Background: Mounting evidence indicates that the gut microbiome (GMB) plays an essential role in kidney stone (KS) formation. In this study, we conducted a systematic review and meta-analysis to compare the composition of gut microbiota in kidney stone patients and healthy individuals, and further understand the role of gut microbiota in nephrolithiasis. Results: Six databases were searched to find taxonomy-based comparison studies on the GMB until September 2022. Meta-analyses were performed using RevMan 5.3 to estimate the overall relative abundance of gut microbiota in KS patients and healthy subjects. Eight studies were included with 356 nephrolithiasis patients and 347 healthy subjects. The meta-analysis suggested that KS patients had a higher abundance of Bacteroides (35.11% vs 21.25%, Z = 3.56, P = 0.0004) and Escherichia_Shigella (4.39% vs 1.78%, Z = 3.23, P = 0.001), and a lower abundance of Prevotella_9 (8.41% vs 10.65%, Z = 4.49, P < 0.00001). Qualitative analysis revealed that beta-diversity was different between the two groups (P < 0.05); Ten taxa (Bacteroides, Phascolarctobacterium, Faecalibacterium, Flavobacterium, Akkermansia, Lactobacillus, Escherichia coli, Rhodobacter and Gordonia) helped the detection of kidney stones (P < 0.05); Genes or protein families of the GMB involved in oxalate degradation, glycan synthesis, and energy metabolism were altered in patients (P < 0.05). Conclusions: There is a characteristic gut microbiota dysbiosis in kidney stone patients. Individualized therapies like microbial supplementation, probiotic or synbiotic preparations and adjusted diet patterns based on individual gut microbial characteristics of patients may be more effective in preventing stone formation and recurrence.

Metastatic urothelial carcinoma is generally incurable with current systemic therapies. Chromatin modifiers are frequently mutated in bladder cancer, with ARID1A -inactivating mutations present in about 20% of tumors. EZH2, a histone methyltransferase, acts as an oncogene that functionally opposes ARID1A. In addition, PI3K signaling is activated in more than 20% of bladder cancers. Using a combination of in vitro and in vivo data, including patient-derived xenografts, we show that ARID1A-mutant tumors were more sensitive to EZH2 inhibition than ARID1A WT tumors. Mechanistic studies revealed that (a) ARID1A deficiency results in a dependency on PI3K/AKT/mTOR signaling via upregulation of a noncanonical PI3K regulatory subunit, PIK3R3, and downregulation of MAPK signaling and (b) EZH2 inhibitor sensitivity is due to upregulation of PIK3IP1, a protein inhibitor of PI3K signaling. We show that PIK3IP1 inhibited PI3K signaling by inducing proteasomal degradation of PIK3R3. Furthermore, ARID1A-deficient bladder cancer was sensitive to combination therapies with EZH2 and PI3K inhibitors in a synergistic manner. Thus, our studies suggest that bladder cancers with ARID1A mutations can be treated with inhibitors of EZH2 and/or PI3K and revealed mechanistic insights into the role of noncanonical PI3K constituents in bladder cancer biology.

The potential association between calcium oxalate stones and renal fibrosis has been extensively investigated; however, the underlying mechanisms remain unclear. Ferroptosis is a novel form of cell death characterized by iron-dependent lipid peroxidation and regulated by acyl coenzyme A synthase long-chain family member 4 (ACSL4). Yes-associated protein (YAP), a transcriptional co-activator in the Hippo pathway, promotes ferroptosis by modulating ACSL4 expression. Nevertheless, the involvement of YAP–ACSL4 axis-mediated ferroptosis in calcium oxalate crystal deposition-induced renal fibrosis and its molecular mechanisms have not been elucidated. In this study, we investigated ACSL4 expression and ferroptosis activation in the kidney tissues of patients with calcium oxalate stones and in mice using single-cell sequencing, transcriptome RNA sequencing, immunohistochemical analysis, and Western blot analysis. In vivo and in vitro experiments demonstrated that inhibiting ferroptosis or ACSL4 mitigated calcium oxalate crystal-induced renal fibrosis. Furthermore, YAP expression was elevated in the kidney tissues of patients with calcium oxalate stones and in calcium oxalate crystal-stimulated human renal tubular epithelial cell lines. Mechanistically, in calcium oxalate crystal-stimulated human renal tubular epithelial cell lines, activated YAP translocated to the nucleus and enhanced ACSL4 expression, consequently inducing cellular ferroptosis. Moreover, YAP silencing suppressed ferroptosis by downregulating ACSL4 expression, thereby attenuating calcium oxalate crystal-induced renal fibrosis. Conclusively, our findings suggest that YAP–ACSL4-mediated ferroptosis represents an important mechanism underlying the induction of renal fibrosis by calcium oxalate crystal deposition. Targeting the YAP–ACSL4 axis and ferroptosis may therefore hold promise as a potential therapeutic approach for preventing renal fibrosis in patients with kidney stones.

Calcium oxalate (CaOx) crystals are known to cause renal injury and trigger inflammatory responses. However, the role of exosome-mediated epithelial-macrophage communication in CaOx-induced kidney injury remains unclear. To identify key molecules, miRNA sequencing was conducted on exosomes derived from CaOx-treated (CaOx-exo) and control (Ctrl-exo) epithelial cells, identifying miR-93-3p as significantly upregulated. A combination of dual-luciferase reporter assays, Western blot, RT-qPCR, immunofluorescence staining, flow cytometry, electrophoretic mobility shift assay (EMSA), and chromatin immunoprecipitation-qPCR (CHIP-qPCR) was used to explore the regulation of miR-93-3p by CREB1/CRTC2 and its downstream effects on NFAT5/Akt1/NIK/NF-κB2 signaling in macrophages. The functional roles of NFAT5 in macrophage polarization and macrophage extracellular traps (METs) formation were further evaluated both in vitro and in vivo. Epithelial exosomes stimulated by CaOx crystals were found to promote kidney injury via macrophage polarization and METs formation. Treatment with NIK SMI1, a NIK inhibitor, or CI-amidine, a METs inhibitor, mitigated crystal deposition and CaOx-induced kidney damage. Overexpression of NFAT5 in a CaOx-induced mouse model reduced renal injury and crystal deposition, downregulated NIK and NF-κB2 levels, and decreased the number of M1-polarized macrophages. Mechanistic studies revealed that miR-93-3p directly targets NFAT5 mRNA, as confirmed by dual-luciferase assays, qRT-PCR, and Western blot. Additionally, we demonstrated that CREB1/CRTC2 acts as a transcriptional activator of miR-93-3p. Inhibition of miR-93-3p partially reversed NIK/NF-κB2 activation and alleviated kidney injury. CaOx crystals exacerbate renal interstitial injury by promoting M1 macrophage polarization and METs formation through the CREB1/CRTC2–exosomal miR-93-3p–NIK/NF-κB2 signaling pathway. Targeting this pathway may provide therapeutic avenues for mitigating crystal deposition-induced kidney damage.

Purpose: Kidney stones is a common medical issue that mediates kidney injury and even kidney function loss. However, the exact pathogenesis still remains unclear. This study aimed to explore the potential competing endogenous RNA (ceRNA)-related pathogenesis of kidney stones and identify the corresponding immune infiltration signature.Methods: One mRNA and one long non-coding RNA (lncRNA) microarray dataset was obtained from the GEO database. Subsequently, we compared differentially expressed mRNAs (DE-mRNAs) and lncRNAs between Randall’s plaques in patients with calcium oxalate (CaOx) stones and controls with normal papillary tissues. lncRNA-targeted miRNAs and miRNA–mRNA pairs were predicted using the online databases. lncRNA-related DE-mRNAs were identified using the Venn method, and GO and KEGG enrichment analyses were subsequently performed. The immune-related lncRNA–miRNA–mRNA ceRNA network was developed. The CIBERSORT algorithm was used to estimate the rate of immune cell infiltration in Randall’s plaques. The ceRNA network and immune infiltration were validated in the glyoxylate-induced hyperoxaluric mouse model and oxalate-treated HK-2 cells.Results: We identified 2,340 DE-mRNAs and 929 DE-lncRNAs between Randall’s plaques in patients with CaOx stones and controls with normal papillary tissues. lncRNA-related DE-mRNAs were significantly enriched in extracellular matrix organization and collagen-containing extracellular matrix, which were associated with kidney interstitial fibrosis. The immune-related ceRNA network included 10 lncRNAs, 23 miRNAs, and 20 mRNAs. Moreover, we found that M2 macrophages and resting mast cells were differentially expressed between Randall’s plaques and normal tissues. Throughout kidney stone development, kidney tubular injury, crystal deposition, collagen fiber deposition, TGF-β expression, infiltration of M1 macrophages, and activation of mast cells were more frequent in glyoxylate-induced hyperoxaluric mice compared with control mice. Nevertheless, M2 macrophage infiltration increased in early stages (day 6) and decreased as kidney stones progressed (day 12). Furthermore, treatment with 0.25 and 0.5 mM of oxalate for 48 h significantly upregulated NEAT1, PVT1, CCL7, and ROBO2 expression levels and downregulated hsa-miR-23b-3p, hsa-miR-429, and hsa-miR-139-5p expression levels in the HK-2 cell line in a dose-dependent manner.Conclusion: We found that significant expressions of ceRNAs (NEAT1, PVT1, hsa-miR-23b-3p, hsa-miR-429, hsa-miR-139-5p, CCL7, and ROBO2) and infiltrating immune cells (macrophages and mast cells) may be involved in kidney stone pathogenesis. These findings provide novel potential therapeutic targets for kidney stones.

Background Nephrolithiasis, a common urinary system disorder, exhibits high morbidity and recurrence rates, correlating with renal dysfunction and the increased risk of chronic kidney disease. Nonetheless, the precise role of disrupted cellular metabolism in renal injury induced by calcium oxalate (CaOx) crystal deposition is unclear. The purpose of this study is to investigate the involvement of the ubiquitin-like protein containing PHD and RING finger structural domain 1 (UHRF1) in CaOx-induced renal fibrosis and its impacts on cellular lipid metabolism. Methods Various approaches, including snRNA-seq, transcriptome RNA-seq, immunohistochemistry, and western blot analyses, were employed to assess UHRF1 expression in kidneys of nephrolithiasis patients, hyperoxaluric mice, and CaOx-induced renal tubular epithelial cells. Subsequently, knockdown of UHRF1 in mice and cells corroborated its effect of UHRF1 on fibrosis, ectopic lipid deposition (ELD) and fatty acid oxidation (FAO). Rescue experiments using AICAR, ND-630 and Compound-C were performed in UHRF1-knockdown cells to explore the involvement of the AMPK pathway. Then we confirmed the bridging molecule and its regulatory pathway in vitro. Experimental results were finally confirmed using AICAR and chemically modified si-UHRF1 in vivo of hyperoxaluria mice model. Results Mechanistically, UHRF1 was found to hinder the activation of the AMPK/ACC1 pathway during CaOx-induced renal fibrosis, which was mitigated by employing AICAR, an AMPK agonist. As a nuclear protein, UHRF1 facilitates nuclear translocation of AMPK and act as a molecular link targeting the protein phosphatase PP2A to dephosphorylate AMPK and inhibit its activity. Conclusion This study revealed that UHRF1 promotes CaOx -induced renal fibrosis by enhancing lipid accumulation and suppressing FAO via inhibiting the AMPK pathway. These findings underscore the feasible therapeutic implications of targeting UHRF1 to prevent renal fibrosis due to stones. Graphical abstract