Oncotarget

Research Papers:

Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data

Mahmoud Ahmed, Huynh Quoc Nguyen, Jin Seok Hwang, Sahib Zada, Trang Huyen Lai, Sang Soo Kang and Deok Ryong Kim _

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Oncotarget. 2018; 9:15526-15541. https://doi.org/10.18632/oncotarget.24506

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Abstract

Mahmoud Ahmed1, Huynh Quoc Nguyen1, Jin Seok Hwang1, Sahib Zada1, Trang Huyen Lai1, Sang Soo Kang2 and Deok Ryong Kim1

1Department of Biochemistry and Convergence Medical Sciences and Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju 527-27, Republic of Korea

2Department of Anatomy and Convergence Medical Sciences and Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju 527-27, Republic of Korea

Correspondence to:

Deok Ryong Kim, email: drkim@gnu.ac.kr

Keywords: autophagy; adipocyte differentiation; 3T3-L1; RNA-seq; gene ontology

Received: June 24, 2017     Accepted: February 10, 2018     Epub: February 15, 2018     Published: March 20, 2018

ABSTRACT

Autophagy contributes to reorganizing intracellular components and forming fat droplets during the adipocyte differentiation. Here, we systematically describe the role of autophagy-related genes and gene sets during the differentiation of adipocytes. We used a public dataset from the European Nucleotide Archive from an RNA-seq experiment in which 3T3-L1 cells were induced by a differentiation induction medium, total RNA was extracted and sequenced at four different time points. Raw reads were aligned to the UCSC mouse reference genome (mm10) using HISAT2, and aligned reads were summarized at the gene or exon level using HTSeq. DESeq2 and DEXSeq were used to model the gene and exon counts and test for differential expression and relative exon usage, respectively. After applying the appropriate transformation, gene counts were used to perform the gene set and pathway enrichment analysis. Data were obtained, processed and annotated using R and Bioconductor. Several autophagy-related genes and autophagy gene sets, as defined in the Gene Ontology, were actively regulated during the course of the adipocyte differentiation. We further characterized these gene sets by clustering their members to a few distinct temporal profiles. Other potential functionally related genes were identified using a machine learning procedure. In summary, we characterized the autophagy gene sets and their members to biologically meaningful groups and elected a number of genes to be functionally related based on their expression patterns, suggesting that autophagy plays a critical role in removal of some intracellular components and supply of energy sources for lipid biogenesis during adipogenesis.


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