Infections by carbapenem-resistant Enterobacteriaceae (CRE) are difficult to manage owing to broad antibiotic resistance profiles and because of the inability of clinically-used β-lactamase inhibitors to counter the activity of metallo-β-lactamases often harbored by these pathogens. Of particular importance is New Delhi metallo-β-lactamase (NDM), which requires a dinuclear zinc ion cluster for catalytic activity. Here, we compare the structures and functions of clinical NDM variants 1-17. The impact of NDM variants on structure is probed by comparing comparing melting temperature and refolding efficiency and also by spectroscopy (UV-Vis, 1 H-NMR, and EPR) of di-cobalt metalloforms. The impact of NDM variants on function is probed by determining of minimum inhibitory concentrations of various antibiotics, pre-steady state and steadystate kinetics, inhibitor binding, and zincdependence of resistance and activity. We observed only minor differences among the fullloaded dizinc enzymes, but most NDM variants had more distinguishable selective advantages in experiments that mimicked zinc scarcity imposed by typical host defenses. Most NDM variants http://www.jbc.org/ Downloaded from 2 exhibited improved thermostability (up to ~10 °C increased Tm) and improved zinc affinity (up to ~10-fold decreased Kd, Zn2). We also provide first evidence that some NDM variants have evolved the ability to function as monozinc enzymes with high catalytic efficiency (NDM-15, ampicillin: kcat/KM = 5 × 10 6 M -1 s -1 ). These findings reveal the molecular mechanisms that NDM variants have evolved to overcome the combined selective pressures of β-lactam antibiotics and zinc deprivation.Carbapenem-resistant Enterobacteriaceae (CRE) continue to be classified as an "urgent threat," the highest hazard level assigned by the Centers for Disease Control and Prevention(1). The five carbapenemases currently of primary public concern include Klebsiella pneumonia carbapanemase (KPC), New Delhi metallo-β-lactamase (NDM), Verona integrin encoded metallo-β-lactamase (VIM), imipenemase (IMP), and oxacillinase-48-like carbapenemase (OXA-48)(2). Three of these carbapenemases (NDM, VIM, and IMP) are metal-dependent β-lactamases that are not susceptible to any of the β-lactamase inhibitors incorporated into combination drugs used in the clinic. Of these three β-lactamases, NDM is the most widespread in U.S. patients, with infections bearing a blaNDM gene reported in 34 / 50 states (as of December 2017)(3).The genes encoding NDM continue to evolve, with discovery of more than 20 variants (NDM-1 through NDM-21 at the time of writing, 16 at the start of this project). Most of these mutations occur at sites distant from the active site, and the functions they confer are not immediately obvious. A comparison of NDM-1 through NDM-8 showed only minor differences in kcat/KM values (≤ 5-fold) for a panel of diverse β-lactam drugs(4). However, a considerable increase in thermostability was noted for many of the variants, suggesting the functional impact of NDM...
Background Ferroptosis is a new type of iron- and reactive oxygen species-dependent cell death, studies on ferroptosis-related long noncoding RNAs (FerLncRNAs) in clear cell renal cell carcinoma (ccRCC) are limited. The purpose of this study was to investigate the potential prognostic value of FerLncRNAs and their relationship with the immune microenvironment and immunotherapy response of ccRCC. Methods RNA sequencing data of 526 patients with ccRCC were downloaded from The Cancer Genome Atlas (TCGA) database. The patients with ccRCC in TCGA were randomly divided (1:1) into a training and testing cohort. ICGC and GEO databases were used for validation. Screening for FerLncRNAs was performed using Pearson’s correlation analysis with the reported ferroptosis-related genes. A FerLncRNA signature was constructed using univariate, LASSO, and multivariate Cox regression analyses in the training cohort. Internal and external datasets were performed to verify the FRlncRNA signature. Four major FRlncRNAs were verified through in vitro experiment. Results We identified seven FerLncRNAs (LINC00894, DUXAP8, LINC01426, PVT1, PELATON, LINC02609, and MYG1-AS1), and established a risk signature and nomogram for predicting the prognosis of ccRCC. Four major FRlncRNAs were verified with the prognosis of ccRCC in the GEPIA and K-M Plotter databases, and their expressions were validated by realtime PCR. The risk signature can also effectively reflect the immune environment, immunotherapy response and drug sensitivity of ccRCC. These FRlncRNAs have great significance to the implementation of individualized treatment and disease monitoring of ccRCC patients.
δ‐Catenin is a unique member of the catenin family and is proved to be overexpressed in diverse human cancer types. However, the clinical significance and underling mechanism of δ‐catenin expression in renal cell carcinoma (RCC) remain elusive. Herein, we detected the protein expression of δ‐catenin in 28 clinical specimens of paired renal cancer tissues and normal renal tissues by Western blot analysis. δ‐Catenin expression in 58 cases of renal cell carcinoma was also examined by immunohistochemistry, and its association with clinicopathological factors was analyzed by statistical analysis. In vitro and in vivo assays were employed to further explore the biological role of δ‐catenin in RCC. The results showed that δ‐catenin was highly expressed in both clinical samples and cell lines of RCC. RCC patients with higher δ‐catenin expression had a more advanced pTNM stage and tumor stage as well as lymph nodes metastasis than those with lower expression. By regulating the nuclear translocation of β‐catenin and β‐catenin‐mediated oncogenic signals, δ‐catenin promoted proliferation and inhibited apoptosis in RCC. In vivo assay indicated δ‐catenin facilitated tumor growth in ACHN cell xenograft mouse model. Taken together, our study suggests that δ‐catenin might be considered as a novel prognostic indicator and actionable target for gene therapy in renal cell carcinoma.
Background:Ferroptosis is a new type of iron- and reactive oxygen species-dependent cell death, which is observed in a variety of disease conditions and plays an important role in cancer. However, studies on ferroptosis-related long noncoding RNAs (FerLncRNAs) in clear cell renal cell carcinoma (ccRCC) are limited. The purpose of this study was to investigate the potential prognostic value of FerLncRNAs and their relationship with the immune microenvironment and immunotherapy response of ccRCC.Methods: RNA sequencing data of 526 patients with ccRCC were downloaded from The Cancer Genome Atlas (TCGA) database. The patients with ccRCC in TCGA were randomly divided (1:1) into a training and testing cohort. ICGC and GEO databases were used for validation. Screening for FerLncRNAs was performed using Pearson’s correlation analysis with the reported ferroptosis-related genes. A FerLncRNA signature was constructed using univariate, LASSO, and multivariate Cox regression analyses in the training cohort. Internal and external datasets were performed to verify the FRlncRNA signature. Four major FRlncRNAs were verified through in vitro experiment.Results: A FerLncRNA signature (LINC00894, DUXAP8, LINC01426, PVT1, PELATON, LINC02609, and MYG1-AS1) was established. Patients in the high-risk group had a worse prognosis than those in the low-risk group. Analysis of the area under the time-dependent ROC curve (AUC) confirmed the predictive accuracy of the signature was better than the traditional evaluation factors; the AUC value for 5-year survival reached 0.772 in the total cohort. Multivariate Cox regression analysis showed that the risk score was an independent prognostic indicator. A nomogram was established based on the risk signature and clinical features to accurately predict the survival of patients with ccRCC. Four major FRlncRNAs (LINC00894, LINC01426, PVT1, and DUXAP8) were verified with the prognosis of ccRCC in the GEPIA and K-M Plotter databases, their expressions were validated by realtime PCR. Gene set enrichment analysis revealed the immune and tumor-related pathways in the individuals from the two risk groups. The immune cell infiltration landscapes and expression levels of immune checkpoints showed significantly different between the low- and high-risk groups. Finally, TIDE and ImmuCellAI analyses showed that patients in the low-risk group were more inclined to respond to immunotherapy than patients in the high-risk group. In addition, drug sensitivity analysis indicated that our risk signature had potential predictive value for chemotherapeutics and targeted therapy. Conclusions: Our study established a novel FerLncRNA signature with robust predictive ability for survival and efficiency in predicting the response to immunotherapy, chemotherapy and targeted therapy in ccRCC patients. Its component FerLncRNAs may serve as therapeutic targets for ccRCC.
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