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A model for predicting postoperative persistent acute kidney injury (AKI) in AKI after cardiac surgery patients with normal baseline renal function.
Chen, Y, Mo, Z, Chu, H, Hu, P, Fan, W, Wu, Y, Song, L, Zhang, L, Li, Z, Liu, S, et al
Clinical cardiology. 2024;(1):e24168
Abstract
BACKGROUND Persistent acute kidney injury (AKI) after cardiac surgery is not uncommon and linked to poor outcomes. HYPOTHESIS The purpose was to develop a model for predicting postoperative persistent AKI in patients with normal baseline renal function who experienced AKI after cardiac surgery. METHODS Data from 5368 patients with normal renal function at baseline who experienced AKI after cardiopulmonary bypass cardiac surgery in our hospital were retrospectively evaluated. Among them, 3768 patients were randomly assigned to develop the model, while the remaining patients were used to validate the model. The new model was developed using logistic regression with variables selected using least absolute shrinkage and selection operator regression. RESULTS The incidence of persistent AKI was 50.6% in the development group. Nine variables were selected for the model, including age, hypertension, diabetes, coronary heart disease, cardiopulmonary bypass time, AKI stage at initial diagnosis after cardiac surgery, postoperative serum magnesium level of <0.8 mmol/L, postoperative duration of mechanical ventilation, and postoperative intra-aortic balloon pump use. The model's performance was good in the validation group. The area under the receiver operating characteristic curve was 0.761 (95% confidence interval: 0.737-0.784). Observations and predictions from the model agreed well in the calibration plot. The model was also clinically useful based on decision curve analysis. CONCLUSIONS It is feasible by using the model to identify persistent AKI after cardiac surgery in patients with normal baseline renal function who experienced postoperative AKI, which may aid in patient stratification and individualized precision treatment strategy.
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Dynamic N6 -methyladenosine RNA modification regulates peanut resistance to bacterial wilt.
Zhao, K, Li, Z, Ke, Y, Ren, R, Cao, Z, Li, Z, Wang, K, Wang, X, Wang, J, Ma, Q, et al
The New phytologist. 2024;(1):231-246
Abstract
N6 -methyladenosine (m6 A) is the most abundant mRNA modification in eukaryotes and is an important regulator of gene expression as well as many other critical biological processes. However, the characteristics and functions of m6 A in peanut (Arachis hypogea L.) resistance to bacterial wilt (BW) remain unknown. Here, we analyzed the dynamic of m6 A during infection of resistant (H108) and susceptible (H107) peanut accessions with Ralstonia solanacearum (R. solanacearum), the causative agent of BW. Throughout the transcriptome, we identified 'URUAY' as a highly conserved motif for m6 A in peanut. The majority of differential m6 A located within the 3' untranslated region (UTR) of the transcript, with fewer in the exons. Integrative analysis of RNA-Seq and m6 A methylomes suggests the correlation between m6 A and gene expression in peanut R. solanacearum infection, and functional analysis reveals that m6 A-associated genes were related to plant-pathogen interaction. Our experimental analysis suggests that AhALKBH15 is an m6 A demethylase in peanut, leading to decreased m6 A levels and upregulation of the resistance gene AhCQ2G6Y. The upregulation of AhCQ2G6Y expression appears to promote BW resistance in the H108 accession.
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Identification and characterization of the TetR family transcriptional regulator NffT in Rhizobium johnstonii.
Li, X, Li, Z, Wei, Y, Chen, Z, Xie, S
Applied and environmental microbiology. 2024;(3):e0185123
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Abstract
Symbiotic nitrogen fixation (SNF) by rhizobia is not only the main natural bionitrogen-source for organisms but also a green process leveraged to increase the fertility of soil for agricultural production. However, an insufficient understanding of the regulatory mechanism of SNF hinders its practical application. During SNF, nifA-fixA signaling is essential for the biosynthesis of nitrogenases and electron transfer chain proteins. In the present study, the TetR regulator NffT, whose mutation increased fixA expression, was discovered through a fixA-promoter-β-glucuronidase fusion assay performed with Rhizobium johnstonii. Real-time quantitative PCR analysis showed that nffT deletion increased the expression of symbiotic genes including nifA and fixA in nifA-fixA signaling, and fixL, fixK, fnrN, and fixN9 in fixL-fixN signaling. nffT overexpression resulted in disordered nodules and reduced nitrogen-fixing efficiency. Electrophoretic mobility shift assays revealed that NffT directly regulated the transcription of RL0091-93, which encode an ATP-binding ABC transporter predicted to be involved in carbohydrate transport. Purified His-tagged NffT bound to a 68 bp DNA sequence located -32 to -99 bp upstream of RL0091-93 and NffT deletion significantly increased the expression of RL0091-93. nffT-promoter-β-glucuronidase fusion assay indicated that nffT expression was regulated by the cobNTS genes and cobalamin. Mutations in cobNTS significantly decreased the expression of nffT, and cobalamin restored its expression. These results revealed that NffT affects nodule development and nitrogen-fixing reaction by participating in a complex regulatory network of symbiotic and carbohydrate metabolic genes and, thus, plays a pivotal regulatory role during symbiosis of R. johnstonii-Pisum sativum.IMPORTANCESymbiotic nitrogen fixation (SNF) by rhizobia is a green way to maintain soil fertility without causing environmental pollution or consuming chemical energy. A detailed understanding of the regulatory mechanism of this complex process is essential for promoting sustainable agriculture. In this study, we discovered the TetR-type regulator NffT, which suppressed the expression of fixA in Rhizobium johnstonii. Furthermore, NffT was confirmed to play pleiotropic roles in R. johnstonii-Pisum sativum symbiosis; specifically, it inhibited rhizobial growth, nodule differentiation, and nitrogen-fixing reactions. We revealed that NffT indirectly affected R. johnstonii-P. sativum symbiosis by participating in a complex regulatory network of symbiotic and carbohydrate metabolic genes. Furthermore, cobalamin, a chemical molecule, was reported for the first time to be involved in TetR-type protein transcription during symbiosis. Thus, NffT identification connects SNF regulation with genetic, metabolic, and chemical signals and provides new insights into the complex regulation of SNF, laying an experimental basis for the targeted construction of rhizobial strains with highly efficient nitrogen-fixing capacity.
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Potassium levels and the risk of all-cause and cardiovascular mortality among patients with cardiovascular diseases: a meta-analysis of cohort studies.
Fan, Y, Wu, M, Li, X, Zhao, J, Shi, J, Ding, L, Jiang, H, Li, Z, Zhang, W, Ma, T, et al
Nutrition journal. 2024;(1):8
Abstract
BACKGROUND Abnormal blood potassium levels are associated with an increased risk of cardiometabolic diseases and mortality in the general population; however, evidence regarding the association between dyskalemia and mortality among patients with cardiovascular disease (CVD) remains inconclusive. This study aimed to evaluate the association of potassium levels with all-cause and cardiovascular mortality among patients with CVD. METHODS PubMed, Embase, Web of Science, and Cochrane Library databases were searched up to August 2023 to identify relevant cohort studies among patients with CVD, such as myocardial infarction, stroke, and heart failure. Abnormal potassium levels were considered as hypokalemia or hyperkalemia. The primary outcomes were all-cause mortality based on follow-up length (including in-hospital, short-term and long-term mortality) and cardiovascular mortality. The methodological quality of included studies was assessed by using the Newcastle-Ottawa Scale. The pooled relative risks (RRs) and 95% confidence intervals (CIs) were calculated using random-effects models. Restricted cubic splines were applied to explore the dose-response relationship. RESULTS Thirty-one cohort studies involving 227,645 participants with an average age of 68.3 years were included in the meta-analysis, all of which achieved moderate to high quality. Hyperkalemia was significantly associated with an approximately 3.0-fold increased risk of all-cause in-hospital mortality (RR:2.78,95CI%:1.92,4.03), 1.8-fold of all-cause short-term mortality (RR:1.80, 95CI%:1.44,2.27), 1.3-fold of all-cause long-term mortality (RR:1.33, 95CI%:1.19,1.48) and 1.2-fold of cardiovascular mortality (RR:1.19, 95CI%:1.04,1.36). Similar positive associations were also observed between hypokalemia and risk of all-cause mortality and cardiovascular mortality. The RRs of all-cause in-hospital, short-term, long-term mortality and cardiovascular mortality with hyperkalemia were attenuated to 2.21 (95CI%:1.60,3.06), 1.46(95CI%:1.25,1.71), 1.23 (95CI%:1.09,1.39) and 1.13 (95CI%:1.00,1.27) when treating hypokalemia together with normokalemia as the reference group. A U-shaped association was observed between potassium levels and mortality, with the lowest risk at around 4.2 mmol/L. CONCLUSIONS Both hypokalemia and hyperkalemia were positively associated with the risk of mortality in patients with CVD. Our results support the importance of potassium homeostasis for improving the CVD management. REGISTRATION PROSPERO, CRD42022324337.
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Design strategies and recent development of bioactive modulators for glutamine transporters.
Cheng, X, Wang, Y, Gong, G, Shen, P, Li, Z, Bian, J
Drug discovery today. 2024;(2):103880
Abstract
Glutamine transporters are integral to the metabolism of glutamine in both healthy tissues and cancerous cells, playing a pivotal role in maintaining amino acid balance, synthesizing biomolecules, and regulating redox equilibrium. Their critical functions in cellular metabolism make them promising targets for oncological therapies. Recent years have witnessed substantial progress in the field of glutamine transporters, marked by breakthroughs in understanding of their protein structures and the discovery of novel inhibitors, prodrugs, and radiotracers. This review provides a comprehensive update on the latest advancements in modulators targeting the glutamine transporter, with special attention given to LAT1 and ASCT2. It also discusses innovative approaches in drug design aimed at these transporters.
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StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides.
Wang, D, Jin, J, Li, Z, Wang, Y, Fan, M, Liang, S, Su, R, Wei, L
Bioinformatics (Oxford, England). 2024;(2)
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Abstract
MOTIVATION Diabetes is a chronic metabolic disorder that has been a major cause of blindness, kidney failure, heart attacks, stroke, and lower limb amputation across the world. To alleviate the impact of diabetes, researchers have developed the next generation of anti-diabetic drugs, known as dipeptidyl peptidase IV inhibitory peptides (DPP-IV-IPs). However, the discovery of these promising drugs has been restricted due to the lack of effective peptide-mining tools. RESULTS Here, we presented StructuralDPPIV, a deep learning model designed for DPP-IV-IP identification, which takes advantage of both molecular graph features in amino acid and sequence information. Experimental results on the independent test dataset and two wet experiment datasets show that our model outperforms the other state-of-art methods. Moreover, to better study what StructuralDPPIV learns, we used CAM technology and perturbation experiment to analyze our model, which yielded interpretable insights into the reasoning behind prediction results. AVAILABILITY AND IMPLEMENTATION The project code is available at https://github.com/WeiLab-BioChem/Structural-DPP-IV.
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Targeting gut microbial nitrogen recycling and cellular uptake of ammonium to improve bortezomib resistance in multiple myeloma.
Zhu, Y, Jian, X, Chen, S, An, G, Jiang, D, Yang, Q, Zhang, J, Hu, J, Qiu, Y, Feng, X, et al
Cell metabolism. 2024;(1):159-175.e8
Abstract
The gut microbiome has been found to play a crucial role in the treatment of multiple myeloma (MM), which is still considered incurable due to drug resistance. In previous studies, we demonstrated that intestinal nitrogen-recycling bacteria are enriched in patients with MM. However, their role in MM relapse remains unclear. This study highlights the specific enrichment of Citrobacter freundii (C. freundii) in patients with relapsed MM. Through fecal microbial transplantation experiments, we demonstrate that C. freundii plays a critical role in inducing drug resistance in MM by increasing levels of circulating ammonium. The ammonium enters MM cells through the transmembrane channel protein SLC12A2, promoting chromosomal instability and drug resistance by stabilizing the NEK2 protein. We show that furosemide sodium, a loop diuretic, downregulates SLC12A2, thereby inhibiting ammonium uptake by MM cells and improving progression-free survival and curative effect scores. These findings provide new therapeutic targets and strategies for the intervention of MM progression and drug resistance.
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Genetic variation in targets of lipid-lowering drugs and amyotrophic lateral sclerosis risk: a Mendelian randomization study.
Li, Z, Tian, M, Jia, H, Li, X, Liu, Q, Zhou, X, Li, R, Dong, H, Liu, Y
Amyotrophic lateral sclerosis & frontotemporal degeneration. 2024;(1-2):197-206
Abstract
BACKGROUND The use of lipid-lowering drugs is still highly controversial in patients with amyotrophic lateral sclerosis (ALS). We performed a drug-target Mendelian randomization (MR) analysis to investigate the effect of targeted lipid-lowering drugs on the risk of ALS. METHODS First, we evaluated the causal relationship between HMG-CoA (3-hydroxy-3-methylglutaryl coenzyme A) reductase (HMGCR) inhibitors-taking trait and ALS using a bidirectional two-sample MR study. Second, we investigated the causal relationship between lipid-lowering drugs and ALS through a drug-target MR approach. The summary data for HMGCR inhibitors-taking traits were extracted from a genome-wide association study (GWAS) of medication use and associated disease in the UK Biobank. The summary data for low-density lipoprotein cholesterol and apolipoprotein B (apoB) were extracted from a meta-analysis of GWAS in individuals of European ancestry in the UKB. The GWAS summary data of ALS were obtained from the Project MinE. RESULTS Our bidirectional two-sample MR showed that genetically determined increased HMGCR inhibitors-taking trait was an independent risk factor for ALS (odds ratio [OR] = 1.090, 95% confidence interval [CI] = 1.035-1.150, p = 0.001). The results of drug-target MR showed that the increased expression of the HMGCR gene in blood with the higher risk of ALS (OR = 1.21, 95% CI = 1.01-1.46; p = 0.042) through SMR method and the apoB level mediated by the APOB gene increased the risk of ALS (OR = 1.15; 95% CI =1.05-1.25; p = 0.001) through inverse-variance weighted MR method. CONCLUSION This present study provides genetic support for a positive causal effect of HMGCR inhibitors-taking trait and ALS. The reason for this may be due to the underlying disease condition behind the medication, rather than the medication itself. Our findings also suggested that HMGCR and apoB inhibitors may have potential protective effects on ALS.
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Effects of Chinese heart-healthy diet on blood lipids, glucose, and estimated 10-y cardiovascular disease risk among Chinese adults: results on secondary outcomes of a randomized controlled trial.
Li, Q, Feng, L, Sun, J, Zhu, H, Zeng, G, Gao, P, Yuan, J, Zhao, Y, Li, S, Lan, X, et al
The American journal of clinical nutrition. 2024;(2):333-343
Abstract
BACKGROUND Healthy diet is essential for cardiovascular disease risk management, but its effects among Chinese patients, whose diets differ from Western diets, remain largely unknown. METHODS In this multicenter, patient- and outcome assessor-blind, randomized controlled feeding trial, 265 Chinese adults with baseline systolic blood pressure 130 to 159 mmHg were randomly assigned into Chinese heart-healthy (CHH) diet or usual diet for a 28-d intervention after a 7-d run-in period on usual diet. Blood lipids and glucose were measured from overnight fasting blood samples before and after the intervention. Ten-year cardiovascular disease risk was estimated using models previously developed and validated in Chinese. The changes in secondary outcomes of serum total cholesterol (TC), blood glucose, and 10-y cardiovascular disease risk over the intervention period were compared between intervention groups, adjusting for center, among participants with baseline and follow-up blood samples available. Sensitivity analyses were done with further adjustment for baseline values and covariables; missing data imputed; and among per-protocol population. RESULTS Among 256 eligible participants (130 on CHH diet, 126 on control diet), 42% had hypercholesterolemia and 15% had diabetes at baseline. In the control group, TC and 10-y cardiovascular disease risk decreased after the intervention by 0.16 mmol/L and 0.91%, respectively, but blood glucose increased by 0.25 mmol/L. Compared with usual diet, the CHH diet lowered TC (-0.14 mmol/L, P = 0.017) and 10-y cardiovascular disease risk (-1.24%, P = 0.001) further. No effect on blood glucose was found. All sensitivity analyses confirmed the results on TC and 10-y cardiovascular disease risk, and analysis with multiple variables adjusted showed a borderline significant effect on blood glucose (-0.17 mmol/L, P = 0.051). The differences in intake of nutrients and food groups between intervention groups explained the results. CONCLUSIONS The CHH diet reduced TC and 10-y cardiovascular disease risk and was likely to reduce blood glucose among Chinese adults with mild hypertension. Further studies with longer terms are warranted. This trial was registered at clinicaltrials.gov as NCT03882645.
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Association of possible sarcopenia with all-cause mortality in patients with solid cancer: A nationwide multicenter cohort study.
Yin, L, Song, C, Cui, J, Lin, X, Li, N, Fan, Y, Zhang, L, Liu, J, Chong, F, Cong, M, et al
The journal of nutrition, health & aging. 2024;(1):100023
Abstract
OBJECTIVES The concept of possible sarcopenia (PS) was recently introduced to enable timely intervention in settings without the technologies required to make a full diagnosis of sarcopenia. This study aimed to investigate the association between PS and all-cause mortality in patients with solid cancer. DESIGN Retrospective observational study. SETTING AND PARTICIPANTS 13,736 patients with 16 types of solid cancer who were ≥18 years old. MEASUREMENTS The presence of both a low calf circumference (men <34 cm or women <33 cm) and low handgrip strength (men <28 kg or women <18 kg) was considered to indicate PS. Harrell's C-index was used to assess prognostic value and the association of PS with mortality was estimated by calculating multivariable-adjusted hazard ratios (HRs). RESULTS The study enrolled 7207 men and 6529 women (median age = 57.8 years). During a median follow-up of 43 months, 3150 deaths occurred. PS showed higher Harrell's C-index (0.549, 95%CI = [0.541, 0.557]) than the low calf circumference (0.541, 95%CI = [0.531, 0.551], P = 0.037) or low handgrip strength (0.542, 95%CI = [0.532, 0.552], P = 0.026). PS was associated with increased mortality risk in both univariate (HR = 1.587, 95%CI = [1.476, 1.708]) and multivariable-adjusted models (HR = 1.190, 95%CI = [1.094, 1.293]). Sensitivity analyses showed that the association of PS with mortality was robust in different covariate subgroups, which also held after excluding those patients who died within the first 3 months (HR = 1.162, 95%CI = [1.060, 1.273]), 6 months (HR = 1.150, 95%CI = [1.039, 1.274]) and 12 months (HR = 1.139, 95%CI = [1.002, 1.296]) after enrollment. CONCLUSION PS could independently and robustly predict all-cause mortality in patients with solid cancer. These findings imply the importance of including PS assessment in routine cancer care to provide significant prognostic information to help mitigate sarcopenia-related premature deaths.