Analysis of gene expression profiles at different stages during preadipocyte differentiation in rabbits
Received date: 2019-09-04
Revised date: 2019-12-11
Online published: 2020-01-13
Supported by
Supported by the Earmarked Fund for China Agriculture Research System No(CARS-44-A-2)
Excessive accumulation of fat is harmful to human health. The preadipocyte differentiation is a critical process of fat development. Studying the expression profiles of genes related to preadipocyte differentiation contributes to understanding of the mechanism of fat accumulation. Despite being considered an ideal animal model for studying adipogenesis, little is known about the gene expression profiles at different stages during preadipocyte differentiation in rabbits. In the present study, rabbit preadipocytes were cultured in vitro and induced for differentiation, and gene expression profiles of adipocytes collected at days 0, 3, and 9 of differentiation were analyzed by RNA-seq. We identified 1352 differentially expressed genes (DEGs) when comparing day 3 with day 0 and identified 888 DEGs when comparing day 9 with day 3. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the PPAR signaling pathway and PI3K-Akt signaling pathway were significantly enriched by the DEGs that up-regulated within the period of day 0 - day 3, and the GO terms and KEGG pathways that were associated with cell cycle were enriched by the DEGs that up-regulated within the period of day 3 - day 9. The DEGs that specifically up-regulated within the period of day 0 - day 3 might play roles in the cytoplasm, and the DEGs that specifically up-regulated within the period of day 3 - day 9 might act in the nucleus. The protein-protein interaction (PPI) network constructed by DEGs showed that hub node genes might modulate rabbit preadipocyte differentiation via regulating cell cycle.
Key words： adipocytes; differentiation; rabbits; preadipocytes; RNA-seq
Kun Du, Chuyang Mao, Anyong Ren, Xuemei Wu, Qingling Li, Tingting Chen, Shiyi Chen, Songjia Lai . Analysis of gene expression profiles at different stages during preadipocyte differentiation in rabbits[J]. Hereditas(Beijing), 2020 , 42(3) : 309 -320 . DOI: 10.16288/j.yczz.19-265
| [1] | Saxena A, Tiwari P, Wahi N, Soni A, Bansiwal RC, Kumar A, Sharma B, Punjabi P, Gupta N, Malik B, Medicherla KM, Suravajhala P, Mathur SK . Transcriptome profiling reveals association of peripheral adipose tissue pathology with type-2 diabetes in Asian Indians. Adipocyte, 2019,8(1):125-136. |
| [2] | Fox CS, Massaro JM, Hoffmann U, Pou KM, Maurovich- Horvat P, Liu CY, Vasan RS, Murabito JM, Meigs JB, Cupples LA, D'Agostino RB Sr, O'Donnell CJ. Abdominal visceral and subcutaneous adipose tissue compartments: Association with metabolic risk factors in the framingham heart study. Circulation, 2007,116(1):39-48. |
| [3] | Kershaw EE, Flier JS . Adipose tissue as an endocrine organ. J Clin Endocrinol Metab, 2004,89(6):2548-2556. |
| [4] | Zhang T, Zhang XQ, Han KP, Zhang GX, Wang JY, Xie KZ, Xue Q . Genome-Wide analysis of lncRNA and mRNA expression during differentiation of abdominal preadipocytes in the chicken. G3 (Bethesda), 2017,7(3):953-966. |
| [5] | Zhang JW, Luo Y, Wang YH, He LJ, Li MZ, Wang X . MicroRNA regulates animal adipocyte differentiation. Hereditas(Beijing), 2015,37(12):1175-1184. |
| [5] | 张进威, 罗毅, 王宇豪, 何刘军, 李明洲, 王讯 . MicroRNA调控动物脂肪细胞分化研究进展. 遗传, 2015,37(12):1175-1184. |
| [6] | Lee MJ . Hormonal regulation of adipogenesis. Compr Physiol, 2017,7(4):1151-1195. |
| [7] | Sarjeant K, Stephens JM . Adipogenesis. Cold Spring Harb Perspect Biol, 2012,4(9):a008417. |
| [8] | Tontonoz P, Hu E, Spiegelman BM . Stimulation of adipogenesis in fibroblasts by PPARγ2, a lipid-activated transcription factor. Cell, 1994,79(7):1147-1156. |
| [9] | Wang L, Na W, Wang YX, Wang YB, Wang N, Wang QG, Li YM, Li H . Characterization of chicken PPARγ expression and its impact on adipocyte proliferation and differentiation. Hereditas(Beijing), 2012,34(4):454-464. |
| [9] | 王丽, 那威, 王宇祥, 王彦博, 王宁, 王启贵, 李玉茂, 李辉 . 鸡PPARγ基因的表达特性及其对脂肪细胞增殖分化的影响. 遗传, 2012,34(4):454-464. |
| [10] | Lin FT, Lane MD . CCAAT/enhancer binding protein alpha is sufficient to initiate the 3T3-L1 adipocyte differentiation program. Proc Natl Acad Sci USA, 1994,91(19):8757-8761. |
| [11] | Deng TM, Wang YH, Wang CC, Yan H . FABP4 silencing ameliorates hypoxia reoxygenation injury through the attenuation of endoplasmic reticulum stress-mediated apoptosis by activating PI3K/Akt pathway. Life Sci, 2019,224:149-156. |
| [12] | Liu Y, Peng WQ, Guo YY, Liu Y, Tang QQ, Guo L . Krüppel-like factor 10 (KLF10) is transactivated by the transcription factor C/EBPβ and involved in early 3T3-L1 preadipocyte differentiation. J Biol Chem, 2018,293(36):14012-14021. |
| [13] | Tang Q, Chen C, Zhang Y, Dai MJ, Jiang YC, Wang H, Yu M, Jing W, Tian WD . Wnt5a regulates the cell proliferation and adipogenesis via MAPK-independent pathway in early stage of obesity. Cell Biol Int, 2018,42(1):63-74. |
| [14] | Yuan YY, Xi Y, Chen JY, Zhu P, Kang JY, Zou ZQ, Wang FY, Bu SZ . STAT3 stimulates adipogenic stem cell proliferation and cooperates with HMGA2 during the early stage of differentiation to promote adipogenesis. Biochem Biophys Res Commun, 2017,482(4):1360-1366. |
| [15] | Desando G, Cavallo C, Sartoni F, Martini L, Parrilli A, Veronesi F, Fini M, Giardino R, Facchini A, Grigolo B . Intra-articular delivery of adipose derived stromal cells attenuates osteoarthritis progression in an experimental rabbit model. Arthritis Res Ther, 2013,15(1):R22. |
| [16] | Gong LL, Wang C, Li YR, Sun QZ, Li GZ, Wang DR . Effects of human adipose-derived stem cells on the viability of rabbit random pattern flaps. Cytotherapy, 2014,16(4):496-507. |
| [17] | Maneschi E, Vignozzi L, Morelli A, Mello T, Filippi S, Cellai I, Comeglio P, Sarchielli E, Calcagno A, Mazzanti B, Vettor R, Vannelli GB, Adorini L, Maggi M . FXR activation normalizes insulin sensitivity in visceral preadipocytes of a rabbit model of MetS. J Endocrinol, 2013,218(2):215-231. |
| [18] | Zebisch K, Voigt V, Wabitsch M, Brandsch M . Protocol for effective differentiation of 3T3-L1 cells to adipocytes. Anal Biochem, 2012,425(1):88-90. |
| [19] | Chen SF, Zhou YQ, Chen YR, Gu J . Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 2018,34(17):i884-i890. |
| [20] | Kim D, Langmead B, Salzberg SL . HISAT: a fast spliced aligner with low memory requirements. Nat Methods, 2015,12(4):357-360. |
| [21] | Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL . Transcript-level expression analysis of RNA-seq experiments with HISAT, stringtie and ballgown. Nat Protoc, 2016,11(9):1650-1667. |
| [22] | Love MI, Huber W, Anders S . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 2014,15(12):550. |
| [23] | Huang Da W, Sherman BT, Lempicki RA . Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc, 2009,4(1):44-57. |
| [24] | Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C, . The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res, 2017,45(D1):D362-D368. |
| [25] | Chin CH, Chen SH, Wu HH, Ho CW, Ko MT, Lin CY . CytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol, 2014,8(Suppl.4):S11. |
| [26] | Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res, 2003,13(11):2498-2504. |
| [27] | Huang WL, Zhang XX, Li A, Miao XY . Identification of differentially expressed genes between subcutaneous and intramuscular adipose tissue of large white pig using RNA-seq. Hereditas(Beijing), 2017,39(6):501-511. |
| [27] | 黄万龙, 张秀秀, 李嫒, 苗向阳 . 利用RNA-seq技术筛选大白猪皮下和肌内脂肪组织差异表达基因. 遗传, 2017,39(6):501-511. |
| [28] | Chang HR, Kim HJ, Xu X, Ferrante AW Jr . Macrophage and adipocyte IGF1 maintain adipose tissue homeostasis during metabolic stresses. Obesity (Silver Spring), 2016,24(1):172-183. |
| [29] | Tang QQ, Lane MD . Adipogenesis: from stem cell to adipocyte. Annu Rev Biochem, 2012,81:715-736. |
| [30] | Hu L, Yang GD, H?gg D, Sun GM, Ahn JM, Jiang N, Ricupero CL, Wu J, Rodhe CH, Ascherman JA, Chen LL, Mao JJ . IGF1 promotes adipogenesis by a lineage bias of endogenous adipose stem/progenitor cells. Stem Cells, 2015,33(8):2483-2495. |
| [31] | Pei Z, Yang Y, Kiess W, Sun CJ, Luo FH . Dynamic profile and adipogenic role of growth differentiation factor 5 (GDF5) in the differentiation of 3T3-L1 preadipocytes. Arch Biochem Biophys, 2014,560:27-35. |
| [32] | Mota de Sá P, Richard AJ, Hang H, Stephens JM . Transcriptional regulation of adipogenesis. Compr Physiol, 2017,7(2):635-674. |
| [33] | ?widerska E, Podolska M, Strycharz J, Szwed M, Abramczyk H, Bro?ek-Pluska B, Wróblewski A, Szemraj J, Majsterek I, Drzewoski J, ?liwińska A . Hyperglycemia changes expression of key adipogenesis markers (C/EBPα and PPAR?) and morphology of differentiating Human visceral adipocytes. Nutrients, 2019,11(8):E1835. |
| [34] | Cai R, Tang GR, Zhang Q, Yong WL, Zhang WR, Xiao JY, Wei CS, He C, Yang GS, Pang WJ . A Novel lnc-RNA, Named lnc-ORA, Is identified by RNA-Seq analysis, and its knockdown inhibits adipogenesis by regulating the PI3K/AKT/mTOR signaling pathway. Cells, 2019,8(5):E477. |
| [35] | Chen JH, Ren XY, Li LM, Lu SY, Cheng T, Tan LT, Liang SD, He DL, Luo QB, Nie QH, Zhang XQ, Luo W . The cell cycle pathway regulates chicken abdominal fat deposition as revealed by transcriptome sequencing. Hereditas (Beijing), 2019,41(10):962-973. |
| [35] | 陈家辉, 任学义, 李丽敏, 卢诗意, 程湉, 谭量天, 梁少东, 何丹林, 罗庆斌, 聂庆华, 张细权, 罗文 . 转录组测序揭示细胞周期通路参与鸡腹脂沉积. 遗传, 2019,41(10):962-973. |
| [36] | He J, Chen DL, Samocha-Bonet D, Gillinder KR, Barclay JL, Magor GW, Perkins AC, Greenfield JR, Yang G, Whitehead JP . Fibroblast growth factor-1 (FGF-1) promotes adipogenesis by downregulation of carboxypeptidase A4 (CPA4) - a negative regulator of adipogenesis implicated in the modulation of local and systemic insulin sensitivity. Growth Factors, 2016,34(5-6):210-216. |
| [37] | Huang Q, Liu ML, Du XL, Zhang RH, Xue Y, Zhang YY, Zhu WD, Li D, Zhao AL, Liu Y . Role of p53 in preadipocyte differentiation. Cell Biol Int, 2014,38(12):1384-1393. |
| [38] | Dalton S . Linking the cell cycle to cell fate decisions. Trends Cell Biol, 2015,25(10):592-600. |
| [39] | Soufi A, Dalton S . Cycling through developmental decisions: how cell cycle dynamics control pluripotency, differentiation and reprogramming. Development, 2016,143(23):4301-4311. |
| [40] | Wu RF, Liu YH, Yao YX, Zhao YL, Bi Z, Jiang Q, Liu Q, Cai M, Wang FQ, Wang YZ, Wang XX . FTO regulates adipogenesis by controlling cell cycle progression via m 6A-YTHDF2 dependent mechanism . Biochim Biophys Acta Mol Cell Biol Lipids, 2018,1863(10):1323-1330. |
| [41] | Lee Y, Yang H, Hur G, Yu J, Park S, Kim JH, Yoon Park JH, Shin HS, Kim JE, Lee KW . 5-(3°,4°-Dihydroxyphenyl)- γ-valerolactone, a metabolite of procyanidins in cacao, suppresses MDI-induced adipogenesis by regulating cell cycle progression through direct inhibition of CDK2/ cyclin O. Food Funct, 2019,10(5):2958-2969. |
| [42] | Dasgupta N, Thakur BK, Ta A, Das S, Banik G, Das S . Polo-like kinase 1 expression is suppressed by CCAAT/ enhancer-binding protein α to mediate colon carcinoma cell differentiation and apoptosis. Biochim Biophys Acta Gen Subj, 2017,1861(7):1777-1787. |
| [43] | Fujimori A, Itoh K, Goto S, Hirakawa H, Wang B, Kokubo T, Kito S, Tsukamoto S, Fushiki S . Disruption of Aspm causes microcephaly with abnormal neuronal differentiation. Brain Dev, 2014,36(8):661-669. |
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