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Gastelum S, Michael AF, Bolger TA. Saccharomyces cerevisiae as a research tool for RNA-mediated human disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1814. [PMID: 37671427 DOI: 10.1002/wrna.1814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 09/07/2023]
Abstract
The budding yeast, Saccharomyces cerevisiae, has been used for decades as a powerful genetic tool to study a broad spectrum of biological topics. With its ease of use, economic utility, well-studied genome, and a highly conserved proteome across eukaryotes, it has become one of the most used model organisms. Due to these advantages, it has been used to study an array of complex human diseases. From broad, complex pathological conditions such as aging and neurodegenerative disease to newer uses such as SARS-CoV-2, yeast continues to offer new insights into how cellular processes are affected by disease and how affected pathways might be targeted in therapeutic settings. At the same time, the roles of RNA and RNA-based processes have become increasingly prominent in the pathology of many of these same human diseases, and yeast has been utilized to investigate these mechanisms, from aberrant RNA-binding proteins in amyotrophic lateral sclerosis to translation regulation in cancer. Here we review some of the important insights that yeast models have yielded into the molecular pathology of complex, RNA-based human diseases. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Stephanie Gastelum
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Allison F Michael
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Timothy A Bolger
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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2
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Freitas-Andrade M, Comin CH, Van Dyken P, Ouellette J, Raman-Nair J, Blakeley N, Liu QY, Leclerc S, Pan Y, Liu Z, Carrier M, Thakur K, Savard A, Rurak GM, Tremblay MÈ, Salmaso N, da F Costa L, Coppola G, Lacoste B. Astroglial Hmgb1 regulates postnatal astrocyte morphogenesis and cerebrovascular maturation. Nat Commun 2023; 14:4965. [PMID: 37587100 PMCID: PMC10432480 DOI: 10.1038/s41467-023-40682-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
Astrocytes are intimately linked with brain blood vessels, an essential relationship for neuronal function. However, astroglial factors driving these physical and functional associations during postnatal brain development have yet to be identified. By characterizing structural and transcriptional changes in mouse cortical astrocytes during the first two postnatal weeks, we find that high-mobility group box 1 (Hmgb1), normally upregulated with injury and involved in adult cerebrovascular repair, is highly expressed in astrocytes at birth and then decreases rapidly. Astrocyte-selective ablation of Hmgb1 at birth affects astrocyte morphology and endfoot placement, alters distribution of endfoot proteins connexin43 and aquaporin-4, induces transcriptional changes in astrocytes related to cytoskeleton remodeling, and profoundly disrupts endothelial ultrastructure. While lack of astroglial Hmgb1 does not affect the blood-brain barrier or angiogenesis postnatally, it impairs neurovascular coupling and behavior in adult mice. These findings identify astroglial Hmgb1 as an important player in postnatal gliovascular maturation.
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Affiliation(s)
| | - Cesar H Comin
- Federal University of São Carlos, Department of Computer Science, São Carlos, Brazil
| | - Peter Van Dyken
- Cellular & Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Julie Ouellette
- Neuroscience Program, The Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Cellular & Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Joanna Raman-Nair
- Neuroscience Program, The Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Cellular & Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Nicole Blakeley
- Neuroscience Program, The Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Cellular & Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Qing Yan Liu
- National Research Council of Canada, Human Health and Therapeutics, Ottawa, ON, Canada
- Department of Biochemistry Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Sonia Leclerc
- National Research Council of Canada, Human Health and Therapeutics, Ottawa, ON, Canada
| | - Youlian Pan
- Digital Technologies, National Research Council of Canada, Ottawa, ON, Canada
| | - Ziying Liu
- Digital Technologies, National Research Council of Canada, Ottawa, ON, Canada
| | - Micaël Carrier
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Karan Thakur
- Neuroscience Program, The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Alexandre Savard
- Neuroscience Program, The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Gareth M Rurak
- Department of Neuroscience, Carleton University, Ottawa, ON, Canada
| | - Marie-Ève Tremblay
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Natalina Salmaso
- Department of Neuroscience, Carleton University, Ottawa, ON, Canada
| | - Luciano da F Costa
- University of São Paulo, São Carlos Institute of Physics, FCM-USP, São Paulo, Brazil
| | | | - Baptiste Lacoste
- Neuroscience Program, The Ottawa Hospital Research Institute, Ottawa, ON, Canada.
- Cellular & Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, Canada.
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Guo Q, Wang Y, Wang Q, Qian Y, Jiang Y, Dong X, Chen H, Chen X, Liu X, Yu S, Zhu J, Shan S, Wu B, Zhou W, Wang H. In the developing cerebral cortex: axonogenesis, synapse formation, and synaptic plasticity are regulated by SATB2 target genes. Pediatr Res 2023; 93:1519-1527. [PMID: 36028553 DOI: 10.1038/s41390-022-02260-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/23/2022] [Accepted: 07/29/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Special AT-rich sequence-binding protein 2 is essential for the development of cerebral cortex and key molecular node for the establishment of proper neural circuitry and function. Mutations in the SATB2 gene lead to SATB2-associated syndrome, which is characterized by abnormal development of skeleton and central nervous systems. METHODS We generated Satb2 knockout mouse model through CRISPR-Cas9 technology and performed RNA-seq and ChIP-seq of embryonic cerebral cortex. We conducted RT-qPCR, western blot, immunofluorescence staining, luciferase reporter assay and behavioral analysis for experimental verification. RESULTS We identified 1363 downstream effector genes of Satb2 and correlation analysis of Satb2-targeted genes and neurological disease genes showed that Satb2 contribute to cognitive and mental disorders from the early developmental stage. We found that Satb2 directly regulate the expression of Ntng1, Cdh13, Kitl, genes important for axon guidance, synaptic formation, neuron migration, and Satb2 directly activates the expression of Mef2c. We also showed that Satb2 heterozygous knockout mice showed impaired spatial learning and memory. CONCLUSIONS Taken together, our study supportsroles of Satb2 in the regulation of axonogenesis and synaptic formation at the early developmental stage and provides new insights into the complicated regulatory mechanism of Satb2 and new evidence to elucidate the pathogen of SATB2-associated syndrome. IMPACT 1363 downstream effector genes of Satb2 were classified into 5 clusters with different temporal expression patterns. We identified Plxnd1, Ntng1, Efnb2, Ephb1, Plxna2, Epha3, Plxna4, Unc5c, and Flrt2 as axon guidance molecules to regulate axonogenesis. 168 targeted genes of Satb2 were found to regulate synaptic formation in the early development of the cerebral cortex. Transcription factor Mef2c is positively regulated by Satb2, and 28 Mef2c-targeted genes can be directly regulated by Satb2. In the Morris water maze test, Satb2+/- mice showed impaired spatial learning and memory, further strengthening that Satb2 can regulate synaptic functions.
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Affiliation(s)
- Qiufang Guo
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
- Berry Genomics Co, 102206, Beijing, China
| | - Yaqiong Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Qing Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Yanyan Qian
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Yinmo Jiang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Huiyao Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Xiang Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Xiuyun Liu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Sha Yu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Jitao Zhu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Shifang Shan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China.
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Key Laboratory of Neonatal Diseases, Ministry of Health, 201102, Shanghai, China.
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China.
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Dysregulated miRNAs as Biomarkers and Therapeutical Targets in Neurodegenerative Diseases. J Pers Med 2022; 12:jpm12050770. [PMID: 35629192 PMCID: PMC9143965 DOI: 10.3390/jpm12050770] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 12/20/2022] Open
Abstract
Alzheimer’s disease (AD), Parkinson’s disease (PD), and Amyotrophic Lateral Sclerosis (ALS) are representative neurodegenerative diseases (NDs) characterized by degeneration of selective neurons, as well as the lack of effective biomarkers and therapeutic treatments. In the last decade, microRNAs (miRNAs) have gained considerable interest in diagnostics and therapy of NDs, owing to their aberrant expression and their ability to target multiple molecules and pathways. Here, we provide an overview of dysregulated miRNAs in fluids (blood or cerebrospinal fluid) and nervous tissue of AD, PD, and ALS patients. By emphasizing those that are commonly dysregulated in these NDs, we highlight their potential role as biomarkers or therapeutical targets and describe the use of antisense oligonucleotides as miRNA therapies.
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Kulkarni R, Thakur A, Kumar H. Microtubule Dynamics Following Central and Peripheral Nervous System Axotomy. ACS Chem Neurosci 2022; 13:1358-1369. [PMID: 35451811 DOI: 10.1021/acschemneuro.2c00189] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Disturbance in the neuronal network leads to instability in the microtubule (MT) railroad of axons, causing hindrance in the intra-axonal transport and making it difficult to re-establish the broken network. Peripheral nervous system (PNS) neurons can stabilize their MTs, leading to the formation of regeneration-promoting structures called "growth cones". However, central nervous system (CNS) neurons lack this intrinsic reparative capability and, instead, form growth-incompetent structures called "retraction bulbs", which have a disarrayed MT network. It is evident from various studies that although axonal regeneration depends on both cell-extrinsic and cell-intrinsic factors, any therapy that aims at axonal regeneration ultimately converges onto MTs. Understanding the neuronal MT dynamics will help develop effective therapeutic strategies in diseases where the MT network gets disrupted, such as spinal cord injury, traumatic brain injury, multiple sclerosis, and amyotrophic lateral sclerosis. It is also essential to know the factors that aid or inhibit MT stabilization. In this review, we have discussed the MT dynamics postaxotomy in the CNS and PNS, and factors that can directly influence MT stability in various diseases.
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Affiliation(s)
- Riya Kulkarni
- National Institute of Pharmaceutical Education and Research, Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat 382355, India
| | - Akshata Thakur
- National Institute of Pharmaceutical Education and Research, Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat 382355, India
| | - Hemant Kumar
- National Institute of Pharmaceutical Education and Research, Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat 382355, India
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Utility of RGNEF in the Prediction of Clinical Prognosis in Patients with Rectal Cancer Receiving Preoperative Concurrent Chemoradiotherapy. Life (Basel) 2021; 12:life12010018. [PMID: 35054411 PMCID: PMC8778573 DOI: 10.3390/life12010018] [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: 11/14/2021] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 11/17/2022] Open
Abstract
Rectal cancer is a heterogeneous malignancy with different clinical responses to preoperative concurrent chemoradiotherapy (CCRT). To discover the significant genes associated with CCRT response, we performed data mining of a transcriptomic dataset (GSE35452), including 46 rectal cancer patients who received preoperative CCRT and underwent standardized curative resection. We identified ARHGEF28 as the most significantly upregulated gene correlated with resistance to CCRT among the genes related to Rho guanyl-nucleotide exchange factor activity (GO:0005085). We enrolled 172 patients with rectal cancer receiving CCRT with radical surgery. The expression of ARHGEF28 encoded protein, Rho guanine nucleotide exchange factor (RGNEF), was assessed using immunohistochemistry. The results showed that upregulated RGNEF immunoexpression was considerably correlated with poor response to CCRT (p = 0.018), pre-CCRT positive nodal status (p = 0.004), and vascular invasion (p < 0.001). Furthermore, high RGNEF expression was significantly associated with worse local recurrence-free survival (p < 0.0001), metastasis-free survival (MeFS) (p = 0.0029), and disease-specific survival (DSS) (p < 0.0001). The multivariate analysis demonstrated that RGNEF immunoexpression status was an independent predictor of DSS (p < 0.001) and MeFS (p < 0.001). Using Gene Ontology enrichment analysis, we discovered that ARHGEF28 overexpression might be linked to Wnt/β-catenin signaling in rectal cancer progression. In conclusion, high RGNEF expression was related to unfavorable pathological characteristics and independently predicted worse clinical prognosis in patients with rectal cancer undergoing CCRT, suggesting its role in risk stratification and clinical decision making.
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Petropavlovskiy AA, Tauro MG, Lajoie P, Duennwald ML. A Quantitative Imaging-Based Protocol for Yeast Growth and Survival on Agar Plates. STAR Protoc 2020; 1:100182. [PMID: 33377076 PMCID: PMC7757406 DOI: 10.1016/j.xpro.2020.100182] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We present a detailed protocol that describes the evaluation of the growth and survival of yeast cells by quantitatively analyzing spotting assays. This simple method reproducibly detects and quantifies subtle differences in growth by measuring the density of cells within a single spot of defined size on an image of a spotting assay. Our protocol is tailored specifically for low-throughput applications, can be easily adapted for specific experimental conditions, and is accessible to yeast experts and non-experts alike. For an example of the execution of this protocol, please refer to DiGregorio et al. (Di Gregorio et al., 2020). Experimental considerations for enabling spotting assay quantification A step-by-step procedure for spotting yeast cultures on agar plates Quantification and statistical analysis of spotting assay data
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Affiliation(s)
| | - Michael G Tauro
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Patrick Lajoie
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Martin L Duennwald
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 3K7, Canada.,Department of Biology, The University of Western Ontario, London, ON N6A 3K7, Canada.,Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 3K7, Canada
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