Integrative Analysis of Whole-genome Expression Profiling and Regulatory Network Identifies Novel Biomarkers for Insulin Resistance in Leptin Receptor-deficient Mice

Author(s): Yuchi Zhang, Xinyu Wu, Cong Zhao, Kai Li, Yi Zheng, Jing Zhao, Pengling Ge*

Journal Name: Medicinal Chemistry

Volume 16 , Issue 5 , 2020

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Graphical Abstract:


Background: Molecular characterization of insulin resistance, a growing health issue worldwide, will help to develop novel strategies and accurate biomarkers for disease diagnosis and treatment.

Objective: Integrative analysis of gene expression profiling and gene regulatory network was exploited to identify potential biomarkers early in the development of insulin resistance.

Methods: RNA was isolated from livers of animals at three weeks of age, and whole-genome expression profiling was performed and analyzed with Agilent mouse 4×44K microarrays. Differentially expressed genes were subsequently validated by qRT-PCR. Functional characterizations of genes and their interactions were performed by Gene Ontology (GO) analysis and gene regulatory network (GRN) analysis.

Results: A total of 197 genes were found to be differentially expressed by fold change ≥2 and P < 0.05 in BKS-db +/+ mice relative to sex and age-matched controls. Functional analysis suggested that these differentially expressed genes were enriched in the regulation of phosphorylation and generation of precursor metabolites which are closely associated with insulin resistance. Then a gene regulatory network associated with insulin resistance (IRGRN) was constructed by integration of these differentially expressed genes and known human protein-protein interaction network. The principal component analysis demonstrated that 67 genes in IRGRN could clearly distinguish insulin resistance from the non-disease state. Some of these candidate genes were further experimentally validated by qRT-PCR, highlighting the predictive role as biomarkers in insulin resistance.

Conclusion: Our study provides new insight into the pathogenesis and treatment of insulin resistance and also reveals potential novel molecular targets and diagnostic biomarkers for insulin resistance.

Keywords: Biomarkers, expression profiling, gene regulatory network, insulin resistance, integrative analysis, leptin receptor gene.

Rao, G. Insulin resistance syndrome. Am. Fam. Physician, 2001, 63(6), 1159-1163, 1165-1166.
[PMID: 11277552]
Suh, Y.H.; Kim, Y.; Bang, J.H.; Choi, K.S.; Lee, J.W.; Kim, W.H.; Oh, T.J.; An, S.; Jung, M.H. Analysis of gene expression profiles in insulin-sensitive tissues from pre-diabetic and diabetic Zucker diabetic fatty rats. J. Mol. Endocrinol., 2005, 34(2), 299-315.
[] [PMID: 15821098]
Wang, L.; Shen, M.; Wang, F.; Ma, L. GRK5 ablation contributes to insulin resistance. Biochem. Biophys. Res. Commun., 2012, 429(1-2), 99-104.
[] [PMID: 23111327]
Soto-Urquieta, M.G.; López-Briones, S.; Pérez-Vázquez, V.; Saavedra-Molina, A.; González-Hernández, G.A.; Ramírez-Emiliano, J. Curcumin restores mitochondrial functions and decreases lipid peroxidation in liver and kidneys of diabetic db/db mice. Biol. Res., 2014, 47, 74.
[] [PMID: 25723052]
Davis, R.C.; Castellani, L.W.; Hosseini, M.; Ben-Zeev, O.; Mao, H.Z.; Weinstein, M.M.; Jung, D.Y.; Jun, J.Y.; Kim, J.K.; Lusis, A.J.; Péterfy, M. Early hepatic insulin resistance precedes the onset of diabetes in obese C57BLKS-db/db mice. Diabetes, 2010, 59(7), 1616-1625.
[] [PMID: 20393148]
Yun, K.U.; Ryu, C.S.; Lee, J.Y.; Noh, J.R.; Lee, C.H.; Lee, H.S.; Kang, J.S.; Park, S.K.; Kim, B.H.; Kim, S.K. Hepatic metabolism of sulfur amino acids in db/db mice. Food Chem. Toxicol., 2013, 53, 180-186.
[] [PMID: 23220616]
Puff, R.; Dames, P.; Weise, M.; Göke, B.; Seissler, J.; Parhofer, K.G.; Lechner, A. Reduced proliferation and a high apoptotic frequency of pancreatic beta cells contribute to genetically-determined diabetes susceptibility of db/db BKS mice. Horm. Metab. Res., 2011, 43(5), 306-311.
[] [PMID: 21412687]
Lin, E.; Tsai, S.J. Genome-wide microarray analysis of gene expression profiling in major depression and antidepressant therapy. Prog. Neuropsychopharmacol. Biol. Psychiatry, 2016, 64, 334-340.
[] [PMID: 25708651]
Fujimaki, S.; Kuwabara, T. Diabetes-induced dysfunction of mitochondria and stem cells in skeletal muscle and the nervous system. Int. J. Mol. Sci., 2017, 18(10), 2147.
[] [PMID: 29036909]
Newsholme, P.; Gaudel, C.; Krause, M. Mitochondria and diabetes. An intriguing pathogenetic role. Adv. Exp. Med. Biol., 2012, 942, 235-247.
[] [PMID: 22399425]
Foti, D.; Chiefari, E.; Fedele, M.; Iuliano, R.; Brunetti, L.; Paonessa, F.; Manfioletti, G.; Barbetti, F.; Brunetti, A.; Croce, C.M.; Fusco, A.; Brunetti, A. Lack of the architectural factor HMGA1 causes insulin resistance and diabetes in humans and mice. Nat. Med., 2005, 11(7), 765-773.
[] [PMID: 15924147]
Suliman, S.G.; Stanik, J.; McCulloch, L.J.; Wilson, N.; Edghill, E.L.; Misovicova, N.; Gasperikova, D.; Sandrikova, V.; Elliott, K.S.; Barak, L.; Ellard, S.; Volpi, E.V.; Klimes, I.; Gloyn, A.L. Severe insulin resistance and intrauterine growth deficiency associated with haploinsufficiency for INSR and CHN2: new insights into synergistic pathways involved in growth and metabolism. Diabetes, 2009, 58(12), 2954-2961.
[] [PMID: 19720790]
Okamoto, H.; Obici, S.; Accili, D.; Rossetti, L. Restoration of liver insulin signaling in Insr knockout mice fails to normalize hepatic insulin action. J. Clin. Invest., 2005, 115(5), 1314-1322.
[] [PMID: 15864351]
Boura-Halfon, S.; Zick, Y. Phosphorylation of IRS proteins, insulin action, and insulin resistance. Am. J. Physiol. Endocrinol. Metab., 2009, 296(4), E581-E591.
[] [PMID: 18728222]
Rojas, F.A.; Hirata, A.E.; Saad, M.J. Regulation of insulin receptor substrate-2 tyrosine phosphorylation in animal models of insulin resistance. Endocrine, 2003, 21(2), 115-122.
[] [PMID: 12897373]
Yi, Z.; Langlais, P.; De Filippis, E.A.; Luo, M.; Flynn, C.R.; Schroeder, S.; Weintraub, S.T.; Mapes, R.; Mandarino, L.J. Global assessment of regulation of phosphorylation of insulin receptor substrate-1 by insulin in vivo in human muscle. Diabetes, 2007, 56(6), 1508-1516.
[] [PMID: 17360977]
Murakami, N.; Bolton, D.C.; Kida, E.; Xie, W.; Hwang, Y.W. Phosphorylation by Dyrk1A of clathrin coated vesicle-associated proteins: identification of the substrate proteins and the effects of phosphorylation. PLoS One, 2012, 7(4) e34845
[] [PMID: 22514676]
Himpel, S.; Tegge, W.; Frank, R.; Leder, S.; Joost, H.G.; Becker, W. Specificity determinants of substrate recognition by the protein kinase DYRK1A. J. Biol. Chem., 2000, 275(4), 2431-2438.
[] [PMID: 10644696]
Hao, L.; Nishimura, T.; Wo, H.; Fernandez-Patron, C. Vascular responses to alpha1-adrenergic receptors in small rat mesenteric arteries depend on mitochondrial reactive oxygen species. Arterioscler. Thromb. Vasc. Biol., 2006, 26(4), 819-825.
[] [PMID: 16424353]
Nagareddy, P.R.; MacLeod, K.M.; McNeill, J.H. GPCR agonistinduced transactivation of the EGFR upregulates MLC II expression and promotes hypertension in insulin-resistant rats. Cardiovasc. Res., 2010, 87(1), 177-186.
[] [PMID: 20110336]
Vairaktaris, E.; Goutzanis, L.; Yapijakis, C.; Vassiliou, S.; Spyridonidou, S.; Vylliotis, A.; Nkenke, E.; Lazaris, A.C.; Strantzias, P.; Patsouris, E. Diabetes enhances the expression of H-ras and suppresses the expression of EGFR leading to increased cell proliferation. Histol. Histopathol., 2009, 24(5), 531-539.
[PMID: 19283661]
Akahori, Y.; Takamoto, N.; Masumoto, A.; Inoue, S.; Nakatsukasa, H.; Masuyama, H.; Hiramatsu, Y. Circulating levels of ciliary neurotrophic factor in normal pregnancy and preeclampsia. Acta Med. Okayama, 2010, 64(2), 129-136.
[PMID: 20424668]
Rezende, L.F.; Santos, G.J.; Santos-Silva, J.C.; Carneiro, E.M.; Boschero, A.C. Ciliary neurotrophic factor (CNTF) protects non-obese Swiss mice against type 2 diabetes by increasing beta cell mass and reducing insulin clearance. Diabetologia, 2012, 55(5), 1495-1504.
[] [PMID: 22349107]
Kowluru, A.; Matti, A. Hyperactivation of protein phosphatase 2A in models of glucolipotoxicity and diabetes: potential mechanisms and functional consequences. Biochem. Pharmacol., 2012, 84(5), 591-597.
[] [PMID: 22583922]
Galbo, T.; Perry, R.J.; Nishimura, E.; Samuel, V.T.; Quistorff, B.; Shulman, G.I. PP2A inhibition results in hepatic insulin resistance despite Akt2 activation. Aging (Albany NY), 2013, 5(10), 770-781.
[] [PMID: 24150286]
Batut, J.; Schmierer, B.; Cao, J.; Raftery, L.A.; Hill, C.S.; Howell, M. Two highly related regulatory subunits of PP2A exert opposite effects on TGF-beta/Activin/Nodal signalling. Development, 2008, 135(17), 2927-2937.
[] [PMID: 18697906]
Rönn, T.; Poulsen, P.; Tuomi, T.; Isomaa, B.; Groop, L.; Vaag, A.; Ling, C. Genetic variation in ATP5O is associated with skeletal muscle ATP50 mRNA expression and glucose uptake in young twins. PLoS One, 2009, 4(3) e4793
[] [PMID: 19274082]
Nagy, N.; Malik, G.; Tosaki, A.; Ho, Y.S.; Maulik, N.; Das, D.K. Overexpression of glutaredoxin-2 reduces myocardial cell death by preventing both apoptosis and necrosis. J. Mol. Cell. Cardiol., 2008, 44(2), 252-260.
[] [PMID: 18076901]
de la Monte, S.; Derdak, Z.; Wands, J.R. Alcohol, insulin resistance and the liver-brain axis. J. Gastroenterol. Hepatol., 2012, 27(Suppl. 2), 33-41.
[] [PMID: 22320914]
He, Z.; Opland, D.M.; Way, K.J.; Ueki, K.; Bodyak, N.; Kang, P.M.; Izumo, S.; Kulkarni, R.N.; Wang, B.; Liao, R.; Kahn, C.R.; King, G.L. Regulation of vascular endothelial growth factor expression and vascularization in the myocardium by insulin receptor and PI3K/Akt pathways in insulin resistance and ischemia. Arterioscler. Thromb. Vasc. Biol., 2006, 26(4), 787-793.
[] [PMID: 16469952]
Zhu, S.; Sun, F.; Li, W.; Cao, Y.; Wang, C.; Wang, Y.; Liang, D.; Zhang, R.; Zhang, S.; Wang, H.; Cao, F. Apelin stimulates glucose uptake through the PI3K/Akt pathway and improves insulin resistance in 3T3-L1 adipocytes. Mol. Cell. Biochem., 2011, 353(1-2), 305-313.
[] [PMID: 21461612]
Adhikari, S.; Uren, A.; Roy, R. Excised damaged base determines the turnover of human N-methylpurine-DNA glycosylase. DNA Repair (Amst.), 2009, 8(10), 1201-1206.
[] [PMID: 19616486]
Derdak, Z.; Lang, C.H.; Villegas, K.A.; Tong, M.; Mark, N.M.; de la Monte, S.M.; Wands, J.R. Activation of p53 enhances apoptosis and insulin resistance in a rat model of alcoholic liver disease. J. Hepatol., 2011, 54(1), 164-172.
[] [PMID: 20961644]
Song, S.; Xing, G.; Yuan, L.; Wang, J.; Wang, S.; Yin, Y.; Tian, C.; He, F.; Zhang, L. N-methylpurine DNA glycosylase inhibits p53-mediated cell cycle arrest and coordinates with p53 to determine sensitivity to alkylating agents. Cell Res., 2012, 22(8), 1285-1303.
[] [PMID: 22801474]
Liang, C.; Zhang, X.; Song, S.; Tian, C.; Yin, Y.; Xing, G.; He, F.; Zhang, L. Identification of UHRF1/2 as new N-methylpurine DNA glycosylase-interacting proteins. Biochem. Biophys. Res. Commun., 2013, 433(4), 415-419.
[] [PMID: 23537643]

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Article Details

Year: 2020
Published on: 07 August, 2020
Page: [635 - 642]
Pages: 8
DOI: 10.2174/1573406415666191004135450
Price: $65

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