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Aryal S, Anand D, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery. Hum Genet 2023; 142:927-947. [PMID: 37191732 PMCID: PMC10680127 DOI: 10.1007/s00439-023-02570-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3300 proteins per sample (n = 5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis-termed "in silico WB-subtraction"-with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ≥ 2.5 average spectral counts, ≥ 2.0 fold-enrichment, false discovery rate < 0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE ( https://research.bioinformatics.udel.edu/iSyTE/ ), to allow effective visualization of this information and facilitate eye gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19713, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Larry L David
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19713, USA.
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2
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Aryal S, Anand D, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery. RESEARCH SQUARE 2023:rs.3.rs-2652395. [PMID: 36993571 PMCID: PMC10055508 DOI: 10.21203/rs.3.rs-2652395/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3,300 proteins per sample (n=5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis-termed "in silico WB-subtraction"-with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ³2.5 average spectral counts, ³2.0 fold-enrichment, False Discovery Rate <0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE (https://research.bioinformatics.udel.edu/iSyTE/), to allow effective visualization of this information and facilitate eye gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Hongzhan Huang
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713 USA
| | - Ashok P. Reddy
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Phillip A. Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Larry L. David
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713 USA
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A 69 kb Deletion in chr19q13.42 including PRPF31 Gene in a Chinese Family Affected with Autosomal Dominant Retinitis Pigmentosa. J Clin Med 2022; 11:jcm11226682. [PMID: 36431159 PMCID: PMC9695658 DOI: 10.3390/jcm11226682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/20/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
We aimed to identify the genetic cause of autosomal dominant retinitis pigmentosa (adRP) and characterize the underlying molecular mechanisms of incomplete penetrance in a Chinese family affected with adRP. All enrolled family members underwent ophthalmic examinations. Whole-genome sequencing (WGS), multiplex ligation-dependent probe amplification (MLPA), linkage analysis and haplotype construction were performed in all participants. RNA-seq was performed to analyze the regulating mechanism of incomplete penetrance among affected patients, mutation carriers and healthy controls. In the studied family, 14 individuals carried a novel heterozygous large deletion of 69 kilobase (kb) in 19q13.42 encompassing exon 1 of the PRPF31 gene and five upstream genes: TFPT, OSCAR, NDUFA3, TARM1, and VSTM1. Three family members were sequenced and diagnosed as non-penetrant carriers (NPCs). RNA-seq showed significant differential expression of genes in deletion between mutation carriers and healthy control. The RP11 pedigree in this study was the largest pedigree compared to other reported RP11 pedigrees with large deletions. Early onset in all affected members in this pedigree was considered to be a special phenotype and was firstly reported in a RP11 family for the first time. Differential expression of PRPF31 between affected and unaffected subjects indicates a haploinsufficiency to cause the disease in the family. The other genes with significant differential expression might play a cooperative effect on the penetrance of RP11.
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Song C, Yue Q, Moseley A, Al-Khalili O, Wynne BM, Ma H, Wang L, Eaton DC. Myristoylated alanine-rich C kinase substrate-like protein-1 regulates epithelial sodium channel activity in renal distal convoluted tubule cells. Am J Physiol Cell Physiol 2020; 319:C589-C604. [PMID: 32639874 DOI: 10.1152/ajpcell.00218.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The epithelial sodium channel (ENaC) regulates blood pressure by fine-tuning distal nephron sodium reabsorption. Our previous work has shown that ENaC gating is regulated by anionic phospholipid phosphates, including phosphatidylinositol 4,5-bisphosphate (PIP2). The PIP2-dependent regulation of ENaC is mediated by the myristoylated alanine-rich protein kinase C substrate-like protein-1 (MLP-1). MLP-1 binds to and is a reversible source of PIP2 at the plasma membrane. We examined MLP-1 regulation of ENaC in distal convoluted tubule clonal cell line DCT-15 cells. Wild-type MLP-1 runs at an apparent molecular mass of 52 kDa despite having a predicted molecular mass of 21 kDa. Native MLP-1 consists of several distinct structural elements: an effector domain that is highly positively charged, sequesters PIP2, contains serines that are the target of PKC, and controls MLP-1 association with the membrane; a myristoylation domain that promotes association with the membrane; and a multiple homology 2 domain of previously unknown function. To further examine MLP-1 in DCT-15 cells, we constructed several MLP-1 mutants: WT, a full-length wild-type protein; S3A, three substitutions in the effector domain to prevent phosphorylation; S3D mimicked constitutive phosphorylation by replacing three serines with aspartates; and GA replaced the myristoylation site glycine with alanine, so GA could not be myristoylated. Each mutant was tagged with either NH2-terminal 3XFLAG or COOH-terminal mCherry or V5. Transfection with MLP mutants modified ENaC activity in DCT-15 cells: activity was highest in S3A and lowest in S3D, and the activity after transfection with either construct was significantly different from WT. In Western blots, when transfected with 3XFLAG-tagged MLP-1 mutants, the expression of the full length of MLP-1 at 52 kDa increased in mutant S3A-MLP-1-transfected DCT-15 cells and decreased in S3D-MLP-1-transfected DCT-15 cells. Several lower molecular mass bands were also detected that correspond to potential presumptive calpain cleavage products. Confocal imaging shows that the different mutants localize in different subcellular compartments consistent with their preferred location in the membrane or in the cytosol. Activation of protein kinase C increases phosphorylation of endogenous MLP-1 and reduces ENaC activity. Our results suggest a complicated role for proteolytic processing in MLP-1 regulation of ENaC.
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Affiliation(s)
- Chang Song
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Division of Nephrology, Department of Medicine, Emory University, Atlanta, Georgia.,Department of Physiology, Emory University, Atlanta, Georgia
| | - Qiang Yue
- Division of Nephrology, Department of Medicine, Emory University, Atlanta, Georgia
| | - Auriel Moseley
- Division of Nephrology, Department of Medicine, Emory University, Atlanta, Georgia
| | - Otor Al-Khalili
- Division of Nephrology, Department of Medicine, Emory University, Atlanta, Georgia
| | - Brandi M Wynne
- Division of Nephrology & Hypertension, Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Heping Ma
- Department of Physiology, Emory University, Atlanta, Georgia
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Douglas C Eaton
- Division of Nephrology, Department of Medicine, Emory University, Atlanta, Georgia
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Liang W, Gao R, Yang M, Wang X, Cheng K, Shi X, He C, Li Y, Wu Y, Shi L, Chen J, Yu X. MARCKSL1 promotes the proliferation, migration and invasion of lung adenocarcinoma cells. Oncol Lett 2020; 19:2272-2280. [PMID: 32194726 PMCID: PMC7039154 DOI: 10.3892/ol.2020.11313] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 08/06/2019] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is the most common cancer in males and females and ~40% of lung cancer cases are adenocarcinomas. Previous studies have demonstrated that myristoylated alanine rich protein kinase C substrate (MARCKS) is upregulated in several types of cancer and is associated with poor prognosis in patients with breast cancer. However, its expression level and role in lung adenocarcinoma remain unknown. Therefore, the aim of the present study was to investigate the expression level and biological functions of MARCKS like 1 (MARCKSL1), a member of the MARCKS family, in lung adenocarcinoma. The expression level of MARCKSL1 was examined in human lung adenocarcinoma tissues and cell lines. MARCKSL1-specific small interfering RNAs effectively suppressed its expression level and significantly inhibited the proliferation, migration and invasion of lung adenocarcinoma cells. Additionally, the role of MARCKSLI in the regulation of metastasis was examined. Silencing MARCKSL1 decreased the expression of the epithelial-mesenchymal transition (EMT)-associated proteins E-cadherin, N-cadherin, vimentin and snail family transcriptional repressor 2, and decreased the phosphorylation level of AKT. The results obtained in the current study suggested that MARCKSL1 promoted the progression of lung adenocarcinoma by regulating EMT. MARCKSLI may have prognostic value and serve as a novel therapeutic target in lung adenocarcinoma.
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Affiliation(s)
- Wenjun Liang
- Department of Respiratory Medicine, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, Jiangsu 213000, P.R. China
| | - Ruichen Gao
- Department of Respiratory Medicine, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, Jiangsu 213000, P.R. China
| | - Mingxia Yang
- Department of Respiratory Medicine, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, Jiangsu 213000, P.R. China
| | - Xiaohua Wang
- Department of Respiratory Medicine, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, Jiangsu 213000, P.R. China
| | - Kewei Cheng
- Department of Respiratory Medicine, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, Jiangsu 213000, P.R. China
| | - Xuejun Shi
- Department of Respiratory Medicine, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, Jiangsu 213000, P.R. China
| | - Chen He
- Department of Respiratory Medicine, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, Jiangsu 213000, P.R. China
| | - Yemei Li
- Department of Respiratory Medicine, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, Jiangsu 213000, P.R. China
| | - Yuying Wu
- Department of Respiratory Medicine, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, Jiangsu 213000, P.R. China
| | - Lei Shi
- Department of Respiratory Medicine, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, Jiangsu 213000, P.R. China
| | - Jingtao Chen
- Department of Respiratory Medicine, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, Jiangsu 213000, P.R. China
| | - Xiaowei Yu
- Department of Respiratory Medicine, Affiliated Changzhou Second Hospital of Nanjing Medical University, Changzhou, Jiangsu 213000, P.R. China
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6
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Yao B, Zhang M, Leng X, Zhao D. Proteomic analysis of the effects of antler extract on chondrocyte proliferation, differentiation and apoptosis. Mol Biol Rep 2019; 46:1635-1648. [DOI: 10.1007/s11033-019-04612-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/17/2019] [Indexed: 01/09/2023]
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7
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Juma AR, Hall NE, Wong J, Gasperoni JG, Watanabe Y, Sahota A, Damdimopoulou PE, Grommen SVH, De Groef B. PLAG1 expression and target genes in the hypothalamo-pituitary system in male mice. Mol Cell Endocrinol 2018; 478:77-83. [PMID: 30048678 DOI: 10.1016/j.mce.2018.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/28/2018] [Accepted: 07/23/2018] [Indexed: 12/26/2022]
Abstract
Knockout of pleomorphic adenoma gene 1 (PLAG1) in mice results in reduced fertility. To investigate whether PLAG1 is involved in reproductive control by the hypothalamo-pituitary system in males, we determined PLAG1 expression sites and compared gene expression between hypothalami and pituitary glands from Plag1 knockout and wildtype animals. Abundant expression of PLAG1 was detected throughout the pituitary gland, including gonadotropes and somatotropes. The hypothalamus also contained a large number of PLAG1-expressing cells. PLAG1 was expressed in some gonadotropin-releasing hormone neurons, but not in kisspeptin neurons. Gene ontology analysis indicated upregulation of cell proliferation in both structures, and of cholesterol biosynthesis in the hypothalamus, but functional confirmation is required. Expression levels of pituitary gonadotropins and gonadotropin-releasing hormone receptor, and of brain gonadotropin-releasing hormone and kisspeptin mRNA were unaffected in knockout mice. We conclude that PLAG1 deficiency does not have a major impact on the reproductive control by the hypothalamo-pituitary system.
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Affiliation(s)
- Almas R Juma
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Nathan E Hall
- Department of Biochemistry and Genetics and La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Joanne Wong
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Jemma G Gasperoni
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Yugo Watanabe
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Akashdeep Sahota
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Pauliina E Damdimopoulou
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institute, Karolinska University Hospital, 14183, Huddinge, Sweden
| | - Sylvia V H Grommen
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Bert De Groef
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, 3086, Australia.
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El Amri M, Fitzgerald U, Schlosser G. MARCKS and MARCKS-like proteins in development and regeneration. J Biomed Sci 2018; 25:43. [PMID: 29788979 PMCID: PMC5964646 DOI: 10.1186/s12929-018-0445-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/07/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Myristoylated Alanine-Rich C-kinase Substrate (MARCKS) and MARCKS-like protein 1 (MARCKSL1) have a wide range of functions, ranging from roles in embryonic development to adult brain plasticity and the inflammatory response. Recently, both proteins have also been identified as important players in regeneration. Upon phosphorylation by protein kinase C (PKC) or calcium-dependent calmodulin-binding, MARCKS and MARCKSL1 translocate from the membrane into the cytosol, modulating cytoskeletal actin dynamics and vesicular trafficking and activating various signal transduction pathways. As a consequence, the two proteins are involved in the regulation of cell migration, secretion, proliferation and differentiation in many different tissues. MAIN BODY Throughout vertebrate development, MARCKS and MARCKSL1 are widely expressed in tissues derived from all germ layers, with particularly strong expression in the nervous system. They have been implicated in the regulation of gastrulation, myogenesis, brain development, and other developmental processes. Mice carrying loss of function mutations in either Marcks or Marcksl1 genes die shortly after birth due to multiple deficiencies including detrimental neural tube closure defects. In adult vertebrates, MARCKS and MARCKL1 continue to be important for multiple regenerative processes including peripheral nerve, appendage, and tail regeneration, making them promising targets for regenerative medicine. CONCLUSION This review briefly summarizes the molecular interactions and cellular functions of MARCKS and MARCKSL1 proteins and outlines their vital roles in development and regeneration.
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Affiliation(s)
- Mohamed El Amri
- Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway, Biomedical Sciences Building, Newcastle Road, Galway, Ireland
| | - Una Fitzgerald
- Galway Neuroscience Centre, School of Natural Sciences, Biomedical Sciences Building, National University of Ireland, Newcastle Road, Galway, Ireland
| | - Gerhard Schlosser
- Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway, Biomedical Sciences Building, Newcastle Road, Galway, Ireland. .,School of Natural Sciences and Regenerative Medicine Institute (REMEDI), National University of Ireland, Galway, Biomedical Sciences Building, Newcastle Road, Galway, Ireland.
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9
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Ricci L, Srivastava M. Wound-induced cell proliferation during animal regeneration. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 7:e321. [PMID: 29719123 DOI: 10.1002/wdev.321] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 03/20/2018] [Accepted: 03/20/2018] [Indexed: 12/19/2022]
Abstract
Many animal species are capable of replacing missing tissues that are lost upon injury or amputation through the process of regeneration. Although the extent of regeneration is variable across animals, that is, some animals can regenerate any missing cell type whereas some can only regenerate certain organs or tissues, regulated cell proliferation underlies the formation of new tissues in most systems. Notably, many species display an increase in proliferation within hours or days upon wounding. While different cell types proliferate in response to wounding in various animal taxa, comparative molecular data are beginning to point to shared wound-induced mechanisms that regulate cell division during regeneration. Here, we synthesize current insights about early molecular pathways of regeneration from diverse model and emerging systems by considering these species in their evolutionary contexts. Despite the great diversity of mechanisms underlying injury-induced cell proliferation across animals, and sometimes even in the same species, similar pathways for proliferation have been implicated in distantly related species (e.g., small diffusible molecules, signaling from apoptotic cells, growth factor signaling, mTOR and Hippo signaling, and Wnt and Bmp pathways). Studies that explicitly interrogate molecular and cellular regenerative mechanisms in understudied animal phyla will reveal the extent to which early pathways in the process of regeneration are conserved or independently evolved. This article is categorized under: Comparative Development and Evolution > Body Plan Evolution Adult Stem Cells, Tissue Renewal, and Regeneration > Regeneration Comparative Development and Evolution > Model Systems.
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Affiliation(s)
- Lorenzo Ricci
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
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10
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Kuribayashi H, Tsuhako A, Kikuchi M, Yoshida N, Koso H, Watanabe S. Role of transcription factor Tgif2 in photoreceptor differentiation in the mouse retina. Exp Eye Res 2016; 152:34-42. [DOI: 10.1016/j.exer.2016.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 09/09/2016] [Accepted: 09/13/2016] [Indexed: 10/21/2022]
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11
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Prieto D, Zolessi FR. Functional Diversification of the Four MARCKS Family Members in Zebrafish Neural Development. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 328:119-138. [PMID: 27554589 DOI: 10.1002/jez.b.22691] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 06/01/2016] [Accepted: 06/20/2016] [Indexed: 12/25/2022]
Abstract
Myristoylated alanin-rich C-kinase substrate (MARCKS) and MARCKS-like 1, each encoded by a different gene, comprise a very small family of actin-modulating proteins with essential roles in mammalian neural development. We show here that four genes (two marcks and two marcksl1) are present in teleosts including zebrafish, while ancient actinopterigians, sarcopterigian fishes, and chondrichtyans only have two. No marcks genes were found in agnaths or invertebrates. All four zebrafish genes are expressed during development, and we show here how their early knockdown causes defects in neural development, with some phenotypical differences. Knockdown of marcksa generated embryos with smaller brain and eyes, while marcksb caused different morphogenetic defects, such as larger hindbrain ventricle and folded retina. marcksl1a and marcksl1b morpholinos also caused smaller eyes and brain, although marcksl1a alone generated larger brain ventricles. At 24 hpf, marcksb caused a wider angle of the hindbrain walls, while marcksl1a showed a "T-shaped" neural tube and alterations in neuroepithelium organization. The double knockdown surprisingly produced new features, which included an increased neuroepithelial disorganization and partial neural tube duplications evident at 48 hpf, suggesting defects in convergent extension. This disorganization was also evident in the retina, although retinal ganglion cells were still able to differentiate. marcksl1b morphants presented a unique retinal phenotype characterized by the occurrence of sporadic ectopic neuronal differentiation. Although only marcksl1a morphant had a clear "ciliary phenotype," all presented significantly shorter cilia. Altogether, our data show that all marcks genes have functions in zebrafish neural development, with some differences that suggest the onset of protein diversification.
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Affiliation(s)
- Daniel Prieto
- Facultad de Ciencias, Sección Biología Celular, Universidad de la República, Montevideo, Uruguay
| | - Flavio R Zolessi
- Facultad de Ciencias, Sección Biología Celular, Universidad de la República, Montevideo, Uruguay.,Cell Biology of Neural Development Lab, Institut Pasteur de Montevideo, Montevideo, Uruguay
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12
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Ng L, Lau C, Sunkin SM, Bernard A, Chakravarty MM, Lein ES, Jones AR, Hawrylycz M. Surface-based mapping of gene expression and probabilistic expression maps in the mouse cortex. Methods 2009; 50:55-62. [PMID: 19818854 DOI: 10.1016/j.ymeth.2009.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 10/01/2009] [Indexed: 10/20/2022] Open
Abstract
The Allen Brain Atlas (ABA, www.brain-map.org) is a genome wide, spatially registered collection of cellular resolution in situ hybridization gene expression image data of the C57Bl/6J mouse brain. Derived from the ABA, the Anatomic Gene Expression Atlas (AGEA, http://mouse.brain-map.org/agea) has demonstrated both laminar and areal spatial gene expression correlations in the mouse cortex. While the mouse cortex is lissencephalic, its curvature and substantial bending in boundary areas renders it difficult to visualize and analyze laminar versus areal effects in a rectilinear coordinate framework. In context of human and non-human primate cortex, surface-based representation has proven useful for understanding relative locations of laminar, columnar, and areal features. In this paper, we describe a methodology for constructing surface-based flatmaps of the mouse cortex that enables mapping of gene expression data from individual genes in the ABA, or probabilistic expression maps from the AGEA, to identify and visualize genetic relationships between layers and areas.
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Affiliation(s)
- Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98103, USA
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13
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Sakai M, Furuya M, Endo H, Yamaoka K, Kondo S, Koike T. An Efficient Identification Method of a Specific Binding Protein for a Bioactive Compound Using On-Bead Digestion and Mass Spectrometry. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2008. [DOI: 10.1246/bcsj.81.1599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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Satoh S, Watanabe S. TGIF, a homeodomain transcription factor, regulates retinal progenitor cell differentiation. Exp Eye Res 2008; 87:571-9. [PMID: 18926818 DOI: 10.1016/j.exer.2008.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2008] [Revised: 09/09/2008] [Accepted: 09/12/2008] [Indexed: 12/29/2022]
Abstract
TG-interacting factor (TGIF) is a TALE homeodomain protein expressed predominantly in the central nervous system and functions as a transcriptional repressor. Several mutations in TGIF have been identified in patients with holoprosencephaly, the most common congenital malformation of the developing human forebrain. However, the precise role of TGIF in neural development is not well understood. We found that TGIF was expressed strongly in the mouse retina during early stages of development, and that its expression gradually decreased as retinal development progressed. In vitro explant cultures of mouse retina mimic the in vivo development of retinal subtypes. Forced expression of TGIF using a retrovirus in explant culture induced the differentiation of amacrine cells from retinal progenitor cells. A TGIF paralog, TGIF2, showed a similar transition in expression during retinal development, and TGIF2 also promoted amacrine cell differentiation in a retinal explant culture system. However, no apparent difference between wild-type and TGIF-knockout mouse retina was observed, suggesting that TGIF and TGIF2 function redundantly in that tissue. Forced expression of TGIF homeodomain (HD)-EnR (repressing) rather than TGIF HD-VP16 (activating) resulted in a phenotype similar to that induced by wild-type TGIF, suggesting that TGIFs may act as transcriptional repressors to induce amacrine genesis.
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Affiliation(s)
- Shinya Satoh
- Department of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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Zhao J, Iida A, Ouchi Y, Satoh S, Watanabe S. M6a is expressed in the murine neural retina and regulates neurite extension. Mol Vis 2008; 14:1623-30. [PMID: 18776950 PMCID: PMC2529470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Accepted: 08/21/2008] [Indexed: 10/26/2022] Open
Abstract
PURPOSE Glycoprotein m6a (M6a) is a cell-surface glycoprotein that belongs to the myelin proteolipid protein family. M6a is expressed mainly in the nervous system, and its expression and function in mammalian retina have not been described. Using proteomics analysis of mouse retinal membrane fractions, we identified M6a as a retinal membrane protein that is strongly expressed at embryonic stages. Our aim was to reveal the function of M6a in development of mouse retina in this work. METHODS Detailed expression pattern of M6a was examined by immunostaining using frozen sections of mouse retina obtained at various developmental stages. For functional analysis of M6a in mouse retinal development, we performed retorovirus-mediated overexpression of M6a in mouse retinal explant culture. Then, cell differentiation, proliferation and structural maturation of the cells were examined. RESULTS M6a transcripts were strongly expressed in embryonic retina. After completion of retinal differentiation, the level of expression decreased as mouse development progressed. Immunohistochemistry showed that in the immature mouse retina, M6a was strongly expressed in the axons of retinal ganglion cells. After birth, M6a expression was confined to the inner plexiform layer, and finally, to the inner and outer plexiform layers of adult mouse retina. M6a expression was completely paralleled by that of the synaptic marker, synaptophysin. Mouse retinal progenitor cells that overexpressed M6a following retrovirus-mediated gene transfer were subjected to in vitro explant or monolayer cultures. The neurite outgrowth of M6a-overexpressing retinal cells was strikingly enhanced, although M6a did not affect differentiation and proliferation. CONCLUSIONS These results suggest that M6a plays a role in retinal development by regulating neurites, and it may also function to modulate synaptic activities in the adult retina.
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