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Negi R, Srivastava A, Srivastava AK, Vatsa P, Ansari UA, Khan B, Singh H, Pandeya A, Pant AB. Proteomic-miRNA Biomics Profile Reveals 2D Cultures of Human iPSC-Derived Neural Progenitor Cells More Sensitive than 3D Spheroid System Against the Experimental Exposure to Arsenic. Mol Neurobiol 2024; 61:5754-5770. [PMID: 38228842 DOI: 10.1007/s12035-024-03924-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024]
Abstract
The iPSC-derived 3D models are considered to be a connective link between 2D culture and in vivo studies. However, the sensitivity of such 3D models is yet to be established. We assessed the sensitivity of the hiPSC-derived 3D spheroids against 2D cultures of neural progenitor cells. The sub-toxic dose of Sodium Arsenite (SA) was used to investigate the alterations in miRNA-proteins in both systems. Though SA exposure induced significant alterations in the proteins in both 2D and 3D systems, these proteins were uncommon except for 20 proteins. The number and magnitude of altered proteins were higher in the 2D system compared to 3D. The association of dysregulated miRNAs with the target proteins showed their involvement primarily in mitochondrial bioenergetics, oxidative and ER stress, transcription and translation mechanism, cytostructure, etc., in both culture systems. Further, the impact of dysregulated miRNAs and associated proteins on these functions and ultrastructural changes was compared in both culture systems. The ultrastructural studies revealed a similar pattern of mitochondrial damage, while the cellular bioenergetics studies confirm a significantly higher energy failure in the 2D system than to 3D. Such a higher magnitude of changes could be correlated with a higher amount of internalization of SA in 2D cultures than in 3D spheroids. Our findings demonstrate that a 2D culture system seems better responsive than a 3D spheroid system against SA exposure.
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Affiliation(s)
- R Negi
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - A Srivastava
- Department of Biochemistry, University of Lucknow, Lucknow, Uttar Pradesh, 226007, India
| | - A K Srivastava
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India
| | - P Vatsa
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - U A Ansari
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - B Khan
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India
| | - H Singh
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India
| | - A Pandeya
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India
| | - A B Pant
- Systems Toxicology Group, CSIR-Indian Institute of Toxicology Research Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, P.O. Box No. 80, Lucknow, 226 001, Uttar Pradesh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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Leitner D, Kavanagh T, Kanshin E, Balcomb K, Pires G, Thierry M, Suazo JI, Schneider J, Ueberheide B, Drummond E, Wisniewski T. Differences in the cerebral amyloid angiopathy proteome in Alzheimer's disease and mild cognitive impairment. Acta Neuropathol 2024; 148:9. [PMID: 39039355 PMCID: PMC11263258 DOI: 10.1007/s00401-024-02767-1] [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: 04/04/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024]
Abstract
Cerebral amyloid angiopathy (CAA) is characterized by amyloid beta (Aβ) deposition in cerebrovasculature. It is prevalent with aging and Alzheimer's disease (AD), associated with intracerebral hemorrhage, and contributes to cognitive deficits. To better understand molecular mechanisms, CAA(+) and CAA(-) vessels were microdissected from paraffin-embedded autopsy temporal cortex of age-matched Control (n = 10), mild cognitive impairment (MCI; n = 4), and sporadic AD (n = 6) cases, followed by label-free quantitative mass spectrometry. 257 proteins were differentially abundant in CAA(+) vessels compared to neighboring CAA(-) vessels in MCI, and 289 in AD (p < 0.05, fold-change > 1.5). 84 proteins changed in the same direction in both groups, and many changed in the same direction among proteins significant in at least one group (p < 0.0001, R2 = 0.62). In CAA(+) vessels, proteins significantly increased in both AD and MCI were particularly associated with collagen-containing extracellular matrix, while proteins associated with ribonucleoprotein complex were significantly decreased in both AD and MCI. In neighboring CAA(-) vessels, 61 proteins were differentially abundant in MCI, and 112 in AD when compared to Control cases. Increased proteins in CAA(-) vessels were associated with extracellular matrix, external encapsulating structure, and collagen-containing extracellular matrix in MCI; collagen trimer in AD. Twenty two proteins were increased in CAA(-) vessels of both AD and MCI. Comparison of the CAA proteome with published amyloid-plaque proteomic datasets identified many proteins similarly enriched in CAA and plaques, as well as a protein subset hypothesized as preferentially enriched in CAA when compared to plaques. SEMA3G emerged as a CAA specific marker, validated immunohistochemically and with correlation to pathology levels (p < 0.0001; R2 = 0.90). Overall, the CAA(-) vessel proteomes indicated changes in vessel integrity in AD and MCI in the absence of Aβ, and the CAA(+) vessel proteome was similar in MCI and AD, which was associated with vascular matrix reorganization, protein translation deficits, and blood brain barrier breakdown.
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Affiliation(s)
- Dominique Leitner
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Tomas Kavanagh
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Evgeny Kanshin
- Proteomics Laboratory, Division of Advanced Research Technologies and Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Kaleah Balcomb
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Geoffrey Pires
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Manon Thierry
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Jianina I Suazo
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Julie Schneider
- Department Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison Street, Suite 1000, Chicago, IL, 60612, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
- Department of Pathology, Rush University Medical Center, Chicago, IL, USA
| | - Beatrix Ueberheide
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies and Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Eleanor Drummond
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia.
| | - Thomas Wisniewski
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, 10016, USA.
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Tilliole P, Fix S, Godin JD. hnRNPs: roles in neurodevelopment and implication for brain disorders. Front Mol Neurosci 2024; 17:1411639. [PMID: 39086926 PMCID: PMC11288931 DOI: 10.3389/fnmol.2024.1411639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/17/2024] [Indexed: 08/02/2024] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) constitute a family of multifunctional RNA-binding proteins able to process nuclear pre-mRNAs into mature mRNAs and regulate gene expression in multiple ways. They comprise at least 20 different members in mammals, named from A (HNRNP A1) to U (HNRNP U). Many of these proteins are components of the spliceosome complex and can modulate alternative splicing in a tissue-specific manner. Notably, while genes encoding hnRNPs exhibit ubiquitous expression, increasing evidence associate these proteins to various neurodevelopmental and neurodegenerative disorders, such as intellectual disability, epilepsy, microcephaly, amyotrophic lateral sclerosis, or dementias, highlighting their crucial role in the central nervous system. This review explores the evolution of the hnRNPs family, highlighting the emergence of numerous new members within this family, and sheds light on their implications for brain development.
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Affiliation(s)
- Pierre Tilliole
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
- Centre National de la Recherche Scientifique, CNRS, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Simon Fix
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
- Centre National de la Recherche Scientifique, CNRS, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Juliette D. Godin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
- Centre National de la Recherche Scientifique, CNRS, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
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Bonomi CG, Bruno M, Colona VL, Bengala M, Martorana A. A case of hereditary dementia: Is it Alzheimer's disease or not? J Neurol Sci 2024; 458:122947. [PMID: 38448253 DOI: 10.1016/j.jns.2024.122947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Affiliation(s)
| | - Matilde Bruno
- Memory Clinic, University of Rome Tor Vergata, Viale Oxford 81, 00133 Roma, Italy
| | - Vito Luigi Colona
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy
| | - Mario Bengala
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy.
| | - Alessandro Martorana
- Memory Clinic, University of Rome Tor Vergata, Viale Oxford 81, 00133 Roma, Italy.
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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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Khalil B, Linsenmeier M, Smith CL, Shorter J, Rossoll W. Nuclear-import receptors as gatekeepers of pathological phase transitions in ALS/FTD. Mol Neurodegener 2024; 19:8. [PMID: 38254150 PMCID: PMC10804745 DOI: 10.1186/s13024-023-00698-1] [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: 06/05/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are fatal neurodegenerative disorders on a disease spectrum that are characterized by the cytoplasmic mislocalization and aberrant phase transitions of prion-like RNA-binding proteins (RBPs). The common accumulation of TAR DNA-binding protein-43 (TDP-43), fused in sarcoma (FUS), and other nuclear RBPs in detergent-insoluble aggregates in the cytoplasm of degenerating neurons in ALS/FTD is connected to nuclear pore dysfunction and other defects in the nucleocytoplasmic transport machinery. Recent advances suggest that beyond their canonical role in the nuclear import of protein cargoes, nuclear-import receptors (NIRs) can prevent and reverse aberrant phase transitions of TDP-43, FUS, and related prion-like RBPs and restore their nuclear localization and function. Here, we showcase the NIR family and how they recognize cargo, drive nuclear import, and chaperone prion-like RBPs linked to ALS/FTD. We also discuss the promise of enhancing NIR levels and developing potentiated NIR variants as therapeutic strategies for ALS/FTD and related neurodegenerative proteinopathies.
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Affiliation(s)
- Bilal Khalil
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
| | - Miriam Linsenmeier
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, U.S.A
| | - Courtney L Smith
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
- Mayo Clinic Graduate School of Biomedical Sciences, Neuroscience Track, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, U.S.A..
| | - Wilfried Rossoll
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A..
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Xu Y, Liu W, Ren L. Emerging roles and mechanism of m6A methylation in rheumatoid arthritis. Biomed Pharmacother 2024; 170:116066. [PMID: 38157641 DOI: 10.1016/j.biopha.2023.116066] [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: 11/20/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024] Open
Abstract
Rheumatoid arthritis (RA) is a multifaceted autoimmune disease characterized by systemic inflammation, affecting both articular and extra-articular structures. This condition results in inflammation of joints and synovial membranes, accompanied by the development of systemic comorbidities. Despite extensive research, the precise pathogenic mechanisms responsible for RA have yet to be completely understood. RNA methylation, a burgeoning epigenetic alteration, assumes a pivotal function in the regulation of a myriad of biological phenomena, encompassing immunity, DNA damage response, tumorigenesis, metastasis, stem cell renewal, adipocyte differentiation, circadian rhythms, cellular development and differentiation, and cell division. The N6-methyladenosine (m6A) modification is the most prevalent among the various RNA modifications found in mammalian mRNA. Recent studies have provided evidence of the significant role played by m6A modification in the pathophysiological progression of RA. This review aims to provide a comprehensive analysis of the progress made in research focused on m6A modification in the context of RA, consolidate the underlying mechanisms involved in m6A modification during the initiation of RA and discuss the potential of targeting m6A modification as a viable therapeutic approach for RA.
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Affiliation(s)
- Yayun Xu
- Department of Neurology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China
| | - Wenqiang Liu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei 230000, China; The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Hefei 230000, China
| | - Lijie Ren
- Department of Neurology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China.
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Chen K, Luo M, Lv Y, Luo Z, Yang H. Undervalued and novel roles of heterogeneous nuclear ribonucleoproteins in autoimmune diseases: Resurgence as potential biomarkers and targets. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1806. [PMID: 37365887 DOI: 10.1002/wrna.1806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/28/2023]
Abstract
Autoimmune diseases are mainly characterized by the abnormal autoreactivity due to the loss of tolerance to specific autoantigens, though multiple pathways associated with the homeostasis of immune responses are involved in initiating or aggravating the conditions. The heterogeneous nuclear ribonucleoproteins (hnRNPs) are a major category of RNA-binding proteins ubiquitously expressed in a multitude of cells and have attracted great attentions especially with their distinctive roles in nucleic acid metabolisms and the pathogenesis in diseases like neurodegenerative disorders and cancers. Nevertheless, the interplay between hnRNPs and autoimmune disorders has not been fully elucidated. Virtually various family members of hnRNPs are increasingly identified as immune players and are pertinent to all kinds of immune-related processes including immune system development and innate or adaptive immune responses. Specifically, hnRNPs have been extensively recognized as autoantigens within and even beyond a myriad of autoimmune diseases, yet their diagnostic and prognostic values are seemingly underestimated. Molecular mimicry, epitope spreading and bystander activation may represent major putative mechanisms underlying the presence of autoantibodies to hnRNPs. Besides, hnRNPs play critical parts in regulating linchpin genes expressions that control genetic susceptibility, disease-linked functional pathways, or immune responses by interacting with other components particularly like microRNAs and long non-coding RNAs, thereby contributing to inflammation and autoimmunity as well as specific disease phenotypes. Therefore, comprehensive unraveling of the roles of hnRNPs is conducive to establishing potential biomarkers and developing better intervention strategies by targeting these hnRNPs in the corresponding disorders. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Kangzhi Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Mengchuan Luo
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanzhi Lv
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhaohui Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Clinical Research Center for Epileptic Disease of Hunan Province, Central South University, Changsha, China
| | - Huan Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
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Muttuvelu DV, Cehofski LJ, Utheim TP, Chen X, Vorum H, Rasmussen MLR, Heegaard S, Khan AM, Abduljabar AB, Honoré B. Tear film proteome changes following Tobradex ® therapy in anterior blepharitis. Acta Ophthalmol 2023. [PMID: 37837306 DOI: 10.1111/aos.15792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/18/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
PURPOSE The management of blepharitis continues to challenge clinicians due to the poorly understood aetiology of the condition. We recently identified the family of intracellular plakin proteins as essential driving forces underlying anterior blepharitis. A large-scale protein analysis was used to study if a topical dexamethasone/tobramycin solution could be used to reverse the expression of plakin proteins. METHODS Tear film samples from treatment naïve patients with anterior blepharitis (n = 15) were collected with Schirmer filtration paper. A subgroup of the patients (n = 10) received treatment with a dexamethasone/tobramycin 1 + 3 mg/mL ophthalmic suspension (Tobradex® ) for 3 weeks and collection of tear film samples was repeated. The samples were analysed with label-free quantification nano liquid chromatography-tandem mass spectrometry requiring quantification in at least 70% of the samples in each group. Proteins were considered differentially expressed if p < 0.05. RESULTS Following Tobradex® intervention, 27 proteins were upregulated while 61 proteins were downregulated. Regulated proteins after Tobradex® treatment were involved in intermediate filament cytoskeleton organization including downregulation of the plakin proteins envoplakin, epiplakin and periplakin. Plectin, a protein of the plakin family, remained unchanged after Tobradex® therapy. Tobradex® treatment resulted in the regulation of proteins involved in translation including a cluster of downregulated ribosomal proteins. Tobradex® intervention was associated with the regulation of proteins involved in fructose metabolism and glycolytic processes including fructose-1.6-bisphosphatase 1, fructose-bisphosphate aldolases A and B, pyruvate kinase PKM and transketolase. Ig lambda chain V-I region, prominin-1, and protein Niban were upregulated after Tobradex® treatment. CONCLUSIONS Tobradex treatment reversed the expression of plakin proteins in anterior blepharitis. Topical solutions which inhibit the expression of plakin proteins may have the potential to restore the ocular surface integrity in anterior blepharitis and should be explored further.
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Affiliation(s)
| | - Lasse Jørgensen Cehofski
- Department of Ophthalmology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Tor Paaske Utheim
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- The Norwegian Dry Eye Clinic, Oslo, Norway
| | | | - Henrik Vorum
- Department of Ophthalmology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | | | - Steffen Heegaard
- Department of Ophthalmology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Bent Honoré
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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10
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Feng Q, Xia W, Feng Z, Tan Y, Zhang Y, Liu D, Zhang G. The accelerated organ senescence and proteotoxicity in thyrotoxicosis mice. J Cell Physiol 2023; 238:2481-2498. [PMID: 37750538 DOI: 10.1002/jcp.31108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 09/27/2023]
Abstract
The mechanism of aging has always been the focus of research, because aging is related to disease susceptibility and seriously affects people's quality of life. The diseases also accelerate the aging process, especially the pathological changes of substantive organs, such as cardiac hypertrophy, severely shortened lifespan. So, lesions in organs are both a consequence and a cause of aging. However, the disease in a given organ is not in isolation but is a systemic problem. Our previous study found that thyrotoxicosis mice model has aging characteristics including immunosenescence, lipotoxicity, malnutrition. But all these characteristics will lead to organ senescence, therefore, this study continued to study the aging changes of important organs such as heart, liver, and kidney in thyrotoxicosis mice using tandem mass tags (TMT) proteomics method. The results showed that the excess thyroxine led to cardiac hypertrophy. In the liver, the ability to synthesize functional proteins, detoxify, and metabolism were declined. The effect on the kidney was the decreased ability of detoxify and metabolism. The main finding of the present study was that the acceleration of organ senescence by excess thyroxine was due to proteotoxicity. The shared cause of proteotoxicity in the three organs included the intensify of oxidative phosphorylation, the redundancy production of ribosomes, and the lack of splicing and ubiquitin proteasome system function. Totally, proteotoxicity was another parallel between thyrotoxicosis and aging in addition to lipotoxicity. Our research provided a convenient and appropriate animal model for exploring aging mechanism and antiaging drugs.
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Affiliation(s)
- Qin Feng
- State Key Laboratory of Integration and Innovation of Classic Formula and Modern Chinese Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi, Shandong, China
| | - Wenkai Xia
- State Key Laboratory of Integration and Innovation of Classic Formula and Modern Chinese Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi, Shandong, China
| | - Zhong Feng
- State Key Laboratory of Integration and Innovation of Classic Formula and Modern Chinese Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi, Shandong, China
- School of Pharmaceutical Sciences, Sun Yat-sen University, Shenzhen, China
| | - Yujun Tan
- State Key Laboratory of Integration and Innovation of Classic Formula and Modern Chinese Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi, Shandong, China
| | - Yongxia Zhang
- State Key Laboratory of Integration and Innovation of Classic Formula and Modern Chinese Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi, Shandong, China
| | - Deshan Liu
- Department of Traditional Chinese Medicine, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Guimin Zhang
- State Key Laboratory of Integration and Innovation of Classic Formula and Modern Chinese Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi, Shandong, China
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11
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Li Z, Wei H, Hu D, Li X, Guo Y, Ding X, Guo H, Zhang L. Research Progress on the Structural and Functional Roles of hnRNPs in Muscle Development. Biomolecules 2023; 13:1434. [PMID: 37892116 PMCID: PMC10604023 DOI: 10.3390/biom13101434] [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: 09/04/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a superfamily of RNA-binding proteins consisting of more than 20 members. These proteins play a crucial role in various biological processes by regulating RNA splicing, transcription, and translation through their binding to RNA. In the context of muscle development and regeneration, hnRNPs are involved in a wide range of regulatory mechanisms, including alternative splicing, transcription regulation, miRNA regulation, and mRNA stability regulation. Recent studies have also suggested a potential association between hnRNPs and muscle-related diseases. In this report, we provide an overview of our current understanding of how hnRNPs regulate RNA metabolism and emphasize the significance of the key members of the hnRNP family in muscle development. Furthermore, we explore the relationship between the hnRNP family and muscle-related diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Linlin Zhang
- Key Laboratory of Animal Breeding and Healthy Livestock Farming, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300392, China; (Z.L.); (H.W.); (D.H.); (X.L.); (Y.G.); (X.D.); (H.G.)
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12
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Rodriguez Gallo MC, Uhrig RG. Phosphorylation mediated regulation of RNA splicing in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1249057. [PMID: 37780493 PMCID: PMC10539000 DOI: 10.3389/fpls.2023.1249057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/22/2023] [Indexed: 10/03/2023]
Abstract
For the past two decades, the study of alternative splicing (AS) and its involvement in plant development and stress response has grown in popularity. Only recently however, has the focus shifted to the study of how AS regulation (or lack-thereof) affects downstream mRNA and protein landscapes and how these AS regulatory events impact plant development and stress tolerance. In humans, protein phosphorylation represents one of the predominant mechanisms by which AS is regulated and thus the protein kinases governing these phosphorylation events are of interest for further study. Large-scale phosphoproteomic studies in plants have consistently found that RNA splicing-related proteins are extensively phosphorylated, however, the signaling pathways involved in AS regulation have not been resolved. In this mini-review, we summarize our current knowledge of the three major splicing-related protein kinase families in plants that are suggested to mediate AS phospho-regulation and draw comparisons to their metazoan orthologs. We also summarize and contextualize the phosphorylation events identified as occurring on splicing-related protein families to illustrate the high degree to which splicing-related proteins are modified, placing a new focus on elucidating the impacts of AS at the protein and PTM-level.
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Affiliation(s)
| | - R. Glen Uhrig
- University of Alberta, Department of Biological Sciences, Edmonton, AB, Canada
- University of Alberta, Department of Biochemistry, Edmonton, AB, Canada
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13
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Niggl E, Bouman A, Briere LC, Hoogenboezem RM, Wallaard I, Park J, Admard J, Wilke M, Harris-Mostert EDRO, Elgersma M, Bain J, Balasubramanian M, Banka S, Benke PJ, Bertrand M, Blesson AE, Clayton-Smith J, Ellingford JM, Gillentine MA, Goodloe DH, Haack TB, Jain M, Krantz I, Luu SM, McPheron M, Muss CL, Raible SE, Robin NH, Spiller M, Starling S, Sweetser DA, Thiffault I, Vetrini F, Witt D, Woods E, Zhou D, Elgersma Y, van Esbroeck ACM. HNRNPC haploinsufficiency affects alternative splicing of intellectual disability-associated genes and causes a neurodevelopmental disorder. Am J Hum Genet 2023; 110:1414-1435. [PMID: 37541189 PMCID: PMC10432175 DOI: 10.1016/j.ajhg.2023.07.005] [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: 01/26/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 08/06/2023] Open
Abstract
Heterogeneous nuclear ribonucleoprotein C (HNRNPC) is an essential, ubiquitously abundant protein involved in mRNA processing. Genetic variants in other members of the HNRNP family have been associated with neurodevelopmental disorders. Here, we describe 13 individuals with global developmental delay, intellectual disability, behavioral abnormalities, and subtle facial dysmorphology with heterozygous HNRNPC germline variants. Five of them bear an identical in-frame deletion of nine amino acids in the extreme C terminus. To study the effect of this recurrent variant as well as HNRNPC haploinsufficiency, we used induced pluripotent stem cells (iPSCs) and fibroblasts obtained from affected individuals. While protein localization and oligomerization were unaffected by the recurrent C-terminal deletion variant, total HNRNPC levels were decreased. Previously, reduced HNRNPC levels have been associated with changes in alternative splicing. Therefore, we performed a meta-analysis on published RNA-seq datasets of three different cell lines to identify a ubiquitous HNRNPC-dependent signature of alternative spliced exons. The identified signature was not only confirmed in fibroblasts obtained from an affected individual but also showed a significant enrichment for genes associated with intellectual disability. Hence, we assessed the effect of decreased and increased levels of HNRNPC on neuronal arborization and neuronal migration and found that either condition affects neuronal function. Taken together, our data indicate that HNRNPC haploinsufficiency affects alternative splicing of multiple intellectual disability-associated genes and that the developing brain is sensitive to aberrant levels of HNRNPC. Hence, our data strongly support the inclusion of HNRNPC to the family of HNRNP-related neurodevelopmental disorders.
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Affiliation(s)
- Eva Niggl
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands.
| | - Lauren C Briere
- Center for Genomic Medicine and Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Ilse Wallaard
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; NGS Competence Center Tübingen, Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Emilio D R O Harris-Mostert
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Minetta Elgersma
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Jennifer Bain
- Department of Neurology Division of Child Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, S5 7AU Sheffield, UK; Department of Oncology & Metabolism, University of Sheffield, S5 7AU Sheffield, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | - Paul J Benke
- Division of Clinical Genetics, Joe DiMaggio Children's Hospital, Hollywood, FL 33021, USA
| | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Alyssa E Blesson
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | - Jamie M Ellingford
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | | | - Dana H Goodloe
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; Center for Rare Diseases, University of Tübingen, 72076 Tübingen, Germany
| | - Mahim Jain
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Ian Krantz
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sharon M Luu
- Waisman Center, University of Wisconsin Hospitals and Clinics, Madison, WI 53704, USA; Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Molly McPheron
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Candace L Muss
- Nemours / AI DuPont Hospital for Children, Wilmington, DE 19803, USA
| | - Sarah E Raible
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Michael Spiller
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Susan Starling
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO 64108, USA; School of Medicine, University of Missouri- Kansas City, Kansas City, MO 64108, USA
| | - David A Sweetser
- Center for Genomic Medicine and Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Isabelle Thiffault
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO 64108, USA; Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA; Undiagnosed Rare Disease Clinic (URDC), Indiana University, Indianapolis, IN 46202, USA
| | - Dennis Witt
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Emily Woods
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, S5 7AU Sheffield, UK
| | - Dihong Zhou
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO 64108, USA; School of Medicine, University of Missouri- Kansas City, Kansas City, MO 64108, USA
| | - Ype Elgersma
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands.
| | - Annelot C M van Esbroeck
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
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14
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Kelvington BA, Abel T. hnRNPH2 gain-of-function mutations reveal therapeutic strategies and a role for RNA granules in neurodevelopmental disorders. J Clin Invest 2023; 133:e171499. [PMID: 37463443 DOI: 10.1172/jci171499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Abstract
hnRNPH2-related neurodevelopmental disorder (NDD) is caused by mutations in the HNRNPH2 gene and is associated with substantial challenges, including developmental delay, intellectual disability, growth delay, and epilepsy. There is currently no therapeutic intervention available to those with hnRNPH2-related NDD that addresses its underlying mechanisms. In this issue of the JCI, Korff et al. studied specific gain-of-function mutations associated with hnRNPH2-related NDD, with the help of mouse models that recapitulate key features of the condition in humans. Their work paves the way for therapeutic approaches that aim to reduce the expression of mutant hnRNPH2 and highlights a role for disrupted RNA granules in neurodevelopmental and neurodegenerative disorders.
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15
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Lodde V, Floris M, Zoroddu E, Zarbo IR, Idda ML. RNA-binding proteins in autoimmunity: From genetics to molecular biology. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1772. [PMID: 36658783 DOI: 10.1002/wrna.1772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/18/2022] [Accepted: 12/05/2022] [Indexed: 01/21/2023]
Abstract
Autoimmune diseases (ADs) are chronic pathologies generated by the loss of immune tolerance to the body's own cells and tissues. There is growing recognition that RNA-binding proteins (RBPs) critically govern immunity in healthy and pathological conditions by modulating gene expression post-transcriptionally at all levels: nuclear mRNA splicing and modification, export to the cytoplasm, as well as cytoplasmic mRNA transport, storage, editing, stability, and translation. Despite enormous efforts to identify new therapies for ADs, definitive solutions are not yet available in many instances. Recognizing that many ADs have a strong genetic component, we have explored connections between the molecular biology and the genetics of RBPs in ADs. Here, we review the genetics and molecular biology of RBPs in four major ADs, multiple sclerosis (MS), type 1 diabetes mellitus (T1D), systemic lupus erythematosus (SLE), and rheumatoid arthritis (RA). We anticipate that gaining insights into the genetics and biology of ADs can facilitate the discovery of new therapies. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Valeria Lodde
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Matteo Floris
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Enrico Zoroddu
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Ignazio Roberto Zarbo
- Department of Medical, Surgical and Experimental Sciences, University of Sassari - Neurology Unit Azienza Ospedaliera Universitaria (AOU), Sassari, Italy
| | - Maria Laura Idda
- Institute for Genetic and Biomedical Research - National Research Council (IRGB-CNR), Sassari, Italy
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16
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Zaqout S, Mannaa A, Klein O, Krajewski A, Klose J, Luise-Becker L, Elsabagh A, Ferih K, Kraemer N, Ravindran E, Makridis K, Kaindl AM. Proteome changes in autosomal recessive primary microcephaly. Ann Hum Genet 2023; 87:50-62. [PMID: 36448252 DOI: 10.1111/ahg.12489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022]
Abstract
BACKGROUND/AIM Autosomal recessive primary microcephaly (MCPH) is a rare and genetically heterogeneous group of disorders characterized by intellectual disability and microcephaly at birth, classically without further organ involvement. MCPH3 is caused by biallelic variants in the cyclin-dependent kinase 5 regulatory subunit-associated protein 2 gene CDK5RAP2. In the corresponding Cdk5rap2 mutant or Hertwig's anemia mouse model, congenital microcephaly as well as defects in the hematopoietic system, germ cells and eyes have been reported. The reduction in brain volume, particularly affecting gray matter, has been attributed mainly to disturbances in the proliferation and survival of early neuronal progenitors. In addition, defects in dendritic development and synaptogenesis exist that affect the excitation-inhibition balance. Here, we studied proteomic changes in cerebral cortices of Cdk5rap2 mutant mice. MATERIAL AND METHODS We used large-gel two-dimensional gel (2-DE) electrophoresis to separate cortical proteins. 2-DE gels were visualized by a trained observer on a light box. Spot changes were considered with respect to presence/absence, quantitative variation and altered mobility. RESULT We identified a reduction in more than 30 proteins that play a role in processes such as cell cytoskeleton dynamics, cell cycle progression, ciliary functions and apoptosis. These proteome changes in the MCPH3 model can be associated with various functional and morphological alterations of the developing brain. CONCLUSION Our results shed light on potential protein candidates for the disease-associated phenotype reported in MCPH3.
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Affiliation(s)
- Sami Zaqout
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Atef Mannaa
- Higher Institute of Engineering and Technology, New Borg AlArab City, Alexandria, Egypt.,Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM), Université de Lille, Lille, France
| | - Oliver Klein
- BIH Center for Regenerative Therapies BCRT, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Charité-Universitätsmedizin Berlin (BIH), Berlin, Germany
| | - Angelika Krajewski
- BIH Center for Regenerative Therapies BCRT, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Charité-Universitätsmedizin Berlin (BIH), Berlin, Germany
| | - Joachim Klose
- Charité-Universitätsmedizin, Institute of Human Genetics, Berlin, Germany
| | - Lena Luise-Becker
- Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Berlin, Germany.,Department of Pediatric Neurology, Charité-Universitätsmedizin, Berlin, Germany
| | - Ahmed Elsabagh
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Khaled Ferih
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Nadine Kraemer
- Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Berlin, Germany.,Department of Pediatric Neurology, Charité-Universitätsmedizin, Berlin, Germany
| | - Ethiraj Ravindran
- Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Berlin, Germany.,Department of Pediatric Neurology, Charité-Universitätsmedizin, Berlin, Germany
| | - Konstantin Makridis
- Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Berlin, Germany.,Department of Pediatric Neurology, Charité-Universitätsmedizin, Berlin, Germany
| | - Angela M Kaindl
- Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Berlin, Germany.,Department of Pediatric Neurology, Charité-Universitätsmedizin, Berlin, Germany
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17
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Kurihara M, Mano T, Eto F, Yao I, Sato K, Ohtomo G, Bannai T, Shibata S, Ishiura H, Ikemura M, Matsubara T, Morishima M, Saito Y, Murayama S, Toda T, Setou M, Iwata A. Proteomic profile of nuclei containing p62-positive inclusions in a patient with neuronal intranuclear inclusion disease. Neurobiol Dis 2023; 177:105989. [PMID: 36621630 DOI: 10.1016/j.nbd.2023.105989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/19/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023] Open
Abstract
Neuronal intranuclear inclusion disease (NIID) is a neurodegenerative disease characterized by eosinophilic hyaline intranuclear inclusions in the neurons, glial cells, and other somatic cells. Although CGG repeat expansions in NOTCH2NLC have been identified in most East Asian patients with NIID, the pathophysiology of NIID remains unclear. Ubiquitin- and p62-positive intranuclear inclusions are the pathological hallmark of NIID. Targeted immunostaining studies have identified several other proteins present in these inclusions. However, the global molecular changes within nuclei with these inclusions remained unclear. Herein, we analyzed the proteomic profile of nuclei with p62-positive inclusions in a NIID patient with CGG repeat expansion in NOTCH2NLC to discover candidate proteins involved in the NIID pathophysiology. We used fluorescence-activated cell sorting and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to quantify each protein identified in the nuclei with p62-positive inclusions. The distribution of increased proteins was confirmed via immunofluorescence in autopsy brain samples from three patients with genetically confirmed NIID. Overall, 526 proteins were identified, of which 243 were consistently quantified using MS. A 1.4-fold increase was consistently observed for 20 proteins in nuclei with p62-positive inclusions compared to those without. Fifteen proteins identified with medium or high confidence in the LC-MS/MS analysis were further evaluated. Gene ontology enrichment analysis showed enrichment of several terms, including poly(A) RNA binding, nucleosomal DNA binding, and protein binding. Immunofluorescence studies confirmed that the fluorescent intensities of increased RNA-binding proteins identified by proteomic analysis, namely hnRNP A2/B1, hnRNP A3, and hnRNP C1/C2, were higher in the nuclei with p62-positive inclusions than in those without, which were not confined to the intranuclear inclusions. We identified several increased proteins in nuclei with p62-positive inclusions. Although larger studies are needed to validate our results, these proteomic data may form the basis for understanding the pathophysiology of NIID.
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Affiliation(s)
- Masanori Kurihara
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Neurology, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan
| | - Tatsuo Mano
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Fumihiro Eto
- Department of Cellular and Molecular Anatomy and International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Ikuko Yao
- Department of Cellular and Molecular Anatomy and International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan; Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, Japan
| | - Kenichiro Sato
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Neuropathology, Graduate School of Medicine, The University of Tokyo. Tokyo, Japan
| | - Gaku Ohtomo
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Taro Bannai
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shota Shibata
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masako Ikemura
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoyasu Matsubara
- Department of Neuropathology (the Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan
| | - Maho Morishima
- Department of Neuropathology (the Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan
| | - Yuko Saito
- Department of Neuropathology (the Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan
| | - Shigeo Murayama
- Department of Neuropathology (the Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan; Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Osaka, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mitsutoshi Setou
- Department of Cellular and Molecular Anatomy and International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Atsushi Iwata
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Neurology, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan.
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18
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Kenkpen AK, Storey JJ, Olson ER, Guden TE, Card TT, Jensen AS, Ahrens JL, Hellmann Whitaker RA. Developing Connections Between LINC00298 RNA and Alzheimer's Disease Through Mapping Its Interactome and Through Biochemical Characterization. J Alzheimers Dis 2023; 95:641-661. [PMID: 37574728 DOI: 10.3233/jad-230057] [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] [Indexed: 08/15/2023]
Abstract
BACKGROUND Long non-coding RNAs are ubiquitous throughout the human system, yet many of their biological functions remain unknown. LINC00298 RNA, a long intergenic non-coding RNA, has been shown to have preferential expression in the central nervous system where it contributes to neuronal differentiation and development. Furthermore, previous research has indicated that LINC00298 RNA is known to be a genetic risk factor for the development of Alzheimer's disease. OBJECTIVE To biochemically characterize LINC00298 RNA and to elucidate its biological function within hippocampal neuronal cells, thereby providing a greater understanding of its role in Alzheimer's disease pathogenesis. METHODS LINC00298 RNA was in vitro transcribed and then subjected to structural analysis using circular dichroism, and UV-Vis spectroscopy. Additionally, affinity column chromatography was used to capture LINC00298 RNA's protein binding partners from hippocampal neuronal cells, which were then identified using liquid chromatography and mass spectrometry (LC/MS). RESULTS LINC00298 RNA is comprised of stem-loop secondary structural elements, with a cylindrical tertiary structure that has highly dynamic regions, which result in high positional entropy. LC/MS identified 24 proteins within the interactome of LINC00298 RNA. CONCLUSION Through analysis of LINC00298 RNA's 24 protein binding partners, it was determined that LINC00298 RNA may play significant roles in neuronal development, proliferation, and cellular organization. Furthermore, analysis of LINC00298 RNA's interactome indicated that LINC00298 RNA is capable of intracellular motility with dual localization in the nucleus and the cytosol. This biochemical characterization of LINC00298 RNA has shed light on its role in Alzheimer's disease pathogenesis.
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Affiliation(s)
- Angel K Kenkpen
- Department of Chemistry, Bemidji State University, Bemidji, MN, USA
| | - Joshua J Storey
- Department of Chemistry, Bemidji State University, Bemidji, MN, USA
| | - Emma R Olson
- Department of Chemistry, Bemidji State University, Bemidji, MN, USA
| | - Ty E Guden
- Department of Chemistry, Bemidji State University, Bemidji, MN, USA
| | - Tate T Card
- Department of Chemistry, Bemidji State University, Bemidji, MN, USA
| | - Ashley S Jensen
- Department of Chemistry, Bemidji State University, Bemidji, MN, USA
| | - Jordyn L Ahrens
- Department of Chemistry, Bemidji State University, Bemidji, MN, USA
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19
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Singh AK. Hsrω and Other lncRNAs in Neuronal Functions and Disorders in Drosophila. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010017. [PMID: 36675966 PMCID: PMC9865238 DOI: 10.3390/life13010017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/27/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Long noncoding RNAs (lncRNAs) have a crucial role in epigenetic, transcriptional and posttranscriptional regulation of gene expression. Many of these regulatory lncRNAs, such as MALAT1, NEAT1, HOTAIR, etc., are associated with different neurodegenerative diseases in humans. The lncRNAs produced by the hsrω gene are known to modulate neurotoxicity in polyQ and amyotrophic lateral sclerosis disease models of Drosophila. Elevated expression of hsrω lncRNAs exaggerates, while their genetic depletion through hsrω-RNAi or in an hsrω-null mutant background suppresses, the disease pathogenicity. This review discusses the possible mechanistic details and implications of the functions of hsrω lncRNAs in the modulation of neurodegenerative diseases.
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Affiliation(s)
- Anand Kumar Singh
- Interdisciplinary School of Life Sciences, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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20
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Heterogeneous nuclear ribonucleoprotein A/B: an emerging group of cancer biomarkers and therapeutic targets. Cell Death Dis 2022; 8:337. [PMID: 35879279 PMCID: PMC9314375 DOI: 10.1038/s41420-022-01129-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 11/20/2022]
Abstract
Heterogeneous nuclear ribonucleoprotein A/B (hnRNPA/B) is one of the core members of the RNA binding protein (RBP) hnRNPs family, including four main subtypes, A0, A1, A2/B1 and A3, which share the similar structure and functions. With the advance in understanding the molecular biology of hnRNPA/B, it has been gradually revealed that hnRNPA/B plays a critical role in almost the entire steps of RNA life cycle and its aberrant expression and mutation have important effects on the occurrence and progression of various cancers. This review focuses on the clinical significance of hnRNPA/B in various cancers and systematically summarizes its biological function and molecular mechanisms.
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21
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Ma L, He LN, Kang S, Gu B, Gao S, Zuo Z. Advances in detecting N6-methyladenosine modification in circRNAs. Methods 2022; 205:234-246. [PMID: 35878749 DOI: 10.1016/j.ymeth.2022.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of noncoding RNAs with covalently single-stranded closed loop structures derived from back-splicing event of linear precursor mRNAs (pre-mRNAs). N6-methyladenosine (m6A), the most abundant epigenetic modification in eukaryotic RNAs, has been shown to play a crucial role in regulating the fate and biological function of circRNAs, and thus affecting various physiological and pathological processes. Accurate identification of m6A modification in circRNAs is an essential step to fully elucidate the crosstalk between m6A and circRNAs. In recent years, the rapid development of high-throughput sequencing technology and bioinformatic methodology has propelled the establishment of a multitude of approaches to detect circRNAs and m6A modification, including in vitro-based and in silico methods. Based on this, the research community has started on a new journey to develop methods for identification of m6A modification in circRNAs. In this review, we provide a comprehensive review and evaluation of the existing methods responsible for detecting circRNAs, m6A modification, and especially, m6A modification in circRNAs, which mainly focused on those developed based on high-throughput technologies and methodology of bioinformatics. This handy reference can help researchers figure out towards which direction this field will go.
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Affiliation(s)
- Lixia Ma
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital (College of Clinical Medical) of Henan University of Science and Technology, Luoyang, China
| | - Li-Na He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shiyang Kang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Bianli Gu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital (College of Clinical Medical) of Henan University of Science and Technology, Luoyang, China
| | - Shegan Gao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital (College of Clinical Medical) of Henan University of Science and Technology, Luoyang, China.
| | - Zhixiang Zuo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
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22
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Paron F, Barattucci S, Cappelli S, Romano M, Berlingieri C, Stuani C, Laurents D, Mompeán M, Buratti E. Unravelling the toxic effects mediated by the neurodegenerative disease-associated S375G mutation of TDP-43 and its S375E phosphomimetic variant. J Biol Chem 2022; 298:102252. [PMID: 35835219 PMCID: PMC9364110 DOI: 10.1016/j.jbc.2022.102252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 12/05/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is a nucleic acid–binding protein found in the nucleus that accumulates in the cytoplasm under pathological conditions, leading to proteinopathies, such as frontotemporal dementia and ALS. An emerging area of TDP-43 research is represented by the study of its post-translational modifications, the way they are connected to disease-associated mutations, and what this means for pathological processes. Recently, we described a novel mutation in TDP-43 in an early onset ALS case that was affecting a potential phosphorylation site in position 375 (S375G). A preliminary characterization showed that both the S375G mutation and its phosphomimetic variant, S375E, displayed altered nuclear–cytoplasmic distribution and cellular toxicity. To better investigate these effects, here we established cell lines expressing inducible WT, S375G, and S375E TDP-43 variants. Interestingly, we found that these mutants do not seem to affect well-studied aspects of TDP-43, such as RNA splicing or autoregulation, or protein conformation, dynamics, or aggregation, although they do display dysmorphic nuclear shape and cell cycle alterations. In addition, RNA-Seq analysis of these cell lines showed that although the disease-associated S375G mutation and its phosphomimetic S375E variant regulate distinct sets of genes, they have a common target in mitochondrial apoptotic genes. Taken together, our data strongly support the growing evidence that alterations in TDP-43 post-translational modifications can play a potentially important role in disease pathogenesis and provide a further link between TDP-43 pathology and mitochondrial health.
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Affiliation(s)
- Francesca Paron
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Simone Barattucci
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Sara Cappelli
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Christian Berlingieri
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Cristiana Stuani
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy
| | - Douglas Laurents
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Miguel Mompeán
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Emanuele Buratti
- Molecular Pathology, International Centre for Genetic and Engineering Biotechnology (ICGEB), Trieste, Italy.
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23
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Emerging Roles of RNA-Binding Proteins in Neurodevelopment. J Dev Biol 2022; 10:jdb10020023. [PMID: 35735914 PMCID: PMC9224834 DOI: 10.3390/jdb10020023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
Diverse cell types in the central nervous system (CNS) are generated by a relatively small pool of neural stem cells during early development. Spatial and temporal regulation of stem cell behavior relies on precise coordination of gene expression. Well-studied mechanisms include hormone signaling, transcription factor activity, and chromatin remodeling processes. Much less is known about downstream RNA-dependent mechanisms including posttranscriptional regulation, nuclear export, alternative splicing, and transcript stability. These important functions are carried out by RNA-binding proteins (RBPs). Recent work has begun to explore how RBPs contribute to stem cell function and homeostasis, including their role in metabolism, transport, epigenetic regulation, and turnover of target transcripts. Additional layers of complexity are provided by the different target recognition mechanisms of each RBP as well as the posttranslational modifications of the RBPs themselves that alter function. Altogether, these functions allow RBPs to influence various aspects of RNA metabolism to regulate numerous cellular processes. Here we compile advances in RNA biology that have added to our still limited understanding of the role of RBPs in neurodevelopment.
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24
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Drongitis D, Caterino M, Verrillo L, Santonicola P, Costanzo M, Poeta L, Attianese B, Barra A, Terrone G, Lioi MB, Paladino S, Di Schiavi E, Costa V, Ruoppolo M, Miano MG. Deregulation of microtubule organization and RNA metabolism in Arx models for lissencephaly and developmental epileptic encephalopathy. Hum Mol Genet 2022; 31:1884-1908. [PMID: 35094084 PMCID: PMC9169459 DOI: 10.1093/hmg/ddac028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/10/2022] [Accepted: 01/26/2022] [Indexed: 11/18/2022] Open
Abstract
X-linked lissencephaly with abnormal genitalia (XLAG) and developmental epileptic encephalopathy-1 (DEE1) are caused by mutations in the Aristaless-related homeobox (ARX) gene, which encodes a transcription factor responsible for brain development. It has been unknown whether the phenotypically diverse XLAG and DEE1 phenotypes may converge on shared pathways. To address this question, a label-free quantitative proteomic approach was applied to the neonatal brain of Arx knockout (ArxKO/Y) and knock-in polyalanine (Arx(GCG)7/Y) mice that are respectively models for XLAG and DEE1. Gene ontology and protein-protein interaction analysis revealed that cytoskeleton, protein synthesis and splicing control are deregulated in an allelic-dependent manner. Decreased α-tubulin content was observed both in Arx mice and Arx/alr-1(KO) Caenorhabditis elegans ,and a disorganized neurite network in murine primary neurons was consistent with an allelic-dependent secondary tubulinopathy. As distinct features of Arx(GCG)7/Y mice, we detected eIF4A2 overexpression and translational suppression in cortex and primary neurons. Allelic-dependent differences were also established in alternative splicing (AS) regulated by PUF60 and SAM68. Abnormal AS repertoires in Neurexin-1, a gene encoding multiple pre-synaptic organizers implicated in synaptic remodelling, were detected in Arx/alr-1(KO) animals and in Arx(GCG)7/Y epileptogenic brain areas and depolarized cortical neurons. Consistent with a conserved role of ARX in modulating AS, we propose that the allelic-dependent secondary synaptopathy results from an aberrant Neurexin-1 repertoire. Overall, our data reveal alterations mirroring the overlapping and variant effects caused by null and polyalanine expanded mutations in ARX. The identification of these effects can aid in the design of pathway-guided therapy for ARX endophenotypes and NDDs with overlapping comorbidities.
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Affiliation(s)
- Denise Drongitis
- Institute of Genetics and Biophysics ``Adriano Buzzati-Traverso'', National Research Council of Italy, 80131, Naples, Italy
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy
- CEINGE - Biotecnologie Avanzate s.c.a.r.l., 80145 Naples, Italy
| | - Lucia Verrillo
- Institute of Genetics and Biophysics ``Adriano Buzzati-Traverso'', National Research Council of Italy, 80131, Naples, Italy
| | - Pamela Santonicola
- Institute of Biosciences and BioResources, National Research Council of Italy, 80131, Naples, Italy
| | - Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy
- CEINGE - Biotecnologie Avanzate s.c.a.r.l., 80145 Naples, Italy
| | - Loredana Poeta
- Institute of Genetics and Biophysics ``Adriano Buzzati-Traverso'', National Research Council of Italy, 80131, Naples, Italy
- Department of Science, University of Basilicata, 85100 Potenza, Italy
| | - Benedetta Attianese
- Institute of Genetics and Biophysics ``Adriano Buzzati-Traverso'', National Research Council of Italy, 80131, Naples, Italy
| | - Adriano Barra
- Institute of Genetics and Biophysics ``Adriano Buzzati-Traverso'', National Research Council of Italy, 80131, Naples, Italy
| | - Gaetano Terrone
- Department of Translational Medicine, Child Neurology Unit, University of Naples “Federico II”, 80131 Naples, Italy
| | | | - Simona Paladino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy
| | - Elia Di Schiavi
- Institute of Biosciences and BioResources, National Research Council of Italy, 80131, Naples, Italy
| | - Valerio Costa
- Institute of Genetics and Biophysics ``Adriano Buzzati-Traverso'', National Research Council of Italy, 80131, Naples, Italy
| | - Margherita Ruoppolo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy
- CEINGE - Biotecnologie Avanzate s.c.a.r.l., 80145 Naples, Italy
| | - Maria Giuseppina Miano
- Institute of Genetics and Biophysics ``Adriano Buzzati-Traverso'', National Research Council of Italy, 80131, Naples, Italy
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25
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Taylor J, Spiller M, Ranguin K, Vitobello A, Philippe C, Bruel A, Cappuccio G, Brunetti‐Pierri N, Willems M, Isidor B, Park K, Balasubramanian M. Expanding the phenotype of HNRNPU-related neurodevelopmental disorder with emphasis on seizure phenotype and review of literature. Am J Med Genet A 2022; 188:1497-1514. [PMID: 35138025 PMCID: PMC9305207 DOI: 10.1002/ajmg.a.62677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/05/2022] [Accepted: 01/13/2022] [Indexed: 11/12/2022]
Abstract
Pathogenic variants in heterogeneous nuclear ribonucleoprotein U (HNRNPU) results in a novel neurodevelopmental disorder recently delineated. Here, we report on 17 previously unpublished patients carrying HNRNPU pathogenic variants. All patients were found to harbor de novo loss-of-function variants except for one individual where the inheritance could not be determined, as a parent was unavailable for testing. All patients had seizures which started in early childhood, global developmental delay, intellectual disability, and dysmorphic features. In addition, hypotonia, behavioral abnormalities (such as autistic features, aggression, anxiety, and obsessive-compulsive behaviors), and cardiac (septal defects) and/or brain abnormalities (ventriculomegaly and corpus callosum thinning/agenesis) were frequently observed. We have noted four recurrent variants in the literature (c.1089G>A p.(Trp363*), c.706_707del p.(Glu236Thrfs*6), c.847_857del p.(Phe283Serfs*5), and c.1681dels p.(Gln561Serfs*45)).
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Affiliation(s)
- James Taylor
- Medical SchoolUniversity of SheffieldSheffieldUK
| | - Michael Spiller
- Sheffield Diagnostic Genetics ServiceSheffield Children's NHS Foundation TrustSheffieldUK
| | - Kara Ranguin
- Department of GeneticsReference Centre for Rare Diseases and Developmental AnomaliesCaenFrance
| | - Antonio Vitobello
- Inserm, UMR1231, Equipe GAD, Bâtiment B3Université de Bourgogne Franche ComtéDijon CedexFrance
| | - Christophe Philippe
- Inserm, UMR1231, Equipe GAD, Bâtiment B3Université de Bourgogne Franche ComtéDijon CedexFrance
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies RaresDijonFrance
| | - Ange‐Line Bruel
- Inserm, UMR1231, Equipe GAD, Bâtiment B3Université de Bourgogne Franche ComtéDijon CedexFrance
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies RaresDijonFrance
| | - Gerarda Cappuccio
- Department of Translational MedicineUniversity of Naples Federico IINaplesItaly
| | - Nicola Brunetti‐Pierri
- Department of Translational MedicineUniversity of Naples Federico IINaplesItaly
- Telethon Institute of Genetics and MedicinePozzuoliItaly
| | - Marjolaine Willems
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Reference Center AD SOOR, AnDDI‐RARE, Groupe DI, Inserm U1298, INMMontpellier University, Centre Hospitalier Universitaire de MontpellierMontpellierFrance
| | | | - Kristen Park
- Department of Paediatrics and NeurologyUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - Meena Balasubramanian
- Department of Oncology & MetabolismUniversity of SheffieldSheffieldUK
- Sheffield Clinical Genetics ServiceSheffield Children's NHS Foundation TrustSheffieldUK
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26
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Targeting HNRNPM Inhibits Cancer Stemness and Enhances Antitumor Immunity in Wnt-activated Hepatocellular Carcinoma. Cell Mol Gastroenterol Hepatol 2022; 13:1413-1447. [PMID: 35158098 PMCID: PMC8938476 DOI: 10.1016/j.jcmgh.2022.02.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 01/10/2023]
Abstract
BACKGROUND & AIMS Cancer stemness and immune evasion are closely associated and play critical roles in tumor development and resistance to immunotherapy. However, little is known about the underlying molecular mechanisms that coordinate this association. METHODS The expressions of heterogeneous nuclear ribonucleoprotein M (HNRNPM) in 240 hepatocellular carcinoma (HCC) samples, public databases, and liver development databases were analyzed. Chromatin immunoprecipitation assays were performed to explore the associations between stem-cell transcription factors and HNRNPM. HNRNPM-regulated alternative splicing (AS) and its binding motif were identified by RNA-seq and RIP-seq. HNRNPM-specific antisense oligonucleotides were developed to explore potential therapeutic targets in HCC. CD8+ T cells that were co-cultured with tumor cells were sorted by flow cytometry assays. RESULTS We identified an elevated oncofetal splicing factor in HCC, HNRNPM, that unifies and regulates the positive association between cancer stemness and immune evasion. HNRNPM knockdown abolished HCC tumorigenesis and diminished cancer stem cell properties in vitro and in vivo. Mechanistically, HNRNPM regulated the AS of MBD2 by binding its flanking introns, whose isoforms played opposing roles. Although MBD2a and MBD2c competitively bound to CpG islands in the FZD3 promoter, MBD2a preferentially increased FZD3 expression and then activated the WNT/β-catenin pathway. Interestingly, FZD3 and β-catenin further provided additional regulation by targeting OCT4 and SOX2. We found that HNRNPM inhibition significantly promoted CD8+ T cell activation and that HNRNPM- antisense oligonucleotides effectively inhibited WNT/β-catenin to enhance anti-programmed cell death protein-1 immunotherapy by promoting CD8+ T cell infiltration. CONCLUSIONS HNRNPM has a tumor-intrinsic function in generating an immunosuppressive HCC environment through an AS-dependent mechanism and demonstrates proof of the concept of targeting HNRNPM in tailoring HCC immunotherapeutic approaches.
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27
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Abstract
The 14-3-3 family proteins are vital scaffold proteins that ubiquitously expressed in various tissues. They interact with numerous protein targets and mediate many cellular signaling pathways. The 14-3-3 binding motifs are often embedded in intrinsically disordered regions which are closely associated with liquid-liquid phase separation (LLPS). In the past ten years, LLPS has been observed for a variety of proteins and biological processes, indicating that LLPS plays a fundamental role in the formation of membraneless organelles and cellular condensates. While extensive investigations have been performed on 14-3-3 proteins, its involvement in LLPS is overlooked. To date, 14-3-3 proteins have not been reported to undergo LLPS alone or regulate LLPS of their binding partners. To reveal the potential involvement of 14-3-3 proteins in LLPS, in this review, we summarized the LLPS propensity of 14-3-3 binding partners and found that about one half of them may undergo LLPS spontaneously. We further analyzed the phase separation behavior of representative 14-3-3 binders and discussed how 14-3-3 proteins may be involved. By modulating the conformation and valence of interactions and recruiting other molecules, we speculate that 14-3-3 proteins can efficiently regulate the functions of their targets in the context of LLPS. Considering the critical roles of 14-3-3 proteins, there is an urgent need for investigating the involvement of 14-3-3 proteins in the phase separation process of their targets and the underling mechanisms.
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28
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Nahalka J. Transcription of the Envelope Protein by 1-L Protein-RNA Recognition Code Leads to Genes/Proteins That Are Relevant to the SARS-CoV-2 Life Cycle and Pathogenesis. Curr Issues Mol Biol 2022; 44:791-816. [PMID: 35723340 PMCID: PMC8928949 DOI: 10.3390/cimb44020055] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/21/2022] [Accepted: 02/03/2022] [Indexed: 12/02/2022] Open
Abstract
The theoretical protein-RNA recognition code was used in this study to research the compatibility of the SARS-CoV-2 envelope protein (E) with mRNAs in the human transcriptome. According to a review of the literature, the spectrum of identified genes showed that the virus post-transcriptionally promotes or represses the genes involved in the SARS-CoV-2 life cycle. The identified genes/proteins are also involved in adaptive immunity, in the function of the cilia and wound healing (EMT and MET) in the pulmonary epithelial tissue, in Alzheimer's and Parkinson's disease and in type 2 diabetes. For example, the E-protein promotes BHLHE40, which switches off the IL-10 inflammatory "brake" and inhibits antiviral THαβ cells. In the viral cycle, E supports the COPII-SCAP-SREBP-HSP90α transport complex by the lowering of cholesterol in the ER and by the repression of insulin signaling, which explains the positive effect of HSP90 inhibitors in COVID-19 (geldanamycin), and E also supports importin α/β-mediated transport to the nucleus, which explains the positive effect of ivermectin, a blocker of importins α/β. In summary, transcription of the envelope protein by the 1-L protein-RNA recognition code leads to genes/proteins that are relevant to the SARS-CoV-2 life cycle and pathogenesis.
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Affiliation(s)
- Jozef Nahalka
- Centre for Glycomics, Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, SK-84538 Bratislava, Slovakia
- Centre of Excellence for White-Green Biotechnology, Institute of Chemistry, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovakia
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29
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Tang F, Chen L, Gao H, Xiao D, Li X. m6A: An Emerging Role in Programmed Cell Death. Front Cell Dev Biol 2022; 10:817112. [PMID: 35141221 PMCID: PMC8819724 DOI: 10.3389/fcell.2022.817112] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/10/2022] [Indexed: 12/20/2022] Open
Abstract
Programmed cell death is an active extinction process, including autophagy, ferroptosis, pyroptosis, apoptosis, and necroptosis. m6A is a reversible RNA modification which undergoes methylation under the action of methylases (writers), and is demethylated under the action of demethylases (erasers). The RNA base site at which m6A is modified is recognized by specialized enzymes (readers) which regulate downstream RNA translation, decay, and stability. m6A affects many aspects of mRNA metabolism, and also plays an important role in promoting the maturation of miRNA, the translation and degradation of circRNA, and the stability of lncRNA. The regulatory factors including writers, erasers and readers promote or inhibit programmed cell death via up-regulating or down-regulating downstream targets in a m6A-dependent manner to participate in the process of disease. In this review, we summarize the functions of m6A with particular reference to its role in programmed cell death.
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Affiliation(s)
- Fajuan Tang
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Lin Chen
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Hu Gao
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Dongqiong Xiao
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- *Correspondence: Dongqiong Xiao, ; Xihong Li,
| | - Xihong Li
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- *Correspondence: Dongqiong Xiao, ; Xihong Li,
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30
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Affiliation(s)
- Caroline Ward
- Department of Pediatrics, Division of Child Neurology, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Udai Bhan Pandey
- Department of Pediatrics, Division of Child Neurology; Department of Human Genetics, School of Public Health, University of Pittsburgh; Center for Neuroscience Institute, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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31
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Influence of N6-Methyladenosine Modification Gene HNRNPC on Cell Phenotype in Parkinson's Disease. PARKINSON'S DISEASE 2021; 2021:9919129. [PMID: 34966539 PMCID: PMC8712163 DOI: 10.1155/2021/9919129] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 12/20/2022]
Abstract
This study aimed to explore the N6-methyladenosine (m6A) modification genes involved in the pathogenesis of Parkinson's disease (PD) through data analysis of the two data sets GSE120306 and GSE22491 in the GEO database and further explore its influence on cell phenotype in PD. We analyzed the differentially expressed genes and function enrichment analysis of the two sets of data and found that the expression of the m6A-modification gene HNRNPC was significantly downregulated in the PD group, and it played an important role in DNA metabolism, RNA metabolism, and RNA processing and may be involved in PD. Then, we constructed the HNRNPC differential expression cell line to study the role of this gene in the pathogenesis of PD. The results showed that overexpression of HNRNPC can promote the proliferation of PC12 cells, inhibit their apoptosis, and inhibit the expression of inflammatory factors IFN-β, IL-6, and TNF-α, suggesting that HNRNPC may cause PD by inhibiting the proliferation of dopaminergic nerve cells, promoting their apoptosis, and causing immune inflammation. Our study also has certain limitations. For example, the data of the experimental group and the validation group come from different cell types, and the data of the experimental group involve individuals with G2019S LRRK2 mutations. In addition, due to the low expression of HNRNPC in PC12 cells, we used the method of overexpressing this gene to study its function. All these factors may cause our conclusions to be biased. Therefore, more research is still needed to corroborate it in the future.
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Montalbano M, Jaworski E, Garcia S, Ellsworth A, McAllen S, Routh A, Kayed R. Tau Modulates mRNA Transcription, Alternative Polyadenylation Profiles of hnRNPs, Chromatin Remodeling and Spliceosome Complexes. Front Mol Neurosci 2021; 14:742790. [PMID: 34924950 PMCID: PMC8678415 DOI: 10.3389/fnmol.2021.742790] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Tau protein is a known contributor in several neurodegenerative diseases, including Alzheimer’s disease (AD) and frontotemporal dementia (FTD). It is well-established that tau forms pathological aggregates and fibrils in these diseases. Tau has been observed within the nuclei of neurons, but there is a gap in understanding regarding the mechanism by which tau modulates transcription. We are interested in the P301L mutation of tau, which has been associated with FTD and increased tau aggregation. Our study utilized tau-inducible HEK (iHEK) cells to reveal that WT and P301L tau distinctively alter the transcription and alternative polyadenylation (APA) profiles of numerous nuclear precursors mRNAs, which then translate to form proteins involved in chromatin remodeling and splicing. We isolated total mRNA before and after over-expressing tau and then performed Poly(A)-ClickSeq (PAC-Seq) to characterize mRNA expression and APA profiles. We characterized changes in Gene Ontology (GO) pathways using EnrichR and Gene Set Enrichment Analysis (GSEA). We observed that P301L tau up-regulates genes associated with reactive oxygen species responsiveness as well as genes involved in dendrite, microtubule, and nuclear body/speckle formation. The number of genes regulated by WT tau is greater than the mutant form, which indicates that the P301L mutation causes loss-of-function at the transcriptional level. WT tau up-regulates genes contributing to cytoskeleton-dependent intracellular transport, microglial activation, microtubule and nuclear chromatin organization, formation of nuclear bodies and speckles. Interestingly, both WT and P301L tau commonly down-regulate genes responsible for ubiquitin-proteosome system. In addition, WT tau significantly down-regulates several genes implicated in chromatin remodeling and nucleosome organization. Although there are limitations inherent to the model systems used, this study will improve understanding regarding the nuclear impact of tau at the transcriptional and post-transcriptional level. This study also illustrates the potential impact of P301L tau on the human brain genome during early phases of pathogenesis.
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Affiliation(s)
- Mauro Montalbano
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Stephanie Garcia
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Anna Ellsworth
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Salome McAllen
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Andrew Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
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Knock-Down of Heterogeneous Nuclear Ribonucleoprotein A1 Results in Neurite Damage, Altered Stress Granule Biology, and Cellular Toxicity in Differentiated Neuronal Cells. eNeuro 2021; 8:ENEURO.0350-21.2021. [PMID: 34697074 PMCID: PMC8607908 DOI: 10.1523/eneuro.0350-21.2021] [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: 08/23/2021] [Revised: 09/29/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is an RNA binding protein (RBP) that is localized within neurons and plays crucial roles in RNA metabolism. Its importance in neuronal functioning is underscored from the study of its pathogenic features in many neurodegenerative diseases where neuronal hnRNP A1 is mislocalized from the nucleus to the cytoplasm resulting in loss of hnRNP A1 function. Here, we model hnRNP A1 loss-of-function by siRNA-mediated knock-down in differentiated Neuro-2a cells. Through RNA sequencing (RNA-seq) followed by gene ontology (GO) analyses, we show that hnRNP A1 is involved in important biological processes, including RNA metabolism, neuronal function, neuronal morphology, neuronal viability, and stress granule (SG) formation. We further confirmed several of these roles by showing that hnRNP A1 knock-down results in a reduction of neurite outgrowth, increase in cell cytotoxicity and changes in SG formation. In summary, these findings indicate that hnRNP A1 loss-of-function contributes to neuronal dysfunction and cell death and implicates hnRNP A1 dysfunction in the pathogenesis of neurodegenerative diseases.
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Molecular Pathogenesis and Peripheral Monitoring of Adult Fragile X-Associated Syndromes. Int J Mol Sci 2021; 22:ijms22168368. [PMID: 34445074 PMCID: PMC8395059 DOI: 10.3390/ijms22168368] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/16/2022] Open
Abstract
Abnormal trinucleotide expansions cause rare disorders that compromise quality of life and, in some cases, lifespan. In particular, the expansions of the CGG-repeats stretch at the 5’-UTR of the Fragile X Mental Retardation 1 (FMR1) gene have pleiotropic effects that lead to a variety of Fragile X-associated syndromes: the neurodevelopmental Fragile X syndrome (FXS) in children, the late-onset neurodegenerative disorder Fragile X-associated tremor-ataxia syndrome (FXTAS) that mainly affects adult men, the Fragile X-associated primary ovarian insufficiency (FXPOI) in adult women, and a variety of psychiatric and affective disorders that are under the term of Fragile X-associated neuropsychiatric disorders (FXAND). In this review, we will describe the pathological mechanisms of the adult “gain-of-function” syndromes that are mainly caused by the toxic actions of CGG RNA and FMRpolyG peptide. There have been intensive attempts to identify reliable peripheral biomarkers to assess disease progression and onset of specific pathological traits. Mitochondrial dysfunction, altered miRNA expression, endocrine system failure, and impairment of the GABAergic transmission are some of the affectations that are susceptible to be tracked using peripheral blood for monitoring of the motor, cognitive, psychiatric and reproductive impairment of the CGG-expansion carriers. We provided some illustrative examples from our own cohort. Understanding the association between molecular pathogenesis and biomarkers dynamics will improve effective prognosis and clinical management of CGG-expansion carriers.
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Bain JM, Ardalan A, Goldman S. Deliberate paradigm shift in research in rare neurodevelopmental disorders. Orphanet J Rare Dis 2021; 16:263. [PMID: 34107995 PMCID: PMC8188744 DOI: 10.1186/s13023-021-01885-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 05/21/2021] [Indexed: 11/10/2022] Open
Abstract
Diagnosis and management of children with rare neurodevelopmental disorders (RNDDs) are complex. The COVID-19 pandemic has forced us to rethink the research activities critical to improve our understanding and treatment of RNDDs, such as creating large international registries and developing natural history studies. In this communication, we reflect on our latest effort in conducting research remotely while providing support, education and feedback to families affected by a specific RNDD. Specifically, we advocate for a deliberate paradigm shift towards virtual family meetings as ecological platforms to enroll and assess individuals with rare disorders. Herein, we demonstrate that such a shift is crucial to substantially increasing geographical and age range coverage, which are essential for capturing the phenotypic variations in RNDDs. Finally, we call on the community to invest in building integrated technological platforms necessary for effective remote research activities, through standardization, collaboration and training.
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Affiliation(s)
- Jennifer M. Bain
- Department of Neurology, Division of Child Neurology, Columbia University Irving Medical Center, 180 Fort Washington Avenue, 5th Floor, New York, NY 10032 USA
| | - Adel Ardalan
- Zuckerman Mind Brain Behavior Institute, Columbia University, 3227 Broadway, New York, NY 10027 USA
| | - Sylvie Goldman
- Department of Neurology, Division of Child Neurology, Columbia University Irving Medical Center, 180 Fort Washington Avenue, 5th Floor, New York, NY 10032 USA
- Department of Neurology, Division of Cognitive Neuroscience, Columbia University Irving Medical Center, 622 West 168th Street, PH18-331, New York, NY 10032 USA
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Klaric JA, Wüst S, Panier S. New Faces of old Friends: Emerging new Roles of RNA-Binding Proteins in the DNA Double-Strand Break Response. Front Mol Biosci 2021; 8:668821. [PMID: 34026839 PMCID: PMC8138124 DOI: 10.3389/fmolb.2021.668821] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions. To protect genomic stability and ensure cell homeostasis, cells mount a complex signaling-based response that not only coordinates the repair of the broken DNA strand but also activates cell cycle checkpoints and, if necessary, induces cell death. The last decade has seen a flurry of studies that have identified RNA-binding proteins (RBPs) as novel regulators of the DSB response. While many of these RBPs have well-characterized roles in gene expression, it is becoming increasingly clear that they also have non-canonical functions in the DSB response that go well beyond transcription, splicing and mRNA processing. Here, we review the current understanding of how RBPs are integrated into the cellular response to DSBs and describe how these proteins directly participate in signal transduction, amplification and repair at damaged chromatin. In addition, we discuss the implications of an RBP-mediated DSB response for genome instability and age-associated diseases such as cancer and neurodegeneration.
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Affiliation(s)
- Julie A Klaric
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Stas Wüst
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Stephanie Panier
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD) Research Center, University of Cologne, Cologne, Germany
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