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Basudan AM, Aziz MA, Yang Y. Implications of zonal architecture on differential gene expression profiling and altered pathway expressions in mandibular condylar cartilage. Sci Rep 2021; 11:16915. [PMID: 34413358 PMCID: PMC8376865 DOI: 10.1038/s41598-021-96071-7] [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: 02/21/2021] [Accepted: 08/04/2021] [Indexed: 11/09/2022] Open
Abstract
Mandibular condylar cartilage (MCC) is a multi-zonal heterogeneous fibrocartilage containing different types of cells, but the factors/mechanisms governing the phenotypic transition across the zones have not been fully understood. The reliability of molecular studies heavily rely on the procurement of pure cell populations from the heterogeneous tissue. We used a combined laser-capture microdissection and microarray analysis approach which allowed identification of differential zone-specific gene expression profiling and altered pathways in the MCC of 5-week-old rats. The bioinformatics analysis demonstrated that the MCC cells clearly exhibited distinguishable phenotypes from the articular chondrocytes. Additionally, a set of genes has been determined as potential markers to identify each MCC zone individually; Crab1 gene showed the highest enrichment while Clec3a was the most downregulated gene at the superficial layer, which consists of fibrous (FZ) and proliferative zones (PZ). Ingenuity Pathway Analysis revealed numerous altered signaling pathways; Leukocyte extravasation signaling pathway was predicted to be activated at all MCC zones, in particular mature and hypertrophic chondrocytes zones (MZ&HZ), when compared with femoral condylar cartilage (FCC). Whereas Superpathway of Cholesterol Biosynthesis showed predicted activation in both FZ and PZ as compared with deep MCC zones and FCC. Determining novel zone-specific differences of large group of potential genes, upstream regulators and pathways in healthy MCC would improve our understanding of molecular mechanisms on regional (zonal) basis, and provide new insights for future therapeutic strategies.
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Affiliation(s)
- Aisha M Basudan
- Division of Orthodontics, Dental Services Department, KAMC/KAIMRC/King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard-Health Affairs (MNGHA), Riyadh, 11426, Saudi Arabia.
| | - Mohammad Azhar Aziz
- King Abdullah International Medical Research Center (KAIMRC)/King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Colorectal Cancer Research Program, MNGHA, Riyadh, 11426, Saudi Arabia
| | - Yanqi Yang
- Division of Paediatric Dentistry and Orthodontics, Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong, SAR, China
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Lin YL, Lin YW, Nhieu J, Zhang X, Wei LN. Sonic Hedgehog-Gli1 Signaling and Cellular Retinoic Acid Binding Protein 1 Gene Regulation in Motor Neuron Differentiation and Diseases. Int J Mol Sci 2020; 21:ijms21114125. [PMID: 32527063 PMCID: PMC7312406 DOI: 10.3390/ijms21114125] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 12/22/2022] Open
Abstract
Cellular retinoic acid-binding protein 1 (CRABP1) is highly expressed in motor neurons. Degenerated motor neuron-like MN1 cells are engineered by introducing SODG93A or AR-65Q to model degenerated amyotrophic lateral sclerosis (ALS) or spinal bulbar muscular atrophy neurons. Retinoic acid (RA)/sonic hedgehog (Shh)-induced embryonic stem cells differentiation into motor neurons are employed to study up-regulation of Crabp1 by Shh. In SODG93A or AR-65Q MN1 neurons, CRABP1 level is reduced, revealing a correlation of motor neuron degeneration with Crabp1 down-regulation. Up-regulation of Crabp1 by Shh is mediated by glioma-associated oncogene homolog 1 (Gli1) that binds the Gli target sequence in Crabp1′s neuron-specific regulatory region upstream of minimal promoter. Gli1 binding triggers chromatin juxtaposition with minimal promoter, activating transcription. Motor neuron differentiation and Crabp1 up-regulation are both inhibited by blunting Shh with Gli inhibitor GANT61. Expression data mining of ALS and spinal muscular atrophy (SMA) motor neurons shows reduced CRABP1, coincided with reduction in Shh-Gli1 signaling components. This study reports motor neuron degeneration correlated with down-regulation in Crabp1 and Shh-Gli signaling. Shh-Gli up-regulation of Crabp1 involves specific chromatin remodeling. The physiological and pathological implication of this regulatory pathway in motor neuron degeneration is supported by gene expression data of ALS and SMA patients.
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Affiliation(s)
| | | | | | | | - Li-Na Wei
- Correspondence: ; Tel.: +1-612-6259402
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Lin YL, Persaud SD, Nhieu J, Wei LN. Cellular Retinoic Acid-Binding Protein 1 Modulates Stem Cell Proliferation to Affect Learning and Memory in Male Mice. Endocrinology 2017; 158:3004-3014. [PMID: 28911165 PMCID: PMC5659671 DOI: 10.1210/en.2017-00353] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/14/2017] [Indexed: 01/05/2023]
Abstract
Retinoic acid (RA) is the active ingredient of vitamin A. It exerts its canonical activity by binding to nuclear RA receptors (RARs) to regulate gene expression. Increasingly, RA is also known to elicit nongenomic RAR-independent activities, most widely detected in activating extracellular regulated kinase (ERK)1/2. This study validated the functional role of cellular retinoic acid-binding protein 1 (Crabp1) in mediating nongenomic activity in RA, specifically activating ERK1/2 to rapidly augment the cell cycle by expanding the growth 1 phase and slowing down embryonic stem cell and neural stem cell (NSC) proliferation. The study further uncovered the physiological activity of Crabp1 in modulating NSC proliferation and animal behavior. In the Crabp1 knockout mouse hippocampus, where Crabp1 is otherwise detected in the subgranular zone, neurogenesis and NSC proliferation increased and hippocampus-dependent brain functions such as learning and memory correspondingly improved. This study established the physiological role of Crabp1 in modulating stem cell proliferation and hippocampus-dependent brain activities such as learning and memory.
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Affiliation(s)
- Yu-Lung Lin
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455
| | - Shawna D. Persaud
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455
| | - Jennifer Nhieu
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455
| | - Li-Na Wei
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455
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Sleat DE, Tannous A, Sohar I, Wiseman JA, Zheng H, Qian M, Zhao C, Xin W, Barone R, Sims KB, Moore DF, Lobel P. Proteomic Analysis of Brain and Cerebrospinal Fluid from the Three Major Forms of Neuronal Ceroid Lipofuscinosis Reveals Potential Biomarkers. J Proteome Res 2017; 16:3787-3804. [PMID: 28792770 DOI: 10.1021/acs.jproteome.7b00460] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Clinical trials have been conducted for the neuronal ceroid lipofuscinoses (NCLs), a group of neurodegenerative lysosomal diseases that primarily affect children. Whereas clinical rating systems will evaluate long-term efficacy, biomarkers to measure short-term response to treatment would be extremely valuable. To identify candidate biomarkers, we analyzed autopsy brain and matching CSF samples from controls and three genetically distinct NCLs due to deficiencies in palmitoyl protein thioesterase 1 (CLN1 disease), tripeptidyl peptidase 1 (CLN2 disease), and CLN3 protein (CLN3 disease). Proteomic and biochemical methods were used to analyze lysosomal proteins, and, in general, we find that changes in protein expression compared with control were most similar between CLN2 disease and CLN3 disease. This is consistent with previous observations of biochemical similarities between these diseases. We also conducted unbiased proteomic analyses of CSF and brain using isobaric labeling/quantitative mass spectrometry. Significant alterations in protein expression were identified in each NCL, including reduced STXBP1 in CLN1 disease brain. Given the confounding variable of post-mortem changes, additional validation is required, but this study provides a useful starting set of candidate NCL biomarkers for further evaluation.
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Affiliation(s)
- David E Sleat
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States.,Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences , Piscataway, New Jersey 08854, United States
| | - Abla Tannous
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States
| | - Istvan Sohar
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States
| | - Jennifer A Wiseman
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States
| | - Meiqian Qian
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States
| | - Caifeng Zhao
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States
| | - Winnie Xin
- Neurogenetics DNA Diagnostic Laboratory, Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Rosemary Barone
- Neurogenetics DNA Diagnostic Laboratory, Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Katherine B Sims
- Neurogenetics DNA Diagnostic Laboratory, Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Dirk F Moore
- Department of Biostatistics, School of Public Health, Rutgers - The State University of New Jersey , Piscataway, New Jersey 08854, United States
| | - Peter Lobel
- Center for Advanced Biotechnology and Medicine , Piscataway, New Jersey 08854, United States.,Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences , Piscataway, New Jersey 08854, United States
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Ethanol exposure alters protein expression in a mouse model of fetal alcohol spectrum disorders. INTERNATIONAL JOURNAL OF PROTEOMICS 2012; 2012:867141. [PMID: 22745907 PMCID: PMC3382221 DOI: 10.1155/2012/867141] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 04/01/2012] [Accepted: 04/01/2012] [Indexed: 11/18/2022]
Abstract
Alcohol exposure during development can result in variable growth retardation and facial dysmorphology known as fetal alcohol spectrum disorders. Although the mechanisms underlying the disorder are not fully understood, recent progress has been made that alcohol induces aberrant changes in gene expression and in the epigenome of embryos. To inform the gene and epigenetic changes in alcohol-induced teratology, we used whole-embryo culture to identify the alcohol-signature protein profile of neurulating C6 mice. Alcohol-treated and control cultures were homogenized, isoelectrically focused, and loaded for 2D gel electrophoresis. Stained gels were cross matched with analytical software. We identified 40 differentially expressed protein spots (P < 0.01), and 9 spots were selected for LC/MS-MS identification. Misregulated proteins include serotransferrin, triosephosphate isomerase and ubiquitin-conjugating enzyme E2 N. Misregulation of serotransferrin and triosephosphate isomerase was confirmed with immunologic analysis. Alteration of proteins with roles in cellular function, cell cycle, and the ubiquitin-proteasome pathway was induced by alcohol. Several misregulated proteins interact with effectors of the NF-κB and Myc transcription factor cascades. Using a whole-embryo culture, we have identified misregulated proteins known to be involved in nervous system development and function.
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Toro S, Wegner J, Muller M, Westerfield M, Varga ZM. Identification of differentially expressed genes in the zebrafish hypothalamic-pituitary axis. Gene Expr Patterns 2009; 9:200-8. [PMID: 19166982 DOI: 10.1016/j.gep.2008.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Revised: 12/12/2008] [Accepted: 12/16/2008] [Indexed: 10/21/2022]
Abstract
The vertebrate hypothalamic-pituitary axis (HP) is the main link between the central nervous system and endocrine system. Although several signal pathways and regulatory genes have been implicated in adenohypophysis ontogenesis, little is known about hypothalamic-neurohypophysial development or when the HP matures and becomes functional. To identify markers of the HP, we constructed subtractive cDNA libraries between adult zebrafish hypothalamus and pituitary. We identified previously published genes, ESTs and novel zebrafish genes, some of which were predicted by genomic database analysis. We also analyzed expression patterns of these genes and found that several are expressed in the embryonic and larval hypothalamus, neurohypophysis, and/or adenohypophysis. Expression at these stages makes these genes useful markers to study HP maturation and function.
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Affiliation(s)
- Sabrina Toro
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR 97403, USA
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