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Retinal Genomic Fabric Remodeling after Optic Nerve Injury. Genes (Basel) 2021; 12:genes12030403. [PMID: 33799827 PMCID: PMC7999523 DOI: 10.3390/genes12030403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/14/2021] [Accepted: 02/19/2021] [Indexed: 12/16/2022] Open
Abstract
Glaucoma is a multifactorial neurodegenerative disease, characterized by degeneration of the retinal ganglion cells (RGCs). There has been little progress in developing efficient strategies for neuroprotection in glaucoma. We profiled the retina transcriptome of Lister Hooded rats at 2 weeks after optic nerve crush (ONC) and analyzed the data from the genomic fabric paradigm (GFP) to bring additional insights into the molecular mechanisms of the retinal remodeling after induction of RGC degeneration. GFP considers three independent characteristics for the expression of each gene: level, variability, and correlation with each other gene. Thus, the 17,657 quantified genes in our study generated a total of 155,911,310 values to analyze. This represents 8830x more data per condition than a traditional transcriptomic analysis. ONC led to a 57% reduction in RGC numbers as detected by retrograde labeling with 1,1'-dioctadecyl-3,3,3,3'-tetramethylindocarbocyanine perchlorate (DiI). We observed a higher relative expression variability after ONC. Gene expression stability was used as a measure of transcription control and disclosed a robust reduction in the number of very stably expressed genes. Predicted protein-protein interaction (PPI) analysis with STRING revealed axon and neuron projection as mostly decreased processes, consistent with RGC degeneration. Conversely, immune response PPIs were found among upregulated genes. Enrichment analysis showed that complement cascade and Notch signaling pathway, as well as oxidative stress and kit receptor pathway were affected after ONC. To expand our studies of altered molecular pathways, we examined the pairwise coordination of gene expressions within each pathway and within the entire transcriptome using Pearson correlations. ONC increased the number of synergistically coordinated pairs of genes and the number of similar profiles mainly in complement cascade and Notch signaling pathway. This deep bioinformatic study provided novel insights beyond the regulation of individual gene expression and disclosed changes in the control of expression of complement cascade and Notch signaling functional pathways that may be relevant for both RGC degeneration and remodeling of the retinal tissue after ONC.
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Iacobas DA, Mgbemena VE, Iacobas S, Menezes KM, Wang H, Saganti PB. Genomic Fabric Remodeling in Metastatic Clear Cell Renal Cell Carcinoma (ccRCC): A New Paradigm and Proposal for a Personalized Gene Therapy Approach. Cancers (Basel) 2020; 12:cancers12123678. [PMID: 33302383 PMCID: PMC7762545 DOI: 10.3390/cancers12123678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/05/2020] [Indexed: 12/30/2022] Open
Abstract
Simple Summary We applied the genomic fabric principles for personalized gene therapy to a case of clear cell renal cell carcinoma (ccRCC). Despite decades of research, the process of finding the molecular mechanisms responsible for the disease and, more importantly, the therapeutic solution is still a work in progress. We analyzed the transcriptomes of the chest wall metastasis, two distinct cancer nodules, and the cancer-free surrounding tissue in the surgically removed right kidney of a Fuhrman grade 3 metastatic ccRCC patient. The studies revealed that even histopathologically equally classified cancer nodules from the same kidney have different transcriptomic topologies, requiring tailored therapeutic solutions not only for each patient but even for each cancer nodule. We identified death-associated protein kinase 3 (DAPK3); transcription activation suppressor (TASOR); family with sequence similarity 27, member C, long non-coding RNA (FAM27C); and UDP-N-acetylglucosaminyltransferase subunit (ALG13) as the gene master regulators of the four profiled regions and proposed molecular mechanisms by which expression manipulation of TASOR and ALG13 may selectively destroy the cancer cells without affecting many of the normal cells. Abstract Published transcriptomic data from surgically removed metastatic clear cell renal cell carcinoma samples were analyzed from the genomic fabric paradigm (GFP) perspective to identify the best targets for gene therapy. GFP considers the transcriptome as a multi-dimensional mathematical object constrained by a dynamic set of expression controls and correlations among genes. Every gene in the chest wall metastasis, two distinct cancer nodules, and the surrounding normal tissue of the right kidney was characterized by three independent measures: average expression level, relative expression variation, and expression correlation with each other gene. The analyses determined the cancer-induced regulation, control, and remodeling of the chemokine and vascular endothelial growth factor (VEGF) signaling, apoptosis, basal transcription factors, cell cycle, oxidative phosphorylation, renal cell carcinoma, and RNA polymerase pathways. Interestingly, the three cancer regions exhibited different transcriptomic organization, suggesting that the gene therapy should not be personalized only for every patient but also for each major cancer nodule. The gene hierarchy was established on the basis of gene commanding height, and the gene master regulators DAPK3,TASOR, FAM27C and ALG13 were identified in each profiled region. We delineated the molecular mechanisms by which TASOR overexpression and ALG13 silencing would selectively affect the cancer cells with little consequences for the normal cells.
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Affiliation(s)
- Dumitru A. Iacobas
- Personalized Genomics Laboratory, CRI Center for Computational Systems Biology, Roy G Perry College of Engineering, Prairie View A&M University, Prairie View, TX 77446, USA
- Correspondence: (D.A.I.); (P.B.S.); Tel.: +1-(936)-261-9626 (D.A.I.)
| | - Victoria E. Mgbemena
- Department of Biology, MD and S Brailsford College of Arts and Sciences, Prairie View A&M University, Prairie View, TX 77446, USA;
| | - Sanda Iacobas
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA;
| | - Kareena M. Menezes
- CRI Radiation Institute for Science & Engineering, MD and S Brailsford College of Arts and Sciences, Prairie View A&M University, Prairie View, TX 77446, USA; (K.M.M.); (H.W.)
| | - Huichen Wang
- CRI Radiation Institute for Science & Engineering, MD and S Brailsford College of Arts and Sciences, Prairie View A&M University, Prairie View, TX 77446, USA; (K.M.M.); (H.W.)
| | - Premkumar B. Saganti
- CRI Radiation Institute for Science & Engineering, MD and S Brailsford College of Arts and Sciences, Prairie View A&M University, Prairie View, TX 77446, USA; (K.M.M.); (H.W.)
- Department of Physics, MD and S Brailsford College of Arts and Sciences, Prairie View A&M University, Prairie View, TX 77446, USA
- Correspondence: (D.A.I.); (P.B.S.); Tel.: +1-(936)-261-9626 (D.A.I.)
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Iacobas DA. Powerful quantifiers for cancer transcriptomics. World J Clin Oncol 2020; 11:679-704. [PMID: 33033692 PMCID: PMC7522543 DOI: 10.5306/wjco.v11.i9.679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/06/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
Every day, investigators find a new link between a form of cancer and a particular alteration in the sequence or/and expression level of a key gene, awarding this gene the title of “biomarker”. The clinician may choose from numerous available panels to assess the type of cancer based on the mutation or expression regulation (“transcriptomic signature”) of “driver” genes. However, cancer is not a “one-gene show” and, together with the alleged biomarker, hundreds other genes are found as mutated or/and regulated in cancer samples. Regardless of the platform, a well-designed transcriptomic study produces three independent features for each gene: Average expression level, expression variability and coordination with expression of each other gene. While the average expression level is used in all studies to identify what genes were up-/down-regulated or turn on/off, the other two features are unfairly ignored. We use all three features to quantify the transcriptomic change during the progression of the disease and recovery in response to a treatment. Data from our published microarray experiments on cancer nodules and surrounding normal tissue from surgically removed tumors prove that the transcriptomic topologies are not only different in histopathologically distinct regions of a tumor but also dynamic and unique for each human being. We show also that the most influential genes in cancer nodules [the Gene Master Regulators (GMRs)] are significantly less influential in the normal tissue. As such, “smart” manipulation of the cancer GMRs expression may selectively kill cancer cells with little consequences on the normal ones. Therefore, we strongly recommend a really personalized approach of cancer medicine and present the experimental procedure and the mathematical algorithm to identify the most legitimate targets (GMRs) for gene therapy.
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Affiliation(s)
- Dumitru Andrei Iacobas
- Personalized Genomics Laboratory, CRI Center for Computational Systems Biology, Roy G Perry College of Engineering, Prairie View A&M University, Prairie View, TX 77446, United States
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Nisimura LM, Coelho LL, de Melo TG, Vieira PDC, Victorino PH, Garzoni LR, Spray DC, Iacobas DA, Iacobas S, Tanowitz HB, Adesse D. Trypanosoma cruzi Promotes Transcriptomic Remodeling of the JAK/STAT Signaling and Cell Cycle Pathways in Myoblasts. Front Cell Infect Microbiol 2020; 10:255. [PMID: 32626662 PMCID: PMC7313395 DOI: 10.3389/fcimb.2020.00255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/30/2020] [Indexed: 12/12/2022] Open
Abstract
Chagas disease is responsible for more than 10,000 deaths per year and about 6 to 7 million infected people worldwide. In its chronic stage, patients can develop mega-colon, mega-esophagus, and cardiomyopathy. Differences in clinical outcomes may be determined, in part, by the genetic background of the parasite that causes Chagas disease. Trypanosoma cruzi has a high genetic diversity, and each group of strains may elicit specific pathological responses in the host. Conflicting results have been reported in studies using various combinations of mammalian host-T. cruzi strains. We previously profiled the transcriptomic signatures resulting from infection of L6E9 rat myoblasts with four reference strains of T. cruzi (Brazil, CL, Y, and Tulahuen). The four strains induced similar overall gene expression alterations in the myoblasts, although only 21 genes were equally affected by all strains. Cardiotrophin-like cytokine factor 1 (Clcf1) was one of the genes found to be consistently upregulated by the infection with all four strains of T. cruzi. This cytokine is a member of the interleukin-6 family that binds to glycoprotein 130 receptor and activates the JAK/STAT signaling pathway, which may lead to muscle cell hypertrophy. Another commonly upregulated gene was tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta (Ywhaq, 14-3-3 protein Θ), present in the Cell Cycle Pathway. In the present work, we reanalyzed our previous microarray dataset, aiming at understanding in more details the transcriptomic impact that each strain has on JAK/STAT signaling and Cell Cycle pathways. Using Pearson correlation analysis between the expression levels of gene pairs in biological replicas from each pathway, we determined the coordination between such pairs in each experimental condition and the predicted protein interactions between the significantly altered genes by each strain. We found that although these highlighted genes were similarly affected by all four strains, the downstream genes or their interaction partners were not necessarily equally affected, thus reinforcing the idea of the role of parasite background on host cell transcriptome. These new analyses provide further evidence to the mechanistic understanding of how distinct T. cruzi strains lead to diverse remodeling of host cell transcriptome.
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Affiliation(s)
- Lindice M. Nisimura
- Laboratório de Pesquisa em Apicomplexa, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Brazil
| | - Laura L. Coelho
- Laboratório de Inovações em Terapias, Ensino e Bioprodutos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Tatiana G. de Melo
- Laboratório de Ultraestrutura Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Paloma de Carvalho Vieira
- Laboratório de Biologia Estrutural, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Pedro H. Victorino
- Laboratório de Neurogênese, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciana R. Garzoni
- Laboratório de Inovações em Terapias, Ensino e Bioprodutos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - David C. Spray
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY, United States
| | - Dumitru A. Iacobas
- Personalized Genomics Laboratory, Center for Computational Systems Biology, Prairie View A&M University, Prairie View, TX, United States
| | - Sanda Iacobas
- Department of Pathology, New York Medical College, Valhalla, NY, United States
| | - Herbert B. Tanowitz
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, United States
| | - Daniel Adesse
- Laboratório de Biologia Estrutural, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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Iacobas DA, Iacobas S, Stout RF, Spray DC. Cellular Environment Remodels the Genomic Fabrics of Functional Pathways in Astrocytes. Genes (Basel) 2020; 11:genes11050520. [PMID: 32392822 PMCID: PMC7290327 DOI: 10.3390/genes11050520] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/27/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023] Open
Abstract
We profiled the transcriptomes of primary mouse cortical astrocytes cultured alone or co-cultured with immortalized precursor oligodendrocytes (Oli-neu cells). Filters between the cell types prevented formation of hetero-cellular gap junction channels but allowed for free exchange of the two culture media. We previously reported that major functional pathways in the Oli-neu cells are remodeled by the proximity of non-touching astrocytes and that astrocytes and oligodendrocytes form a panglial transcriptomic syncytium in the brain. Here, we present evidence that the astrocyte transcriptome likewise changes significantly in the proximity of non-touching Oli-neu cells. Our results indicate that the cellular environment strongly modulates the transcriptome of each cell type and that integration in a heterocellular tissue changes not only the expression profile but also the expression control and networking of the genes in each cell phenotype. The significant decrease of the overall transcription control suggests that in the co-culture astrocytes are closer to their normal conditions from the brain. The Oli-neu secretome regulates astrocyte genes known to modulate neuronal synaptic transmission and remodels calcium, chemokine, NOD-like receptor, PI3K-Akt, and thyroid hormone signaling, as well as actin-cytoskeleton, autophagy, cell cycle, and circadian rhythm pathways. Moreover, the co-culture significantly changes the gene hierarchy in the astrocytes.
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Affiliation(s)
- Dumitru A Iacobas
- Personalized Genomics Laboratory, Center for Computational Systems Biology, RG Perry College of Engineering, Prairie View A&M University, Prairie View, TX 77446, USA
- DP Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY 10461, USA
- Correspondence: ; Tel.: +1-936-261-9926
| | - Sanda Iacobas
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA;
| | - Randy F Stout
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA;
| | - David C Spray
- DP Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY 10461, USA
- Department of Medicine, Albert Einstein College of Medicine, New York, NY 10461, USA;
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Iacobas DA, Iacobas S, Lee PR, Cohen JE, Fields RD. Coordinated Activity of Transcriptional Networks Responding to the Pattern of Action Potential Firing in Neurons. Genes (Basel) 2019; 10:genes10100754. [PMID: 31561430 PMCID: PMC6826514 DOI: 10.3390/genes10100754] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Transcriptional responses to the appropriate temporal pattern of action potential firing are essential for long-term adaption of neuronal properties to the functional activity of neural circuits and environmental experience. However, standard transcriptome analysis methods can be too limited in identifying critical aspects that coordinate temporal coding of action potential firing with transcriptome response. A Pearson correlation analysis was applied to determine how pairs of genes in the mouse dorsal root ganglion (DRG) neurons are coordinately expressed in response to stimulation producing the same number of action potentials by two different temporal patterns. Analysis of 4728 distinct gene-pairs related to calcium signaling, 435,711 pairs of transcription factors, 820 pairs of voltage-gated ion channels, and 86,862 pairs of calcium signaling genes with transcription factors indicated that genes become coordinately activated by distinct action potential firing patterns and this depends on the duration of stimulation. Moreover, a measure of expression variance revealed that the control of transcripts abundances is sensitive to the pattern of stimulation. Thus, action potentials impact intracellular signaling and the transcriptome in dynamic manner that not only alter gene expression levels significantly (as previously reported) but also affects the control of their expression fluctuations and profoundly remodel the transcriptional networks.
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Affiliation(s)
- Dumitru A Iacobas
- Personalized Genomics Laboratory, Center for Computational Systems Biology, Prairie View A&M University, Prairie View, TX 77446, USA.
- DP Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Sanda Iacobas
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA.
| | - Philip R Lee
- Section on Nervous System Development and Plasticity, the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD 20892, USA.
| | - Jonathan E Cohen
- Division of Medical Imaging Products, U.S. Food and Drug Administration, Silver Spring, 20993 MD, USA.
| | - R Douglas Fields
- Section on Nervous System Development and Plasticity, the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD 20892, USA.
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Iacobas DA. The Genomic Fabric Perspective on the Transcriptome Between Universal Quantifiers and Personalized Genomic Medicine. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s13752-016-0245-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Bosone C, Andreu A, Echevarria D. GAP junctional communication in brain secondary organizers. Dev Growth Differ 2016; 58:446-55. [PMID: 27273333 DOI: 10.1111/dgd.12297] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/05/2016] [Accepted: 05/05/2016] [Indexed: 11/28/2022]
Abstract
Gap junctions (GJs) are integral membrane proteins that enable the direct cytoplasmic exchange of ions and low molecular weight metabolites between adjacent cells. They are formed by the apposition of two connexons belonging to adjacent cells. Each connexon is formed by six proteins, named connexins (Cxs). Current evidence suggests that gap junctions play an important part in ensuring normal embryo development. Mutations in connexin genes have been linked to a variety of human diseases, although the precise role and the cell biological mechanisms of their action remain almost unknown. Among the big family of Cxs, several are expressed in nervous tissue but just a few are expressed in the anterior neural tube of vertebrates. Many efforts have been made to elucidate the molecular bases of Cxs cell biology and how they influence the morphogenetic signal activity produced by brain signaling centers. These centers, orchestrated by transcription factors and morphogenes determine the axial patterning of the mammalian brain during its specification and regionalization. The present review revisits the findings of GJ composed by Cx43 and Cx36 in neural tube patterning and discuss Cx43 putative enrollment in the control of Fgf8 signal activity coming from the well known secondary organizer, the isthmic organizer.
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Affiliation(s)
- Camilla Bosone
- Instituto de Neurociencias, Universidad Miguel Hernández & Consejo Superior de Investigaciones Científicas, 03550, Sant Joan d'Alacant, Spain
| | - Abraham Andreu
- Institut de Biologie Paris-Seine (IBPS), Developmental Biology Laboratory, University Pierre and Marie Curie, Paris, France
| | - Diego Echevarria
- Instituto de Neurociencias, Universidad Miguel Hernández & Consejo Superior de Investigaciones Científicas, 03550, Sant Joan d'Alacant, Spain
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Dienel GA. The metabolic trinity, glucose-glycogen-lactate, links astrocytes and neurons in brain energetics, signaling, memory, and gene expression. Neurosci Lett 2015; 637:18-25. [PMID: 25725168 DOI: 10.1016/j.neulet.2015.02.052] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 02/23/2015] [Indexed: 10/23/2022]
Abstract
Glucose, glycogen, and lactate are traditionally identified with brain energetics, ATP turnover, and pathophysiology. However, recent studies extend their roles to include involvement in astrocytic signaling, memory consolidation, and gene expression. Emerging roles for these brain fuels and a readily-diffusible by-product are linked to differential fluxes in glycolytic and oxidative pathways, astrocytic glycogen dynamics, redox shifts, neuron-astrocyte interactions, and regulation of astrocytic activities by noradrenaline released from the locus coeruleus. Disproportionate utilization of carbohydrate compared with oxygen during brain activation is influenced by catecholamines, but its physiological basis is not understood and its magnitude may be affected by technical aspects of metabolite assays. Memory consolidation and gene expression are impaired by glycogenolysis blockade, and prevention of these deficits by injection of abnormally-high concentrations of lactate was interpreted as a requirement for astrocyte-to-neuron lactate shuttling in memory and gene expression. However, lactate transport was not measured and evidence for presumed shuttling is not compelling. In fact, high levels of lactate used to preserve memory consolidation and induce gene expression are sufficient to shut down neuronal firing via the HCAR1 receptor. In contrast, low lactate levels activate a receptor in locus coeruleus that stimulates noradrenaline release that may activate astrocytes throughout brain. Physiological relevance of exogenous concentrations of lactate used to mimic and evaluate metabolic, molecular, and behavioral effects of lactate requires close correspondence with the normal lactate levels, the biochemical and cellular sources and sinks, and specificity of lactate delivery to target cells.
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Affiliation(s)
- Gerald A Dienel
- Department of Neurology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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O'Carroll SJ, Becker DL, Davidson JO, Gunn AJ, Nicholson LFB, Green CR. The use of connexin-based therapeutic approaches to target inflammatory diseases. Methods Mol Biol 2014; 1037:519-46. [PMID: 24029957 DOI: 10.1007/978-1-62703-505-7_31] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Alterations in Connexin43 (Cx43) expression levels have been shown to play a role in inflammatory processes including skin wounding and neuroinflammation. Cx43 protein levels increase following a skin wound and can inhibit wound healing. Increased Cx43 has been observed following stroke, epilepsy, ischemia, optic nerve damage, and spinal cord injury with gap junctional communication and hemichannel opening leading to increased secondary damage via the inflammatory response. Connexin43 modulation has been identified as a potential target for protection and repair in neuroinflammation and skin wound repair. This review describes the use of a Cx43 specific antisense oligonucleotide (Cx43 AsODN) and peptide mimetics of the connexin extracellular loop domain to modulate Cx43 expression and/or function in inflammatory disorders of the skin and central nervous system. An overview of the role of connexin43 in inflammatory conditions, how antisense and peptide have allowed us to elucidate the role of Cx43 in these diseases, create models of diseases to test interventions and their potential for use clinically or in current clinical trials is presented. Antisense oligonucleotides are applied topically and have been used to improve wound healing following skin injury. They have also been used to develop ex vivo models of neuroinflammatory diseases that will allow testing of intervention strategies. The connexin mimetic peptides have shown potential in a number of neuroinflammatory disorders in ex vivo models as well as in vivo when delivered directly to the injury site or when delivered systemically.
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Affiliation(s)
- Simon J O'Carroll
- Department of Anatomy with Radiology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
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Kurtenbach S, Kurtenbach S, Zoidl G. Gap junction modulation and its implications for heart function. Front Physiol 2014; 5:82. [PMID: 24578694 PMCID: PMC3936571 DOI: 10.3389/fphys.2014.00082] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/10/2014] [Indexed: 01/04/2023] Open
Abstract
Gap junction communication (GJC) mediated by connexins is critical for heart function. To gain insight into the causal relationship of molecular mechanisms of disease pathology, it is important to understand which mechanisms contribute to impairment of gap junctional communication. Here, we present an update on the known modulators of connexins, including various interaction partners, kinases, and signaling cascades. This gap junction network (GJN) can serve as a blueprint for data mining approaches exploring the growing number of publicly available data sets from experimental and clinical studies.
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Affiliation(s)
- Stefan Kurtenbach
- Department of Psychology, Faculty of Health, York University Toronto, ON, Canada
| | - Sarah Kurtenbach
- Department of Psychology, Faculty of Health, York University Toronto, ON, Canada
| | - Georg Zoidl
- Department of Psychology, Faculty of Health, York University Toronto, ON, Canada ; Department of Biology, Faculty of Science, York University Toronto, ON, Canada ; Center for Vision Research, York University Toronto, ON, Canada
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Nielsen MS, Axelsen LN, Sorgen PL, Verma V, Delmar M, Holstein-Rathlou NH. Gap junctions. Compr Physiol 2013; 2:1981-2035. [PMID: 23723031 DOI: 10.1002/cphy.c110051] [Citation(s) in RCA: 289] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Gap junctions are essential to the function of multicellular animals, which require a high degree of coordination between cells. In vertebrates, gap junctions comprise connexins and currently 21 connexins are known in humans. The functions of gap junctions are highly diverse and include exchange of metabolites and electrical signals between cells, as well as functions, which are apparently unrelated to intercellular communication. Given the diversity of gap junction physiology, regulation of gap junction activity is complex. The structure of the various connexins is known to some extent; and structural rearrangements and intramolecular interactions are important for regulation of channel function. Intercellular coupling is further regulated by the number and activity of channels present in gap junctional plaques. The number of connexins in cell-cell channels is regulated by controlling transcription, translation, trafficking, and degradation; and all of these processes are under strict control. Once in the membrane, channel activity is determined by the conductive properties of the connexin involved, which can be regulated by voltage and chemical gating, as well as a large number of posttranslational modifications. The aim of the present article is to review our current knowledge on the structure, regulation, function, and pharmacology of gap junctions. This will be supported by examples of how different connexins and their regulation act in concert to achieve appropriate physiological control, and how disturbances of connexin function can lead to disease.
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Affiliation(s)
- Morten Schak Nielsen
- Department of Biomedical Sciences and The Danish National Research Foundation Centre for Cardiac Arrhythmia, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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Iacobas DA, Iacobas S, Chachua T, Goletiani C, Sidyelyeva G, Velíšková J, Velíšek L. Prenatal corticosteroids modify glutamatergic and GABAergic synapse genomic fabric: insights from a novel animal model of infantile spasms. J Neuroendocrinol 2013; 25:964-79. [PMID: 23763471 PMCID: PMC3855178 DOI: 10.1111/jne.12061] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/25/2013] [Accepted: 06/09/2013] [Indexed: 12/16/2022]
Abstract
Prenatal exposure to corticosteroids has long-term postnatal somatic and neurodevelopmental consequences. Animal studies indicate that corticosteroid exposure-associated alterations in the nervous system include hypothalamic function. Infants with infantile spasms, a devastating epileptic syndrome of infancy with characteristic spastic seizures, chaotic irregular waves on interictal electroencephalogram (hypsarhythmia) and mental deterioration, have decreased concentrations of adrenocorticotrophic hormone (ACTH) and cortisol in cerebrospinal fluid, strongly suggesting hypothalamic dysfunction. We have exploited this feature to develop a model of human infantile spasms by using repeated prenatal exposure to betamethasone and a postnatal trigger of developmentally relevant spasms with NMDA. The spasms triggered in prenatally primed rats are more severe compared to prenatally saline-injected ones and respond to ACTH, a treatment of choice for infantile spasms in humans. Using autoradiography and immunohistochemistry, we have identified a link between the spasms in our model and the hypothalamus, especially the arcuate nucleus. Transcriptomic analysis of the arcuate nucleus after prenatal priming with betamethasone but before trigger of spasms indicates that prenatal betamethasone exposure down-regulates genes encoding several important proteins participating in glutamatergic and GABAergic transmission. Interestingly, there were significant sex-specific alterations after prenatal betamethasone in synapse-related gene expression but no such sex differences were found in prenatally saline-injected controls. A pairwise relevance analysis revealed that, although the synapse gene expression in controls was independent of sex, these genes form topologically distinct gene fabrics in males and females and these fabrics are altered by betamethasone in a sex-specific manner. These findings may explain the sex differences with respect to both normal behaviour and the occurrence and severity of infantile spasms. Changes in transcript expression and their coordination may contribute to a molecular substrate of permanent neurodevelopmental changes (including infantile spasms) found after prenatal exposure to corticosteroids.
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Affiliation(s)
- D A Iacobas
- Department of Pathology, New York Medical College, Valhalla, NY, USA
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14
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Friedman LK, Mancuso J, Patel A, Kudur V, Leheste JR, Iacobas S, Botta J, Iacobas DA, Spray DC. Transcriptome profiling of hippocampal CA1 after early-life seizure-induced preconditioning may elucidate new genetic therapies for epilepsy. Eur J Neurosci 2013; 38:2139-52. [PMID: 23551718 DOI: 10.1111/ejn.12168] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 01/28/2013] [Accepted: 01/28/2013] [Indexed: 11/30/2022]
Abstract
Injury of the CA1 subregion induced by a single injection of kainic acid (1 × KA) in juvenile animals (P20) is attenuated in animals with two prior sustained neonatal seizures on P6 and P9. To identify gene candidates involved in the spatially protective effects produced by early-life conditioning seizures we profiled and compared the transcriptomes of CA1 subregions from control, 1 × KA- and 3 × KA-treated animals. More genes were regulated following 3 × KA (9.6%) than after 1 × KA (7.1%). Following 1 × KA, genes supporting oxidative stress, growth, development, inflammation and neurotransmission were upregulated (e.g. Cacng1, Nadsyn1, Kcng1, Aven, S100a4, GFAP, Vim, Hrsp12 and Grik1). After 3 × KA, protective genes were differentially over-expressed [e.g. Cat, Gpx7, Gad1, Hspa12A, Foxn1, adenosine A1 receptor, Ca(2+) adaptor and homeostasis proteins, Cacnb4, Atp2b2, anti-apoptotic Bcl-2 gene members, intracellular trafficking protein, Grasp and suppressor of cytokine signaling (Socs3)]. Distinct anti-inflammatory interleukins (ILs) not observed in adult tissues [e.g. IL-6 transducer, IL-23 and IL-33 or their receptors (IL-F2 )] were also over-expressed. Several transcripts were validated by real-time polymerase chain reaction (QPCR) and immunohistochemistry. QPCR showed that casp 6 was increased after 1 × KA but reduced after 3 × KA; the pro-inflammatory gene Cox1 was either upregulated or unchanged after 1 × KA but reduced by ~70% after 3 × KA. Enhanced GFAP immunostaining following 1 × KA was selectively attenuated in the CA1 subregion after 3 × KA. The observed differential transcriptional responses may contribute to early-life seizure-induced pre-conditioning and neuroprotection by reducing glutamate receptor-mediated Ca(2+) permeability of the hippocampus and redirecting inflammatory and apoptotic pathways. These changes could lead to new genetic therapies for epilepsy.
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Affiliation(s)
- L K Friedman
- Basic Sciences, Cell Biology & Anatomy, New York Medical College, 50 Dana Rd, Valhalla, NY 10595, USA.
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15
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Iacobas S, Neal-Perry G, Iacobas DA. Analyzing the Cytoskeletal Transcriptome: Sex Differences in Rat Hypothalamus. THE CYTOSKELETON 2013. [DOI: 10.1007/978-1-62703-266-7_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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16
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Iacobas S, Iacobas DA, Spray DC, Scemes E. The connexin43-dependent transcriptome during brain development: importance of genetic background. Brain Res 2012; 1487:131-9. [PMID: 22771707 PMCID: PMC3501561 DOI: 10.1016/j.brainres.2012.05.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 05/31/2012] [Indexed: 01/27/2023]
Abstract
Use of null mutant mice is a powerful way to evaluate the role of specific proteins in brain function. Studies performed on knockout mice have revealed some unexpected roles of the gap junction proteins (connexins). Thus, analyses of gene expression in connexin43 (Cx43) null brains indicated that deletion of a single gene (Gja1) induced expression level change of numerous other genes located on all chromosomes and involved in a wide diversity of functional pathways. The significant overlap between alterations in gene expression level, control and coordination in Cx43 knockout and knockdown astrocytes raised the possibility that Gja1 represents a transcriptomic node of gene regulatory networks. However, conditional deletion of Gja1 in astrocytes of two mouse strains resulted in remarkably different phenotypes. In order to evaluate the influence of the genetic background on the transcriptome, we performed microarray studies on brains of GFAP-Cre:Cx43(f/f) C57Bl/6 and 129/SvEv mice. The surprisingly low number of Cx43 core genes (regulated in all Cx43 nulls regardless of strain) and the high number of differently regulated genes in the two Cx43 conditional knockouts indicate high influence of mouse strain on brain transcriptome. This article is part of a Special Issue entitled Electrical Synapses.
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Affiliation(s)
- S Iacobas
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1410, Pelham Parkway, Kennedy Center, Room 203, Bronx, NY 10461, USA
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17
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Overexpression of the gap junction protein Cx43 as found in diabetic foot ulcers can retard fibroblast migration. Cell Biol Int 2012; 36:661-7. [DOI: 10.1042/cbi20110628] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Lazarowski ER. Vesicular and conductive mechanisms of nucleotide release. Purinergic Signal 2012; 8:359-73. [PMID: 22528679 DOI: 10.1007/s11302-012-9304-9] [Citation(s) in RCA: 228] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 01/21/2012] [Indexed: 12/22/2022] Open
Abstract
Extracellular nucleotides and nucleosides promote a vast range of physiological responses, via activation of cell surface purinergic receptors. Virtually all tissues and cell types exhibit regulated release of ATP, which, in many cases, is accompanied by the release of uridine nucleotides. Given the relevance of extracellular nucleotide/nucleoside-evoked responses, understanding how ATP and other nucleotides are released from cells is an important physiological question. By facilitating the entry of cytosolic nucleotides into the secretory pathway, recently identified vesicular nucleotide and nucleotide-sugar transporters contribute to the exocytotic release of ATP and UDP-sugars not only from endocrine/exocrine tissues, but also from cell types in which secretory granules have not been biochemically characterized. In addition, plasma membrane connexin hemichannels, pannexin channels, and less-well molecularly defined ATP conducting anion channels have been shown to contribute to the release of ATP (and UTP) under a variety of conditions.
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Affiliation(s)
- Eduardo R Lazarowski
- School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7248, USA.
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19
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Iacobas S, Thomas NM, Iacobas DA. Plasticity of the myelination genomic fabric. Mol Genet Genomics 2012; 287:237-46. [PMID: 22246408 DOI: 10.1007/s00438-012-0673-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 01/03/2012] [Indexed: 01/11/2023]
Abstract
This study aimed to quantify the influence of the astrocyte proximity on myelination genomic fabric (MYE) of oligodendrocytes, defined as the most interconnected and stably expressed gene web responsible for myelination. Such quantitation is important to evaluate whether astrocyte signaling may contribute to demyelination when impaired and remyelination when properly restored. For this, we compared changes in the gene expression profiles of immortalized precursor oligodendrocytes (Oli-neu), stimulated to differentiate by the proximity of nontouching astrocytes or treatment with db-cAMP. In a previous paper, we reported that the astrocyte proximity upregulated or turned-on a large number of myelination genes and substantially enriched the Ca(2+)-signaling and cytokine receptor regulatory networks of MYE in Oli-neu cells. Here, we introduce the "transcriptomic distance" to evaluate fabric remodeling and "pair-wise relevance" to identify the most influential gene pairs. Together with the prominence gene analysis used to select and rank the fabric genes, these novel analytical tools provide a comprehensively quantitative view of the physio/pathological transformations of the transcriptomic programs of myelinating cells. Applied to our data, the analyses revealed not only that the astrocyte neighborhood is a substantially more powerful regulator of myelination than the differentiating treatment but also the molecular mechanisms of the two differentiating paradigms are different. By inducing a profound remodeling of MYE and regulatory transcriptomic networks, the astrocyte-oligodendrocyte intercommunication may be considered as a major player in both pathophysiology and therapy of neurodegenerative diseases related to myelination.
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Affiliation(s)
- Sanda Iacobas
- D.P. Purpura Department of Neuroscience, Kennedy Center, Albert Einstein College of Medicine of Yeshiva University, Room 713, 1300 Morris Park Avenue, Bronx-New York, NY, 10461, USA
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Lazarowski ER, Sesma JI, Seminario-Vidal L, Kreda SM. Molecular mechanisms of purine and pyrimidine nucleotide release. ADVANCES IN PHARMACOLOGY 2011; 61:221-61. [PMID: 21586361 DOI: 10.1016/b978-0-12-385526-8.00008-4] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Given the widespread importance of purinergic receptor-evoked signaling, understanding how ATP and other nucleotides are released from cells in a regulated manner is an essential physiological question. Nonlytic release of ATP, UTP, UDP-glucose, and other nucleotides occurs in all cell types and tissues via both constitutive mechanisms, that is, in the absence of external stimuli, and to a greater extent in response to biochemical or mechanical/physical stimuli. However, a molecular understanding of the processes regulating nucleotide release has only recently begun to emerge. It is generally accepted that nucleotide release occurs in two different scenarios, exocytotic release from the secretory pathway or via conductive/transport mechanisms, and a critical review of our current understanding of these mechanisms is presented in this chapter.
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Affiliation(s)
- Eduardo R Lazarowski
- Cystic Fibrosis/Pulmonary Research & Treatment Center, School of Medicine, University of North Carolina, Chapel Hill, USA
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21
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Blankenship AG, Hamby AM, Firl A, Vyas S, Maxeiner S, Willecke K, Feller MB. The role of neuronal connexins 36 and 45 in shaping spontaneous firing patterns in the developing retina. J Neurosci 2011; 31:9998-10008. [PMID: 21734291 PMCID: PMC3142875 DOI: 10.1523/jneurosci.5640-10.2011] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 05/17/2011] [Accepted: 05/23/2011] [Indexed: 12/27/2022] Open
Abstract
Gap junction coupling synchronizes activity among neurons in adult neural circuits, but its role in coordinating activity during development is less known. The developing retina exhibits retinal waves--spontaneous depolarizations that propagate among retinal interneurons and drive retinal ganglion cells (RGCs) to fire correlated bursts of action potentials. During development, two connexin isoforms, connexin 36 (Cx36) and Cx45, are expressed in bipolar cells and RGCs, and therefore provide a potential substrate for coordinating network activity. To determine whether gap junctions contribute to retinal waves, we compared spontaneous activity patterns using calcium imaging, whole-cell recording, and multielectrode array recording in control, single-knock-out (ko) mice lacking Cx45 and double-knock-out (dko) mice lacking both isoforms. Wave frequency, propagation speed, and bias in propagation direction were similar in control, Cx36ko, Cx45ko, and Cx36/45dko retinas. However, the spontaneous firing rate of individual retinal ganglion cells was elevated in Cx45ko retinas, similar to Cx36ko retinas (Hansen et al., 2005; Torborg and Feller, 2005), a phenotype that was more pronounced in Cx36/45dko retinas. As a result, spatial correlations, as assayed by nearest-neighbor correlation and functional connectivity maps, were significantly altered. In addition, Cx36/45dko mice had reduced eye-specific segregation of retinogeniculate afferents. Together, these findings suggest that although Cx36 and Cx45 do not play a role in gross spatial and temporal propagation properties of retinal waves, they strongly modulate the firing pattern of individual RGCs, ensuring strongly correlated firing between nearby RGCs and normal patterning of retinogeniculate projections.
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Affiliation(s)
- Aaron G. Blankenship
- Neurosciences Graduate Program, University of California, San Diego, La Jolla, California 92093
- Department of Molecular and Cell Biology
| | | | - Alana Firl
- Vision Sciences Graduate Program, Department of Optometry, and
| | - Shri Vyas
- Department of Molecular and Cell Biology
| | - Stephan Maxeiner
- LIMES (Life and Medical Sciences) Institute, University of Bonn, 53115 Bonn, Germany
| | - Klaus Willecke
- LIMES (Life and Medical Sciences) Institute, University of Bonn, 53115 Bonn, Germany
| | - Marla B. Feller
- Department of Molecular and Cell Biology
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, California 94720, and
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Kang SG, Roh YM, Lau A, Westaway D, McKenzie D, Aiken J, Kim YS, Yoo HS. Establishment and characterization of Prnp knockdown neuroblastoma cells using dual microRNA-mediated RNA interference. Prion 2011; 5:93-102. [PMID: 21494092 DOI: 10.4161/pri.5.2.15621] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Prion diseases are fatal transmissible neurodegenerative disorders. In the pathogenesis of the disease, the cellular prion protein (PrPC) is required for replication of abnormal prion (PrPSc), which results in accumulation of PrPSc. Although there have been extensive studies using Prnp knockout systems, the normal function of PrPC remains ambiguous. Compared with conventional germline knockout technologies and transient naked siRNA-dependent knockdown systems, newly constructed durable chained-miRNA could provide a cell culture model that is closer to the disease status and easier to achieve with no detrimental sequelae. The selective silencing of a target gene by RNA interference (RNAi) is a powerful approach to investigate the unknown function of genes in vitro and in vivo. To reduce PrPC expression, a novel dual targeting-microRNA (miRdual) was constructed. The miRdual, which targets N- and C- termini of Prnp simultaneously, more effectively suppressed PrPC expression compared with conventional single site targeting. Furthermore, to investigate the cellular change following PrPC depletion, gene expression analysis of PrPC interacting and/or associating genes and several assays including proliferation, viability and apoptosis were performed. The transcripts 670460F02Rik and Plk3, Ppp2r2b and Csnk2a1 increase in abundance and are reported to be involved in cell proliferation and mitochondrial-mediated apoptosis. Dual-targeting RNAi with miRdual against Prnp will be useful for analyzing the physiological function of PrPC in neuronal cell lines and may provide a potential therapeutic intervention for prion diseases in the future.
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Affiliation(s)
- Sang-Gyun Kang
- Department of Infectious Diseases, College of Veterinary Medicine, KRF Zoonotic Disease Priority Research Institute and BK21 Program for Veterinary Science, Seoul National University, Seoul, Korea
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Abstract
Extensive literature documented that astrocytes release neurotransmitters, cytokines and other signaling molecules to modulate migration, maturation and myelin synthesis of oligodendrocytes through mechanisms primarily converging on cytosolic [Ca2+] transients. Considering the long-term effects, it is expected that astrocyte-conditioned medium is a major regulator of gene expression in oligodendrocytes even in the absence of cytosol-to-cytosol communication via astrocyte-oligodendrocyte gap junction channels. Indeed, by comparing the transcriptomes of immortalized precursor oligodendrocyte (Oli-neu) cells when cultured alone and co-cultured with non-touching astrocytes we found profound changes in the gene expression level, control and networking. Remarkably, the astrocyte proximity was more effective in remodeling the myelination (MYE) gene fabric and its control by cytokine receptor (CYR)-modulated intercellular Ca2+-signaling (ICS) transcriptomic network than the dibutyryl-cAMP (db-cAMP) treatment-induced transformation into myelin-associated glycoprotein-positive oligodendrocyte-like cells. Moreover, astrocyte proximity up-regulated 37 MYE genes and switched on another 14 MYE, 23 ICS and 4 CYR genes, enhancing the roles of the leukemia inhibitory factor receptor and connexins Cx29 and Cx47. The novel prominent gene analysis identified the enhancer of zeste homolog 2 as the most relevant MYE gene in the astrocyte proximity, notch gene homolog 1 in control and B-cell leukemia/lymphoma 2 in differentiated Oli-neu cells.
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Iacobas DA, Iacobas S, Thomas N, Spray DC. Sex-dependent gene regulatory networks of the heart rhythm. Funct Integr Genomics 2009; 10:73-86. [PMID: 19756788 DOI: 10.1007/s10142-009-0137-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 08/19/2009] [Accepted: 08/22/2009] [Indexed: 01/27/2023]
Abstract
Expression level, control, and intercoordination of 66 selected heart rhythm determinant (HRD) genes were compared in atria and ventricles of four male and four female adult mice. We found that genes encoding various adrenergic receptors, ankyrins, ion channels and transporters, connexins, cadherins, plakophilins, and other components of the intercalated discs form a complex network that is chamber dependent and differs between the two sexes. In addition, most HRD genes in atria had higher expression in males than in females, while in ventricles, expression levels were mostly higher in females than in males. Moreover, significant chamber differences were observed between the sexes, with higher expression in atria than ventricles for males and higher expression in ventricles than atria for females. We have ranked the selected genes according to their prominence (new concept) within the HRD gene web defined as extent of expression coordination with the other web genes and stability of expression. Interestingly, the prominence hierarchy was substantially different between the two sexes. Taken together, these findings indicate that the organizational principles of the heart rhythm transcriptome are sex dependent, with the newly introduced prominence analysis allowing identification of genes that are pivotal for the sexual dichotomy.
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Affiliation(s)
- D A Iacobas
- Dominick P Purpura Department of Neuroscience, Albert Einstein College of Medicine, Kennedy Center, New York, NY 10461, USA.
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25
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Voss LJ, Jacobson G, Sleigh JW, Steyn-Ross A, Steyn-Ross M. Excitatory effects of gap junction blockers on cerebral cortex seizure-like activity in rats and mice. Epilepsia 2009; 50:1971-8. [PMID: 19486358 DOI: 10.1111/j.1528-1167.2009.02087.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PURPOSE The role of gap junctions in seizures is an area of intense research. Many groups have reported anticonvulsant effects of gap junction blockade, strengthening the case for a role for gap junctions in ictogenesis. The cerebral cortex is underrepresented in this body of research. We have investigated the effect of gap junction blockade on seizure-like activity in rat and mouse cerebral cortex slices. METHODS Seizure-like activity was induced by perfusing with low-magnesium artificial cerebrospinal fluid. The effect of three gap junction blockers was investigated in rat cortical slices; quinine (200 and 400 microm), quinidine (100 and 200 microm), and carbenoxolone (100 and 200 microm). In addition, the effect of mefloquine was investigated in wild-type mice and connexin36 knockout mice. The data were analyzed for the effect on frequency and amplitude of seizure-like events. RESULTS Paradoxical excitatory effects on seizure-like activity were observed for all three agents in rat cortical slices. Quinine (200 microm) and carbenoxolone (100 microm) increased both the frequency and amplitude of seizure-like events. Quinidine (100 microm) increased the frequency of events. Higher doses of quinine (400 microm) and carbenoxolone (200 microm) had biphasic excitatory-inhibitory effects. Similar excitatory effects were observed in adult wild-type mouse cortical slices perfused with mefloquine (5 microm or 10 microm), but were absent in slices from connexin36-deficient mice. DISCUSSION In conclusion, we have shown a paradoxical proseizure effect of pharmacologic gap junction blockade in a cortical model of seizure-like activity. We suggest that this effect is probably due to a disruption of inhibitory interneuron coupling secondary to connexin36 blockade.
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Affiliation(s)
- Logan J Voss
- Department of Anesthesiology, Waikato Clinical School, University of Auckland, Waikato Hospital, New Zealand.
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Cook JE, Becker DL. Gap-Junction Proteins in Retinal Development: New Roles for the “Nexus”. Physiology (Bethesda) 2009; 24:219-30. [DOI: 10.1152/physiol.00007.2009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Gap-junction channels, the cytoplasmic proteins that associate with them, and the transcriptional networks that regulate them are increasingly being viewed as critical communications hubs for cell signaling in health and disease. As a result, the term “nexus,” which was the original structural name for these focal intercellular links, is coming back into use with new proteomic and transcriptomic meanings. The retina is better understood than any other part of the vertebrate central nervous system in respect of its developmental patterning, its diverse neuronal types and circuits, and the emergence of its definitive structure-function correlations. Thus, studies of the junctional and nonjunctional nexus roles of gap-junction proteins in coordinating retinal development should throw useful light on cell signaling in other developing nervous tissues.
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Affiliation(s)
- Jeremy E. Cook
- Department of Cell and Developmental Biology, University College London, Gower Street, London, United Kingdom
| | - David L. Becker
- Department of Cell and Developmental Biology, University College London, Gower Street, London, United Kingdom
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Fort AG, Spray DC. Trifluoroethanol reveals helical propensity at analogous positions in cytoplasmic domains of three connexins. Biopolymers 2009; 92:173-82. [PMID: 19226516 DOI: 10.1002/bip.21166] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cytoplasmic domains of gap junction proteins (connexins) are involved in channel gating, voltage and pH sensitivity, and contain binding sites for partner proteins. However, their secondary structure is incompletely characterized and comparisons among the connexins is totally lacking. Circular dichroism (CD) was used to study the conformational properties of synthetic peptides corresponding to the highly divergent amino acid sequences of cytoplasmic domains of connexin (Cx)32, Cx36, and Cx43. We report that whereas peptides were largely unstructured in aqueous buffer, certain peptides in 30% trifluoroethanol (TFE) showed considerable helical content. These structured peptides correspond to analogous regions in each of the three connexin cytoplasmic domains. This first comparative study of conformational properties of connexin cytoplasmic domains reveals protein domains that may play similar roles in channel function and protein-protein interactions.
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Affiliation(s)
- Alfredo G Fort
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA.
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28
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Scemes E, Spray DC, Meda P. Connexins, pannexins, innexins: novel roles of "hemi-channels". Pflugers Arch 2008; 457:1207-26. [PMID: 18853183 DOI: 10.1007/s00424-008-0591-5] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Accepted: 09/17/2008] [Indexed: 12/11/2022]
Affiliation(s)
- Eliana Scemes
- The Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY, USA
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Iacobas DA, Iacobas S, Urban-Maldonado M, Scemes E, Spray DC. Similar transcriptomic alterations in Cx43 knockdown and knockout astrocytes. ACTA ACUST UNITED AC 2008; 15:195-206. [PMID: 18649190 DOI: 10.1080/15419060802014222] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Previous findings of widespread transcriptomic alteration in tissues from connexin null mice raise the issue of whether the transcriptomic changes are directly due to connexin down-regulation or to "compensatory" developmental alterations for the missing gene. To start addressing this question, the authors compared with wild-type control the gene expression profiles of connexin 43 (Cx43) knockout and Cx43siRNA knockdown wild-type cortical astrocytes. Array analysis revealed remarkable parallelism of transcriptomic changes in knockout and knockdown astrocytes, with similarly altered genes being located on all chromosomes and encoding proteins involved in a wide diversity of cell functions. Moreover, gene expression variability was analogously higher in Cx43 null and siRNA-treated astrocytes, and expression interlinkages were similarly altered among a selected subset of genes. This highly significant overlap between transcriptomic alterations in Cx43 knockout and knockdown astrocytes suggests that the widespread changes more likely reflect connexin-dependent Gene Regulatory Networks rather than developmental compensation for the missing gene.
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Affiliation(s)
- Dumitru A Iacobas
- Dominick P Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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30
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Integrated transcriptomic response to cardiac chronic hypoxia: translation regulators and response to stress in cell survival. Funct Integr Genomics 2008; 8:265-75. [PMID: 18446526 DOI: 10.1007/s10142-008-0082-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 03/31/2008] [Accepted: 04/06/2008] [Indexed: 12/12/2022]
Abstract
Complementary deoxyribonucleic acid microarray data from 36 mice subjected for 1, 2, or 4 weeks of their early life to normal atmospheric conditions (normoxia) or chronic intermittent (CIH) or constant (CCH) hypoxia were analyzed to extract organizational principles of the developing heart transcriptome and determine the integrated response to oxygen deprivation. Although both CCH and CIH regulated numerous genes involved in a wide diversity of processes, the changes in maturational profile, expression stability, and coordination were vastly different between the two treatments, indicating the activation of distinct regulatory mechanisms of gene transcription. The analysis focused on the main regulators of translation and response to stress because of their role in the cardiac hypertrophy and cell survival in hypoxia. On average, the expression of each heart gene was tied to the expression of about 20% of other genes in normoxia but to only 8% in CCH and 9% in CIH, indicating a strong decoupling effect of hypoxia. In contrast to the general tendency, the interlinkages among components of the translational machinery and response to stress increased significantly in CIH and much more in CCH, suggesting a coordinated response to the hypoxic stress. Moreover, the transcriptomic networks were profoundly and differently remodeled by CCH and CIH.
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Abstract
Gap junctions facilitate direct cytoplasmic communication between neighboring cells, facilitating the transfer of small molecular weight molecules involved in cell signaling and metabolism. Gap junction channels are formed by the joining of two hemichannels from adjacent cells, each composed of six oligomeric protein subunits called connexins. Of paramount importance to CNS homeostasis are astrocyte networks formed by gap junctions, which play a critical role in maintaining the homeostatic regulation of extracellular pH, K+, and glutamate levels. Inflammation is a hallmark of several diseases afflicting the CNS. Within the past several years, the number of publications reporting effects of cytokines and pathogenic stimuli on glial gap junction communication has increased dramatically. The purpose of this review is to discuss recent observations characterizing the consequences of inflammatory stimuli on homocellular gap junction coupling in astrocytes and microglia as well as changes in connexin expression during various CNS inflammatory conditions.
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Affiliation(s)
- Tammy Kielian
- Department of Neurobiology and Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA.
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Elias LAB, Kriegstein AR. Gap junctions: multifaceted regulators of embryonic cortical development. Trends Neurosci 2008; 31:243-50. [PMID: 18403031 DOI: 10.1016/j.tins.2008.02.007] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 02/01/2008] [Accepted: 02/01/2008] [Indexed: 10/22/2022]
Abstract
The morphological development of the cerebral cortex from a primitive neuroepithelium into a complex laminar structure underlying higher cognition must rely on a network of intercellular signaling. Gap junctions are widely expressed during embryonic development and provide a means of cell-cell contact and communication. We review the roles of gap junctions in regulating the proliferation of neural progenitors as well as the migration and differentiation of young neurons in the embryonic cerebral cortex. There is substantial evidence that although gap junctions act in the classical manner coupling neural progenitors, they also act as hemichannels mediating the spread of calcium waves across progenitor cell populations and as adhesive molecules aiding neuronal migration. Gap junctions are thus emerging as multifaceted regulators of cortical development playing diverse roles in intercellular communication.
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Affiliation(s)
- Laura A B Elias
- Neuroscience Graduate Program, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
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Iacobas DA, Iacobas S, Werner P, Scemes E, Spray DC. Alteration of transcriptomic networks in adoptive-transfer experimental autoimmune encephalomyelitis. Front Integr Neurosci 2007; 1:10. [PMID: 18958238 PMCID: PMC2526015 DOI: 10.3389/neuro.07.010.2007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Accepted: 12/03/2007] [Indexed: 01/09/2023] Open
Abstract
Adoptive transfer experimental autoimmune encephalomyelitis (AT-EAE) is an inflammatory demyelination that recapitulates in mouse spinal cord (SC) the human multiple sclerosis disease. We now analyze previously reported cDNA array data from age-matched young female adult control and passively myelin antigen-sensitized EAE mice with regard to organizational principles of the SC transcriptome in autoimmune demyelination. Although AT-EAE had a large impact on immune response genes, broader functional and chromosomal gene cohorts were neither significantly regulated nor showed significant changes in expression coordination. However, overall transcriptional control was increased in AT-EAE and the proportions of transcript abundances were perturbed within each cohort. Striking likenesses and oppositions were identified in the coordination profiles of genes related to myelination, calcium signaling, and inflammatory response in controls that were substantially altered in AT-EAE. We propose that up- or down-regulation of genes linked to those targeted by the disease could potentially compensate for the pathological transcriptomic changes.
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Affiliation(s)
- Dumitru A Iacobas
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine USA.
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