Identification of Potential Candidate Genes From Co-Expression Module Analysis During Preadipocyte Differentiation in Landrace Pig

Preadipocyte differentiation plays an important role in lipid deposition and affects fattening efficiency in pigs. In the present study, preadipocytes isolated from the subcutaneous adipose tissue of three Landrace piglets were induced into mature adipocytes in vitro. Gene clusters associated with fat deposition were investigated using RNA sequencing data at four time points during preadipocyte differentiation. Twenty-seven co-expression modules were subsequently constructed using weighted gene co-expression network analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses revealed three modules (blue, magenta, and brown) as being the most critical during preadipocyte differentiation. Based on these data and our previous differentially expressed gene analysis, angiopoietin-like 4 (ANGPTL4) was identified as a key regulator of preadipocyte differentiation and lipid metabolism. After inhibition of ANGPTL4, the expression of adipogenesis-related genes was reduced, except for that of lipoprotein lipase (LPL), which was negatively regulated by ANGPTL4 during preadipocyte differentiation. Our findings provide a new perspective to understand the mechanism of fat deposition.

[1]  T. Efferth,et al.  Identification of novel drug resistance mechanisms by genomic and transcriptomic profiling of glioblastoma cells with mutation-activated EGFR. , 2021, Life sciences.

[2]  Jiying Wang,et al.  Muscle Transcriptome Analysis Reveals Potential Candidate Genes and Pathways Affecting Intramuscular Fat Content in Pigs , 2020, Frontiers in Genetics.

[3]  M. Čandek-Potokar,et al.  Lipid Deposition and Metabolism in Local and Modern Pig Breeds: A Review , 2020, Animals : an open access journal from MDPI.

[4]  Yibing Liu,et al.  Transcriptome Analysis of Landrace Pig Subcutaneous Preadipocytes during Adipogenic Differentiation , 2019, Genes.

[5]  A. Wen,et al.  Molecular Characterization of Microtubule Affinity-Regulating Kinase4 from Sus scrofa and Promotion of Lipogenesis in Primary Porcine Placental Trophoblasts , 2019, International journal of molecular sciences.

[6]  M. Ploug,et al.  On the mechanism of angiopoietin-like protein 8 for control of lipoprotein lipase activity , 2019, Journal of Lipid Research.

[7]  Qisheng Zuo,et al.  Acetyl‐coenzyme A acyltransferase 2 promote the differentiation of sheep precursor adipocytes into adipocytes , 2018, Journal of cellular biochemistry.

[8]  Si Yang,et al.  Identification of key gene pathways and coexpression networks of islets in human type 2 diabetes , 2018, Diabetes, metabolic syndrome and obesity : targets and therapy.

[9]  S. Kersten,et al.  Angiopoietin-like 4 promotes the intracellular cleavage of lipoprotein lipase by PCSK3/furin in adipocytes , 2018, The Journal of Biological Chemistry.

[10]  T. Horvath,et al.  Brown adipose tissue derived ANGPTL4 controls glucose and lipid metabolism and regulates thermogenesis , 2018, Molecular metabolism.

[11]  Xiaohui Chen,et al.  Knockdown expression of IL-10Rα gene inhibits PRRSV replication and elevates immune responses in PBMCs of Tibetan pig in vitro , 2018, Veterinary Research Communications.

[12]  Min Zhang,et al.  MicroRNA-134 Promotes the Development of Atherosclerosis Via the ANGPTL4/LPL Pathway in Apolipoprotein E Knockout Mice , 2017, Journal of atherosclerosis and thrombosis.

[13]  K. Shubham,et al.  Systems-level organization of non-alcoholic fatty liver disease progression network. , 2017, Molecular bioSystems.

[14]  C. Lents,et al.  Production of a gonadotropin-releasing hormone 2 receptor knockdown (GNRHR2 KD) swine line , 2017, Transgenic Research.

[15]  C. Maltecca,et al.  Gene co-expression network analysis identifies porcine genes associated with variation in metabolizing fenbendazole and flunixin meglumine in the liver , 2017, Scientific Reports.

[16]  Jingyuan Fu,et al.  Inter-Tissue Gene Co-Expression Networks between Metabolically Healthy and Unhealthy Obese Individuals , 2016, PloS one.

[17]  J. B. Kim,et al.  Adipose Tissue Remodeling: Its Role in Energy Metabolism and Metabolic Disorders , 2016, Front. Endocrinol..

[18]  Jing Liu,et al.  Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease , 2016, BMC Cardiovascular Disorders.

[19]  W. D. van Marken Lichtenbelt,et al.  ANGPTL4 mediates shuttling of lipid fuel to brown adipose tissue during sustained cold exposure , 2015, eLife.

[20]  Matthew J. Silva,et al.  ASXL2 Regulates Glucose, Lipid, and Skeletal Homeostasis. , 2015, Cell reports.

[21]  Y. Wang,et al.  Integration of Transcriptome and Whole Genomic Resequencing Data to Identify Key Genes Affecting Swine Fat Deposition , 2015, PloS one.

[22]  Susanna Cirera,et al.  Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model , 2014, BMC Medical Genomics.

[23]  N. Sharma,et al.  An Approach to Identify SNPs in the Gene Encoding Acetyl-CoA Acetyltransferase-2 (ACAT-2) and Their Proposed Role in Metabolic Processes in Pig , 2014, PloS one.

[24]  S. Kersten,et al.  Angptl4 serves as an endogenous inhibitor of intestinal lipid digestion. , 2014, Molecular metabolism.

[25]  N. Tan,et al.  Fatty acid-inducible ANGPTL4 governs lipid metabolic response to exercise , 2014, Proceedings of the National Academy of Sciences.

[26]  Jonathan E. Clark,et al.  Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer , 2013, BMC Systems Biology.

[27]  S. Kersten,et al.  Linking nutritional regulation of Angptl4, Gpihbp1, and Lmf1 to lipoprotein lipase activity in rodent adipose tissue , 2012, BMC Physiology.

[28]  Guangchuang Yu,et al.  clusterProfiler: an R package for comparing biological themes among gene clusters. , 2012, Omics : a journal of integrative biology.

[29]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[30]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[31]  S. Young,et al.  GPIHBP1 is responsible for the entry of lipoprotein lipase into capillaries. , 2010, Cell metabolism.

[32]  J. Heinrich,et al.  Role of FADS1 and FADS2 polymorphisms in polyunsaturated fatty acid metabolism. , 2010, Metabolism: clinical and experimental.

[33]  Bing Zhang,et al.  Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression , 2010, BMC Systems Biology.

[34]  J. Auwerx,et al.  Interdependence of AMPK and SIRT1 for metabolic adaptation to fasting and exercise in skeletal muscle. , 2010, Cell metabolism.

[35]  Y. Hu,et al.  GPIHBP1 stabilizes lipoprotein lipase and prevents its inhibition by angiopoietin-like 3 and angiopoietin-like 4 , 2009, Journal of Lipid Research.

[36]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[37]  Robert V Farese,et al.  Angiopoietin-like 4 (ANGPTL4, Fasting-induced Adipose Factor) Is a Direct Glucocorticoid Receptor Target and Participates in Glucocorticoid-regulated Triglyceride Metabolism* , 2009, The Journal of Biological Chemistry.

[38]  Junjun Zhang,et al.  BioMart Central Portal—unified access to biological data , 2009, Nucleic Acids Res..

[39]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[40]  S. Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[41]  W. Cawthorn,et al.  TNF‐α and adipocyte biology , 2008 .

[42]  Defa Li,et al.  CLA differently regulates adipogenesis in stromal vascular cells from porcine subcutaneous adipose and skeletal muscle Published, JLR Papers in Press, May 11, 2007. , 2007, Journal of Lipid Research.

[43]  S. Horvath,et al.  Weighted gene coexpression network analysis strategies applied to mouse weight , 2007, Mammalian Genome.

[44]  O. MacDougald,et al.  Adipocyte differentiation from the inside out , 2006, Nature Reviews Molecular Cell Biology.

[45]  S. Horvath,et al.  Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target , 2006, Proceedings of the National Academy of Sciences.

[46]  J. Berndt,et al.  Semaphorin 3d promotes cell proliferation and neural crest cell development downstream of TCF in the zebrafish hindbrain , 2006, Development.

[47]  J. Zierath,et al.  AMP-activated protein kinase signaling in metabolic regulation. , 2006, The Journal of clinical investigation.

[48]  Deborah H. Anderson.  Role of lipids in the MAPK signaling pathway. , 2006, Progress in lipid research.

[49]  S. Horvath,et al.  A General Framework for Weighted Gene Co-Expression Network Analysis , 2005, Statistical applications in genetics and molecular biology.

[50]  Frank Eisenhaber,et al.  Fat Mobilization in Adipose Tissue Is Promoted by Adipose Triglyceride Lipase , 2004, Science.

[51]  H. Sul,et al.  Desnutrin, an Adipocyte Gene Encoding a Novel Patatin Domain-containing Protein, Is Induced by Fasting and Glucocorticoids , 2004, Journal of Biological Chemistry.

[52]  D. Auclair,et al.  BAY 43-9006 Exhibits Broad Spectrum Oral Antitumor Activity and Targets the RAF/MEK/ERK Pathway and Receptor Tyrosine Kinases Involved in Tumor Progression and Angiogenesis , 2004, Cancer Research.

[53]  T. Lallier.  Semaphorin Profiling of Periodontal Fibroblasts and Osteoblasts , 2004, Journal of dental research.

[54]  Namjin Chung,et al.  Sirt1 promotes fat mobilization in white adipocytes by repressing PPAR-γ , 2004, Nature.

[55]  J. Flier,et al.  Adipose Tissue as an Endocrine Organ , 2014 .

[56]  P. Shannon,et al.  Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks , 2003 .

[57]  S. Homma,et al.  Lipoprotein lipase (LpL) on the surface of cardiomyocytes increases lipid uptake and produces a cardiomyopathy. , 2003, The Journal of clinical investigation.

[58]  Kenichi Yoshida,et al.  Angiopoietin-like protein 4 is a potent hyperlipidemia-inducing factor in mice and inhibitor of lipoprotein lipase Published, JLR Papers in Press, September 16, 2002. DOI 10.1194/jlr.C200010-JLR200 , 2002, Journal of Lipid Research.

[59]  R. Zechner,et al.  Hormone-sensitive Lipase Deficiency in Mice Causes Diglyceride Accumulation in Adipose Tissue, Muscle, and Testis* , 2002, The Journal of Biological Chemistry.

[60]  M. Karin,et al.  AP-1 in cell proliferation and survival , 2001, Oncogene.

[61]  J. Mourot,et al.  Lipids in monogastric animal meat. , 2001, Reproduction, nutrition, development.

[62]  H. Ogata,et al.  The effects of dietary retinoic acid on body lipid deposition in juvenile red sea bream (Pagrus major); a preliminary study , 2001 .

[63]  R. Morrison,et al.  Hormonal signaling and transcriptional control of adipocyte differentiation. , 2000, The Journal of nutrition.

[64]  J. Flier,et al.  Obesity and insulin resistance. , 2000, The Journal of clinical investigation.

[65]  M. Lane,et al.  Role of the CCAAT enhancer binding proteins (C/EBPs) in adipocyte differentiation. , 1999, Biochemical and biophysical research communications.

[66]  W. Verbeke,et al.  Consumer perception, facts and possibilities to improve acceptability of health and sensory characteristics of pork. , 1999, Meat science.

[67]  A. Kimmel,et al.  Perilipins, ADRP, and other proteins that associate with intracellular neutral lipid droplets in animal cells. , 1999, Seminars in cell & developmental biology.

[68]  H. Beug,et al.  TGFβ signaling is necessary for carcinoma cell invasiveness and metastasis , 1998, Current Biology.

[69]  Christopher K. Glass,et al.  The peroxisome proliferator-activated receptor-γ is a negative regulator of macrophage activation , 1998, Nature.

[70]  E. Zandi,et al.  AP-1 function and regulation. , 1997, Current opinion in cell biology.

[71]  M. Lazar,et al.  Transcriptional Activation by Peroxisome Proliferator-activated Receptor γ Is Inhibited by Phosphorylation at a Consensus Mitogen-activated Protein Kinase Site* , 1997, The Journal of Biological Chemistry.

[72]  A. Suryawan,et al.  Effect of age on the differentiation of porcine adipose stromal-vascular cells in culture. , 1994, Journal of animal science.

[73]  A. Greenberg,et al.  Perilipin, a major hormonally regulated adipocyte-specific phosphoprotein associated with the periphery of lipid storage droplets. , 1991, The Journal of biological chemistry.

[74]  Hui Shen,et al.  Identification of Novel Potentially Pleiotropic Variants Associated With Osteoporosis and Obesity Using the cFDR Method , 2018, The Journal of clinical endocrinology and metabolism.

[75]  R. Pelikan,et al.  Modulation of lipid metabolic defects rescues cleft palate in Tgfbr2 mutant mice. , 2014, Human molecular genetics.