1
|
Văcăraş V, Vulturar R, Chiş A, Damian L. Inclusion body myositis, viral infections, and TDP-43: a narrative review. Clin Exp Med 2024; 24:91. [PMID: 38693436 PMCID: PMC11062973 DOI: 10.1007/s10238-024-01353-9] [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: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 05/03/2024]
Abstract
The ubiquitous RNA-processing molecule TDP-43 is involved in neuromuscular diseases such as inclusion body myositis, a late-onset acquired inflammatory myopathy. TDP-43 solubility and function are disrupted in certain viral infections. Certain viruses, high viremia, co-infections, reactivation of latent viruses, and post-acute expansion of cytotoxic T cells may all contribute to inclusion body myositis, mainly in an age-shaped immune landscape. The virally induced senescent, interferon gamma-producing cytotoxic CD8+ T cells with increased inflammatory, and cytotoxic features are involved in the occurrence of inclusion body myositis in most such cases, in a genetically predisposed host. We discuss the putative mechanisms linking inclusion body myositis, TDP-43, and viral infections untangling the links between viruses, interferon, and neuromuscular degeneration could shed a light on the pathogenesis of the inclusion body myositis and other TDP-43-related neuromuscular diseases, with possible therapeutic implications.
Collapse
Affiliation(s)
- Vitalie Văcăraş
- Department of Neurosciences, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, 43, Victor Babeş St, 400012, Cluj-Napoca, Romania
- Neurology Department of Cluj, County Emergency Hospital, 3-5, Clinicilor St, 400347, Cluj-Napoca, Romania
| | - Romana Vulturar
- Department of Molecular Sciences, "Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, 6, Pasteur St, 400349, Cluj-Napoca, Romania
- Cognitive Neuroscience Laboratory, University Babeş-Bolyai, 30, Fântânele St, 400294, Cluj-Napoca, Romania
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St, 400497, Cluj-Napoca, Romania
| | - Adina Chiş
- Department of Molecular Sciences, "Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, 6, Pasteur St, 400349, Cluj-Napoca, Romania.
- Cognitive Neuroscience Laboratory, University Babeş-Bolyai, 30, Fântânele St, 400294, Cluj-Napoca, Romania.
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St, 400497, Cluj-Napoca, Romania.
| | - Laura Damian
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St, 400497, Cluj-Napoca, Romania
- Department of Rheumatology, Centre for Rare Autoimmune and Autoinflammatory Diseases, Emergency, Clinical County Hospital Cluj, 2-4, Clinicilor St, 400006, Cluj-Napoca, Romania
- CMI Reumatologie Dr. Damian, 6-8, Petru Maior St, 400002, Cluj-Napoca, Romania
| |
Collapse
|
2
|
Castro-Gomez S, Heneka MT. Innate immune activation in neurodegenerative diseases. Immunity 2024; 57:790-814. [PMID: 38599171 DOI: 10.1016/j.immuni.2024.03.010] [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: 01/12/2024] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024]
Abstract
Activation of the innate immune system following pattern recognition receptor binding has emerged as one of the major pathogenic mechanisms in neurodegenerative disease. Experimental, epidemiological, pathological, and genetic evidence underscores the meaning of innate immune activation during the prodromal as well as clinical phases of several neurodegenerative disorders including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal dementia. Importantly, innate immune activation and the subsequent release of inflammatory mediators contribute mechanistically to other hallmarks of neurodegenerative diseases such as aberrant proteostatis, pathological protein aggregation, cytoskeleton abnormalities, altered energy homeostasis, RNA and DNA defects, and synaptic and network disbalance and ultimately to the induction of neuronal cell death. In this review, we discuss common mechanisms of innate immune activation in neurodegeneration, with particular emphasis on the pattern recognition receptors (PRRs) and other receptors involved in the detection of damage-associated molecular patterns (DAMPs).
Collapse
Affiliation(s)
- Sergio Castro-Gomez
- Center for Neurology, Department of Parkinson, Sleep and Movement Disorders, University Hospital Bonn, 53127 Bonn, Germany; Institute of Physiology II, University Hospital Bonn, 53115 Bonn, Germany
| | - Michael T Heneka
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg; Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, USA.
| |
Collapse
|
3
|
Banazadeh M, Abiri A, Poortaheri MM, Asnaashari L, Langarizadeh MA, Forootanfar H. Unexplored power of CRISPR-Cas9 in neuroscience, a multi-OMICs review. Int J Biol Macromol 2024; 263:130413. [PMID: 38408576 DOI: 10.1016/j.ijbiomac.2024.130413] [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: 02/03/2023] [Revised: 05/27/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
The neuroscience and neurobiology of gene editing to enhance learning and memory is of paramount interest to the scientific community. The advancements of CRISPR system have created avenues to treat neurological disorders by means of versatile modalities varying from expression to suppression of genes and proteins. Neurodegenerative disorders have also been attributed to non-canonical DNA secondary structures by affecting neuron activity through controlling gene expression, nucleosome shape, transcription, translation, replication, and recombination. Changing DNA regulatory elements which could contribute to the fate and function of neurons are thoroughly discussed in this review. This study presents the ability of CRISPR system to boost learning power and memory, treat or cure genetically-based neurological disorders, and alleviate psychiatric diseases by altering the activity and the irritability of the neurons at the synaptic cleft through DNA manipulation, and also, epigenetic modifications using Cas9. We explore and examine how each different OMIC techniques can come useful when altering DNA sequences. Such insight into the underlying relationship between OMICs and cellular behaviors leads us to better neurological and psychiatric therapeutics by intelligently designing and utilizing the CRISPR/Cas9 technology.
Collapse
Affiliation(s)
- Mohammad Banazadeh
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA
| | | | - Lida Asnaashari
- Student Research Committee, Kerman Universiy of Medical Sciences, Kerman, Iran
| | - Mohammad Amin Langarizadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Forootanfar
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran.
| |
Collapse
|
4
|
Eck RJ, Stair JG, Kraemer BC, Liachko NF. Simple models to understand complex disease: 10 years of progress from Caenorhabditis elegans models of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Front Neurosci 2024; 17:1300705. [PMID: 38239833 PMCID: PMC10794587 DOI: 10.3389/fnins.2023.1300705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/28/2023] [Indexed: 01/22/2024] Open
Abstract
The nematode Caenorhabditis elegans are a powerful model system to study human disease, with numerous experimental advantages including significant genetic and cellular homology to vertebrate animals, a short lifespan, and tractable behavioral, molecular biology and imaging assays. Beginning with the identification of SOD1 as a genetic cause of amyotrophic lateral sclerosis (ALS), C. elegans have contributed to a deeper understanding of the mechanistic underpinnings of this devastating neurodegenerative disease. More recently this work has expanded to encompass models of other types of ALS and the related disease frontotemporal lobar degeneration (FTLD-TDP), including those characterized by mutation or accumulation of the proteins TDP-43, C9orf72, FUS, HnRNPA2B1, ALS2, DCTN1, CHCHD10, ELP3, TUBA4A, CAV1, UBQLN2, ATXN3, TIA1, KIF5A, VAPB, GRN, and RAB38. In this review we summarize these models and the progress and insights from the last ten years of using C. elegans to study the neurodegenerative diseases ALS and FTLD-TDP.
Collapse
Affiliation(s)
- Randall J. Eck
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, United States
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Jade G. Stair
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
| | - Brian C. Kraemer
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Nicole F. Liachko
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
| |
Collapse
|
5
|
Taylor M, Marx O, Norris A. TDP-1 and FUST-1 co-inhibit exon inclusion and control fertility together with transcriptional regulation. Nucleic Acids Res 2023; 51:9610-9628. [PMID: 37587694 PMCID: PMC10570059 DOI: 10.1093/nar/gkad665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/20/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023] Open
Abstract
Gene expression is a multistep process and crosstalk among regulatory layers plays an important role in coordinating gene expression. To identify functionally relevant gene expression coordination, we performed a systematic reverse-genetic interaction screen in C. elegans, combining RNA binding protein (RBP) and transcription factor (TF) mutants to generate over 100 RBP;TF double mutants. We identified many unexpected double mutant phenotypes, including two strong genetic interactions between the ALS-related RBPs, fust-1 and tdp-1, and the homeodomain TF ceh-14. Losing any one of these genes alone has no effect on the health of the organism. However, fust-1;ceh-14 and tdp-1;ceh-14 double mutants both exhibit strong temperature-sensitive fertility defects. Both double mutants exhibit defects in gonad morphology, sperm function, and oocyte function. RNA-Seq analysis of double mutants identifies ceh-14 as the main controller of transcript levels, while fust-1 and tdp-1 control splicing through a shared role in exon inhibition. A skipped exon in the polyglutamine-repeat protein pqn-41 is aberrantly included in tdp-1 mutants, and genetically forcing this exon to be skipped in tdp-1;ceh-14 double mutants rescues their fertility. Together our findings identify a novel shared physiological role for fust-1 and tdp-1 in promoting C. elegans fertility and a shared molecular role in exon inhibition.
Collapse
Affiliation(s)
- Morgan Taylor
- Southern Methodist University, Dallas, TX 75205, USA
| | - Olivia Marx
- Southern Methodist University, Dallas, TX 75205, USA
| | - Adam Norris
- Southern Methodist University, Dallas, TX 75205, USA
| |
Collapse
|
6
|
Milstead RA, Link CD, Xu Z, Hoeffer CA. TDP-43 knockdown in mouse model of ALS leads to dsRNA deposition, gliosis, and neurodegeneration in the spinal cord. Cereb Cortex 2023; 33:5808-5816. [PMID: 36443249 PMCID: PMC10183735 DOI: 10.1093/cercor/bhac461] [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: 08/12/2022] [Revised: 10/28/2022] [Accepted: 10/29/2022] [Indexed: 11/30/2022] Open
Abstract
Transactive response DNA binding protein 43 kilodaltons (TDP-43) is a DNA and RNA binding protein associated with severe neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), primarily affecting motor neurons in the brain and spinal cord. Partial knockdown of TDP-43 expression in a mouse model (the amiR-TDP-43 mice) leads to progressive, age-related motor dysfunction, as observed in ALS patients. Work in Caenorhabditis elegans suggests that TDP-43 dysfunction can lead to deficits in chromatin processing and double-stranded RNA (dsRNA) accumulation, potentially activating the innate immune system and promoting neuroinflammation. To test this hypothesis, we used immunostaining to investigate dsRNA accumulation and other signs of CNS pathology in the spinal cords of amiR-TDP-43 mice. Compared with wild-type controls, TDP-43 knockdown animals show increases in dsRNA deposition in the dorsal and ventral horns of the spinal cord. Additionally, animals with heavy dsRNA expression show markedly increased levels of astrogliosis and microgliosis. Interestingly, areas of high dsRNA expression and microgliosis overlap with regions of heavy neurodegeneration, indicating that activated microglia could contribute to the degeneration of spinal cord neurons. This study suggests that loss of TDP-43 function could contribute to neuropathology by increasing dsRNA deposition and subsequent innate immune system activation.
Collapse
Affiliation(s)
- Ryan A Milstead
- Department of Integrative Physiology, University of Colorado, Boulder, Boulder CO 80303
- Institute for Behavioral Genetics, University of Colorado, Boulder, Boulder, CO 80303
| | - Christopher D Link
- Department of Integrative Physiology, University of Colorado, Boulder, Boulder CO 80303
| | - Zuoshang Xu
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01655
| | - Charles A Hoeffer
- Department of Integrative Physiology, University of Colorado, Boulder, Boulder CO 80303
- Institute for Behavioral Genetics, University of Colorado, Boulder, Boulder, CO 80303
- Linda Crnic Institute, Anschutz Medical Center, Aurora, CO 80217
| |
Collapse
|
7
|
Licht-Murava A, Meadows SM, Palaguachi F, Song SC, Jackvony S, Bram Y, Zhou C, Schwartz RE, Froemke RC, Orr AL, Orr AG. Astrocytic TDP-43 dysregulation impairs memory by modulating antiviral pathways and interferon-inducible chemokines. SCIENCE ADVANCES 2023; 9:eade1282. [PMID: 37075107 PMCID: PMC10115456 DOI: 10.1126/sciadv.ade1282] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Transactivating response region DNA binding protein 43 (TDP-43) pathology is prevalent in dementia, but the cell type-specific effects of TDP-43 pathology are not clear, and therapeutic strategies to alleviate TDP-43-linked cognitive decline are lacking. We found that patients with Alzheimer's disease or frontotemporal dementia have aberrant TDP-43 accumulation in hippocampal astrocytes. In mouse models, induction of widespread or hippocampus-targeted accumulation in astrocytic TDP-43 caused progressive memory loss and localized changes in antiviral gene expression. These changes were cell-autonomous and correlated with impaired astrocytic defense against infectious viruses. Among the changes, astrocytes had elevated levels of interferon-inducible chemokines, and neurons had elevated levels of the corresponding chemokine receptor CXCR3 in presynaptic terminals. CXCR3 stimulation altered presynaptic function and promoted neuronal hyperexcitability, akin to the effects of astrocytic TDP-43 dysregulation, and blockade of CXCR3 reduced this activity. Ablation of CXCR3 also prevented TDP-43-linked memory loss. Thus, astrocytic TDP-43 dysfunction contributes to cognitive impairment through aberrant chemokine-mediated astrocytic-neuronal interactions.
Collapse
Affiliation(s)
- Avital Licht-Murava
- Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Samantha M. Meadows
- Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Fernando Palaguachi
- Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Soomin C. Song
- Skirball Institute, Neuroscience Institute, Department of Otolaryngology, New York University Grossman School of Medicine, New York, NY, USA
| | - Stephanie Jackvony
- Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Yaron Bram
- Department of Medicine, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY, USA
| | - Constance Zhou
- Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Medicine–Rockefeller–Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY USA
| | - Robert E. Schwartz
- Department of Medicine, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY, USA
| | - Robert C. Froemke
- Skirball Institute, Neuroscience Institute, Department of Otolaryngology, New York University Grossman School of Medicine, New York, NY, USA
| | - Adam L. Orr
- Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Anna G. Orr
- Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Medicine–Rockefeller–Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY USA
| |
Collapse
|
8
|
Taylor M, Marx O, Norris A. TDP-1 and FUST-1 co-inhibit exon inclusion and control fertility together with transcriptional regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537345. [PMID: 37131843 PMCID: PMC10153140 DOI: 10.1101/2023.04.18.537345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Gene expression is a multistep, carefully controlled process, and crosstalk between regulatory layers plays an important role in coordinating gene expression. To identify functionally relevant coordination between transcriptional and post-transcriptional gene regulation, we performed a systematic reverse-genetic interaction screen in C. elegans . We combined RNA binding protein (RBP) and transcription factor (TF) mutants, creating over 100 RBP; TF double mutants. This screen identified a variety of unexpected double mutant phenotypes, including two strong genetic interactions between the ALS-related RBPs, fust-1 and tdp-1 , and the homeodomain TF ceh-14 . Losing any one of these genes alone has no significant effect on the health of the organism. However, fust-1; ceh-14 and tdp-1; ceh-14 double mutants both exhibit strong temperature-sensitive fertility defects. Both double mutants exhibit defects in gonad morphology, sperm function, and oocyte function. RNA-seq analysis of double mutants identifies ceh-14 as the main controller of transcript levels, while fust-1 and tdp-1 control splicing through a shared role in exon inhibition. We identify a cassette exon in the polyglutamine-repeat protein pqn-41 which tdp-1 inhibits. Loss of tdp-1 causes the pqn-41 exon to be aberrantly included, and forced skipping of this exon in tdp-1; ceh-14 double mutants rescues fertility. Together our findings identify a novel shared physiological role for fust-1 and tdp-1 in promoting C. elegans fertility in a ceh-14 mutant background and reveal a shared molecular function of fust-1 and tdp-1 in exon inhibition.
Collapse
|
9
|
Henriquez G, Ahlawat J, Fairman R, Narayan M. Citric Acid-Derived Carbon Quantum Dots Attenuate Paraquat-Induced Neuronal Compromise In Vitro and In Vivo. ACS Chem Neurosci 2022; 13:2399-2409. [PMID: 35942850 DOI: 10.1021/acschemneuro.2c00099] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The potent environmental herbicide and weedicide paraquat is linked to neuromotor defects and Parkinson's disease (PD). We have evaluated the neuroprotective role of citric acid-sourced carbon quantum dots (Cit-CQDs) on paraquat-insulted human neuroblastoma-derived SH-SY5Y cell lines and on a paraquat-exposed nematode (Caenorhabditis elegans). Our data reveal that Cit-CQDs are able to scavenge free radicals in test tube assays and mitigate paraquat-elevated reactive oxygen species (ROS) levels in SH-SY5Y cells. Furthermore, Cit-CQDs protect the cell line from paraquat, which otherwise elicits cell death. Cit-CQDs-challenged nematodes demonstrate enhanced survival rates 72 h post-paraquat exposure compared to controls. Paraquat ablates dopamine (DA) neurons, which results in compromised locomotor function in nematodes. However, the neurons remained intact when the nematodes were incubated with Cit-CQDs prior to neurotoxicant exposure. The collective data suggest Cit-CQDs offer neuroprotection for cell lines and organisms from xenotoxicant-associated neuronal injury and death. The study suggests Cit-CQDs as a potentially viable green chemistry-synthesized, biobased nanomaterial for intervention in neurodegenerative disorders.
Collapse
Affiliation(s)
- Gabriela Henriquez
- Department of Environmental Science and Engineering, The University of Texas at El Paso (UTEP), El Paso, Texas 79968, United States
| | - Jyoti Ahlawat
- Department of Chemistry and Biochemistry, The University of Texas at El Paso (UTEP), El Paso, Texas 79968, United States
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041, United States
| | - Mahesh Narayan
- Department of Chemistry and Biochemistry, The University of Texas at El Paso (UTEP), El Paso, Texas 79968, United States
| |
Collapse
|
10
|
Hayes LR, Kalab P. Emerging Therapies and Novel Targets for TDP-43 Proteinopathy in ALS/FTD. Neurotherapeutics 2022; 19:1061-1084. [PMID: 35790708 PMCID: PMC9587158 DOI: 10.1007/s13311-022-01260-5] [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] [Accepted: 06/03/2022] [Indexed: 10/17/2022] Open
Abstract
Nuclear clearance and cytoplasmic mislocalization of the essential RNA binding protein, TDP-43, is a pathologic hallmark of amyotrophic lateral sclerosis, frontotemporal dementia, and related neurodegenerative disorders collectively termed "TDP-43 proteinopathies." TDP-43 mislocalization causes neurodegeneration through both loss and gain of function mechanisms. Loss of TDP-43 nuclear RNA processing function destabilizes the transcriptome by multiple mechanisms including disruption of pre-mRNA splicing, the failure of repression of cryptic exons, and retrotransposon activation. The accumulation of cytoplasmic TDP-43, which is prone to aberrant liquid-liquid phase separation and aggregation, traps TDP-43 in the cytoplasm and disrupts a host of downstream processes including the trafficking of RNA granules, local translation within axons, and mitochondrial function. In this review, we will discuss the TDP-43 therapy development pipeline, beginning with therapies in current and upcoming clinical trials, which are primarily focused on accelerating the clearance of TDP-43 aggregates. Then, we will look ahead to emerging strategies from preclinical studies, first from high-throughput genetic and pharmacologic screens, and finally from mechanistic studies focused on the upstream cause(s) of TDP-43 disruption in ALS/FTD. These include modulation of stress granule dynamics, TDP-43 nucleocytoplasmic shuttling, RNA metabolism, and correction of aberrant splicing events.
Collapse
Affiliation(s)
- Lindsey R Hayes
- Johns Hopkins School of Medicine, Dept. of Neurology, Baltimore, MD, USA.
| | - Petr Kalab
- Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| |
Collapse
|
11
|
Choi S, Meyer MO, Bevilacqua PC, Keating CD. Phase-specific RNA accumulation and duplex thermodynamics in multiphase coacervate models for membraneless organelles. Nat Chem 2022; 14:1110-1117. [PMID: 35773489 DOI: 10.1038/s41557-022-00980-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 05/20/2022] [Indexed: 12/20/2022]
Abstract
Liquid-liquid phase separation has emerged as an important means of intracellular RNA compartmentalization. Some membraneless organelles host two or more compartments serving different putative biochemical roles. The mechanisms for, and functional consequences of, this subcompartmentalization are not yet well understood. Here we show that adjacent phases of decapeptide-based multiphase model membraneless organelles differ markedly in their interactions with RNA. Single- and double-stranded RNAs preferentially accumulate in different phases within the same droplet, and one phase is more destabilizing for RNA duplexes than the other. Single-phase peptide droplets did not capture this behaviour. Phase coexistence introduces new thermodynamic equilibria that alter RNA duplex stability and RNA sorting by hybridization state. These effects require neither biospecific RNA-binding sites nor full-length proteins. As such, they are more general and point to primitive versions of mechanisms operating in extant biology that could aid understanding and enable the design of functional artificial membraneless organelles.
Collapse
Affiliation(s)
- Saehyun Choi
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - McCauley O Meyer
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA. .,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA. .,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
| | - Christine D Keating
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
| |
Collapse
|
12
|
Naranjo-Galindo FJ, Ai R, Fang EF, Nilsen HL, SenGupta T. C. elegans as an Animal Model to Study the Intersection of DNA Repair, Aging and Neurodegeneration. FRONTIERS IN AGING 2022; 3:916118. [PMID: 35821838 PMCID: PMC9261396 DOI: 10.3389/fragi.2022.916118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022]
Abstract
Since its introduction as a genetic model organism, Caenorhabditis elegans has yielded insights into the causes of aging. In addition, it has provided a molecular understanding of mechanisms of neurodegeneration, one of the devastating effects of aging. However, C. elegans has been less popular as an animal model to investigate DNA repair and genomic instability, which is a major hallmark of aging and also a cause of many rare neurological disorders. This article provides an overview of DNA repair pathways in C. elegans and the impact of DNA repair on aging hallmarks, such as mitochondrial dysfunction, telomere maintenance, and autophagy. In addition, we discuss how the combination of biological characteristics, new technical tools, and the potential of following precise phenotypic assays through a natural life-course make C. elegans an ideal model organism to study how DNA repair impact neurodegeneration in models of common age-related neurodegenerative diseases.
Collapse
Affiliation(s)
- Francisco José Naranjo-Galindo
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
- Section of Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
| | - Ruixue Ai
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
| | - Evandro Fei Fang
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
| | - Hilde Loge Nilsen
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
- Section of Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- *Correspondence: Hilde Loge Nilsen, ; Tanima SenGupta,
| | - Tanima SenGupta
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
- Section of Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
- *Correspondence: Hilde Loge Nilsen, ; Tanima SenGupta,
| |
Collapse
|
13
|
Azpurua J, El-Karim EG, Tranquille M, Dubnau J. A behavioral screen for mediators of age-dependent TDP-43 neurodegeneration identifies SF2/SRSF1 among a group of potent suppressors in both neurons and glia. PLoS Genet 2021; 17:e1009882. [PMID: 34723963 PMCID: PMC8584670 DOI: 10.1371/journal.pgen.1009882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/11/2021] [Accepted: 10/15/2021] [Indexed: 11/19/2022] Open
Abstract
Cytoplasmic aggregation of Tar-DNA/RNA binding protein 43 (TDP-43) occurs in 97 percent of amyotrophic lateral sclerosis (ALS), ~40% of frontotemporal dementia (FTD) and in many cases of Alzheimer's disease (AD). Cytoplasmic TDP-43 inclusions are seen in both sporadic and familial forms of these disorders, including those cases that are caused by repeat expansion mutations in the C9orf72 gene. To identify downstream mediators of TDP-43 toxicity, we expressed human TDP-43 in a subset of Drosophila motor neurons. Such expression causes age-dependent deficits in negative geotaxis behavior. Using this behavioral readout of locomotion, we conducted an shRNA suppressor screen and identified 32 transcripts whose knockdown was sufficient to ameliorate the neurological phenotype. The majority of these suppressors also substantially suppressed the negative effects on lifespan seen with glial TDP-43 expression. In addition to identification of a number of genes whose roles in neurodegeneration were not previously known, our screen also yielded genes involved in chromatin regulation and nuclear/import export- pathways that were previously identified in the context of cell based or neurodevelopmental suppressor screens. A notable example is SF2, a conserved orthologue of mammalian SRSF1, an RNA binding protein with roles in splicing and nuclear export. Our identification SF2/SRSF1 as a potent suppressor of both neuronal and glial TDP-43 toxicity also provides a convergence with C9orf72 expansion repeat mediated neurodegeneration, where this gene also acts as a downstream mediator.
Collapse
Affiliation(s)
- Jorge Azpurua
- Department of Anesthesiology, Stony Brook School of Medicine, Stony Brook, New York, United States of America
| | - Enas Gad El-Karim
- Department of Anesthesiology, Stony Brook School of Medicine, Stony Brook, New York, United States of America
| | - Marvel Tranquille
- Department of Physiology and Biophysics, M.S. Program, Stony Brook School of Medicine, Stony Brook, New York, United States of America
| | - Josh Dubnau
- Department of Anesthesiology, Stony Brook School of Medicine, Stony Brook, New York, United States of America
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
| |
Collapse
|
14
|
Rodriguez S, Sahin A, Schrank BR, Al-Lawati H, Costantino I, Benz E, Fard D, Albers AD, Cao L, Gomez AC, Evans K, Ratti E, Cudkowicz M, Frosch MP, Talkowski M, Sorger PK, Hyman BT, Albers MW. Genome-encoded cytoplasmic double-stranded RNAs, found in C9ORF72 ALS-FTD brain, propagate neuronal loss. Sci Transl Med 2021; 13:13/601/eaaz4699. [PMID: 34233951 DOI: 10.1126/scitranslmed.aaz4699] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 06/29/2020] [Accepted: 03/15/2021] [Indexed: 12/12/2022]
Abstract
Triggers of innate immune signaling in the CNS of patients with amyotrophic lateral sclerosis and frontotemporal degeneration (ALS/FTD) remain elusive. We report the presence of cytoplasmic double-stranded RNA (cdsRNA), an established trigger of innate immunity, in ALS-FTD brains carrying C9ORF72 intronic hexanucleotide expansions that included genomically encoded expansions of the G4C2 repeat sequences. The presence of cdsRNA in human brains was coincident with cytoplasmic TAR DNA binding protein 43 (TDP-43) inclusions, a pathologic hallmark of ALS/FTD. Introducing cdsRNA into cultured human neural cells induced type I interferon (IFN-I) signaling and death that was rescued by FDA-approved JAK inhibitors. In mice, genomically encoded dsRNAs expressed exclusively in a neuronal class induced IFN-I and death in connected neurons non-cell-autonomously. Our findings establish that genomically encoded cdsRNAs trigger sterile, viral-mimetic IFN-I induction and propagated death within neural circuits and may drive neuroinflammation and neurodegeneration in patients with ALS/FTD.
Collapse
Affiliation(s)
- Steven Rodriguez
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA.,Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
| | - Asli Sahin
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Benjamin R Schrank
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Hawra Al-Lawati
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Isabel Costantino
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Eric Benz
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Darian Fard
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Alefiya D Albers
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA.,Department of Psychology, Endicott College, Beverly, MA 01915, USA
| | - Luxiang Cao
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Alexis C Gomez
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Kyle Evans
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA.,Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
| | - Elena Ratti
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Merit Cudkowicz
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Matthew P Frosch
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael Talkowski
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Mark W Albers
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA. .,Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
15
|
Dunker W, Ye X, Zhao Y, Liu L, Richardson A, Karijolich J. TDP-43 prevents endogenous RNAs from triggering a lethal RIG-I-dependent interferon response. Cell Rep 2021; 35:108976. [PMID: 33852834 PMCID: PMC8109599 DOI: 10.1016/j.celrep.2021.108976] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/01/2021] [Accepted: 03/19/2021] [Indexed: 12/16/2022] Open
Abstract
RIG-I-like receptors (RLRs) are involved in the discrimination of self versus non-self via the recognition of double-stranded RNA (dsRNA). Emerging evidence suggests that immunostimulatory dsRNAs are ubiquitously expressed but are disrupted or sequestered by cellular RNA binding proteins (RBPs). TDP-43 is an RBP associated with multiple neurological disorders and is essential for cell viability. Here, we demonstrate that TDP-43 regulates the accumulation of immunostimulatory dsRNA. The immunostimulatory RNA is identified as RNA polymerase III transcripts, including 7SL and Alu retrotransposons, and we demonstrate that the RNA-binding activity of TDP-43 is required to prevent immune stimulation. The dsRNAs activate a RIG-I-dependent interferon (IFN) response, which promotes necroptosis. Genetic inactivation of the RLR-pathway rescues the interferon-mediated cell death associated with loss of TDP-43. Collectively, our study describes a role for TDP-43 in preventing the accumulation of endogenous immunostimulatory dsRNAs and uncovers an intricate relationship between the control of cellular gene expression and IFN-mediated cell death.
Collapse
MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/immunology
- Alu Elements
- Cell Line, Tumor
- Cell Survival
- Cytokines/genetics
- Cytokines/immunology
- DEAD Box Protein 58/antagonists & inhibitors
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/immunology
- DNA-Binding Proteins/deficiency
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/immunology
- Epithelial Cells/immunology
- Epithelial Cells/virology
- Gene Expression Regulation
- HEK293 Cells
- Herpesvirus 8, Human/genetics
- Herpesvirus 8, Human/growth & development
- Herpesvirus 8, Human/immunology
- Humans
- Immunization
- Interferons/genetics
- Interferons/immunology
- Interleukin-6/genetics
- Interleukin-6/immunology
- Necroptosis/genetics
- Necroptosis/immunology
- Neurons/immunology
- Neurons/virology
- RNA Polymerase III/genetics
- RNA Polymerase III/immunology
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/immunology
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- RNA, Small Cytoplasmic/genetics
- RNA, Small Cytoplasmic/immunology
- RNA, Viral/genetics
- RNA, Viral/immunology
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/immunology
- Receptors, Immunologic/antagonists & inhibitors
- Receptors, Immunologic/genetics
- Receptors, Immunologic/immunology
- Signal Recognition Particle/genetics
- Signal Recognition Particle/immunology
- Signal Transduction
- Tumor Necrosis Factor-alpha/genetics
- Tumor Necrosis Factor-alpha/immunology
- Ubiquitins/genetics
- Ubiquitins/immunology
Collapse
Affiliation(s)
- William Dunker
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-2363, USA
| | - Xiang Ye
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-2363, USA
| | - Yang Zhao
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-2363, USA
| | - Lanxi Liu
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-2363, USA
| | - Antiana Richardson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-2363, USA
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-2363, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-2363, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37232-2363, USA; Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN 37232-2363, USA; Vanderbilt Center for Immunobiology, Nashville, TN 37232-2363, USA.
| |
Collapse
|
16
|
Pathway from TDP-43-Related Pathology to Neuronal Dysfunction in Amyotrophic Lateral Sclerosis and Frontotemporal Lobar Degeneration. Int J Mol Sci 2021; 22:ijms22083843. [PMID: 33917673 PMCID: PMC8068029 DOI: 10.3390/ijms22083843] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 12/15/2022] Open
Abstract
Transactivation response DNA binding protein 43 kDa (TDP-43) is known to be a pathologic protein in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). TDP-43 is normally a nuclear protein, but affected neurons of ALS or FTLD patients exhibit mislocalization of nuclear TDP-43 and cytoplasmic inclusions. Basic studies have suggested gain-of-neurotoxicity of aggregated TDP-43 or loss-of-function of intrinsic, nuclear TDP-43. It has also been hypothesized that the aggregated TDP-43 functions as a propagation seed of TDP-43 pathology. However, a mechanistic discrepancy between the TDP-43 pathology and neuronal dysfunctions remains. This article aims to review the observations of TDP-43 pathology in autopsied ALS and FTLD patients and address pathways of neuronal dysfunction related to the neuropathological findings, focusing on impaired clearance of TDP-43 and synaptic alterations in TDP-43-related ALS and FTLD. The former may be relevant to intraneuronal aggregation of TDP-43 and exocytosis of propagation seeds, whereas the latter may be related to neuronal dysfunction induced by TDP-43 pathology. Successful strategies of disease-modifying therapy might arise from further investigation of these subcellular alterations.
Collapse
|
17
|
Giunti S, Andersen N, Rayes D, De Rosa MJ. Drug discovery: Insights from the invertebrate Caenorhabditis elegans. Pharmacol Res Perspect 2021; 9:e00721. [PMID: 33641258 PMCID: PMC7916527 DOI: 10.1002/prp2.721] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/06/2021] [Indexed: 12/18/2022] Open
Abstract
Therapeutic drug development is a long, expensive, and complex process that usually takes 12-15 years. In the early phases of drug discovery, in particular, there is a growing need for animal models that ensure the reduction in both cost and time. Caenorhabditis elegans has been traditionally used to address fundamental aspects of key biological processes, such as apoptosis, aging, and gene expression regulation. During the last decade, with the advent of large-scale platforms for screenings, this invertebrate has also emerged as an essential tool in the pharmaceutical research industry to identify novel drugs and drug targets. In this review, we discuss the reasons why C. elegans has been positioned as an outstanding cost-effective option for drug discovery, highlighting both the advantages and drawbacks of this model. Particular attention is paid to the suitability of this nematode in large-scale genetic and pharmacological screenings. High-throughput screenings in C. elegans have indeed contributed to the breakthrough of a wide variety of candidate compounds involved in extensive fields including neurodegeneration, pathogen infections and metabolic disorders. The versatility of this nematode, which enables its instrumentation as a model of human diseases, is another attribute also herein underscored. As illustrative examples, we discuss the utility of C. elegans models of both human neurodegenerative diseases and parasitic nematodes in the drug discovery industry. Summing up, this review aims to demonstrate the impact of C. elegans models on the drug discovery pipeline.
Collapse
Affiliation(s)
- Sebastián Giunti
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
| | - Natalia Andersen
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
| | - Diego Rayes
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
| | - María José De Rosa
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
| |
Collapse
|
18
|
Kim ES, Chung CG, Park JH, Ko BS, Park SS, Kim YH, Cha IJ, Kim J, Ha CM, Kim HJ, Lee SB. C9orf72-associated arginine-rich dipeptide repeats induce RNA-dependent nuclear accumulation of Staufen in neurons. Hum Mol Genet 2021; 30:1084-1100. [PMID: 33783499 PMCID: PMC8188407 DOI: 10.1093/hmg/ddab089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 12/24/2022] Open
Abstract
RNA-binding proteins (RBPs) play essential roles in diverse cellular processes through post-transcriptional regulation of RNAs. The subcellular localization of RBPs is thus under tight control, the breakdown of which is associated with aberrant cytoplasmic accumulation of nuclear RBPs such as TDP-43 and FUS, well-known pathological markers for amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). Here, we report in Drosophila model for ALS/FTD that nuclear accumulation of a cytoplasmic RBP Staufen may be a new pathological feature. We found that in Drosophila C4da neurons expressing PR36, one of the arginine-rich dipeptide repeat proteins (DPRs), Staufen accumulated in the nucleus in Importin- and RNA-dependent manner. Notably, expressing Staufen with exogenous NLS—but not with mutated endogenous NLS—potentiated PR-induced dendritic defect, suggesting that nuclear-accumulated Staufen can enhance PR toxicity. PR36 expression increased Fibrillarin staining in the nucleolus, which was enhanced by heterozygous mutation of stau (stau+/−), a gene that codes Staufen. Furthermore, knockdown of fib, which codes Fibrillarin, exacerbated retinal degeneration mediated by PR toxicity, suggesting that increased amount of Fibrillarin by stau+/− is protective. stau+/− also reduced the amount of PR-induced nuclear-accumulated Staufen and mitigated retinal degeneration and rescued viability of flies expressing PR36. Taken together, our data show that nuclear accumulation of Staufen in neurons may be an important pathological feature contributing to the pathogenesis of ALS/FTD.
Collapse
Affiliation(s)
- Eun Seon Kim
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea.,Dementia research group, Korea Brain Research Institute (KBRI), Daegu 41068, Republic of Korea
| | - Chang Geon Chung
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea
| | - Jeong Hyang Park
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea
| | - Byung Su Ko
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea
| | - Sung Soon Park
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea
| | - Yoon Ha Kim
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea
| | - In Jun Cha
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea
| | - Jaekwang Kim
- Dementia research group, Korea Brain Research Institute (KBRI), Daegu 41068, Republic of Korea
| | - Chang Man Ha
- Research Division and Brain Research Core Facilities of Korea Brain Research Institute (KBRI), Daegu 41068, Republic of Korea
| | - Hyung-Jun Kim
- Dementia research group, Korea Brain Research Institute (KBRI), Daegu 41068, Republic of Korea
| | - Sung Bae Lee
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea.,Dementia research group, Korea Brain Research Institute (KBRI), Daegu 41068, Republic of Korea
| |
Collapse
|
19
|
Houri-Zeevi L, Teichman G, Gingold H, Rechavi O. Stress resets ancestral heritable small RNA responses. eLife 2021; 10:65797. [PMID: 33729152 PMCID: PMC8021399 DOI: 10.7554/elife.65797] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
Transgenerational inheritance of small RNAs challenges basic concepts of heredity. In Caenorhabditis elegans nematodes, small RNAs are transmitted across generations to establish a transgenerational memory trace of ancestral environments and distinguish self-genes from non-self-elements. Carryover of aberrant heritable small RNA responses was shown to be maladaptive and to lead to sterility. Here, we show that various types of stress (starvation, high temperatures, and high osmolarity) induce resetting of ancestral small RNA responses and a genome-wide reduction in heritable small RNA levels. We found that mutants that are defective in various stress pathways exhibit irregular RNAi inheritance dynamics even in the absence of stress. Moreover, we discovered that resetting of ancestral RNAi responses is specifically orchestrated by factors that function in the p38 MAPK pathway and the transcription factor SKN-1/Nrf2. Stress-dependent termination of small RNA inheritance could protect from run-on of environment-irrelevant heritable gene regulation.
Collapse
Affiliation(s)
- Leah Houri-Zeevi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Guy Teichman
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Hila Gingold
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
20
|
Bowling EA, Wang JH, Gong F, Wu W, Neill NJ, Kim IS, Tyagi S, Orellana M, Kurley SJ, Dominguez-Vidaña R, Chung HC, Hsu TYT, Dubrulle J, Saltzman AB, Li H, Meena JK, Canlas GM, Chamakuri S, Singh S, Simon LM, Olson CM, Dobrolecki LE, Lewis MT, Zhang B, Golding I, Rosen JM, Young DW, Malovannaya A, Stossi F, Miles G, Ellis MJ, Yu L, Buonamici S, Lin CY, Karlin KL, Zhang XHF, Westbrook TF. Spliceosome-targeted therapies trigger an antiviral immune response in triple-negative breast cancer. Cell 2021; 184:384-403.e21. [PMID: 33450205 PMCID: PMC8635244 DOI: 10.1016/j.cell.2020.12.031] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/29/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022]
Abstract
Many oncogenic insults deregulate RNA splicing, often leading to hypersensitivity of tumors to spliceosome-targeted therapies (STTs). However, the mechanisms by which STTs selectively kill cancers remain largely unknown. Herein, we discover that mis-spliced RNA itself is a molecular trigger for tumor killing through viral mimicry. In MYC-driven triple-negative breast cancer, STTs cause widespread cytoplasmic accumulation of mis-spliced mRNAs, many of which form double-stranded structures. Double-stranded RNA (dsRNA)-binding proteins recognize these endogenous dsRNAs, triggering antiviral signaling and extrinsic apoptosis. In immune-competent models of breast cancer, STTs cause tumor cell-intrinsic antiviral signaling, downstream adaptive immune signaling, and tumor cell death. Furthermore, RNA mis-splicing in human breast cancers correlates with innate and adaptive immune signatures, especially in MYC-amplified tumors that are typically immune cold. These findings indicate that dsRNA-sensing pathways respond to global aberrations of RNA splicing in cancer and provoke the hypothesis that STTs may provide unexplored strategies to activate anti-tumor immune pathways.
Collapse
Affiliation(s)
- Elizabeth A Bowling
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jarey H Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fade Gong
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - William Wu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nicholas J Neill
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ik Sun Kim
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Siddhartha Tyagi
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mayra Orellana
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah J Kurley
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rocio Dominguez-Vidaña
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hsiang-Ching Chung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tiffany Y-T Hsu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julien Dubrulle
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander B Saltzman
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Heyuan Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jitendra K Meena
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gino M Canlas
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Srinivas Chamakuri
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Swarnima Singh
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lukas M Simon
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Calla M Olson
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lacey E Dobrolecki
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael T Lewis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ido Golding
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey M Rosen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Damian W Young
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malovannaya
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - George Miles
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lihua Yu
- H3Biomedicine, Cambridge, MA 02139, USA
| | | | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kristen L Karlin
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiang H-F Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas F Westbrook
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
21
|
Durnaoglu S, Kim HS, Ahnn J, Lee SK. Human Endogenous Retrovirus K (HERV-K) can drive gene expression as a promoter in Caenorhabditis elegans. BMB Rep 2020. [PMID: 32867919 PMCID: PMC7607151 DOI: 10.5483/bmbrep.2020.53.10.150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Endogenous retroviruses (ERVs) are retrotransposons present in various metazoan genomes and have been implicated in metazoan evolution as well as in nematodes and humans. The long terminal repeat (LTR) retrotransposons contain several regulatory sequences including promoters and enhancers that regulate endogenous gene expression and thereby control organismal development and response to environmental change. ERVs including the LTR retrotransposons constitute 8% of the human genome and less than 0.6% of the Caenorhabditis elegans (C.elegans) genome, a nematode genetic model system. To investigate the evolutionarily conserved mechanism behind the transcriptional activity of retrotransposons, we generated a transgenic worm model driving green fluorescent protein (GFP) expression using Human endogenous retroviruses (HERV)-K LTR as a promoter. The promoter activity of HERV-K LTR was robust and fluorescence was observed in various tissues throughout the developmental process. Interestingly, persistent GFP expression was specifically detected in the adult vulva muscle. Using deletion constructs, we found that the region from positions 675 to 868 containing the TATA box was necessary for promoter activity driving gene expression in the vulva. Interestingly, we found that the promoter activity of the LTR was dependent on che-1 transcription factor, a sensory neuron driver, and lin-15b, a negative regulator of RNAi and germline gene expression. These results suggest evolutionary conservation of the LTR retrotransposon activity in transcriptional regulation as well as the possibility of che-1 function in non-neuronal tissues.
Collapse
Affiliation(s)
- Serpen Durnaoglu
- Department of Life Science, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea
| | - Joohong Ahnn
- Department of Life Science, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Sun-Kyung Lee
- Department of Life Science, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| |
Collapse
|
22
|
Loss of Nuclear TDP-43 Is Associated with Decondensation of LINE Retrotransposons. Cell Rep 2020; 27:1409-1421.e6. [PMID: 31042469 PMCID: PMC6508629 DOI: 10.1016/j.celrep.2019.04.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 02/14/2019] [Accepted: 03/27/2019] [Indexed: 12/13/2022] Open
Abstract
Loss of the nuclear RNA binding protein TAR DNA binding protein-43 (TDP-43) into cytoplasmic aggregates is the strongest correlate to neurodegeneration in amyotrophic lateral sclerosis and frontotemporal degeneration. The molecular changes associated with the loss of nuclear TDP-43 in human tissues are not entirely known. Using subcellular fractionation andfluorescent-activated cell sorting to enrich for diseased neuronal nuclei without TDP-43 from post-mortem frontotemporal degeneration-amyotro-phic lateral sclerosis (FTD-ALS) human brain, we characterized the effects of TDP-43 loss on the transcriptome and chromatin accessibility. Nuclear TDP-43 loss is associated with gene expression changes that affect RNA processing, nucleocytoplas-mic transport, histone processing, and DNA damage. Loss of nuclear TDP-43 is also associated with chromatin decondensation around long interspersed nuclear elements (LINEs) and increased LINE1 DNA content. Moreover, loss of TDP-43 leads to increased retrotransposition that can be inhibited with antiretro-viral drugs, suggesting that TDP-43 neuropathology is associated with altered chromatin structure including decondensation of LINEs. Liu et al. fractionated and sorted for diseased neuronal nuclei from post-mortem FTD-ALS human brains and showed that loss of an RNA-binding protein, TDP-43, altered the transcriptome and chromatin accessibility. Their results suggest that loss of nuclear TDP-43 is associated with decondensation of LINE retrotransposons.
Collapse
|
23
|
Arribere JA, Kuroyanagi H, Hundley HA. mRNA Editing, Processing and Quality Control in Caenorhabditis elegans. Genetics 2020; 215:531-568. [PMID: 32632025 PMCID: PMC7337075 DOI: 10.1534/genetics.119.301807] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 05/03/2020] [Indexed: 02/06/2023] Open
Abstract
While DNA serves as the blueprint of life, the distinct functions of each cell are determined by the dynamic expression of genes from the static genome. The amount and specific sequences of RNAs expressed in a given cell involves a number of regulated processes including RNA synthesis (transcription), processing, splicing, modification, polyadenylation, stability, translation, and degradation. As errors during mRNA production can create gene products that are deleterious to the organism, quality control mechanisms exist to survey and remove errors in mRNA expression and processing. Here, we will provide an overview of mRNA processing and quality control mechanisms that occur in Caenorhabditis elegans, with a focus on those that occur on protein-coding genes after transcription initiation. In addition, we will describe the genetic and technical approaches that have allowed studies in C. elegans to reveal important mechanistic insight into these processes.
Collapse
Affiliation(s)
| | - Hidehito Kuroyanagi
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan, and
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Indiana 47405
| |
Collapse
|
24
|
Nguyen TM, Kabotyanski EB, Reineke LC, Shao J, Xiong F, Lee JH, Dubrulle J, Johnson H, Stossi F, Tsoi PS, Choi KJ, Ellis AG, Zhao N, Cao J, Adewunmi O, Ferreon JC, Ferreon ACM, Neilson JR, Mancini MA, Chen X, Kim J, Ma L, Li W, Rosen JM. The SINEB1 element in the long non-coding RNA Malat1 is necessary for TDP-43 proteostasis. Nucleic Acids Res 2020; 48:2621-2642. [PMID: 31863590 PMCID: PMC7049706 DOI: 10.1093/nar/gkz1176] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 01/12/2023] Open
Abstract
Transposable elements (TEs) comprise a large proportion of long non-coding RNAs (lncRNAs). Here, we employed CRISPR to delete a short interspersed nuclear element (SINE) in Malat1, a cancer-associated lncRNA, to investigate its significance in cellular physiology. We show that Malat1 with a SINE deletion forms diffuse nuclear speckles and is frequently translocated to the cytoplasm. SINE-deleted cells exhibit an activated unfolded protein response and PKR and markedly increased DNA damage and apoptosis caused by dysregulation of TDP-43 localization and formation of cytotoxic inclusions. TDP-43 binds stronger to Malat1 without the SINE and is likely 'hijacked' by cytoplasmic Malat1 to the cytoplasm, resulting in the depletion of nuclear TDP-43 and redistribution of TDP-43 binding to repetitive element transcripts and mRNAs encoding mitotic and nuclear-cytoplasmic regulators. The SINE promotes Malat1 nuclear retention by facilitating Malat1 binding to HNRNPK, a protein that drives RNA nuclear retention, potentially through direct interactions of the SINE with KHDRBS1 and TRA2A, which bind to HNRNPK. Losing these RNA-protein interactions due to the SINE deletion likely creates more available TDP-43 binding sites on Malat1 and subsequent TDP-43 aggregation. These results highlight the significance of lncRNA TEs in TDP-43 proteostasis with potential implications in both cancer and neurodegenerative diseases.
Collapse
Affiliation(s)
- Tuan M Nguyen
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Elena B Kabotyanski
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lucas C Reineke
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiaofang Shao
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX 77030, USA
| | - Feng Xiong
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX 77030, USA
| | - Joo-Hyung Lee
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX 77030, USA
| | - Julien Dubrulle
- Integrated Microscopy Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hannah Johnson
- Integrated Microscopy Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fabio Stossi
- Integrated Microscopy Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Phoebe S Tsoi
- Department of Pharmacology and Chemical Biology, Houston, TX 77030, USA
| | - Kyoung-Jae Choi
- Department of Pharmacology and Chemical Biology, Houston, TX 77030, USA
| | - Alexander G Ellis
- Michael E. DeBakey High School for Health Professions, Houston, TX 77030, USA
| | - Na Zhao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jin Cao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Oluwatoyosi Adewunmi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Joel R Neilson
- Department of Molecular Physiology and Biophysics, Houston, TX 77030, USA
| | - Michael A Mancini
- Integrated Microscopy Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xi Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jongchan Kim
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX 77030, USA
| | - Jeffrey M Rosen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
25
|
Tam OH, Rozhkov NV, Shaw R, Kim D, Hubbard I, Fennessey S, Propp N, Fagegaltier D, Harris BT, Ostrow LW, Phatnani H, Ravits J, Dubnau J, Gale Hammell M. Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia. Cell Rep 2019; 29:1164-1177.e5. [PMID: 31665631 PMCID: PMC6866666 DOI: 10.1016/j.celrep.2019.09.066] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/03/2019] [Accepted: 09/20/2019] [Indexed: 12/14/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive loss of motor neurons. While several pathogenic mutations have been identified, the vast majority of ALS cases have no family history of disease. Thus, for most ALS cases, the disease may be a product of multiple pathways contributing to varying degrees in each patient. Using machine learning algorithms, we stratify the transcriptomes of 148 ALS postmortem cortex samples into three distinct molecular subtypes. The largest cluster, identified in 61% of patient samples, displays hallmarks of oxidative and proteotoxic stress. Another 19% of the samples shows predominant signatures of glial activation. Finally, a third group (20%) exhibits high levels of retrotransposon expression and signatures of TARDBP/TDP-43 dysfunction. We further demonstrate that TDP-43 (1) directly binds a subset of retrotransposon transcripts and contributes to their silencing in vitro, and (2) pathological TDP-43 aggregation correlates with retrotransposon de-silencing in vivo.
Collapse
Affiliation(s)
- Oliver H Tam
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Regina Shaw
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Duyang Kim
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
| | - Isabel Hubbard
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
| | - Samantha Fennessey
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
| | - Nadia Propp
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
| | - Delphine Fagegaltier
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
| | - Brent T Harris
- The NYGC ALS Consortium; Department of Neurology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Lyle W Ostrow
- The NYGC ALS Consortium; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA; The NYGC ALS Consortium
| | - John Ravits
- The NYGC ALS Consortium; Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Josh Dubnau
- The NYGC ALS Consortium; Department of Anesthesiology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY 11794, USA
| | - Molly Gale Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; The NYGC ALS Consortium.
| |
Collapse
|
26
|
TDP-43 regulates transcription at protein-coding genes and Alu retrotransposons. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194434. [PMID: 31655156 DOI: 10.1016/j.bbagrm.2019.194434] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022]
Abstract
The 43-kDa transactive response DNA-binding protein (TDP-43) is an example of an RNA-binding protein that regulates RNA metabolism at multiple levels from transcription and splicing to translation. Its role in post-transcriptional RNA processing has been a primary focus of recent research, but its role in regulating transcription has been studied for only a few human genes. We characterized the effects of TDP-43 on transcription genome-wide and found that TDP-43 broadly affects transcription of protein-coding and noncoding RNA genes. Among protein-coding genes, the effects of TDP-43 were greatest for genes <30 thousand base pairs in length. Surprisingly, we found that the loss of TDP-43 resulted in increased evidence for transcription activity near repetitive Alu elements found within expressed genes. The highest densities of affected Alu elements were found in the shorter genes, whose transcription was most affected by TDP-43. Thus, in addition to its role in post-transcriptional RNA processing, TDP-43 plays a critical role in maintaining the transcriptional stability of protein-coding genes and transposable DNA elements.
Collapse
|
27
|
Chang YH, Dubnau J. The Gypsy Endogenous Retrovirus Drives Non-Cell-Autonomous Propagation in a Drosophila TDP-43 Model of Neurodegeneration. Curr Biol 2019; 29:3135-3152.e4. [PMID: 31495585 PMCID: PMC6783360 DOI: 10.1016/j.cub.2019.07.071] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/11/2019] [Accepted: 07/23/2019] [Indexed: 12/16/2022]
Abstract
A hallmark of neurodegenerative disease is focal onset of pathological protein aggregation, followed by progressive spread of pathology to connected brain regions. In amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), pathology is often associated with aggregation of TAR DNA-binding protein 43 (TDP-43). Although aggregated TDP-43 protein moves between cells, it is not clear whether and how this movement propagates the degeneration. Here, we have established a Drosophila model of human TDP-43 in which we initiated toxic expression of human TDP-43 focally within small groups of glial cells. We found that this focal onset kills adjacent neurons. Surprisingly, we show that this spreading death is caused by an endogenous retrovirus within the glia, which leads to DNA damage and death in adjacent neurons. These findings suggest a possible mechanism by which human retroviruses such as HERV-K might contribute to TDP-43-mediated propagation of neurodegeneration.
Collapse
Affiliation(s)
- Yung-Heng Chang
- Department of Anesthesiology, Stony Brook School of Medicine, NY 11794, USA
| | - Josh Dubnau
- Department of Anesthesiology, Stony Brook School of Medicine, NY 11794, USA; Department of Neurobiology and Behavior, Stony Brook University, NY 11794, USA.
| |
Collapse
|
28
|
RNase L Reprograms Translation by Widespread mRNA Turnover Escaped by Antiviral mRNAs. Mol Cell 2019; 75:1203-1217.e5. [PMID: 31494035 DOI: 10.1016/j.molcel.2019.07.029] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/13/2019] [Accepted: 07/18/2019] [Indexed: 12/27/2022]
Abstract
In response to foreign and endogenous double-stranded RNA (dsRNA), protein kinase R (PKR) and ribonuclease L (RNase L) reprogram translation in mammalian cells. PKR inhibits translation initiation through eIF2α phosphorylation, which triggers stress granule (SG) formation and promotes translation of stress responsive mRNAs. The mechanisms of RNase L-driven translation repression, its contribution to SG assembly, and its regulation of dsRNA stress-induced mRNAs are unknown. We demonstrate that RNase L drives translational shut-off in response to dsRNA by promoting widespread turnover of mRNAs. This alters stress granule assembly and reprograms translation by allowing translation of mRNAs resistant to RNase L degradation, including numerous antiviral mRNAs such as interferon (IFN)-β. Individual cells differentially activate dsRNA responses revealing variation that can affect cellular outcomes. This identifies bulk mRNA degradation and the resistance of antiviral mRNAs as the mechanism by which RNase L reprograms translation in response to dsRNA.
Collapse
|
29
|
TDP-43 knockdown causes innate immune activation via protein kinase R in astrocytes. Neurobiol Dis 2019; 132:104514. [PMID: 31229690 DOI: 10.1016/j.nbd.2019.104514] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/26/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022] Open
Abstract
TAR-DNA binding protein 43 (TDP-43) is a multifunctional RNA binding protein directly implicated in the etiology of amyotrophic lateral sclerosis (ALS). Previous studies have demonstrated that loss of TDP-43 function leads to intracellular accumulation of non-coding repetitive element transcripts and double-stranded RNA (dsRNA). These events could cause immune activation and contribute to the neuroinflammation observed in ALS, but this possibility has not been investigated. Here, we knock down TDP-43 in primary rat astrocytes via siRNA, and we use RNA-seq, immunofluorescence, and immunoblotting to show that this results in: 1) accumulation of repetitive element transcripts and dsRNA; and 2) pro-inflammatory gene and protein expression consistent with innate immune signaling and astrocyte activation. We also show that both chemical inhibition and siRNA knockdown of protein kinase R (PKR), a dsRNA-activated kinase implicated in the innate immune response, block the expression of all activation markers assayed. Based on these findings, we suggest that intracellular accumulation of endogenous dsRNA may be a novel and important mechanism underlying the pathogenesis of ALS (and perhaps other neurodegenerative diseases), and that PKR inhibitors may have the potential to prevent reactive astrocytosis in ALS.
Collapse
|
30
|
Campbell AE, Belleville AE, Resnick R, Shadle SC, Tapscott SJ. Facioscapulohumeral dystrophy: activating an early embryonic transcriptional program in human skeletal muscle. Hum Mol Genet 2019; 27:R153-R162. [PMID: 29718206 DOI: 10.1093/hmg/ddy162] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 04/27/2018] [Indexed: 12/12/2022] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is the third most prevalent muscular dystrophy. A progressive disease, it presents clinically as weakness and wasting of the face, shoulder and upper arm muscles, with later involvement of the trunk and lower extremities. FSHD develops through complex genetic and epigenetic events that converge on a common mechanism of toxicity with mis-expression of the transcription factor double homeobox 4 (DUX4). There is currently no treatment available for FSHD. However, the consensus that ectopic DUX4 expression in skeletal muscle is the root cause of FSHD pathophysiology has allowed research efforts to turn toward cultivating a deeper understanding of DUX4 biology and the pathways that underlie FSHD muscle pathology, and to translational studies aimed at developing targeted therapeutics using ever more sophisticated cell and animal-based models of FSHD. This review summarizes recent advances in our understanding of FSHD, including the regulation and activity of DUX4 in its normal developmental roles as well as its pathological contexts. We highlight how these advances raise new questions and challenges for the field as it moves into the next decade of FSHD research.
Collapse
Affiliation(s)
- Amy E Campbell
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrea E Belleville
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rebecca Resnick
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.,Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Sean C Shadle
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Stephen J Tapscott
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Neurology, University of Washington, Seattle, WA, USA
| |
Collapse
|
31
|
Van Treeck B, Parker R. Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies. Cell 2019; 174:791-802. [PMID: 30096311 DOI: 10.1016/j.cell.2018.07.023] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/05/2018] [Accepted: 07/20/2018] [Indexed: 12/22/2022]
Abstract
Eukaryotic cells contain large assemblies of RNA and protein, referred to as ribonucleoprotein (RNP) granules, which include cytoplasmic P-bodies, stress granules, and neuronal and germinal granules, as well as nuclear paraspeckles, Cajal bodies, and RNA foci formed from repeat expansion RNAs. Recent evidence argues that intermolecular RNA-RNA interactions play a role in forming and determining the composition of certain RNP granules. We hypothesize that intermolecular RNA-RNA interactions are favored in cells yet are limited by RNA-binding proteins, helicases, and ribosomes, thereby allowing normal RNA function. An over-abundance of intermolecular RNA-RNA interactions may be toxic since perturbations that increase RNA-RNA interactions such as long repeat expansion RNAs, arginine-containing dipeptide repeat polypeptides, and sequestration or loss of abundant RNA-binding proteins can contribute to degenerative diseases.
Collapse
Affiliation(s)
- Briana Van Treeck
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA.
| |
Collapse
|
32
|
Melnick M, Gonzales P, Cabral J, Allen MA, Dowell RD, Link CD. Heat shock in C. elegans induces downstream of gene transcription and accumulation of double-stranded RNA. PLoS One 2019; 14:e0206715. [PMID: 30958820 PMCID: PMC6453478 DOI: 10.1371/journal.pone.0206715] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/25/2019] [Indexed: 12/14/2022] Open
Abstract
We observed that heat shock of Caenorhabditis elegans leads to the formation of nuclear double-stranded RNA (dsRNA) foci, detectable with a dsRNA-specific monoclonal antibody. These foci significantly overlap with nuclear HSF-1 granules. To investigate the molecular mechanism(s) underlying dsRNA foci formation, we used RNA-seq to globally characterize total RNA and immunoprecipitated dsRNA from control and heat shocked worms. We find a subset of both sense and antisense transcripts enriched in the dsRNA pool by heat shock overlap with dsRNA transcripts enriched by deletion of tdp-1, which encodes the C. elegans ortholog of TDP-43. Interestingly, transcripts involved in translation are over-represented in the dsRNAs induced by either heat shock or deletion of tdp-1. Also enriched in the dsRNA transcripts are sequences downstream of annotated genes (DoGs), which we globally quantified with a new algorithm. To validate these observations, we used fluorescence in situ hybridization (FISH) to confirm both antisense and downstream of gene transcription for eif-3.B, one of the affected loci we identified.
Collapse
Affiliation(s)
- Marko Melnick
- Integrative Physiology, University of Colorado, Boulder, Colorado, United States of America
| | - Patrick Gonzales
- Integrative Physiology, University of Colorado, Boulder, Colorado, United States of America
| | - Joseph Cabral
- Integrative Physiology, University of Colorado, Boulder, Colorado, United States of America
| | - Mary A. Allen
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
| | - Robin D. Dowell
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Christopher D. Link
- Integrative Physiology, University of Colorado, Boulder, Colorado, United States of America
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, United States of America
| |
Collapse
|
33
|
Abstract
Long double-stranded RNAs (dsRNAs) are abundantly expressed in animals, in which they frequently occur in introns and 3' untranslated regions of mRNAs. Functions of long, cellular dsRNAs are poorly understood, although deficiencies in adenosine deaminases that act on RNA, or ADARs, promote their recognition as viral dsRNA and an aberrant immune response. Diverse dsRNA-binding proteins bind cellular dsRNAs, hinting at additional roles. Understanding these roles is facilitated by mapping the genomic locations that express dsRNA in various tissues and organisms. ADAR editing provides a signature of dsRNA structure in cellular transcripts. In this review, we detail approaches to map ADAR editing sites and dsRNAs genome-wide, with particular focus on high-throughput sequencing methods and considerations for their successful application to the detection of editing sites and dsRNAs.
Collapse
Affiliation(s)
- Daniel P Reich
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112
| | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112
| |
Collapse
|
34
|
Zhang YJ, Guo L, Gonzales PK, Gendron TF, Wu Y, Jansen-West K, O'Raw AD, Pickles SR, Prudencio M, Carlomagno Y, Gachechiladze MA, Ludwig C, Tian R, Chew J, DeTure M, Lin WL, Tong J, Daughrity LM, Yue M, Song Y, Andersen JW, Castanedes-Casey M, Kurti A, Datta A, Antognetti G, McCampbell A, Rademakers R, Oskarsson B, Dickson DW, Kampmann M, Ward ME, Fryer JD, Link CD, Shorter J, Petrucelli L. Heterochromatin anomalies and double-stranded RNA accumulation underlie C9orf72 poly(PR) toxicity. Science 2019; 363:eaav2606. [PMID: 30765536 PMCID: PMC6524780 DOI: 10.1126/science.aav2606] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/07/2018] [Accepted: 01/14/2019] [Indexed: 12/12/2022]
Abstract
How hexanucleotide GGGGCC (G4C2) repeat expansions in C9orf72 cause frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) is not understood. We developed a mouse model engineered to express poly(PR), a proline-arginine (PR) dipeptide repeat protein synthesized from expanded G4C2 repeats. The expression of green fluorescent protein-conjugated (PR)50 (a 50-repeat PR protein) throughout the mouse brain yielded progressive brain atrophy, neuron loss, loss of poly(PR)-positive cells, and gliosis, culminating in motor and memory impairments. We found that poly(PR) bound DNA, localized to heterochromatin, and caused heterochromatin protein 1α (HP1α) liquid-phase disruptions, decreases in HP1α expression, abnormal histone methylation, and nuclear lamina invaginations. These aberrations of histone methylation, lamins, and HP1α, which regulate heterochromatin structure and gene expression, were accompanied by repetitive element expression and double-stranded RNA accumulation. Thus, we uncovered mechanisms by which poly(PR) may contribute to the pathogenesis of C9orf72-associated FTD and ALS.
Collapse
Affiliation(s)
- Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Lin Guo
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrick K Gonzales
- Department of Integrative Physiology, Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Yanwei Wu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Aliesha D O'Raw
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Sarah R Pickles
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Yari Carlomagno
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Mariam A Gachechiladze
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Connor Ludwig
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, and Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ruilin Tian
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, and Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jeannie Chew
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Michael DeTure
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Wen-Lang Lin
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Jimei Tong
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Mei Yue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yuping Song
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Aishe Kurti
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | | | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, and Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - John D Fryer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Christopher D Link
- Department of Integrative Physiology, Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| |
Collapse
|
35
|
Saldi TK, Gonzales PK, LaRocca TJ, Link CD. Neurodegeneration, Heterochromatin, and Double-Stranded RNA. J Exp Neurosci 2019; 13:1179069519830697. [PMID: 30792577 PMCID: PMC6376497 DOI: 10.1177/1179069519830697] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/23/2019] [Indexed: 12/15/2022] Open
Abstract
Changes in chromatin and epigenetic modifications have been associated with aging and aging-associated neurodegenerative diseases, although the causal relationship between these changes and disease-related pathology has been unclear. Recent studies have now made direct connections between neurodegeneration-associated proteins and derepression of repetitive element transcription due to changes in heterochromatin. We suggest that this derepression leads to an increased accumulation of intracellular double-stranded RNA (dsRNA), with an attendant induction of innate immune responses that contribute to the neuroinflammation found in essentially all age-associated neurodegenerative diseases.
Collapse
Affiliation(s)
- Tassa K Saldi
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, USA
| | - Patrick K Gonzales
- Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Thomas J LaRocca
- Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Christopher D Link
- Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| |
Collapse
|
36
|
Reich DP, Bass BL. Inverted repeat structures are associated with essential and highly expressed genes on C. elegans autosome distal arms. RNA (NEW YORK, N.Y.) 2018; 24:1634-1646. [PMID: 30190375 PMCID: PMC6239182 DOI: 10.1261/rna.067405.118] [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] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
Complementary sequences in cellular transcripts base-pair to form double-stranded RNA (dsRNA) structures. Because transposon-derived repeats often give rise to self-complementary sequences, dsRNA structures are prevalent in eukaryotic genomes, typically occurring in gene introns and untranslated regions (UTRs). However, the regulatory impact of double-stranded structures within genes is not fully understood. We used three independent methods to define loci in Caenorhabditis elegans predicted to form dsRNA and correlated these structures with patterns of gene expression, gene essentiality, and genome organization. As previously observed, dsRNA loci are enriched on distal arms of C. elegans autosomes, where genes typically show less conservation and lower overall expression. In contrast, we find that dsRNAs are associated with essential genes on autosome arms, and dsRNA-associated genes exhibit higher-than-expected expression and histone modification patterns associated with transcriptional elongation. Genes with significant repetitive sequence content are also highly expressed, and, thus, observed gene expression trends may relate either to dsRNA structures or to repeat content. Our results raise the possibility that as-yet-undescribed mechanisms promote expression of loci that produce dsRNAs, despite their well-characterized roles in gene silencing.
Collapse
Affiliation(s)
- Daniel P Reich
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
| |
Collapse
|
37
|
Saldi TK, Gonzales P, Garrido-Lecca A, Dostal V, Roberts CM, Petrucelli L, Link CD. The Caenorhabditis elegans Ortholog of TDP-43 Regulates the Chromatin Localization of the Heterochromatin Protein 1 Homolog HPL-2. Mol Cell Biol 2018; 38:e00668-17. [PMID: 29760282 PMCID: PMC6048318 DOI: 10.1128/mcb.00668-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/04/2018] [Accepted: 05/01/2018] [Indexed: 12/13/2022] Open
Abstract
TDP-1 is the Caenorhabditis elegans ortholog of mammalian TDP-43, which is strongly implicated in the etiology of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). We discovered that deletion of the tdp-1 gene results in enhanced nuclear RNA interference (RNAi). As nuclear RNAi in C. elegans involves chromatin changes moderated by HPL-2, a homolog of heterochromatin protein 1 (HP1), we investigated the interaction of TDP-1 and HPL-2. We found that TDP-1 and HPL-2 interact directly and that loss of TDP-1 dramatically alters the chromatin association of HPL-2. We showed previously that deletion of the tdp-1 gene results in transcriptional alterations and the accumulation of double-stranded RNA (dsRNA). These molecular changes are replicated in an hpl-2 deletion strain, consistent with HPL-2 acting in consort with TDP-1 to modulate these aspects of RNA metabolism. Our observations identify novel mechanisms by which HP1 homologs can be recruited to chromatin and by which nuclear depletion of human TDP-43 may lead to changes in RNA metabolism that are relevant to disease.
Collapse
Affiliation(s)
- Tassa K Saldi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Patrick Gonzales
- Integrative Physiology, University of Colorado, Boulder, Colorado, USA
| | - Alfonso Garrido-Lecca
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Vishantie Dostal
- Integrative Physiology, University of Colorado, Boulder, Colorado, USA
| | | | | | - Christopher D Link
- Integrative Physiology, University of Colorado, Boulder, Colorado, USA
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA
| |
Collapse
|
38
|
Guo C, Jeong HH, Hsieh YC, Klein HU, Bennett DA, De Jager PL, Liu Z, Shulman JM. Tau Activates Transposable Elements in Alzheimer's Disease. Cell Rep 2018; 23:2874-2880. [PMID: 29874575 PMCID: PMC6181645 DOI: 10.1016/j.celrep.2018.05.004] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 03/19/2018] [Accepted: 05/01/2018] [Indexed: 02/06/2023] Open
Abstract
Aging and neurodegenerative disease are characterized by genomic instability in neurons, including aberrant activation and mobilization of transposable elements (TEs). Integrating studies of human postmortem brain tissue and Drosophila melanogaster models, we investigate TE activation in association with Tau pathology in Alzheimer's disease (AD). Leveraging RNA sequencing from 636 human brains, we discover differential expression for several retrotransposons in association with neurofibrillary tangle burden and highlight evidence for global TE transcriptional activation among the long interspersed nuclear element 1 and endogenous retrovirus clades. In addition, we detect Tau-associated, active chromatin signatures at multiple HERV-Fc1 genomic loci. To determine whether Tau is sufficient to induce TE activation, we profile retrotransposons in Drosophila expressing human wild-type or mutant Tau throughout the brain. We discover heterogeneous response profiles, including both age- and genotype-dependent activation of TE expression by Tau. Our results implicate TE activation and associated genomic instability in Tau-mediated AD mechanisms.
Collapse
Affiliation(s)
- Caiwei Guo
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurologic Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Hyun-Hwan Jeong
- Jan and Dan Duncan Neurologic Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi-Chen Hsieh
- Jan and Dan Duncan Neurologic Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hans-Ulrich Klein
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA; Cell Circuits Program, Broad Institute, Cambridge, MA 02142, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA; Cell Circuits Program, Broad Institute, Cambridge, MA 02142, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurologic Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joshua M Shulman
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurologic Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
39
|
Shelkovnikova TA, Kukharsky MS, An H, Dimasi P, Alexeeva S, Shabir O, Heath PR, Buchman VL. Protective paraspeckle hyper-assembly downstream of TDP-43 loss of function in amyotrophic lateral sclerosis. Mol Neurodegener 2018; 13:30. [PMID: 29859124 PMCID: PMC5984788 DOI: 10.1186/s13024-018-0263-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/25/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Paraspeckles are subnuclear bodies assembled on a long non-coding RNA (lncRNA) NEAT1. Their enhanced formation in spinal neurons of sporadic amyotrophic lateral sclerosis (ALS) patients has been reported but underlying mechanisms are unknown. The majority of ALS cases are characterized by TDP-43 proteinopathy. In current study we aimed to establish whether and how TDP-43 pathology may augment paraspeckle assembly. METHODS Paraspeckle formation in human samples was analysed by RNA-FISH and laser capture microdissection followed by qRT-PCR. Mechanistic studies were performed in stable cell lines, mouse primary neurons and human embryonic stem cell-derived neurons. Loss and gain of function for TDP-43 and other microRNA pathway factors were modelled by siRNA-mediated knockdown and protein overexpression. RESULTS We show that de novo paraspeckle assembly in spinal neurons and glial cells is a hallmark of both sporadic and familial ALS with TDP-43 pathology. Mechanistically, loss of TDP-43 but not its cytoplasmic accumulation or aggregation augments paraspeckle assembly in cultured cells. TDP-43 is a component of the microRNA machinery, and recently, paraspeckles have been shown to regulate pri-miRNA processing. Consistently, downregulation of core protein components of the miRNA pathway also promotes paraspeckle assembly. In addition, depletion of these proteins or TDP-43 results in accumulation of endogenous dsRNA and activation of type I interferon response which also stimulates paraspeckle formation. We demonstrate that human or mouse neurons in vitro lack paraspeckles, but a synthetic dsRNA is able to trigger their de novo formation. Finally, paraspeckles are protective in cells with compromised microRNA/dsRNA metabolism, and their assembly can be promoted by a small-molecule microRNA enhancer. CONCLUSIONS Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA.
Collapse
Affiliation(s)
| | - Michail S Kukharsky
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.,Institute of Physiologically Active Compounds Russian Academy of Sciences, 1 Severniy proezd, Chernogolovka, Moscow Region, Russian Federation, 142432
| | - Haiyan An
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Pasquale Dimasi
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Svetlana Alexeeva
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Osman Shabir
- The Sheffield Institute for Translational Neuroscience, 385A Glossop Road, Sheffield, S10 2HQ, UK
| | - Paul R Heath
- The Sheffield Institute for Translational Neuroscience, 385A Glossop Road, Sheffield, S10 2HQ, UK
| | - Vladimir L Buchman
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.,Institute of Physiologically Active Compounds Russian Academy of Sciences, 1 Severniy proezd, Chernogolovka, Moscow Region, Russian Federation, 142432
| |
Collapse
|
40
|
Krestel H, Meier JC. RNA Editing and Retrotransposons in Neurology. Front Mol Neurosci 2018; 11:163. [PMID: 29875629 PMCID: PMC5974252 DOI: 10.3389/fnmol.2018.00163] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/30/2018] [Indexed: 12/28/2022] Open
Abstract
Compared to sites in protein-coding sequences many more targets undergoing adenosine to inosine (A-to-I) RNA editing were discovered in non-coding regions of human cerebral transcripts, particularly in genetic transposable elements called retrotransposons. We review here the interaction mechanisms of RNA editing and retrotransposons and their impact on normal function and human neurological diseases. Exemplarily, A-to-I editing of retrotransposons embedded in protein-coding mRNAs can contribute to protein abundance and function via circular RNA formation, alternative splicing, and exonization or silencing of retrotransposons. Interactions leading to disease are not very well understood. We describe human diseases with involvement of the central nervous system including inborn errors of metabolism, neurodevelopmental disorders, neuroinflammatory and neurodegenerative and paroxysmal diseases, in which retrotransposons (Alu and/or L1 elements) appear to be causally involved in genetic rearrangements. Sole binding of single-stranded retrotransposon transcripts by RNA editing enzymes rather than enzymatic deamination may have a homeostatic effect on retrotransposon turnover. We also review evidence in support of the emerging pathophysiological function of A-to-I editing of retrotransposons in inflammation and its implication for different neurological diseases including amyotrophic lateral sclerosis, frontotemporal dementia, Alzheimer's and Parkinson's disease, and epilepsy.
Collapse
Affiliation(s)
- Heinz Krestel
- Department of Neurology, Bern University Hospital and University of Bern, Bern, Switzerland.,Department for BioMedical Research, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Jochen C Meier
- Division Cell Physiology, Zoological Institute, Technical University Braunschweig, Braunschweig, Germany
| |
Collapse
|
41
|
Dubnau J. The Retrotransposon storm and the dangers of a Collyer's genome. Curr Opin Genet Dev 2018; 49:95-105. [PMID: 29705598 PMCID: PMC5975205 DOI: 10.1016/j.gde.2018.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/08/2018] [Accepted: 04/11/2018] [Indexed: 12/13/2022]
Abstract
Like the famous Collyer's mansion in NY, our genomes have accumulated vast quantities of sequences that have been referred to as 'junk DNA,' much of which consists of retrotransposons (RTEs). A recent literature establishes the phenomenology that many RTEs become expressed at progressively higher levels during the course of normal aging. This seems to reflect gradual loss of heterochromatin in old age. In addition, RTEs appear to be precociously expressed in brains of younger animals that are experiencing neurodegenerative decline. Although it is difficult to distinguish cause from consequence, several recent studies support the contention that RTE expression, and even perhaps transposition, causally contribute to both the normal deterioration seen with age and to the precipitous decline in some neurodegenerative disorders. This may reflect a two hit model in which normal age-dependent loss of heterochromatin synergizes with a disruption to posttranscriptional silencing of RTEs caused by genetic and environmental stress.
Collapse
Affiliation(s)
- Josh Dubnau
- Department of Anesthesiology, State University of New York at Stony Brook, Stony Brook, NY 11794-8480, United States; Department of Neurobiology & Behavior, Stony Brook University & Stony Brook School of Medicine, Stony Brook, NY 11794-8480, United States.
| |
Collapse
|
42
|
RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome. Proc Natl Acad Sci U S A 2018; 115:2734-2739. [PMID: 29483269 DOI: 10.1073/pnas.1800038115] [Citation(s) in RCA: 309] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Stress granules are higher order assemblies of nontranslating mRNAs and proteins that form when translation initiation is inhibited. Stress granules are thought to form by protein-protein interactions of RNA-binding proteins. We demonstrate RNA homopolymers or purified cellular RNA forms assemblies in vitro analogous to stress granules. Remarkably, under conditions representative of an intracellular stress response, the mRNAs enriched in assemblies from total yeast RNA largely recapitulate the stress granule transcriptome. We suggest stress granules are formed by a summation of protein-protein and RNA-RNA interactions, with RNA self-assembly likely to contribute to other RNP assemblies wherever there is a high local concentration of RNA. RNA assembly in vitro is also increased by GR and PR dipeptide repeats, which are known to increase stress granule formation in cells. Since GR and PR dipeptides are involved in neurodegenerative diseases, this suggests that perturbations increasing RNA-RNA assembly in cells could lead to disease.
Collapse
|
43
|
Biology and Pathobiology of TDP-43 and Emergent Therapeutic Strategies. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a024554. [PMID: 27920024 DOI: 10.1101/cshperspect.a024554] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cytoplasmic TDP-43 mislocalization and aggregation is a pathological hallmark of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. TDP-43 is an RNA-binding protein (RBP) with a prion-like domain (PrLD) that promotes TDP-43 misfolding. PrLDs possess compositional similarity to canonical prion domains of various yeast proteins, including Sup35. Strikingly, disease-causing TDP-43 mutations reside almost exclusively in the PrLD and can enhance TDP-43 misfolding and toxicity. Another ∼70 human RBPs harbor PrLDs, including FUS, TAF15, EWSR1, hnRNPA1, and hnRNPA2, which have surfaced in the etiology of neurodegenerative diseases. Importantly, PrLDs enable RBP function and mediate phase transitions that partition functional ribonucleoprotein compartments. This PrLD activity, however, renders RBPs prone to populating deleterious oligomers or self-templating fibrils that might spread disease, and disease-linked PrLD mutations can exacerbate this risk. Several strategies have emerged to counter TDP-43 proteinopathies, including engineering enhanced protein disaggregases based on Hsp104.
Collapse
|
44
|
McKerrow WH, Savva YA, Rezaei A, Reenan RA, Lawrence CE. Predicting RNA hyper-editing with a novel tool when unambiguous alignment is impossible. BMC Genomics 2017; 18:522. [PMID: 28693467 PMCID: PMC5502491 DOI: 10.1186/s12864-017-3898-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/22/2017] [Indexed: 12/13/2022] Open
Abstract
Background Repetitive elements are now known to have relevant cellular functions, including self-complementary sequences that form double stranded (ds) RNA. There are numerous pathways that determine the fate of endogenous dsRNA, and misregulation of endogenous dsRNA is a driver of autoimmune disease, particularly in the brain. Unfortunately, the alignment of high-throughput, short-read sequences to repeat elements poses a dilemma: Such sequences may align equally well to multiple genomic locations. In order to differentiate repeat elements, current alignment methods depend on sequence variation in the reference genome. Reads are discarded when no such variations are present. However, RNA hyper-editing, a possible fate for dsRNA, introduces enough variation to distinguish between repeats that are otherwise identical. Results To take advantage of this variation, we developed a new algorithm, RepProfile, that simultaneously aligns reads and predicts novel variations. RepProfile accurately aligns hyper-edited reads that other methods discard. In particular we predict hyper-editing of Drosophila melanogaster repeat elements in vivo at levels previously described only in vitro, and provide validation by Sanger sequencing sixty-two individual cloned sequences. We find that hyper-editing is concentrated in genes involved in cell-cell communication at the synapse, including some that are associated with neurodegeneration. We also find that hyper-editing tends to occur in short runs. Conclusions Previous studies of RNA hyper-editing discarded ambiguously aligned reads, ignoring hyper-editing in long, perfect dsRNA – the perfect substrate for hyper-editing. We provide a method that simulation and Sanger validation show accurately predicts such RNA editing, yielding a superior picture of hyper-editing. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3898-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Wilson H McKerrow
- Division of Applied Mathematics, Brown University, Providence, 02912, RI, USA.
| | - Yiannis A Savva
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, 02912, RI, USA
| | - Ali Rezaei
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, 02912, RI, USA
| | - Robert A Reenan
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, 02912, RI, USA
| | - Charles E Lawrence
- Division of Applied Mathematics, Brown University, Providence, 02912, RI, USA
| |
Collapse
|
45
|
Medina J, Charvet B, Leblanc P, Germi R, Horvat B, Marche PN, Perron H. [Endogenous retroviral sequences in the human genome can play a physiological or pathological role]. Med Sci (Paris) 2017; 33:397-403. [PMID: 28497735 DOI: 10.1051/medsci/20173304009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Human endogenous retroviruses (HERV) represent a large part of our genome and the few elements that have retained a potential of expression still remain "dormant" in physiological conditions. In some instances, they can be awakened by environmental factors activating their expression. The best studied conditions of HERV activation are infections caused by microorganisms such as viruses of the Herpesvirus family. This activation can thus lead to the expression of pathogenic proteins such as envelope proteins belonging to the HERV-W and HERV-K families, respectively involved in Multiple Sclerosis (MS) and amyotrophic lateral sclerosis (ALS). Endogenous retroviral proteins can also acquire a physiological function beneficial for humans. This is the case of Syncytin-1 from the HERV-W family, that is involved in placenta formation.
Collapse
Affiliation(s)
- Julie Medina
- GeNeuro Innovation, Bioparc Laënnec, 60, avenue Rockefeller, 69008 Lyon, France
| | - Benjamin Charvet
- CIRI, Centre International de Recherche en Infectiologie; - Inserm, U1111, Lyon, France - CNRS, UMR5308, Lyon, France - Université Lyon-1, Faculté de Médecine Laënnec, 69008 Lyon, France - Institut NeuroMyogène (INMG), CNRS UMR5310, Inserm U1217, LBMC, École Normale Supérieure de Lyon, France - Laboratoire d'Excellence ECOFECT, Lyon, France
| | - Pascal Leblanc
- Institut NeuroMyogène (INMG), CNRS UMR5310, Inserm U1217, LBMC, École Normale Supérieure de Lyon, France - UMR 5239 CNRS-ENS, Université Lyon 1, Lyon, France
| | - Raphaële Germi
- Laboratoire de Virologie, Institut de Biologie et Pathologie, CHU de Grenoble, France - Institut de Biologie Structurale, UMR 5075 CEA/CNRS/UGA, Grenoble, France
| | - Branka Horvat
- CIRI, Centre International de Recherche en Infectiologie; - Inserm, U1111, Lyon, France - CNRS, UMR5308, Lyon, France - Université Lyon-1, Faculté de Médecine Laënnec, 69008 Lyon, France - Institut NeuroMyogène (INMG), CNRS UMR5310, Inserm U1217, LBMC, École Normale Supérieure de Lyon, France - Laboratoire d'Excellence ECOFECT, Lyon, France
| | - Patrice N Marche
- Inserm U1209, Grenoble, France - Institut Advance Biosciences, CNRS UMR5309, Université Grenoble Alpes
| | - Hervé Perron
- GeNeuro Innovation, Bioparc Laënnec, 60, avenue Rockefeller, 69008 Lyon, France - Université Lyon-1, Faculté de Médecine Laënnec, 69008 Lyon, France - GeNeuro, 18, chemin des Aulx, 1228 Plan-Les-Ouates, Genève, Suisse
| |
Collapse
|
46
|
DUX4-induced dsRNA and MYC mRNA stabilization activate apoptotic pathways in human cell models of facioscapulohumeral dystrophy. PLoS Genet 2017; 13:e1006658. [PMID: 28273136 PMCID: PMC5362247 DOI: 10.1371/journal.pgen.1006658] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 03/22/2017] [Accepted: 02/26/2017] [Indexed: 12/19/2022] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is caused by the mis-expression of DUX4 in skeletal muscle cells. DUX4 is a transcription factor that activates genes normally associated with stem cell biology and its mis-expression in FSHD cells results in apoptosis. To identify genes and pathways necessary for DUX4-mediated apoptosis, we performed an siRNA screen in an RD rhabdomyosarcoma cell line with an inducible DUX4 transgene. Our screen identified components of the MYC-mediated apoptotic pathway and the double-stranded RNA (dsRNA) innate immune response pathway as mediators of DUX4-induced apoptosis. Further investigation revealed that DUX4 expression led to increased MYC mRNA, accumulation of nuclear dsRNA foci, and activation of the dsRNA response pathway in both RD cells and human myoblasts. Nuclear dsRNA foci were associated with aggregation of the exon junction complex component EIF4A3. The elevation of MYC mRNA, dsRNA accumulation, and EIF4A3 nuclear aggregates in FSHD muscle cells suggest that these processes might contribute to FSHD pathophysiology. Facioscapulohumeral dystrophy (FSHD) is a common form of muscular dystrophy which is currently untreatable. It is caused by the inappropriate expression in skeletal muscle of the gene DUX4 that encodes a transcription factor normally expressed in some stem cells. When DUX4 is expressed in cultured human or mouse skeletal muscle cells, it activates a program of cell death. Knowing the molecular basis for the cell death induced by DUX4 is important to determine the mechanism of muscle damage in FSHD. We used a molecular screening approach to identify genes and pathways necessary for DUX4 to induce the cell death program. We found that DUX4 activated a known MYC-induced cell death pathway, at least in part through stabilization of MYC mRNA. We also found that DUX4 expression led to an accumulation of double stranded RNAs (dsRNAs) that induced a cell death pathway evolved to protect against viral infections. This dsRNA accumulation was accompanied by aggregation of the EIF4A3 protein, a factor involved in mRNA surveillance and decay, which may provide a partial mechanism for how DUX4 can inhibit RNA quality control pathways in cells. Because FSHD muscle cells have increased MYC mRNA, dsRNA accumulation, and EIF4A3 nuclear aggregates, we conclude that these processes might contribute to FSHD pathophysiology.
Collapse
|
47
|
Krug L, Chatterjee N, Borges-Monroy R, Hearn S, Liao WW, Morrill K, Prazak L, Rozhkov N, Theodorou D, Hammell M, Dubnau J. Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS. PLoS Genet 2017; 13:e1006635. [PMID: 28301478 PMCID: PMC5354250 DOI: 10.1371/journal.pgen.1006635] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 02/14/2017] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable neurodegenerative disorders that exist on a symptomological spectrum and share both genetic underpinnings and pathophysiological hallmarks. Functional abnormality of TAR DNA-binding protein 43 (TDP-43), an aggregation-prone RNA and DNA binding protein, is observed in the vast majority of both familial and sporadic ALS cases and in ~40% of FTLD cases, but the cascade of events leading to cell death are not understood. We have expressed human TDP-43 (hTDP-43) in Drosophila neurons and glia, a model that recapitulates many of the characteristics of TDP-43-linked human disease including protein aggregation pathology, locomotor impairment, and premature death. We report that such expression of hTDP-43 impairs small interfering RNA (siRNA) silencing, which is the major post-transcriptional mechanism of retrotransposable element (RTE) control in somatic tissue. This is accompanied by de-repression of a panel of both LINE and LTR families of RTEs, with somewhat different elements being active in response to hTDP-43 expression in glia versus neurons. hTDP-43 expression in glia causes an early and severe loss of control of a specific RTE, the endogenous retrovirus (ERV) gypsy. We demonstrate that gypsy causes the degenerative phenotypes in these flies because we are able to rescue the toxicity of glial hTDP-43 either by genetically blocking expression of this RTE or by pharmacologically inhibiting RTE reverse transcriptase activity. Moreover, we provide evidence that activation of DNA damage-mediated programmed cell death underlies both neuronal and glial hTDP-43 toxicity, consistent with RTE-mediated effects in both cell types. Our findings suggest a novel mechanism in which RTE activity contributes to neurodegeneration in TDP-43-mediated diseases such as ALS and FTLD.
Collapse
Affiliation(s)
- Lisa Krug
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Nabanita Chatterjee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | | | - Stephen Hearn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Wen-Wei Liao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Kathleen Morrill
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Lisa Prazak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Department of Biology, Farmingdale State College, Farmingdale, NY United States of America
| | - Nikolay Rozhkov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Delphine Theodorou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Josh Dubnau
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Department of Anesthesiology, Stony Brook School of Medicine, Stony Brook, New York, United States of America
- Department of Neurobiology and Behavior, Stony Brook School of Medicine, Stony Brook, New York, United States of America
| |
Collapse
|
48
|
Tang AY. RNA processing-associated molecular mechanisms of neurodegenerative diseases. J Appl Genet 2015; 57:323-33. [DOI: 10.1007/s13353-015-0330-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/22/2015] [Accepted: 11/26/2015] [Indexed: 12/13/2022]
|
49
|
Abstract
The degeneration of motor neurons in amyotrophic lateral sclerosis (ALS) inevitably causes paralysis and death within a matter of years. Mounting genetic and functional evidence suggest that abnormalities in RNA processing and metabolism underlie motor neuron loss in sporadic and familial ALS. Abnormal localization and aggregation of essential RNA-binding proteins are fundamental pathological features of sporadic ALS, and mutations in genes encoding RNA processing enzymes cause familial disease. Also, expansion mutations occurring in the noncoding region of C9orf72-the most common cause of inherited ALS-result in nuclear RNA foci, underscoring the link between abnormal RNA metabolism and neurodegeneration in ALS. This review summarizes the current understanding of RNA dysfunction in ALS, and builds upon this knowledge base to identify converging mechanisms of neurodegeneration in ALS. Potential targets for therapy development are highlighted, with particular emphasis on early and conserved pathways that lead to motor neuron loss in ALS.
Collapse
Affiliation(s)
- Sami J Barmada
- Department of Neurology, University of Michigan, 109 Zina Pitcher Place, 5015 Biomedical Sciences Research Building, SSPC 2200, Ann Arbor, MI, 48109, USA,
| |
Collapse
|