Diagnostic performance of machine learning in systemic infection following percutaneous nephrolithotomy and identification of associated risk factors.

Objective: This study aims to investigate the predictive performance of machine learning in predicting the occurrence of systemic inflammatory response syndrome (SIRS) and urosepsis after percutaneous nephrolithotomy (PCNL). Methods: A retrospective analysis was conducted on patients who underwent PCNL treatment between January 2016 and July 2022. Machine learning techniques were employed to establish and select the best predictive model for postoperative systemic infection. The feasibility of using relevant risk factors as predictive markers was explored through interpretability with Machine Learning. Results: A total of 1067 PCNL patients were included in this study, with 111 (10.4 %) patients developing SIRS and 49 (4.5 %) patients developing urosepsis. In the validation set, the risk model based on the GBM protocol demonstrated a predictive power of 0.871 for SIRS and 0.854 for urosepsis. Preoperative and postoperative platelet changes were identified as the most significant predictors. Both thrombocytopenia and thrombocytosis were found to be risk factors for SIRS or urosepsis after PCNL. Furthermore, it was observed that when the change in platelet count before and after PCNL surgery exceeded 30*109/L (whether an increase or decrease), the risk of developing SIRS or urosepsis significantly increased. Conclusion: Machine learning can be effectively utilized for predicting the occurrence of SIRS or urosepsis after PCNL. The changes in platelet count before and after PCNL surgery serve as important predictors.

Elucidating the reversible and irreversible self-assembly mechanisms of low-complexity aromatic-rich kinked peptides and steric zipper peptides.

Many RNA-binding proteins such as fused-in sarcoma (FUS) can self-assemble into reversible liquid droplets and fibrils through the self-association of their low-complexity (LC) domains. Recent experiments have revealed that SYG-rich segments in the FUS LC domains play critical roles in the reversible self-assembly behaviors of FUS. These FUS LC segments alone can self-assemble into reversible kinked fibrils, which are markedly different from the canonical irreversible steric zipper ß-sheet fibrils. However, the molecular determinants underlying the reversible and irreversible self-assembly are poorly understood. Herein we conducted extensive all-atom and coarse-grained molecular dynamics simulations of four representative hexapeptides: two low-complexity aromatic-rich kinked peptides from the amyotrophic lateral sclerosis-related FUS protein, FUS37-42 (SYSGYS) and FUS54-59 (SYSSYG); and two steric zipper peptides from Alzheimer's-associated Aß and Tau proteins, Aß16-21 (KLVFFA) and Tau306-311 (VQIVYK). We dissected their reversible and irreversible self-assembly dynamics, predicted their phase separation behaviors, and elucidated the underpinning molecular interactions. Our simulations showed that alternating stickers (Tyr) and spacers (Gly and Ser) in FUS37-42 and FUS54-59 facilitate the formation of highly dynamic coil-rich oligomers and lead to reversible self-assembly, while consecutive hydrophobic residues of LVFF in Aß16-21 and IVY in Tau306-311 act as hydrophobic patches, favoring the formation of stable ß-sheet-rich oligomers and driving the irreversible self-assembly. Intriguingly, we found that FUS37-42 and FUS54-59 peptides, possessing the same amino acid composition and the same number of sticker and spacer residues, display differential self-assembly propensities. This finding suggests that the self-assembly behaviors of FUS peptides are fine-tuned by the site-specific patterning of spacer residues (Ser and Gly). This study provides significant mechanistic insights into reversible and irreversible peptide self-assembly, which would be helpful for understanding the molecular mechanisms underlying the formation of biological liquid condensates and pathological solid amyloid fibrils.

The effects of iron-based nanomaterials (Fe NMs) on plants under stressful environments: Machine learning-assisted meta-analysis.

Mitigating the adverse effects of stressful environments on crops and promoting plant recovery in contaminated sites are critical to agricultural development and environmental remediation. Iron-based nanomaterials (Fe NMs) can be used as environmentally friendly nano-fertilizer and as a means of ecological remediation. A meta-analysis was conducted on 58 independent studies from around the world to evaluate the effects of Fe NMs on plant development and antioxidant defense systems in stressful environments. The application of Fe NMs significantly enhanced plant biomass (mean = 25%, CI = 20%-30%), while promoting antioxidant enzyme activity (mean = 14%, CI = 10%-18%) and increasing antioxidant metabolite content (mean = 10%, CI = 6%-14%), reducing plant oxidative stress (mean = -15%, CI = -20%∼-10%), and alleviating the toxic effects of stressful environments. The observed response was dependent on a number of factors, which were ranked in terms of a Random Forest Importance Analysis. Plant species was the most significant factor, followed by Fe NM particle size, duration of application, dose level, and Fe NM type. The meta-analysis has demonstrated the potential of Fe NMs in achieving sustainable agriculture and the future development of phytoremediation.

Procoagulant genes may affect angiogenesis, epithelial-mesenchymal transition, survival prognosis and tumor immune microenvironment in patients with urothelial carcinoma.

Factors related to coagulation regulation are closely related to angiogenesis, epithelial-mesenchymal transition, tumor proliferation and metastasis, and tumor immune microenvironment remodeling in tumors. To date, there are no quantitative indicators of coagulation associated with urothelial cancer. We classified urothelial cancer into high coagulation and low coagulation subtypes by screening for procoagulant-related molecular features and screened out relevant genes representing the coagulation state of urothelial carcinoma. Tumors with increased procoagulant gene expression were consistently associated with higher T-staging (p < 0.001), lymph node metastasis (p < 0.001), stage (p < 0.001), and grade (p = 0.046). Furthermore, high expression of procoagulant genes predicts a worse prognosis, a higher tumor proliferation rate and increased angiogenesis within the tumor. In addition, according to cibersort algorithm, the increased expression of procoagulant gene was negatively correlated with the degree of T-lymphocyte infiltration and positively correlated with the degree of M2 macrophage infiltration. Increased expression of procoagulant genes in data sets treated with immune checkpoints also predicted worse response and worse prognosis. At the same time, the expression of procoagulant genes in bladder cancer promoted the activation of coagulation, EMT, TGF-ß and WNT pathways.

Effects of the application of nanoscale zero-valent iron on plants: Meta analysis, mechanism, and prospects.

In order to determine the ideal conditions for the application of nanoscale zero-valent iron (nZVI) in agricultural production, this review studies the effects of nZVI application on plant physiological parameters, presents its mechanism and prospective outcomes. In this research, it was observed that the application of nZVI had both favorable and unfavorable effects on plant growth, photosynthesis, oxidative stress, and nutrient absorption levels. Specifically, the application of nZVI significantly increased the biomass and length of plants, and greatly reduced the germination rate of seeds. In terms of photosynthesis, there was no significant effect for the application of nZVI on the synthesis of photosynthetic pigments (chlorophyll and carotenoids). In terms of oxidative stress, plants respond by increasing the activity of antioxidant enzyme under mild nZVI stress and trigger oxidative burst under severe stress. In addition, the application of nZVI significantly increased the absorption of nutrients (B, K, P, S, Mg, Zn, and Fe). In summary, the application of nZVI can affect the plant physiological parameters, and the degree of influence varies depending on the concentration, preparation method, application method, particle size, and action time of nZVI. These findings are important for evaluating nZVI-related risks and enhancing nZVI safety in agricultural production.

Single-cell and spatial transcriptomics reveal 5-methylcytosine RNA methylation regulators immunologically reprograms tumor microenvironment characterizations, immunotherapy response and precision treatment of clear cell renal cell carcinoma.

Clear cell Renal Cell Carcinoma (ccRCC) is a highly heterogeneous disease, making it challenging to predict prognosis and therapy efficacy. In this study, we aimed to explore the role of 5-methylcytosine (m5C) RNA modification in ccRCC and its potential as a predictor for therapy response and overall survival (OS). We established a novel 5-methylcytosine RNA modification-related gene index (M5CRMRGI) and studied its effect on the tumor microenvironment (TME) using single-cell sequencing data for in-depth analysis, and verified it using spatial sequencing data. Our results showed that M5CRMRGI is an independent predictor of OS in multiple datasets and exhibited outstanding performance in predicting the OS of ccRCC. Distinct mutation profiles, hallmark pathways, and infiltration of immune cells in TME were observed between high- and low-M5CRMRGI groups. Single-cell/spatial transcriptomics revealed that M5CRMRGI could reprogram the distribution of tumor-infiltrating immune cells. Moreover, significant differences in tumor immunogenicity and tumor immune dysfunction and exclusion (TIDE) were observed between the two risk groups, suggesting a better response to immune checkpoint blockade therapy of the high-risk group. We also predicted six potential drugs binding to the core target of the M5CRMRGI signature via molecular docking. Real-world treatment cohort data proved once again that high-risk patients were appropriate for immune checkpoint blockade therapy, while low-risk patients were appropriate for Everolimus. Our study shows that the m5C modification landscape plays a role in TME distribution. The proposed M5CRMRGI-guided strategy for predicting survival and immunotherapy efficacy, we reported here, might also be applied to more cancers other than ccRCC.

Iron clusters regulate local charge distribution in Fe-N4 sites to boost oxygen electroreduction.

The atomically-dispersed and nitrogen-coordinated iron (FeNC) on a carbon catalyst is a potential non-noble metal catalyst that can replace precious metal electrocatalysts. However, its activity is often unsatisfactory owing to the symmetric charge distribution around the iron matrix. In this study, atomically- dispersed Fe-N4 and Fe nanoclusters loaded with N-doped porous carbon (FeNCs/FeSAs-NC-Z8@34) were rationally fabricated by introducing homologous metal clusters and increasing the N content of the support. FeNCs/FeSAs-NC-Z8@34 exhibited a half-wave potential of 0.918 V, which exceeded that of the commercial benchmark Pt/C catalyst. Theoretical calculations verified that introducing Fe nanoclusters can break the symmetric electronic structure of Fe-N4, thus inducing charge redistribution. Furthermore, it can optimize a part of Fe 3d occupancy orbitals and accelerate OO fracture in OOH* (rate-determining step), thus significantly improving oxygen reduction reaction activity. This work provides a reasonably advanced pathway to modulate the electronic structure of the single-atom center and optimize the catalytic activity of single-atom catalysts.

Robot-assisted partial nephrectomy for large complex renal cancer: step-by-step segmental artery unclamping

ABSTRACT Introduction Main renal artery clamping and selective arterial clamping are two conventional devascularization methods for robot-assisted partial nephrectomy (RAPN) (1, 2). Decreasing warm ischemic (WI) time (3, 4) and improving clear surgical visualization (5) are the main surgically modifiable factors for RAPN, especially in large complex renal cancer (6). In this study, we described our surgical technique, focusing on gradual segmental artery unclamping on patients with large renal tumors. Material and methods Two patients (R.E.N.A.L score 10 and 11) underwent RAPN with gradual segmental artery unclamping (Figures 1 and 2). The unclamping included five key steps. First, all renal segmental arteries were identified as tumor feeding vessel(s) and the vessels for normal kidney parenchyma under the guidance of CT angiography (CTA) 3-division (3D) reconstruction. Second, all segmental arteries were isolated, and the feeding one(s) should be blocked before other arteries were blocked. Third, the tumor was resected outside the pseudocapsule, and the deep resection bed was sutured for initial hemostasis. Fourth, the segmental arteries were reopened except for the tumor feeding one(s), and normal kidney parenchyma restored blood supply. And fifth, the resection bed was completely sutured, and the feeding vessel supplying the tumor was opened after the suture. Warm ischemia time (WIT) was defined as the time measured between clamping and unclamping of the renal artery. WIT1 was the time for normal kidney parenchyma and WIT2 was the time for resection area. Patient demographics, perioperative variables, and warm ischemic time were included in our study. And we presented the details of gradual segmental artery unclamping in the video. Results In both cases, the total operation times were 215 and 130 mins for patient 1 and patient 2, respectively. WIT1 and WIT2 for patient 1 were 15 min and 33 min., and WIT1 and WIT2 for patient 2 were 21 min and 32 min, respectivelly. The maximum diameters of the masses resected were 10.8 and 7.3 cm, and surgical margins were negative. No patient had complications after operation. Preoperative and postoperative eGFR did not change significantly. Pre- and postoperative eGFR were 111 and 108 mL/min for patient 1, 91 and 83 mL/min for patient 2, respectively. Key hints for outcomes optimization during RAPN on patients with large complex renal tumors: 1) Each segmental renal artery is precised clamped before we excise the tumor, and an excellent surgical vision is essential for precising excision and shortening clamping time, 2) Other segmental renal arteries are unclamped except tumor feeding branch after suturing deep layer of parenchyma, and most normal parenchyma restores blood supply, 3) Preoperative high-resolution computed tomography angiography (CTA) and 3D reconstructive renal structure serve as a guide to clear the approach to find the tumor and segmental arteries (7, 8). Conclusions Gradual segmental artery unclamping is feasible and efficient to excise large complex renal cancer. Compared with main renal artery clamping, it can shorten the warm ischemic time of normal parenchyma; On the other hand, compared with selective segmental arterial clamping, the technique can reduce bleeding from the deep resection bed, keep a clear surgical vision, and decrease the incidence of positive margin.

Dissecting the Effect of ALS Mutation G335D on the Early Aggregation of the TDP-43 Amyloidogenic Core Peptide: Helix-to-ß-Sheet Transition and Conformational Shift.

The aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) into fibrillary deposits is associated with amyotrophic lateral sclerosis (ALS). The 311-360 fragment of TDP-43 (TDP-43311-360), the amyloidogenic core region, can spontaneously aggregate into fibrils, and the ALS-associated mutation G335D has an enhanced effect on TDP-43311-360 fibrillization. However, the molecular mechanism underlying G335D-enhanced aggregation at atomic level remains largely unknown. By utilizing all-atom molecular dynamics (MD) and replica exchange with solute tempering 2 (REST2) simulations, we investigated influences of G335D on the dimerization (the first step of aggregation) and conformational ensemble of the TDP-43311-360 peptide. Our simulations show that G335D mutation increases inter-peptide interactions, especially inter-peptide hydrogen-bonding interactions in which the mutant site has a relatively large contribution, and enhances the dimerization of TDP-43311-360 peptides. The α-helix regions in the NMR-resolved conformation of the TDP-43311-360 monomer (321-330 and 335-343) play an essential role in the formation of the dimer. G335D mutation induces helix unfolding and promotes α-to-ß conversion. G335D mutation alters the conformational distribution of TDP-43311-360 dimers and causes population shift from helix-rich to ß-sheet-rich conformations, which facilitates the fibrillization of the TDP-43311-360 peptide. Our MD and REST2 simulation results suggest that the 321-330 region is of paramount importance to α-to-ß transition and could be the initiation site for TDP-43311-360 fibrillization. Our work reveals the mechanism underlying the enhanced aggregation propensity of the G335D TDP-43311-360 peptide, which provides atomistic insights into the G335D mutation-caused pathogenicity of TDP-43 protein.

Dissecting how ALS-associated D290V mutation enhances pathogenic aggregation of hnRNPA2286-291 peptides: Dynamics and conformational ensembles.

The aggregation of RNA binding proteins, including hnRNPA1/2, TDP-43 and FUS, is heavily implicated in causing or increasing disease risk for a series of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). A recent experimental study demonstrated that an ALS-related D290V mutation in the low complexity domain (LCD) of hnRNPA2 can enhance the aggregation propensity of wild type (WT) hnRNPA2286-291 peptide. However, the underlying molecular mechanisms remain elusive. Herein, we investigated effects of D290V mutation on aggregation dynamics of hnRNPA2286-291 peptide and the conformational ensemble of hnRNPA2286-291 oligomers by performing all-atom molecular dynamic and replica-exchange molecular dynamic simulations. Our simulations demonstrate that D290V mutation greatly reduces the dynamics of hnRNPA2286-291 peptide and that D290V oligomers possess higher compactness and ß-sheet content than WT, indicative of mutation-enhanced aggregation capability. Specifically, D290V mutation strengthens inter-peptide hydrophobic, main-chain hydrogen bonding and side-chain aromatic stacking interactions. Those interactions collectively lead to the enhancement of aggregation capability of hnRNPA2286-291 peptides. Overall, our study provides insights into the dynamics and thermodynamic mechanisms underlying D290V-induced disease-causing aggregation of hnRNPA2286-291, which could contribute to better understanding of the transitions from reversible condensates to irreversible pathogenic aggregates of hnRNPA2 LCD in ALS-related diseases.

Robot-assisted partial nephrectomy for large complex renal cancer: step-by-step segmental artery unclamping.

INTRODUCTION: Main renal artery clamping and selective arterial clamping are two conventional devascularization methods for robot-assisted partial nephrectomy (RAPN) (1, 2). Decreasing warm ischemic (WI) time (3, 4) and improving clear surgical visualization (5) are the main surgically modifiable factors for RAPN, especially in large complex renal cancer (6). In this study, we described our surgical technique, focusing on gradual segmental artery unclamping on patients with large renal tumors. MATERIAL AND METHODS: Two patients (R.E.N.A.L score 10 and 11) underwent RAPN with gradual segmental artery unclamping (Figures 1 and 2). The unclamping included five key steps. First, all renal segmental arteries were identified as tumor feeding vessel(s) and the vessels for normal kidney parenchyma under the guidance of CT angiography (CTA) 3-division (3D) reconstruction. Second, all segmental arteries were isolated, and the feeding one(s) should be blocked before other arteries were blocked. Third, the tumor was resected outside the pseudocapsule, and the deep resection bed was sutured for initial hemostasis. Fourth, the segmental arteries were reopened except for the tumor feeding one(s), and normal kidney parenchyma restored blood supply. And fifth, the resection bed was completely sutured, and the feeding vessel supplying the tumor was opened after the suture. Warm ischemia time (WIT) was defined as the time measured between clamping and unclamping of the renal artery. WIT1 was the time for normal kidney parenchyma and WIT2 was the time for resection area. Patient demographics, perioperative variables, and warm ischemic time were included in our study. And we presented the details of gradual segmental artery unclamping in the video. RESULTS: In both cases, the total operation times were 215 and 130 mins for patient 1 and patient 2, respectively. WIT1 and WIT2 for patient 1 were 15 min and 33 min., and WIT1 and WIT2 for patient 2 were 21 min and 32 min, respectivelly. The maximum diameters of the masses resected were 10.8 and 7.3 cm, and surgical margins were negative. No patient had complications after operation. Preoperative and postoperative eGFR did not change significantly. Pre- and postoperative eGFR were 111 and 108 mL/min for patient 1, 91 and 83 mL/min for patient 2, respectively. Key hints for outcomes optimization during RAPN on patients with large complex renal tumors: 1) Each segmental renal artery is precised clamped before we excise the tumor, and an excellent surgical vision is essential for precising excision and shortening clamping time, 2) Other segmental renal arteries are unclamped except tumor feeding branch after suturing deep layer of parenchyma, and most normal parenchyma restores blood supply, 3) Preoperative high-resolution computed tomography angiography (CTA) and 3D reconstructive renal structure serve as a guide to clear the approach to find the tumor and segmental arteries (7, 8). CONCLUSIONS: Gradual segmental artery unclamping is feasible and efficient to excise large complex renal cancer. Compared with main renal artery clamping, it can shorten the warm ischemic time of normal parenchyma; On the other hand, compared with selective segmental arterial clamping, the technique can reduce bleeding from the deep resection bed, keep a clear surgical vision, and decrease the incidence of positive margin.

Identification of mRNA vaccines and conserved ferroptosis related immune landscape for individual precision treatment in bladder cancer.

Background: The aim of this study was to identify the ferroptosis induced tumor microenvironment (FeME) landscape in bladder cancer (BCa) for mRNA vaccine development and selecting suitable patients for precision treatment. Methods: Gene expression profiles and clinical information of 1216 BCa patients were extracted from TCGA-BLCA, three GEO databases and IMvigor210 cohort. We comprehensively established the FeME landscape of 1216 BCa samples based on 290 ferroptosis related genes (FRGs), and systematically correlated these regulation patterns with TME cell-infiltrating characteristics. Besides, we identified the patients' ferroptosis risk index (FRI) to predict the prognosis of BCa for precise treatment. Results: Six over-expressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in BCa. Furthermore, we demonstrated the evaluation of FeME within individual tumors could predict stages of tumor inflammation, subtypes, genetic variation, and patient prognosis. Then, 5-lncRNA signature was mined to produce the FRI. Low FRI was also linked to increased mutation load, better prognosis and enhanced response to anti-PD-L1 immunotherapy. Besides, an immunotherapy cohort confirmed patients with lower FRI demonstrated significant therapeutic advantages and clinical benefits. Conclusions: TFRC, SCD, G6PD, FADS2, SQLE, and SLC3A2 are potent antigens for developing anti-BCa mRNA vaccine. Establishment of FRI will contribute to enhancing our cognition of TME infiltration characterization and guiding more effective immunotherapy strategies and selecting appropriate patients for tumor vaccine therapy. Supplementary Information: The online version contains supplementary material available at 10.1186/s40537-022-00641-z.

Insights into the Atomistic Mechanisms of Phosphorylation in Disrupting Liquid-Liquid Phase Separation and Aggregation of the FUS Low-Complexity Domain.

Fused in sarcoma (FUS), a nuclear RNA binding protein, can not only undergo liquid-liquid phase separation (LLPS) to form dynamic biomolecular condensates but also aggregate into solid amyloid fibrils which are associated with the pathology of amyotrophic lateral sclerosis and frontotemporal lobar degeneration diseases. Phosphorylation in the FUS low-complexity domain (FUS-LC) inhibits FUS LLPS and aggregation. However, it remains largely elusive what are the underlying atomistic mechanisms of this inhibitory effect and whether phosphorylation can disrupt preformed FUS fibrils, reversing the FUS gel/solid phase toward the liquid phase. Herein, we systematically investigate the impacts of phosphorylation on the conformational ensemble of the FUS37-97 monomer and dimer and the structure of the FUS37-97 fibril by performing extensive all-atom molecular dynamics simulations. Our simulations reveal three key findings: (1) phosphorylation shifts the conformations of FUS37-97 from the ß-rich, fibril-competent state toward a helix-rich, fibril-incompetent state; (2) phosphorylation significantly weakens protein-protein interactions and enhances protein-water interactions, which disfavor FUS-LC LLPS as well as aggregation and facilitate the dissolution of the preformed FUS-LC fibril; and (3) the FUS37-97 peptide displays a high ß-strand probability in the region spanning residues 52-67, and phosphorylation at S54 and S61 residues located in this region is crucial for the disruption of LLPS and aggregation of FUS-LC. This study may pave the way for ameliorating phase-separation-related pathologies via site-specific phosphorylation.

Deciphering the mechanisms of HPV E6 mutations in the destabilization of E6/E6AP/p53 complex.

In epithelial tumors, oncoprotein E6 binds with the ubiquitin ligase E6AP to form E6/E6AP heterodimer; then this heterodimer recruits p53 to form E6/E6AP/p53 heterotrimer and induces p53 degradation. Recent experiments demonstrated that three E6 single-site mutants (F47R, R102A, and L50E) can inhibit the E6/E6AP/p53 heterotrimer formation and rescue p53 from the degradation pathway. However, the molecular mechanism underlying mutation-induced heterotrimer inhibition remains largely elusive. Herein, we performed extensive molecular dynamics simulations (totally ∼13 µs) on both heterodimer and heterotrimer to elucidate at an atomic level how each p53-degradation-defective HPV16 E6 mutant reduces the structural stabilities of the two complexes. Our simulations reveal that the three E6 mutations destabilize the structure of E6/E6AP/p53 complex through distinct mechanisms. Although F47RE6 mutation has no effect on the structure of E6/E6AP heterodimer, it results in an electrostatic repulsion between R47E6 and R290p53, which is unfavorable for E6-p53 binding. R102AE6 mutation destabilizes the structure of E6/E6AP heterodimer and significantly disrupts hydrophobic and cation-π interactions between F47E6 and E286p53/L298p53/R290p53. L50EE6 mutation impairs both E6 interdomain interactions (especially F47-K108 cation-π interaction) and E6-E6AP intermolecular interactions important for the stabilization of E6/E6AP heterodimer. This study identifies the intra- and intermolecular interactions crucial for the complex stability, which may provide mechanistic insights into the inhibition of complex formation by the three HPV16 E6 mutations.

The impact of tumor size on the survival of patients with small renal masses: A population-based study.

BACKGROUND: Active surveillance (AS) with delayed intervention has gained acceptance as a management strategy for small renal masses (SRMs). However, during AS, there is a risk of tumor growth. Thus, we aim to investigate whether tumor growth in patients with SRMs leads to tumor progress. METHODS: In this study, we enrolled 16,070 patients from the Surveillance, Epidemiology, and End Results database with T1a renal cell carcinoma (RCC) between 2004 and 2017. The 16,070 patients were divided into three groups: 10,526 in the partial nephrectomy (PN) group, 2768 in the local ablation (LA) group, and 2776 in the AS group. Associations of tumor size with all-cause and cancer-specific mortality were evaluated using Kaplan-Meier analyses and Cox regression models. RESULTS: Four tumor size categories were delineated (≤1, >1-2, >2-3, and > 3-4 cm in diameter), and 10-year all-cause and cancer-specific mortality both significantly increased with increasing tumor size in the PN, LA, and AS groups (all p < 0.05). Tumors were substaged based on diameter: T1aA (≤2 cm) and T1aB (>2-4 cm). All-cause and cancer-specific mortality were significantly higher in T1aB tumors than T1aA tumors in each group (hazard ratio = 1.395 and 1.538, respectively; all p < 0.05). CONCLUSIONS: Tumor growth relates to worse prognosis of T1a RCC, and 2 cm serves as a size threshold that is prognostically relevant for patients with T1a RCC. Because of the lack of accurate predictors of tumor growth rate, AS for patients with SRMs incurs a risk of tumor progression.

TP53/BRAF mutation as an aid in predicting response to immune-checkpoint inhibitor across multiple cancer types.

Immunotherapy with checkpoint inhibitors, such as PD-1/PD-L1 blockage, is becoming standard of practice for an increasing number of cancer types. However, the response rate is only 10%-40%. Thus, identifying biomarkers that could accurately predict the ICI-therapy response is critically important. We downloaded somatic mutation data for 46,697 patients and tumor-infiltrating immune cells levels data for 11070 patients, then combined TP53 and BRAF mutation status into a biomarker model and found that the predict ability of TP53/BRAF mutation model is more powerful than some past models. Commonly, patients with high-TMB status have better response to ICI therapy than patients with low-TMB status. However, the genotype of TP53MUTBRAFWT in high-TMB status cohort have poorer response to ICI therapy than the genotype of BRAFMUTTP53WT in low-TMB status (Median, 18 months vs 47 month). Thus, TP53/BRAF mutation model can add predictive value to TMB in identifying patients who benefited from ICI treatment, which can enable more informed treatment decisions.

Mechanistic insight into the destabilization of p53TD tetramer by cancer-related R337H mutation: a molecular dynamics study.

The p53 protein is a tumor suppressor crucial for cell cycle and genome integrity. In a very large proportion of human cancers, p53 is frequently inactivated by mutations located in its DNA-binding domain (DBD). Some experimental studies reported that the inherited R337H mutation located in the p53 tetramerization domain (p53TD) can also result in destabilization of the p53 protein, and consequently lead to an organism prone to cancer setup. However, the underlying R337H mutation-induced structural destabilization mechanism is not well understood. Herein, we investigate the structural stability and dynamic property of the wild type p53TD tetramer and its cancer-related R337H mutant by performing multiple microsecond molecular dynamics simulations. It is found that R337H mutation destroys the R337-D352 hydrogen bonds, weakens the F341-F341 π-π stacking interaction and the hydrophobic interaction between aliphatic hydrocarbons of R337 and M340, leading to more solvent exposure of all the hydrophobic cores, and thus disrupting the structural integrity of the tetramer. Importantly, our simulations show for the first time that R337H mutation results in unfolding of the α-helix starting from the N-terminal region (residues 335RER(H)FEM340). Consistently, community network analyses reveal that R337H mutation reduces dynamical correlation and global connectivity of p53TD tetramer, which destabilizes the structure of the p53TD tetramer. This study provides the atomistic mechanism of R337H mutation-induced destabilization of p53TD tetramer, which might be helpful for in-depth understanding of the p53 loss-of-function mechanism.

circCHST15 is a novel prognostic biomarker that promotes clear cell renal cell carcinoma cell proliferation and metastasis through the miR-125a-5p/EIF4EBP1 axis.

BACKGROUND: Circular RNAs (circRNAs) have been indicated as potentially critical mediators in various types of tumor progression, generally acting as microRNA (miRNA) sponges to regulate downstream gene expression. However, the aberrant expression profile and dysfunction of circRNAs in human clear cell renal cell carcinoma (ccRCC) need to be further investigated. This study mined key prognostic circRNAs and elucidates the potential role and molecular mechanism of circRNAs in regulating the proliferation and metastasis of ccRCC. METHODS: circCHST15 (hsa_circ_0020303) was identified by mining two circRNA microarrays from the Gene Expression Omnibus database and comparing matched tumor versus adjacent normal epithelial tissue pairs or matched primary versus metastatic tumor tissue pairs. These results were validated by quantitative real-time polymerase chain reaction and agarose gel electrophoresis. We demonstrated the biological effect of circCHST15 in ccRCC both in vitro and in vivo. To test the interaction between circCHST15 and miRNAs, we conducted a number of experiments, including RNA pull down assay, dual-luciferase reporter assay and fluorescence in situ hybridization. RESULTS: The expression of circCHST15 was higher in ccRCC tissues compared to healthy adjacent kidney tissue and higher in RCC cell lines compared to normal kidney cell lines. The level of circCHST15 was positively correlated with aggressive clinicopathological characteristics, and circCHST15 served as an independent prognostic indicator for overall survival and progression-free survival in patients with ccRCC after surgical resection. Our in vivo and in vitro data indicate that circCHST15 promotes the proliferation, migration, and invasion of ccRCC cells. Mechanistically, we found that circCHST15 directly interacts with miR-125a-5p and acts as a microRNA sponge to regulate EIF4EBP1 expression. CONCLUSIONS: We found that sponging of miR-125a-5p to promote EIF4EBP1 expression is the underlying mechanism of hsa_circ_0020303-induced ccRCC progression. This prompts further investigation of circCHST15 as a potential prognostic biomarker and therapeutic target for ccRCC.

Functional characterization of the immunomodulatory properties of human urine-derived stem cells.

BACKGROUND: Urine-derived stem cells (USCs) have been widely researched as a novel cell source for stem cell therapy, but their immunomodulatory characteristics remain to be investigated. This study aimed to characterize the immunomodulatory properties of human USCs. METHODS: Human USCs were isolated from fresh voiding urine samples from healthy male donors and expanded. Their cell surface markers were characterized by flow cytometry analysis and the telomerase activities for several USCs clones were determined. The immunosuppressive potential of USCs was evaluated by the performing the mixed lymphocyte reaction (MLR) [co-culture with peripheral blood mononuclear cells (PBMNCs)] and natural killer cells (NK) cytotoxicity assay. USCs cytokines release profile was determined by using human cytokine proteome array. RESULTS: USCs exhibited high cell surface expression of embryonic/mesenchymal stem cells (MSCs) markers CD29, CD44, CD54, CD73, CD90, CD146, and CD166, while lacked expression of hematopoietic stem cell markers CD11, CD14, CD19, CD31, CD34, CD45, B cell marker CD79, and co-stimulatory factors CD80 and CD86, thus, exhibiting the phenotype of MSCs. MLR indicated that USCs significantly inhibited the proliferation of PBMNCs, as compared to that of the human smooth muscle cells (SMCs). In cell cytotoxicity assays, NK cells displayed less cytotoxicity against USCs than against bone marrow mesenchymal stem cells (BMSCs) and SMCs. Furthermore, upon PBMNCs stimulation, USCs secreted higher levels of immunomodulatory cytokines, including IL-6, IL-8, MCP-1, RANTES, GROα, and GM-CSF, compared to those of BMSCs, especially when directly contact mix-culture with PBMNCs. CONCLUSIONS: USCs secreted immunoregulatory cytokines and possessed immunomodulatory properties, comparable to those of BMSCs.

Localization of external urethral orifice in coronary sulcus during urethroplasty in case of severe hypospadias accompanied by prostatic utricle cyst.

BACKGROUND: To explore whether opening the external urethral orifice in the coronal sulcus can reduce the incidence of epididymitis after operating on hypospadias with prostatic utricle cyst (PUC) connecting to the vas deferens. Group A consisted of 3 patients with severe hypospadias and PUC undergoing cystostomy, hypospadias correction and urethroplasty, along with the relocation of the external orifice of the urethra to the coronal sulcus. Group B consisted of 4 patients having initial hypospadias repaired with meatus in the orthotopic position in the glans, presenting with multiple epididymitis after hypospadias surgery and unsuccessful conservative treatment. MR confirmed that all the Group B patients had PUC connecting to the vas deferens. Group B patients underwent urethral dilatation along with urethral catheterization, cutting of the original corpus cavernosum that encapsulated the urethra, and extension of the position of the external urethral orifice to the coronal sulcus. RESULTS: In group A, 3 children underwent bladder fistula removal 2 weeks after the operation. The penis developed normally without any complications. Four children in group B underwent stent removal 12 weeks after operation, and one patient was still stenosed and dilated again. All patients in group B were followed without epididymitis recurrence. CONCLUSIONS: For patients with hypospadias complicating with a PUC, connecting to one side of the vas deferens, the positioning of the external urethral orifice in the coronary sulcus would be helpful to reduce the occurrence of epididymitis.