Bioinformatics analysis of biomarkers of aristolochic acid‑induced early nephrotoxicity in embryonic stem cells

Wang,Li; Man,Shanshan; Bian,Yuhong

doi:10.3892/etm.2021.9939

Bioinformatics analysis of biomarkers of aristolochic acid‑induced early nephrotoxicity in embryonic stem cells

Authors:
- Li Wang
- Shanshan Man
- Yuhong Bian
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Affiliations: Pharmaceutical Sector, Tianjin Second People's Hospital, Tianjin Institute of Liver Disease, Tianjin 300192, P.R. China, School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, P.R. China
Published online on: March 18, 2021 https://doi.org/10.3892/etm.2021.9939
Article Number: 508
Copyright: © Wang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

The present study aimed to identify key genes as potential biomarkers for early nephrotoxicity induced by aristolochic acid (AA) in embryonic stem cells (ESCs). An MTT assay was performed to determine the cytotoxicity of AA in ESCs. Differentially expressed genes (DEGs) were identified using the DNA‑Chip Analyzer following microarray analysis. Gene Ontology analysis was performed to determine functional terms enriched by the DEGs in the categories biological process, cellular component and molecular function. Furthermore, the DEGs were subjected to Kyoto Encyclopedia of Genes and Genomes analysis to determine pathways they were accumulated in. Furthermore, a protein‑protein interaction network was constructed using Cytoscape 3.2 software. Tumor protein 53 apoptosis effector (Perp), cation transport regulator‑like 1 (Chac1), adrenoceptor β2 and Wnt6 were selected for confirmation by reverse transcription‑quantitative (RT‑q) PCR analysis. A total of 72 DEGs (49 upregulated and 23 downregulated) were identified. The DEGs were enriched in functional terms and pathways associated with nephrotoxicity and participated in 92 pathways. A total of two hub genes, fructose‑1,6‑bisphosphatase (Fbp)1 and Fbp2, were filtered out from the interaction network. Perp and phorbol‑12‑myristate‑13‑acetate‑induced protein 1 were demonstrated to have vital roles in the p53 signaling pathway which was indicated in the interaction network. The results of the RT‑qPCR analysis were consistent with the microarray data. Taken together, the present study suggested that hub genes involved in the p53 pathway, including Fbp1, Fbp2 and Perp, may serve as potential biomarkers for early nephrotoxicity induced by AA.

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1	Yun KY, Xu ZU and Song JY: Traditional Chinese medicine containing aristolochic acids and their detection. Sci Sin Vitae. 49:238–249. 2019.
2	Kuo PC, Li YC and Wu TS: Chemical constituents and pharmacology of the aristolochia (mădōu ling) species. J Tradit Complement Med. 2:249–266. 2012.PubMed/NCBI View Article : Google Scholar
3	Li J and Zhang L, Jiang Z, Shu B, Li F, Bao Q and Zhang L: Toxicities of aristolochic acid I and aristololactam I in cultured renal epithelial cells. Toxicol In Vitro. 24:1092–1097. 2010.PubMed/NCBI View Article : Google Scholar
4	Honarpisheh M, Foresto-Neto O, Steiger S, Kraft F, Koehler P, von Rauchhaupt E, Potempa J, Adamowicz K, Koziel J and Lech M: Aristolochic acid I determine the phenotype and activation of macrophages in acute and chronic kidney disease. Sci Rep. 8(12169)2018.PubMed/NCBI View Article : Google Scholar
5	Yang L, Li X and Wang H: Possible mechanisms explaining the tendency towards interstitial fibrosis in aristolochic acid-induced acute tubular necrosis. Nephrol Dial Transplant. 22:445–456. 2007.PubMed/NCBI View Article : Google Scholar
6	Debelle FD, Vanherweghem JL and Nortier JL: Aristolochic acid nephropathy: A worldwide problem. Kidney Int. 74:158–169. 2008.PubMed/NCBI View Article : Google Scholar
7	Chen D, Tang Z, Luo C, Chen H and Liu Z: Clinical and pathological spectrums of aristolochic acid nephropathy. Clin Nephrol. 78:54–60. 2012.PubMed/NCBI View Article : Google Scholar
8	Bastek H, Zubel T, Stemmer K, Mangerich A, Beneke S and Dietrich DR: Comparison of aristolochic acid I derived DNA adduct levels in human renal toxicity models. Toxicology. 420:29–38. 2019.PubMed/NCBI View Article : Google Scholar
9	Fuchs TC and Hewitt P: Biomarkers for drug-induced renal damage and nephrotoxicity-an overview for applied toxicology. AAPS J. 13:615–631. 2011.PubMed/NCBI View Article : Google Scholar
10	Mori Y, Kondo C, Tonomura Y, Torii M and Uehara T: Identification of potential genomic biomarkers for early detection of chemically induced cardiotoxicity in rats. Toxicology. 271:36–44. 2010.PubMed/NCBI View Article : Google Scholar
11	Pal R, Mamidi MK, Das AK and Bhonde R: Human embryonic stem cell proliferation and differentiation as parameters to evaluate developmental toxicity. J Cell Physiol. 226:1583–1595. 2011.PubMed/NCBI View Article : Google Scholar
12	Ahuja YR, Vijayalakshmi V and Polasa K: Stem cell test: A practical tool in toxicogenomics. Toxicology. 231:1–10. 2007.PubMed/NCBI View Article : Google Scholar
13	Cezar GG, Quam JA, Smith AM, Rosa GJ, Piekarczyk MS, Brown JF, Gage FH and Muotri AR: Identification of small molecules from human embryonic stem cells using metabolomics. Stem Cells Dev. 16:869–882. 2007.PubMed/NCBI View Article : Google Scholar
14	Asaba A, Okabe S, Nagasawa M, Kato M, Koshida N, Osakada T, Mogi K and Kikusui T: Developmental social environment imprints female preference for male song in mice. PLoS One. 9(e87186)2014.PubMed/NCBI View Article : Google Scholar
15	Fagundez CB, Loresi MA, Ojea Quintana ME, Delcourt SM, Testa R, Gogorza SJ and Argibay PF: A simple approach for mouse embryonic stem cells isolation and differentiation inducing embryoid body formation. Cell Biol Int. 33:1196–1200. 2009.PubMed/NCBI View Article : Google Scholar
16	West PR, Weir AM, Smith AM, Donley EL and Cezar GG: Predicting human developmental toxicity of pharmaceuticals using human embryonic stem cells and metabolomics. Toxicol Appl Pharmacol. 247:18–27. 2010.PubMed/NCBI View Article : Google Scholar
17	Li C and Wing H: DNA-Chip Analyzer (dChip). The analysis of gene expression data: Methods and software. Parmigiani G, Garrett ES, Irizarry R and Zeger SL (eds). Springer, New York, pp120-141, 2003.
18	Livak KJ and Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods. 25:402–408. 2001.PubMed/NCBI View Article : Google Scholar
19	Mei N, Arlt VM, Phillips DH, Heflich RH and Chen T: DNA adduct formation and mutation induction by aristolochic acid in rat kidney and liver. Mutat Res. 602:83–91. 2006.PubMed/NCBI View Article : Google Scholar
20	De Broe ME, Curhan GC and Forman JP: Nephropathy induced by aristolochic acid (AA) containing herbs. UpToDate, 2018.
21	Singaravelu K, Devalaraja-Narashimha K, Lastovica B and Padanilam BJ: PERP, a p53 proapoptotic target, mediates apoptotic cell death in renal ischemia. Am J Physiol Renal Physiol. 296:F847–F858. 2009.PubMed/NCBI View Article : Google Scholar
22	Singaravelu K and Padanilam B: The role of p53 pro-apoptotic target, PERP, induces mitochondrial permeability and apoptosis in hypoxic renal cells. FASEB J. 22 (1 Suppl)(730.11)2008.PubMed/NCBI View Article : Google Scholar
23	Lord GM, Hollstein M, Arlt VM, Roufosse C, Pusey CD, Cook T and Schmeiser HH: DNA adducts and p53 mutations in a patient with aristolochic acid-associated nephropathy. Am J Kidney Dis. 43:e11–e17. 2004.PubMed/NCBI View Article : Google Scholar
24	Schimmack G, Defronzo RA and Musi N: AMP-activated protein kinase: Role in metabolism and therapeutic implications. Diabetes Obes Metab. 8:591–602. 2006.PubMed/NCBI View Article : Google Scholar
25	Shi L, He C, Li Z, Wang Z and Zhang Q: FBP1 modulates cell metabolism of breast cancer cells by inhibiting the expression of HIF-1α. Neoplasma. 64:535–542. 2017.PubMed/NCBI View Article : Google Scholar
26	Kępka A, Dariusz Szajda S, Stypułkowska A, Waszkiewicz N, Jankowska A, Chojnowska S and Zwierz K: Urinary fructose-1, 6-bisphosphatase activity as a marker of the damage to the renal proximal tubules in children with idiopathic nephrotic syndrome. Clin Chem Lab Med. 46:831–835. 2008.PubMed/NCBI View Article : Google Scholar
27	Kepka A, Szajda SD and Zwierz K: Fructose-1, 6-bisphosphatase-marker of damage to proximal renal tubules. Pol Merkur Lekarski. 24:125–130. 2008.PubMed/NCBI View Article : Google Scholar : (In Polish).
28	Upadhyaya Y, Xie L, Salama P, Cao S, Nho K, Saykin AJ and Yan J: For The Alzheimer's Disease Neuroimaging Initiative. Differential co-expression analysis reveals early stage transcriptomic decoupling in alzheimer's disease. BMC Med Genomics. 13 (Suppl 5)(S53)2020.PubMed/NCBI View Article : Google Scholar
29	Hsin YH, Cheng CH, Tzen JT, Wu MJ, Shu KH and Chen HC: Effect of aristolochic acid on intracellular calcium concentration and its links with apoptosis in renal tubular cells. Apoptosis. 11:2167–2177. 2006.PubMed/NCBI View Article : Google Scholar
30	Itäranta P, Lin Y, Peräsaari J, Roël G, Destrée O and Vainio S: Wnt-6 is expressed in the ureter bud and induces kidney tubule development in vitro. Genesis. 32:259–268. 2002.PubMed/NCBI View Article : Google Scholar
31	Crawford RR, Prescott ET, Sylvester CF, Higdon AN, Shan J, Kilberg MS and Mungrue IN: Human CHAC1 protein degrades glutathione, and mRNA induction is regulated by the transcription factors ATF4 and ATF3 and a bipartite ATF/CRE regulatory element. J Biol Chem. 290:15878–15891. 2015.PubMed/NCBI View Article : Google Scholar
32	Choi YM, Cho HY, Anwar MA, Kim HK, Kwon JW and Choi S: ATF3 attenuates cyclosporin A-induced nephrotoxicity by downregulating CHOP in HK-2 cells. Biochem Biophys Res Commun. 448:182–188. 2014.PubMed/NCBI View Article : Google Scholar