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

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.

Autophagy in Adipocyte Browning: Emerging Drug Target for Intervention in Obesity

“…Lipophagy is the selective removal of lipid droplets in cytosolic organelles by lysosomes, which are derived from stimulated autophagy markers such as LC3 and p62 (Singh and Cuervo, 2012; Ward et al, 2016). Lipogenesis, often considered identical to adipogenesis, is focused on the formation of lipid droplets during white adipocyte differentiation with autophagy activation; lipolysis, on the other hand, is the secretion of glycerol and fatty acid partially resulting from the degradation of lipid droplets by autophagy (Cingolani and Czaja, 2016; Ahmed et al, 2018). The balance between lipogenesis and lipolysis plays a vital role in regulating the lipid metabolism in white and brown adipocytes (Singh and Cuervo, 2012; Martinez-Lopez et al, 2016; Zechner et al, 2017).…”

“…Adipogenesis is a unique adipocyte differentiation process that generates lipid droplets with triglycerides and fatty acids inside the lipid vacuoles (Rosen and Spiegelman, 2006; Ro et al, 2013; Ahmed et al, 2018). Autophagy for non-selective bulk degradation of proteins and lipids through the fusion of autophagosomes and lysosomes is suggested as one of the major types of autophagy in adipocytes (Singh et al, 2009b; Singh and Cuervo, 2012; Ro et al, 2013).…”

“…The relationship between adipogenesis and autophagy has drawn much attention over the past decade regarding the potential link to metabolic diseases such as obesity. Autophagy is necessary and activated when white adipocyte undergoes differentiation (Singh et al, 2009b; Singh and Cuervo, 2012; Zhang et al, 2012; Ahmed et al, 2018). Chloroquine treatment and autophagy-related protein (ATG) 5 knockdown decreases adipogenesis of mouse embryonic fibroblast (MEF) cells.…”

Co-Expression Network Analysis of AMPK and Autophagy Gene Products during Adipocyte Differentiation

“…On the other hand, this process likely involves a wide range of changes in transcription, translation and protein modification. In a previous study from our laboratory, we suggested that many autophagy genes were functionally associated with adipocyte differentiation using the RNA-Seq expression data [ 19 ]. We also showed that the mRNA level of key autophagy genes is specifically regulated at different time points, and clusters of these genes respond to the differentiation stimulus in a time-dependent manner.…”

“…3T3-L1 pre-adipocytes were cultured and induced for differentiation using MDI protocol as described before [ 19 ]. Total RNA was collected at four different time points corresponding the the major differentiation stages of the adipocytes (−2 day, full confluence; 0 day, undifferentiated; 10 h differentiating; and −6 day, maturating).…”