NeuroMuscleDB: a Database of Genes Associated with Muscle Development, Neuromuscular Diseases, Ageing, and Neurodegeneration

Baig, Mohammad Hassan; Rashid, Iliyas; Srivastava, Prachi; Ahmad, Khurshid; Jan, Arif Tasleem; Rabbani, Gulam; Choi, Dukhwan; Barreto, George E.; Ashraf, Ghulam Md; Lee, Eun Ju

doi:10.1007/s12035-019-1478-5

Cited by 14 publications

(9 citation statements)

References 40 publications

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“…The developmental process of multinucleated myofibers with contractile capability from MSCs is termed myogenesis, and involves cell cycle arrest, cell fusion, increases in nuclear sizes, and the peripheral localization of nuclei (Charge and Rudnicki, 2004). Myogenesis is a decidedly regulated mechanism that is determined by the co-expressions of Pax3, Pax7, and myogenicregulatory factors such as Myf5, Mrf4, MyoD, and myogenin in MSCs (Zammit and Beauchamp, 2001;Relaix et al, 2005;Baig et al, 2019;Kim et al, 2019;Lee et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Cross-Talk Between Extracellular Matrix and Skeletal Muscle: Implications for Myopathies

et al. 2020

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Skeletal muscle (SM) comprises around 40% of total body weight and is among the most important plastic tissues, as it supports skeletal development, controls body temperature, and manages glucose levels. Extracellular matrix (ECM) maintains the integrity of SM, enables biochemical signaling, provides structural support, and plays a vital role during myogenesis. Several human diseases are coupled with dysfunctions of the ECM, and several ECM components are involved in disease pathologies that affect almost all organ systems. Thus, mutations in ECM genes that encode proteins and their transmembrane receptors can result in diverse SM diseases, a large proportion of which are types of fibrosis and muscular dystrophy. In this review, we present major ECM components of SMs related to muscle-associated diseases, and discuss two major ECM myopathies, namely, collagen myopathy and laminin myopathies, and their therapeutic managements. A comprehensive understanding of the mechanisms underlying these ECM-related myopathies would undoubtedly aid the discovery of novel treatments for these devastating diseases.

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Section: Introductionmentioning

confidence: 99%

Cross-Talk Between Extracellular Matrix and Skeletal Muscle: Implications for Myopathies

et al. 2020

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“…It induces the myogenic cells and maintains a balance between proliferation and differentiation [4,5,6]. Progression of MSCs along the myogenic lineage is initiated with the co-expression of paired box transcription factors (Pax3/Pax7) along with myogenic-regulatory factors (MRFs; including Myf5, MyoD, Mrf4, and myogenin) [7,8,9].…”

Section: Introductionmentioning

confidence: 99%

Dermatopontin in Skeletal Muscle Extracellular Matrix Regulates Myogenesis

Kim

Ahmad

Shaikh

et al. 2019

Cells

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Dermatopontin (DPT) is an extensively distributed non-collagenous component of the extracellular matrix predominantly found in the dermis of the skin, and consequently expressed in several tissues. In this study, we explored the role of DPT in myogenesis and perceived that it enhances the cell adhesion, reduces the cell proliferation and promotes the myoblast differentiation in C2C12 cells. Our results reveal an inhibitory effect with fibronectin (FN) in myoblast differentiation. We also observed that DPT and fibromodulin (FMOD) regulate positively to each other and promote myogenic differentiation. We further predicted the 3D structure of DPT, which is as yet unknown, and validated it using state-of-the-art in silico tools. Furthermore, we explored the in-silico protein-protein interaction between DPT-FMOD, DPT-FN, and FMOD-FN, and perceived that the interaction between FMOD-FN is more robust than DPT-FMOD and DPT-FN. Taken together, our findings have determined the role of DPT at different stages of the myogenic process.

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“…NeuroMuscleDB 5 is a database of genes associated with muscle development, neuromuscular diseases, aging, and neurodegeneration ( Baig et al, 2019 ).…”

Section: Large Data Collections For Aging: a Survey Of Available Databases And Datasetsmentioning

confidence: 99%

“…A strength of this database is that analytical tools, containing PCR primer design and sequence analysis, were also implemented to support the laboratory analyses of candidate genes and sequences. More details are available in Baig et al (2019) .…”

Section: Large Data Collections For Aging: a Survey Of Available Databases And Datasetsmentioning

confidence: 99%

Omics in a Digital World: The Role of Bioinformatics in Providing New Insights Into Human Aging

et al. 2021

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BackgroundAging is a complex phenotype influenced by a combination of genetic and environmental factors. Although many studies addressed its cellular and physiological age-related changes, the molecular causes of aging remain undetermined. Considering the biological complexity and heterogeneity of the aging process, it is now clear that full understanding of mechanisms underlying aging can only be achieved through the integration of different data types and sources, and with new computational methods capable to achieve such integration.Recent AdvancesIn this review, we show that an omics vision of the age-dependent changes occurring as the individual ages can provide researchers with new opportunities to understand the mechanisms of aging. Combining results from single-cell analysis with systems biology tools would allow building interaction networks and investigate how these networks are perturbed during aging and disease. The development of high-throughput technologies such as next-generation sequencing, proteomics, metabolomics, able to investigate different biological markers and to monitor them simultaneously during the aging process with high accuracy and specificity, represents a unique opportunity offered to biogerontologists today.Critical IssuesAlthough the capacity to produce big data drastically increased over the years, integration, interpretation and sharing of high-throughput data remain major challenges. In this paper we present a survey of the emerging omics approaches in aging research and provide a large collection of datasets and databases as a useful resource for the scientific community to identify causes of aging. We discuss their peculiarities, emphasizing the need for the development of methods focused on the integration of different data types.Future DirectionsWe critically review the contribution of bioinformatics into the omics of aging research, and we propose a few recommendations to boost collaborations and produce new insights. We believe that significant advancements can be achieved by following major developments in bioinformatics, investing in diversity, data sharing and community-driven portable bioinformatics methods. We also argue in favor of more engagement and participation, and we highlight the benefits of new collaborations along these lines. This review aims at being a useful resource for many researchers in the field, and a call for new partnerships in aging research.

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NeuroMuscleDB: a Database of Genes Associated with Muscle Development, Neuromuscular Diseases, Ageing, and Neurodegeneration

Cited by 14 publications

References 40 publications

Cross-Talk Between Extracellular Matrix and Skeletal Muscle: Implications for Myopathies

Cross-Talk Between Extracellular Matrix and Skeletal Muscle: Implications for Myopathies

Dermatopontin in Skeletal Muscle Extracellular Matrix Regulates Myogenesis

Omics in a Digital World: The Role of Bioinformatics in Providing New Insights Into Human Aging

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