Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis
Sarcopenia is an age-related disease characterized by the loss of muscle mass and muscle function. A proper understanding of its pathogenesis and mechanisms may lead to new strategies for diagnosis and treatment of the disease. This study aims to discover the underlying genes, proteins, and pathways...
Main Authors: | , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
PeerJ Inc.
2018-09-01
|
Series: | PeerJ |
Subjects: | |
Online Access: | https://peerj.com/articles/5239.pdf |
id |
doaj-794e10f5754f4bef8dbef6c174a2261d |
---|---|
record_format |
Article |
spelling |
doaj-794e10f5754f4bef8dbef6c174a2261d2020-11-24T21:34:46ZengPeerJ Inc.PeerJ2167-83592018-09-016e523910.7717/peerj.5239Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysisGita Shafiee0Yazdan Asgari1Akbar Soltani2Bagher Larijani3Ramin Heshmat4Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, IranDepartment of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, IranEndocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, IranEndocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, IranChronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, IranSarcopenia is an age-related disease characterized by the loss of muscle mass and muscle function. A proper understanding of its pathogenesis and mechanisms may lead to new strategies for diagnosis and treatment of the disease. This study aims to discover the underlying genes, proteins, and pathways associated with sarcopenia in both genders. Integrated analysis of microarray datasets has been performed to identify differentially expressed genes (DEGs) between old and young skeletal muscles. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then performed to uncover the functions of the DEGs. Moreover, a protein–protein interaction (PPI) network was constructed based on the DEGs. We have identified 41,715 DEGs, including 19 downregulated and 41,696 upregulated ones, in men. Among women, 3,015 DEGs have been found, with 2,874 of them being upregulated and 141 downregulated genes. Among the top up-regulated and downregulated genes, the ribosome biogenesis genes and genes involved in lipid storage may be closely related to aging muscles in men and women respectively. Also, the DEGs were enriched in the pathways including those of ribosome and Peroxisome proliferator-activated receptor (PPAR) in men and women, respectively. In the PPI network, Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1), Cullin 3 (CUL3) and P53 have been identified as significant hub proteins in both genders. Using the integrated analysis of multiple gene expression profiles, we propose that the ribosome biogenesis genes and those involved in lipid storage would be promising markers for sarcopenia in men and women, respectively. In the reconstructed PPI network, neurotrophic factors expressed in skeletal muscle are essential for motoneuron survival and muscle fiber innervation during development. Cullin E3 ubiquitin ligase (Cul3) is an important component of the ubiquitin–proteasome system—it regulates the proteolysis. P53 is recognized as a central regulator of the cell cycle and apoptosis. These proteins, which have been identified as the most significant hubs, may be involved in aging muscle and sarcopenia.https://peerj.com/articles/5239.pdfSkeletal muscleStructural analysisSarcopeniaAging |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Gita Shafiee Yazdan Asgari Akbar Soltani Bagher Larijani Ramin Heshmat |
spellingShingle |
Gita Shafiee Yazdan Asgari Akbar Soltani Bagher Larijani Ramin Heshmat Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis PeerJ Skeletal muscle Structural analysis Sarcopenia Aging |
author_facet |
Gita Shafiee Yazdan Asgari Akbar Soltani Bagher Larijani Ramin Heshmat |
author_sort |
Gita Shafiee |
title |
Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis |
title_short |
Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis |
title_full |
Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis |
title_fullStr |
Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis |
title_full_unstemmed |
Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis |
title_sort |
identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis |
publisher |
PeerJ Inc. |
series |
PeerJ |
issn |
2167-8359 |
publishDate |
2018-09-01 |
description |
Sarcopenia is an age-related disease characterized by the loss of muscle mass and muscle function. A proper understanding of its pathogenesis and mechanisms may lead to new strategies for diagnosis and treatment of the disease. This study aims to discover the underlying genes, proteins, and pathways associated with sarcopenia in both genders. Integrated analysis of microarray datasets has been performed to identify differentially expressed genes (DEGs) between old and young skeletal muscles. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then performed to uncover the functions of the DEGs. Moreover, a protein–protein interaction (PPI) network was constructed based on the DEGs. We have identified 41,715 DEGs, including 19 downregulated and 41,696 upregulated ones, in men. Among women, 3,015 DEGs have been found, with 2,874 of them being upregulated and 141 downregulated genes. Among the top up-regulated and downregulated genes, the ribosome biogenesis genes and genes involved in lipid storage may be closely related to aging muscles in men and women respectively. Also, the DEGs were enriched in the pathways including those of ribosome and Peroxisome proliferator-activated receptor (PPAR) in men and women, respectively. In the PPI network, Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1), Cullin 3 (CUL3) and P53 have been identified as significant hub proteins in both genders. Using the integrated analysis of multiple gene expression profiles, we propose that the ribosome biogenesis genes and those involved in lipid storage would be promising markers for sarcopenia in men and women, respectively. In the reconstructed PPI network, neurotrophic factors expressed in skeletal muscle are essential for motoneuron survival and muscle fiber innervation during development. Cullin E3 ubiquitin ligase (Cul3) is an important component of the ubiquitin–proteasome system—it regulates the proteolysis. P53 is recognized as a central regulator of the cell cycle and apoptosis. These proteins, which have been identified as the most significant hubs, may be involved in aging muscle and sarcopenia. |
topic |
Skeletal muscle Structural analysis Sarcopenia Aging |
url |
https://peerj.com/articles/5239.pdf |
work_keys_str_mv |
AT gitashafiee identificationofcandidategenesandproteinsinagingskeletalmusclesarcopeniausinggeneexpressionandstructuralanalysis AT yazdanasgari identificationofcandidategenesandproteinsinagingskeletalmusclesarcopeniausinggeneexpressionandstructuralanalysis AT akbarsoltani identificationofcandidategenesandproteinsinagingskeletalmusclesarcopeniausinggeneexpressionandstructuralanalysis AT bagherlarijani identificationofcandidategenesandproteinsinagingskeletalmusclesarcopeniausinggeneexpressionandstructuralanalysis AT raminheshmat identificationofcandidategenesandproteinsinagingskeletalmusclesarcopeniausinggeneexpressionandstructuralanalysis |
_version_ |
1725947539023200256 |