Automatic Text-Mining Approach to Identify Molecular Target Candidates Associated with Metabolic Processes for Myotonic Dystrophy Type 1
Abstract
:1. Introduction
2. Material and Methods
2.1. Search Approach
2.2. Automatic Text-Mining Analysis Using VOSviewer
2.3. DisGeNET Search
2.4. Protein–Protein Interaction Network Construction
2.5. Gene Ontology Functional and Pathway Enrichment Analyses
3. Results
3.1. Literature Search and Automatic Text-Mining Analysis to Unveil Novel Metabolism Molecular Targets in DM1
3.2. Comparative Analysis of the Novel Identified Metabolism-Associated Molecular Targets in DM1 Using VOSviewer with Molecular Associations Previously Described in DisGeNET
3.3. Characterization and Functional Enrichment Analysis of the Novel Identified Metabolism Associated Molecular Targets in DM1
4. Discussion
4.1. Dysregulation of Biological Processes and Signaling Pathways Associated with DM1
4.1.1. Muscle Function and Associated Pathways
4.1.2. NGF and TRK Signaling Pathways
4.1.3. Insulin Signaling Pathways
4.1.4. Myogenesis- and Signaling-Associated Pathways
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Rank | Keyword | Total Link Strength |
---|---|---|
1 | Myotonic dystrophy | 29,037 |
2 | Metabolism | 28,505 |
3 | Gene expression | 15,044 |
4 | Skeletal muscle | 14,660 |
5 | Muscle, skeletal | 13,750 |
6 | RNA-binding proteins | 10,329 |
UniProt Accession Number | Gene Name | Protein Name | Biological Process |
---|---|---|---|
Q09013 | DMPK | Myotonic dystrophy protein kinase | Muscle cell apoptotic processing; intercellular signal transduction; regulation of excitatory postsynaptic membrane potential in skeletal muscle contraction; cellular calcium ion homeostasis |
Q9NR56 | MBNL1 | Muscleblind Like Splicing Regulator 1 | Neurogenesis; mRNA splicing; mRNA processing; myoblast differentiation |
Q92879 | CELF1 | CUGBP Elav-Like Family Member 1 | mRNA processing; germ cell development; positive regulation of gene expression and cell death |
P06213 | INSR | Insulin Receptor | Carbohydrate metabolism; activation and positive regulation of protein kinase activity; glucose homeostasis; insulin receptor signaling pathway |
P05231 | IL-6 | Interleukin 6 | Acute-phase inflammatory response; cellular response to lipopolysaccharide; glucose homeostasis; negative regulation of lipid storage; positive regulation of MAPK cascade |
P05019 | IGF-1 | Insulin-like growth factor 1 | Myogenesis; ERK1 and ERK2 cascade; glycolate metabolic process; muscle hypertrophy; myoblast differentiation and proliferation |
P11532 | DMD | Dystrophin | Myogenesis; actin cytoskeleton organization; muscle cell development; regulation of muscle system process; skeletal muscle tissue development |
P17252 | PRKCA | Protein Kinase C alpha | Cell adhesion; neurotransmitter; angiogenesis; protein synthesis inhibitor; positive regulation of bone resorption; protein phosphorylation; regulation of mRNA stability |
P60709 | ACTB | Beta-actin | Blood coagulation; rotamase; cell motility; axongenesis |
O14983 | ATP2A1 | ATPase Sarcoplasmic/Endoplasmic Reticulum Ca2+ Transporting 1 | Blood coagulation; calcium transport; ATP synthesis; maintenance of mitochondrion location; negative regulation of striated muscle contraction |
P16615 | ATP2A2 | ATPase Sarcoplasmic/Endoplasmic Reticulum Ca2+ Transporting 2 | Cell adhesion; blood coagulation; translocation; transport; ATP synthesis |
P21817 | RYR-1 | Ryanodine receptor 1 | Calcium transport; muscle contraction; skeletal muscle fiber development |
P42574 | CASP3 | Caspase 3 | Protease; apoptosis; DNA damage; proteolysis; protein processing |
P01137 | TGFB1 | Transforming Growth Factor Beta 1 | ATP synthesis; growth arrest; inflammatory response; DNA replication inhibition; neurodegeneration; MAPK cascade |
P06732 | CKM | Creatine kinase, M-type | Creatine metabolic process; phosphocreatine biosynthetic process |
UniProt ID | Gene/miRNA | Protein | Biological Process | Generic Gene Role/Function in DM1 | VOSviewer Occurrences | Reference |
---|---|---|---|---|---|---|
Q5T8P6 | RBM26 | RNA-binding protein 26 | mRNA processing | - Protein-coding gene critical for PAXT-mediated nuclear RNA. | 478 | [32] |
Q75NE6 | MIR17HG | Putative microRNA 17 host gene protein | - | - Exhibits complex links to cancer metastasis. | 253 | [33] |
P01398 | INS | Insulin | Glucose metabolism, sigma factor, transcription | - INS is linked with the regulation of muscle protein synthesis, through which reduced insulin sensitivity effects occur in lower muscle mass. - Insulin signaling is known to be a significant contributor to DM1. | 196 | [34] |
P13591 | NCAM1 | Neural cell adhesion molecule 1 | Cell adhesion plasma membrane, virus receptor activity | - Its site of expression/function in the membrane protein - Known to occur more frequently in nuclear clump fibers in DM2 than in DM1. | 188 | [35] |
Q9Y6E0 | STK24 | Serine/threonine-protein kinase 24 | Protein phosphorylation, signal transduction | - Promotes apoptosis in response to caspase activation and stress stimuli. | 162 | [36] |
Q9UHP9 | SMPX | Small muscular protein | Striated muscle contraction | - Functions to promote myocyte fusion by increasing the activity of the nuclear factor of activated T cells and MEF2 transcription factors through IGF1 signaling. - Important for muscle fiber organization and distal myopathy. | 145 | [37] |
P68133 | ACTA1 | Actin, alpha skeletal muscle | Muscle contraction, skeletal muscle fiber adaption and development, skeletal muscle thin filament assembly | - Plays a role in the integrity, motility, and structure of all eukaryotic cells. It is also expressed in skeletal muscle. - Mutations in this gene are likely to cause various kinds of myopathy. - ACTA1 mutations are a notable cause of serious congenital myopathies with no treatment. | 128 | [38] |
Q8TCT8 | SPPL2A | Signal peptide peptidase-like 2A | Membrane protein ectodomain proteolysis, membrane protein proteolysis | - Plays a key role in the development and purpose of antigen-presenting cells such as dendritic cells. - Shows a druggable pharmacological target, with the potential to provide a novel approach for treating autoimmune diseases by targeting dendritic cells and B cells. | 112 | [39] |
Q8N5C6 | SRBD1 | S1 RNA-binding domain-containing protein 1 | Translation, nucleobase-containing compound metabolic process | - SRBD1 is an RNA-binding protein usually identified in E.coli. - Participates maintainence of homeostasis, cell growth, induction of apoptosis, and protein synthesis. - SRBD1 is known to be sensitive to early-onset normal tension glaucoma, although the functions of this gene in other fields are unclear. | 112 | [40] |
O60356 | NUPR1 | Nuclear protein 1 | Detoxification, protein acetylation, skeletal muscle cell differentiation | - Little information about NUPR1 is available in relation to DM1, nuclear envelope alterations are observed in DM1 primary myoblasts. | 101 | [41] |
P40692 | MLH1 | DNA mismatch repair protein MLH1 | Spermatogenesis, oogenesis, mismatch repair | - Provides instructions to make proteins that play a role in repairing DNA. | 92 | [42] |
Q13464 | ROCK1 | Rho-associated protein kinase 1 | Regulation of cell adhesion, signal transduction | - Destabilizes the actin cytoskeleton via regulation of myosin light chain 2 (MLC2) phosphorylation. | 89 | [43] |
P41134 | ID1 | DNA-binding protein inhibitor ID-1 | DNA-directed RNA polymerase transcription, apoptosis, angiogenesis, antibiotic resistance | - Helix–loop–helix protein involved in cellular growth and processes that has no basic region and does not bind to DNA. - ID1 inhibits skeletal muscle but has no direct association with DM1. | 78 | [44] |
P10636 | MAPT | Microtubule-associated protein tau | rRNA metabolic process, protein homo-oligomerization | - Contributes to microtubule assembly and stability. | 78 | [45] |
P12882 | MYH1 | Myosin-1 | Muscle contraction | - Myosin changes chemical energy into mechanical energy via the hydrolysis of ATP. | 77 | [46] |
P51114 | FXR1 | Fragile X mental retardation syndrome-related protein 1 | Apoptotic process, muscle organ development, skeletal muscle organ development | - FXR1 splicing is key for muscle development and biomolecular condensates in muscle cells. | 74 | [47] |
P01138 | NGF | Beta nerve growth factor | Apoptosis, inflammatory response | - Provides directions for the manufacture of a protein called nerve growth factor beta (NGFβ). - Contributes to the development and survival of nerve cells. | 71 | [48] |
Q86TN4 | TRPT1 | tRNA 2’-phosphotransferase 1 | tRNA processing, regulation of protein kinase activity | - Predicted to enable tRNA 2’-phosphotransferase activity. - Anticipated to be involved in tRNA splicing through ligation and endonucleolytic cleavage. | 68 | [49] |
P15923 | TCF3 | Transcription factor E2-alpha | DNA-directed RNA polymerase, transcription, transcription, regulation, apoptosis | - Plays a vital role in embryogenesis. | 66 | [50] |
P31749 | AKT1 | Protein kinase B | Cell differentiation, glucose metabolic process, protein kinase B signaling, protein phosphorylation | - AKT1 regulates processes including cell survival, metabolism, and angiogenesis. This gene plays a role in various signaling pathways in neurodegenerative diseases. - Impairment of AKT signaling in DM1 pathogenesis causes surges in apoptosis and autophagy, which can be affected in DM1 by AMPK downregulation. | 65 | [51] |
Q9BPY8 | HOPX | Homeodomain-only protein | DNA-directed RNA polymerase, Transcription, regulation of protein binding | - Involved in the regulation of growth and differentiation of myocytes, stem cells, and lymphocytes. | 61 | [52] |
Q14344 | GNA13 | Guanine nucleotide-binding protein subunit alpha-13 | Transduction, blood coagulation, differentiation, cell shape | - Contributes to bone homeostasis, angiogenesis, platelet activation, and localization of germinal B cells. | 60 | [53] |
P17028 | ZNF24 | Zinc finger protein 24 | DNA-directed RNA polymerase, transcription, myelination | - Controls proliferation, differentiation, and migration in many kinds of cells. | 60 | [54] |
P01730 | CD4 | T-cell surface glycoprotein CD4 | Transduction, cell adhesion, innate immunity | - CD4 (T cells) fights infection. - Crucial role in adaptive immune responses, such as the stimulation of cytotoxic lymphocytes. - HIV particles are reproduced by infected CD4 T cells. | 57 | [55] |
P28482 | MAPK1 | Mitogen-activated protein kinase 1 | DNA-directed RNA polymerase, cytosine metabolic process, ERK1 and ERK2 cascade, protein phosphorylation | - Involved in muscular dystrophies. - Many researchers have reported the activation of extracellular signal-related kinases (ERKs), c-Jun N-terminal kinases (JNKs), and p-38 MAPK in skeletal and cardiac muscle of Duchenne muscular dystrophies. - ERKs were also found to be deregulated in DM1. - MAPKs are targets of PKC proteins. | 55 | [56,57] |
Q9ULG6 | CCPG1 | Cell cycle progression protein 1 | Positive regulation of cell cycle, positive regulation of cell population proliferation | - Cell cycle progression gene 1 and has no known physiological role. - This gene is important for ER-phagy and pancreatic ER proteostasis. | 53 | [58] |
P17661 | DES | Desmin | Cytoskeleton organization, muscle contraction | - A class III intermediate filament used as a marker of myogenic cells. - Found in cardiac and skeletal muscle. | 53 | [59] |
Q15669 | RHOH | Rho-related GTP-binding protein RhoH | Sigma factor, transcription regulation | - Rho genes are part of the Ras superfamily of GTPases. - Alteration of signal transduction by Rho GTPases is a repeated theme in the flow of human malignancies. | 48 | [60] |
P60953 | CDC42 | Cell division control protein 42 homolog | Actin cytoskeleton organization, actin filament branching | - Plays an essential role in local F-actin organization by several kinase and non-kinase effector proteins - Cell cycle regulator. | 45 | [61] |
Q9NRG0 | CHRAC1 | Chromatin accessibility complex protein 1 | Nucleosome assembly and mobilization, regulation of DNA replication | - A potential target for lung cancer. | 45 | [62] |
P15172 | MYOD1 | Myoblast determination protein 1 | Muscle organ development, positive regulation of muscle cell differentiation, protein phosphorylation | - Encodes a nuclear protein and is known to be involved in muscle regeneration and differentiation. | 45 | [63] |
Q2TAM9 | TUSC1 | Tumor suppressor candidate gene 1 protein | - | - Known to exhibit tumor-suppressor activity as a candidate tumor suppressor gene. | 44 | [64] |
Q13698 | CACNA1S | Voltage-dependent L-type calcium channel subunit alpha-1S. | Muscle contraction, calcium ion import and transport | - Delivers directions to make a subunit of a structure called a calcium channel. | 43 | [65] |
P15173 | MYOG | Myogenin | Positive regulation of muscle atrophy, regulation of myoblast fusion, skeletal muscle cell differentiation | - Plays a role in muscle atrophy, muscle differentiation, and embryonic skeletal fiber muscle differentiation. | 43 | [66] |
P0CG48 | UBC | Polyubiquitin-C | Protein ubiquitination | - The ubiquitin (Ub) system plays a vital role in protein homeostasis. | 43 | [67] |
P0DMV8 | HSPA1A | Heat shock 70 kDa protein 1A | ATP metabolic process, cellular response to heat, lysosomal transport, protein refolding and stabilization | - Important role in the protein quality control system. - Ensures the correct folding of proteins and controls the targeting of proteins for upcoming degradation. | 42 | [68] |
P45378 | TNNT3 | Troponin T, fast skeletal muscle | Muscle contraction, skeletal muscle contraction | - Provides instructions to make a protein called troponin T. - Troponin T is found in skeletal muscles, which are used for movement. - This gene is linked to impaired muscle function. | 42 | [69] |
Q9NRR1 | CYTL1 | Cytokine-like protein 1 | Signaling receptor binding, extracellular space, cartilage homeostasis | - Features of a secretory protein. - Linked with conditions such as smoking, cardiac fibrosis, and various tumors. | 40 | [70] |
P61925 | PKIA | cAMP-dependent protein kinase inhibitor alpha | Negative regulation of protein import into the nucleus | - Protein kinase inhibitors are widely referenced in the literature. - However, because the DMPK gene encodes for myotonic dystrophy protein kinase, a serine–threonine kinase with similarity to adenosine monophosphate-dependent protein kinases undergoes self-phosphorylation, in contrast to other membrane proteins. | 40 | [71] |
P12814 | ACTN1 | Alpha-actinin-1 | Actin cytoskeleton organization, focal adhesion assembly, muscle cell development | - Cytoskeletal proteins known to exhibit non-muscle functions. - Important for glioma cell motility. | 39 | [72] |
O15085 | ARHGEF11 | Rho guanine nucleotide exchange factor 11 | Striated muscle contraction, G-protein-coupled receptor | - Promotes tumor metastasis in glioblastoma and ovarian cancer. | 38 | [73] |
P42336 | PIK3CA | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform | Glucose metabolism, response to muscle stretching, positive regulation of smooth muscle cell proliferation | - Produces an enzyme called PI3K, which has been associated with DM1 - Participates in cellular signaling in response to different growth factors. - The PIK3CA gene mainly plays a role in breast cancer and causes mutations in different human malignancies. | 38 | [57,74] |
P53567 | CEBPG | CCAAT/enhancer-binding protein gamma | mRNA metabolic process, positive regulation of DNA binding and repair | - Potential biomarkers for cancer prognosis. - Plays a role in gastric cancer progression and breast cancer cell migration. | 36 | [75] |
P11047 | LAMC1 | Laminin subunit gamma 1 | Cell adhesion, tissue development | - Associated with the development and occurrence of tubal cancer and other malignant tumors. - Its molecular mechanism remains unclear. | 36 | [76] |
P51816 | AFF2 | AF4/FMR2 family member 2 | mRNA processing, RNA splicing, regulation of gene expression | - Encodes a recognized transcriptional activator. - conserved and expressed in the human brain. | ND | [77] |
Q13936 | CACNA1C | Voltage-dependent L-type calcium channel subunit alpha-1C | Cardiac muscle cell action potential involved in contraction, cardiac conduction | - Encodes calcium channels in heart tissue and its gain-of-purpose mutations in arrhythmias and sudden death. - CACNA1C and GJA1 upregulation may contribute to cardiac impairment observed in DM1 patients. | ND | [78] |
Q8IX12 | CCAR1 | Cell division cycle and apoptosis regulator protein 1 | DNA-directed RNA polymerase, transcription, sigma factor, transcription, Regulation, mRNA splicing | - Functions as a key proliferation-inducing gene and p35 coactivator. | ND | [79] |
Q8WWK9 | CKAP2 | Cytoskeleton-associated protein 2 | Apoptotic process, mitotic cytokinesis | - A powerful microtubule growth factor. - Plays important roles as an oncogene and spindle protein and in proliferation. | ND | [80] |
P51116 | FXR2 | Fragile X mental retardation syndrome-related protein 2 | Regulation of mRNA stability, positive regulation of protein phosphorylation | - FXR2 is an RNA-binding protein known to play a role in fragile X cognitive disability syndrome. | ND | [81] |
P34931 | HSPA1L | Heat shock 70 kDa protein 1-like | Unfolded protein response, vesicle-mediated transport | - Encodes a 70kDa heat shock protein. - Ensures protein quality control of the cell. | ND | [82] |
P04792 | HSPB1 | Heat shock protein beta 1 | Regulation of protein phosphorylation, chaperon-mediated protein folding | - Preserves cellular proteostasis during the course of stress conditions. | ND | [83] |
Q02363 | ID2 | DNA-binding protein inhibitor ID-2 | Developmental protein, regulation of lipid metabolic process, cellular senescence | - Regulator of developmentally associated genes and tumor growth in vitro, as well as in vivo, in Ewing sarcoma tumors. - Involved in cellular growth. | ND | [84] |
P25391 | LAMA1 | Laminin subunit alpha 1 | Cell adhesion, tissue development, protein phosphorylation | - Encodes the alpha 1 subunits of laminin. - Implicated in various biological processes such as migration, cell adhesion, signaling, differentiation, and metastasis. - Mutations in this gene may be related to Poretti-Boltshauser syndrome. | ND | [85] |
P07942 | LAMB1 | Laminin subunit beta 1 | Cell adhesion, cell migration, tissue development | - Plays significant roles in different kinds of tumors, including breast cancer, glioblastoma multiforme, prostate cancer, and hepatocellular carcinoma. | ND | [86] |
P43246 | MLH2 | DNA mismatch repair protein Msh2 | DNA repair, oxidative phosphorylation, mismatch repair | - Delivers instructions for making a protein that play an important role in DNA repair. | ND | [87] |
O15146 | MUSK | Muscle, skeletal receptor tyrosine-protein kinase | Skeletal muscle acetylcholine-gated channel clustering | - Encodes a muscle-specific tyrosine kinase receptor that plays a role in clustering of the acetylcholine receptor in postsynaptic neuromuscular connections. - Mutations in this gene have been related to congenital myasthenic syndrome. | ND | [88] |
Q9UKX2 | MYH2 | Myosin-2 | Muscle contraction, muscle filament sliding | - Needed for cytoskeleton organization and muscle contraction. | ND | [89] |
P04629 | NTRK1 | High affinity nerve growth factor receptor | Aging, nerve growth factor signaling pathway | NTRK plays a role in the growth and normal functioning of the nervous system. However, tropomyosin receptor kinase (trk) is involved in different kinds of cancer. | ND | [90] |
Q9Y2B9 | PKIG | cAMP-dependent protein kinase inhibitor gamma | Negative regulation of protein import into the nucleus | - Protein kinase inhibitors are broadly referenced in the literature. - However, because the DMPK gene encodes for myotonic dystrophy protein kinase, a serine–threonine kinase with similarity to adenosine monophosphate-dependent protein kinases undergoes self-phosphorylation, in contrast to other membrane proteins. | ND | [71] |
P52756 | RBM5 | RNA-binding protein 5 | Apoptosis, mRNA splicing | - Acts as a tumor suppressor. - Controls cell growth, cell cycle progression, and apoptosis in cell homeostasis. - RBM5 expression may be a potential curative target for drug-resistant lung cancer. | ND | [91] |
O75116 | ROCK2 | Rho-associated protein kinase 2 | Actin cytoskeleton organization, positive regulation of MAPK cascade | - Stabilizes actin cytoskeleton via regulation of cofilin phosphorylation. | ND | [43] |
Q14493 | SLBP | Histone RNA hairpin-binding protein | mRNA processing, mRNA transport | - Essential for the coordinate synthesis of DNA and histone proteins. - Needed for progression through the cell division cycle. | ND | [92] |
Q9ULZ2 | STAP1 | Signal-transducing adaptor protein 1 | Transduction, positive regulation of gene expression | - Candidate gene related to familial hypercholesterolemia. - STAP1 is observed in immune cells. | ND | [93] |
Q9UGK3 | STAP2 | Signal-transducing adaptor protein 2 | --- | - Regulates different intercellular signaling pathways and promotes prostate cancer flow via EGFR activation. | ND | [94] |
Q15208 | STK38 | Serine/threonine-protein kinase 38 | Protein phosphorylation | - Negative regulator of MAPK1/2 signaling. | ND | [95] |
P04637 | TB53 | Cellular tumor antigen p53 | Cell aging, protein stabilization, regulation of cell cycle | - Acts as a tumor suppressor in various tumor types. - Regulates in DNA repair, autophagy, senescence, and cell cycle arrest. | ND | [96] |
P13805 | TNNT1 | Troponin T, slow skeletal muscle | Muscle contraction, skeletal muscle contraction | - TNNT1 is known as the slow skeletal troponin T subunit. - Mutations in this gene lead to nemaline myopathy type 5. - Causes most troponin-related skeletal myopathies. | ND | [97] |
P45379 | TNNT2 | Troponin T, cardiac muscle | Muscle contraction, muscle filament sliding, actin crosslink formation | - It is unclear whether TNNT2 mis-splicing can be considered a specific cardiac biomarker in adult skeletal muscles of DM1 patients, suggesting that alternative splicing of this gene may be useful as a cardiac biomarker. | ND | [98] |
P25490 | YY1 | Transcriptional repressor protein YY1 | DNA-directed RNA polymerase, transcription, differentiation spermatogenesis, DNA damage | - Involved in regulating the expression of a large number of genes and binds to interferon-beta (IFN-β) promoter to either repress or activate its expression. - It could play a role in modulating the cellular response to dsRNA. | ND | [99] |
P17036 | ZNF3 | Zinc finger protein 3 (isoform) | Cell differentiation, leukocyte activation | - Serves as a specific RNA-binding domain, which helps MBNL to identify various target mRNAs by binding to a wide area of motifs. | ND | [100] |
Q6NUN9 | ZNF746 | Zinc finger protein 746 | DNA-directed RNA polymerase, transcription | - Performs the function of promoting the occurrence of hepatocellular carcinoma. - Recognized as a substrate of E3 ligase Parkin, and its accumulation is related to Parkinson’s disease. | ND | [101] |
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Kuntawala, D.H.; Martins, F.; Vitorino, R.; Rebelo, S. Automatic Text-Mining Approach to Identify Molecular Target Candidates Associated with Metabolic Processes for Myotonic Dystrophy Type 1. Int. J. Environ. Res. Public Health 2023, 20, 2283. https://doi.org/10.3390/ijerph20032283
Kuntawala DH, Martins F, Vitorino R, Rebelo S. Automatic Text-Mining Approach to Identify Molecular Target Candidates Associated with Metabolic Processes for Myotonic Dystrophy Type 1. International Journal of Environmental Research and Public Health. 2023; 20(3):2283. https://doi.org/10.3390/ijerph20032283
Chicago/Turabian StyleKuntawala, Dhvani H., Filipa Martins, Rui Vitorino, and Sandra Rebelo. 2023. "Automatic Text-Mining Approach to Identify Molecular Target Candidates Associated with Metabolic Processes for Myotonic Dystrophy Type 1" International Journal of Environmental Research and Public Health 20, no. 3: 2283. https://doi.org/10.3390/ijerph20032283