MethParquet: an R package for rapid and efficient DNA methylation association analysis adopting Apache Parquet.

SUMMARY: Genome-wide DNA methylation (DNAm) profiling is indispensable for unveiling how DNAm regulates biological pathways and individual phenotypes. However, managing and analyzing extensive DNAm data generated from large cohort studies present computational obstacles. Apache Parquet is a data file format that allows for efficient data storage, retrieval, and manipulation, alleviating computational hurdles associated with conventional row-based formats. We here introduce MethParquet, the first R package leveraging the columnar Parquet format for efficient DNAm data analysis. It can be used for data extraction, methylation risk score calculation, epigenome-wide association analyses, and other standard post-quality control tasks. The package flexibly implements diverse regression models. Via a public methylation dataset, we show the efficiency of this package in reducing running time and RAM usage in large-scale EWAS. AVAILABILITY AND IMPLEMENTATION: The MethParquet R package is publicly available on the GitHub repository https://github.com/ZWangTen/MethParquet. It includes a vignette and a toy dataset derived from a public resource.

A Review of Transition Metal Boride, Carbide, Pnictide, and Chalcogenide Water Oxidation Electrocatalysts.

Transition metal borides, carbides, pnictides, and chalcogenides (X-ides) have emerged as a class of materials for the oxygen evolution reaction (OER). Because of their high earth abundance, electrical conductivity, and OER performance, these electrocatalysts have the potential to enable the practical application of green energy conversion and storage. Under OER potentials, X-ide electrocatalysts demonstrate various degrees of oxidation resistance due to their differences in chemical composition, crystal structure, and morphology. Depending on their resistance to oxidation, these catalysts will fall into one of three post-OER electrocatalyst categories: fully oxidized oxide/(oxy)hydroxide material, partially oxidized core@shell structure, and unoxidized material. In the past ten years (from 2013 to 2022), over 890 peer-reviewed research papers have focused on X-ide OER electrocatalysts. Previous review papers have provided limited conclusions and have omitted the significance of "catalytically active sites/species/phases" in X-ide OER electrocatalysts. In this review, a comprehensive summary of (i) experimental parameters (e.g., substrates, electrocatalyst loading amounts, geometric overpotentials, Tafel slopes, etc.) and (ii) electrochemical stability tests and post-analyses in X-ide OER electrocatalyst publications from 2013 to 2022 is provided. Both mono and polyanion X-ides are discussed and classified with respect to their material transformation during the OER. Special analytical techniques employed to study X-ide reconstruction are also evaluated. Additionally, future challenges and questions yet to be answered are provided in each section. This review aims to provide researchers with a toolkit to approach X-ide OER electrocatalyst research and to showcase necessary avenues for future investigation.

Aerobic Thiols Oxidative Coupling to Disulfides over Robust CoOx Nanoclusters Confined within Hierarchical Silicalite-1 Zeolite.

Disulfide is an important organic reagent and synthetic intermediate that is widely used in organic synthesis, polymers, and other fields, but its synthesis still suffers from many environmental pollution and economic problems. Here, we present an environmentally friendly and efficient base-free aerobic oxidative thiol coupling catalyzed by heterogeneous CoOx nanoclusters entrapped in hierarchical silicalite-1 zeolite, synthesized by combining silane pore expansion and metal coordination methods under hydrothermal conditions. It is confirmed that open hierarchical channels favor mass diffusion, and the chemical valence of Co species in CoOx/h-S-1-H is +2, which is different from that of Co3O4 particles in CoOx/h-S-1-I. CoOx nanoclusters, are strongly fixed in the channels of silicalite-1 zeolite via Co-O-Si bonds, which is of great importance for the high catalytic activity in both symmetrical and unsymmetrical oxidative thiol coupling reactions. After recycling experiments four times, the CoOx/h-S-1-H used has almost the same chemical state and the same distribution of Co(II) species as the fresh catalysts. Based on DFT calculations and inhibition experiments, the oxidative coupling of thiols undergoes a free radical mechanism in which Co(III) causes RS-H cleavage into RS· and H· species. Subsequently, two RS· radicals are coupled to disulfides, while H· radicals react with the O species to form H2O molecules. This work not only provides guidance on catalyst design and parameter optimization for oxidative thiol coupling but also advances the understanding of the aerobic oxidation mechanism.

Association between asthma and COVID-19 severity during Omicron epidemic: a retrospective cohort study using real-world data.

BACKGROUND: The available evidence presented inconsistencies and inconclusive findings regarding the associations between co-existing asthma and mortality among COVID-19 patients. The objective of the current study is to investigate the relationship between asthma and severe outcomes after SARS-CoV-2 Omicron infection in an infection-naïve population. METHODS: A retrospective cohort study using propensity score matching was conducted. The COVID-19 patients requiring hospitalisation in Hong Kong from January 1, 2022, to November 13, 2022, an Omicron-predominated period, were identified. Severe clinical outcomes were defined as ICU admission and inpatient death after the first positive PCR results as well as a composite outcome of both. RESULTS: Of the 74,396 hospitalised COVID-19 patients admitted, 1,290 asthma patients and 18,641 non-asthma patients were included in the matched cohort. The rates of death and the composite outcome were 15·3% and 17·2%, respectively, among the non-asthma patients,12·2% and 13·6%, respectively, among the asthma patients, with adjusted hazard ratios equal to 0·775 (95% CI: 0·660-0·909) and 0·770 (95% CI: 0·662-0·895), respectively. The negative association was more apparent in the elderly and female groups. Asthma remained a factor that lowered the risk of disease severity even though the patients were not fully vaccinated with at least two doses. CONCLUSIONS: We used real-world data to demonstrate that asthma was not a risk factor for COVID-19 severity of the infections of Omicron variant, even though the patients were not fully vaccinated.

TLT-1 Promotes Platelet-Monocyte Aggregate Formation to Induce IL-10-Producing B Cells in Tuberculosis.

The immunoregulation of platelets and platelet-monocyte aggregates (PMAs) is increasingly recognized, but it roles in tuberculosis (TB) remain to be elucidated. In this study, we found that CD14+CD41+ PMAs were increased in peripheral blood of patients with active TB. CD14+CD41+ PMAs highly expressed triggering receptors expressed on myeloid cells (TREMs)-like transcript-1 (TLT-1), P-selectin (CD62P), and CD40L. Our in vitro study found that platelets from patients with active TB aggregate with monocytes to induce IL-1ß and IL-6 production by monocytes. Importantly, we identified that TLT-1 was required for formation of PMAs. The potential TLT-1 ligand was expressed and increased on CD14+ monocytes of patients with TB determined by using TLT-1 fusion protein (TLT-1 Fc). Blocking of ligand-TLT-1 interaction with TLT-1 Fc reduced PMA formation and IL-1ß and IL-6 production by monocytes. Further results demonstrated that PMAs induced IL-10 production by B cells (B10) dependent on IL-1ß, IL-6, and CD40L signals in a coculture system. Moreover, TLT-1 Fc treatment suppressed B10 polarization via blocking PMA formation. Taking all of these data together, we elucidated that TLT-1 promoted PMA-mediated B10 polarization through enhancing IL-1ß, IL-6, and CD40L origin from PMAs, which may provide potential targeting strategies for TB disease treatment.

Mechanistic study of transcription factor Sox18 during heart development.

Heart development is a delicate and complex process regulated by coordination of various signaling pathways. In this study, we investigated the role of sox18 in heart development by modulating Wnt/ß-Catenin signaling pathways. Our spatiotemporal expression analysis revealed that sox18 is mainly expressed in the heart, branchial arch, pharyngeal arch, spinal cord, and intersegmental vessels at the tailbud stage of Xenopus tropicalis embryo. Overexpression of sox18 in the X. tropicalis embryos causes heart edema, while loss-of-function of sox18 can change the signal of developmental heart marker gata4 at different stages, suggesting that sox18 plays an essential role in the development of the heart. Knockdown of SOX18 in human umbilical vein endothelial cells suggests a link between Sox18 and ß-CATENIN, a key regulator of the Wnt signaling pathway. Sox18 negatively regulates islet1 and tbx3, the downstream factors of Wnt/ß-Catenin signaling, during the linear heart tube formation and the heart looping stage. Taken together, our findings highlight the crucial role of Sox18 in the development of the heart via inhibiting Wnt/ß-Catenin signaling.

Mass Transfer Limitation within Molecular Crowding Electrolyte Reorienting (100) and (101) Texture for Dendrite-Free Zinc Metal Batteries.

Aqueous zinc metal batteries are emerging as a promising alternative for energy storage due to their high safety and low cost. However, their development is hindered by the formation of Zn dendrites and side reactions. Herein, a macromolecular crowding electrolyte (MCE40) is prepared by incorporating polyvinylpyrrolidone (PVP) into the aqueous solutions, exhibiting an enlarged electrochemical stability window and anti-freezing properties. Notably, through electrochemical measurements and characterizations, it is discovered that the mass transfer limitation near the electrode surface within the MCE40 electrolyte inhibits the (002) facets. This leads to the crystallographic reorientation of Zn deposition to expose the (100) and (101) textures, which undergo a "nucleation-merge-growth" process to form a uniform and compact Zn deposition. Consequently, the MCE40 enables highly reversible and stable Zn plating/stripping in Zn/Cu half cells over 600 cycles and in Zn/Zn symmetric cells for over 3000 hours at 1.0 mA cm-2. Furthermore, Na0.33V2O5/Zn and α-MnO2/Zn full cells display promising capacity and sustained stability over 500 cycles at room and sub-zero temperatures. This study highlights a novel electrochemical mechanism for achieving preferential Zn deposition, introducing a unique strategy for fabricating dendrite-free zinc metal batteries.

High-Entropy Electrolyte Driven by Multi-Solvation Structures for Long-Lifespan Aqueous Zinc Metal Pouch Cells.

Aqueous zinc metal batteries (AZMBs) are promising for grid-scale energy storage due to their low cost and high safety. However, poor stability and an unfavorable freezing point hinder their actual application. Herein, a ternary salts-based high-entropy electrolyte (HEE) composed of Zn0.2Na0.4Li0.4(ClO4)1.2·7H2O is proposed to address the above issues. The addition of perchlorate salts with different cations reduces the size of ion clusters, significantly increases the solvation structure species, and promotes the anion-rich Zn2+ solvation structures, resulting in an enlarged electrochemical stability window, favorable viscosity and ionic conductivity, and low freezing point. Furthermore, characterization and calculations confirm that multiple types of solvation structures effectively increase the electrolyte entropy. As a consequence, the Zn/Zn symmetric cells in HEE can sustainably cycle for at least 1000 hours and 1500 hours under room and subzero temperatures, respectively. The Na0.33V2O5/Zn and polyaniline/Zn full cells can even last for 30000 and 20000 cycles without capacity decay at -20 °C, respectively. The pouch cells employing HEE deliver promising capacity and stability, even at high mass loading of active materials. This strategy of introducing multiple salts with different cations to construct a high-entropy environment provides a facile approach for high-performance and long-lifespan AZMBs across a wide temperature range.

Protective effects of chlorogenic acid on growth, intestinal inflammation, hepatic antioxidant capacity, muscle development and skin color in channel catfish Ictalurus punctatus fed an oxidized fish oil diet.

Under oxidative stress condition, the protective effects of dietary chlorogenic acid (CGA) supplementation on liver antioxidant capacity, intestinal inflammation and barrier function, muscle development and skin coloration in channel catfish Ictalurus punctatus were explored in the current study. With that purpose, I. punctatus were fed five experimental diets containing 2% fresh fish oil (FFO, 9.2 meqO2/kg) or 2% oxidized fish oil (OFO, 897.4 meqO2/kg) without or with CGA supplementation (0.02%, 0.04% and 0.08%) for 8 weeks. Upon comparative analysis, the oxidized fish oil consumption significantly lowered weight gain rate, decreased intestinal villi length and muscular thickness values and the tight junction proteins mRNA abundance, augmented the intestinal proinflammatory factors, attenuated hepatic antioxidant enzymes activities and related genes mRNA expression levels, influenced the myogenic regulatory factors expression profile and impacted the myocyte density, myocyte area values as well as the skin pigments contents compared to the FFO treatment. Collectively, long-term feeding of the oxidized fish oil diet suppressed the growth performance, destroyed intestinal structural integrity, caused intestinal inflammation and hepatic oxidative stress, impacted the skeletal development and skin color of I. punctatus. Whereas CGA supplementation in oxidized fish oil diets partially counteracted the negative effects of the oxidized fish oil on I. punctatus in terms of increasing the growth performance, improving the intestinal mucosal structure, alleviating hepatic oxidative stress and intestinal inflammation, recompiling the myogenic regulatory factors expression and improving skin color. In conclusion, CGA has great potential to be an aquatic feed additive.

Lipoprotein(a) in patients with breast cancer after chemotherapy: exploring potential strategies for cardioprotection.

Developments in neoadjuvant and adjuvant chemotherapy (CHT) have led to an increase in the number of breast cancer survivors. The determination of an appropriate follow-up for these patients is of increasing importance. Deaths due to cardiovascular disease (CVD) are an important part of mortality in patients with breast cancer.This review suggests that chemotherapeutic agents may influence lipoprotein(a) (Lp(a)) concentrations in breast cancer survivors after CHT based on many convincing evidence from epidemiologic and observational researches. Usually, the higher the Lp(a) concentration, the higher the median risk of developing CVD. However, more clinical trial results are needed in the future to provide clear evidence of a possible causal relationship. This review also discuss the existing and emerging therapies for lowering Lp(a) concentrations in the clinical setting. Hormone replacement therapy, statins, proprotein convertase subtilisin/kexin-type 9 (PCSK9) inhibitors, Antisense oligonucleotides, small interfering RNA, etc. may reduce circulating Lp(a) or decrease the incidence of CVD.

A Bayesian phase I-II clinical trial design to find the biological optimal dose on drug combination.

In recent years, combined therapy shows expected treatment effect as they increase dose intensity, work on multiple targets and benefit more patients for antitumor treatment. However, dose -finding designs for combined therapy face a number of challenges. Therefore, under the framework of phase I-II, we propose a two-stage dose -finding design to identify the biologically optimal dose combination (BODC), defined as the one with the maximum posterior mean utility under acceptable safety. We model the probabilities of toxicity and efficacy by using linear logistic regression models and conduct Bayesian model selection (BMS) procedure to define the most likely pattern of dose-response surface. The BMS can adaptively select the most suitable model during the trial, making the results robust. We investigated the operating characteristics of the proposed design through simulation studies under various practical scenarios and showed that the proposed design is robust and performed well.

CD177+ cells produce neutrophil extracellular traps that promote biliary atresia.

BACKGROUND & AIMS: We have previously reported on the potential pathogenic role of neutrophils in biliary atresia (BA). Herein, we aimed to delineate the role of CD177+ neutrophils in the pathogenesis of BA. METHODS: Immune cells from the livers of mice with rhesus rotavirus-induced BA were analysed. Single-cell RNA-sequencing was performed to specifically analyse Gr-1+ (Ly6C/Ly6G+) cells in the liver. Gene expression profiles of CD177+ cells were analysed using the Smart-Seq RNA-sequencing method, and the pathogenesis of BA was examined in Cd177-/- mice. Neutrophil extracellular trap (NET) inhibitors were used to determine the role of CD177+ cell-derived NETs in BA-associated bile duct damage, and a pilot clinical study evaluated the potential effects of N-acetylcysteine on NET release in BA. RESULTS: Increased levels of Gr-1+ cells were observed in the livers of mice with rhesus rotavirus-induced BA. RNA-sequencing analysis revealed that CD177+ cells were the main population of Gr-1+ cells and expressed elevated levels of both interferon-stimulated and neutrophil degranulation genes. Cd177-/- BALB/c mice exhibited delayed disease onset and reduced morbidity and mortality. High numbers of mitochondria were detected in CD177+ cells derived from mice with BA; these cells were associated with increased levels of reactive oxygen species and increased NET formation, which induced the apoptosis of biliary epithelial cells in cocultures. In a pilot clinical study, the administration of N-acetylcysteine to patients with BA reduced CD177+ cell numbers and reactive oxygen species levels, indicating a potential beneficial effect. CONCLUSIONS: Our data indicate that CD177+ cells play an important role in the initiation of BA pathogenesis via NET formation. CLINICAL TRIAL REGISTRATION: The pilot study of N-acetylcysteine treatment in patients with BA was registered on the Chinese Clinical Trial Registry (ChiCTR2000040505). LAY SUMMARY: Neutrophils (a type of innate immune cell, i.e. an immune cell that doesn't target a specific antigen) are thought to play a role in the development of biliary atresia (a rare but potentially lethal condition of the bile ducts that occurs in infants). Herein, we found that neutrophils expressing a particular protein (CD177) played an important role in bile duct damage by releasing a special structure (NET) that can trap and kill pathogens but that can also cause severe tissue damage. A pilot study in patients with biliary atresia showed that inhibiting NETs could have a beneficial effect.

Effect of therapeutic versus prophylactic anticoagulation therapy on clinical outcomes in COVID-19 patients: a systematic review with an updated meta-analysis.

BACKGROUND: Previous studies demonstrate a reduced risk of thrombosis and mortality with anticoagulant treatment in patients with COVID-19 than in those without anticoagulation treatment. However, an open question regarding the efficacy and safety of therapeutic anticoagulation (T-AC) versus a lower dose, prophylaxis anticoagulation (P-AC) in COVID-19 patients is still controversial. METHODS: We systematically reviewed currently available randomized clinical trials (RCTs) and observational studies (OBs) from January 8, 2019, to January 8, 2022, and compared prophylactic and therapeutic anticoagulant treatment in COVID-19 patients. The primary outcomes were risk of mortality, major bleeding, and the secondary outcomes included venous and arterial thromboembolism. Subgroup analysis was also performed between critically ill and non-critically ill patients with COVID-19 and between patients with higher and lower levels of D-dimer. Sensitivity analysis was performed to decrease the bias and the impact of population heterogeneity. RESULTS: We identified 11 RCTs and 17 OBs fulfilling our inclusion criteria. In the RCTs analyses, there was no statistically significant difference in the relative risk of mortality between COVID-19 patients with T-AC treatment and those treated with P-AC (RR 0.95, 95% CI, 0.78-1.15, P = 0.60). Similar results were also found in the OBs analyses (RR 1.21, 95% CI, 0.98-1.49, P = 0.08). The pooling meta-analysis using a random-effects model combined with effect sizes showed that in the RCTs and OBs analyses, patients with COVID-19 who received T-AC treatment had a significantly higher relative risk of the major bleeding event than those with P-AC treatment in COVID-19 patients (RCTs: RR 1.76, 95% CI, 1.19-2.62, P = 0.005; OBs: RR 2.39, 95% CI, 1.56-3.68, P < 0.0001). Compared with P-AC treatment in COVID-19 patients, patients with T-AC treatment significantly reduced the incidence of venous thromboembolism (RR 0.51, 95% CI, 0.39-0.67, P<0.00001), but it is not associated with arterial thrombosis events (RR 0.97, 95% CI, 0.66-1.42, P = 0.87). The subgroup analysis of OBs shows that the mortality risk significantly reduces in critically ill COVID-19 patients treated with T-AC compared with those with P-AC treatment (RR 0.58, 95% CI, 0.39-0.86, P = 0.007), while the mortality risk significantly increases in non-critically ill COVID-19 patients treated with T-AC (RR 1.56, 95% CI, 1.34-1.80, P < 0.00001). In addition, T-AC treatment does not reduce the risk of mortality in COVID-19 patients with high d-dimer levels in RCTs. Finally, the overall sensitivity analysis after excluding two RCTs studies remains consistent with the previous results. CONCLUSIONS: In our integrated analysis of included RCTs and OBs, there is no significant difference between the mortality of T-AC and P-AC treatment in unselected patients with COVID-19. T-AC treatment in COVID-19 patients significantly reduced the incidence of venous thromboembolism but showed a higher risk of bleeding than those with P-AC treatment. In addition, P-AC treatment was superior to T-AC treatment in non-critically ill COVID-19 patients, the evidence supporting the necessity for T-AC treatment in critically ill COVID-19 patients came only from OBs. TRIAL REGISTRATION: Protocol registration: The protocol was registered at PROSPERO (CRD42021293294).

Theoretical insights into graphenylene-based triple-atom catalysts for efficient nitrogen fixation.

Ammonia synthesis from the electrochemical nitrogen reduction reaction, which can weaken but not directly break the inert NN bond via multiple progressive protonation steps under mild conditions, has been recognized as one of the most attractive alternatives for the production of NH3. In this work, the potential of employing graphenylene-based triple-atom catalysts for the nitrogen reduction reaction was investigated by using first-principles calculations. The performance of these catalysts was studied focusing on configuration optimization, thermal stability, catalyst selectivity and activity and the interaction mechanism. There was electron transfer between the transition metal atoms and the graphenylene substrate, which strengthens the structure stability of the complex systems and brings about sufficient catalytic activity. A more negative ΔG (N2) for the nitrogen reduction reaction than ΔG (H) for the hydrogen evolution reaction is selected as an evaluation standard of good selectivity. Moreover, ΔG (*N*NH) or ΔG (*NNH) < 0.6 eV is used as a screening criterion for good activity. By screening, Mo3@GP is found to show the best nitrogen reduction reaction performance with a low limiting potential of -0.39 V through a consecutive pathway. The excellent performance derives from the largest electron transfer ability of Mo3 atoms and the electronic reservoir function of the GP substrate.

Synthesis of Aliphatic Polycarbonates from Diphenyl Carbonate and Diols over Zinc (II) Acetylacetonate.

APCs (aliphatic polycarbonates) are one of the most important types of biodegradable polymers and widely used in the fields of solid electrolyte, biological medicine and biodegradable plastics. Zinc-based catalysts have the advantages of being low cost, being non-toxic, having high activity, and having excellent environmental and biological compatibility. Zinc (II) acetylacetonate (Zn(Acac)2) was first reported as a highly effective catalyst for the melt transesterification of biphenyl carbonate with 1,4-butanediol to synthesize poly(1,4-butylene carbonate)(PBC). It was found that the weight-average molecular weight of PBC derived from Zn(Acac)2 could achieve 143,500 g/mol with a yield of 85.6% under suitable reaction conditions. The Lewis acidity and steric hindrance of Zn2+ could obviously affect the catalytic performance of Zn-based catalysts for this reaction. The main reasons for the Zn(Acac)2 catalyst displaying a higher yield and Mw than other zinc-based catalysts should be ascribed to the presence of the interaction between acetylacetone ligand and Zn2+, which can provide this melt transesterification reaction with the appropriate Lewis acidity as well as the steric hindrance.

Transcriptional response of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. leaves grown under full and partial daylight conditions.

BACKGROUND: Asarum heterotropides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. is an important medicinal and industrial plant, which is used in the treatment of various diseases. The main bioactive ingredient is the volatile oil having more than 82 identified components of which methyleugenol, safrole, myristicin, and toluene account for about 70% of the total volume. As a sciophyte plant, the amount of light it absorbs through leaves is an important factor for growth and metabolism. RESULTS: We grew Asarum plants under full, 50, 28, and 12% sunlight conditions to investigate the effect of different light irradiances on the four major volatile oil components. We employed de novo transcriptome sequencing to understand the transcriptional behavior of Asarum leaves regarding the biosynthetic pathways of the four volatile oil components, photosynthesis and biomass accumulation, and hormone signaling. Our results demonstrated that the increasing light conditions promoted higher percent of the four components. Under full sunlight conditions, cinnamyl alcohol dehydrogenase and cytochrome p450719As were upregulated and led the increased methyleugenol, safrole, and myristicin. The transcriptomic data also showed that Asarum leaves, under full sunlight conditions, adjust their photosynthesis-antenna proteins as a photoprotective response with the help of carotenoids. Plant hormone-signaling related genes were also differentially expressed between full sunlight and low light conditions. CONCLUSIONS: High light induces accumulation of major bioactive ingredients A. heterotropides volatile oil and this is ascribed to upregulation of key genes such as cinnamyl alcohol dehydrogenase and cytochrome p450719As. The transcriptome data presented here lays the foundation of further understanding of light responses in sciophytes and provides guidance for increasing bioactive molecules in Asarum.

Detection of Metabolite-Protein Interactions in Complex Biological Samples by High-Resolution Relaxometry: Toward Interactomics by NMR.

Metabolomics, the systematic investigation of metabolites in biological fluids, cells, or tissues, reveals essential information about metabolism and diseases. Metabolites have functional roles in a myriad of biological processes, as substrates and products of enzymatic reactions but also as cofactors and regulators of large numbers of biochemical mechanisms. These functions involve interactions of metabolites with macromolecules. Yet, methods to systematically investigate these interactions are still scarce to date. In particular, there is a need for techniques suited to identify and characterize weak metabolite-macromolecule interactions directly in complex media such as biological fluids. Here, we introduce a method to investigate weak interactions between metabolites and macromolecules in biological fluids. Our approach is based on high-resolution NMR relaxometry and does not require any invasive procedure or separation step. We show that we can detect interactions between small and large molecules in human blood serum and quantify the size of the complex. Our work opens the way for investigations of metabolite (or other small molecules)-protein interactions in biological fluids for interactomics or pharmaceutical applications.

Comparison of the effects between MPL and JAK2V617F on thrombosis and peripheral blood cell counts in patients with essential thrombocythemia: a meta-analysis.

To assess the effects between MPL and JAK2V617F on the thrombosis risk and peripheral blood cell counts in patients with essential thrombocythemia (ET), we identified eligible studies from PubMed, Embase, and the Cochrane Library. Seven studies were ultimately included in this meta-analysis. All studies reported the peripheral blood cell counts of ET patients, and three of them reported the eligible thrombotic events. In comparing the effect of MPL versus JAK2V617F on thrombosis, 1257 ET patients (73 MPL + and 1184 JAK2V617F +) were included. MPL-positive (MPL +) ET patients had a higher risk of thrombosis than JAK2V617F-positive (JAK2V617F +) ET patients [RR = 1.80 (1.08-3.01), P = 0.025]. And 3453 ET patients (138 MPL + and 3315 JAK2V617F +) were included in the comparison of peripheral blood cell counts. Platelet counts of MPL + ET patients were higher than that of JAK2V617F + ET patients [WMD = 81.18 (31.77-130.60), P = 0.001]. MPL + ET patients had lower hemoglobin [WMD = - 11.66 (- 14.32 to - 9.00), P = 0.000] and white blood cell counts [WMD = - 1.01 (- 1.47 to - 0.56), P = 0.000] than JAK2V617F + ET patients. These findings indicate that the MPL mutation is a high-risk factor for thrombosis in ET patients, and it may be rational to include MPL mutation in the revised IPSET as a criterion for thrombosis prediction scores. And given the differences in peripheral blood, it is necessary to further study whether MPL + ET patients differ from JAK2V617F + ET patients in bleeding and survival.

Prognostic value of ASXL1 mutations in patients with primary myelofibrosis and its relationship with clinical features: a meta-analysis.

Additional sex combs like 1 (ASXL1) mutations are one of the most common molecular biological abnormalities in patients with primary myelofibrosis (PMF), and the effect of these mutations on prognosis remains controversial. Hence, we conducted a meta-analysis to assess the prognostic value and clinical characteristics of ASXL1 mutations in PMF patients. Eligible studies were systematically searched from PubMed, Embase, and the Cochrane Library. We extracted the hazard ratios (HRs) and their 95% confidence intervals (CIs) of overall survival (OS) and leukemia-free survival (LFS), the number of patients transformed to acute leukemia, and clinical characteristics to carry out a meta-analysis by fixed effect model or random effect model according to the heterogeneity between studies. A total of 4501 PMF patients from 16 cohorts of 14 studies were included in this meta-analysis. The results revealed that ASXL1 mutations might predict a shorter OS (HR = 2.30, 95% CI: 1.79-2.94, P < 0.00001) and a higher probability of transformation to acute leukemia (LFS: HR = 1.77, 95% CI: 1.30-2.42, P = 0.0003; the rate of acute leukemia transformation: OR = 2.06, 95% CI: 1.50-2.83, P < 0.00001). Furthermore, ASXL1 mutations were correlated with patients older than 65 years old, male, a lower level of platelet counts, and a higher risk of the international prognostic score system. These findings indicate that ASXL1 mutations have a significant adverse impact on the prognosis of PMF patients and may contribute to risk stratification and prognostic assessment for PMF patients.

Apatinib induced ferroptosis by lipid peroxidation in gastric cancer.

BACKGROUND: Apatinib, a competitive inhibitor of VEGFR2, has anti-angiogenesis and anticancer activities through different mechanisms, but it still cannot fully explain the drug efficacy of apatinib. Ferroptosis, associated with lethal lipid peroxidation, has emerged to play an important role in cancer biology, however, the exact role of ferroptosis in apatinib-mediating anticancer treatment are still not clear. METHODS: The effects of (1S, 3R)-RSL3 and apatinib were evaluated in different GC cell lines and in normal human gastric epithelial cells. Further, the effects of apatinib and inhibition of antioxidant defense enzyme glutathione peroxidase (GPX4) on cell viability, cell death, glutathione (GSH) levels, lipid ROS production, cellular malondialdehyde (MDA) levels and protein expression were evaluated in vitro as well as in a mouse tumor xenograft model. The expression level of GPX4 in GC tissues and paracancerous tissues was measured by immunohistochemistry. RESULTS: (1S, 3R)-RSL3 selectively killed GC cells, but not normal cells. Apatinib induced ferroptosis in GC cells by decreasing cellular GSH levels and increasing lipid peroxidation levels. This effect was blocked by co-incubation with ferrostatin-1, liproxstatin-1, GSH, or vitamin E. Further investigation revealed that apatinib down-regulated GPX4 expression via inhibition of the transcription factors Sterol regulatory element-binding protein-1a (SREBP-1a). Besides, we found that multi-drug resistant GC cells were vulnerable to apatinib-induced GPX4 inhibition. CONCLUSIONS: In summary, we show that apatinib could induce the lipid peroxidation through GPX4 mediated by SREBP-1a, then negatively regulate the GC cell, even the multi-drug-resistant GC cell, ferroptosis.