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Chen S, Jiang Q, Fan J, Cheng H. Nuclear mRNA export. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39243141 DOI: 10.3724/abbs.2024145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2024] Open
Abstract
In eukaryotic cells, gene expression begins with transcription in the nucleus, followed by the maturation of messenger RNAs (mRNAs). These mRNA molecules are then exported to the cytoplasm through the nuclear pore complex (NPC), a process that serves as a critical regulatory phase of gene expression. The export of mRNA is intricately linked to precursor mRNA (pre-mRNA) processing, ensuring that only properly processed mRNA reaches the cytoplasm. This coordination is essential, as recent studies have revealed that mRNA export factors not only assist in transport but also influence upstream processing steps, adding a layer of complexity to gene regulation. Furthermore, the export process competes with RNA processing and degradation pathways, maintaining a delicate balance vital for accurate gene expression. While these mechanisms are generally conserved across eukaryotes, significant differences exist between yeast and higher eukaryotic cells, particularly due to the more genome complexity of the latter. This review delves into the current research on mRNA export in higher eukaryotic cells, focusing on its role in the broader context of gene expression regulation and highlighting how it interacts with other gene expression processes to ensure precise and efficient gene functionality in complex organisms.
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Affiliation(s)
- Suli Chen
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, Hangzhou 310024, University of Chinese Academy of Sciences, China
| | - Qingyi Jiang
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jing Fan
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Hong Cheng
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, Hangzhou 310024, University of Chinese Academy of Sciences, China
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
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2
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Neuronal activity stimulates a genetic program to rapidly generate synapses during development. Nat Neurosci 2024; 27:1641-1642. [PMID: 39117771 DOI: 10.1038/s41593-024-01729-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
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3
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Yee C, Xiao Y, Chen H, Reddy AR, Xu B, Medwig-Kinney TN, Zhang W, Boyle AP, Herbst WA, Xiang YK, Matus DQ, Shen K. An activity-regulated transcriptional program directly drives synaptogenesis. Nat Neurosci 2024; 27:1695-1707. [PMID: 39103556 PMCID: PMC11374667 DOI: 10.1038/s41593-024-01728-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 07/11/2024] [Indexed: 08/07/2024]
Abstract
Although the molecular composition and architecture of synapses have been widely explored, much less is known about what genetic programs directly activate synaptic gene expression and how they are modulated. Here, using Caenorhabditis elegans dopaminergic neurons, we reveal that EGL-43/MECOM and FOS-1/FOS control an activity-dependent synaptogenesis program. Loss of either factor severely reduces presynaptic protein expression. Both factors bind directly to promoters of synaptic genes and act together with CUT homeobox transcription factors to activate transcription. egl-43 and fos-1 mutually promote each other's expression, and increasing the binding affinity of FOS-1 to the egl-43 locus results in increased presynaptic protein expression and synaptic function. EGL-43 regulates the expression of multiple transcription factors, including activity-regulated factors and developmental factors that define multiple aspects of dopaminergic identity. Together, we describe a robust genetic program underlying activity-regulated synapse formation during development.
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Affiliation(s)
- Callista Yee
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA, USA
| | - Yutong Xiao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | - Hongwen Chen
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA, USA
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anay R Reddy
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA, USA
| | - Bing Xu
- Department of Pharmacology, University of California, Davis, Davis, CA, USA
- VA Northern California Healthcare System, Mather, CA, USA
| | - Taylor N Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Alan P Boyle
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Wendy A Herbst
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA, USA
| | - Yang Kevin Xiang
- Department of Pharmacology, University of California, Davis, Davis, CA, USA
- VA Northern California Healthcare System, Mather, CA, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Kang Shen
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
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4
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Zeng X, Fan L, Li M, Qin Q, Pang X, Shi S, Zheng D, Jiang Y, Wang H, Wu L, Liang S. Resveratrol regulates Thoc5 to improve maternal immune activation-induced autism-like behaviors in adult mouse offspring. J Nutr Biochem 2024; 129:109638. [PMID: 38583499 DOI: 10.1016/j.jnutbio.2024.109638] [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: 10/04/2023] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Maternal infection during pregnancy is an important cause of autism spectrum disorder (ASD) in offspring, and inflammatory infiltration caused by maternal immune activation (MIA) can cause neurodevelopmental disorders in the fetus. Medicine food homologous (MFH) refers to a traditional Chinese medicine (TCM) concept, which effectively combines food functions and medicinal effects. However, no previous study has screened, predicted, and validated the potential targets of MFH herbs for treating ASD. Therefore, in this study, we used comprehensive bioinformatics methods to screen and analyze MFH herbs and drug targets on a large scale, and identified resveratrol and Thoc5 as the best small molecular ingredient and drug target, respectively, for the treatment of MIA-induced ASD. Additionally, the results of in vitro experiments revealed that resveratrol increased the expression of Thoc5 and effectively inhibited lipopolysaccharide-induced inflammatory factor production by BV2 cells. Moreover, in vivo, resveratrol increased the expression of Thoc5 and effectively inhibited placental and fetal brain inflammation in MIA pregnancy mice, and improved ASD-like behaviors in offspring.
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Affiliation(s)
- Xin Zeng
- Department of Child and Adolescent Health, Public Health College, Harbin Medical University, Harbin, 150081, China
| | - Linlin Fan
- Department of Child and Adolescent Health, Public Health College, Harbin Medical University, Harbin, 150081, China
| | - Mengyue Li
- Department of Child and Adolescent Health, Public Health College, Harbin Medical University, Harbin, 150081, China
| | - Qian Qin
- Department of Child and Adolescent Health, Public Health College, Harbin Medical University, Harbin, 150081, China
| | - Xiuming Pang
- Outpatient Department, The Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Shanyi Shi
- Traditional Chinese Medicine Prevention and Treatment Center, The Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Danyang Zheng
- Department of Child and Adolescent Health, Public Health College, Harbin Medical University, Harbin, 150081, China
| | - Yutong Jiang
- Department of Child and Adolescent Health, Public Health College, Harbin Medical University, Harbin, 150081, China
| | - Han Wang
- Department of Child and Adolescent Health, Public Health College, Harbin Medical University, Harbin, 150081, China
| | - Lijie Wu
- Department of Child and Adolescent Health, Public Health College, Harbin Medical University, Harbin, 150081, China.
| | - Shuang Liang
- Department of Child and Adolescent Health, Public Health College, Harbin Medical University, Harbin, 150081, China.
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5
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Prusty AB, Hirmer A, Sierra-Delgado JA, Huber H, Guenther UP, Schlosser A, Dybkov O, Yildirim E, Urlaub H, Meyer KC, Jablonka S, Erhard F, Fischer U. RNA helicase IGHMBP2 regulates THO complex to ensure cellular mRNA homeostasis. Cell Rep 2024; 43:113802. [PMID: 38368610 DOI: 10.1016/j.celrep.2024.113802] [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: 08/03/2023] [Revised: 12/21/2023] [Accepted: 01/31/2024] [Indexed: 02/20/2024] Open
Abstract
RNA helicases constitute a large protein family implicated in cellular RNA homeostasis and disease development. Here, we show that the RNA helicase IGHMBP2, linked to the neuromuscular disorder spinal muscular atrophy with respiratory distress type 1 (SMARD1), associates with polysomes and impacts translation of mRNAs containing short, GC-rich, and structured 5' UTRs. The absence of IGHMBP2 causes ribosome stalling at the start codon of target mRNAs, leading to reduced translation efficiency. The main mRNA targets of IGHMBP2-mediated regulation encode for components of the THO complex (THOC), linking IGHMBP2 to mRNA production and nuclear export. Accordingly, failure of IGHMBP2 regulation of THOC causes perturbations of the transcriptome and its encoded proteome, and ablation of THOC subunits phenocopies these changes. Thus, IGHMBP2 is an upstream regulator of THOC. Of note, IGHMBP2-dependent regulation of THOC is also observed in astrocytes derived from patients with SMARD1 disease, suggesting that deregulated mRNA metabolism contributes to SMARD1 etiology and may enable alternative therapeutic avenues.
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Affiliation(s)
| | - Anja Hirmer
- Department of Biochemistry 1, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | | | - Hannes Huber
- Department of Biochemistry 1, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | | | - Andreas Schlosser
- Rudolf-Virchow-Center, Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Olexandr Dybkov
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Ezgi Yildirim
- Institute of Clinical Neurobiology, University Hospital Würzburg, 97078 Würzburg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Department of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences, University of Göttingen, Göttingen, Germany
| | - Kathrin C Meyer
- Nationwide Children's Hospital, Center for Gene Therapy, Columbus, OH 43205, USA; Department of Pediatrics, Ohio State University, Columbus, OH 43210, USA
| | - Sibylle Jablonka
- Institute of Clinical Neurobiology, University Hospital Würzburg, 97078 Würzburg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, 97078 Würzburg, Germany; Faculty for Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany.
| | - Utz Fischer
- Department of Biochemistry 1, Biocenter, University of Würzburg, 97074 Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany.
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6
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Werren EA, LaForce GR, Srivastava A, Perillo DR, Li S, Johnson K, Baris S, Berger B, Regan SL, Pfennig CD, de Munnik S, Pfundt R, Hebbar M, Jimenez-Heredia R, Karakoc-Aydiner E, Ozen A, Dmytrus J, Krolo A, Corning K, Prijoles EJ, Louie RJ, Lebel RR, Le TL, Amiel J, Gordon CT, Boztug K, Girisha KM, Shukla A, Bielas SL, Schaffer AE. TREX tetramer disruption alters RNA processing necessary for corticogenesis in THOC6 Intellectual Disability Syndrome. Nat Commun 2024; 15:1640. [PMID: 38388531 PMCID: PMC10884030 DOI: 10.1038/s41467-024-45948-y] [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: 10/02/2022] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
THOC6 variants are the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 is critical for mammalian Transcription Export complex (TREX) tetramer formation, which is composed of four six-subunit THO monomers. The TREX tetramer facilitates mammalian RNA processing, in addition to the nuclear mRNA export functions of the TREX dimer conserved through yeast. Human and mouse TIDS model systems revealed novel THOC6-dependent, species-specific TREX tetramer functions. Germline biallelic Thoc6 loss-of-function (LOF) variants result in mouse embryonic lethality. Biallelic THOC6 LOF variants reduce the binding affinity of ALYREF to THOC5 without affecting the protein expression of TREX members, implicating impaired TREX tetramer formation. Defects in RNA nuclear export functions were not detected in biallelic THOC6 LOF human neural cells. Instead, mis-splicing was detected in human and mouse neural tissue, revealing novel THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for key signaling pathways known to regulate the transition from proliferative to neurogenic divisions during human corticogenesis. Together, these findings implicate altered RNA processing in the developmental biology of TIDS neuropathology.
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Affiliation(s)
- Elizabeth A Werren
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Anshika Srivastava
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
| | - Delia R Perillo
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Shaokun Li
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Katherine Johnson
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Safa Baris
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Brandon Berger
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Samantha L Regan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Christian D Pfennig
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sonja de Munnik
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, 6524, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, 6524, the Netherlands
| | - Malavika Hebbar
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 98195, Seattle, WA, USA
| | - Raúl Jimenez-Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
| | - Elif Karakoc-Aydiner
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Ahmet Ozen
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Jasmin Dmytrus
- Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Ana Krolo
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
| | - Ken Corning
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - E J Prijoles
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | | | - Robert Roger Lebel
- Section of Medical Genetics, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Thuy-Linh Le
- Imagine Institute, INSERM U1163, Paris Cité University, Paris, 75015, France
| | - Jeanne Amiel
- Imagine Institute, INSERM U1163, Paris Cité University, Paris, 75015, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, 75015, France
| | | | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
- Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, 1090, Austria
- St. Anna Children's Hospital and Children's Cancer Research Institute, Department of Pediatrics, Medical University of Vienna, Vienna, 1090, Austria
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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7
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Castillo-Armengol J, Marzetta F, Rodriguez Sanchez-Archidona A, Fledelius C, Evans M, McNeilly A, McCrimmon RJ, Ibberson M, Thorens B. Disrupted hypothalamic transcriptomics and proteomics in a mouse model of type 2 diabetes exposed to recurrent hypoglycaemia. Diabetologia 2024; 67:371-391. [PMID: 38017352 PMCID: PMC10789691 DOI: 10.1007/s00125-023-06043-x] [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: 04/18/2023] [Accepted: 09/07/2023] [Indexed: 11/30/2023]
Abstract
AIMS/HYPOTHESIS Repeated exposures to insulin-induced hypoglycaemia in people with diabetes progressively impairs the counterregulatory response (CRR) that restores normoglycaemia. This defect is characterised by reduced secretion of glucagon and other counterregulatory hormones. Evidence indicates that glucose-responsive neurons located in the hypothalamus orchestrate the CRR. Here, we aimed to identify the changes in hypothalamic gene and protein expression that underlie impaired CRR in a mouse model of defective CRR. METHODS High-fat-diet fed and low-dose streptozocin-treated C57BL/6N mice were exposed to one (acute hypoglycaemia [AH]) or multiple (recurrent hypoglycaemia [RH]) insulin-induced hypoglycaemic episodes and plasma glucagon levels were measured. Single-nuclei RNA-seq (snRNA-seq) data were obtained from the hypothalamus and cortex of mice exposed to AH and RH. Proteomic data were obtained from hypothalamic synaptosomal fractions. RESULTS The final insulin injection resulted in similar plasma glucose levels in the RH group and AH groups, but glucagon secretion was significantly lower in the RH group (AH: 94.5±9.2 ng/l [n=33]; RH: 59.0±4.8 ng/l [n=37]; p<0.001). Analysis of snRNA-seq data revealed similar proportions of hypothalamic cell subpopulations in the AH- and RH-exposed mice. Changes in transcriptional profiles were found in all cell types analysed. In neurons from RH-exposed mice, we observed a significant decrease in expression of Avp, Pmch and Pcsk1n, and the most overexpressed gene was Kcnq1ot1, as compared with AH-exposed mice. Gene ontology analysis of differentially expressed genes (DEGs) indicated a coordinated decrease in many oxidative phosphorylation genes and reduced expression of vacuolar H+- and Na+/K+-ATPases; these observations were in large part confirmed in the proteomic analysis of synaptosomal fractions. Compared with AH-exposed mice, oligodendrocytes from RH-exposed mice had major changes in gene expression that suggested reduced myelin formation. In astrocytes from RH-exposed mice, DEGs indicated reduced capacity for neurotransmitters scavenging in tripartite synapses as compared with astrocytes from AH-exposed mice. In addition, in neurons and astrocytes, multiple changes in gene expression suggested increased amyloid beta (Aβ) production and stability. The snRNA-seq analysis of the cortex showed that the adaptation to RH involved different biological processes from those seen in the hypothalamus. CONCLUSIONS/INTERPRETATION The present study provides a model of defective counterregulation in a mouse model of type 2 diabetes. It shows that repeated hypoglycaemic episodes induce multiple defects affecting all hypothalamic cell types and their interactions, indicative of impaired neuronal network signalling and dysegulated hypoglycaemia sensing, and displaying features of neurodegenerative diseases. It also shows that repeated hypoglycaemia leads to specific molecular adaptation in the hypothalamus when compared with the cortex. DATA AVAILABILITY The transcriptomic dataset is available via the GEO ( http://www.ncbi.nlm.nih.gov/geo/ ), using the accession no. GSE226277. The proteomic dataset is available via the ProteomeXchange data repository ( http://www.proteomexchange.org ), using the accession no. PXD040183.
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Affiliation(s)
- Judit Castillo-Armengol
- Novo Nordisk A/S, Måløv, Denmark
- Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland
| | - Flavia Marzetta
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - Mark Evans
- IMS Metabolic Research Laboratories, Addenbrookes Biomedical Campus, Cambridge, UK
| | | | | | - Mark Ibberson
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Bernard Thorens
- Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland.
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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8
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Fujita KI, Ito M, Irie M, Harada K, Fujiwara N, Ikeda Y, Yoshioka H, Yamazaki T, Kojima M, Mikami B, Mayeda A, Masuda S. Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes. Nat Commun 2024; 15:455. [PMID: 38225262 PMCID: PMC10789772 DOI: 10.1038/s41467-023-44217-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024] Open
Abstract
mRNA export is an essential pathway for the regulation of gene expression. In humans, closely related RNA helicases, UAP56 and URH49, shape selective mRNA export pathways through the formation of distinct complexes, known as apo-TREX and apo-AREX complexes, and their subsequent remodeling into similar ATP-bound complexes. Therefore, defining the unidentified components of the apo-AREX complex and elucidating the molecular mechanisms underlying the formation of distinct apo-complexes is key to understanding their functional divergence. In this study, we identify additional apo-AREX components physically and functionally associated with URH49. Furthermore, by comparing the structures of UAP56 and URH49 and performing an integrated analysis of their chimeric mutants, we exhibit unique structural features that would contribute to the formation of their respective complexes. This study provides insights into the specific structural and functional diversification of these two helicases that diverged from the common ancestral gene Sub2.
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Affiliation(s)
- Ken-Ichi Fujita
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan.
- Division of Gene Expression Mechanism, Center for Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan.
- Division of Cancer Stem Cell, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Misa Ito
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Midori Irie
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Kotaro Harada
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Naoko Fujiwara
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Yuya Ikeda
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Hanae Yoshioka
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Tomohiro Yamazaki
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Masaki Kojima
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Bunzo Mikami
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, 611-0011, Japan
- Institute of Advanced Energy, Kyoto University, Kyoto, 611-0011, Japan
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Center for Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
| | - Seiji Masuda
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan.
- Department of Food Science and Nutrition, Faculty of Agriculture Kindai University, Nara, Nara, 631-8505, Japan.
- Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Nara, 631-8505, Japan.
- Antiaging Center, Kindai University, Higashiosaka, Osaka, 577-8502, Japan.
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9
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Braz CU, Passamonti MM, Khatib H. Characterization of genomic regions escaping epigenetic reprogramming in sheep. ENVIRONMENTAL EPIGENETICS 2023; 10:dvad010. [PMID: 38496251 PMCID: PMC10944287 DOI: 10.1093/eep/dvad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 03/19/2024]
Abstract
The mammalian genome undergoes two global epigenetic reprogramming events during the establishment of primordial germ cells and in the pre-implantation embryo after fertilization. These events involve the erasure and re-establishment of DNA methylation marks. However, imprinted genes and transposable elements (TEs) maintain their DNA methylation signatures to ensure normal embryonic development and genome stability. Despite extensive research in mice and humans, there is limited knowledge regarding environmentally induced epigenetic marks that escape epigenetic reprogramming in other species. Therefore, the objective of this study was to examine the characteristics and locations of genomic regions that evade epigenetic reprogramming in sheep, as well as to explore the biological functions of the genes within these regions. In a previous study, we identified 107 transgenerationally inherited differentially methylated cytosines (DMCs) in the F1 and F2 generations in response to a paternal methionine-supplemented diet. These DMCs were found in TEs, non-repetitive regions, and imprinted and non-imprinted genes. Our findings suggest that genomic regions, rather than TEs and imprinted genes, have the propensity to escape reprogramming and serve as potential candidates for transgenerational epigenetic inheritance. Notably, 34 transgenerational methylated genes influenced by paternal nutrition escaped reprogramming, impacting growth, development, male fertility, cardiac disorders, and neurodevelopment. Intriguingly, among these genes, 21 have been associated with neural development and brain disorders, such as autism, schizophrenia, bipolar disease, and intellectual disability. This suggests a potential genetic overlap between brain and infertility disorders. Overall, our study supports the concept of transgenerational epigenetic inheritance of environmentally induced marks in mammals.
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Affiliation(s)
- Camila U Braz
- Department of Animal Sciences, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition, Universit’a Cattolica del Sacro Cuore, Piacenza, 29122, Italy
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI 53706, USA
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10
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Werren E, LaForce G, Srivastava A, Perillo D, Johnson K, Berger B, Regan S, Pfennig C, Baris S, de Munnik S, Pfundt R, Hebbar M, Jimenez Heredia R, Karakoc-Aydiner E, Ozen A, Dmytrus J, Krolo A, Corning K, Prijoles E, Louie R, Lebel R, Le TL, Amiel J, Gordon C, Boztug K, Girisha K, Shukla A, Bielas S, Schaffer A. Mechanisms of mRNA processing defects in inherited THOC6 intellectual disability syndrome. RESEARCH SQUARE 2023:rs.3.rs-2126145. [PMID: 37720017 PMCID: PMC10503840 DOI: 10.21203/rs.3.rs-2126145/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
THOC6 is the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 facilitates the formation of the Transcription Export complex (TREX) tetramer, composed of four THO monomers. The TREX tetramer supports mammalian mRNA processing that is distinct from yeast TREX dimer functions. Human and mouse TIDS model systems allow novel THOC6-dependent TREX tetramer functions to be investigated. Biallelic loss-of-functon(LOF) THOC6 variants do not influence the expression and localization of TREX members in human cells, but our data suggests reduced binding affinity of ALYREF. Impairment of TREX nuclear export functions were not detected in cells with biallelic THOC6 LOF. Instead, mRNA mis-splicing was observed in human and mouse neural tissue, revealing novel insights into THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for regulation of key signaling pathways in human corticogenesis that dictate the transition from proliferative to neurogenic divisions that may inform TIDS neuropathology.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jasmin Dmytrus
- CeMM Research Centre for Molecular Medicine of the Austrian Academy of Sciences
| | - Ana Krolo
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases
| | | | | | | | | | - Thuy-Linh Le
- Imagine Institute, INSERM U1163, Paris Descartes University
| | | | - Christopher Gordon
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases
| | - Katta Girisha
- Kasturba Medical College, Manipal, Manipal Academy of Higher Education
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11
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Yue Z, Hu B, Chen Z, Zheng G, Wang Y, Yang C, Cao P, Wu X, Liang L, Zang F, Wang J, Li J, Zhang T, Wu J, Chen H. Continuous release of mefloquine featured in electrospun fiber membranes alleviates epidural fibrosis and aids in sensory neurological function after lumbar laminectomy. Mater Today Bio 2022; 17:100469. [PMID: 36340590 PMCID: PMC9633751 DOI: 10.1016/j.mtbio.2022.100469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/11/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022] Open
Abstract
Recurrent low back pain after spinal surgeries, such as lumbar laminectomy, is a major complication of excessive epidural fibrosis. Although multiple preclinical and clinical methods have been aimed at ameliorating epidural fibrosis, their safety and efficacy remain largely unclear. Single implanted electrospun fibrous membranes provide physical barriers that can decrease tissue fibrosis after surgery; however, they also trigger local inflammation due to the implantation of a foreign body, thus subsequently attenuating their anti-fibrosis properties. Here, we designed a strategy that permits easy incorporation of mefloquine into polylactic acid membranes, and stable long-term mefloquine release, to potentially improve anti-fibrosis effects and relieve or prevent low back pain. The electrospun fibrous membranes grafted with mefloquine showed a well-controlled early temporary peak release, and secondary drug release occurred smoothly over several weeks. Histopathological and histomorphometric results indicated that the drug-loaded membranes had excellent anti-fibrosis effects after laminectomy in rats. Inflammation and neovascularization at the surgical site indicated that the mefloquine-grafted electrospun fibrous membranes provided sustained anti-inflammatory outcomes while effectively alleviating associated neuropathic pain hypersensitivity. In summary, our study indicated that polylactic acid-mefloquine grafted electrospun fibrous membranes may be a potential local agent to mitigate epidural fibrosis and support sensory neurological function after laminectomy, thereby potentially improving patients' postoperative outcomes.
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Affiliation(s)
- Zhihao Yue
- Spine Center, Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Bo Hu
- Spine Center, Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Zhe Chen
- Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai, China
| | - Genjiang Zheng
- Spine Center, Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yunhao Wang
- Spine Center, Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Chen Yang
- Spine Center, Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Peng Cao
- Spine Center, Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xiaodong Wu
- Spine Center, Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Lei Liang
- Spine Center, Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Fazhi Zang
- Spine Center, Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jianxi Wang
- Spine Center, Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jing Li
- Spine Center, Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
- Department of Bioinformatics, Center for Translational Medicine, Naval Medical University, Shanghai, 200433, China
| | - Tao Zhang
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, 200030, Shanghai, China
| | - Jinglei Wu
- Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai, China
| | - Huajiang Chen
- Spine Center, Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, China
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12
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Chou YJ, Lin CC, Hsu YC, Syu JL, Tseng LM, Chiu JH, Lo JF, Lin CH, Fu SL. Andrographolide suppresses the malignancy of triple-negative breast cancer by reducing THOC1-promoted cancer stem cell characteristics. Biochem Pharmacol 2022; 206:115327. [PMID: 36330949 DOI: 10.1016/j.bcp.2022.115327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 12/14/2022]
Abstract
Triple-negative breast cancers (TNBCs) are difficult to cure and currently lack of effective treatment strategies. Cancer stem cells (CSCs) are highly associated with the poor clinical outcome of TNBCs. Thoc1 is a core component of the THO complex (THOC) that regulates the elongation, processing and nuclear export of mRNA. The function of thoc1 in TNBC and whether Thoc1 serves as a drug target are poorly understood. In this study, we demonstrated that thoc1 expression is elevated in TNBC cell lines and human TNBC patient tissues. Knockdown of thoc1 decreased cancer stem cell populations, reduced mammosphere formation, impaired THOC function, and downregulated the expression of stemness-related proteins. Moreover, the thoc1-knockdown 4T1 cells showed less lung metastasis in an orthotopic breast cancer mouse model. Overexpression of Thoc1 promoted TNBC malignancy and the mRNA export of stemness-related genes. Furthermore, treatment of TNBC cells with the natural compound andrographolide reduced the expression of Thoc1 expression, impaired homeostasis of THOC, suppressed CSC properties, and delayed tumor growth in a 4T1-implanted orthotopic mouse model. Andrographolide also reduced the activity of NF-κB, an upstream transcriptional regulator of Thoc1. Notably, thoc1 overexpression attenuates andrographolide-suppressed cellular proliferation. Altogether, our results demonstrate that THOC1 promotes cancer stem cell characteristics of TNBC, and andrographolide is a potential natural compound for eliminating CSCs of TNBCs by downregulating the NF-κB-thoc1 axis.
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Affiliation(s)
- Yi-Ju Chou
- Program in Molecular Medicine, School of Life Sciences, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 11221, Taiwan
| | - Ching-Cheng Lin
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Ya-Chi Hsu
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Jia-Ling Syu
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Ling-Ming Tseng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jen-Hwey Chiu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jeng-Fan Lo
- Institute of Oral Biology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Chao-Hsiung Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Shu-Ling Fu
- Program in Molecular Medicine, School of Life Sciences, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 11221, Taiwan; Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan.
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13
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Kamp JA, Lemmens BBLG, Romeijn RJ, González-Prieto R, Olsen J, Vertegaal ACO, van Schendel R, Tijsterman M. THO complex deficiency impairs DNA double-strand break repair via the RNA surveillance kinase SMG-1. Nucleic Acids Res 2022; 50:6235-6250. [PMID: 35670662 PMCID: PMC9226523 DOI: 10.1093/nar/gkac472] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/11/2022] [Accepted: 06/02/2022] [Indexed: 12/25/2022] Open
Abstract
The integrity and proper expression of genomes are safeguarded by DNA and RNA surveillance pathways. While many RNA surveillance factors have additional functions in the nucleus, little is known about the incidence and physiological impact of converging RNA and DNA signals. Here, using genetic screens and genome-wide analyses, we identified unforeseen SMG-1-dependent crosstalk between RNA surveillance and DNA repair in living animals. Defects in RNA processing, due to viable THO complex or PNN-1 mutations, induce a shift in DNA repair in dividing and non-dividing tissues. Loss of SMG-1, an ATM/ATR-like kinase central to RNA surveillance by nonsense-mediated decay (NMD), restores DNA repair and radio-resistance in THO-deficient animals. Mechanistically, we find SMG-1 and its downstream target SMG-2/UPF1, but not NMD per se, to suppress DNA repair by non-homologous end-joining in favour of single strand annealing. We postulate that moonlighting proteins create short-circuits in vivo, allowing aberrant RNA to redirect DNA repair.
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Affiliation(s)
| | | | - Ron J Romeijn
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Román González-Prieto
- Department of Cell & Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Alfred C O Vertegaal
- Department of Cell & Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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14
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Park HS, Lee J, Lee HS, Ahn SH, Ryu HY. Nuclear mRNA Export and Aging. Int J Mol Sci 2022; 23:5451. [PMID: 35628261 PMCID: PMC9142925 DOI: 10.3390/ijms23105451] [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: 04/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
The relationship between transcription and aging is one that has been studied intensively and experimentally with diverse attempts. However, the impact of the nuclear mRNA export on the aging process following its transcription is still poorly understood, although the nuclear events after transcription are coupled closely with the transcription pathway because the essential factors required for mRNA transport, namely TREX, TREX-2, and nuclear pore complex (NPC), physically and functionally interact with various transcription factors, including the activator/repressor and pre-mRNA processing factors. Dysregulation of the mediating factors for mRNA export from the nucleus generally leads to the aberrant accumulation of nuclear mRNA and further impairment in the vegetative growth and normal lifespan and the pathogenesis of neurodegenerative diseases. The optimal stoichiometry and density of NPC are destroyed during the process of cellular aging, and their damage triggers a defect of function in the nuclear permeability barrier. This review describes recent findings regarding the role of the nuclear mRNA export in cellular aging and age-related neurodegenerative disorders.
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Affiliation(s)
- Hyun-Sun Park
- Department of Biochemistry, Inje University College of Medicine, Busan 50834, Korea;
| | - Jongbok Lee
- Department of Biological and Chemical Engineering, Hongik University, 2639, Sejong-ro, Jochiwon-eup, Sejong-si 30016, Korea;
| | - Hyun-Shik Lee
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Korea;
| | - Seong Hoon Ahn
- Department of Molecular and Life Science, College of Science and Convergence Technology, ERICA Campus, Hanyang University, Ansan 15588, Korea
| | - Hong-Yeoul Ryu
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Korea;
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15
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Kow RL, Black AH, Saxton AD, Liachko NF, Kraemer BC. Loss of aly/ALYREF suppresses toxicity in both tau and TDP-43 models of neurodegeneration. GeroScience 2022; 44:747-761. [PMID: 35122183 PMCID: PMC9135935 DOI: 10.1007/s11357-022-00526-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/27/2022] [Indexed: 11/04/2022] Open
Abstract
Neurodegenerative diseases with tau pathology, or tauopathies, include Alzheimer's disease and related dementia disorders. Previous work has shown that loss of the poly(A) RNA-binding protein gene sut-2/MSUT2 strongly suppressed tauopathy in Caenorhabditis elegans, human cell culture, and mouse models of tauopathy. However, the mechanism of suppression is still unclear. Recent work has shown that MSUT2 protein interacts with the THO complex and ALYREF, which are components of the mRNA nuclear export complex. Additionally, previous work showed ALYREF homolog Ref1 modulates TDP-43 and G4C2 toxicity in Drosophila melanogaster models. We used transgenic C. elegans models of tau or TDP-43 toxicity to investigate the effects of loss of ALYREF function on tau and TDP-43 toxicity. In C. elegans, three genes are homologous to human ALYREF: aly-1, aly-2, and aly-3. We found that loss of C. elegans aly gene function, especially loss of both aly-2 and aly-3, suppressed tau-induced toxic phenotypes. Loss of aly-2 and aly-3 was also able to suppress TDP-43-induced locomotor behavior deficits. However, loss of aly-2 and aly-3 had divergent effects on mRNA and protein levels as total tau protein levels were reduced while mRNA levels were increased, but no significant effects were seen on total TDP-43 protein or mRNA levels. Our results suggest that although aly genes modulate both tau and TDP-43-induced toxicity phenotypes, the molecular mechanisms of suppression are different and separated from impacts on mRNA and protein levels. Altogether, this study highlights the importance of elucidating RNA-related mechanisms in both tau and TDP-43-induced toxicity.
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Affiliation(s)
- Rebecca L Kow
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, S182, 1660 South Columbian Way, Seattle, WA, 98108, USA.
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, 98104, USA.
| | - Aristide H Black
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, S182, 1660 South Columbian Way, Seattle, WA, 98108, USA
| | - Aleen D Saxton
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, S182, 1660 South Columbian Way, Seattle, WA, 98108, USA
| | - Nicole F Liachko
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, S182, 1660 South Columbian Way, Seattle, WA, 98108, USA
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, 98104, USA
| | - Brian C Kraemer
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, S182, 1660 South Columbian Way, Seattle, WA, 98108, USA.
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, 98104, USA.
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA.
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16
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Montalbano M, Jaworski E, Garcia S, Ellsworth A, McAllen S, Routh A, Kayed R. Tau Modulates mRNA Transcription, Alternative Polyadenylation Profiles of hnRNPs, Chromatin Remodeling and Spliceosome Complexes. Front Mol Neurosci 2021; 14:742790. [PMID: 34924950 PMCID: PMC8678415 DOI: 10.3389/fnmol.2021.742790] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Tau protein is a known contributor in several neurodegenerative diseases, including Alzheimer’s disease (AD) and frontotemporal dementia (FTD). It is well-established that tau forms pathological aggregates and fibrils in these diseases. Tau has been observed within the nuclei of neurons, but there is a gap in understanding regarding the mechanism by which tau modulates transcription. We are interested in the P301L mutation of tau, which has been associated with FTD and increased tau aggregation. Our study utilized tau-inducible HEK (iHEK) cells to reveal that WT and P301L tau distinctively alter the transcription and alternative polyadenylation (APA) profiles of numerous nuclear precursors mRNAs, which then translate to form proteins involved in chromatin remodeling and splicing. We isolated total mRNA before and after over-expressing tau and then performed Poly(A)-ClickSeq (PAC-Seq) to characterize mRNA expression and APA profiles. We characterized changes in Gene Ontology (GO) pathways using EnrichR and Gene Set Enrichment Analysis (GSEA). We observed that P301L tau up-regulates genes associated with reactive oxygen species responsiveness as well as genes involved in dendrite, microtubule, and nuclear body/speckle formation. The number of genes regulated by WT tau is greater than the mutant form, which indicates that the P301L mutation causes loss-of-function at the transcriptional level. WT tau up-regulates genes contributing to cytoskeleton-dependent intracellular transport, microglial activation, microtubule and nuclear chromatin organization, formation of nuclear bodies and speckles. Interestingly, both WT and P301L tau commonly down-regulate genes responsible for ubiquitin-proteosome system. In addition, WT tau significantly down-regulates several genes implicated in chromatin remodeling and nucleosome organization. Although there are limitations inherent to the model systems used, this study will improve understanding regarding the nuclear impact of tau at the transcriptional and post-transcriptional level. This study also illustrates the potential impact of P301L tau on the human brain genome during early phases of pathogenesis.
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Affiliation(s)
- Mauro Montalbano
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Stephanie Garcia
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Anna Ellsworth
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Salome McAllen
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Andrew Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
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17
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Phongpreecha T, Gajera CR, Liu CC, Vijayaragavan K, Chang AL, Becker M, Fallahzadeh R, Fernandez R, Postupna N, Sherfield E, Tebaykin D, Latimer C, Shively CA, Register TC, Craft S, Montine KS, Fox EJ, Poston KL, Keene CD, Angelo M, Bendall SC, Aghaeepour N, Montine TJ. Single-synapse analyses of Alzheimer's disease implicate pathologic tau, DJ1, CD47, and ApoE. SCIENCE ADVANCES 2021; 7:eabk0473. [PMID: 34910503 PMCID: PMC8673771 DOI: 10.1126/sciadv.abk0473] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Synaptic molecular characterization is limited for Alzheimer’s disease (AD). Our newly invented mass cytometry–based method, synaptometry by time of flight (SynTOF), was used to measure 38 antibody probes in approximately 17 million single-synapse events from human brains without pathologic change or with pure AD or Lewy body disease (LBD), nonhuman primates (NHPs), and PS/APP mice. Synaptic molecular integrity in humans and NHP was similar. Although not detected in human synapses, Aβ was in PS/APP mice single-synapse events. Clustering and pattern identification of human synapses showed expected disease-specific differences, like increased hippocampal pathologic tau in AD and reduced caudate dopamine transporter in LBD, and revealed previously unidentified findings including increased hippocampal CD47 and lowered DJ1 in AD and higher ApoE in AD with dementia. Our results were independently supported by multiplex ion beam imaging of intact tissue. This highlights the higher depth and breadth of insight on neurodegenerative diseases obtainable through SynTOF.
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Affiliation(s)
- Thanaphong Phongpreecha
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | | | - Candace C. Liu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Alan L. Chang
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Martin Becker
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Ramin Fallahzadeh
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | - Nadia Postupna
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Emily Sherfield
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Dmitry Tebaykin
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Caitlin Latimer
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Carol A. Shively
- Department of Pathology/Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Thomas C. Register
- Department of Pathology/Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Suzanne Craft
- Department of Internal Medicine–Geriatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | - Edward J. Fox
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kathleen L. Poston
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - C. Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sean C. Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Thomas J. Montine
- Department of Pathology, Stanford University, Stanford, CA, USA
- Corresponding author.
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18
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Lee GY, Sohn J, Lee SJV. Combinatorial Approach Using Caenorhabditis elegans and Mammalian Systems for Aging Research. Mol Cells 2021; 44:425-432. [PMID: 34248055 PMCID: PMC8334350 DOI: 10.14348/molcells.2021.0080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 12/13/2022] Open
Abstract
Aging is associated with functional and structural declines in organisms over time. Organisms as diverse as the nematode Caenorhabditis elegans and mammals share signaling pathways that regulate aging and lifespan. In this review, we discuss recent combinatorial approach to aging research employing C. elegans and mammalian systems that have contributed to our understanding of evolutionarily conserved aging-regulating pathways. The topics covered here include insulin/IGF-1, mechanistic target of rapamycin (mTOR), and sirtuin signaling pathways; dietary restriction; autophagy; mitochondria; and the nervous system. A combinatorial approach employing high-throughput, rapid C. elegans systems, and human model mammalian systems is likely to continue providing mechanistic insights into aging biology and will help develop therapeutics against age-associated disorders.
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Affiliation(s)
- Gee-Yoon Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Jooyeon Sohn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Seung-Jae V. Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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19
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Shan S, Xu F, Brenig B. Genome-Wide Association Studies Reveal Neurological Genes for Dog Herding, Predation, Temperament, and Trainability Traits. Front Vet Sci 2021; 8:693290. [PMID: 34368281 PMCID: PMC8335642 DOI: 10.3389/fvets.2021.693290] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
Genome-wide association study (GWAS) using dog breed standard values as phenotypic measurements is an efficient way to identify genes associated with morphological and behavioral traits. As a result of strong human purposeful selections, several specialized behavioral traits such as herding and hunting have been formed in different modern dog breeds. However, genetic analyses on this topic are rather limited due to the accurate phenotyping difficulty for these complex behavioral traits. Here, 268 dog whole-genome sequences from 130 modern breeds were used to investigate candidate genes underlying dog herding, predation, temperament, and trainability by GWAS. Behavioral phenotypes were obtained from the American Kennel Club based on dog breed standard descriptions or groups (conventional categorization of dog historical roles). The GWAS results of herding behavior (without body size as a covariate) revealed 44 significantly associated sites within five chromosomes. Significantly associated sites on CFA7, 9, 10, and 20 were located either in or near neuropathological or neuronal genes including THOC1, ASIC2, MSRB3, LLPH, RFX8, and CHL1. MSRB3 and CHL1 genes were reported to be associated with dog fear. Since herding is a restricted hunting behavior by removing killing instinct, 36 hounds and 55 herding dogs were used to analyze predation behavior. Three neuronal-related genes (JAK2, MEIS1, and LRRTM4) were revealed as candidates for predation behavior. The significantly associated variant of temperament GWAS was located within ACSS3 gene. The highest associated variant in trainability GWAS is located on CFA22, with no variants detected above the Bonferroni threshold. Since dog behaviors are correlated with body size, we next incorporate body mass as covariates into GWAS; and significant signals around THOC1, MSRB3, LLPH, RFX8, CHL1, LRRTM4, and ACSS3 genes were still detected for dog herding, predation, and temperament behaviors. In humans, these candidate genes are either involved in nervous system development or associated with mental disorders. In conclusion, our results imply that these neuronal or psychiatric genes might be involved in biological processes underlying dog herding, predation, and temperament behavioral traits.
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Affiliation(s)
- Shuwen Shan
- Department of Animal Sciences, Faculty of Agricultural Sciences, Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
| | - Fangzheng Xu
- Department of Animal Sciences, Faculty of Agricultural Sciences, Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
| | - Bertram Brenig
- Department of Animal Sciences, Faculty of Agricultural Sciences, Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
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20
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Yao F, Zhang K, Feng C, Gao Y, Shen L, Liu X, Ni J. Protein Biomarkers of Autism Spectrum Disorder Identified by Computational and Experimental Methods. Front Psychiatry 2021; 12:554621. [PMID: 33716802 PMCID: PMC7947305 DOI: 10.3389/fpsyt.2021.554621] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 01/19/2021] [Indexed: 12/27/2022] Open
Abstract
Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that affects millions of people worldwide. However, there are currently no reliable biomarkers for ASD diagnosis. Materials and Methods: The strategy of computational prediction combined with experimental verification was used to identify blood protein biomarkers for ASD. First, brain tissue-based transcriptome data of ASD were collected from Gene Expression Omnibus database and analyzed to find ASD-related genes by bioinformatics method of significance analysis of microarrays. Then, a prediction program of blood-secretory proteins was applied on these genes to predict ASD-related proteins in blood. Furthermore, ELISA was used to verify these proteins in plasma samples of ASD patients. Results: A total of 364 genes were identified differentially expressed in brain tissue of ASD, among which 59 genes were predicted to encode ASD-related blood-secretory proteins. After functional analysis and literature survey, six proteins were chosen for experimental verification and five were successfully validated. Receiver operating characteristic curve analyses showed that the area under the curve of SLC25A12, LIMK1, and RARS was larger than 0.85, indicating that they are more powerful in discriminating ASD cases from controls. Conclusion: SLC25A12, LIMK1, and RARS might serve as new potential blood protein biomarkers for ASD. Our findings provide new insights into the pathogenesis and diagnosis of ASD.
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Affiliation(s)
- Fang Yao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Kaoyuan Zhang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China.,Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Chengyun Feng
- Department of Child Healthcare, Maternal and Child Health Hospital of Baoan, Shenzhen, China
| | - Yan Gao
- Department of Child Healthcare, Maternal and Child Health Hospital of Baoan, Shenzhen, China
| | - Liming Shen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Xukun Liu
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Jiazuan Ni
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
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21
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Krum BN, Martins AC, Queirós L, Ferrer B, Milne GL, Soares FAA, Fachinetto R, Aschner M. Haloperidol Interactions with the dop-3 Receptor in Caenorhabditis elegans. Mol Neurobiol 2020; 58:304-316. [PMID: 32935232 DOI: 10.1007/s12035-020-02124-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/05/2020] [Indexed: 11/29/2022]
Abstract
Haloperidol is a typical antipsychotic drug commonly used to treat a broad range of psychiatric disorders related to dysregulations in the neurotransmitter dopamine (DA). DA modulates important physiologic functions and perturbations in Caenorhabditis elegans (C. elegans) and, its signaling have been associated with alterations in behavioral, molecular, and morphologic properties in C. elegans. Here, we evaluated the possible involvement of dopaminergic receptors in the onset of these alterations followed by haloperidol exposure. Haloperidol increased lifespan and decreased locomotor behavior (basal slowing response, BSR, and locomotion speed via forward speed) of the worms. Moreover, locomotion speed recovered to basal conditions upon haloperidol withdrawal. Haloperidol also decreased DA levels, but it did not alter neither dop-1, dop-2, and dop-3 gene expression, nor CEP dopaminergic neurons' morphology. These effects are likely due to haloperidol's antagonism of the D2-type DA receptor, dop-3. Furthermore, this antagonism appears to affect mechanistic pathways involved in the modulation and signaling of neurotransmitters such as octopamine, acetylcholine, and GABA, which may underlie at least in part haloperidol's effects. These pathways are conserved in vertebrates and have been implicated in a range of disorders. Our novel findings demonstrate that the dop-3 receptor plays an important role in the effects of haloperidol.
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Affiliation(s)
- Bárbara Nunes Krum
- Departamento de Fisiologia e Farmacologia, Centro de Ciências da Saúde, Universidade Federal de Santa Maria, Camobi, Santa Maria, RS, 97105-900, Brazil.,Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Forccheimer 209, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Airton C Martins
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Forccheimer 209, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Libânia Queirós
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Forccheimer 209, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.,Department of Biology and CESAM (Centre for Environmental and Marine Studies), University of Aveiro, 3810-193, Aveiro, Portugal
| | - Beatriz Ferrer
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Forccheimer 209, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Ginger L Milne
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, 37240, USA
| | - Félix Alexandre Antunes Soares
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Forccheimer 209, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.,Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Camobi, Santa Maria, RS, 97105-900, Brazil
| | - Roselei Fachinetto
- Departamento de Fisiologia e Farmacologia, Centro de Ciências da Saúde, Universidade Federal de Santa Maria, Camobi, Santa Maria, RS, 97105-900, Brazil
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Forccheimer 209, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.
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22
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Harnessing the power of genetics: fast forward genetics in Caenorhabditis elegans. Mol Genet Genomics 2020; 296:1-20. [PMID: 32888055 DOI: 10.1007/s00438-020-01721-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 08/27/2020] [Indexed: 12/23/2022]
Abstract
Forward genetics is a powerful tool to unravel molecular mechanisms of diverse biological processes. The success of genetic screens primarily relies on the ease of genetic manipulation of an organism and the availability of a plethora of genetic tools. The roundworm Caenorhabditis elegans has been one of the favorite models for genetic studies due to its hermaphroditic lifestyle, ease of maintenance, and availability of various genetic manipulation tools. The strength of C. elegans genetics is highlighted by the leading role of this organism in the discovery of several conserved biological processes. In this review, the principles and strategies for forward genetics in C. elegans are discussed. Further, the recent advancements that have drastically accelerated the otherwise time-consuming process of mutation identification, making forward genetic screens a method of choice for understanding biological functions, are discussed. The emphasis of the review has been on providing practical and conceptual pointers for designing genetic screens that will identify mutations, specifically disrupting the biological processes of interest.
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23
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Wang L, Nie Q, Gao M, Yang L, Xiang JW, Xiao Y, Liu FY, Gong XD, Fu JL, Wang Y, Nguyen QD, Liu Y, Liu M, Li DWC. The transcription factor CREB acts as an important regulator mediating oxidative stress-induced apoptosis by suppressing αB-crystallin expression. Aging (Albany NY) 2020; 12:13594-13617. [PMID: 32554860 PMCID: PMC7377838 DOI: 10.18632/aging.103474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 05/03/2020] [Indexed: 12/17/2022]
Abstract
The general transcription factor, CREB has been shown to play an essential role in promoting cell proliferation, neuronal survival and synaptic plasticity in the nervous system. However, its function in stress response remains to be elusive. In the present study, we demonstrated that CREB plays a major role in mediating stress response. In both rat lens organ culture and mouse lens epithelial cells (MLECs), CREB promotes oxidative stress-induced apoptosis. To confirm that CREB is a major player mediating the above stress response, we established stable lines of MLECs stably expressing CREB and found that they are also very sensitive to oxidative stress-induced apoptosis. To define the underlying mechanism, RNAseq analysis was conducted. It was found that CREB significantly suppressed expression of the αB-crystallin gene to sensitize CREB-expressing cells undergoing oxidative stress-induced apoptosis. CREB knockdown via CRISPR/CAS9 technology led to upregulation of αB-crystallin and enhanced resistance against oxidative stress-induced apoptosis. Moreover, overexpression of exogenous human αB-crystallin can restore the resistance against oxidative stress-induced apoptosis. Finally, we provided first evidence that CREB directly regulates αB-crystallin gene. Together, our results demonstrate that CREB is an important transcription factor mediating stress response, and it promotes oxidative stress-induced apoptosis by suppressing αB-crystallin expression.
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Affiliation(s)
- Ling Wang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510230, Guangdong, China
| | - Qian Nie
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510230, Guangdong, China
| | - Meng Gao
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
- Medical College, Henan University of Science and Technology, Luoyang 471000, Henan, China
| | - Lan Yang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510230, Guangdong, China
| | - Jia-Wen Xiang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510230, Guangdong, China
- Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA 94303, USA
| | - Yuan Xiao
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510230, Guangdong, China
| | - Fang-Yuan Liu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510230, Guangdong, China
| | - Xiao-Dong Gong
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510230, Guangdong, China
| | - Jia-Ling Fu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510230, Guangdong, China
| | - Yan Wang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510230, Guangdong, China
| | - Quan Dong Nguyen
- Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA 94303, USA
| | - Yizhi Liu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510230, Guangdong, China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - David Wan-Cheng Li
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510230, Guangdong, China
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24
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A Genetic Screen for Human Genes Suppressing FUS Induced Toxicity in Yeast. G3-GENES GENOMES GENETICS 2020; 10:1843-1852. [PMID: 32276960 PMCID: PMC7263679 DOI: 10.1534/g3.120.401164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
FUS is a nucleic acid binding protein that, when mutated, cause a subset of familial amyotrophic lateral sclerosis (ALS). Expression of FUS in yeast recapitulates several pathological features of the disease-causing mutant proteins, including nuclear to cytoplasmic translocation, formation of cytoplasmic inclusions, and cytotoxicity. Genetic screens using the yeast model of FUS have identified yeast genes and their corresponding human homologs suppressing FUS induced toxicity in yeast, neurons and animal models. To expand the search for human suppressor genes of FUS induced toxicity, we carried out a genome-scale genetic screen using a newly constructed library containing 13570 human genes cloned in an inducible yeast-expression vector. Through multiple rounds of verification, we found 37 human genes that, when overexpressed, suppress FUS induced toxicity in yeast. Human genes with DNA or RNA binding functions are overrepresented among the identified suppressor genes, supporting that perturbations of RNA metabolism is a key underlying mechanism of FUS toxicity.
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25
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Assembly of the presynaptic active zone. Curr Opin Neurobiol 2020; 63:95-103. [PMID: 32403081 DOI: 10.1016/j.conb.2020.03.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/29/2020] [Accepted: 03/18/2020] [Indexed: 12/11/2022]
Abstract
In a presynaptic nerve terminal, the active zone is composed of sophisticated protein machinery that enables secretion on a submillisecond time scale and precisely targets it toward postsynaptic receptors. The past two decades have provided deep insight into the roles of active zone proteins in exocytosis, but we are only beginning to understand how a neuron assembles active zone protein complexes into effective molecular machines. In this review, we outline the fundamental processes that are necessary for active zone assembly and discuss recent advances in understanding assembly mechanisms that arise from genetic, morphological and biochemical studies. We further outline the challenges ahead for understanding this important problem.
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26
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Mechanism and Regulation of Co-transcriptional mRNP Assembly and Nuclear mRNA Export. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:1-31. [DOI: 10.1007/978-3-030-31434-7_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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27
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Feldmann KG, Chowdhury A, Becker JL, McAlpin N, Ahmed T, Haider S, Richard Xia JX, Diaz K, Mehta MG, Mano I. Non-canonical activation of CREB mediates neuroprotection in a Caenorhabditis elegans model of excitotoxic necrosis. J Neurochem 2018; 148:531-549. [PMID: 30447010 DOI: 10.1111/jnc.14629] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/26/2018] [Accepted: 11/13/2018] [Indexed: 12/11/2022]
Abstract
Excitotoxicity, caused by exaggerated neuronal stimulation by Glutamate (Glu), is a major cause of neurodegeneration in brain ischemia. While we know that neurodegeneration is triggered by overstimulation of Glu-receptors (GluRs), the subsequent mechanisms that lead to cellular demise remain controversial. Surprisingly, signaling downstream of GluRs can also activate neuroprotective pathways. The strongest evidence involves activation of the transcription factor cAMP response element-binding protein (CREB), widely recognized for its importance in synaptic plasticity. Canonical views describe CREB as a phosphorylation-triggered transcription factor, where transcriptional activation involves CREB phosphorylation and association with CREB-binding protein. However, given CREB's ubiquitous cross-tissue expression, the multitude of cascades leading to CREB phosphorylation, and its ability to regulate thousands of genes, it remains unclear how CREB exerts closely tailored, differential neuroprotective responses in excitotoxicity. A non-canonical, alternative cascade for activation of CREB-mediated transcription involves the CREB co-factor cAMP-regulated transcriptional co-activator (CRTC), and may be independent of CREB phosphorylation. To identify cascades that activate CREB in excitotoxicity we used a Caenorhabditis elegans model of neurodegeneration by excitotoxic necrosis. We demonstrated that CREB's neuroprotective effect was conserved, and seemed most effective in neurons with moderate Glu exposure. We found that factors mediating canonical CREB activation were not involved. Instead, phosphorylation-independent CREB activation in nematode excitotoxic necrosis hinged on CRTC. CREB-mediated transcription that depends on CRTC, but not on CREB phosphorylation, might lead to expression of a specific subset of neuroprotective genes. Elucidating conserved mechanisms of excitotoxicity-specific CREB activation can help us focus on core neuroprotective programs in excitotoxicity. Cover Image for this issue: doi: 10.1111/jnc.14494.
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Affiliation(s)
- K Genevieve Feldmann
- Department of Molecular, Cellular and Biomedical Sciences, CDI Cluster on Neural Development and Repair, The CUNY School of Medicine, City College (CCNY), The City University of New York (CUNY), New York City, New York, USA.,The CUNY Neuroscience Collaborative PhD Program, CUNY Graduate Center, New York City, New York, USA
| | - Ayesha Chowdhury
- Department of Molecular, Cellular and Biomedical Sciences, CDI Cluster on Neural Development and Repair, The CUNY School of Medicine, City College (CCNY), The City University of New York (CUNY), New York City, New York, USA.,The CUNY Neuroscience Collaborative PhD Program, CUNY Graduate Center, New York City, New York, USA
| | - Jessica L Becker
- Undergraduate Program in Biology, CCNY, CUNY, New York City, New York, USA
| | - N'Gina McAlpin
- Undergraduate Program in Biology, CCNY, CUNY, New York City, New York, USA
| | - Taqwa Ahmed
- The Sophie Davis BS/MD program, CUNY School of Medicine, New York City, New York, USA
| | - Syed Haider
- Undergraduate Program in Biology, CCNY, CUNY, New York City, New York, USA
| | - Jian X Richard Xia
- The Sophie Davis BS/MD program, CUNY School of Medicine, New York City, New York, USA
| | - Karina Diaz
- The Sophie Davis BS/MD program, CUNY School of Medicine, New York City, New York, USA
| | - Monal G Mehta
- Robert Wood Johnson Medical School, Rutgers - The State University of New Jersey, Piscataway, New Jersey, USA
| | - Itzhak Mano
- Department of Molecular, Cellular and Biomedical Sciences, CDI Cluster on Neural Development and Repair, The CUNY School of Medicine, City College (CCNY), The City University of New York (CUNY), New York City, New York, USA.,The CUNY Neuroscience Collaborative PhD Program, CUNY Graduate Center, New York City, New York, USA.,The Sophie Davis BS/MD program, CUNY School of Medicine, New York City, New York, USA
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28
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Oranth A, Schultheis C, Tolstenkov O, Erbguth K, Nagpal J, Hain D, Brauner M, Wabnig S, Steuer Costa W, McWhirter RD, Zels S, Palumbos S, Miller III DM, Beets I, Gottschalk A. Food Sensation Modulates Locomotion by Dopamine and Neuropeptide Signaling in a Distributed Neuronal Network. Neuron 2018; 100:1414-1428.e10. [DOI: 10.1016/j.neuron.2018.10.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/14/2018] [Accepted: 10/12/2018] [Indexed: 01/02/2023]
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