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Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of Egr1, Rxra and Max in kidney stone disease

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Abstract

Nephrolithiasis is one of the most common and frequent urologic diseases worldwide. The molecular mechanism of kidney stone formation is complex and remains to be illustrated. Transcript factors (TFs) that influenced the expression pattern of multiple genes, as well as microRNAs, important posttranscriptional modulators, play vital roles in this disease progression. Datasets of nephrolithiasis mice and kidney stone patients were acquired from Gene Expression Omnibus repository. TFs were predicted from differentially expressed genes by RcisTarget. The target genes of differential-expressed microRNAs were predicted by miRWalk. MicroRNA-mRNA network and PPI network were constructed. Functional enrichment analysis was performed via Metascape and Cytoscape identified hub genes. The assay of quantitative real-time PCR (q-PCR) and immunochemistry and the datasets of oxalate diet-induced nephrolithiasis mice kidneys and kidney stone patients’ samples were utilized to validate the bioinformatic results. We identified three potential key TFs (Egr1, Rxra, Max), which can be modulated by miR-181a-5p, miR-7b-3p and miR-22-3p, respectively. The TFs and their regulated hub genes influenced the progression of nephrolithiasis via altering the expression of genes enriched in the functions of fibrosis, cell proliferation and molecular transportation and metabolism. The expression changes of transcription factors were consistent in q-PCR and immunochemistry results. For regulated hub genes, they showed consistent expression changes in oxalate diet-induced nephrolithiasis mice model and human kidneys with stones. The identified and verified three TFs, which may be modulated by microRNAs in nephrolithiasis disease progression, mainly influence biological processes responding to fibrosis, proliferation and molecular transportation and metabolism. The transcript influence showed consistency in multiple nephrolithiasis mice models and kidney stone patients.

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Data availability

All datasets analysed in this study are available in online websites. Further inquiries can be directed to the corresponding author.

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Acknowledgements

This study was supported by National Natural Science Foundation of China (82173369, 82070692 and 31771511), Foundation strengthening program in technical field of China (2019-JCJQ-JJ-068).

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  1. Linxi Huang, Yuxuan Shi and Junjie Hu contributed equally to this work.

Authors and Affiliations

  1. Department of Nephrology, Changhai Hospital, Naval Medical University (Second Military Medical University), 168 Changhai Road, Shanghai, 200433, People’s Republic of China

    Linxi Huang, Yuxuan Shi, Jiarong Ding & Zhiyong Guo

  2. Department of Cell Biology, Naval Medical University (Second Military Medical University), 800 Xiangyin Road, Shanghai, 200433, People’s Republic of China

    Linxi Huang, Junjie Hu & Bing Yu

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Contributions

All authors contributed to the study’s conception and design. Data collection and analysis were performed by LH, YS and JH. The first draft of the manuscript was written by LH and BY. JD edited the manuscript. Critical revision of the manuscript was written by ZG. All authors read and approved the final manuscript.

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Huang, L., Shi, Y., Hu, J. et al. Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of Egr1, Rxra and Max in kidney stone disease. Urolithiasis 51, 13 (2023). https://doi.org/10.1007/s00240-022-01384-5

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