735
Views
0
CrossRef citations to date
0
Altmetric
Research Paper

A comparative assessment of reference genes in mouse brown adipocyte differentiation and thermogenesis in vitro

, , , , &
Article: 2330355 | Received 15 Nov 2023, Accepted 06 Mar 2024, Published online: 25 Mar 2024

References

  • Wang GX, Zhao XY, Lin JD. The brown fat secretome: metabolic functions beyond thermogenesis. Trends Endocrinol Metab. 2015;26(5):231–14. doi: 10.1016/j.tem.2015.03.002
  • Townsend KL, Tseng YH. Brown fat fuel utilization and thermogenesis. Trends Endocrinol Metab. 2014;25(4):168–177. doi: 10.1016/j.tem.2013.12.004
  • Betz MJ, Enerbäck S. Targeting thermogenesis in brown fat and muscle to treat obesity and metabolic disease. Nat Rev Endocrinol. 2018;14(2):77–87. doi: 10.1038/nrendo.2017.132
  • Kajimura S, Spiegelman BM, Seale P. Brown and beige fat: physiological roles beyond heat generation. Cell Metab. 2015;22(4):546–559. doi: 10.1016/j.cmet.2015.09.007
  • Luijten IHN, Cannon B, Nedergaard J. Glucocorticoids and brown adipose tissue: do glucocorticoids really inhibit thermogenesis? Mol Aspects Med. 2019;68(July):42–59. doi: 10.1016/j.mam.2019.07.002
  • Ballinger MA, Andrews MT, Suarez, RK., et al. Nature’s fat-burning machine: brown adipose tissue in a hibernating mammal. J. Exp. Biol. 2018;221(Suppl 1):jeb162586. doi:10.1242/jeb.162586
  • Ikeda K, Yamada T. UCP1 Dependent and Independent Thermogenesis in Brown and Beige Adipocytes. Front Endocrinol. 2020;11(July):1–6. doi: 10.3389/fendo.2020.00498
  • Oeckl J, Janovska P, Adamcova K, et al. Loss of UCP1 function augments recruitment of futile lipid cycling for thermogenesis in murine brown fat. Mol Metab. 2022;61(April):101499. doi: 10.1016/j.molmet.2022.101499
  • Galmozzi A, Sonne SB, Altshuler-Keylin S, et al. ThermoMouse: an in vivo Model to identify modulators of UCP1 expression in brown adipose tissue. Cell Rep. 2014;9(5):1584–1593. doi: 10.1016/j.celrep.2014.10.066
  • Kalinovich AV, de Jong JMA, Cannon B, et al. UCP1 in adipose tissues: two steps to full browning. Biochimie. 2017;134:127–137. doi: 10.1016/j.biochi.2017.01.007
  • Fedorenko A, Lishko PV, Kirichok Y. Mechanism of fatty-acid-dependent UCP1 uncoupling in brown fat mitochondria. Cell. 2012;151(2):400–413. doi: 10.1016/j.cell.2012.09.010
  • Duteil D, Metzger E, Willmann D, et al. LSD1 promotes oxidative metabolism of white adipose tissue. Nat Commun. 2014;5(1):4093. doi: 10.1038/ncomms5093
  • Kusudo T, Hashimoto M, Kataoka N, et al. CREG1 promotes uncoupling protein 1 expression and brown adipogenesis in vitro. J Biochem. 2019;165(1):47–55. doi: 10.1093/JB/MVY083
  • Lefterova MI, Zhang Y, Steger DJ, et al. Ppargamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev. 2008;22(21):2941–2952. doi: 10.1101/gad.1709008
  • Ahmed M, Lai TH, Hwang JS, et al. Transcriptional regulation of autophagy genes via stage-specific activation of CEBPB and PPARG during adipogenesis: a systematic study using public gene expression and transcription factor binding datasets. Cells. 2019;8(11):1321. doi: 10.3390/cells8111321
  • Loft A, Forss I, Siersbæk MS, et al. Browning of human adipocytes requires KLF11 and reprogramming of PPARγ superenhancers. Genes Dev. 2015;29(1):7–22. doi: 10.1101/gad.250829.114
  • Townsend KL, Tseng Y-H. Of mice and men: novel insights regarding constitutive and recruitable brown adipocytes. Int J Obes Suppl. 2015;5(S1):S15–S20. doi: 10.1038/ijosup.2015.5
  • Fundel K, Haag J, Gebhard PM, et al. Normalization strategies for mRNA expression data in cartilage research. Osteoarthr Cartil. 2008;16(8):947–955. doi: 10.1016/J.JOCA.2007.12.007
  • Almeida-Oliveira F, Leandro JGB, Ausina P, et al. Reference genes for quantitative PCR in the adipose tissue of mice with metabolic disease. Biomed Pharmacother. 2017;88:948–955. doi: 10.1016/j.biopha.2017.01.091
  • Ho KH, Patrizi A. Assessment of common housekeeping genes as reference for gene expression studies using RT-qPCR in mouse choroid plexus. Sci Rep. 2021;11(1):1–15. doi: 10.1038/s41598-021-82800-5
  • Silver N, Best S, Jiang J, et al. Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR. BMC Mol Biol. 2006;7(1):1–9. doi:10.1186/1471-2199-7-33
  • Nevone A, Lattarulo F, Russo M, et al. A strategy for the selection of RT-qPCR reference genes based on publicly available transcriptomic datasets. Biomedicines. 2023;11(4):1079. doi: 10.3390/biomedicines11041079
  • Mu J, Wang Y, Wang M, et al. Identification of reliable reference genes for gene expression studies in mouse models under microplastics stress. Ecotoxicol Environ Saf. 2023;252(January):114569. doi: 10.1016/j.ecoenv.2023.114569
  • Hayashi M, Nagasaka T. Suppression of norepinephrine-induced thermogenesis in brown adipose tissue by fasting. Am J Physiol. 1983;245(6):E582–E586. doi: 10.1152/AJPENDO.1983.245.6.E582
  • Cannon B, Nedergaard J. Brown adipose tissue: function and physiological significance. Physiol Rev. 2004;84(1):277–359. doi: 10.1152/PHYSREV.00015.2003
  • van Marken Lichtenbelt WD, Daanen HAM. Cold-induced metabolism. Curr Opin Clin Nutr Metab Care. 2003;6(4):469–475. doi: 10.1097/01.MCO.0000078992.96795.5F
  • O’Leary NA, Wright MW, Brister JR, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44(D1):D733–D745. doi: 10.1093/NAR/GKV1189
  • Ye J, Coulouris G, Zaretskaya I, et al. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinf. 2012;13(1):134. doi: 10.1186/1471-2105-13-134
  • Larionov A, Krause A, Miller WR. A standard curve based method for relative real time PCR data processing. BMC Bioinf. 2005;6(1):62. doi: 10.1186/1471-2105-6-62
  • Xie F, Wang J, Zhang B. RefFinder: a web-based tool for comprehensively analyzing and identifying reference genes. Funct Integr Genomics. 2023;23(2):125. doi: 10.1007/S10142-023-01055-7
  • Livak KJ, Schmittgen TD Analysis of relative gene expression data using real-time quantitative PCR and the double delta CT method. Methods. 2001;25(4):402–408. doi: 10.1006/meth.2001.1262
  • Pfaffl MW, Tichopad A, Prgomet C, et al. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper–Excel-based tool using pair-wise correlations. Biotechnol Lett. 2004;26(6):509–515. doi: 10.1023/B:BILE.0000019559.84305.47
  • Andersen CL, Jensen JL, TF Ørntoft. Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 2004;64(15):5245–5250. doi: 10.1158/0008-5472.CAN-04-0496
  • Vandesompele J, De Preter K, Pattyn F, et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002;3(7):1–12. doi: 10.1186/gb-2002-3-7-research0034
  • Shinde AB, Song A, Wang QA. Brown adipose tissue heterogeneity, energy metabolism, and beyond. Front Endocrinol. 2021;12(April):1–13. doi: 10.3389/fendo.2021.651763
  • Tontonoz P, Hu E, Spiegelman BM. Stimulation of adipogenesis in fibroblasts by PPARγ2, a lipid-activated transcription factor. Cell. 1994;79(7):1147–1156. doi: 10.1016/0092-8674(94)90006-X
  • Wang QA, Zhang F, Jiang L, et al. Peroxisome proliferator-activated receptor γ and its role in adipocyte homeostasis and thiazolidinedione-mediated insulin sensitization. 2018;38(10). doi: 10.1128/MCB.00677-17
  • Colas C, Mouchiroud M, Al Dow M, et al. DEPTOR loss impairs brown adipocyte development in vitro but has limited impacts in mice. Mol Metab. 2023;67:67. doi: 10.1016/J.MOLMET.2022.101660
  • Chang CF, Gunawan AL, Liparulo I, et al. CoQ regulates brown adipose tissue respiration and uncoupling protein 1 expression. Antioxidants (Basel). 2022;12(1):14. doi: 10.3390/ANTIOX12010014
  • Li X, Yang Q, Bai J, et al. Evaluation of eight reference genes for quantitative polymerase chain reaction analysis in human T lymphocytes co-cultured with mesenchymal stem cells. Mol Med Rep. 2015;12(5):7721–7727. doi: 10.3892/mmr.2015.4396
  • Wang Y, Shan Q, Meng Y, et al. Mrpl10 and Tbp are suitable reference genes for peripheral nerve crush injury. Int J Mol Sci. 2017;18(2):263. doi: 10.3390/IJMS18020263
  • Chen J, Bao Z, Huang Y, et al. Selection of suitable reference genes for qPCR gene expression analysis of HepG2 and L02 in four different liver cell Injured models. Biomed Res Int. 2020;2020:1–11. doi: 10.1155/2020/8926120
  • Franko N, Vrščaj LA, Zore T, et al. TBP, PPIA, YWHAZ and EF1A1 are the most stably expressed genes during Osteogenic Differentiation. Int J Mol Sci. 2022;23(8):4257. doi:10.3390/IJMS23084257
  • González-Bermúdez L, Anglada T, Genescà A, et al. Identification of reference genes for RT-qPCR data normalisation in aging studies. Sci Rep 91. 2019;9(1):1–11. doi:10.1038/s41598-019-50035-0
  • Schiera G, Di Liegro CM, Di Liegro I. Molecular determinants of malignant brain cancers: from intracellular alterations to invasion mediated by extracellular vesicles. Int J Mol Sci. 2017;18(12):2774. doi: 10.3390/ijms18122774
  • Sato K, Nishikawa SI, Nakano A. Membrane protein retrieval from the golgi apparatus to the endoplasmic reticulum (ER): characterization of the RER1 gene product as a component involved in ER localization of Sec12p. Mol Biol Cell. 1995;6(11):1459–1477. doi: 10.1091/MBC.6.11.1459
  • Hara T, Maejima I, Akuzawa T, et al. Rer1-mediated quality control system is required for neural stem cell maintenance during cerebral cortex development. PloS Genet. 2018;14(9):1–22. doi: 10.1371/journal.pgen.1007647
  • Krautgasser C, Mandl M, Hatzmann FM, et al. Reliable reference genes for expression analysis of proliferating and adipogenically differentiating human adipose stromal cells. Cell Mol Biol Lett. 2019;24(1). doi: 10.1186/s11658-019-0140-6
  • du Sert NP, Hurst V, Ahluwalia A, et al. The arrive guidelines 2.0: Updated guidelines for reporting animal research. PLoS Biol. 2020;18(7):1–12. doi: 10.1371/journal.pbio.3000410
  • Kawano M, Morikawa K, Suda T, et al. Chimeric SV40 virus-like particles induce specific cytotoxicity and protective immunity against influenza a virus without the need of adjuvants. Virology. 2014;448:159–167. doi: 10.1016/j.virol.2013.10.010
  • Ahmed M, Kim DR. Pcr: an R package for quality assessment, analysis and testing of qPCR data. PeerJ. 2018;6(3):e4473. doi: 10.7717/peerj.4473
  • Xie F, Xiao P, Chen D, et al. miRdeepfinder: a miRNA analysis tool for deep sequencing of plant small RNAs. Plant Mol Biol. 2012;80(1):75–84. doi: 10.1007/S11103-012-9885-2
  • R Core Team. R: a language and environment for statistical computing. 2021. Available from: https://www.r-project.org/
  • Gentleman RC, Carey VJ, Bates DM, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):1–16.
  • Xu S, Chen M, Feng T, et al. Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers. Front Genet. 2021;12:2122. doi: 10.3389/fgene.2021.774846
  • Shapiro SS, Wilk MB. An analysis of variance test for normality (complete samples). Biometrika. 1965;52(3–4):591–611. doi: 10.1093/biomet/52.3-4.591