Comprehensive analyses of the microRNA-messenger RNA-transcription factor regulatory network in mouse and human renal fibrosis

Identification of Stable Housekeeping Genes for miRNA Expression Studies in a Mouse Unilateral Ureteral Obstruction Model

Recently, several studies have aimed to establish the role of microRNAs (miRNAs) in the unilateral ureteral obstruction (UUO) model. Therefore, it is essential to identify the best housekeeping genes (HKG) to correctly estimate the expression levels of miRNAs. The present study aimed to identify suitable HKG to normalize the expression of miRNAs by RT-qPCR in kidney samples from the UUO mice model. We analyzed the stability of twelve endogenous reference genes of small non-coding RNAs (Snord61, Snord68, Snord72, Snord95, Snord96a, U6, let-7e-5p, let-7i-3p, miR-15b-5p, miR-16a-5p, miR-26a-5p, and miR-30c-5p) by using four software packages: NormFinder, GeNorm, ΔCt method, and BestKeeper. The optimal number of genes was calculated using GenEx software analysis. To validate the best HKG, we normalized the expression of miR-18a-5p, miR-21a-3p, and miR-29b-3p. In silico analysis revealed that Snord61, Snord68, and Snord72 were the most stable HKG between the groups. Using GenEX software and Pearson's correlation, we determined that the combination of Snord61 and Snord68 or the combination of Snord68 and Snord72, provided the best HKG association. These results along with the correlation analyses establish that the association of Snord68 and Snord72 is the best choice for miRNA expression analysis by RT-qPCR in the UUO model.

Transcription factor specificity protein (SP) family in renal physiology and diseases

Dysregulated specificity proteins (SPs), members of the C2H2 zinc-finger family, are crucial transcription factors (TFs) with implications for renal physiology and diseases. This comprehensive review focuses on the role of SP family members, particularly SP1 and SP3, in renal physiology and pathology. A detailed analysis of their expression and cellular localization in the healthy human kidney is presented, highlighting their involvement in fatty acid metabolism, electrolyte regulation, and the synthesis of important molecules. The review also delves into the diverse roles of SPs in various renal diseases, including renal ischemia/reperfusion injury, diabetic nephropathy, renal interstitial fibrosis, and lupus nephritis, elucidating their molecular mechanisms and potential as therapeutic targets. The review further discusses pharmacological modulation of SPs and its implications for treatment. Our findings provide a comprehensive understanding of SPs in renal health and disease, offering new avenues for targeted therapeutic interventions and precision medicine in nephrology.

LncRNA-associated competing endogenous RNA network analysis uncovered key lncRNAs involved in temozolomide resistance and tumor recurrence of glioblastoma

Temozolomide (TMZ) is a common alkylating chemotherapeutic agent used to treat brain tumors such as glioblastoma multiforme (GBM) and anaplastic astrocytoma. GBM patients develop resistance to this drug, which has an unclear and complicated molecular mechanism. The competing endogenous RNAs (ceRNAs) play critical roles in tumorigenesis, drug resistance, and tumor recurrence in cancers. This study aims to predict ceRNAs, their possible involvement, and underlying molecular mechanisms in TMZ resistance. Therefore, we analyzed coding and non-coding RNA expression levels in TMZ-resistant GBM samples compared to sensitive GBM samples and performed pathway analysis of mRNAs differentially expressed (DE) in TMZ-resistant samples. We next applied a mathematical model on 950 DE long non-coding RNAs (lncRNAs), 116 microRNAs (miRNAs), and 7977 mRNAs and obtained 10 lncRNA-associated ceRNAs that may be regulating potential target genes involved in cancer-related pathways by sponging 25 miRNAs in TMZ-resistant GBM. Among these, two lncRNAs named ARFRP1 and RUSC2 regulate five target genes (IRS1, FOXG1, GNG2, RUNX2, and CACNA1E) involved in AMPK, AKT, mTOR, and TGF-β signaling pathways that activate or inhibit autophagy causing TMZ resistance. The novel lncRNA-associated ceRNA network predicted in GBM offers a fresh viewpoint on TMZ resistance, which might contribute to treating this malignancy.

Pioglitazone Protects Tubular Epithelial Cells during Kidney Fibrosis by Attenuating miRNA Dysregulation and Autophagy Dysfunction Induced by TGF-β

Excessive renal TGF-β production and pro-fibrotic miRNAs are important drivers of kidney fibrosis that lack any efficient treatment. Dysfunctional autophagy might play an important role in the pathogenesis. We aimed to study the yet unknown effects of peroxisome proliferator-activated receptor-γ (PPARγ) agonist pioglitazone (Pio) on renal autophagy and miRNA dysregulation during fibrosis. Mouse primary tubular epithelial cells (PTEC) were isolated, pre-treated with 5 µM pioglitazone, and then stimulated with 10 ng/mL TGF-β1 for 24 h. Male 10-week-old C57Bl6 control (CTL) and TGF-β overexpressing mice were fed with regular chow (TGF) or Pio-containing chow (20 mg/kg/day) for 5 weeks (TGF + Pio). PTEC and kidneys were evaluated for mRNA and protein expression. In PTEC, pioglitazone attenuated (p < 0.05) the TGF-β-induced up-regulation of Col1a1 (1.4-fold), Tgfb1 (2.2-fold), Ctgf (1.5-fold), Egr2 (2.5-fold) mRNAs, miR-130a (1.6-fold), and miR-199a (1.5-fold), inhibited epithelial-to-mesenchymal transition, and rescued autophagy function. In TGF mice, pioglitazone greatly improved kidney fibrosis and related dysfunctional autophagy (increased LC3-II/I ratio and reduced SQSTM1 protein content (p < 0.05)). These were accompanied by 5-fold, 3-fold, 12-fold, and 2-fold suppression (p < 0.05) of renal Ccl2, Il6, C3, and Lgals3 mRNA expression, respectively. Our results implicate that pioglitazone counteracts multiple pro-fibrotic processes in the kidney, including autophagy dysfunction and miRNA dysregulation.