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1.
Decoding the gene regulatory network of endosperm differentiation in maize.
Yuan, Y, Huo, Q, Zhang, Z, Wang, Q, Wang, J, Chang, S, Cai, P, Song, KM, Galbraith, DW, Zhang, W, et al
Nature communications. 2024;(1):34
Abstract
The persistent cereal endosperm constitutes the majority of the grain volume. Dissecting the gene regulatory network underlying cereal endosperm development will facilitate yield and quality improvement of cereal crops. Here, we use single-cell transcriptomics to analyze the developing maize (Zea mays) endosperm during cell differentiation. After obtaining transcriptomic data from 17,022 single cells, we identify 12 cell clusters corresponding to five endosperm cell types and revealing complex transcriptional heterogeneity. We delineate the temporal gene-expression pattern from 6 to 7 days after pollination. We profile the genomic DNA-binding sites of 161 transcription factors differentially expressed between cell clusters and constructed a gene regulatory network by combining the single-cell transcriptomic data with the direct DNA-binding profiles, identifying 181 regulons containing genes encoding transcription factors along with their high-confidence targets, Furthermore, we map the regulons to endosperm cell clusters, identify cell-cluster-specific essential regulators, and experimentally validated three predicted key regulators. This study provides a framework for understanding cereal endosperm development and function at single-cell resolution.
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Cost-Effectiveness of Salt Substitute and Salt Supply Restriction in Eldercare Facilities: The DECIDE-Salt Cluster Randomized Clinical Trial.
Lai, X, Yuan, Y, Wang, H, Zhang, R, Qiao, Q, Feng, X, Jin, A, Li, H, Li, J, Si, L, et al
JAMA network open. 2024;(2):e2355564
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Abstract
IMPORTANCE Salt substitution has been reported to be a cost-saving sodium reduction strategy that has not yet been replicated in different contexts. OBJECTIVE To estimate the cost-effectiveness of sodium reduction strategies within the DECIDE-Salt trial. DESIGN, SETTING, AND PARTICIPANTS The DECIDE-Salt trial cluster randomized in a 1:1:1:1 ratio 48 eldercare facilities in China into 4 groups for evaluation of 2 sodium reduction strategies for 2 years: 1 with both strategies, 2 with either strategy, and 1 with neither strategy. The trial was conducted from September 25, 2017, through October 24, 2020. INTERVENTIONS The 2 intervention strategies were replacing regular salt with salt substitute and progressively restricting salt supply to kitchens. MAIN OUTCOMES AND MEASURES The main outcomes included per-participant costs of intervention implementation and medical treatments for hypertension and major adverse cardiovascular events (MACEs) against mean reductions in systolic blood pressure, hypertension prevalence, MACE incidence, and mortality. The incremental cost-utility ratio was then assessed as the additional mean cost per quality-adjusted life-year gained. Analyses were conducted separately for each strategy, comparing groups assigned and not assigned the test strategy. Disease outcomes followed the intention-to-treat principle and adopted different models as appropriate. One-way and probabilistic sensitivity analyses were conducted to explore uncertainty, and data analyses were performed between August 13, 2022, and April 5, 2023. RESULTS A total of 1612 participants (1230 males [76.3%]) with a mean (SD) age of 71.0 (9.5) years were enrolled. Replacing regular salt with salt substitute reduced mean systolic blood pressure by 7.14 (95% CI, 3.79-10.48) mm Hg, hypertension prevalence by 5.09 (95% CI, 0.37-9.80) percentage points, and cumulative MACEs by 2.27 (95% CI, 0.09-4.45) percentage points. At the end of the 2-year intervention, the mean cost was $25.95 less for the salt substitute group than the regular salt group due to substantial savings in health care costs for MACEs (mean [SD], $72.88 [$9.11] vs $111.18 [$13.90], respectively). Sensitivity analysis showed robust cost savings. By contrast, the salt restriction strategy did not show significant results. If the salt substitution strategy were rolled out to all eldercare facilities in China, 48 101 MACEs and 107 857 hypertension cases were estimated to be averted and $54 982 278 saved in the first 2 years. CONCLUSIONS AND RELEVANCE The findings of this cluster randomized clinical trial indicate that salt substitution may be a cost-saving strategy for hypertension control and cardiovascular disease prevention for residents of eldercare facilities in China. The substantial health benefit savings in preventing MACEs and moderate operating costs offer strong evidence to support the Chinese government and other countries in planning or implementing sodium intake reduction and salt substitute campaigns. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT03290716.
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Clinical metabolomics characteristics of diabetic kidney disease: A meta-analysis of 1875 cases with diabetic kidney disease and 4503 controls.
Yuan, Y, Huang, L, Yu, L, Yan, X, Chen, S, Bi, C, He, J, Zhao, Y, Yang, L, Ning, L, et al
Diabetes/metabolism research and reviews. 2024;(3):e3789
Abstract
AIMS: Diabetic Kidney Disease (DKD), one of the major complications of diabetes, is also a major cause of end-stage renal disease. Metabolomics can provide a unique metabolic profile of the disease and thus predict or diagnose the development of the disease. Therefore, this study summarises a more comprehensive set of clinical biomarkers related to DKD to identify functional metabolites significantly associated with the development of DKD and reveal their driving mechanisms for DKD. MATERIALS AND METHODS We searched PubMed, Embase, the Cochrane Library and Web of Science databases through October 2022. A meta-analysis was conducted on untargeted or targeted metabolomics research data based on the strategy of standardized mean differences and the process of ratio of means as the effect size, respectively. We compared the changes in metabolite levels between the DKD patients and the controls and explored the source of heterogeneity through subgroup analyses, sensitivity analysis and meta-regression analysis. RESULTS The 34 clinical-based metabolomics studies clarified the differential metabolites between DKD and controls, containing 4503 control subjects and 1875 patients with DKD. The results showed that a total of 60 common differential metabolites were found in both meta-analyses, of which 5 metabolites (p < 0.05) were identified as essential metabolites. Compared with the control group, metabolites glycine, aconitic acid, glycolic acid and uracil decreased significantly in DKD patients; cysteine was significantly higher. This indicates that amino acid metabolism, lipid metabolism and pyrimidine metabolism in DKD patients are disordered. CONCLUSIONS We have identified 5 metabolites and metabolic pathways related to DKD which can serve as biomarkers or targets for disease prevention and drug therapy.
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Copper and Copper Complexes in Tumor Therapy.
Wang, Y, Tang, T, Yuan, Y, Li, N, Wang, X, Guan, J
ChemMedChem. 2024;:e202400060
Abstract
Copper (Cu), a crucial trace element in physiological processes, has garnered significant interest for its involvement in cancer progression and potential therapeutic applications. The regulation of cellular copper levels is essential for maintaining copper homeostasis, as imbalances can lead to toxicity and cell death. The development of drugs that target copper homeostasis has emerged as a promising strategy for anticancer treatment, with a particular focus on copper chelators, copper ionophores, and novel copper complexes. Recent research has also investigated the potential of copper complexes in cancer therapy.
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Preoperative prognostic nutritional index value as a predictive factor for postoperative delirium in older adult patients with hip fractures: a secondary analysis.
Mi, X, Jia, Y, Song, Y, Liu, K, Liu, T, Han, D, Yang, N, Wang, G, Guo, X, Yuan, Y, et al
BMC geriatrics. 2024;(1):21
Abstract
BACKGROUND Malnutrition is a common geriatric syndrome and can be targeted preoperatively to decrease the risk of postoperative delirium (POD) in older adult patients. To analyze the value of the prognostic nutritional index (PNI) to predict the incidence of POD in older adult patients with hip fractures. METHODS This was a prospective, observational, cohort study of older adult patients with hip fractures. Preoperative PNI was calculated as 10 × serum albumin (g/dL) + 0.005 × total lymphocyte count (/μL) using preoperative laboratory results. Patients were divided into POD and non-POD groups using the Confusion Assessment Method (CAM). The risk factors associated with POD as well as the relationship between PNI values and the incidence of POD were analyzed using univariate and multivariate logistic regression analyses. The predictive value of PNI for POD was assessed using receiver operating characteristic curve analysis. RESULTS In this cohort of 369 patients who underwent hip fracture surgery, 67 patients (18.2%) were diagnosed with POD by the CAM results. Low PNI increased the risk of POD (odds ratio (OR) = 0.928, 95% confidence interval (CI): 0.864-0.997). General anesthesia (OR = 2.307, 95% CI: 1.279-4.162) and Mini-Mental State Examination (MMSE) score (OR = 0.956, 95% CI: 0.920-0.994) were also identified as risk factors for POD. Receiver operating characteristic curve analysis suggested that PNI combined with the anesthetic method and MMSE score may be used as a potential predictive indicator of POD after hip fracture surgery. CONCLUSION Preoperative PNI value is related to POD in older adult patients with hip fractures. TRIAL REGISTRATION This secondary analysis study was approved by the Peking University Third Hospital Medical Science Research Ethics Committee (approval No. M2022578) and registered in the Chinese Clinical Trial Registry (ChiCTR2300070569).
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Human milk sphingomyelin: Function, metabolism, composition and mimicking.
Yuan, Y, Zhao, J, Liu, Q, Liu, Y, Liu, Y, Tian, X, Qiao, W, Zhao, Y, Liu, Y, Chen, L
Food chemistry. 2024;:138991
Abstract
Human milk, which contains various nutrients, is the "gold standard" for infant nutrition. Healthy human milk meets all the nutritional needs of early infant development. Polar lipids mainly exist in the milk fat globule membrane, accounting for approximately 1-2% of human milk lipids; sphingomyelin (SM) accounts for approximately 21-24% of polar lipids. SM plays an important role in promoting the development of the brain and nervous system, regulating intestinal flora, and improving skin barriers. Though SM could be synthesized de novo, SM nutrition from dietary is also important for infants. The content and composition of SM in human milk has been reported, however, the molecular mechanisms of nutritional functions of SM for infants required further research. This review summarizes the functional mechanisms, metabolic pathways, and compositional, influencing factors, and mimicking of SM in human milk, and highlights the challenges of improving maternal and infant early/long-term nutrition.
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Identification of formononetin as the active compound of CR-SR in hepatocellular carcinoma treatment: An integrated approach combining network pharmacology and weighted gene co-expression networks.
Li, C, Xie, Y, Hu, S, Yu, H, Xu, Y, Shen, H, Yuan, Y, Gu, L, Pu, B
Chemical biology & drug design. 2024;(1):e14363
Abstract
Hepatocellular carcinoma (HCC) is a life-threatening disease for which there is no cure. Traditional Chinese medicine is a treasure trove of Medicinals that has been used for thousands of years. In China, the traditional herb pair, Curcumae Rhizoma and Sparganii Rhizoma (CR-SR) represent a classic herbal combination used for the treatment of HCC. However, the drug targets and pharmacological mechanism of action of CR-SR in the treatment of HCC are unclear. To address this, we screened the active components and drug targets of CR-SR from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database and a high-throughput experiment- and reference-guided database of traditional Chinese medicines (HERB database). Combined with the weighted co-expression network analysis of dataset GSE76427, we constructed an active component-target-disease regulatory network. It was found that CR-SR's active components for HCC treatment included trans-gondoic acid, beta-sitosterol, stigmasterol, hederagenin, and formononetin. These compounds specifically targeted the genes Estrogen Receptor 1 (ESR1), Cyclin A2 (CCNA2), Checkpoint Kinase 1 (CHEK1), and Nuclear Receptor Coactivator 2 (NCOA2). ESR1, CCNA2, and CHEK1 genes showed significant differences in survival prognosis, expression levels, and statistical significance during the pathological stage. Moreover, their high affinity for formononetin was determined through molecular docking analysis. Cell assays and high-throughput sequencing were performed to reveal that the inhibitory effect of formononetin on HepG2 cell proliferation was related to hepatocyte metabolism and cell cycle regulation-related pathways. This study provides insights into potential HCC treatments.
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The clinical efficacy and safety of berberine in the treatment of non-alcoholic fatty liver disease: a meta-analysis and systematic review.
Nie, Q, Li, M, Huang, C, Yuan, Y, Liang, Q, Ma, X, Qiu, T, Li, J
Journal of translational medicine. 2024;(1):225
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is becoming increasingly prevalent worldwide, emerging as a significant health issue on a global scale. Berberine exhibits potential for treating NAFLD, but clinical evidence remains inconclusive. This meta-analysis was conducted to assess the efficacy and safety of berberine for treating NAFLD. METHODS This study was registered with PROSPERO (No. CRD42023462338). Identification of randomized controlled trials (RCTs) involved searching 6 databases covering the period from their initiation to 9 September 2023. The primary outcomes comprised liver function markers such as glutamyl transpeptidase (GGT), alanine transaminase (ALT), aspartate transaminase (AST), lipid indices including total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL-C) and high-density lipoprotein cholesterol (HDL-C), homeostasis model assessment for insulin resistance (HOMA-IR) and body mass index (BMI). Review Manager 5.4 and STATA 17.0 were applied for analysis. RESULTS Among 10 RCTs involving 811 patients, berberine demonstrated significant reductions in various parameters: ALT (standardized mean difference (SMD) = - 0.72), 95% confidence interval (Cl) [- 1.01, - 0.44], P < 0.00001), AST (SMD = - 0.79, 95% CI [- 1.17, - 0.40], P < 0.0001), GGT (SMD = - 0.62, 95% CI [- 0.95, - 0.29], P = 0.0002), TG (SMD = - 0.59, 95% CI [- 0.86, - 0.31], P < 0.0001), TC(SMD = - 0.74, 95% CI [- 1.00, - 0.49], P < 0.00001), LDL-C (SMD = - 0.53, 95% CI [- 0.88, - 0.18], P = 0.003), HDL-C (SMD = - 0.51, 95% CI [- 0.12, 1.15], P = 0.11), HOMA-IR (SMD = - 1.56, 95% CI [- 2.54, - 0.58], P = 0.002), and BMI (SMD = - 0.58, 95% CI [- 0.77, - 0.38], P < 0.00001). Importantly, Berberine exhibited a favorable safety profile, with only mild gastrointestinal adverse events reported. CONCLUSION This meta-analysis demonstrates berberine's efficacy in improving liver enzymes, lipid profile, and insulin sensitivity in NAFLD patients. These results indicate that berberine shows promise as an adjunct therapy for NAFLD. Trial registration The protocol was registered with PROSPERO (No. CRD42023462338). Registered on September 27, 2023.
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Magnetic two-dimensional nanocomposites for multimodal antitumor therapy: a recent review.
Yuan, Y, Chen, B, Song, L, An, X, Zhang, Q, Lu, H, Li, CM, Guo, C
Journal of materials chemistry. B. 2024;(6):1404-1428
Abstract
Magnetic two-dimensional nanocomposites (M2D NCs) that synergistically combine magnetic nanomedicine and 2D nanomaterials have emerged in multimodal antitumor therapy, attracting great interest in materials science and biomedical engineering. This review provides a summary of the recent advances of M2D NCs and their multimodal antitumor applications. We first introduce the design and fabrication of M2D NCs, followed by discussing new types of M2D NCs that have been recently reported. Then, a detailed analysis and discussions about the different types of M2D NCs are presented based on the structural categories of 2D NMs, including 2D graphene, transition metal dichalcogenides (TMDs), transition metal carbides/nitrides/carbonitrides (MXenes), black phosphorus (BP), layered double hydroxides (LDHs), metal organic frameworks (MOFs), covalent organic frameworks (COFs) and other 2D nanomaterials. In particular, we focus on the synthesis strategies, magnetic or optical responsive performance, and the versatile antitumor applications, which include magnetic hyperthermia therapy (MHT), photothermal therapy (PTT), photodynamic therapy (PDT), drug delivery, immunotherapy and multimodal imaging. We conclude the review by proposing future developments with an emphasis on the mass production and biodegradation mechanism of the M2D NCs. This work is expected to provide a comprehensive overview to researchers and engineers who are interested in such a research field and promote the clinical translation of M2D NCs in practical applications.
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The Role of Methionine Restriction in Gastric Cancer: A Summary of Mechanisms and a Discussion on Tumor Heterogeneity.
Zou, Y, Yuan, Y, Zhou, Q, Yue, Z, Liu, J, Fan, L, Xu, H, Xin, L
Biomolecules. 2024;(2)
Abstract
Gastric cancer is ranked as the fifth most prevalent cancer globally and has long been a topic of passionate discussion among numerous individuals. However, the incidence of gastric cancer in society has not decreased, but instead has shown a gradual increase in recent years. For more than a decade, the treatment effect of gastric cancer has not been significantly improved. This is attributed to the heterogeneity of cancer, which makes popular targeted therapies ineffective. Methionine is an essential amino acid, and many studies have shown that it is involved in the development of gastric cancer. Our study aimed to review the literature on methionine and gastric cancer, describing its mechanism of action to show that tumor heterogeneity in gastric cancer does not hinder the effectiveness of methionine-restricted therapies. This research also aimed to provide insight into the inhibition of gastric cancer through metabolic reprogramming with methionine-restricted therapies, thereby demonstrating their potential as adjuvant treatments for gastric cancer.