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Yang Y, Zou J, Li M, Yun Y, Li J, Bai J. Extraction and characterization of polysaccharides from blackcurrant fruits and its inhibitory effects on acetylcholinesterase. Int J Biol Macromol 2024; 262:130047. [PMID: 38336315 DOI: 10.1016/j.ijbiomac.2024.130047] [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: 06/26/2023] [Revised: 01/11/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Microwave assisted aqueous two-phase system (MA-ATPS) was used to simultaneously extract two polysaccharides from blackcurrant. Under the suitable ATPS (ethanol/(NH4)2SO4, 26.75 %/18.98 %) combining with the optimal MA conditions (liquid-to-material ratio 58.5 mL/g, time 9.5 min, temperature 60.5 °C, power 587 W) predicted by response surface methodology, the yields of the top/bottom phase polysaccharides were 13.08 ± 0.37 % and 42.65 ± 0.89 %, respectively. After purification through column chromatography, the top phase polysaccharide (PRTP) and bottom phase polysaccharide (PRBP) were obtained. FT-IR, methylation and NMR analyses confirmed that the repeating unit in the backbone of PRTP was →2, 5)-α-L-Araf-(1 → 3)-α-D-Manp-(1 → 6)-β-D-Galp-(1 → 6)-α-D-Glcp-(1 → 4)-α-L-Rhap-(1 → 4)-α-D-GalAp-(1→, while the possible unit in PRBP was →4)-α-L-Rhap-(1 → 3)-α-D-Manp-(1 → 6)-β-D-Galp-(1 → 6)-α-D-Glcp-(1 → 2, 5)-α-L-Araf-(1 → 4)-α-D-GalAp-(1→. PRBP with relatively low molecular weight exhibited better stability, rheological property, free radical scavenging and acetylcholinesterase (AChE) inhibitory activities than PRTP. PRTP and PRBP were reversible mixed-type inhibitors for AChE, and the conformation of AChE was changed after binding with the polysaccharides. Molecular docking, fluorescence and isothermal titration calorimetry assays revealed that PRTP and PRBP quenched the fluorescence through static quenching mechanism, and the van der Waals interactions and hydrogen bonding played key roles in the stability of polysaccharide-enzyme complexes. This study provided a theoretical basis for blackcurrant polysaccharides as AChE inhibitors to treat Alzheimer's disease.
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Affiliation(s)
- Yu Yang
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Jiaheng Zou
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Miao Li
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yang Yun
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Jianqiang Li
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Jingwen Bai
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China.
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Ahmad K, Shaikh S, Lim JH, Ahmad SS, Chun HJ, Lee EJ, Choi I. Therapeutic application of natural compounds for skeletal muscle-associated metabolic disorders: A review on diabetes perspective. Biomed Pharmacother 2023; 168:115642. [PMID: 37812896 DOI: 10.1016/j.biopha.2023.115642] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/19/2023] [Accepted: 10/03/2023] [Indexed: 10/11/2023] Open
Abstract
Skeletal muscle (SM) plays a vital role in energy and glucose metabolism by regulating insulin sensitivity, glucose uptake, and blood glucose homeostasis. Impaired SM metabolism is strongly linked to several diseases, particularly type 2 diabetes (T2D). Insulin resistance in SM may result from the impaired activities of insulin receptor tyrosine kinase, insulin receptor substrate 1, phosphoinositide 3-kinase, and AKT pathways. This review briefly discusses SM myogenesis and the critical roles that SM plays in insulin resistance and T2D. The pharmacological targets of T2D which are associated with SM metabolism, such as DPP4, PTB1B, SGLT, PPARγ, and GLP-1R, and their potential modulators/inhibitors, especially natural compounds, are discussed in detail. This review highlights the significance of SM in metabolic disorders and the therapeutic potential of natural compounds in targeting SM-associated T2D targets. It may provide novel insights for the future development of anti-diabetic drug therapies. We believe that scientists working on T2D therapies will benefit from this review by enhancing their knowledge and updating their understanding of the subject.
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Affiliation(s)
- Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea
| | - Sibhghatulla Shaikh
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea
| | - Jeong Ho Lim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea
| | - Syed Sayeed Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea
| | - Hee Jin Chun
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, South Korea
| | - Eun Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea.
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Emerging Perspectives on Gene Therapy Delivery for Neurodegenerative and Neuromuscular Disorders. J Pers Med 2022; 12:jpm12121979. [PMID: 36556200 PMCID: PMC9788053 DOI: 10.3390/jpm12121979] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022] Open
Abstract
Neurodegenerative disorders (NDDs), such as Alzheimer's disease (AD) and Parkinson's Disease (PD), are a group of heterogeneous diseases that mainly affect central nervous system (CNS) functions. A subset of NDDs exhibit CNS dysfunction and muscle degeneration, as observed in Gangliosidosis 1 (GM1) and late stages of PD. Neuromuscular disorders (NMDs) are a group of diseases in which patients show primary progressive muscle weaknesses, including Duchenne Muscular Dystrophy (DMD), Pompe disease, and Spinal Muscular Atrophy (SMA). NDDs and NMDs typically have a genetic component, which affects the physiological functioning of critical cellular processes, leading to pathogenesis. Currently, there is no cure or efficient treatment for most of these diseases. More than 200 clinical trials have been completed or are currently underway in order to establish safety, tolerability, and efficacy of promising gene therapy approaches. Thus, gene therapy-based therapeutics, including viral or non-viral delivery, are very appealing for the treatment of NDDs and NMDs. In particular, adeno-associated viral vectors (AAV) are an attractive option for gene therapy for NDDs and NMDs. However, limitations have been identified after systemic delivery, including the suboptimal capacity of these therapies to traverse the blood-brain barrier (BBB), degradation of the particles during the delivery, high reactivity of the patient's immune system during the treatment, and the potential need for redosing. To circumvent these limitations, several preclinical and clinical studies have suggested intrathecal (IT) delivery to target the CNS and peripheral organs via cerebrospinal fluid (CSF). CSF administration can vastly improve the delivery of small molecules and drugs to the brain and spinal cord as compared to systemic delivery. Here, we review AAV biology and vector design elements, different therapeutic routes of administration, and highlight CSF delivery as an attractive route of administration. We discuss the different aspects of neuromuscular and neurodegenerative diseases, such as pathogenesis, the landscape of mutations, and the biological processes associated with the disease. We also describe the hallmarks of NDDs and NMDs as well as discuss current therapeutic approaches and clinical progress in viral and non-viral gene therapy and enzyme replacement strategies for those diseases.
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Durai P, Beeraka NM, Ramachandrappa HVP, Krishnan P, Gudur P, Raghavendra NM, Ravanappa PKB. Advances in PPARs Molecular Dynamics and Glitazones as a Repurposing Therapeutic Strategy through Mitochondrial Redox Dynamics against Neurodegeneration. Curr Neuropharmacol 2022; 20:893-915. [PMID: 34751120 PMCID: PMC9881103 DOI: 10.2174/1570159x19666211109141330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/20/2021] [Accepted: 09/17/2021] [Indexed: 11/22/2022] Open
Abstract
Peroxisome proliferator-activated receptors (PPARs) activity has significant implications for the development of novel therapeutic modalities against neurodegenerative diseases. Although PPAR-α, PPAR-β/δ, and PPAR-γ nuclear receptor expressions are significantly reported in the brain, their implications in brain physiology and other neurodegenerative diseases still require extensive studies. PPAR signaling can modulate various cell signaling mechanisms involved in the cells contributing to on- and off-target actions selectively to promote therapeutic effects as well as the adverse effects of PPAR ligands. Both natural and synthetic ligands for the PPARα, PPARγ, and PPARβ/δ have been reported. PPARα (WY 14.643) and PPARγ agonists can confer neuroprotection by modulating mitochondrial dynamics through the redox system. The pharmacological effect of these agonists may deliver effective clinical responses by protecting vulnerable neurons from Aβ toxicity in Alzheimer's disease (AD) patients. Therefore, the current review delineated the ligands' interaction with 3D-PPARs to modulate neuroprotection, and also deciphered the efficacy of numerous drugs, viz. Aβ aggregation inhibitors, vaccines, and γ-secretase inhibitors against AD; this review elucidated the role of PPAR and their receptor isoforms in neural systems, and neurodegeneration in human beings. Further, we have substantially discussed the efficacy of PPREs as potent transcription factors in the brain, and the role of PPAR agonists in neurotransmission, PPAR gamma coactivator-1α (PGC-1α) and mitochondrial dynamics in neuroprotection during AD conditions. This review concludes with the statement that the development of novel PPARs agonists may benefit patients with neurodegeneration, mainly AD patients, which may help mitigate the pathophysiology of dementia, subsequently improving overall the patient's quality of life.
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Affiliation(s)
- Priya Durai
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru 570 015, India and JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | - Narasimha M. Beeraka
- Center of Excellence in Regenerative Medicine and Molecular Biology (CEMR), Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research, Mysuru 570 015, Karnataka, India;,I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119146, Russia
| | - Hemanth Vikram Poola Ramachandrappa
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru 570 015, India and JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | | | - Pranesh Gudur
- Swamy Vivekananda Yoga Anusandhana Samsthana Deemed University, Bengaluru 560 105, India
| | | | - Prashantha Kumar Bommenahally Ravanappa
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru 570 015, India and JSS Academy of Higher Education & Research, Mysuru, Karnataka, India;,Address correspondence to this author at the Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru 570 015, India and JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka, India; E-mail:
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Ahmad K, Lim JH, Lee EJ, Chun HJ, Ali S, Ahmad SS, Shaikh S, Choi I. Extracellular Matrix and the Production of Cultured Meat. Foods 2021; 10:foods10123116. [PMID: 34945667 PMCID: PMC8700801 DOI: 10.3390/foods10123116] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/05/2021] [Accepted: 12/13/2021] [Indexed: 12/28/2022] Open
Abstract
Cultured meat production is an evolving method of producing animal meat using tissue engineering techniques. Cells, chemical factors, and suitable biomaterials that serve as scaffolds are all essential for the cultivation of muscle tissue. Scaffolding is essential for the development of organized meat products resembling steaks because it provides the mechanical stability needed by cells to attach, differentiate, and mature. In in vivo settings, extracellular matrix (ECM) ensures substrates and scaffolds are provided for cells. The ECM of skeletal muscle (SM) maintains tissue elasticity, creates adhesion points for cells, provides a three-dimensional (3D) environment, and regulates biological processes. Consequently, creating mimics of native ECM is a difficult task. Animal-derived polymers like collagen are often regarded as the gold standard for producing scaffolds with ECM-like properties. Animal-free scaffolds are being investigated as a potential source of stable, chemically defined, low-cost materials for cultured meat production. In this review, we explore the influence of ECM on myogenesis and its role as a scaffold and vital component to improve the efficacy of the culture media used to produce cultured meat.
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Affiliation(s)
- Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (K.A.); (J.-H.L.); (E.-J.L.); (H.-J.C.); (S.A.); (S.S.A.); (S.S.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Jeong-Ho Lim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (K.A.); (J.-H.L.); (E.-J.L.); (H.-J.C.); (S.A.); (S.S.A.); (S.S.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Eun-Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (K.A.); (J.-H.L.); (E.-J.L.); (H.-J.C.); (S.A.); (S.S.A.); (S.S.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Hee-Jin Chun
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (K.A.); (J.-H.L.); (E.-J.L.); (H.-J.C.); (S.A.); (S.S.A.); (S.S.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Shahid Ali
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (K.A.); (J.-H.L.); (E.-J.L.); (H.-J.C.); (S.A.); (S.S.A.); (S.S.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Syed Sayeed Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (K.A.); (J.-H.L.); (E.-J.L.); (H.-J.C.); (S.A.); (S.S.A.); (S.S.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Sibhghatulla Shaikh
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (K.A.); (J.-H.L.); (E.-J.L.); (H.-J.C.); (S.A.); (S.S.A.); (S.S.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (K.A.); (J.-H.L.); (E.-J.L.); (H.-J.C.); (S.A.); (S.S.A.); (S.S.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
- Correspondence:
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Dato S, Crocco P, Rambaldi Migliore N, Lescai F. Omics in a Digital World: The Role of Bioinformatics in Providing New Insights Into Human Aging. Front Genet 2021; 12:689824. [PMID: 34178042 PMCID: PMC8225294 DOI: 10.3389/fgene.2021.689824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background Aging 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 Advances In 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 Issues Although 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 Directions We 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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Affiliation(s)
- Serena Dato
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Paolina Crocco
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | | | - Francesco Lescai
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
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Yubero D, Natera-de Benito D, Pijuan J, Armstrong J, Martorell L, Fernàndez G, Maynou J, Jou C, Roldan M, Ortez C, Nascimento A, Hoenicka J, Palau F. The Increasing Impact of Translational Research in the Molecular Diagnostics of Neuromuscular Diseases. Int J Mol Sci 2021; 22:4274. [PMID: 33924139 PMCID: PMC8074304 DOI: 10.3390/ijms22084274] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
The diagnosis of neuromuscular diseases (NMDs) has been progressively evolving from the grouping of clinical symptoms and signs towards the molecular definition. Optimal clinical, biochemical, electrophysiological, electrophysiological, and histopathological characterization is very helpful to achieve molecular diagnosis, which is essential for establishing prognosis, treatment and genetic counselling. Currently, the genetic approach includes both the gene-targeted analysis in specific clinically recognizable diseases, as well as genomic analysis based on next-generation sequencing, analyzing either the clinical exome/genome or the whole exome or genome. However, as of today, there are still many patients in whom the causative genetic variant cannot be definitely established and variants of uncertain significance are often found. In this review, we address these drawbacks by incorporating two additional biological omics approaches into the molecular diagnostic process of NMDs. First, functional genomics by introducing experimental cell and molecular biology to analyze and validate the variant for its biological effect in an in-house translational diagnostic program, and second, incorporating a multi-omics approach including RNA-seq, metabolomics, and proteomics in the molecular diagnosis of neuromuscular disease. Both translational diagnostics programs and omics are being implemented as part of the diagnostic process in academic centers and referral hospitals and, therefore, an increase in the proportion of neuromuscular patients with a molecular diagnosis is expected. This improvement in the process and diagnostic performance of patients will allow solving aspects of their health problems in a precise way and will allow them and their families to take a step forward in their lives.
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Affiliation(s)
- Dèlia Yubero
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Daniel Natera-de Benito
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.N.-d.B.); (C.O.)
| | - Jordi Pijuan
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Judith Armstrong
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Loreto Martorell
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Guerau Fernàndez
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Joan Maynou
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Cristina Jou
- Department of Pathology, Hospital Sant Joan de Déu, Pediatric Biobank for Research, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Mònica Roldan
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Confocal Microscopy and Cellular Imaging Unit, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain
| | - Carlos Ortez
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.N.-d.B.); (C.O.)
- Division of Pediatrics, Clinic Institute of Medicine & Dermatology, Hospital Clínic, University of Barcelona School of Medicine and Health Sciences, 08950 Barcelona, Spain
| | - Andrés Nascimento
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.N.-d.B.); (C.O.)
| | - Janet Hoenicka
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Francesc Palau
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
- Department of Pathology, Hospital Sant Joan de Déu, Pediatric Biobank for Research, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
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Asplund O, Rung J, Groop L, Prasad B R, Hansson O. MuscleAtlasExplorer: a web service for studying gene expression in human skeletal muscle. Database (Oxford) 2020; 2020:baaa111. [PMID: 33338203 PMCID: PMC7747357 DOI: 10.1093/database/baaa111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/13/2020] [Accepted: 12/14/2020] [Indexed: 01/30/2023]
Abstract
MuscleAtlasExplorer is a freely available web application that allows for the exploration of gene expression data from human skeletal muscle. It draws from an extensive publicly available dataset of 1654 skeletal muscle expression microarray samples. Detailed, manually curated, patient phenotype data, with information such as age, sex, BMI and disease status, are combined with skeletal muscle gene expression to provide insights into gene function in skeletal muscle. It aims to facilitate easy exploration of the data using powerful data visualization functions, while allowing for sample selection, in-depth inspection and further analysis using external tools. Availability: MuscleAtlasExplorer is available at https://mae.crc.med.lu.se/mae2 (username 'muscle' and password 'explorer' pre-publication).
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Affiliation(s)
- Olof Asplund
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenströms gata 35, Malmö 20502, Sweden
| | - Johan Rung
- SciLifeLab, BMC, Husargatan 3, Uppsala University, Uppsala 751 22, Sweden
| | - Leif Groop
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenströms gata 35, Malmö 20502, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 800290 Helsinki, Finland
| | - Rashmi Prasad B
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenströms gata 35, Malmö 20502, Sweden
| | - Ola Hansson
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenströms gata 35, Malmö 20502, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 800290 Helsinki, Finland
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MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons. Sci Rep 2020; 10:8593. [PMID: 32451429 PMCID: PMC7248120 DOI: 10.1038/s41598-020-65319-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 04/28/2020] [Indexed: 12/14/2022] Open
Abstract
Muscular atrophy or muscle loss is a multifactorial clinical condition during many critical illnesses like cancer, cardiovascular diseases, diabetes, pulmonary diseases etc. leading to fatigue and weakness and contributes towards a decreased quality of life. The proportion of older adults (>65 y) in the overall population is also growing and aging is another important factor causing muscle loss. Some muscle miRNAs (myomiRs) and their target genes have even been proposed as potential diagnostic, therapeutic and predictive markers for muscular atrophy. MyomirDB (http://www.myomirdb.in/) is a unique resource that provides a comprehensive, curated, user- friendly and detailed compilation of various miRNA bio-molecular interactions; miRNA-Transcription Factor-Target Gene co-regulatory networks and ~8000 tripartite regulons associated with 247 myomiRs which have been experimentally validated to be associated with various muscular atrophy conditions. For each database entry, MyomirDB compiles source organism, muscle atrophic condition, experiment duration, its level of expression, fold change, tissue of expression, experimental validation, disease and drug association, tissue-specific expression level, Gene Ontology and KEGG pathway associations. The web resource is a unique server platform which uses in-house scripts to construct miRNA-Transcription Factor-Target Gene co-regulatory networks and extract tri-partite regulons also called Feed Forward Loops. These unique features helps to offer mechanistic insights in disease pathology. Hence, MyomirDB is a unique platform for researchers working in this area to explore, fetch, compare and analyse atrophy associated miRNAs, their co-regulatory networks and FFL regulons.
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Ahmad K, Shaikh S, Ahmad SS, Lee EJ, Choi I. Cross-Talk Between Extracellular Matrix and Skeletal Muscle: Implications for Myopathies. Front Pharmacol 2020; 11:142. [PMID: 32184725 PMCID: PMC7058629 DOI: 10.3389/fphar.2020.00142] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 02/04/2020] [Indexed: 12/13/2022] Open
Abstract
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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Affiliation(s)
- Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Sibhghatulla Shaikh
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Syed Sayeed Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Eun Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
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Kim T, Ahmad K, Shaikh S, Jan AT, Seo MG, Lee EJ, Choi I. Dermatopontin in Skeletal Muscle Extracellular Matrix Regulates Myogenesis. Cells 2019; 8:cells8040332. [PMID: 30970625 PMCID: PMC6523808 DOI: 10.3390/cells8040332] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/06/2019] [Accepted: 04/09/2019] [Indexed: 12/31/2022] Open
Abstract
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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Affiliation(s)
- Taeyeon Kim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.
| | - Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.
| | - Sibhghatulla Shaikh
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.
| | - Arif Tasleem Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185236, India.
| | - Myung-Gi Seo
- Department of Veterinary Histology, College of Veterinary Medicine, Kyungpook National University, Daegu 702-701, Korea.
| | - Eun Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.
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