Block CJ, Mitchell AV, Wu L, Glassbrook J, Craig D, Chen W, Dyson G, DeGracia D, Polin L, Ratnam M, Gibson H, Wu G. RNA binding protein RBMS3 is a common EMT effector that modulates triple-negative breast cancer progression via stabilizing PRRX1 mRNA. Oncogene. 2021;46:6430–42. https://doi.org/10.1038/s41388-021-02030-x.

Article  CAS  Google Scholar 

Bosada FM, Rivaud MR, Uhm JS, Verheule S, van Duijvenboden K, Verkerk AO, Christoffels VM, Boukens BJ. A variant noncoding region regulates prrx1 and predisposes to atrial arrhythmias. Circ Res. 2021;3:420–34. https://doi.org/10.1161/CIRCRESAHA.121.319146.

Article  CAS  Google Scholar 

Bridoux F, Leung N, Belmouaz M, Royal V, Ronco P, Nasr SH, Fermand JP. Management of acute kidney injury in symptomatic multiple myeloma. Kidney Int. 2021;3:570–80. https://doi.org/10.1016/j.kint.2020.11.010.

Article  CAS  Google Scholar 

Chen Z, Chen Y, Li Y, Lian W, Zheng K, Zhang Y, Zhang Y, Lin C, Liu C, Sun F, Sun X, Wang J, Zhao L, Ke Y. Prrx1 promotes stemness and angiogenesis via activating TGF-beta/smad pathway and upregulating proangiogenic factors in glioma. Cell Death Dis. 2021;6:615. https://doi.org/10.1038/s41419-021-03882-7.

Article  CAS  Google Scholar 

Chen T, Guo Y, Wang J, Ai L, Ma L, He W, Li Z, Yu X, Li J, Fan X, Gu Y, Liang H. LncRNA CTD-2528L19.6 prevents the progression of IPF by alleviating fibroblast activation. Cell Death Dis. 2021;6:600. https://doi.org/10.1038/s41419-021-03884-5.

Article  CAS  Google Scholar 

Chevalier RL. The proximal tubule is the primary target of injury and progression of kidney disease: Role of the glomerulotubular junction. Am J Physiol Renal Physiol. 2016;1:F145–61. https://doi.org/10.1152/ajprenal.00164.2016.

Article  CAS  Google Scholar 

Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Austine-Orimoloye O, Azov AG, Barnes I, Bennett R, Berry A, Bhai J, Bignell A, Billis K, Boddu S, Brooks L, Charkhchi M, Cummins C, Da RFL, Davidson C, Dodiya K, Donaldson S, El HB, El NT, Fatima R, Giron CG, Genez T, Martinez JG, Guijarro-Clarke C, Gymer A, Hardy M, Hollis Z, Hourlier T, Hunt T, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Marugan JC, Mohanan S, Mushtaq A, Naven M, Ogeh DN, Parker A, Parton A, Perry M, Pilizota I, Prosovetskaia I, Sakthivel MP, Salam A, Schmitt BM, Schuilenburg H, Sheppard D, Perez-Silva JG, Stark W, Steed E, Sutinen K, Sukumaran R, Sumathipala D, Suner MM, Szpak M, Thormann A, Tricomi FF, Urbina-Gomez D, Veidenberg A, Walsh TA, Walts B, Willhoft N, Winterbottom A, Wass E, Chakiachvili M, Flint B, Frankish A, Giorgetti S, Haggerty L, Hunt SE, IIsley GR, Loveland JE, Martin FJ, Moore B, Mudge JM, Muffato M, Perry E, Ruffier M, Tate J, Thybert D, Trevanion SJ, Dyer S, Harrison PW, Howe KL, Yates AD, Zerbino DR, Flicek P. Ensembl. Nucleic Acids Res. 2022;D1:D988–D995. https://doi.org/10.1093/nar/gkab1049.

Du L, Qian X, Li Y, Li XZ, He LL, Xu L, Liu YQ, Li CC, Ma P, Shu FL, Lu Q, Yin XX. Sirt1 inhibits renal tubular cell epithelial-mesenchymal transition through YY1 deacetylation in diabetic nephropathy. Acta Pharmacol Sin. 2021;2:242–51. https://doi.org/10.1038/s41401-020-0450-2.

Article  CAS  Google Scholar 

El-Lateef A, El-Shemi A, Alhammady MS, Yuan R, Zhang Y. LncRNA NEAT2 modulates pyroptosis of renal tubular cells induced by high glucose in diabetic nephropathy (DN) by via miR-206 regulation. Biochem Genet. 2022;5:1733–47. https://doi.org/10.1007/s10528-021-10164-6.

Article  CAS  Google Scholar 

Fan Y, Yi Z, D’Agati VD, Sun Z, Zhong F, Zhang W, Wen J, Zhou T, Li Z, He L, Zhang Q, Lee K, He JC, Wang N. Comparison of kidney transcriptomic profiles of early and advanced diabetic nephropathy reveals potential new mechanisms for disease progression. Diabetes. 2019;12:2301–14. https://doi.org/10.2337/db19-0204.

Article  CAS  Google Scholar 

Feng J, Yang G, Liu Y, Gao Y, Zhao M, Bu Y, Yuan H, Yuan Y, Yun H, Sun M, Gao H, Zhang S, Liu Z, Yin M, Song X, Miao Z, Lin Z, Zhang X. LncRNA PCNAP1 modulates hepatitis B virus replication and enhances tumor growth of liver cancer. Theranostics. 2019;18:5227–45. https://doi.org/10.7150/thno.34273.

Article  CAS  Google Scholar 

Guo J, Fu Z, Wei J, Lu W, Feng J, Zhang S. PRRX1 promotes epithelial-mesenchymal transition through the Wnt/beta-catenin pathway in gastric cancer. Med Oncol. 2015;1:393. https://doi.org/10.1007/s12032-014-0393-x.

Article  CAS  Google Scholar 

Han C, Sun L, Pan Q, Sun Y, Wang W, Chen Y. Polysome profiling followed by quantitative PCR for identifying potential micropeptide encoding long non-coding RNAs in suspension cell lines. STAR Protoc. 2022;1:101037. https://doi.org/10.1016/j.xpro.2021.101037.

Article  CAS  Google Scholar 

Huang M, Ye Y, Chen Y, Zhu J, Xu L, Cheng W, Lu X, Yan F. Identification and validation of an inflammation-related lncRNAs signature for improving outcomes of patients in colorectal cancer. Front Genet. 2022;13:955240. https://doi.org/10.3389/fgene.2022.955240.

Kursa MB. Robustness of random forest-based gene selection methods. BMC Bioinformatics. 2014;15:8. https://doi.org/10.1186/1471-2105-15-8.

Li A, Peng R, Sun Y, Liu H, Peng H, Zhang Z. LincRNA 1700020I14Rik alleviates cell proliferation and fibrosis in diabetic nephropathy via miR-34a-5p/Sirt1/HIF-1alpha signaling. Cell Death Dis. 2018;5:461. https://doi.org/10.1038/s41419-018-0527-8.

Article  CAS  Google Scholar 

Li RH, Tian T, Ge QW, He XY, Shi CY, Li JH, Zhang Z, Liu FZ, Sang LJ, Yang ZZ, Liu YZ, Xiong Y, Yan Q, Li X, Ju HQ, Liu J, Wang LJ, Shao JZ, Wang W, Zhou T, Lin A. A phosphatidic acid-binding lncRNA SNHG9 facilitates LATS1 liquid-liquid phase separation to promote oncogenic YAP signaling. Cell Res. 2021;10:1088–105. https://doi.org/10.1038/s41422-021-00530-9.

Article  CAS  Google Scholar 

Liu B, Qiang L, Wang GD, Duan Q, Liu J. LncRNA MALAT1 facilities high glucose induced endothelial to mesenchymal transition and fibrosis via targeting miR-145/ZEB2 axis. Eur Rev Med Pharmacol Sci. 2019;8:3478–86. https://doi.org/10.26355/eurrev_201904_17713.

Article  Google Scholar 

Liu Y, Li Y, Xu L, Shi J, Yu X, Wang X, Li X, Jiang H, Yang T, Yin X, Du L, Lu Q. Quercetin attenuates podocyte apoptosis of diabetic nephropathy through targeting EGFR signaling. Front Pharmacol. 2021;12:792777. https://doi.org/10.3389/fphar.2021.792777.

Martianov I, Ramadass A, Serra BA, Chow N, Akoulitchev A. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature. 2007;7128:666–70. https://doi.org/10.1038/nature05519.

Article  CAS  Google Scholar 

Meng Z, Chen Y, Wu W, Yan B, Zhang L, Chen H, Meng Y, Liang Y, Yao X, Luo J. PRRX1 is a novel prognostic biomarker and facilitates tumor progression through Epithelial-Mesenchymal transition in uveal melanoma. Front Immunol. 2022;13:754645. https://doi.org/10.3389/fimmu.2022.754645.

Ocana OH, Corcoles R, Fabra A, Moreno-Bueno G, Acloque H, Vega S, Barrallo-Gimeno A, Cano A, Nieto MA. Metastatic colonization requires the repression of the epithelial-mesenchymal transition inducer Prrx1. Cancer Cell. 2012;6:709–24. https://doi.org/10.1016/j.ccr.2012.10.012.

Article  CAS  Google Scholar 

Sanchez-Nino MD, Fernandez-Fernandez B, Ortiz A. Klotho, the elusive kidney-derived anti-ageing factor. Clin Kidney J. 2020;2:125–7. https://doi.org/10.1093/ckj/sfz125.

Article  CAS  Google Scholar 

Smola MJ, Christy TW, Inoue K, Nicholson CO, Friedersdorf M, Keene JD, Lee DM, Calabrese JM, Weeks KM. SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells. Proc Natl Acad Sci U S A. 2016;37:10322–7. https://doi.org/10.1073/pnas.1600008113.

Article  CAS  Google Scholar 

Stekhoven DJ, Buhlmann P. MissForest–non-parametric missing value imputation for mixed-type data. Bioinformatics. 2012;1:112–8. https://doi.org/10.1093/bioinformatics/btr597.

Article  CAS  Google Scholar 

Stevens PE, Levin A. Evaluation and management of chronic kidney disease: Synopsis of the kidney disease: Improving global outcomes 2012 clinical practice guideline. Ann Intern Med. 2013;11:825–30. https://doi.org/10.7326/0003-4819-158-11-201306040-00007.

Article  Google Scholar 

Volders PJ, Anckaert J, Verheggen K, Nuytens J, Martens L, Mestdagh P, Vandesompele J. LNCipedia 5: Towards a reference set of human long non-coding RNAs. Nucleic Acids Res. 2019;D1:D135–9. https://doi.org/10.1093/nar/gky1031.

Article  CAS  Google Scholar 

Wang W, Jia YJ, Yang YL, Xue M, Zheng ZJ, Wang L, Xue YM. LncRNA GAS5 exacerbates renal tubular epithelial fibrosis by acting as a competing endogenous RNA of miR-96–5p. Biomed Pharmacother. 2020;121:109411. https://doi.org/10.1016/j.biopha.2019.109411.

Wang W, Min L, Qiu X, Wu X, Liu C, Ma J, Zhang D, Zhu L. Biological function of long non-coding RNA (LncRNA) xist. Front Cell Dev Biol. 2021;9:645647. https://doi.org/10.3389/fcell.2021.645647.

Wang L, Wang J, Wang Z, Zhou J, Zhang Y. Higher urine exosomal miR-193a is associated with a higher probability of primary focal segmental glomerulosclerosis and an increased risk of poor prognosis among children with nephrotic syndrome. Front Cell Dev Biol 2021;727370. https://doi.org/10.3389/fcell.2021.727370.

Wu S, Cheng C, Zhu W, Yang J, He BB, Li S, Wang X, Guo H, Chen D, Guo YM. Whole transcriptome analysis reveals that immune infiltration- lncRNAs are related to cellular apoptosis in liver transplantation. Front Immunol. 2023;14:1152742. https://doi.org/10.3389/fimmu.2023.1152742.

Xie YEJ, Cai H, Zhong F, Xiao W, Gordon RE, Wang L, Zheng YL, Zhang A, Lee K, He JC. Reticulon-1A mediates diabetic kidney disease progression through endoplasmic reticulum-mitochondrial contacts in tubular epithelial cells. Kidney Int. 2022;2:293–306. https://doi.org/10.1016/j.kint.2022.02.038.

Article  CAS  Google Scholar 

Xu S, Liu D, Chang T, Wen X, Ma S, Sun G, Wang L, Chen S, Xu Y, Zhang H. Cuproptosis-Associated lncRNA establishes new prognostic profile and predicts immunotherapy response in clear cell renal cell carcinoma. Front Genet 2022;13:938259. https://doi.org/10.3389/fgene.2022.938259.

Zhang Y, Zhang L, Wang Y, Ding H, Xue S, Qi H, Li P. MicroRNAs or long noncoding RNAs in diagnosis and prognosis of coronary artery disease. Aging Dis. 2019;2:353–66. https://doi.org/10.14336/AD.2018.0617.

Article  Google Scholar 

Zhang P, Sun Y, Peng R, Chen W, Fu X, Zhang L, Peng H, Zhang Z. Long non-coding RNA Rpph1 promotes inflammation and proliferation of mesangial cells in diabetic nephropathy via an interaction with Gal-3. Cell Death Dis. 2019;7:526. https://doi.org/10.1038/s41419-019-1765-0.

Article  CAS  Google Scholar 

Zhang Y, Li B, Bai Q, Wang P, Wei G, Li Z, Hu L, Tian Q, Zhou J, Huang Q, Wang Z, Yue S, Wu J, Yang L, Zhou X, Jiang L, Ni T, Ye L, Wu Y. The lncRNA Snhg1-Vps13D vesicle trafficking system promotes memory CD8 T cell establishment via regulating the dual effects of IL-7 signaling. Signal Transduct Target Ther. 2021;1:126. https://doi.org/10.1038/s41392-021-00492-9.

Article  CAS  Google Scholar 

Zhao C, Hu J, Wang Z, Cao ZY, Wang L. Serum LncRNA PANDAR may Act as a Novel Serum Biomarker of Diabetic Nephropathy in Patients with Type 2 Diabetes. Clin Lab 2020;66(6):191032. https://doi.org/10.7754/Clin.Lab.2019.191032.

Zheng ZC, Zhu W, Lei L, Liu XQ, Wu YG. Wogonin ameliorates renal inflammation and fibrosis by inhibiting NF-kappaB and TGF-beta1/Smad3 signaling pathways in diabetic nephropathy. Drug Des Devel Ther. 2020;14:4135–4148. https://doi.org/10.2147/DDDT.S274256.

Zhou J, Liu L, Wu P, Zhao L, Wu Y. Identification and characterization of non-coding RNA networks in infected macrophages revealing the pathogenesis of F. Nucleatum-Assoc Dis BMC Genomics. 2022;1:826. https://doi.org/10.1186/s12864-022-09052-z.

Article