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Xu S, Jia M, Guo J, He J, Chen X, Xu Y, Hu W, Wu D, Wu C, Ji X. Ticking Brain: Circadian Rhythm as a New Target for Cerebroprotection. Stroke 2024; 55:2385-2396. [PMID: 39011642 DOI: 10.1161/strokeaha.124.046684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Circadian rhythm is a master process observed in nearly every type of cell throughout the body, and it macroscopically regulates daily physiology. Recent clinical trials have revealed the effects of circadian variation on the incidence, pathophysiological processes, and prognosis of acute ischemic stroke. Furthermore, core clock genes, the cell-autonomous pacemakers of the circadian rhythm, affect the neurovascular unit-composing cells in a nonparallel manner after the same pathophysiological processes of ischemia/reperfusion. In this review, we discuss the influence of circadian rhythms and clock genes on each type of neurovascular unit cell in the pathophysiological processes of acute ischemic stroke.
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Affiliation(s)
- Shuaili Xu
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders (S.X., X.J.), Capital Medical University, Beijing, China
- China-America Institute of Neuroscience, Xuanwu Hospital (S.X., J.G., J.H., X.C., Y.X., W.H., D.W., X.J.), Capital Medical University, Beijing, China
| | - Milan Jia
- Department of Neurology, Xuanwu Hospital (M.J., X.C., Y.X., W.H., C.W., X.J.), Capital Medical University, Beijing, China
| | - Jiaqi Guo
- China-America Institute of Neuroscience, Xuanwu Hospital (S.X., J.G., J.H., X.C., Y.X., W.H., D.W., X.J.), Capital Medical University, Beijing, China
| | - Jiachen He
- China-America Institute of Neuroscience, Xuanwu Hospital (S.X., J.G., J.H., X.C., Y.X., W.H., D.W., X.J.), Capital Medical University, Beijing, China
| | - Xi Chen
- Department of Neurology, Xuanwu Hospital (M.J., X.C., Y.X., W.H., C.W., X.J.), Capital Medical University, Beijing, China
- China-America Institute of Neuroscience, Xuanwu Hospital (S.X., J.G., J.H., X.C., Y.X., W.H., D.W., X.J.), Capital Medical University, Beijing, China
| | - Yi Xu
- Department of Neurology, Xuanwu Hospital (M.J., X.C., Y.X., W.H., C.W., X.J.), Capital Medical University, Beijing, China
- China-America Institute of Neuroscience, Xuanwu Hospital (S.X., J.G., J.H., X.C., Y.X., W.H., D.W., X.J.), Capital Medical University, Beijing, China
| | - Wenbo Hu
- Department of Neurology, Xuanwu Hospital (M.J., X.C., Y.X., W.H., C.W., X.J.), Capital Medical University, Beijing, China
- China-America Institute of Neuroscience, Xuanwu Hospital (S.X., J.G., J.H., X.C., Y.X., W.H., D.W., X.J.), Capital Medical University, Beijing, China
| | - Di Wu
- China-America Institute of Neuroscience, Xuanwu Hospital (S.X., J.G., J.H., X.C., Y.X., W.H., D.W., X.J.), Capital Medical University, Beijing, China
| | - Chuanjie Wu
- Department of Neurology, Xuanwu Hospital (M.J., X.C., Y.X., W.H., C.W., X.J.), Capital Medical University, Beijing, China
| | - Xunming Ji
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders (S.X., X.J.), Capital Medical University, Beijing, China
- Department of Neurology, Xuanwu Hospital (M.J., X.C., Y.X., W.H., C.W., X.J.), Capital Medical University, Beijing, China
- China-America Institute of Neuroscience, Xuanwu Hospital (S.X., J.G., J.H., X.C., Y.X., W.H., D.W., X.J.), Capital Medical University, Beijing, China
- Department of Neurosurgery, Xuanwu Hospital (X.J.), Capital Medical University, Beijing, China
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2
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Li W, Tiedt S, Lawrence JH, Harrington ME, Musiek ES, Lo EH. Circadian Biology and the Neurovascular Unit. Circ Res 2024; 134:748-769. [PMID: 38484026 DOI: 10.1161/circresaha.124.323514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
Mammalian physiology and cellular function are subject to significant oscillations over the course of every 24-hour day. It is likely that these daily rhythms will affect function as well as mechanisms of disease in the central nervous system. In this review, we attempt to survey and synthesize emerging studies that investigate how circadian biology may influence the neurovascular unit. We examine how circadian clocks may operate in neural, glial, and vascular compartments, review how circadian mechanisms regulate cell-cell signaling, assess interactions with aging and vascular comorbidities, and finally ask whether and how circadian effects and disruptions in rhythms may influence the risk and progression of pathophysiology in cerebrovascular disease. Overcoming identified challenges and leveraging opportunities for future research might support the development of novel circadian-based treatments for stroke.
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Affiliation(s)
- Wenlu Li
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (W.L., E.H.L.)
- Consortium International pour la Recherche Circadienne sur l'AVC, Munich, Germany (W.L., S.T., J.H.L., M.E.H., E.S.M., E.H.L.)
| | - Steffen Tiedt
- Consortium International pour la Recherche Circadienne sur l'AVC, Munich, Germany (W.L., S.T., J.H.L., M.E.H., E.S.M., E.H.L.)
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany (S.T.)
| | - Jennifer H Lawrence
- Consortium International pour la Recherche Circadienne sur l'AVC, Munich, Germany (W.L., S.T., J.H.L., M.E.H., E.S.M., E.H.L.)
- Department of Neurology, Washington University School of Medicine, St. Louis, MO (J.H.L., E.S.M.)
| | - Mary E Harrington
- Consortium International pour la Recherche Circadienne sur l'AVC, Munich, Germany (W.L., S.T., J.H.L., M.E.H., E.S.M., E.H.L.)
- Neuroscience Program, Smith College, Northampton, MA (M.E.H.)
| | - Erik S Musiek
- Consortium International pour la Recherche Circadienne sur l'AVC, Munich, Germany (W.L., S.T., J.H.L., M.E.H., E.S.M., E.H.L.)
- Department of Neurology, Washington University School of Medicine, St. Louis, MO (J.H.L., E.S.M.)
| | - Eng H Lo
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (W.L., E.H.L.)
- Consortium International pour la Recherche Circadienne sur l'AVC, Munich, Germany (W.L., S.T., J.H.L., M.E.H., E.S.M., E.H.L.)
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3
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Mitchell JW, Gillette MU. Development of circadian neurovascular function and its implications. Front Neurosci 2023; 17:1196606. [PMID: 37732312 PMCID: PMC10507717 DOI: 10.3389/fnins.2023.1196606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/14/2023] [Indexed: 09/22/2023] Open
Abstract
The neurovascular system forms the interface between the tissue of the central nervous system (CNS) and circulating blood. It plays a critical role in regulating movement of ions, small molecules, and cellular regulators into and out of brain tissue and in sustaining brain health. The neurovascular unit (NVU), the cells that form the structural and functional link between cells of the brain and the vasculature, maintains the blood-brain interface (BBI), controls cerebral blood flow, and surveils for injury. The neurovascular system is dynamic; it undergoes tight regulation of biochemical and cellular interactions to balance and support brain function. Development of an intrinsic circadian clock enables the NVU to anticipate rhythmic changes in brain activity and body physiology that occur over the day-night cycle. The development of circadian neurovascular function involves multiple cell types. We address the functional aspects of the circadian clock in the components of the NVU and their effects in regulating neurovascular physiology, including BBI permeability, cerebral blood flow, and inflammation. Disrupting the circadian clock impairs a number of physiological processes associated with the NVU, many of which are correlated with an increased risk of dysfunction and disease. Consequently, understanding the cell biology and physiology of the NVU is critical to diminishing consequences of impaired neurovascular function, including cerebral bleeding and neurodegeneration.
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Affiliation(s)
- Jennifer W. Mitchell
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL, United States
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Martha U. Gillette
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL, United States
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, United States
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, United States
- Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, United States
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4
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Lu F, Leach LL, Gross JM. A CRISPR-Cas9-mediated F0 screen to identify pro-regenerative genes in the zebrafish retinal pigment epithelium. Sci Rep 2023; 13:3142. [PMID: 36823429 PMCID: PMC9950062 DOI: 10.1038/s41598-023-29046-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/30/2023] [Indexed: 02/25/2023] Open
Abstract
Ocular diseases resulting in death of the retinal pigment epithelium (RPE) lead to vision loss and blindness. There are currently no FDA-approved strategies to restore damaged RPE cells. Stimulating intrinsic regenerative responses within damaged tissues has gained traction as a possible mechanism for tissue repair. Zebrafish possess remarkable regenerative abilities, including within the RPE; however, our understanding of the underlying mechanisms remains limited. Here, we conducted an F0 in vivo CRISPR-Cas9-mediated screen of 27 candidate RPE regeneration genes. The screen involved injection of a ribonucleoprotein complex containing three highly mutagenic guide RNAs per target gene followed by PCR-based genotyping to identify large intragenic deletions and MATLAB-based automated quantification of RPE regeneration. Through this F0 screening pipeline, eight positive and seven negative regulators of RPE regeneration were identified. Further characterization of one candidate, cldn7b, revealed novel roles in regulating macrophage/microglia infiltration after RPE injury and in clearing RPE/pigment debris during late-phase RPE regeneration. Taken together, these data support the utility of targeted F0 screens for validating pro-regenerative factors and reveal novel factors that could regulate regenerative responses within the zebrafish RPE.
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Affiliation(s)
- Fangfang Lu
- grid.21925.3d0000 0004 1936 9000Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA ,grid.452708.c0000 0004 1803 0208Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011 Hunan China
| | - Lyndsay L. Leach
- grid.21925.3d0000 0004 1936 9000Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA ,grid.89336.370000 0004 1936 9924Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712 USA
| | - Jeffrey M. Gross
- grid.21925.3d0000 0004 1936 9000Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA ,grid.89336.370000 0004 1936 9924Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712 USA
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5
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Xiao J, Wang WX. Patterns and Crucial Regulation of Alternative Splicing During Early Development in Zebrafish. J Mol Biol 2022; 434:167821. [PMID: 36087778 DOI: 10.1016/j.jmb.2022.167821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 10/31/2022]
Abstract
Many vertebrate genes generate multiple transcript variants that may encode functionally distinct protein isoforms, but the transcriptomes of various developmental stages are poorly defined. Identifying the transcriptome and its regulation during the normal developmental process is the key to deciphering the developmental stage-specific functions of genes. Here we presented a systematic assessment of the temporal alternative splicing (AS) events during the critical development stages to capture the dynamic gene expression changes and AS in zebrafish. An unexpected transcriptome complexity generated by AS was observed during zebrafish development. The patterns of AS events varied substantially among developmental stages despite the similarities in the total proportion of AS genes. We further found that AS afforded substantial functional diversification of genes through the generation of stage-specific AS events from broadly protein-coding genes as an essential developmental regulatory mechanism. Skipped exon (SE) showed the strongest signals among developmental AS (devAS), suggesting that devAS events generated by SE may be necessary for the normal development of zebrafish. Most developmental genes regulated by AS mechanisms were not modulated in terms of their overall expression levels, indicating that AS shaped the transcriptome independently from transcriptional regulation during development. 128-cell stage was a critical stage for gene transcription during embryonic development. Splicing factors as an essential developmental regulator underwent AS in the potential autoregulatory feedback loop and expressed multiple isoforms. Thus, zebrafish development was shaped by an interplay of programs controlling gene expression levels and AS. Overall, we provided a global view of developmental patterns of AS during zebrafish development and revealed that AS transitions were the crucial regulatory component of zebrafish embryonic development.
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Affiliation(s)
- Jie Xiao
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Wen-Xiong Wang
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China.
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6
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Pandey RS, Krebs MP, Bolisetty MT, Charette JR, Naggert JK, Robson P, Nishina PM, Carter GW. Single-Cell RNA Sequencing Reveals Molecular Features of Heterogeneity in the Murine Retinal Pigment Epithelium. Int J Mol Sci 2022; 23:10419. [PMID: 36142331 PMCID: PMC9499471 DOI: 10.3390/ijms231810419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/09/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Transcriptomic analysis of the mammalian retinal pigment epithelium (RPE) aims to identify cellular networks that influence ocular development, maintenance, function, and disease. However, available evidence points to RPE cell heterogeneity within native tissue, which adds complexity to global transcriptomic analysis. Here, to assess cell heterogeneity, we performed single-cell RNA sequencing of RPE cells from two young adult male C57BL/6J mice. Following quality control to ensure robust transcript identification limited to cell singlets, we detected 13,858 transcripts among 2667 and 2846 RPE cells. Dimensional reduction by principal component analysis and uniform manifold approximation and projection revealed six distinct cell populations. All clusters expressed transcripts typical of RPE cells; the smallest (C1, containing 1-2% of total cells) exhibited the hallmarks of stem and/or progenitor (SP) cells. Placing C1-6 along a pseudotime axis suggested a relative decrease in melanogenesis and SP gene expression and a corresponding increase in visual cycle gene expression upon RPE maturation. K-means clustering of all detected transcripts identified additional expression patterns that may advance the understanding of RPE SP cell maintenance and the evolution of cellular metabolic networks during development. This work provides new insights into the transcriptome of the mouse RPE and a baseline for identifying experimentally induced transcriptional changes in future studies of this tissue.
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Affiliation(s)
- Ravi S. Pandey
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | - Mark P. Krebs
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Mohan T. Bolisetty
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | | | | | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | - Patsy M. Nishina
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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7
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DeVera C, Dixon J, Chrenek MA, Baba K, Le YZ, Iuvone PM, Tosini G. The Circadian Clock in the Retinal Pigment Epithelium Controls the Diurnal Rhythm of Phagocytic Activity. Int J Mol Sci 2022; 23:5302. [PMID: 35628111 PMCID: PMC9141420 DOI: 10.3390/ijms23105302] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 02/04/2023] Open
Abstract
The diurnal peak of phagocytosis by the retinal pigment epithelium (RPE) of photoreceptor outer segments (POS) is under circadian control and believed that this process involves interactions from the retina and RPE. Previous studies have demonstrated that a functional circadian clock exists within multiple retinal cell types and RPE. Thereby, the aim of this study was to determine whether the clock in the retina or RPE controls the diurnal phagocytic peak and whether disruption of the circadian clock in the RPE would affect cellular function and the viability during aging. To that, we generated and validated an RPE tissue-specific KO of the essential clock gene, Bmal1, and then determined the daily rhythm in phagocytic activity by the RPE in mice lacking a functional circadian clock in the retina or RPE. Then, using electroretinography, spectral domain-optical coherence tomography, and optomotor response of visual function we determined the effect of Bmal1 removal in young (6 months) and old (18 months) mice. RPE morphology and lipofuscin accumulation was determined in young and old mice. Our data shows that the clock in the RPE, rather than the retina clock, controls the diurnal phagocytic peak. Surprisingly, absence of a functional RPE clock and phagocytic peak does not result in any detectable age-related degenerative phenotype in the retina or RPE. Thus, our results demonstrate that the circadian clock in the RPE controls the daily peak of phagocytic activity. However, the absence of the clock in the RPE does not result in deterioration of photoreceptors or the RPE during aging.
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Affiliation(s)
- Christopher DeVera
- Department of Pharmacology & Toxicology and Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA; (C.D.); (K.B.)
| | - Jendayi Dixon
- Department of Ophthalmology and Emory Eye Center, Emory University School of Medicine, Atlanta, GA 30322, USA; (J.D.); (M.A.C.); (P.M.I.)
| | - Micah A. Chrenek
- Department of Ophthalmology and Emory Eye Center, Emory University School of Medicine, Atlanta, GA 30322, USA; (J.D.); (M.A.C.); (P.M.I.)
| | - Kenkichi Baba
- Department of Pharmacology & Toxicology and Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA; (C.D.); (K.B.)
| | - Yun Z. Le
- Departments of Medicine, Cell Biology, and Ophthalmology and Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - P. Michael Iuvone
- Department of Ophthalmology and Emory Eye Center, Emory University School of Medicine, Atlanta, GA 30322, USA; (J.D.); (M.A.C.); (P.M.I.)
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gianluca Tosini
- Department of Pharmacology & Toxicology and Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA; (C.D.); (K.B.)
- Department of Ophthalmology and Emory Eye Center, Emory University School of Medicine, Atlanta, GA 30322, USA; (J.D.); (M.A.C.); (P.M.I.)
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8
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Baba K, Goyal V, Tosini G. Circadian Regulation of Retinal Pigment Epithelium Function. Int J Mol Sci 2022; 23:2699. [PMID: 35269840 PMCID: PMC8910459 DOI: 10.3390/ijms23052699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 12/22/2022] Open
Abstract
The retinal pigment epithelium (RPE) is a single layer of cells located between the choriocapillaris vessels and the light-sensitive photoreceptors in the outer retina. The RPE performs physiological processes necessary for the maintenance and support of photoreceptors and visual function. Among the many functions performed by the RPE, the timing of the peak in phagocytic activity by the RPE of the photoreceptor outer segments that occurs 1-2 h. after the onset of light has captured the interest of many investigators and has thus been intensively studied. Several studies have shown that this burst in phagocytic activity by the RPE is under circadian control and is present in nocturnal and diurnal species and rod and cone photoreceptors. Previous investigations have demonstrated that a functional circadian clock exists within multiple retinal cell types and RPE cells. However, the anatomical location of the circadian controlling this activity is not clear. Experimental evidence indicates that the circadian clock, melatonin, dopamine, and integrin signaling play a key role in controlling this rhythm. A series of very recent studies report that the circadian clock in the RPE controls the daily peak in phagocytic activity. However, the loss of the burst in phagocytic activity after light onset does not result in photoreceptor or RPE deterioration during aging. In the current review, we summarized the current knowledge on the mechanism controlling this phenomenon and the physiological role of this peak.
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Affiliation(s)
| | | | - Gianluca Tosini
- Department of Pharmacology & Toxicology and Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310-1495, USA; (K.B.); (V.G.)
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9
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Network Meta-Analysis of Chicken Microarray Data Following Avian Influenza Challenge—A Comparison of Highly and Lowly Pathogenic Strains. Genes (Basel) 2022; 13:genes13030435. [PMID: 35327988 PMCID: PMC8953847 DOI: 10.3390/genes13030435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 02/01/2023] Open
Abstract
The current bioinformatics study was undertaken to analyze the transcriptome of chicken (Gallus gallus) after influenza A virus challenge. A meta-analysis was carried out to explore the host expression response after challenge with lowly pathogenic avian influenza (LPAI) (H1N1, H2N3, H5N2, H5N3 and H9N2) and with highly pathogenic avian influenza (HPAI) H5N1 strains. To do so, ten microarray datasets obtained from the Gene Expression Omnibus (GEO) database were normalized and meta-analyzed for the LPAI and HPAI host response individually. Different undirected networks were constructed and their metrics determined e.g., degree centrality, closeness centrality, harmonic centrality, subgraph centrality and eigenvector centrality. The results showed that, based on criteria of centrality, the CMTR1, EPSTI1, RNF213, HERC4L, IFIT5 and LY96 genes were the most significant during HPAI challenge, with PARD6G, HMG20A, PEX14, RNF151 and TLK1L having the lowest values. However, for LPAI challenge, ZDHHC9, IMMP2L, COX7C, RBM18, DCTN3, and NDUFB1 genes had the largest values for aforementioned criteria, with GTF3C5, DROSHA, ATRX, RFWD2, MED23 and SEC23B genes having the lowest values. The results of this study can be used as a basis for future development of treatments/preventions of the effects of avian influenza in chicken.
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10
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Milićević N, Ait-Hmyed Hakkari O, Bagchi U, Sandu C, Jongejan A, Moerland PD, Ten Brink JB, Hicks D, Bergen AA, Felder-Schmittbuhl MP. Core circadian clock genes Per1 and Per2 regulate the rhythm in photoreceptor outer segment phagocytosis. FASEB J 2021; 35:e21722. [PMID: 34160105 DOI: 10.1096/fj.202100293rr] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/13/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023]
Abstract
Retinal photoreceptors undergo daily renewal of their distal outer segments, a process indispensable for maintaining retinal health. Photoreceptor outer segment (POS) phagocytosis occurs as a daily peak, roughly about 1 hour after light onset. However, the underlying cellular and molecular mechanisms which initiate this process are still unknown. Here we show that, under constant darkness, mice deficient for core circadian clock genes (Per1 and Per2) lack a daily peak in POS phagocytosis. By qPCR analysis, we found that core clock genes were rhythmic over 24 hours in both WT and Per1, Per2 double mutant whole retinas. More precise transcriptomics analysis of laser capture microdissected WT photoreceptors revealed no differentially expressed genes between time points preceding and during the peak of POS phagocytosis. In contrast, we found that microdissected WT retinal pigment epithelium (RPE) had a number of genes that were differentially expressed at the peak phagocytic time point compared to adjacent ones. We also found a number of differentially expressed genes in Per1, Per2 double mutant RPE compared to WT ones at the peak phagocytic time point. Finally, based on STRING analysis, we found a group of interacting genes that potentially drive POS phagocytosis in the RPE. This potential pathway consists of genes such as: Pacsin1, Syp, Camk2b, and Camk2d among others. Our findings indicate that Per1 and Per2 are necessary clock components for driving POS phagocytosis and suggest that this process is transcriptionally driven by the RPE.
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Affiliation(s)
- Nemanja Milićević
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Centre National de la Recherche Scientifique, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Strasbourg, France
| | - Ouafa Ait-Hmyed Hakkari
- Centre National de la Recherche Scientifique, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Strasbourg, France
| | - Udita Bagchi
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Centre National de la Recherche Scientifique, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Strasbourg, France
| | - Cristina Sandu
- Centre National de la Recherche Scientifique, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Strasbourg, France
| | - Aldo Jongejan
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Amsterdam, the Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Amsterdam, the Netherlands
| | - Jacoline B Ten Brink
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - David Hicks
- Centre National de la Recherche Scientifique, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Strasbourg, France
| | - Arthur A Bergen
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Department of Ophthalmology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Netherlands Institute for Neuroscience (NIN-KNAW), Amsterdam, the Netherlands
| | - Marie-Paule Felder-Schmittbuhl
- Centre National de la Recherche Scientifique, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Strasbourg, France
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Brücker L, Kretschmer V, May-Simera HL. The entangled relationship between cilia and actin. Int J Biochem Cell Biol 2020; 129:105877. [PMID: 33166678 DOI: 10.1016/j.biocel.2020.105877] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022]
Abstract
Primary cilia are microtubule-based sensory cell organelles that are vital for tissue and organ development. They act as an antenna, receiving and transducing signals, enabling communication between cells. Defects in ciliogenesis result in severe genetic disorders collectively termed ciliopathies. In recent years, the importance of the direct and indirect involvement of actin regulators in ciliogenesis came into focus as it was shown that F-actin polymerisation impacts ciliation. The ciliary basal body was further identified as both a microtubule and actin organising centre. In the current review, we summarize recent studies on F-actin in and around primary cilia, focusing on different actin regulators and their effect on ciliogenesis, from the initial steps of basal body positioning and regulation of ciliary assembly and disassembly. Since primary cilia are also involved in several intracellular signalling pathways such as planar cell polarity (PCP), subsequently affecting actin rearrangements, the multiple effectors of this pathway are highlighted in more detail with a focus on the feedback loops connecting actin networks and cilia proteins. Finally, we elucidate the role of actin regulators in the development of ciliopathy symptoms and cancer.
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Affiliation(s)
- Lena Brücker
- Cilia Cell Biology, Institute of Molecular Physiology, Johannes-Gutenberg University, Mainz, Germany
| | - Viola Kretschmer
- Cilia Cell Biology, Institute of Molecular Physiology, Johannes-Gutenberg University, Mainz, Germany
| | - Helen Louise May-Simera
- Cilia Cell Biology, Institute of Molecular Physiology, Johannes-Gutenberg University, Mainz, Germany.
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