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1.
Angew Chem Int Ed Engl ; : e202406262, 2024 May 24.
Article En | MEDLINE | ID: mdl-38787604

Single-atom catalysts (SACs) have recently become highly attractive for selective hydrogenation reactions owing to their remarkably high selectivity. However, compared to their nanoparticle counterparts, atomically dispersed metal atoms in SACs often show inferior activity and are prone to aggregate under reaction conditions. Here, by theoretical calculations, we show that tuning the local electronic structures of metal anchor sites on g-C3N4 by doping B atoms (BCN) with relatively lower electronegativity allows achieving zero-valence Pd SACs with reinforced metal-support orbital hybridizations for high stability and upshifted Pd 4d orbitals for high activity in H2 activation. The precise synthesis of Pd SACs on BCN supports with varied B contents substantiated the theoretical prediction. A zero-valence Pd1/BCN SAC was achieved on a BCN support with a relatively low B content. It exhibited much higher stability in a H2 reducing environment, and more strikingly, a hydrogenation activity, approximately 10 and 34 times greater than those high-valence Pd1/g-C3N4 and Pd1/BCN with a high B content, respectively.

2.
Small ; : e2400410, 2024 May 09.
Article En | MEDLINE | ID: mdl-38721986

The construction of defective sites is one of the effective strategies to create high-activity Metal-Organic frameworks (MOFs) catalysts. However, traditional synthesis methods usually suffer from cumbersome synthesis steps and disordered defect structures. Herein, a cluster-cluster co-nucleation (CCCN) strategy is presented that involves the in situ introduction of size-matched functional polyoxometalates (H6P2W18O62, {P2W18}) to intervene the nucleation process of cluster-based MOFs (UiO-66), achieving one-step inducement of exposed defective sites without redundant post-processing. POM-induced UiO-66 ({P2W18}-0.1@UiO-66) exhibits a classical reo topology for well-defined cluster defects. Moreover, the defective sites and the interaction between POM and skeletal cluster nodes are directly observed by Integrated Differential Phase Contrast in Scanning Transmission Electron Microscopy (iDPC-STEM). Owing to the molecular-level proximity between defective sites and POM in the same nano-reaction space, {P2W18}-0.1@UiO-66 exhibits efficient tandem catalysis in the preparation of γ-valerolactone (γ-GVL) from laevulinic acid (LA) by the combination of Lewis and Brønsted acids with 11 times higher performance than defective UiO-66 formed by conventional coordination modulation strategy. The CCCN strategy is applicable to different POM and has the potential to be extended to other cluster-based MOFs, which will pave a new way for the construction of functional MOFs with multi-centered synergistic catalysis.

3.
Clin Cardiol ; 47(6): e24276, 2024 Jun.
Article En | MEDLINE | ID: mdl-38812437

BACKGROUND: The purpose of this study was to explore the association between triglycerides (TGs) and the risk of atrial fibrillation (AF) recurrence. METHODS AND RESULTS: Included were adult patients with AF who underwent radiofrequency catheter ablation in the Affiliated Changzhou Second People's Hospital of Nanjing Medical University. The enrolled patients were divided into the AF recurrence group and the sinus rhythm (SR) maintenance group. The univariate Cox regression analysis and Kaplan-Meier survival curve were performed estimate the association between TG and the risk of AF recurrence. Of the 402 patients, 79 (19.7%) experienced recurrence of AF after ablation. The TG level was significantly higher in the AF recurrence group than in the SR-maintaining group. Patients were grouped by quartile of TG levels, with Quartile 1 and Quartile 2 defined as the low concentration group, Quartile 3 as the moderate concentration group, and Quartile 4 as the high concentration group. Multivariate Cox regression analysis showed that the moderate concentration group (p = .02, hazard ratio [HR]: 2.331, 95% confidence interval [CI]: 1.141-4.762) and high concentration group (p = .007, HR: 2.873, 95% CI: 1.332-6.199) were associated with an increased risk of AF recurrence compared with the low concentration group. The median follow-up was 1.17 years, it is indicated that a higher risk of recurrent AF was observed in the moderate concentration and high concentration group (log-rank: χ2 = 7.540, p = .023). CONCLUSION: Our data suggest that an elevated TG level measured before catheter ablation is associated with an increased risk of AF recurrence.


Atrial Fibrillation , Catheter Ablation , Recurrence , Triglycerides , Humans , Atrial Fibrillation/blood , Atrial Fibrillation/surgery , Male , Female , Catheter Ablation/adverse effects , Retrospective Studies , Triglycerides/blood , Middle Aged , Risk Factors , Biomarkers/blood , China/epidemiology , Time Factors , Treatment Outcome , Risk Assessment/methods , Aged , Follow-Up Studies
4.
Article En | MEDLINE | ID: mdl-38812479

Purpose: To evaluate the efficacy and safety of a pyrotinib-based therapy for human epidermal growth factor receptor 2 (HER2)-positive metastatic breast cancer (MBC) in the real world. Methods: Clinical data of 218 patients with HER2-positive MBC who received a pyrotinib-based therapy from January 2020 to March 2023 at the First Affiliated Hospital of Zhengzhou University were retrospectively analyzed. Results: Finally, 195 patients were included in the efficacy cohort. The median progression-free survival (PFS) in the total population is 12.4 months (95% CI, 9.8-15.0 months). More than half of the patients in the efficacy cohort received pyrotinib mono-targeted therapy (103 cases, 52.8%). Among the remaining patients, 74 (37.9%) patients chose a combined trastuzumab-targeted therapy and 17 (8.7%) chose to combine inetetamab. Median PFS in the pyrotinib group vs pyrotinib plus trastuzumab group was 10.5 months vs 20.1 months (P<0.001). The median PFS of primary trastuzumab resistance population reached to 20.1 months in pyrotinib plus trastuzumab group. Double-targets' advantage was also observed in the brain metastases subgroup (17.9 months vs 10.0 months, P=0.386). The patients who received pyrotinib plus inetetamab as second and higher-line treatment reached a median PFS of 7.9 months (95% CI, 4.0-11.8 months). Forty-one (19.8%) of 207 patients included in the safety cohort experienced grade 3 or higher diarrhea, the most common adverse event in safety analysis, and no adverse event-related deaths. Conclusion: The combination of pyrotinib and trastuzumab demonstrated promising efficacy in the treatment of HER2-positive metastatic breast cancer, including those who had primary resistance to trastuzumab and brain metastases. Pyrotinib plus trastuzumab is expected to be a potent option in the first-line. Additionally, the concurrent administration of pyrotinib and inetetamab could be an alternative to consider in the second and higher-line treatment for metastatic breast cancer. The adverse reactions of pyrotinib were tolerable in general.

5.
BMC Cardiovasc Disord ; 24(1): 216, 2024 Apr 20.
Article En | MEDLINE | ID: mdl-38643093

BACKGROUND: Acute kidney injury (AKI) in patients with acute myocardial infarction (AMI) often indicates a poor prognosis. OBJECTIVE: This study aimed to investigate the association between the TyG index and the risk of AKI in patients with AMI. METHODS: Data were taken from the Medical Information Mart for Intensive Care (MIMIC) database. A 1:3 propensity score (PS) was set to match patients in the AKI and non-AKI groups. Multivariate logistic regression analysis, restricted cubic spline (RCS) regression and subgroup analysis were performed to assess the association between TyG index and AKI. RESULTS: Totally, 1831 AMI patients were included, of which 302 (15.6%) had AKI. The TyG level was higher in AKI patients than in non-AKI patients (9.30 ± 0.71 mg/mL vs. 9.03 ± 0.73 mg/mL, P < 0.001). Compared to the lowest quartile of TyG levels, quartiles 3 or 4 had a higher risk of AKI, respectively (Odds Ratiomodel 4 = 2.139, 95% Confidence Interval: 1.382-3.310, for quartile 4 vs. quartile 1, Ptrend < 0.001). The risk of AKI increased by 34.4% when the TyG level increased by 1 S.D. (OR: 1.344, 95% CI: 1.150-1.570, P < 0.001). The TyG level was non-linearly associated with the risk of AKI in the population within a specified range. After 1:3 propensity score matching, the results were similar and the TyG level remained a risk factor for AKI in patients with AMI. CONCLUSION: High levels of TyG increase the risk of AKI in AMI patients. The TyG level is a predictor of AKI risk in AMI patients, and can be used for clinical management.


Acute Kidney Injury , Myocardial Infarction , Humans , Propensity Score , Acute Kidney Injury/diagnosis , Acute Kidney Injury/epidemiology , Acute Kidney Injury/etiology , Glucose , Myocardial Infarction/complications , Myocardial Infarction/diagnosis , Risk Factors , Triglycerides , Blood Glucose
6.
Int J Nanomedicine ; 19: 3295-3314, 2024.
Article En | MEDLINE | ID: mdl-38606373

Background: Cardiac repair remains a thorny issue for survivors of acute myocardial infarction (AMI), due to the regenerative inertia of myocardial cells. Cell-free therapies, such as exosome transplantation, have become a potential strategy for myocardial injury. The aim of this study was to investigate the role of engineered exosomes in overexpressing Growth Differentiation Factor-15 (GDF-15) (GDF15-EVs) after myocardial injury, and their molecular mechanisms in cardiac repair. Methods: H9C2 cells were transfected with GDF-15 lentivirus or negative control. The exosomes secreted from H9C2 cells were collected and identified. The cellular apoptosis and autophagy of H2O2-injured H9C2 cells were assessed by Western blotting, TUNEL assay, electron microscopy, CCK-8 and caspase 3/7 assay. A rat model of AMI was constructed by ligating the left anterior descending artery. The anti-apoptotic, pro-angiogenic effects of GDF15-EVs treatment, as well as ensuing functional and histological recovery were evaluated. Then, mRNA sequencing was performed to identify the differentially expressed mRNAs after GDF15-EVs treatment. Results: GDF15-EVs inhibited apoptosis and promoted autophagy in H2O2 injured H9C2 cells. GDF15-EVs effectively decreased the infarct area and enhanced the cardiac function in rats with AMI. Moreover, GDF15-EVs hindered inflammatory cell infiltration, inhibited cell apoptosis, and promoted cardiac angiogenesis in rats with AMI. RNA sequence showed that telomerase reverse transcriptase (TERT) mRNA was upregulated in GDF15-EVs-treated H9C2 cells. AMPK signaling was activated after GDF15-EVs. Silencing TERT impaired the protective effects of GDF15-EVs on H2O2-injured H9C2 cells. Conclusion: GDF15-EVs could fulfil their protective effects against myocardial injury by upregulating the expression of TERT and activating the AMPK signaling pathway. GDF15-EVs might be exploited to design new therapies for AMI.


Exosomes , Growth Differentiation Factor 15 , Myocardial Infarction , Animals , Rats , AMP-Activated Protein Kinases/metabolism , AMP-Activated Protein Kinases/pharmacology , Apoptosis , Exosomes/metabolism , Growth Differentiation Factor 15/genetics , Growth Differentiation Factor 15/metabolism , Growth Differentiation Factor 15/pharmacology , Hydrogen Peroxide/pharmacology , Hydrogen Peroxide/metabolism , Myocardial Infarction/genetics , Myocardial Infarction/therapy , Myocardial Infarction/pathology , Myocytes, Cardiac , RNA, Messenger/metabolism
7.
Clin Interv Aging ; 19: 503-515, 2024.
Article En | MEDLINE | ID: mdl-38525316

Objective: This study aimed to explore the association of preoperative neutrophil percentage (NEUT%) with the risk of acute kidney injury (AKI) in patients with acute myocardial infarction (AMI) having undergone coronary interventional therapy. Methods: A single-center, retrospective and observational study was conducted. From December 2012 to June 2021, patients with AMI were enrolled and divided into AKI group and non-AKI group. The NEUT% in the two groups was compared. The association between NEUT% with the risk of post-AMI AKI was analyzed by univariate and multivariable logistic regression. Kaplan-Meier survival curve was drawn to evaluate the prognostic ability of NEUT% for short-term all-cause death following AMI. Results: A total of 3001 consecutive patients were enrolled with an average age of 64.38 years. AKI occurred in 327 (10.9%) patients. The NEUT% was higher in the AKI group than in the non-AKI group ([76.65±11.43]% versus [73.22±11.83]%, P<0.001). NEUT% was also identified as an independent risk factor for AKI in AMI patients after adjustment (OR=1.021, 95% CI: 1.010-1.033, P < 0.001). Compared with those at the lowest quartile of NEUT%, the patients at quartiles 2-4 had a higher risk of AKI (P for trend = 0.003). The odds of AKI increased by 29.0% as NEUT% increased by 1 standard deviation (OR=1.290, 95% CI: 1.087-1.531, P = 0.004). After a median of 35 days follow-up, 93 patients died. Patients with a higher NEUT% presented a higher risk of all-cause death after AMI (Log rank: χ2 =24.753, P<0.001). Conclusion: In AMI patients, the peripheral blood NEUT% was positively associated with the odds of AKI and short-term all-cause mortality. NEUT% may provide physicians with more information about disease development and prognosis.


Acute Kidney Injury , Myocardial Infarction , Humans , Aged , Neutrophils , Retrospective Studies , Prognosis , Myocardial Infarction/complications , Biomarkers , Risk Factors , Acute Kidney Injury/epidemiology , Acute Kidney Injury/etiology
8.
Angew Chem Int Ed Engl ; 63(20): e202401568, 2024 May 13.
Article En | MEDLINE | ID: mdl-38506189

Maintaining high conversion under the premise of high oxygenates selectivity in syngas conversion is important but a formidable challenge in Rh catalysis. Monometallic Rh catalysts provide poor oxygenate conversion efficiency, and efforts have been focused on constructing adjacent polymetallic sites; however, the one-pass yields of C2+ oxygenates over the reported Rh-based catalysts were mostly <20 %. In this study, we constructed a monometallic Rh catalyst encapsulated in UiO-67 (Rh/UiO-67) with enhanced proximity to dual-site Rh1,2-Rhn ensembles. Unexpectedly, this catalyst exhibited high efficacy for oxygenate synthesis from syngas, giving a high oxygenate selectivity of 72.0 % with a remarkable CO conversion of 50.4 %, and the one-pass yield of C2+ oxygenates exceeded 25 %. The state-of-the-art characterizations further revealed the spontaneous formation of an ensemble of Rh single atoms/dimers (Rh1,2) in the proximity of ultrasmall Rh clusters (Rhn) confined within the nanocavity of UiO-67, providing adjacent Rh+-Rh0 dual sites dynamically during the reaction that promote the relay of the undissociated CHO species to the CHx species. Thus, our results open a new route for designing highly efficient Rh catalysts for the conversion of syngas to oxygenates by precisely tuning the ensemble and proximity of the dual active sites in a confined space.

9.
Eur J Clin Pharmacol ; 80(4): 613-620, 2024 Apr.
Article En | MEDLINE | ID: mdl-38319348

OBJECTIVE: Sodium-glucose cotransporter 2 (SGLT2) inhibitors have well-documented effects in reducing hospitalization or cardiovascular mortality, while the association of SGLT2 inhibitor dapagliflozin (DAPA) and the risk of acute kidney injury (AKI) in acute myocardial infarction (AMI) patients has not been comprehensively investigated. Therefore, we aimed to assess the association between DAPA and AKI risk in AMI patients after percutaneous coronary intervention (PCI) therapy. METHODS: Using the Changzhou Acute Myocardial Infarction Registry database, we retrospectively included AMI patients from January 2017 to August 2021 and analyzed the risk of AKI and all-cause mortality after PCI therapy. The patients were divided into two groups according to the use of DAPA (DAPA group and Ctrl group). Patients in the DAPA group started to use DAPA after admission and continued its use during hospitalization and follow-up period. Baseline characteristics were balanced between the two groups with a propensity score matching (PSM) analysis. The outcome was AKI within 7 days after PCI and all-cause mortality during a follow-up of 2 years. Univariate and multivariate logistic regression analyses were used to assess the association between DAPA and AKI risk. RESULTS: A total of 1839 AMI patients undergoing PCI were enrolled. DAPA was used in 278 (15.1%) patients. Postoperative AKI occurred in 351 (19.1%) cases. A 1:1 PSM analysis was used to reduce confounding factors. The multivariate stepwise regression analysis showed that DAPA (odds ratio, OR 0.66; 95% confidence interval, CI 0.44-0.97; P = 0.036) was an independent protective factor in the entire cohort. After matching, the use of DAPA in AMI patients was independently associated with a decline of AKI risk (OR 0.32; 95% CI, 0.19-0.53; P < 0.001) after hospital admission. Meanwhile, there were significant differences in mortality between the DAPA group and Ctrl group (2.5% vs. 7.6%, P = 0.012). CONCLUSION: SGLT2 inhibitor DAPA was associated with lower risks of incident AKI and all-cause mortality in AMI patients after PCI therapy.


Acute Kidney Injury , Benzhydryl Compounds , Glucosides , Myocardial Infarction , Percutaneous Coronary Intervention , Sodium-Glucose Transporter 2 Inhibitors , Humans , Percutaneous Coronary Intervention/adverse effects , Retrospective Studies , Risk Factors
10.
Biomed Pharmacother ; 172: 116224, 2024 Mar.
Article En | MEDLINE | ID: mdl-38308970

OBJECTIVE: Extracellular vesicles (EVs) have garnered considerable attention among researchers as candidates for natural drug delivery systems. This study aimed to investigate whether extracellular vesicle mediated targeting delivery of growth differentiation factor-15 (GDF15) improves myocardial repair by reprogramming macrophages post myocardial injury. METHODS: EVs were isolated from macrophages transfected with GDF15 (EXO-GDF15) and control macrophages (EXO-NC). In vitro and vivo experiments, we compared their reprogram ability of macrophages and regeneration activity. Furthermore, proteomic analysis were employed to determine the specific mechanism by which GDF15 repairs the myocardium. RESULTS: Compared with EXO-NC, EXO-GDF15 significantly regulated macrophage phenotypic shift, inhibited cardiomyocyte apoptosis, and enhanced endothelial cell angiogenesis. Moreover, EXO-GDF15 also significantly regulated macrophage heterogeneity and inflammatory cytokines, reduced fibrotic area, and enhanced cardiac function in infarcted rats. Proteomic analysis revealed a decrease in fatty acid-binding protein 4 (FABP4) protein expression following treatment with EXO-GDF15. Mechanistically, the reprogramming of macrophages by EXO-GDF15 is accomplished through the activation of Smad2/3 phosphorylation, which subsequently inhibits the production of FABP4. CONCLUSIONS: Extracellular vesicle mediated targeting delivery of growth differentiation factor-15 improves myocardial repair by reprogramming macrophages post myocardial injury via down-regulating the expression of FABP4. EXO-GDF15 may serve as a promising approach of immunotherapy.


Exosomes , Extracellular Vesicles , Heart Injuries , Myocardial Infarction , Rats , Animals , Myocardial Infarction/metabolism , Proteomics , Exosomes/metabolism , Myocardium/metabolism , Extracellular Vesicles/metabolism , Macrophages/metabolism , Heart Injuries/metabolism
11.
BMC Cardiovasc Disord ; 24(1): 16, 2024 01 03.
Article En | MEDLINE | ID: mdl-38172656

BACKGROUND: The purpose of this study was to develop a Nomogram model to identify the risk of all-cause mortality during hospitalization in patients with heart failure (HF). METHODS: HF patients who had been registered in the Medical Information Mart for Intensive Care (MIMIC) III and IV databases were included. The primary outcome was the occurrence of all-cause mortality during hospitalization. Two Logistic Regression models (LR1 and LR2) were developed to predict in-hospital death for HF patients from the MIMIC-IV database. The MIMIC-III database were used for model validation. The area under the receiver operating characteristic curve (AUC) was used to compare the discrimination of each model. Calibration curve was used to assess the fit of each developed models. Decision curve analysis (DCA) was used to estimate the net benefit of the predictive model. RESULTS: A total of 16,908 HF patients were finally enrolled through screening, of whom 2,283 (13.5%) presented with in-hospital death. Totally, 48 variables were included and analyzed in the univariate and multifactorial regression analysis. The AUCs for the LR1 and LR2 models in the test cohort were 0.751 (95% CI: 0.735∼0.767) and 0.766 (95% CI: 0.751-0.781), respectively. Both LR models performed well in the calibration curve and DCA process. Nomogram and online risk assessment system were used as visualization of predictive models. CONCLUSION: A new risk prediction tool and an online risk assessment system were developed to predict mortality in HF patients, which performed well and might be used to guide clinical practice.


Heart Failure , Nomograms , Humans , Hospital Mortality , Heart Failure/diagnosis , Heart Failure/therapy , Area Under Curve , Critical Care , Retrospective Studies
12.
Nature ; 625(7993): 148-156, 2024 Jan.
Article En | MEDLINE | ID: mdl-37993710

The continuing emergence of SARS-CoV-2 variants highlights the need to update COVID-19 vaccine compositions. However, immune imprinting induced by vaccination based on the ancestral (hereafter referred to as WT) strain would compromise the antibody response to Omicron-based boosters1-5. Vaccination strategies to counter immune imprinting are critically needed. Here we investigated the degree and dynamics of immune imprinting in mouse models and human cohorts, especially focusing on the role of repeated Omicron stimulation. In mice, the efficacy of single Omicron boosting is heavily limited when using variants that are antigenically distinct from WT-such as the XBB variant-and this concerning situation could be mitigated by a second Omicron booster. Similarly, in humans, repeated Omicron infections could alleviate WT vaccination-induced immune imprinting and generate broad neutralization responses in both plasma and nasal mucosa. Notably, deep mutational scanning-based epitope characterization of 781 receptor-binding domain (RBD)-targeting monoclonal antibodies isolated from repeated Omicron infection revealed that double Omicron exposure could induce a large proportion of matured Omicron-specific antibodies that have distinct RBD epitopes to WT-induced antibodies. Consequently, immune imprinting was largely mitigated, and the bias towards non-neutralizing epitopes observed in single Omicron exposures was restored. On the basis of the deep mutational scanning profiles, we identified evolution hotspots of XBB.1.5 RBD and demonstrated that these mutations could further boost the immune-evasion capability of XBB.1.5 while maintaining high ACE2-binding affinity. Our findings suggest that the WT component should be abandoned when updating COVID-19 vaccines, and individuals without prior Omicron exposure should receive two updated vaccine boosters.


Antibodies, Viral , COVID-19 Vaccines , COVID-19 , Immunization, Secondary , Immunologic Memory , SARS-CoV-2 , Animals , Humans , Mice , Antibodies, Monoclonal/immunology , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/immunology , COVID-19/prevention & control , COVID-19/virology , COVID-19 Vaccines/administration & dosage , COVID-19 Vaccines/immunology , Epitopes, B-Lymphocyte/immunology , Immunologic Memory/immunology , SARS-CoV-2/classification , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Mutation
13.
Genomics ; 116(1): 110769, 2024 Jan.
Article En | MEDLINE | ID: mdl-38141931

Estrogen receptor α (ESR1) is involved in E2 signaling and plays a major role in postmenopausal bone loss. However, the molecular network underlying ESR1 has not been explored. We used systems genetics and bioinformatics to identify important genes associated with Esr1 in postmenopausal bone loss. We identified ~2300 Esr1-coexpressed genes in female BXD bone femur, functional analysis of which revealed 'osteoblast signaling' as the most enriched pathway. PPI network led to the identification of 25 'female bone candidates'. The gene-regulatory analysis revealed RUNX2 as a key TF. ANKRD1 and RUNX2 were significantly different between osteoporosis patients and healthy controls. Sp7, Col1a1 and Pth1r correlated with multiple femur bone phenotypes in BXD mice. miR-3121-3p targeted Csf1, Ankrd1, Sp7 and Runx2. ß-estradiol treatment markedly increased the expression of these candidates in mouse osteoblast. Our study revealed that Esr1-correlated genes Ankrd1, Runx2, Csf1 and Sp7 may play important roles in female bone development.


Osteoporosis, Postmenopausal , Osteoporosis , Humans , Female , Mice , Animals , Osteoporosis, Postmenopausal/genetics , Core Binding Factor Alpha 1 Subunit/genetics , Core Binding Factor Alpha 1 Subunit/metabolism , Bone and Bones/metabolism , Osteoporosis/genetics , Bone Development/genetics , Cell Differentiation
14.
PLoS Pathog ; 19(12): e1011868, 2023 Dec.
Article En | MEDLINE | ID: mdl-38117863

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) XBB lineages have achieved dominance worldwide and keep on evolving. Convergent evolution of XBB lineages on the receptor-binding domain (RBD) L455F and F456L is observed, resulting in variants with substantial growth advantages, such as EG.5, FL.1.5.1, XBB.1.5.70, and HK.3. Here, we show that neutralizing antibody (NAb) evasion drives the convergent evolution of F456L, while the epistatic shift caused by F456L enables the subsequent convergence of L455F through ACE2 binding enhancement and further immune evasion. L455F and F456L evade RBD-targeting Class 1 public NAbs, reducing the neutralization efficacy of XBB breakthrough infection (BTI) and reinfection convalescent plasma. Importantly, L455F single substitution significantly dampens receptor binding; however, the combination of L455F and F456L forms an adjacent residue flipping, which leads to enhanced NAbs resistance and ACE2 binding affinity. The perturbed receptor-binding mode leads to the exceptional ACE2 binding and NAb evasion, as revealed by structural analyses. Our results indicate the evolution flexibility contributed by epistasis cannot be underestimated, and the evolution potential of SARS-CoV-2 RBD remains high.


Angiotensin-Converting Enzyme 2 , COVID-19 , Humans , Angiotensin-Converting Enzyme 2/genetics , SARS-CoV-2/genetics , COVID-19/genetics , COVID-19 Serotherapy , Antibodies, Neutralizing
15.
Proc Natl Acad Sci U S A ; 120(49): e2310367120, 2023 Dec 05.
Article En | MEDLINE | ID: mdl-38011566

Existing single-cell bisulfite-based DNA methylation analysis is limited by low DNA recovery, and the measurement of 5hmC at single-base resolution remains challenging. Here, we present a bisulfite-free single-cell whole-genome 5mC and 5hmC profiling technique, named Cabernet, which can characterize 5mC and 5hmC at single-base resolution with high genomic coverage. Cabernet utilizes Tn5 transposome for DNA fragmentation, which enables the discrimination between different alleles for measuring hemi-methylation status. Using Cabernet, we revealed the 5mC, hemi-5mC and 5hmC dynamics during early mouse embryo development, uncovering genomic regions exclusively governed by active or passive demethylation. We show that hemi-methylation status can be used to distinguish between pre- and post-replication cells, enabling more efficient cell grouping when integrated with 5mC profiles. The property of Tn5 naturally enables Cabernet to achieve high-throughput single-cell methylome profiling, where we probed mouse cortical neurons and embryonic day 7.5 (E7.5) embryos, and constructed the library for thousands of single cells at high efficiency, demonstrating its potential for analyzing complex tissues at substantially low cost. Together, we present a way of high-throughput methylome and hydroxymethylome detection at single-cell resolution, enabling efficient analysis of the epigenetic status of biological systems with complicated nature such as neurons and cancer cells.


5-Methylcytosine , DNA Methylation , Animals , Mice , Sulfites , Sequence Analysis, DNA/methods , Cytosine
17.
Invest Ophthalmol Vis Sci ; 64(12): 25, 2023 09 01.
Article En | MEDLINE | ID: mdl-37707836

Purpose: Glaucoma is a group of heterogeneous optic neuropathies characterized by the progressive degeneration of retinal ganglion cells. However, the underlying mechanisms have not been understood completely. We aimed to elucidate the genetic network associated with the development of pigmentary glaucoma with DBA/2J (D2) mouse model of glaucoma and corresponding genetic control D2-Gpnmb (D2G) mice carrying the wild type (WT) Gpnmb allele. Methods: Retinas isolated from 13 D2 and 12 D2G mice were subdivided into 2 age groups: pre-onset (1-6 months: samples were collected at approximately 1-2, 2-4, and 5-6 months) and post-onset (7-15 months: samples were collected at approximately 7-9, 10-12, and 13-15 months) glaucoma were compared. Differential gene expression (DEG) analysis and gene-set enrichment analyses were performed. To identify micro-RNAs (miRNAs) that target Gpnmb, miRNA expression levels were correlated with time point matched mRNA expression levels. A weighted gene co-expression network analysis (WGCNA) was performed using the reference BXD mouse population. Quantitative real-time PCR (qRT-PCR) was used to validate Gpnmb and miRNA expression levels. Results: A total of 314 and 86 DEGs were identified in the pre-onset and post-onset glaucoma groups, respectively. DEGs in the pre-onset glaucoma group were associated with the crystallin gene family, whereas those in the post-onset group were related to innate immune system response. Of 1329 miRNAs predicted to target Gpnmb, 3 miRNAs (miR-125a-3p, miR-3076-5p, and miR-214-5p) were selected. A total of 47 genes demonstrated overlapping with the identified DEGs between D2 and D2G, segregated into their time-relevant stages. Gpnmb was significantly downregulated, whereas 2 out of 3 miRNAs were significantly upregulated (P < 0.05) in D2 mice at both 3-and 10-month time points. Conclusions: These findings suggest distinct gene-sets involved in pre-and post-glaucoma in the D2 mouse. We identified three miRNAs regulating Gpnmb in the development of murine pigmentary glaucoma.


Glaucoma, Open-Angle , Glaucoma , MicroRNAs , Animals , Mice , Mice, Inbred DBA , Gene Regulatory Networks , Glaucoma, Open-Angle/genetics , Glaucoma/genetics , MicroRNAs/genetics , Transcription Factors
18.
Int J Mol Sci ; 24(16)2023 Aug 14.
Article En | MEDLINE | ID: mdl-37628941

BACKGROUND: Troponin-I interacting kinase encoded by the TNNI3K gene is expressed in nuclei and Z-discs of cardiomyocytes. Mutations in TNNI3K were identified in patients with cardiac conduction diseases, arrhythmias, and cardiomyopathy. METHODS: We performed cardiac gene expression, whole genome sequencing (WGS), and cardiac function analysis in 40 strains of BXD recombinant inbred mice derived from C57BL/6J (B6) and DBA/2J (D2) strains. Expression quantitative trait loci (eQTLs) mapping and gene enrichment analysis was performed, followed by validation of candidate Tnni3k-regulatory genes. RESULTS: WGS identified compound splicing and missense T659I Tnni3k variants in the D2 parent and some BXD strains (D allele) and these strains had significantly lower Tnni3k expression than those carrying wild-type Tnni3k (B allele). Expression levels of Tnni3k significantly correlated with multiple cardiac (heart rate, wall thickness, PR duration, and T amplitude) and metabolic (glucose levels and insulin resistance) phenotypes in BXDs. A significant cis-eQTL on chromosome 3 was identified for the regulation of Tnni3k expression. Furthermore, Tnni3k-correlated genes were primarily involved in cardiac and glucose metabolism-related functions and pathways. Genes Nodal, Gnas, Nfkb1, Bmpr2, Bmp7, Smad7, Acvr1b, Acvr2b, Chrd, Tgfb3, Irs1, and Ppp1cb were differentially expressed between the B and D alleles. CONCLUSIONS: Compound splicing and T659I Tnni3k variants reduce cardiac Tnni3k expression and Tnni3k levels are associated with cardiac and glucose metabolism-related phenotypes.


Carbohydrate Metabolism , Myocytes, Cardiac , Animals , Mice , Mice, Inbred C57BL , Mice, Inbred DBA , Glucose , Protein Serine-Threonine Kinases
19.
J Phys Chem B ; 127(27): 6006-6014, 2023 07 13.
Article En | MEDLINE | ID: mdl-37368753

Single-cell proteomics has attracted a lot of attention in recent years because it offers more functional relevance than single-cell transcriptomics. However, most work to date has focused on cell typing, which has been widely accomplished by single-cell transcriptomics. Here we report the use of single-cell proteomics to measure the correlation between the translational levels of a pair of proteins in a single mammalian cell. In measuring pairwise correlations among ∼1000 proteins in a population of homogeneous K562 cells under a steady-state condition, we observed multiple correlated protein modules (CPMs), each containing a group of highly positively correlated proteins that are functionally interacting and collectively involved in certain biological functions, such as protein synthesis and oxidative phosphorylation. Some CPMs are shared across different cell types while others are cell-type specific. Widely studied in omics analyses, pairwise correlations are often measured by introducing perturbations into bulk samples. However, some correlations of gene or protein expression under the steady-state condition would be masked by perturbation. The single-cell correlations probed in our experiment reflect intrinsic steady-state fluctuations in the absence of perturbation. We note that observed correlations between proteins are experimentally more distinct and functionally more relevant than those between corresponding mRNAs measured in single-cell transcriptomics. By virtue of single-cell proteomics, functional coordination of proteins is manifested through CPMs.


Proteins , Proteomics , Animals , Gene Expression Profiling , Mammals
20.
ACS Appl Mater Interfaces ; 15(21): 25516-25523, 2023 May 31.
Article En | MEDLINE | ID: mdl-37209114

Manipulating the product selectivity of an electrochemical CO2 reduction reaction (CO2RR) is challenging due to the unclear and uncontrollable active sites. Here, we report stable CO2RR operation with tunable product selectivity over a family of molecule-modulated copper catalysts. The coordination environment of Cu in catalysts is modulated by an imidazole-based molecule via different synthetic routes. Various carbonaceous products ranging from carbon monoxide, methane, and ethylene were selectively produced via, respectively, tuning the coordination environment of copper atoms from Cu-N, Cu-C, and Cu-Cu. Density functional theory (DFT) calculations reveal that the Cu-N sites weaken the adsorption energy of the *CO intermediate, which is beneficial for CO desorption. The Cu-C and Cu-Cu sites, respectively, facilitate the formation of *OCOH and *(CO)2 intermediates, favoring the CH4 and C2H4 pathways. This work provides a stable and simple model system for studying the influence of coordination elements on the product selectivity of CO2RR.

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