituto Nacional de Psiquiatría Ramón de La Fuente Muñiz, Colonia San Lorenzo Huipulco, Calzada México-Xochimilco 101, Tlalpan, 14370, Ciudad de Mexico, México
- Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Unidad Profesional Adolfo López Mateos, Av. Wilfrido Massieu 399, Nueva Industrial Vallejo, Gustavo A. Madero, 07738, Ciudad de México, México
| | - Enrique Becerril-Villanueva
- Laboratorio de Psicoinmunología, Instituto Nacional de Psiquiatría Ramón de La Fuente Muñiz, Colonia San Lorenzo Huipulco, Calzada México-Xochimilco 101, Tlalpan, 14370, Ciudad de Mexico, México
| | - Samantha Alvarez-Herrera
- Laboratorio de Psicoinmunología, Instituto Nacional de Psiquiatría Ramón de La Fuente Muñiz, Colonia San Lorenzo Huipulco, Calzada México-Xochimilco 101, Tlalpan, 14370, Ciudad de Mexico, México
| | - Gabriela Leyva-Mascareño
- Laboratorio de Psicoinmunología, Instituto Nacional de Psiquiatría Ramón de La Fuente Muñiz, Colonia San Lorenzo Huipulco, Calzada México-Xochimilco 101, Tlalpan, 14370, Ciudad de Mexico, México
| | - Sandra L González-López
- Laboratorio de Psicoinmunología, Instituto Nacional de Psiquiatría Ramón de La Fuente Muñiz, Colonia San Lorenzo Huipulco, Calzada México-Xochimilco 101, Tlalpan, 14370, Ciudad de Mexico, México
| | - Enrique Estudillo
- Laboratorio de Reprogramación Celular, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Av. Insurgentes Sur 3877 Del. Tlalpan, 14269. Col. La Fama., Ciudad de México, México
| | - Alberto E Fernández-Molina
- Laboratorio de Psicoinmunología, Instituto Nacional de Psiquiatría Ramón de La Fuente Muñiz, Colonia San Lorenzo Huipulco, Calzada México-Xochimilco 101, Tlalpan, 14370, Ciudad de Mexico, México
| | - José Miguel Elizalde-Contreras
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C, Cluster BioMimic®, Carretera Antigua a Coatepec 351, Congregación El Haya, 91073, Xalapa, Veracruz, México
| | - Eliel Ruiz-May
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C, Cluster BioMimic®, Carretera Antigua a Coatepec 351, Congregación El Haya, 91073, Xalapa, Veracruz, México
| | - Aldo Segura-Cabrera
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C, Cluster BioMimic®, Carretera Antigua a Coatepec 351, Congregación El Haya, 91073, Xalapa, Veracruz, México
- Genomic Sciences, GSK, Stevenage, UK
| | - Janeth Jiménez-Genchi
- Hospital Psiquiátrico Fray Bernardino Álvarez. Av, Niño Jesús, San Buenaventura 214000, Tlalpan, Ciudad de Mexico, México
| | - Lenin Pavón
- Laboratorio de Psicoinmunología, Instituto Nacional de Psiquiatría Ramón de La Fuente Muñiz, Colonia San Lorenzo Huipulco, Calzada México-Xochimilco 101, Tlalpan, 14370, Ciudad de Mexico, México
| | - Sergio Roberto Zamudio
- Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Unidad Profesional Adolfo López Mateos, Av. Wilfrido Massieu 399, Nueva Industrial Vallejo, Gustavo A. Madero, 07738, Ciudad de México, México.
| | - Gilberto Pérez-Sánchez
- Laboratorio de Psicoinmunología, Instituto Nacional de Psiquiatría Ramón de La Fuente Muñiz, Colonia San Lorenzo Huipulco, Calzada México-Xochimilco 101, Tlalpan, 14370, Ciudad de Mexico, México.
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Grieco SF, Johnston KG, Gao P, Garduño BM, Tang B, Yi E, Sun Y, Horwitz GD, Yu Z, Holmes TC, Xu X. Anatomical and molecular characterization of parvalbumin-cholecystokinin co-expressing inhibitory interneurons: implications for neuropsychiatric conditions. Mol Psychiatry 2023; 28:5293-5308. [PMID: 37443194 DOI: 10.1038/s41380-023-02153-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/15/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023]
Abstract
Inhibitory interneurons are crucial to brain function and their dysfunction is implicated in neuropsychiatric conditions. Emerging evidence indicates that cholecystokinin (CCK)-expressing interneurons (CCK+) are highly heterogenous. We find that a large subset of parvalbumin-expressing (PV+) interneurons express CCK strongly; between 40 and 56% of PV+ interneurons in mouse hippocampal CA1 express CCK. Primate interneurons also exhibit substantial PV/CCK co-expression. Mouse PV+/CCK+ and PV+/CCK- cells show distinguishable electrophysiological and molecular characteristics. Analysis of single nuclei RNA-seq and ATAC-seq data shows that PV+/CCK+ cells are a subset of PV+ cells, not of synuclein gamma positive (SNCG+) cells, and that they strongly express oxidative phosphorylation (OXPHOS) genes. We find that mitochondrial complex I and IV-associated OXPHOS gene expression is strongly correlated with CCK expression in PV+ interneurons at both the transcriptomic and protein levels. Both PV+ interneurons and dysregulation of OXPHOS processes are implicated in neuropsychiatric conditions, including autism spectrum (ASD) disorder and schizophrenia (SCZ). Analysis of human brain samples from patients with these conditions shows alterations in OXPHOS gene expression. Together these data reveal important molecular characteristics of PV-CCK co-expressing interneurons and support their implication in neuropsychiatric conditions.
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Affiliation(s)
- Steven F Grieco
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
- Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA
| | - Kevin G Johnston
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
- Department of Mathematics, School of Physical Sciences, University of California, Irvine, CA, 92697, USA
| | - Pan Gao
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - B Maximiliano Garduño
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Bryan Tang
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Elsie Yi
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Yanjun Sun
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Gregory D Horwitz
- Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, 98195, USA
| | - Zhaoxia Yu
- Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA
- Department of Statistics, Donald Bren School of Information and Computer Sciences, University of California, Irvine, CA, 92697, USA
| | - Todd C Holmes
- Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA.
- Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA.
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, 92697, USA.
- Department of Biomedical Engineering, University of California, Irvine, CA, 92697, USA.
- Department of Computer Science, University of California, Irvine, CA, 92697, USA.
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Hasan B, Khan A, Lenz C, Asif AR, Ahmed N. Characterization of functional protein complexes from Alzheimer's disease and healthy brain by mass spectrometry-based proteome analysis. Sci Rep 2021; 11:13891. [PMID: 34230543 DOI: 10.1038/s41598-021-93356-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 06/08/2021] [Indexed: 11/09/2022] Open
Abstract
Alzheimer’s disease (AD) is a complex neurodegenerative disorder with impaired protein activities. Proteins in the form of complexes have a ubiquitous role in diverse range of cellular functions. The key challenge is to identify novel disease associated protein complexes and their potential role in the progression of AD pathology. Protein complexes were obtained from AD brain prefrontal cortex and age matched controls by Blue Native-Polyacrylamide Gel Electrophoresis. A proteomic analysis was performed using second dimension SDS-PAGE followed by nano LC–MS/MS. Differentially expressed proteins were mapped to existing biological networks by Ingenuity Pathway Analysis (IPA). A total of 13 protein complexes with their interacting proteins were resolved on SDS-PAGE. We identified 34 protein spots and found significant abundance difference between the two experimental samples. IPA analysis revealed degeneration of neurons and cell death as a major consequence of protein dysregulation. Furthermore, focused network analysis suggested an integrated regulation of the identified proteins through APP and MAPT dependent mechanisms. The interacting differentially expressed proteins in AD were found to be part of concomitant signaling cascades terminating in neuronal cell death. The identified protein networks and pathways warrant further research to study their actual contribution to AD pathology.
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Srivastava A, Singh P, Gupta H, Kaur H, Kanojia N, Guin D, Sood M, Chadda RK, Yadav J, Vohora D, Saso L, Kukreti R. Systems Approach to Identify Common Genes and Pathways Associated with Response to Selective Serotonin Reuptake Inhibitors and Major Depression Risk. Int J Mol Sci 2019; 20:E1993. [PMID: 31018568 DOI: 10.3390/ijms20081993] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/17/2019] [Accepted: 04/20/2019] [Indexed: 12/27/2022] Open
Abstract
Despite numerous studies on major depressive disorder (MDD) susceptibility, the precise underlying molecular mechanism has not been elucidated which restricts the development of etiology-based disease-modifying drug. Major depressive disorder treatment is still symptomatic and is the leading cause of (~30%) failure of the current antidepressant therapy. Here we comprehended the probable genes and pathways commonly associated with antidepressant response and MDD. A systematic review was conducted, and candidate genes/pathways associated with antidepressant response and MDD were identified using an integrative genetics approach. Initially, single nucleotide polymorphisms (SNPs)/genes found to be significantly associated with antidepressant response were systematically reviewed and retrieved from the candidate studies and genome-wide association studies (GWAS). Also, significant variations concerning MDD susceptibility were extracted from GWAS only. We found 245 (Set A) and 800 (Set B) significantly associated genes with antidepressant response and MDD, respectively. Further, gene set enrichment analysis revealed the top five co-occurring molecular pathways (p ≤ 0.05) among the two sets of genes: Cushing syndrome, Axon guidance, cAMP signaling pathway, Insulin secretion, and Glutamatergic synapse, wherein all show a very close relation to synaptic plasticity. Integrative analyses of candidate gene and genome-wide association studies would enable us to investigate the putative targets for the development of disease etiology-based antidepressant that might be more promising than current ones.
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Fernández-Tajes J, Gaulton KJ, van de Bunt M, Torres J, Thurner M, Mahajan A, Gloyn AL, Lage K, McCarthy MI. Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data. Genome Med 2019; 11:19. [PMID: 30914061 PMCID: PMC6436236 DOI: 10.1186/s13073-019-0628-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 03/08/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified several hundred susceptibility loci for type 2 diabetes (T2D). One critical, but unresolved, issue concerns the extent to which the mechanisms through which these diverse signals influencing T2D predisposition converge on a limited set of biological processes. However, the causal variants identified by GWAS mostly fall into a non-coding sequence, complicating the task of defining the effector transcripts through which they operate. METHODS Here, we describe implementation of an analytical pipeline to address this question. First, we integrate multiple sources of genetic, genomic and biological data to assign positional candidacy scores to the genes that map to T2D GWAS signals. Second, we introduce genes with high scores as seeds within a network optimization algorithm (the asymmetric prize-collecting Steiner tree approach) which uses external, experimentally confirmed protein-protein interaction (PPI) data to generate high-confidence sub-networks. Third, we use GWAS data to test the T2D association enrichment of the "non-seed" proteins introduced into the network, as a measure of the overall functional connectivity of the network. RESULTS We find (a) non-seed proteins in the T2D protein-interaction network so generated (comprising 705 nodes) are enriched for association to T2D (p = 0.0014) but not control traits, (b) stronger T2D-enrichment for islets than other tissues when we use RNA expression data to generate tissue-specific PPI networks and (c) enhanced enrichment (p = 3.9 × 10- 5) when we combine the analysis of the islet-specific PPI network with a focus on the subset of T2D GWAS loci which act through defective insulin secretion. CONCLUSIONS These analyses reveal a pattern of non-random functional connectivity between candidate causal genes at T2D GWAS loci and highlight the products of genes including YWHAG, SMAD4 or CDK2 as potential contributors to T2D-relevant islet dysfunction. The approach we describe can be applied to other complex genetic and genomic datasets, facilitating integration of diverse data types into disease-associated networks.
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Affiliation(s)
- Juan Fernández-Tajes
- 0000 0004 1936 8948grid.4991.5Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kyle J. Gaulton
- 0000 0001 2107 4242grid.266100.3Department of Pediatrics, University of California, San Diego, CA USA
| | - Martijn van de Bunt
- 0000 0004 1936 8948grid.4991.5Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK ,0000 0004 1936 8948grid.4991.5Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK ,Present Address: Department of Bioinformatics and Data Mining, Novo Nordisk A/S, Maaloev, Denmark
| | - Jason Torres
- 0000 0004 1936 8948grid.4991.5Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK ,0000 0004 1936 8948grid.4991.5Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Matthias Thurner
- 0000 0004 1936 8948grid.4991.5Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK ,0000 0004 1936 8948grid.4991.5Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Anubha Mahajan
- 0000 0004 1936 8948grid.4991.5Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Anna L. Gloyn
- 0000 0004 1936 8948grid.4991.5Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK ,0000 0004 1936 8948grid.4991.5Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK ,0000 0004 0488 9484grid.415719.fOxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Kasper Lage
- 0000 0004 0386 9924grid.32224.35Department of Surgery, Massachusetts, General Hospital, Boston, MA USA ,grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA
| | - Mark I. McCarthy
- 0000 0004 1936 8948grid.4991.5Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK ,0000 0004 1936 8948grid.4991.5Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK ,0000 0004 0488 9484grid.415719.fOxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
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Kasture AS, Bartel D, Steinkellner T, Sucic S, Hummel T, Freissmuth M. Distinct contribution of axonal and somatodendritic serotonin transporters in drosophila olfaction. Neuropharmacology 2019; 161:107564. [PMID: 30851308 DOI: 10.1016/j.neuropharm.2019.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/11/2019] [Accepted: 03/03/2019] [Indexed: 01/07/2023]
Abstract
The serotonin transporter (SERT) regulates serotonergic neurotransmission by retrieving released serotonin and replenishing vesicular stores. SERT is not only delivered to axons but it is also present on the neuronal soma and on dendrites. It has not been possible to restrict the distribution of SERT without affecting transporter function. Hence, the physiological role of somatodendritic SERT remains enigmatic. The SERT C-terminus harbors a conserved RI-motif, which recruits SEC24C, a cargo receptor in the coatomer protein-II coat. Failure to engage SEC24C precludes axonal enrichment of SERT. Here we introduced a point mutation into the RI-motif of human SERT causing confinement of the resulting - otherwise fully functional - hSERT-R607A on the somatodendritic membrane of primary rat dorsal raphe neurons. Transgenic expression of the corresponding Drosophila mutant dSERT-R599A led to its enrichment in the somatodendritic compartment of serotonergic neurons in the fly brain. We explored the possible physiological role of somatodendritic SERT by comparing flies harboring wild type SERT and dSERT-R599A in a behavioral paradigm for serotonin-modulated odor perception. When globally re-expressed in serotonergic neurons, wild type SERT but not dSERT-R599A restored ethanol preference. In contrast, dSERT-R599A restored ethanol preference after targeted expression in contralaterally projecting, serotonin-immunoreactive deuterocerebral (CSD) interneurons, while expression of wild type SERT caused ethanol aversion. We conclude that, in CSD neurons, (i) somatodendritic SERT supports ethanol attraction, (ii) axonal SERT specifies ethanol aversion, (iii) the effect of axonal SERT can override that of somatodendritic SERT. These observations demonstrate a distinct biological role of somatodendritic and axonal serotonin transport. This article is part of the issue entitled 'Special Issue on Neurotransmitter Transporters'.
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Affiliation(s)
- Ameya Sanjay Kasture
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, A-1090 Vienna, Austria; Department of Neurobiology, University of Vienna, A-1090 Vienna, Austria
| | - Daniela Bartel
- Department of Neurobiology, University of Vienna, A-1090 Vienna, Austria
| | - Thomas Steinkellner
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Sonja Sucic
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Thomas Hummel
- Department of Neurobiology, University of Vienna, A-1090 Vienna, Austria
| | - Michael Freissmuth
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, A-1090 Vienna, Austria.
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Wang HQ, Jia L, Li YT, Farren T, Agrawal SG, Liu FT. Increased autocrine interleukin-6 production is significantly associated with worse clinical outcome in patients with chronic lymphocytic leukemia. J Cell Physiol 2019; 234:13994-14006. [PMID: 30623437 PMCID: PMC6590298 DOI: 10.1002/jcp.28086] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/07/2018] [Indexed: 12/25/2022]
Abstract
Chronic lymphocytic leukemia (CLL) remains incurable with current standard therapy. We have previously reported that an increased expression of interleukin‐6 (IL‐6) receptor CD126 leads to resistance of CLL cells to chemotherapy and worse prognosis for patients with CLL. In this study, we determine whether autocrine IL‐6 production by CLL B cells is associated with poor clinical outcome and explore IL‐6‐mediated survival mechanism in primary CLL cells. Our results demonstrate that higher levels of autocrine IL‐6 are significantly associated with shorter absolute lymphocyte doubling time, patients received treatment, without complete remission, advanced Binet stages, 17p/11q deletion, and shorter time to first time treatment and progression‐free survival. IL‐6 activated both STAT3 and nuclear factor kappa B (NF‐κB) in primary CLL cells. Blocking IL‐6 receptor and JAK2 inhibited IL‐6‐mediated activation of STAT3 and NF‐κB. Our study demonstrates that an increased autocrine IL‐6 production by CLL B‐cells are associated with worse clinical outcome for patients with CLL. IL‐6 promotes CLL cell survival by activating both STAT3 and NF‐κB through diverse signaling cascades. Neutralizing IL‐6 or blocking IL‐6 receptor might contribute overcoming the resistance of CLL cells to chemotherapy. We propose that the measurement of autocrine IL‐6 could be a useful approach to predict clinical outcome.
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Affiliation(s)
- Hua-Qing Wang
- Department of Hematology and Oncology, Tianjin Union Medial Center of Nankai University, Tianjin, China
| | - Li Jia
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Yu-Ting Li
- Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Centre for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Timothy Farren
- Pathology Group, Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Samir G Agrawal
- Division of Haemato-Oncology, St Bartholomew's Hospital, Barts Health NHS Trust and Queen Mary University of London, London, United Kingdom
| | - Feng-Ting Liu
- Department of Hematology and Oncology, Tianjin Union Medial Center of Nankai University, Tianjin, China.,Division of Haemato-Oncology, St Bartholomew's Hospital, Barts Health NHS Trust and Queen Mary University of London, London, United Kingdom
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Morgan S, Duguez S, Duddy W. Personalized Medicine and Molecular Interaction Networks in Amyotrophic Lateral Sclerosis (ALS): Current Knowledge. J Pers Med 2018; 8:E44. [PMID: 30551677 PMCID: PMC6313785 DOI: 10.3390/jpm8040044] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/27/2018] [Accepted: 12/05/2018] [Indexed: 12/12/2022] Open
Abstract
Multiple genes and mechanisms of pathophysiology have been implicated in amyotrophic lateral sclerosis (ALS), suggesting it is a complex systemic disease. With this in mind, applying personalized medicine (PM) approaches to tailor treatment pipelines for ALS patients may be necessary. The modelling and analysis of molecular interaction networks could represent valuable resources in defining ALS-associated pathways and discovering novel therapeutic targets. Here we review existing omics datasets and analytical approaches, in order to consider how molecular interaction networks could improve our understanding of the molecular pathophysiology of this fatal neuromuscular disorder.
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Affiliation(s)
- Stephen Morgan
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, BT47 6SB, Northern Ireland, UK.
| | - Stephanie Duguez
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, BT47 6SB, Northern Ireland, UK.
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, BT47 6SB, Northern Ireland, UK.
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Xiang B, Liu K, Yu M, Liang X, Zhang J, Lei W, Huang C, Chen J, Gu X, Li N, Wu G, Wang Y, He W, Tan J, Zhang T. Systematic genetic analyses of genome-wide association study data reveal an association between the key nucleosome remodeling and deacetylase complex and bipolar disorder development. Bipolar Disord 2018; 20:370-380. [PMID: 29280245 DOI: 10.1111/bdi.12580] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 10/21/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND Genome-wide association studies (GWASs) are used to identify genetic variants for association with bipolar disorder (BD) risk; however, each GWAS can only reveal a small fraction of this association. This study systematically analyzed multiple GWAS data sets to provide further insights into potential causal BD processes by integrating the results of Psychiatric Genomics Consortium Phase I (PGC-I) for BD with core human pathways and functional networks. METHODS The i-Gsea4GwasV2 program was used to analyze data from the PGC-I GWAS for BD (the pathways came from Reactome), as well as the nominally significant pathways. We established a gene network of the significant pathways and performed a gene set analysis for each gene cluster of the Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) GWAS data for the volumes of the intracranial region and seven subcortical regions. RESULTS A total of 30 of 1816 Reactome pathways were identified and showed associations with BD risk. We further revealed 22 interconnected functional and topologically interacting clusters (Clusters 0-21) that were associated with BD risk. Moreover, we obtained brain transcriptome data from BrainSpan and found significant associations between common variants of the genes in Cluster 1 with the hippocampus (HIP; P = .026; family-wise error [FWE] correction) and amygdala (AMY; P = .016; FEW correction) in Cluster 8 with HIP (P = .022; FWE correction). The genes in Cluster 1 were enriched for the transcriptional co-expression profile in the prenatal AMY, and core genes (CDH4, MTA2, RBBP4, and HDAC2) were identified to be involved in regulating early brain development. CONCLUSION This study demonstrated that the HIP and AMY play a central role in neurodevelopment and BD risk.
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Affiliation(s)
- Bo Xiang
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Kezhi Liu
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Minglan Yu
- Medical Laboratory Center, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Xuemei Liang
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Jin Zhang
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Wei Lei
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Chaohua Huang
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Jing Chen
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Xiaochu Gu
- Clinical Laboratory, Su zhou Guang ji Hospital, Suzhou, Jiangsu Province, China
| | - Nian Li
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Guoying Wu
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Yan Wang
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Wenying He
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Jinhua Tan
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Tao Zhang
- Department of Psychiatry, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
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Petrov B, Aldoori A, James C, Yang K, Algorta GP, Lee A, Zhang L, Lin T, Awadhi RA, Parquette JR, Samogyi A, Arnold LE, Fristad MA, Gracious B, Ziouzenkova O. Bipolar disorder in youth is associated with increased levels of vitamin D-binding protein. Transl Psychiatry 2018; 8:61. [PMID: 29531242 DOI: 10.1038/s41398-018-0109-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Genetic, dietary, and inflammatory factors contribute to the etiology of major mood disorders (MMD), thus impeding the identification of specific biomarkers to assist in diagnosis and treatment. We tested association of vitamin D and inflammatory markers in 36 adolescents with bipolar disorder (BD) and major depressive disorder (MDD) forms of MMD and without MMD (non-mood control). We also assessed the overall level of inflammation using a cell-based reporter assay for nuclear factor kappa-B (NFκB) activation and measuring antibodies to oxidized LDL. We found that these factors were similar between non-mood and MMD youth. To identify potential biomarkers, we developed a screening immunoprecipitation-sequencing approach based on inflammatory brain glia maturation factor beta (GMFβ). We discovered that a homolog of GMFβ in human plasma is vitamin D-binding protein (DBP) and validated this finding using immunoprecipitation with anti-DBP antibodies and mass spectrometry/sequencing analysis. We quantified DBP levels in participants by western blot. DBP levels in BD participants were significantly higher (136%) than in participants without MMD (100%). The increase in DBP levels in MDD participants (121.1%) was not statistically different from these groups. The DBP responds early to cellular damage by binding of structural proteins and activating inflammatory cells. A product of enzymatic cleavage of DBP has been described as macrophage-activating factor. Circulating DBP is comprised of heterogenous high and low molecular fractions that are only partially recognized by mono- and polyclonal ELISA and are not suitable for the quantitative comparison of DBP in non-mood and MDD participants. Our data suggest DBP as a marker candidate of BD warranting its validation in a larger cohort of adolescent and adult MMD patients.
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11
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Xie Z, Yang X, Deng X, Ma M, Shu K. A Genome-Wide Association Study and Complex Network Identify Four Core Hub Genes in Bipolar Disorder. Int J Mol Sci 2017; 18:E2763. [PMID: 29257106 DOI: 10.3390/ijms18122763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 11/29/2017] [Accepted: 12/14/2017] [Indexed: 11/25/2022] Open
Abstract
Bipolar disorder is a common and severe mental illness with unsolved pathophysiology. A genome-wide association study (GWAS) has been used to find a number of risk genes, but it is difficult for a GWAS to find genes indirectly associated with a disease. To find core hub genes, we introduce a network analysis after the GWAS was conducted. Six thousand four hundred fifty eight single nucleotide polymorphisms (SNPs) with p < 0.01 were sifted out from Wellcome Trust Case Control Consortium (WTCCC) dataset and mapped to 2045 genes, which are then compared with the protein–protein network. One hundred twelve genes with a degree >17 were chosen as hub genes from which five significant modules and four core hub genes (FBXL13, WDFY2, bFGF, and MTHFD1L) were found. These core hub genes have not been reported to be directly associated with BD but may function by interacting with genes directly related to BD. Our method engenders new thoughts on finding genes indirectly associated with, but important for, complex diseases.
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12
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Safari-Alighiarloo N, Rezaei-Tavirani M, Taghizadeh M, Tabatabaei SM, Namaki S. Network-based analysis of differentially expressed genes in cerebrospinal fluid (CSF) and blood reveals new candidate genes for multiple sclerosis. PeerJ 2016; 4:e2775. [PMID: 28028462 PMCID: PMC5183126 DOI: 10.7717/peerj.2775] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/08/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The involvement of multiple genes and missing heritability, which are dominant in complex diseases such as multiple sclerosis (MS), entail using network biology to better elucidate their molecular basis and genetic factors. We therefore aimed to integrate interactome (protein-protein interaction (PPI)) and transcriptomes data to construct and analyze PPI networks for MS disease. METHODS Gene expression profiles in paired cerebrospinal fluid (CSF) and peripheral blood mononuclear cells (PBMCs) samples from MS patients, sampled in relapse or remission and controls, were analyzed. Differentially expressed genes which determined only in CSF (MS vs. control) and PBMCs (relapse vs. remission) separately integrated with PPI data to construct the Query-Query PPI (QQPPI) networks. The networks were further analyzed to investigate more central genes, functional modules and complexes involved in MS progression. RESULTS The networks were analyzed and high centrality genes were identified. Exploration of functional modules and complexes showed that the majority of high centrality genes incorporated in biological pathways driving MS pathogenesis. Proteasome and spliceosome were also noticeable in enriched pathways in PBMCs (relapse vs. remission) which were identified by both modularity and clique analyses. Finally, STK4, RB1, CDKN1A, CDK1, RAC1, EZH2, SDCBP genes in CSF (MS vs. control) and CDC37, MAP3K3, MYC genes in PBMCs (relapse vs. remission) were identified as potential candidate genes for MS, which were the more central genes involved in biological pathways. DISCUSSION This study showed that network-based analysis could explicate the complex interplay between biological processes underlying MS. Furthermore, an experimental validation of candidate genes can lead to identification of potential therapeutic targets.
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Affiliation(s)
- Nahid Safari-Alighiarloo
- Proteomics Research Center, Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Mohammad Taghizadeh
- Bioinformatics Department, Institute of Biochemistry and Biophysics, Tehran University , Tehran , Iran
| | - Seyyed Mohammad Tabatabaei
- Medical Informatics Department, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Saeed Namaki
- Immunology Department, Faculty of Medical Sciences, Shahid Beheshti University of Medical Sciences , Tehran , Iran
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13
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Abstract
Background Epigenetics of schizophrenia provides important information on how the environmental factors affect the genetic architecture of the disease. DNA methylation plays a pivotal role in etiology for schizophrenia. Previous studies have focused mostly on the discovery of schizophrenia-associated SNPs or genetic variants. As postmortem brain samples became available, more and more recent studies surveyed transcriptomics of the diseases. In this study, we constructed protein-protein interaction (PPI) network using the disease associated SNP (or genetic variants), differentially expressed disease genes and differentially methylated disease genes (or promoters). By combining the different datasets and topological analyses of the PPI network, we established a more comprehensive understanding of the development and genetics of this devastating mental illness. Results We analyzed the previously published DNA methylation profiles of prefrontal cortex from 335 healthy controls and 191 schizophrenic patients. These datasets revealed 2014 CpGs identified as GWAS risk loci with the differential methylation profile in schizophrenia, and 1689 schizophrenic differential methylated genes (SDMGs) identified with predominant hypomethylation. These SDMGs, combined with the PPIs of these genes, were constructed into the schizophrenic differential methylation network (SDMN). On the SDMN, there are 10 hypermethylated SDMGs, including GNA13, CAPNS1, GABPB2, GIT2, LEFTY1, NDUFA10, MIOS, MPHOSPH6, PRDM14 and RFWD2. The hypermethylation to differential expression network (HyDEN) were constructed to determine how the hypermethylated promoters regulate gene expression. The enrichment analyses of biochemical pathways in HyDEN, including TNF alpha, PDGFR-beta signaling, TGF beta Receptor, VEGFR1 and VEGFR2 signaling, regulation of telomerase, hepatocyte growth factor receptor signaling, ErbB1 downstream signaling and mTOR signaling pathway, suggested that the malfunctioning of these pathways contribute to the symptoms of schizophrenia. Conclusions The epigenetic profiles of DNA differential methylation from schizophrenic brain samples were investigated to understand the regulatory roles of SDMGs. The SDMGs interplays with SCZCGs in a coordinated fashion in the disease mechanism of schizophrenia. The protein complexes and pathways involved in SDMN may be responsible for the etiology and potential treatment targets. The SDMG promoters are predominantly hypomethylated. Increasing methylation on these promoters is proposed as a novel therapeutic approach for schizophrenia. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0229-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sheng-An Lee
- Department of Information Management, Kainan University, Taoyuan, Taiwan
| | - Kuo-Chuan Huang
- Department of Psychiatry, Beitou Branch, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan. .,Department of Nursing, Ching Kuo Institute of Management and Health, Keelung, Taiwan.
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14
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Alelú-Paz R, Carmona FJ, Sanchez-Mut JV, Cariaga-Martínez A, González-Corpas A, Ashour N, Orea MJ, Escanilla A, Monje A, Guerrero Márquez C, Saiz-Ruiz J, Esteller M, Ropero S. Epigenetics in Schizophrenia: A Pilot Study of Global DNA Methylation in Different Brain Regions Associated with Higher Cognitive Functions. Front Psychol 2016; 7:1496. [PMID: 27746755 PMCID: PMC5044511 DOI: 10.3389/fpsyg.2016.01496] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/20/2016] [Indexed: 12/29/2022] Open
Abstract
Attempts to discover genes that are involved in the pathogenesis of major psychiatric disorders have been frustrating and often fruitless. Concern is building about the need to understand the complex ways in which nature and nurture interact to produce mental illness. We analyze the epigenome in several brain regions from schizophrenic patients with severe cognitive impairment using high-resolution (450K) DNA methylation array. We identified 139 differentially methylated CpG sites included in known and novel candidate genes sequences as well as in and intergenic sequences which functions remain unknown. We found that altered DNA methylation is not restricted to a particular region, but includes others such as CpG shelves and gene bodies, indicating the presence of different DNA methylation signatures depending on the brain area analyzed. Our findings suggest that epimutations are not relatables between different tissues or even between tissues' regions, highlighting the need to adequately study brain samples to obtain reliable data concerning the epigenetics of schizophrenia.
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Affiliation(s)
- Raúl Alelú-Paz
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of AlcaláMadrid, Spain; Laboratory for Neuroscience of Mental Disorders Elena Pessino, Department of Medicine and Medical Specialties, School of Medicine, University of AlcaláMadrid, Spain; Department of Psychiatry, CIBERSAM, IRYCIS, Hospital Ramón y CajalMadrid, Spain
| | - Francisco J Carmona
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat Barcelona, Spain
| | - José V Sanchez-Mut
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat Barcelona, Spain
| | - Ariel Cariaga-Martínez
- Laboratory for Neuroscience of Mental Disorders Elena Pessino, Department of Medicine and Medical Specialties, School of Medicine, University of Alcalá Madrid, Spain
| | - Ana González-Corpas
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of Alcalá Madrid, Spain
| | - Nadia Ashour
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of Alcalá Madrid, Spain
| | - Maria J Orea
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of Alcalá Madrid, Spain
| | - Ana Escanilla
- Neurological Brain Bank, Parc Sanitari Sant Joan de Déu Barcelona, Spain
| | - Alfonso Monje
- Neurological Brain Bank, Parc Sanitari Sant Joan de Déu Barcelona, Spain
| | | | - Jerónimo Saiz-Ruiz
- Department of Psychiatry, CIBERSAM, IRYCIS, Hospital Ramón y Cajal Madrid, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de LlobregatBarcelona, Spain; Institució Catalana de Recerca i Estudis AvançatsBarcelona, Spain; Department of Physiological Sciences II, School of Medicine, University of BarcelonaBarcelona, Spain
| | - Santiago Ropero
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of Alcalá Madrid, Spain
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15
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Giusti L, Ciregia F, Mazzoni MR, Lucacchini A. Proteomics insight into psychiatric disorders: an update on biological fluid biomarkers. Expert Rev Proteomics 2016; 13:941-950. [DOI: 10.1080/14789450.2016.1230499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Laura Giusti
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Federica Ciregia
- Department of Pharmacy, University of Pisa, Pisa, Italy
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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16
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Shao L, Golbaz K, Honer WG, Beasley CL. Deficits in axon-associated proteins in prefrontal white matter in bipolar disorder but not schizophrenia. Bipolar Disord 2016; 18:342-51. [PMID: 27218831 DOI: 10.1111/bdi.12395] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/25/2016] [Accepted: 02/26/2016] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Brain imaging studies have implicated white matter dysfunction in the pathophysiology of both bipolar disorder (BD) and schizophrenia (SCZ). However, the contribution of axons to white matter pathology in these disorders is not yet understood. Maintenance of neuronal function is dependent on the active transport of biological material, including synaptic proteins, along the axon. In this study, the expression of six proteins associated with axonal transport of synaptic cargoes was quantified in postmortem samples of prefrontal white matter in subjects with BD, those with SCZ, and matched controls, as a measure of axonal dysfunction in these disorders. METHODS Levels of the microtubule-associated proteins β-tubulin and microtubule-associated protein 6 (MAP6), the motor and accessory proteins kinesin-1 and disrupted-in-schizophrenia 1 (DISC1), and the synaptic cargoes synaptotagmin and synaptosomal-associated protein-25 (SNAP-25) were quantified in white matter adjacent to the dorsolateral prefrontal cortex in subjects with BD (n = 34), subjects with SCZ (n = 35), and non-psychiatric controls (n = 35) using immunoblotting and an enzyme-linked immunosorbent assay (ELISA). RESULTS Protein expression of β-tubulin, kinesin-1, DISC1, synaptotagmin, and SNAP-25 was significantly lower in subjects with BD compared to controls. Levels of axon-associated proteins were also lower in subjects with SCZ, but failed to reach statistical significance. CONCLUSIONS These data provide evidence for deficits in axon-associated proteins in prefrontal white matter in BD. Findings are suggestive of decreased axonal density or dysregulation of axonal function in this disorder.
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Affiliation(s)
- Li Shao
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Khashayar Golbaz
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - William G Honer
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Clare L Beasley
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
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17
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Chen C, Shen H, Zhang LG, Liu J, Cao XG, Yao AL, Kang SS, Gao WX, Han H, Cao FH, Li ZG. Construction and analysis of protein-protein interaction networks based on proteomics data of prostate cancer. Int J Mol Med 2016; 37:1576-86. [PMID: 27121963 PMCID: PMC4866967 DOI: 10.3892/ijmm.2016.2577] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 04/15/2016] [Indexed: 12/22/2022] Open
Abstract
Currently, using human prostate cancer (PCa) tissue samples to conduct proteomics research has generated a large amount of data; however, only a very small amount has been thoroughly investigated. In this study, we manually carried out the mining of the full text of proteomics literature that involved comparisons between PCa and normal or benign tissue and identified 41 differentially expressed proteins verified or reported more than 2 times from different research studies. We regarded these proteins as seed proteins to construct a protein-protein interaction (PPI) network. The extended network included one giant network, which consisted of 1,264 nodes connected via 1,744 edges, and 3 small separate components. The backbone network was then constructed, which was derived from key nodes and the subnetwork consisting of the shortest path between seed proteins. Topological analyses of these networks were conducted to identify proteins essential for the genesis of PCa. Solute carrier family 2 (facilitated glucose transporter), member 4 (SLC2A4) had the highest closeness centrality located in the center of each network, and the highest betweenness centrality and largest degree in the backbone network. Tubulin, beta 2C (TUBB2C) had the largest degree in the giant network and subnetwork. In addition, using module analysis of the whole PPI network, we obtained a densely connected region. Functional annotation indicated that the Ras protein signal transduction biological process, mitogen-activated protein kinase (MAPK), neurotrophin and the gonadotropin-releasing hormone (GnRH) signaling pathway may play an important role in the genesis and development of PCa. Further investigation of the SLC2A4, TUBB2C proteins, and these biological processes and pathways may therefore provide a potential target for the diagnosis and treatment of PCa.
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Affiliation(s)
- Chen Chen
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China
| | - Hong Shen
- Department of Modern Technology and Education Center, North China University of Science and Technology and International Science and Technology Cooperation Base of Geriatric Medicine, Tangshan, Hebei 063000, P.R. China
| | - Li-Guo Zhang
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China
| | - Jian Liu
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China
| | - Xiao-Ge Cao
- Tianjin Binhai New Area Hangu No. 1 High School, Tianjin 300480, P.R. China
| | - An-Liang Yao
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China
| | - Shao-San Kang
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China
| | - Wei-Xing Gao
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China
| | - Hui Han
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China
| | - Feng-Hong Cao
- Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China
| | - Zhi-Guo Li
- Medical Research Center, North China University of Science and Technology and International Science and Technology Cooperation Base of Geriatric Medicine, Tangshan, Hebei 063000, P.R. China
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Abstract
The multifactorial origin of most chronic disorders of the brain, including schizophrenia, has been well accepted. Consequently, pharmacotherapy would require multi-targeted strategies. This contrasts to the majority of drug therapies used until now, addressing more or less specifically only one target molecule. Nevertheless, quite some searches for multiple molecular targets specific for mental disorders have been undertaken. For example, genome-wide association studies have been conducted to discover new target genes of disease. Unfortunately, these attempts have not fulfilled the great hopes they have started with. Polypharmacology and network pharmacology approaches of drug treatment endeavor to abandon the one-drug one-target thinking. To this end, most approaches set out to investigate network topologies searching for modules, endowed with “important” nodes, such as “hubs” or “bottlenecks”, encompassing features of disease networks, and being useful as tentative targets of drug therapies. This kind of research appears to be very promising. However, blocking or inhibiting “important” targets may easily result in destruction of network integrity. Therefore, it is suggested here to study functions of nodes with lower centrality for more subtle impact on network behavior. Targeting multiple nodes with low impact on network integrity by drugs with multiple activities (“dirty drugs”) or by several drugs, simultaneously, avoids to disrupt network integrity and may reset deviant dynamics of disease. Natural products typically display multi target functions and therefore could help to identify useful biological targets. Hence, future efforts should consider to combine drug-target networks with target-disease networks using mathematical (graph theoretical) tools, which could help to develop new therapeutic strategies in long-term psychiatric disorders.
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19
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Kos MZ, Carless MA, Peralta J, Blackburn A, Almeida M, Roalf D, Pogue-Geile MF, Prasad K, Gur RC, Nimgaonkar V, Curran JE, Duggirala R, Glahn DC, Blangero J, Gur RE, Almasy L. Exome Sequence Data From Multigenerational Families Implicate AMPA Receptor Trafficking in Neurocognitive Impairment and Schizophrenia Risk. Schizophr Bull 2016; 42:288-300. [PMID: 26405221 PMCID: PMC4753604 DOI: 10.1093/schbul/sbv135] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Schizophrenia is a mental disorder characterized by impairments in behavior, thought, and neurocognitive performance. We searched for susceptibility loci at a quantitative trait locus (QTL) previously reported for abstraction and mental flexibility (ABF), a cognitive function often compromised in schizophrenia patients and their unaffected relatives. Exome sequences were determined for 134 samples in 8 European American families from the original linkage study, including 25 individuals with schizophrenia or schizoaffective disorder. At chromosome 5q32-35.3, we analyzed 407 protein-altering variants for association with ABF and schizophrenia status. For replication, significant, Bonferroni-corrected findings were tested against cognitive traits in Mexican American families (n = 959), as well as interrogated for schizophrenia risk using GWAS results from the Psychiatric Genomics Consortium (PGC). From the gene SYNPO, rs6579797 (MAF = 0.032) shows significant associations with ABF (P = .015) and schizophrenia (P = .040), as well as jointly (P = .0027). In the Mexican American pedigrees, rs6579797 exhibits significant associations with IQ (P = .011), indicating more global effects on neurocognition. From the PGC results, other SYNPO variants were identified with near significant effects on schizophrenia risk, with a local linkage disequilibrium block displaying signatures of positive selection. A second missense variant within the QTL, rs17551608 (MAF = 0.19) in the gene WWC1, also displays a significant effect on schizophrenia in our exome sequences (P = .038). Remarkably, the protein products of SYNPO and WWC1 are interaction partners involved in AMPA receptor trafficking, a brain process implicated in synaptic plasticity. Our study reveals variants in these genes with significant effects on neurocognition and schizophrenia risk, identifying a potential pathogenic mechanism for schizophrenia spectrum disorders.
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Affiliation(s)
- Mark Z. Kos
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, San Antonio, TX;,*To whom correspondence should be addressed; South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, San Antonio, TX 78229, US; tel: 210-585-9772, fax: 210-582-5836, e-mail:
| | - Melanie A. Carless
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Juan Peralta
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, San Antonio, TX
| | - August Blackburn
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Marcio Almeida
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, San Antonio, TX
| | - David Roalf
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | | | - Konasale Prasad
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA
| | - Ruben C. Gur
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | | | - Joanne E. Curran
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, San Antonio, TX
| | - Ravi Duggirala
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, San Antonio, TX
| | - David C. Glahn
- Department of Psychiatry, Olin Neuropsychiatric Research Center, Yale School of Medicine, Hartford, CT
| | - John Blangero
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, San Antonio, TX
| | - Raquel E. Gur
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Laura Almasy
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, San Antonio, TX
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20
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Zamanian Azodi M, Peyvandi H, Rostami-Nejad M, Safaei A, Rostami K, Vafaee R, Heidari M, Hosseini M, Zali MR. Protein-protein interaction network of celiac disease. Gastroenterol Hepatol Bed Bench 2016; 9:268-277. [PMID: 27895852 PMCID: PMC5118851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
AIM The aim of this study is to investigate the Protein-Protein Interaction Network of Celiac Disease. BACKGROUND Celiac disease (CD) is an autoimmune disease with susceptibility of individuals to gluten of wheat, rye and barley. Understanding the molecular mechanisms and involved pathway may lead to the development of drug target discovery. The protein interaction network is one of the supportive fields to discover the pathogenesis biomarkers for celiac disease. MATERIAL AND METHODS In the present study, we collected the articles that focused on the proteomic data in celiac disease. According to the gene expression investigations of these articles, 31 candidate proteins were selected for this study. The networks of related differentially expressed protein were explored using Cytoscape 3.3 and the PPI analysis methods such as MCODE and ClueGO. RESULTS According to the network analysis Ubiquitin C, Heat shock protein 90kDa alpha (cytosolic and Grp94); class A, B and 1 member, Heat shock 70kDa protein, and protein 5 (glucose-regulated protein, 78kDa), T-complex, Chaperon in containing TCP1; subunit 7 (beta) and subunit 4 (delta) and subunit 2 (beta), have been introduced as hub-bottlnecks proteins. HSP90AA1, MKKS, EZR, HSPA14, APOB and CAD have been determined as seed proteins. CONCLUSION Chaperons have a bold presentation in curtail area in network therefore these key proteins beside the other hub-bottlneck proteins may be a suitable candidates biomarker panel for diagnosis, prognosis and treatment processes in celiac disease.
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Affiliation(s)
- Mona Zamanian Azodi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hassan Peyvandi
- Hearing Disorders Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rostami-Nejad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Akram Safaei
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kamran Rostami
- Department of Gastroenterology, Milton Keynes University Hospital United Kingdom
| | - Reza Vafaee
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Mostafa Hosseini
- Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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O'Shea KS, McInnis MG. Neurodevelopmental origins of bipolar disorder: iPSC models. Mol Cell Neurosci 2015; 73:63-83. [PMID: 26608002 DOI: 10.1016/j.mcn.2015.11.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 10/14/2015] [Accepted: 11/18/2015] [Indexed: 12/22/2022] Open
Abstract
Bipolar disorder (BP) is a chronic neuropsychiatric condition characterized by pathological fluctuations in mood from mania to depression. Adoption, twin and family studies have consistently identified a significant hereditary component to BP, yet there is no clear genetic event or consistent neuropathology. BP has been suggested to have a developmental origin, although this hypothesis has been difficult to test since there are no viable neurons or glial cells to analyze, and research has relied largely on postmortem brain, behavioral and imaging studies, or has examined proxy tissues including saliva, olfactory epithelium and blood cells. Neurodevelopmental factors, particularly pathways related to nervous system development, cell migration, extracellular matrix, H3K4 methylation, and calcium signaling have been identified in large gene expression and GWAS studies as altered in BP. Recent advances in stem cell biology, particularly the ability to reprogram adult somatic tissues to a pluripotent state, now make it possible to interrogate these pathways in viable cell models. A number of induced pluripotent stem cell (iPSC) lines from BP patient and healthy control (C) individuals have been derived in several laboratories, and their ability to form cortical neurons examined. Early studies suggest differences in activity, calcium signaling, blocks to neuronal differentiation, and changes in neuronal, and possibly glial, lineage specification. Initial observations suggest that differentiation of BP patient-derived neurons to dorsal telencephalic derivatives may be impaired, possibly due to alterations in WNT, Hedgehog or Nodal pathway signaling. These investigations strongly support a developmental contribution to BP and identify novel pathways, mechanisms and opportunities for improved treatments.
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Affiliation(s)
- K Sue O'Shea
- Department of Cell and Developmental Biology, University of Michigan, 3051 BSRB, 109 Zina Pitcher PL, Ann Arbor, MI 48109-2200, United States; Department of Psychiatry, University of Michigan, 4250 Plymouth Rd, Ann Arbor, MI 48109-5765, United States.
| | - Melvin G McInnis
- Department of Psychiatry, University of Michigan, 4250 Plymouth Rd, Ann Arbor, MI 48109-5765, United States
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de Baumont A, Maschietto M, Lima L, Carraro DM, Olivieri EH, Fiorini A, Barreta LA, Palha JA, Belmonte-de-Abreu P, Moreira Filho CA, Brentani H. Innate immune response is differentially dysregulated between bipolar disease and schizophrenia. Schizophr Res 2015; 161:215-21. [PMID: 25487697 DOI: 10.1016/j.schres.2014.10.055] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 09/22/2014] [Accepted: 10/28/2014] [Indexed: 01/04/2023]
Abstract
Schizophrenia (SZ) and bipolar disorder (BD) are severe psychiatric conditions with a neurodevelopmental component. Genetic findings indicate the existence of an overlap in genetic susceptibility across the disorders. Also, image studies provide evidence for a shared neurobiological basis, contributing to a dimensional diagnostic approach. This study aimed to identify the molecular mechanisms that differentiate SZ and BD patients from health controls but also that distinguish both from health individuals. Comparison of gene expression profiling in post-mortem brains of both disorders and health controls (30 cases), followed by a further comparison between 29 BD and 29 SZ revealed 28 differentially expressed genes. These genes were used in co-expression analysesthat revealed the pairs CCR1/SERPINA1, CCR5/HCST, C1QA/CD68, CCR5/S100A11 and SERPINA1/TLR1 as presenting the most significant difference in co-expression between SZ and BD. Next, a protein-protein interaction (PPI) network using the 28 differentially expressed genes as seeds revealed CASP4, TYROBP, CCR1, SERPINA1, CCR5 and C1QA as having a central role in the diseases manifestation. Both co-expression and network topological analyses pointed to genes related to microglia functions. Based on this data, we suggest that differences between SZ and BP are due to genes involved with response to stimulus, defense response, immune system process and response to stress biological processes, all having a role in the communication of environmental factors to the cells and associated to microglia.
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23
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Huang KC, Yang KC, Lin H, Tsao TTH, Lee SA. Transcriptome alterations of mitochondrial and coagulation function in schizophrenia by cortical sequencing analysis. BMC Genomics 2014; 15 Suppl 9:S6. [PMID: 25522158 PMCID: PMC4290619 DOI: 10.1186/1471-2164-15-s9-s6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Background Transcriptome sequencing of brain samples provides detailed enrichment analysis of differential expression and genetic interactions for evaluation of mitochondrial and coagulation function of schizophrenia. It is implicated that schizophrenia genetic and protein interactions may give rise to biological dysfunction of energy metabolism and hemostasis. These findings may explain the biological mechanisms responsible for negative and withdraw symptoms of schizophrenia and antipsychotic-induced venous thromboembolism. We conducted a comparison of schizophrenic candidate genes from literature reviews and constructed the schizophrenia-mediator network (SCZMN) which consists of schizophrenic candidate genes and associated mediator genes by applying differential expression analysis to BA22 RNA-Seq brain data. The network was searched against pathway databases such as PID, Reactome, HumanCyc, and Cell-Map. The candidate complexes were identified by MCL clustering using CORUM for potential pathogenesis of schizophrenia. Results Published BA22 RNA-Seq brain data of 9 schizophrenic patients and 9 controls samples were analyzed. The differentially expressed genes in the BA22 brain samples of schizophrenia are proposed as schizophrenia candidate marker genes (SCZCGs). The genetic interactions between mitochondrial genes and many under-expressed SCZCGs indicate the genetic predisposition of mitochondria dysfunction in schizophrenia. The biological functions of SCZCGs, as listed in the Pathway Interaction Database (PID), indicate that these genes have roles in DNA binding transcription factor, signal and cancer-related pathways, coagulation and cell cycle regulation and differentiation pathways. In the query-query protein-protein interaction (QQPPI) network of SCZCGs, TP53, PRKACA, STAT3 and SP1 were identified as the central "hub" genes. Mitochondrial function was modulated by dopamine inhibition of respiratory complex I activity. The genetic interaction between mitochondria function and schizophrenia may be revealed by DRD2 linked to NDUFS7 through protein-protein interactions of FLNA and ARRB2. The biological mechanism of signaling pathway of coagulation cascade was illustrated by the PPI network of the SCZCGs and the coagulation-associated genes. The relationship between antipsychotic target genes (DRD2/3 and HTR2A) and coagulation factor genes (F3, F7 and F10) appeared to cascade the following hemostatic process implicating the bottleneck of coagulation genetic network by the bridging of actin-binding protein (FLNA). Conclusions It is implicated that the energy metabolism and hemostatic process have important roles in the pathogenesis for schizophrenia. The cross-talk of genetic interaction by these co-expressed genes and reached candidate genes may address the key network in disease pathology. The accuracy of candidate genes evaluated from different quantification tools could be improved by crosstalk analysis of overlapping genes in genetic networks.
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Podder A, Latha N. New Insights into Schizophrenia Disease Genes Interactome in the Human Brain: Emerging Targets and Therapeutic Implications in the Postgenomics Era. OMICS: A Journal of Integrative Biology 2014; 18:754-66. [DOI: 10.1089/omi.2014.0082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Avijit Podder
- Bioinformatics Infrastructure Facility, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Narayanan Latha
- Bioinformatics Infrastructure Facility, Sri Venkateswara College, University of Delhi, New Delhi, India
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25
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Rakshit H, Rathi N, Roy D. Construction and analysis of the protein-protein interaction networks based on gene expression profiles of Parkinson's disease. PLoS One 2014; 9:e103047. [PMID: 25170921 PMCID: PMC4149362 DOI: 10.1371/journal.pone.0103047] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 06/26/2014] [Indexed: 11/29/2022] Open
Abstract
Background Parkinson's Disease (PD) is one of the most prevailing neurodegenerative diseases. Improving diagnoses and treatments of this disease is essential, as currently there exists no cure for this disease. Microarray and proteomics data have revealed abnormal expression of several genes and proteins responsible for PD. Nevertheless, few studies have been reported involving PD-specific protein-protein interactions. Results Microarray based gene expression data and protein-protein interaction (PPI) databases were combined to construct the PPI networks of differentially expressed (DE) genes in post mortem brain tissue samples of patients with Parkinson's disease. Samples were collected from the substantia nigra and the frontal cerebral cortex. From the microarray data, two sets of DE genes were selected by 2-tailed t-tests and Significance Analysis of Microarrays (SAM), run separately to construct two Query-Query PPI (QQPPI) networks. Several topological properties of these networks were studied. Nodes with High Connectivity (hubs) and High Betweenness Low Connectivity (bottlenecks) were identified to be the most significant nodes of the networks. Three and four-cliques were identified in the QQPPI networks. These cliques contain most of the topologically significant nodes of the networks which form core functional modules consisting of tightly knitted sub-networks. Hitherto unreported 37 PD disease markers were identified based on their topological significance in the networks. Of these 37 markers, eight were significantly involved in the core functional modules and showed significant change in co-expression levels. Four (ARRB2, STX1A, TFRC and MARCKS) out of the 37 markers were found to be associated with several neurotransmitters including dopamine. Conclusion This study represents a novel investigation of the PPI networks for PD, a complex disease. 37 proteins identified in our study can be considered as PD network biomarkers. These network biomarkers may provide as potential therapeutic targets for PD applications development.
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Affiliation(s)
- Hindol Rakshit
- Integrated Science Education & Research Centre (ISERC), Visva-Bharati University, Shantiniketan, Birbhum, West Bengal, India
| | - Nitin Rathi
- Cognizant Technology Solutions India Pvt. Ltd., Rajiv Gandhi Infotech Park, MIDC, Hinjewadi, Pune, Maharashtra, India
| | - Debjani Roy
- Department of Biophysics, Bose Institute, Acharya J.C. Bose Centenary Building, Kolkata, West Bengal, India
- * E-mail:
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McIntyre RS, Cha DS, Jerrell JM, Swardfager W, Kim RD, Costa LG, Baskaran A, Soczynska JK, Woldeyohannes HO, Mansur RB, Brietzke E, Powell AM, Gallaugher A, Kudlow P, Kaidanovich-Beilin O, Alsuwaidan M. Advancing biomarker research: utilizing 'Big Data' approaches for the characterization and prevention of bipolar disorder. Bipolar Disord 2014; 16:531-47. [PMID: 24330342 DOI: 10.1111/bdi.12162] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 10/22/2013] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To provide a strategic framework for the prevention of bipolar disorder (BD) that incorporates a 'Big Data' approach to risk assessment for BD. METHODS Computerized databases (e.g., Pubmed, PsychInfo, and MedlinePlus) were used to access English-language articles published between 1966 and 2012 with the search terms bipolar disorder, prodrome, 'Big Data', and biomarkers cross-referenced with genomics/genetics, transcriptomics, proteomics, metabolomics, inflammation, oxidative stress, neurotrophic factors, cytokines, cognition, neurocognition, and neuroimaging. Papers were selected from the initial search if the primary outcome(s) of interest was (were) categorized in any of the following domains: (i) 'omics' (e.g., genomics), (ii) molecular, (iii) neuroimaging, and (iv) neurocognitive. RESULTS The current strategic approach to identifying individuals at risk for BD, with an emphasis on phenotypic information and family history, has insufficient predictive validity and is clinically inadequate. The heterogeneous clinical presentation of BD, as well as its pathoetiological complexity, suggests that it is unlikely that a single biomarker (or an exclusive biomarker approach) will sufficiently augment currently inadequate phenotypic-centric prediction models. We propose a 'Big Data'- bioinformatics approach that integrates vast and complex phenotypic, anamnestic, behavioral, family, and personal 'omics' profiling. Bioinformatic processing approaches, utilizing cloud- and grid-enabled computing, are now capable of analyzing data on the order of tera-, peta-, and exabytes, providing hitherto unheard of opportunities to fundamentally revolutionize how psychiatric disorders are predicted, prevented, and treated. High-throughput networks dedicated to research on, and the treatment of, BD, integrating both adult and younger populations, will be essential to sufficiently enroll adequate samples of individuals across the neurodevelopmental trajectory in studies to enable the characterization and prevention of this heterogeneous disorder. CONCLUSIONS Advances in bioinformatics using a 'Big Data' approach provide an opportunity for novel insights regarding the pathoetiology of BD. The coordinated integration of research centers, inclusive of mixed-age populations, is a promising strategic direction for advancing this line of neuropsychiatric research.
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Affiliation(s)
- Roger S McIntyre
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada; Department of Pharmacology, University of Toronto, Toronto, ON, Canada; Mood Disorders Psychopharmacology Unit, University Health Network, Toronto, ON, Canada; Institute of Medical Science, University of Toronto, Toronto, ON, Canada
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27
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Abstract
We provide an introduction to network theory, evidence to support a connection between molecular network structure and neuropsychiatric disease, and examples of how network approaches can expand our knowledge of the molecular bases of these diseases. Without systematic methods to derive their biological meanings and inter-relatedness, the many molecular changes associated with neuropsychiatric disease, including genetic variants, gene expression changes, and protein differences, present an impenetrably complex set of findings. Network approaches can potentially help integrate and reconcile these findings, as well as provide new insights into the molecular architecture of neuropsychiatric diseases. Network approaches to neuropsychiatric disease are still in their infancy, and we discuss what might be done to improve their prospects.
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Affiliation(s)
- Kay S Grennan
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
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28
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Zhang F, Liu C, Xu Y, Qi G, Yuan G, Cheng Z, Wang J, Wang G, Wang Z, Zhu W, Zhou Z, Zhao X, Tian L, Jin C, Yuan J, Zhang G, Chen Y, Wang L, Lu T, Yan H, Ruan Y, Yue W, Zhang D. A two-stage association study suggests BRAP as a susceptibility gene for schizophrenia. PLoS One 2014; 9:e86037. [PMID: 24454952 PMCID: PMC3893271 DOI: 10.1371/journal.pone.0086037] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/04/2013] [Indexed: 01/05/2023] Open
Abstract
Schizophrenia (SZ) is a neurodevelopmental disorder in which altered immune function typically plays an important role in mediating the effect of environmental insults and regulation of inflammation. The breast cancer suppressor protein associated protein (BRAP) is suggested to exert vital effects in neurodevelopment by modulating the mitogen-activated protein kinase cascade and inflammation signaling. To explore the possible role of BRAP in SZ, we conducted a two-stage study to examine the association of BRAP polymorphisms with SZ in the Han Chinese population. In stage one, we screened SNPs in BRAP from our GWAS data, which detected three associated SNPs, with rs3782886 being the most significant one (P = 2.31E-6, OR = 0.67). In stage two, we validated these three SNPs in an independently collected population including 1957 patients and 1509 controls, supporting the association of rs3782886 with SZ (P = 1.43E-6, OR = 0.73). Furthermore, cis-eQTL analysis indicates that rs3782886 genotypes are associated with mRNA levels of aldehyde dehydrogenase 2 family (ALDH2) (P = 0.0039) and myosin regulatory light chain 2 (MYL2) (P < 1.0E-4). Our data suggest that the BRAP gene may confer vulnerability for SZ in Han Chinese population, adding further evidence for the involvement of developmental and/or neuroinflammatory cascades in the illness.
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Affiliation(s)
- Fuquan Zhang
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China
- Key Laboratory of Mental Health, Ministry of Health, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
| | - Chenxing Liu
- Key Laboratory of Mental Health, Ministry of Health, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
| | - Yong Xu
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Guoyang Qi
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Guozhen Yuan
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Zaohuo Cheng
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Jidong Wang
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Guoqiang Wang
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Zhiqiang Wang
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Wei Zhu
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Zhenhe Zhou
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Xingfu Zhao
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Lin Tian
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Chunhui Jin
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Janmin Yuan
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Guofu Zhang
- Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China
| | - Yaguang Chen
- Key Laboratory of Mental Health, Ministry of Health, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
| | - Lifang Wang
- Key Laboratory of Mental Health, Ministry of Health, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
| | - Tianlan Lu
- Key Laboratory of Mental Health, Ministry of Health, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
| | - Hao Yan
- Key Laboratory of Mental Health, Ministry of Health, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
| | - Yanyan Ruan
- Key Laboratory of Mental Health, Ministry of Health, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
| | - Weihua Yue
- Key Laboratory of Mental Health, Ministry of Health, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
- * E-mail: (DZ); (WY)
| | - Dai Zhang
- Key Laboratory of Mental Health, Ministry of Health, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
- * E-mail: (DZ); (WY)
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Abstract
From a neurobiological perspective there is no such thing as bipolar disorder. Rather, it is almost certainly the case that many somewhat similar, but subtly different, pathological conditions produce a disease state that we currently diagnose as bipolarity. This heterogeneity - reflected in the lack of synergy between our current diagnostic schema and our rapidly advancing scientific understanding of the condition - limits attempts to articulate an integrated perspective on bipolar disorder. However, despite these challenges, scientific findings in recent years are beginning to offer a provisional "unified field theory" of the disease. This theory sees bipolar disorder as a suite of related neurodevelopmental conditions with interconnected functional abnormalities that often appear early in life and worsen over time. In addition to accelerated loss of volume in brain areas known to be essential for mood regulation and cognitive function, consistent findings have emerged at a cellular level, providing evidence that bipolar disorder is reliably associated with dysregulation of glial-neuronal interactions. Among these glial elements are microglia - the brain's primary immune elements, which appear to be overactive in the context of bipolarity. Multiple studies now indicate that inflammation is also increased in the periphery of the body in both the depressive and manic phases of the illness, with at least some return to normality in the euthymic state. These findings are consistent with changes in the hypothalamic-pituitary-adrenal axis, which are known to drive inflammatory activation. In summary, the very fact that no single gene, pathway, or brain abnormality is likely to ever account for the condition is itself an extremely important first step in better articulating an integrated perspective on both its ontological status and pathogenesis. Whether this perspective will translate into the discovery of innumerable more homogeneous forms of bipolarity is one of the great questions facing the field and one that is likely to have profound treatment implications, given that fact that such a discovery would greatly increase our ability to individualize - and by extension, enhance - treatment.
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Affiliation(s)
- Vladimir Maletic
- Department of Neuropsychiatry and Behavioral Sciences, University of South Carolina School of Medicine , Columbia, SC , USA
| | - Charles Raison
- Department of Psychiatry, University of Arizona , Tucson, AZ , USA ; Norton School of Family and Consumer Sciences, College of Agriculture and Life Sciences, University of Arizona , Tucson, AZ , USA
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Li H, Zuo X, Ouyang P, Lin M, Zhao Z, Liang Y, Zhong S, Rao S. Identifying functional modules for coronary artery disease by a prior knowledge-based approach. Gene 2013; 537:260-8. [PMID: 24389497 DOI: 10.1016/j.gene.2013.12.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/18/2013] [Accepted: 12/20/2013] [Indexed: 12/22/2022]
Abstract
Until recently, the underlying genetic mechanisms for coronary artery disease (CAD) have been largely unknown, with just a list of genes identified accounting for very little of the disease in the population. Hence, a systematic dissection of the sophisticated interplays between these individual disease genes and their functional involvements becomes essential. Here, we presented a novel knowledge-based approach to identify the functional modules for CAD. First, we selected 266 disease genes in CADgene database as the initial seed genes, and used PPI knowledge as a guide to expand these genes into a CAD-specific gene network. Then, we used Newman's algorithm to decompose the primary network into 14 compact modules with high modularity. By analysis of these modules, we further identified 114 hub genes, all either directly or indirectly associated with CAD. Finally, by functional analysis of these modules, we revealed several novel pathogenic mechanisms for CAD (for examples, some yet rarely concerned like peptide YY receptor activity, Fc gamma R-mediated phagocytosis and actin cytoskeleton regulation etc.).
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Affiliation(s)
- Haoli Li
- Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology, School of Public Health, Guangdong Medical College, Dongguan 523808, China
| | - Xiaoyu Zuo
- Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology, School of Public Health, Guangdong Medical College, Dongguan 523808, China; Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Ping Ouyang
- Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology, School of Public Health, Guangdong Medical College, Dongguan 523808, China
| | - Meihua Lin
- Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology, School of Public Health, Guangdong Medical College, Dongguan 523808, China
| | - Zhong Zhao
- Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology, School of Public Health, Guangdong Medical College, Dongguan 523808, China; Department of Statistical Sciences, School of Mathematics and Computational Science, Sun Yat-sen University, Guangzhou 510080, China
| | - Yan Liang
- Department of Internal Cardiovascular Medicine, Maoming People's Hospital, Maoming 525000, China
| | - Shouqiang Zhong
- Department of Internal Cardiovascular Medicine, Maoming People's Hospital, Maoming 525000, China
| | - Shaoqi Rao
- Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology, School of Public Health, Guangdong Medical College, Dongguan 523808, China; Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China; Department of Statistical Sciences, School of Mathematics and Computational Science, Sun Yat-sen University, Guangzhou 510080, China.
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31
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Huang KC, Yang KC, Lin H, Tsao Tsun-Hui T, Lee WK, Lee SA, Kao CY. Analysis of schizophrenia and hepatocellular carcinoma genetic network with corresponding modularity and pathways: novel insights to the immune system. BMC Genomics 2013; 14 Suppl 5:S10. [PMID: 24564241 PMCID: PMC3852078 DOI: 10.1186/1471-2164-14-s5-s10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background Schizophrenic patients show lower incidences of cancer, implicating schizophrenia may be a protective factor against cancer. To study the genetic correlation between the two diseases, a specific PPI network was constructed with candidate genes of both schizophrenia and hepatocellular carcinoma. The network, designated schizophrenia-hepatocellular carcinoma network (SHCN), was analysed and cliques were identified as potential functional modules or complexes. The findings were compared with information from pathway databases such as KEGG, Reactome, PID and ConsensusPathDB. Results The functions of mediator genes from SHCN show immune system and cell cycle regulation have important roles in the eitology mechanism of schizophrenia. For example, the over-expressing schizophrenia candidate genes, SIRPB1, SYK and LCK, are responsible for signal transduction in cytokine production; immune responses involving IL-2 and TREM-1/DAP12 pathways are relevant for the etiology mechanism of schizophrenia. Novel treatments were proposed by searching the target genes of FDA approved drugs with genes in potential protein complexes and pathways. It was found that Vitamin A, retinoid acid and a few other immune response agents modulated by RARA and LCK genes may be potential treatments for both schizophrenia and hepatocellular carcinoma. Conclusions This is the first study showing specific mediator genes in the SHCN which may suppress tumors. We also show that the schizophrenic protein interactions and modulation with cancer implicates the importance of immune system for etiology of schizophrenia.
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Venditti R, Wilson C, De Matteis MA. Exiting the ER: what we know and what we don't. Trends Cell Biol 2013; 24:9-18. [PMID: 24076263 DOI: 10.1016/j.tcb.2013.08.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 08/07/2013] [Accepted: 08/13/2013] [Indexed: 01/17/2023]
Abstract
The vast majority of proteins that are transported to different cellular compartments and secreted from the cell require coat protein complex II (COPII) for export from the endoplasmic reticulum (ER). Many of the molecular mechanisms underlying COPII assembly are understood in great detail, but it is becoming increasingly evident that this basic machinery is insufficient to account for diverse aspects of protein export from the ER that are observed in vivo. Here we review recent data that have furthered our mechanistic understanding of COPII assembly and, in particular, how genetic diseases associated with the early secretory pathway have added fundamental insights into the regulation of ER-derived carrier formation. We also highlight some unresolved issues that future work should address to better understand the physiology of COPII-mediated transport.
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Affiliation(s)
- Rossella Venditti
- Telethon Institute of Genetics and Medicine, Via Pietro Castellino 111, Naples 80131, Italy
| | - Cathal Wilson
- Telethon Institute of Genetics and Medicine, Via Pietro Castellino 111, Naples 80131, Italy
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33
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Fan X, Li D, Lichti CF, Green TA. Dynamic proteomics of nucleus accumbens in response to acute psychological stress in environmentally enriched and isolated rats. PLoS One 2013; 8:e73689. [PMID: 24040027 DOI: 10.1371/journal.pone.0073689] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 07/25/2013] [Indexed: 11/19/2022] Open
Abstract
Our prior research has shown that environmental enrichment (i.e. rats reared in an environment with novel objects, social contact with conspecifics) produces a protective antidepressant-like phenotype in rats and decreases neurobiological effects of acute psychological stress. Although CREB activity has been identified as a major player, the downstream molecular mechanisms remain largely unexplored. Thus, the current study investigates proteomic differences in the accumbens of rats raised in an enriched condition (EC) versus those raised in an isolated control condition (IC) under basal conditions and after 30 min of acute restraint stress. Results showed that under basal conditions, EC rats generally expressed less mitochondria-related proteins, particularly those involved in TCA cycle and electron transport compared to IC rats. After 30 min of acute stress, EC rats displayed increased expression of energy metabolism enzymes (among others) while IC rats exhibited decreased expression of similar proteins. Further, network and pathway analyses also identified links to AKT signaling proteins, 14-3-3 family proteins, heat-shock proteins, and ubiquitin-interacting proteins. The protein ENO1 showed marked differential expression and regulation; EC rats expressed higher levels under basal conditions that increased subsequent to stress, while the basal IC expression was lower and decreased further still after stress. The results of this study define differential protein expression in a protective rat model for major depression and additionally identify a dynamic and coordinated differential response to acute stress between the two groups. These results provide new avenues for exploration of the molecular determinants of depression and the response to acute stress.
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Menniti FS, Lindsley CW, Conn PJ, Pandit J, Zagouras P, Volkmann RA. Allosteric modulators for the treatment of schizophrenia: targeting glutamatergic networks. Curr Top Med Chem 2013; 13:26-54. [PMID: 23409764 DOI: 10.2174/1568026611313010005] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 12/11/2012] [Accepted: 12/15/2012] [Indexed: 12/20/2022]
Abstract
Schizophrenia is a highly debilitating mental disorder which afflicts approximately 1% of the global population. Cognitive and negative deficits account for the lifelong disability associated with schizophrenia, whose symptoms are not effectively addressed by current treatments. New medicines are needed to treat these aspects of the disease. Neurodevelopmental, neuropathological, genetic, and behavioral pharmacological data indicate that schizophrenia stems from a dysfunction of glutamate synaptic transmission, particularly in frontal cortical networks. A number of novel pre- and postsynaptic mechanisms affecting glutamatergic synaptic transmission have emerged as viable targets for schizophrenia. While developing orthosteric glutamatergic agents for these targets has proven extremely difficult, targeting allosteric sites of these targets has emerged as a promising alternative. From a medicinal chemistry perspective, allosteric sites provide an opportunity of finding agents with better drug-like properties and greater target specificity. Furthermore, allosteric modulators are better suited to maintaining the highly precise temporal and spatial aspects of glutamatergic synaptic transmission. Herein, we review neuropathological and genomic/genetic evidence underscoring the importance of glutamate synaptic dysfunction in the etiology of schizophrenia and make a case for allosteric targets for therapeutic intervention. We review progress in identifying allosteric modulators of AMPA receptors, NMDA receptors, and metabotropic glutamate receptors, all with the aim of restoring physiological glutamatergic synaptic transmission. Challenges remain given the complexity of schizophrenia and the difficulty in studying cognition in animals and humans. Nonetheless, important compounds have emerged from these efforts and promising preclinical and variable clinical validation has been achieved.
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Fard Jahromi SS, Shamsir MS. Construction and Analysis of the Cell Surface's Protein Network for Human Sperm-Egg Interaction. ISRN Bioinform 2013; 2013:962760. [PMID: 25937952 DOI: 10.1155/2013/962760] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 07/10/2013] [Indexed: 02/02/2023]
Abstract
Sperm-egg interaction is one of the most impressive processes in sexual reproduction, and understanding the molecular mechanism is crucial in solving problems in infertility and failed in vitro fertilization. The main purpose of this study is to map the sperm-egg interaction network between cell-surface proteins and perform an interaction analysis on this new network. We built the first protein interaction network of human sperm-egg binding and fusion proteins that consists of 84 protein nodes and 112 interactions. The gene ontology analysis identified a number of functional clusters that may be involved in the sperm-egg interaction. These include G-protein coupled receptor protein signaling pathway, cellular membrane fusion, and single fertilization. The PPI network showed a highly interconnected network and identified a set of candidate proteins: ADAM-ZP3, ZP3-CLGN, IZUMO1-CD9, and ADAM2-IZUMO1 that may have an important role in sperm-egg interaction. The result showed that the ADAM2 may mediate interaction between two essential factors CD9 and IZUMO1. The KEGG analysis showed 12 statistically significant pathways with 10 proteins associated with cancer, suggesting a common pathway between tumor fusion and sperm-egg fusion. We believe that the availability of this map will assist future researches in the fertilization mechanism and will also facilitate biological interpretation of sperm-egg interaction.
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Affiliation(s)
- Aiden Corvin
- Department of Psychiatry & Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland.
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Abstract
This article constructs an argument for using blood chromatin (contained in nucleated blood cells) as a protein biosensor to integrate the ambient epigenetic influences in the internal milieu. An analogy is made to blood glycated hemoglobin (HbA1c) in diabetes as an integrated proxy for glucose levels and body-wide protein glycation. Genome-wide chromatin can serve as an organizing principle that bridges the central and peripheral compartments by entraining commensurable gene networks. Chromatin deposition along these networks will be imposed by the totality of epigenetic influences, which incorporates significant contributions from biochemicals that readily traverse the blood-brain barrier. In a clinical trial, these influences would be dominated by pharmaceuticals designed to override pathophysiological signals. In practice, mRNA readouts would be limited to nonsynaptic gene networks whose critical nodes are occupied by a site-specific chromatin modification. Finally, chromatin measurements in peripheral tissue will retain the influences of a patient's lifestyle and unique genomic background.
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Affiliation(s)
- Rajiv P Sharma
- The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St, Chicago, IL 60612, USA.
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Sucic S, Koban F, El-Kasaby A, Kudlacek O, Stockner T, Sitte HH, Freissmuth M. Switching the clientele: a lysine residing in the C terminus of the serotonin transporter specifies its preference for the coat protein complex II component SEC24C. J Biol Chem 2013; 288:5330-41. [PMID: 23288844 PMCID: PMC3581386 DOI: 10.1074/jbc.m112.408237] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The serotonin transporter (SERT) maintains serotonergic neurotransmission via rapid reuptake of serotonin from the synaptic cleft. SERT relies exclusively on the coat protein complex II component SEC24C for endoplasmic reticulum (ER) export. The closely related transporters for noradrenaline and dopamine depend on SEC24D. Here, we show that discrimination between SEC24C and SEC24D is specified by the residue at position +2 downstream from the ER export motif (607RI608 in SERT). Substituting Lys610 with tyrosine, the corresponding residue found in the noradrenaline and dopamine transporters, switched the SEC24 isoform preference: SERT-K610Y relied solely on SEC24D to reach the cell surface. This analysis was extended to other SLC6 (solute carrier 6) transporter family members: siRNA-dependent depletion of SEC24C, but not of SEC24D, reduced surface levels of the glycine transporter-1a, the betaine/GABA transporter and the GABA transporter-4. Experiments with dominant negative versions of SEC24C and SEC24D recapitulated these findings. We also verified that the presence of two ER export motifs (in concatemers of SERT and GABA transporter-1) supported recruitment of both SEC24C and SEC24D. To the best of our knowledge, this is the first report to document a change in SEC24 specificity by mutation of a single residue in the client protein. Our observations allowed for deducing a rule for SLC6 family members: a hydrophobic residue (Tyr or Val) in the +2 position specifies interaction with SEC24D, and a hydrophilic residue (Lys, Asn, or Gln) recruits SEC24C. Variations in SEC24C are linked to neuropsychiatric disorders. The present findings provide a mechanistic explanation. Variations in SEC24C may translate into distinct surface levels of neurotransmitter transporters.
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Affiliation(s)
- Sonja Sucic
- Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University of Vienna, A-1090 Vienna, Austria
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Ranganathan S, Schönbach C, Kelso J, Rost B, Nathan S, Tan TW. Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference. BMC Bioinformatics 2011; 12 Suppl 13:S1. [PMID: 22372736 PMCID: PMC3278825 DOI: 10.1186/1471-2105-12-s13-s1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The 2011 International Conference on Bioinformatics (InCoB) conference, which is the annual scientific conference of the Asia-Pacific Bioinformatics Network (APBioNet), is hosted by Kuala Lumpur, Malaysia, is co-organized with the first ISCB-Asia conference of the International Society for Computational Biology (ISCB). InCoB and the sequencing of the human genome are both celebrating their tenth anniversaries and InCoB’s goalposts for the next decade, implementing standards in bioinformatics and globally distributed computational networks, will be discussed and adopted at this conference. Of the 49 manuscripts (selected from 104 submissions) accepted to BMC Genomics and BMC Bioinformatics conference supplements, 24 are featured in this issue, covering software tools, genome/proteome analysis, systems biology (networks, pathways, bioimaging) and drug discovery and design.
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Affiliation(s)
- Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney NSW 2109, Australia.
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