Identification of circular RNAs and functional competing endogenous RNA networks in human proximal tubular epithelial cells treated with sodium-glucose cotransporter 2 inhibitor dapagliflozin in diabetic kidney disease

References

• Minutolo R, Gabbai FB, Provenzano M, et al. Cardiorenal prognosis by residual proteinuria level in diabetic chronic kidney disease: pooled analysis of four cohort studies. Nephrol Dialysis Trans. 2018;33(11):1942–1949.
   PubMed Web of Science ®Google Scholar
• Li Vecchi M, Fuiano G, Francesco M, et al. Prevalence and severity of anaemia in patients with type 2 diabetic nephropathy and different degrees of chronic renal insufficiency. Nephron Clin Pract. 2007;105(2):c62–c67.
   PubMedGoogle Scholar
• Kondapally Seshasai S R, Kaptoge S, Thompson A, et al. Diabetes mellitus, fasting glucose, and risk of cause-specific death. N Engl J Med. 2011;364:829–841.
   PubMed Web of Science ®Google Scholar
• Garcia-Fernandez N, Jacobs-Cachأ C, JMa M-G, et al. Matrix metalloproteinases in diabetic kidney disease. J Clin Med. 2020;9(2):472.
   PubMed Web of Science ®Google Scholar
• De Nicola L, Gabbai FB, Liberti ME, et al. Sodium/glucose cotransporter 2 inhibitors and prevention of diabetic nephropathy: targeting the renal tubule in diabetes. Am J Kidney Dis. 2014;64(1):16–24.
   PubMed Web of Science ®Google Scholar
• Zinman B, Wanner C, Lachin JM, et al. Empagliflozin, cardiovascular outcomes, and mortality in type 2 diabetes. N Engl J Med. 2015;373(22):2117–2128.
   PubMed Web of Science ®Google Scholar
• Neal B, Perkovic V, Mahaffey KW, et al. Canagliflozin and cardiovascular and renal events in type 2 diabetes. N Engl J Med. 2017;377(7):644–657.
   PubMed Web of Science ®Google Scholar
• Wiviott SD, Raz I, Bonaca MP, et al. Dapagliflozin and cardiovascular outcomes in type 2 diabetes. N Engl J Med. 2019;380(4):347–357.
   PubMed Web of Science ®Google Scholar
• Kidokoro K, Cherney DZI, Bozovic A, et al. Evaluation of glomerular hemodynamic function by empagliflozin in diabetic mice using in vivo imaging. Circulation. 2019;140(4):303–315.
   PubMed Web of Science ®Google Scholar
• Perkovic V, Jardine MJ, Neal B, et al. Canagliflozin and renal outcomes in type 2 diabetes and nephropathy. N Engl J Med. 2019;380(24):2295–2306.
   PubMed Web of Science ®Google Scholar
• Heerspink HJL, Stefأ NBV, Correa-Rotter R, et al. Dapagliflozin in patients with chronic kidney disease. N Engl J Med. 2020;383:1436–1446.
   PubMed Web of Science ®Google Scholar
• Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495(7441):333–338.
   PubMed Web of Science ®Google Scholar
• Salzman J, Chen RE, Olsen MN, et al. Cell-type specific features of circular RNA expression. PLoS Genet. 2013;9(9):e1003777.
   PubMed Web of Science ®Google Scholar
• Suzuki H, Zuo Y, Wang J, et al. Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Res. 2006;34:e638.
   Web of Science ®Google Scholar
• Ma H-B, Yao Y-N, Yu -J-J, et al. Extensive profiling of circular RNAs and the potential regulatory role of circRNA-000284 in cell proliferation and invasion of cervical cancer via sponging miR-506. Am J Transl Res. 2018;10:592–604.
   PubMed Web of Science ®Google Scholar
• Munschauer M, Nguyen CT, Sirokman K, et al. The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. Nature. 2018;561(7721):132–136.
   PubMed Web of Science ®Google Scholar
• Legnini I, Di Timoteo G, Rossi F, et al. Circ-ZNF609 is a circular rna that can be translated and functions in myogenesis. Mol Cell. 2017;66:22–37.e9.
   PubMed Web of Science ®Google Scholar
• Hu W, Han Q, Zhao L, et al. Circular RNA circRNA_15698 aggravates the extracellular matrix of diabetic nephropathy mesangial cells via miR-185/TGF-خ21. J Cell Physiol. 2019;234(2):1469–1476.
   PubMed Web of Science ®Google Scholar
• Peng F, Gong W, Li S, et al. circRNA_010383 acts as a sponge for mir-135a, and its downregulated expression contributes to renal fibrosis in diabetic nephropathy. Diabetes. 2021;70:603–615.
   PubMed Web of Science ®Google Scholar
• Feng T, Li W, Li T, et al. Circular RNA_0037128 aggravates high glucose-induced damage in HK-2 cells via regulation of microRNA-497-5p/nuclear factor of activated T cells 5 axis. Bioengineered. 2021;12(2):10959–10970.
   PubMed Web of Science ®Google Scholar
• van Bommel EJM, Muskiet MHA, van Baar Mljb, et al. The renal hemodynamic effects of the SGLT2 inhibitor dapagliflozin are caused by post-glomerular vasodilatation rather than pre-glomerular vasoconstriction in metformin-treated patients with type 2 diabetes in the randomized, double-blind RED trial. Kidney Int. 2020;97(1):202–212.
   PubMed Web of Science ®Google Scholar
• Tomita I, Kume S, Sugahara S, et al. SGLT2 inhibition mediates protection from diabetic kidney disease by promoting ketone body-induced mTORC1 Inhibition. Cell Metab. 2020;32(3):404–419.e6.
   PubMed Web of Science ®Google Scholar
• Heerspink HJL, Perco P, Mulder S, et al. Canagliflozin reduces inflammation and fibrosis biomarkers: a potential mechanism of action for beneficial effects of SGLT2 inhibitors in diabetic kidney disease. Diabetologia. 2019;62(7):1154–1166.
   PubMed Web of Science ®Google Scholar
• Amar D, Safer H, Shamir R. Dissection of regulatory networks that are altered in disease via differential co-expression. PLoS Comput Biol. 2013;9(3):e1002955.
   PubMed Web of Science ®Google Scholar
• Guttman M, Donaghey J, Carey BW, et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature. 2011;477(7364):295–300.
   PubMed Web of Science ®Google Scholar
• Chen R, She Y, Fu Q, et al. Differentially expressed coding and noncoding RNAs in CoCl2-induced cytotoxicity of C2C12 cells. Epigenomics. 2019;11(4):423–438.
   PubMed Web of Science ®Google Scholar
• Yamamura S, Imai-Sumida M, Tanaka Y, et al. Interaction and cross-talk between non-coding RNAs. Cellular and molecular life sciences. Cmls. 2018;75(3):467–484.
   PubMed Web of Science ®Google Scholar
• Agarwal V, Bell GW, Nam J-W, et al. Predicting effective microRNA target sites in mammalian mRNAs. eLife. 2015;4. DOI:10.7554/eLife.05005
   Web of Science ®Google Scholar
• Wong N, Wang X. An online resource for microRNA target prediction and functional annotations. Nucleic Acids Res. 2015;43(D1):D146–D152.
   PubMed Web of Science ®Google Scholar
• Dudekula DB, Panda AC, Grammatikakis I, et al. CircInteractome: a web tool for exploring circular RNAs and their interacting proteins and microRNAs. RNA Biol. 2016;13(1):34–42.
   PubMed Web of Science ®Google Scholar
• Huang H-Y, Y-c-d L, Li J, et al. miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database. Nucleic Acids Res. 2020;48(D1):D148–D154.
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504.
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Morris JH, Cook H, et al. The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 2017;45(D1):D362–D368.
   PubMed Web of Science ®Google Scholar
• Nangraj AS, Selvaraj G, Kaliamurthi S, et al. Integrated PPI- and WGCNA-retrieval of hub gene signatures shared between barrett’s esophagus and esophageal adenocarcinoma. Front Pharmacol. 2020;11:881.
   PubMed Web of Science ®Google Scholar
• Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Santos A, Von Mering C, et al. STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Res. 2016;44(D1):D380–D384.
   PubMed Web of Science ®Google Scholar
• Piأ±ero J, Ramأ-rez-anguita JM, Saأ¼ch-pitarch J, et al. The DisGeNET knowledge platform for disease genomics: 2019 update. Nucleic Acids Res. 2020;48(D1):D845–D855.
   PubMed Web of Science ®Google Scholar
• Piأ±ero J, Bravo L, Queralt-Rosinach N, et al. DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. Nucleic Acids Res. 2017;45(D1):D833–D839.
   PubMed Web of Science ®Google Scholar
• Sivaskandarajah GA, Jeansson M, Maezawa Y, et al. Vegfa protects the glomerular microvasculature in diabetes. Diabetes. 2012;61(11):2958–2966.
   PubMed Web of Science ®Google Scholar
• Liang X, Wang P, Chen B, et al. Glycogen synthase kinase 3خ2 hyperactivity in urinary exfoliated cells predicts progression of diabetic kidney disease. Kidney Int. 2020;97(1):175–192.
   PubMed Web of Science ®Google Scholar
• Zou H, Zhou B, Xu G. SGLT2 inhibitors: a novel choice for the combination therapy in diabetic kidney disease. Cardiovasc Diabetol. 2017;16(1):65.
   PubMedGoogle Scholar
• Ren H, Shao Y, Wu C, et al. Metformin alleviates oxidative stress and enhances autophagy in diabetic kidney disease via AMPK/SIRT1-FoxO1 pathway. Mol Cell Endocrinol. 2020;500:110628.
   PubMed Web of Science ®Google Scholar
• Liu WJ, Xie SH, Liu YN, et al. Dipeptidyl peptidase IV inhibitor attenuates kidney injury in streptozotocin-induced diabetic rats. J Pharmacol Exp Ther. 2012;340(2):248–255.
   PubMed Web of Science ®Google Scholar
• Foretz M, Guigas B, Bertrand L, et al. Metformin: from mechanisms of action to therapies. Cell Metab. 2014;20(6):953–966.
   PubMed Web of Science ®Google Scholar
• Ye Y, Bajaj M, Yang H-C, et al. SGLT-2 inhibition with dapagliflozin reduces the activation of the Nlrp3/asc inflammasome and attenuates the development of diabetic cardiomyopathy in mice with type 2 diabetes. further augmentation of the effects with saxagliptin, a DPP4 inhibitor. Cardiovasc Drugs Ther. 2017;31(2):119–132.
   PubMed Web of Science ®Google Scholar
• Packer M. Role of impaired nutrient and oxygen deprivation signaling and deficient autophagic flux in diabetic ckd development: implications for understanding the effects of sodium-glucose cotransporter 2-Inhibitors. J Am Soc Nephrol. 2020;31(5):907–919.
   PubMed Web of Science ®Google Scholar
• Fukumoto K, Sakata-Yanagimoto M, Fujisawa M, et al. VAV1 mutations contribute to development of T-cell neoplasms in mice. Blood. 2020;136(26):3018–3032.
   PubMed Web of Science ®Google Scholar
• Kreis -N-N, Louwen F, Yuan J. The multifaceted p21 (Cip1/Waf1/) in cell differentiation, migration and cancer therapy. Cancers (Basel). 2019;11. DOI:10.3390/cancers11091220
   Web of Science ®Google Scholar
• Zhang Y, Nakano D, Guan Y, et al. A sodium-glucose cotransporter 2 inhibitor attenuates renal capillary injury and fibrosis by a vascular endothelial growth factor-dependent pathway after renal injury in mice. Kidney Int. 2018;94(3):524–535.
   PubMed Web of Science ®Google Scholar
• Chen BL, Sheu ML, Tsai KS, et al. CCAAT-enhancer-binding protein homologous protein deficiency attenuates oxidative stress and renal ischemia-reperfusion Injury. Antioxid Redox Signal. 2015;23(15):1233–1245.
   PubMed Web of Science ®Google Scholar
• Huang F, Zhao Y, Wang Q, et al. Dapagliflozin attenuates renal tubulointerstitial fibrosis associated with type 1 diabetes by regulating STAT1/TGFخ21 signaling. Front Endocrinol (Lausanne). 2019;10:441.
   PubMed Web of Science ®Google Scholar
• Mulder S, Hammarstedt A, Nagaraj SB, et al. A metabolomics-based molecular pathway analysis of how the sodium-glucose co-transporter-2 inhibitor dapagliflozin may slow kidney function decline in patients with diabetes. Diabetes Obes Metab. 2020;22(7):1157–1166.
   PubMed Web of Science ®Google Scholar
• Deliؤ‡ D, Eisele C, Schmid R, et al. Urinary exosomal mirna signature in type ii diabetic nephropathy patients. PloS One. 2016;11(3):e0150154.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Li C, Li H, et al. miR-378 activates the pyruvate-PEP futile cycle and enhances lipolysis to ameliorate obesity in mice. EBioMedicine. 2016;5:93–104.
   PubMed Web of Science ®Google Scholar