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Tapken I, Kuhn D, Hoffmann N, Detering NT, Schüning T, Billaud JN, Tugendreich S, Schlüter N, Green J, Krämer A, Claus P. From data to discovery: AI-guided analysis of disease-relevant molecules in spinal muscular atrophy (SMA). Hum Mol Genet 2024:ddae076. [PMID: 38704739 DOI: 10.1093/hmg/ddae076] [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: 01/18/2024] [Revised: 04/04/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024] Open
Abstract
Spinal Muscular Atrophy is caused by partial loss of survival of motoneuron (SMN) protein expression. The numerous interaction partners and mechanisms influenced by SMN loss result in a complex disease. Current treatments restore SMN protein levels to a certain extent, but do not cure all symptoms. The prolonged survival of patients creates an increasing need for a better understanding of SMA. Although many SMN-protein interactions, dysregulated pathways, and organ phenotypes are known, the connections among them remain largely unexplored. Monogenic diseases are ideal examples for the exploration of cause-and-effect relationships to create a network describing the disease-context. Machine learning tools can utilize such knowledge to analyze similarities between disease-relevant molecules and molecules not described in the disease so far. We used an artificial intelligence-based algorithm to predict new genes of interest. The transcriptional regulation of 8 out of 13 molecules selected from the predicted set were successfully validated in an SMA mouse model. This bioinformatic approach, using the given experimental knowledge for relevance predictions, enhances efficient targeted research in SMA and potentially in other disease settings.
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Affiliation(s)
- Ines Tapken
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Feodor-Lynen-Str. 31, Hannover 30625, Germany
- Center for Systems Neuroscience (ZSN), Bünteweg 2, Hannover 30559, Germany
| | - Daniela Kuhn
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Feodor-Lynen-Str. 31, Hannover 30625, Germany
- Hannover Medical School, Department of Conservative Dentistry, Periodontology and Preventive Dentistry, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Nico Hoffmann
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Feodor-Lynen-Str. 31, Hannover 30625, Germany
| | - Nora T Detering
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Feodor-Lynen-Str. 31, Hannover 30625, Germany
- Center for Systems Neuroscience (ZSN), Bünteweg 2, Hannover 30559, Germany
| | - Tobias Schüning
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Feodor-Lynen-Str. 31, Hannover 30625, Germany
| | - Jean-Noël Billaud
- QIAGEN Digital Insights, 1001 Marshall Street,Redwood City, CA 94063, United States
| | - Stuart Tugendreich
- QIAGEN Digital Insights, 1001 Marshall Street,Redwood City, CA 94063, United States
| | - Nadine Schlüter
- Hannover Medical School, Department of Conservative Dentistry, Periodontology and Preventive Dentistry, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Jeff Green
- QIAGEN Digital Insights, 1001 Marshall Street,Redwood City, CA 94063, United States
| | - Andreas Krämer
- QIAGEN Digital Insights, 1001 Marshall Street,Redwood City, CA 94063, United States
| | - Peter Claus
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Feodor-Lynen-Str. 31, Hannover 30625, Germany
- Center for Systems Neuroscience (ZSN), Bünteweg 2, Hannover 30559, Germany
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Hemandhar Kumar S, Tapken I, Kuhn D, Claus P, Jung K. bootGSEA: a bootstrap and rank aggregation pipeline for multi-study and multi-omics enrichment analyses. FRONTIERS IN BIOINFORMATICS 2024; 4:1380928. [PMID: 38633435 PMCID: PMC11021641 DOI: 10.3389/fbinf.2024.1380928] [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: 02/02/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Introduction: Gene set enrichment analysis (GSEA) subsequent to differential expression analysis is a standard step in transcriptomics and proteomics data analysis. Although many tools for this step are available, the results are often difficult to reproduce because set annotations can change in the databases, that is, new features can be added or existing features can be removed. Finally, such changes in set compositions can have an impact on biological interpretation. Methods: We present bootGSEA, a novel computational pipeline, to study the robustness of GSEA. By repeating GSEA based on bootstrap samples, the variability and robustness of results can be studied. In our pipeline, not all genes or proteins are involved in the different bootstrap replicates of the analyses. Finally, we aggregate the ranks from the bootstrap replicates to obtain a score per gene set that shows whether it gains or loses evidence compared to the ranking of the standard GSEA. Rank aggregation is also used to combine GSEA results from different omics levels or from multiple independent studies at the same omics level. Results: By applying our approach to six independent cancer transcriptomics datasets, we showed that bootstrap GSEA can aid in the selection of more robust enriched gene sets. Additionally, we applied our approach to paired transcriptomics and proteomics data obtained from a mouse model of spinal muscular atrophy (SMA), a neurodegenerative and neurodevelopmental disease associated with multi-system involvement. After obtaining a robust ranking at both omics levels, both ranking lists were combined to aggregate the findings from the transcriptomics and proteomics results. Furthermore, we constructed the new R-package "bootGSEA," which implements the proposed methods and provides graphical views of the findings. Bootstrap-based GSEA was able in the example datasets to identify gene or protein sets that were less robust when the set composition changed during bootstrap analysis. Discussion: The rank aggregation step was useful for combining bootstrap results and making them comparable to the original findings on the single-omics level or for combining findings from multiple different omics levels.
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Affiliation(s)
- Shamini Hemandhar Kumar
- Institute for Animal Genomics, University of Veterinary Medicine, Foundation, Hannover, Germany
- Center for Systems Neuroscience (ZSN), University of Veterinary Medicine, Foundation, Hannover, Germany
| | - Ines Tapken
- Center for Systems Neuroscience (ZSN), University of Veterinary Medicine, Foundation, Hannover, Germany
- SMATHERIA gGmbH—Non-Profit Biomedical Research Institute, Hannover, Germany
| | - Daniela Kuhn
- SMATHERIA gGmbH—Non-Profit Biomedical Research Institute, Hannover, Germany
- Clinic for Conservative Dentistry, Periodontology and Preventive Dentistry, Hannover Medical School, Hannover, Germany
| | - Peter Claus
- Center for Systems Neuroscience (ZSN), University of Veterinary Medicine, Foundation, Hannover, Germany
- SMATHERIA gGmbH—Non-Profit Biomedical Research Institute, Hannover, Germany
| | - Klaus Jung
- Institute for Animal Genomics, University of Veterinary Medicine, Foundation, Hannover, Germany
- Center for Systems Neuroscience (ZSN), University of Veterinary Medicine, Foundation, Hannover, Germany
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Signoria I, van der Pol WL, Groen EJN. Innovating spinal muscular atrophy models in the therapeutic era. Dis Model Mech 2023; 16:dmm050352. [PMID: 37787662 PMCID: PMC10565113 DOI: 10.1242/dmm.050352] [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] [Indexed: 10/04/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a severe, monogenetic, neuromuscular disease. A thorough understanding of its genetic cause and the availability of robust models has led to the development and approval of three gene-targeting therapies. This is a unique and exciting development for the field of neuromuscular diseases, many of which remain untreatable. The development of therapies for SMA not only opens the door to future therapeutic possibilities for other genetic neuromuscular diseases, but also informs us about the limitations of such treatments. For example, treatment response varies widely and, for many patients, significant disability remains. Currently available SMA models best recapitulate the severe types of SMA, and these models are genetically and phenotypically more homogeneous than patients. Furthermore, treating patients is leading to a shift in phenotypes with increased variability in SMA clinical presentation. Therefore, there is a need to generate model systems that better reflect these developments. Here, we will first discuss current animal models of SMA and their limitations. Next, we will discuss the characteristics required to future-proof models to assist the field in the development of additional, novel therapies for SMA.
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Affiliation(s)
- Ilaria Signoria
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - W. Ludo van der Pol
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Ewout J. N. Groen
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
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Shamhari A‘A, Jefferi NES, Abd Hamid Z, Budin SB, Idris MHM, Taib IS. The Role of Promyelocytic Leukemia Zinc Finger (PLZF) and Glial-Derived Neurotrophic Factor Family Receptor Alpha 1 (GFRα1) in the Cryopreservation of Spermatogonia Stem Cells. Int J Mol Sci 2023; 24:ijms24031945. [PMID: 36768269 PMCID: PMC9915902 DOI: 10.3390/ijms24031945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 01/20/2023] Open
Abstract
The cryopreservation of spermatogonia stem cells (SSCs) has been widely used as an alternative treatment for infertility. However, cryopreservation itself induces cryoinjury due to oxidative and osmotic stress, leading to reduction in the survival rate and functionality of SSCs. Glial-derived neurotrophic factor family receptor alpha 1 (GFRα1) and promyelocytic leukemia zinc finger (PLZF) are expressed during the self-renewal and differentiation of SSCs, making them key tools for identifying the functionality of SSCs. To the best of our knowledge, the involvement of GFRα1 and PLZF in determining the functionality of SSCs after cryopreservation with therapeutic intervention is limited. Therefore, the purpose of this review is to determine the role of GFRα1 and PLZF as biomarkers for evaluating the functionality of SSCs in cryopreservation with therapeutic intervention. Therapeutic intervention, such as the use of antioxidants, and enhancement in cryopreservation protocols, such as cell encapsulation, cryoprotectant agents (CPA), and equilibrium of time and temperature increase the expression of GFRα1 and PLZF, resulting in maintaining the functionality of SSCs. In conclusion, GFRα1 and PLZF have the potential as biomarkers in cryopreservation with therapeutic intervention of SSCs to ensure the functionality of the stem cells.
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Affiliation(s)
- Asma’ ‘Afifah Shamhari
- Center of Diagnostics, Therapeutics, and Investigative Studies (CODTIS), Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Wilayah Persekutuan, Malaysia
| | - Nur Erysha Sabrina Jefferi
- Center of Diagnostics, Therapeutics, and Investigative Studies (CODTIS), Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Wilayah Persekutuan, Malaysia
| | - Zariyantey Abd Hamid
- Center of Diagnostics, Therapeutics, and Investigative Studies (CODTIS), Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Wilayah Persekutuan, Malaysia
| | - Siti Balkis Budin
- Center of Diagnostics, Therapeutics, and Investigative Studies (CODTIS), Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Wilayah Persekutuan, Malaysia
| | - Muhd Hanis Md Idris
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Puncak Alam Campus, Bandar Puncak Alam 42300, Selangor, Malaysia
| | - Izatus Shima Taib
- Center of Diagnostics, Therapeutics, and Investigative Studies (CODTIS), Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Wilayah Persekutuan, Malaysia
- Correspondence: ; Tel.: +603-928-97608
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Detering NT, Schüning T, Hensel N, Claus P. The phospho-landscape of the survival of motoneuron protein (SMN) protein: relevance for spinal muscular atrophy (SMA). Cell Mol Life Sci 2022; 79:497. [PMID: 36006469 PMCID: PMC11071818 DOI: 10.1007/s00018-022-04522-9] [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: 03/21/2022] [Revised: 07/27/2022] [Accepted: 08/09/2022] [Indexed: 11/03/2022]
Abstract
Spinal muscular atrophy (SMA) is caused by low levels of the survival of motoneuron (SMN) Protein leading to preferential degeneration of lower motoneurons in the ventral horn of the spinal cord and brain stem. However, the SMN protein is ubiquitously expressed and there is growing evidence of a multisystem phenotype in SMA. Since a loss of SMN function is critical, it is important to decipher the regulatory mechanisms of SMN function starting on the level of the SMN protein itself. Posttranslational modifications (PTMs) of proteins regulate multiple functions and processes, including activity, cellular trafficking, and stability. Several PTM sites have been identified within the SMN sequence. Here, we map the identified SMN PTMs highlighting phosphorylation as a key regulator affecting localization, stability and functions of SMN. Furthermore, we propose SMN phosphorylation as a crucial factor for intracellular interaction and cellular distribution of SMN. We outline the relevance of phosphorylation of the spinal muscular atrophy (SMA) gene product SMN with regard to basic housekeeping functions of SMN impaired in this neurodegenerative disease. Finally, we compare SMA patient mutations with putative and verified phosphorylation sites. Thus, we emphasize the importance of phosphorylation as a cellular modulator in a clinical perspective as a potential additional target for combinatorial SMA treatment strategies.
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Affiliation(s)
- Nora Tula Detering
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Hannover, Germany
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Tobias Schüning
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Hannover, Germany
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Niko Hensel
- Ottawa Hospital Research Institute (OHRI), Ottawa, Canada
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Peter Claus
- SMATHERIA gGmbH - Non-Profit Biomedical Research Institute, Hannover, Germany.
- Center for Systems Neuroscience (ZSN), Hannover, Germany.
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Brown SJ, Kline RA, Synowsky SA, Shirran SL, Holt I, Sillence KA, Claus P, Wirth B, Wishart TM, Fuller HR. The Proteome Signatures of Fibroblasts from Patients with Severe, Intermediate and Mild Spinal Muscular Atrophy Show Limited Overlap. Cells 2022; 11:cells11172624. [PMID: 36078032 PMCID: PMC9454632 DOI: 10.3390/cells11172624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 12/04/2022] Open
Abstract
Most research to characterise the molecular consequences of spinal muscular atrophy (SMA) has focused on SMA I. Here, proteomic profiling of skin fibroblasts from severe (SMA I), intermediate (SMA II), and mild (SMA III) patients, alongside age-matched controls, was conducted using SWATH mass spectrometry analysis. Differentially expressed proteomic profiles showed limited overlap across each SMA type, and variability was greatest within SMA II fibroblasts, which was not explained by SMN2 copy number. Despite limited proteomic overlap, enriched canonical pathways common to two of three SMA severities with at least one differentially expressed protein from the third included mTOR signalling, regulation of eIF2 and eIF4 signalling, and protein ubiquitination. Network expression clustering analysis identified protein profiles that may discriminate or correlate with SMA severity. From these clusters, the differential expression of PYGB (SMA I), RAB3B (SMA II), and IMP1 and STAT1 (SMA III) was verified by Western blot. All SMA fibroblasts were transfected with an SMN-enhanced construct, but only RAB3B expression in SMA II fibroblasts demonstrated an SMN-dependent response. The diverse proteomic profiles and pathways identified here pave the way for studies to determine their utility as biomarkers for patient stratification or monitoring treatment efficacy and for the identification of severity-specific treatments.
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Affiliation(s)
- Sharon J. Brown
- School of Pharmacy and Bioengineering (PhaB), Keele University, Keele ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
| | - Rachel A. Kline
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
- Euan MacDonald Centre, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Silvia A. Synowsky
- BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews, St Andrews KY16 9ST, UK
| | - Sally L. Shirran
- BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews, St Andrews KY16 9ST, UK
| | - Ian Holt
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
| | | | - Peter Claus
- SMATHERIA gGmbH—Non-Profit Biomedical Research Institute, 30625 Hannover, Germany
| | - Brunhilde Wirth
- Institute of Human Genetics, University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Rare Diseases, University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Institute for Genetics, University of Cologne, 50931 Cologne, Germany
| | - Thomas M. Wishart
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
- Euan MacDonald Centre, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Heidi R. Fuller
- School of Pharmacy and Bioengineering (PhaB), Keele University, Keele ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
- Correspondence: ; Tel.: +44-(0)1-782-734546
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Detering NT, Zambon A, Hensel N, Kothary R, Swoboda K, Gillingwater TH, Baranello G. 264th ENMC International Workshop: Multi-system involvement in Spinal Muscular Atrophy Hoofddorp, The Netherlands, November 19th – 21th 2021. Neuromuscul Disord 2022; 32:697-705. [DOI: 10.1016/j.nmd.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 06/16/2022] [Indexed: 11/24/2022]
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Kubinski S, Claus P. Protein Network Analysis Reveals a Functional Connectivity of Dysregulated Processes in ALS and SMA. Neurosci Insights 2022; 17:26331055221087740. [PMID: 35372839 PMCID: PMC8966079 DOI: 10.1177/26331055221087740] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/28/2022] [Indexed: 01/09/2023] Open
Abstract
Spinal Muscular Atrophy (SMA) and Amyotrophic Lateral Sclerosis (ALS) are neurodegenerative diseases which are characterized by the loss of motoneurons within the central nervous system. SMA is a monogenic disease caused by reduced levels of the Survival of motoneuron protein, whereas ALS is a multi-genic disease with over 50 identified disease-causing genes and involvement of environmental risk factors. Although these diseases have different causes, they partially share identical phenotypes and pathomechanisms. To analyze and identify functional connections and to get a global overview of altered pathways in both diseases, protein network analyses are commonly used. Here, we used an in silico tool to test for functional associations between proteins that are involved in actin cytoskeleton dynamics, fatty acid metabolism, skeletal muscle metabolism, stress granule dynamics as well as SMA or ALS risk factors, respectively. In network biology, interactions are represented by edges which connect proteins (nodes). Our approach showed that only a few edges are necessary to present a complex protein network of different biological processes. Moreover, Superoxide dismutase 1, which is mutated in ALS, and the actin-binding protein profilin1 play a central role in the connectivity of the aforementioned pathways. Our network indicates functional links between altered processes that are described in either ALS or SMA. These links may not have been considered in the past but represent putative targets to restore altered processes and reveal overlapping pathomechanisms in both diseases.
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Affiliation(s)
- Sabrina Kubinski
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, Hannover, Germany
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Peter Claus
- Center for Systems Neuroscience (ZSN), Hannover, Germany
- SMATHERIA gGmbH – Non-Profit Biomedical Research Institute, Hannover, Germany
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Kray KM, McGovern VL, Chugh D, Arnold WD, Burghes AHM. Dual SMN inducing therapies can rescue survival and motor unit function in symptomatic ∆7SMA mice. Neurobiol Dis 2021; 159:105488. [PMID: 34425216 PMCID: PMC8502210 DOI: 10.1016/j.nbd.2021.105488] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/06/2021] [Accepted: 08/16/2021] [Indexed: 11/24/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive disease characterized by survival motor neuron (SMN) protein deficiency which results in motor neuron loss and muscle atrophy. SMA is caused by a mutation or deletion of the survival motor neuron 1 (SMN1) gene and retention of the nearly identical SMN2 gene. SMN2 contains a C to T change in exon 7 that results in exon 7 exclusion from 90% of transcripts. SMN protein lacking exon 7 is unstable and rapidly degraded. The remaining full-length transcripts from SMN2 are insufficient for normal motor neuron function leading to the development of SMA. Three different therapeutic approaches that increase full-length SMN (FL-SMN) protein production are approved for treatment of SMA patients. Studies in both animal models and humans have demonstrated increasing SMN levels prior to onset of symptoms provides the greatest therapeutic benefit. Treatment of SMA, after some motor neuron loss has occurred, is also effective but to a lesser degree. The SMN∆7 mouse model is a well characterized model of severe or type 1 SMA, dying at 14 days of age. Here we treated three groups of ∆7SMA mice starting before, roughly during, and after symptom onset to determine if combining two mechanistically distinct SMN inducing therapies could improve the therapeutic outcome both before and after motor neuron loss. We found, compared with individual therapies, that morpholino antisense oligonucleotide (ASO) directed against ISS-N1 combined with the small molecule compound RG7800 significantly increased FL-SMN transcript and protein production resulting in improved survival and weight of ∆7SMA mice. Moreover, when give late symptomatically, motor unit function was completely rescued with no loss in function at 100 days of age in the dual treatment group. We have therefore shown that this dual therapeutic approach successfully increases SMN protein and rescues motor function in symptomatic ∆7SMA mice.
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Affiliation(s)
- Kaitlyn M Kray
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, 1060 Carmack Road, Columbus, OH 43210, USA.
| | - Vicki L McGovern
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, 1060 Carmack Road, Columbus, OH 43210, USA.
| | - Deepti Chugh
- Department of Neurology, Neuromuscular Division, The Ohio State University Wexner Medical Center, 395 W. 12(th) Ave, Columbus, OH 43210, USA
| | - W David Arnold
- Department of Neurology, Neuromuscular Division, The Ohio State University Wexner Medical Center, 395 W. 12(th) Ave, Columbus, OH 43210, USA.
| | - Arthur H M Burghes
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, 1060 Carmack Road, Columbus, OH 43210, USA; Department of Neurology, Neuromuscular Division, The Ohio State University Wexner Medical Center, 395 W. 12(th) Ave, Columbus, OH 43210, USA.
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Hensel N, Brickwedde H, Tsaknakis K, Grages A, Braunschweig L, Lüders KA, Lorenz HM, Lippross S, Walter LM, Tavassol F, Lienenklaus S, Neunaber C, Claus P, Hell AK. Altered bone development with impaired cartilage formation precedes neuromuscular symptoms in spinal muscular atrophy. Hum Mol Genet 2021; 29:2662-2673. [PMID: 32644125 DOI: 10.1093/hmg/ddaa145] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 01/04/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a fatal neurodegenerative disease of newborns and children caused by mutations or deletions of the survival of motoneuron gene 1 resulting in low levels of the SMN protein. While neuromuscular degeneration is the cardinal symptom of the disease, the reduction of the ubiquitously expressed SMN additionally elicits non-motoneuron symptoms. Impaired bone development is a key feature of SMA, but it is yet unknown whether this is an indirect functional consequence of muscle weakness or caused by bone-intrinsic mechanisms. Therefore, we radiologically examined SMA patients in a prospective, non-randomized cohort study characterizing bone size and bone mineral density (BMD) and performed equivalent measurements in pre-symptomatic SMA mice. BMD as well as lumbar vertebral body size were significantly reduced in SMA patients. This growth defect but not BMD reduction was confirmed in SMA mice by μCT before the onset of neuromuscular symptoms indicating that it is at least partially independent of neuromuscular degeneration. Interestingly, the number of chondroblasts in the hypertrophic zone of the growth plate was significantly reduced. This was underlined by RNAseq and expression data from developing SMA mice vertebral bodies, which revealed molecular changes related to cell division and cartilage remodeling. Together, these findings suggest a bone intrinsic defect in SMA. This phenotype may not be rescued by novel drugs that enhance SMN levels in the central nervous system only.
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Affiliation(s)
- Niko Hensel
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, Hannover, Germany.,Center for Systems Neurosciences (ZSN), Hannover, Germany
| | - Hermann Brickwedde
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, Hannover, Germany
| | - Konstantinos Tsaknakis
- Pediatric Orthopedics, Department of Trauma, Orthopedic and Plastic Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Antonia Grages
- Pediatric Orthopedics, Department of Trauma, Orthopedic and Plastic Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Lena Braunschweig
- Pediatric Orthopedics, Department of Trauma, Orthopedic and Plastic Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Katja A Lüders
- Pediatric Orthopedics, Department of Trauma, Orthopedic and Plastic Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Heiko M Lorenz
- Pediatric Orthopedics, Department of Trauma, Orthopedic and Plastic Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Sebastian Lippross
- Pediatric Orthopedics, Department of Trauma, Orthopedic and Plastic Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Lisa M Walter
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, Hannover, Germany.,Center for Systems Neurosciences (ZSN), Hannover, Germany
| | - Frank Tavassol
- Department of Oral and Maxillofacial Surgery, Hannover Medical School, Hannover, Germany
| | - Stefan Lienenklaus
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hannover, Germany
| | | | - Peter Claus
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, Hannover, Germany.,Center for Systems Neurosciences (ZSN), Hannover, Germany
| | - Anna K Hell
- Pediatric Orthopedics, Department of Trauma, Orthopedic and Plastic Surgery, University Medical Center Goettingen, Goettingen, Germany
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Impairment of the neurotrophic signaling hub B-Raf contributes to motoneuron degeneration in spinal muscular atrophy. Proc Natl Acad Sci U S A 2021; 118:2007785118. [PMID: 33931501 DOI: 10.1073/pnas.2007785118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a motoneuron disease caused by deletions of the Survival of Motoneuron 1 gene (SMN1) and low SMN protein levels. SMN restoration is the concept behind a number of recently approved drugs which result in impressive yet limited effects. Since SMN has already been enhanced in treated patients, complementary SMN-independent approaches are needed. Previously, a number of altered signaling pathways which regulate motoneuron degeneration have been identified as candidate targets. However, signaling pathways form networks, and their connectivity is still unknown in SMA. Here, we used presymptomatic SMA mice to elucidate the network of altered signaling in SMA. The SMA network is structured in two clusters with AKT and 14-3-3 ζ/δ in their centers. Both clusters are connected by B-Raf as a major signaling hub. The direct interaction of B-Raf with 14-3-3 ζ/δ is important for an efficient neurotrophic activation of the MEK/ERK pathway and crucial for motoneuron survival. Further analyses in SMA mice revealed that both proteins were down-regulated in motoneurons and the spinal cord with B-Raf being reduced at presymptomatic stages. Primary fibroblasts and iPSC-derived motoneurons from SMA patients both showed the same pattern of down-regulation. This mechanism is conserved across species since a Caenorhabditis elegans SMA model showed less expression of the B-Raf homolog lin-45 Accordingly, motoneuron survival was rescued by a cell autonomous lin-45 expression in a C. elegans SMA model resulting in improved motor functions. This rescue was effective even after the onset of motoneuron degeneration and mediated by the MEK/ERK pathway.
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Wirth B. Spinal Muscular Atrophy: In the Challenge Lies a Solution. Trends Neurosci 2021; 44:306-322. [PMID: 33423791 DOI: 10.1016/j.tins.2020.11.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/08/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022]
Abstract
The path from gene discovery to therapy in spinal muscular atrophy (SMA) has been a highly challenging endeavor, but also led to one of the most successful stories in neurogenetics. In SMA, a neuromuscular disorder with an often fatal outcome until recently, with those affected never able to sit, stand, or walk, children now achieve these motoric abilities and almost age-based development when treated presymptomatically. This review summarizes the challenges along this 30-year journey. It is also meant to inspire early-career scientists not to give up when things become difficult but to try to uncover the biological underpinnings and transform the challenge into the next big discovery. Without doubt, the improvements seen with the three therapeutic strategies in SMA are impressive; many open questions remain and are discussed in this review.
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Affiliation(s)
- Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine, Center for Rare Disorders, University of Cologne, Kerpener Str. 34, 50931 Cologne, Germany.
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Spinal muscular atrophy: Broad disease spectrum and sex-specific phenotypes. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166063. [PMID: 33412266 DOI: 10.1016/j.bbadis.2020.166063] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 12/17/2022]
Abstract
Spinal muscular atrophy (SMA) is one of the major genetic disorders associated with infant mortality. More than 90% of cases of SMA result from deletions of or mutations in the Survival Motor Neuron 1 (SMN1) gene. SMN2, a nearly identical copy of SMN1, does not compensate for the loss of SMN1 due to predominant skipping of exon 7. The spectrum of SMA is broad, ranging from prenatal death to infant mortality to survival into adulthood. All tissues, including brain, spinal cord, bone, skeletal muscle, heart, lung, liver, pancreas, gastrointestinal tract, kidney, spleen, ovary and testis, are directly and/or indirectly affected in SMA. Accumulating evidence on impaired mitochondrial biogenesis and defects in X chromosome-linked modifying factors, coupled with the sexual dimorphic nature of many tissues, point to sex-specific vulnerabilities in SMA. Here we review the role of sex in the pathogenesis of SMA.
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Gollapalli K, Kim JK, Monani UR. Emerging concepts underlying selective neuromuscular dysfunction in infantile-onset spinal muscular atrophy. Neural Regen Res 2021; 16:1978-1984. [PMID: 33642371 PMCID: PMC8343306 DOI: 10.4103/1673-5374.308073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Infantile-onset spinal muscular atrophy is the quintessential example of a disorder characterized by a predominantly neurodegenerative phenotype that nevertheless stems from perturbations in a housekeeping protein. Resulting from low levels of the Survival of Motor Neuron (SMN) protein, spinal muscular atrophy manifests mainly as a lower motor neuron disease. Why this is so and whether other cell types contribute to the classic spinal muscular atrophy phenotype continue to be the subject of intense investigation and are only now gaining appreciation. Yet, what is emerging is sometimes as puzzling as it is instructive, arguing for a careful re-examination of recent study outcomes, raising questions about established dogma in the field and making the case for a greater focus on milder spinal muscular atrophy models as tools to identify key mechanisms driving selective neuromuscular dysfunction in the disease. This review examines the evidence for novel molecular and cellular mechanisms that have recently been implicated in spinal muscular atrophy, highlights breakthroughs, points out caveats and poses questions that ought to serve as the basis of new investigations to better understand and treat this and other more common neurodegenerative disorders.
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Affiliation(s)
- Kishore Gollapalli
- Department of Neurology; Center for Motor Neuron Biology and Disease, Columbia University Medical Center, New York, NY, USA
| | - Jeong-Ki Kim
- Department of Neurology; Center for Motor Neuron Biology and Disease, Columbia University Medical Center, New York, NY, USA
| | - Umrao R Monani
- Department of Neurology; Department of Pathology & Cell Biology; Center for Motor Neuron Biology and Disease, Columbia University Medical Center, New York, NY, USA
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Li YJ, Chen TH, Wu YZ, Tseng YH. Metabolic and Nutritional Issues Associated with Spinal Muscular Atrophy. Nutrients 2020; 12:nu12123842. [PMID: 33339220 PMCID: PMC7766651 DOI: 10.3390/nu12123842] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/02/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
Spinal muscular atrophy (SMA), the main genetic cause of infant death, is a neurodegenerative disease characterized by the selective loss of motor neurons in the anterior horn of the spinal cord, accompanied by muscle wasting. Pathomechanically, SMA is caused by low levels of the survival motor neuron protein (SMN) resulting from the loss of the SMN1 gene. However, emerging research extends the pathogenic effect of SMN deficiency beyond motor neurons. A variety of metabolic abnormalities, especially altered fatty acid metabolism and impaired glucose tolerance, has been described in isolated cases of SMA; therefore, the impact of SMN deficiency in metabolic abnormalities has been speculated. Although the life expectancy of these patients has increased due to novel disease-modifying therapies and standardization of care, understanding of the involvement of metabolism and nutrition in SMA is still limited. Optimal nutrition support and metabolic monitoring are essential for patients with SMA, and a comprehensive nutritional assessment can guide personalized nutritional therapy for this vulnerable population. It has recently been suggested that metabolomics studies before and after the onset of SMA in patients can provide valuable information about the direct or indirect effects of SMN deficiency on metabolic abnormalities. Furthermore, identifying and quantifying the specific metabolites in SMA patients may serve as an authentic biomarker or therapeutic target for SMA. Here, we review the main epidemiological and mechanistic findings that link metabolic changes to SMA and further discuss the principles of metabolomics as a novel approach to seek biomarkers and therapeutic insights in SMA.
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Affiliation(s)
- Yang-Jean Li
- Department of Pediatrics, Kaohsiung Municipal United Hospital, Kaohsiung 80455, Taiwan;
| | - Tai-Heng Chen
- Department of Pediatrics, Division of Pediatric Emergency, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (Y.-Z.W.); (Y.-H.T.)
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Correspondence: ; Tel.: +886-7-312-1101; Fax: +886-7-321-2062
| | - Yan-Zhang Wu
- Department of Pediatrics, Division of Pediatric Emergency, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (Y.-Z.W.); (Y.-H.T.)
| | - Yung-Hao Tseng
- Department of Pediatrics, Division of Pediatric Emergency, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (Y.-Z.W.); (Y.-H.T.)
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