The deubiquitinating enzymes-related signature predicts the prognosis and immunotherapy response in breast cancer.

BACKGROUND: Breast cancer is a prevalent disease that has a dismal prognosis for patients and a bad outlook for treatments. Ubiquitination is a reversible biological process that regulates protein production and degradation, as well as plays a vital role in protein transport, localization, and biological activity. METHODS: We obtained the breast cancer patient sample data and used a machine learning technique to create a novel index called Deubiquitinating enzyme related index (DUBRI) by gathering genes associated to deubiquitinating enzymes. Based on DUBRI, we systematically analyze patients' prognosis, clinical characteristics, tumor immune microenvironment, chemotherapy response and immunotherapy response. Finally, the function of OTUB2 was explored in breast cancer cells. RESULTS: DUBRI, which consists of five deubiquitinating enzyme genes (OTUB2, USP41, MINDY2, YOD1, and PSMD7), is a reliable predictor of survival in breast cancer patients. We found that the high DUBRI group presented higher levels of immune cell infiltration. We performed molecular docking prediction of core target proteins in deubiquitinating enzymes. In vitro experiments verified that knockdown of OTUB2 could inhibit the proliferation and migration of breast cancer. CONCLUSIONS: The DUBRI discovered in this research may effectively evaluate the outlook of breast cancer patients and identify groups of patients who would gain advantages from immunotherapy, offering vital knowledge for the future targeted treatment of breast cancer patients.

Short-term outcomes of distal gastrectomy versus total gastrectomy for gastric cancer under enhanced recovery after surgery: a propensity score-matched analysis.

Enhanced recovery after surgery (ERAS) has been used safely and effectively in patients with gastric cancer. Our aim was to evaluate the short-term outcomes of total gastrectomy (TG) versus distal gastrectomy (DG) for gastric cancer under ERAS. A prospectively collected database of 1349 patients with gastric cancer who underwent TG or DG between January 2016 and September 2022 was retrospectively analyzed. Propensity score matching analysis was used at a ratio of 1:1 to reduce confounding effects, and perioperative clinical outcomes were compared between the two groups. The primary outcome was overall postoperative complications (POCs). Secondary outcomes comprised time to bowel function recovery, postoperative hospital stay, mortality, and 30-day readmission rate. Of 1349 identified patients, 296 (21.9%) experienced overall POCs. Before matching, multivariable analysis revealed that age, body mass index, diabetes, operation time, and extent of gastrectomy were independent risk factors for overall POCs. After matching, each group comprised 495 patients, and no significant differences were observed between the groups for all parameters except tumor location. Compared with TG, DG was associated with significantly earlier days to first flatus and to eating a soft diet, and shorter postoperative hospital stay (P < 0.05). The incidence of overall- and severe POCs (Clavien-Dindo grade ≥ IIIa) in the TG group was significantly higher vs. the DG group (P < 0.05). There was no significant difference in the number of days to eating a liquid diet, or mortality and 30-day readmission rates between the groups (P > 0.05). In the subgroup analysis for middle-third gastric cancer, the TG group experienced higher rates of overall- and severe POCs, with a longer postoperative hospital stay. Compared with DG, patients who underwent TG had higher POC rates, slower recovery of bowel function, and longer duration of hospitalization under ERAS. Therefore, caution is needed when initiating early feeding for patients who undergo TG.

Gasdermin D deficiency aborts myeloid calcium influx to drive granulopoiesis in lupus nephritis.

Gasdermin D (GSDMD) is emerging as an important player in autoimmune diseases, but its exact role in lupus nephritis (LN) remains controversial. Here, we identified markedly elevated GSDMD in human and mouse LN kidneys, predominantly in CD11b+ myeloid cells. Global or myeloid-conditional deletion of GSDMD was shown to exacerbate systemic autoimmunity and renal injury in lupus mice with both chronic graft-versus-host (cGVH) disease and nephrotoxic serum (NTS) nephritis. Interestingly, RNA sequencing and flow cytometry revealed that myeloid GSDMD deficiency enhanced granulopoiesis at the hematopoietic sites in LN mice, exhibiting remarkable enrichment of neutrophil-related genes, significant increases in total and immature neutrophils as well as granulocyte/macrophage progenitors (GMPs). GSDMD-deficient GMPs and all-trans-retinoic acid (ATRA)-stimulated human promyelocytes NB4 were further demonstrated to possess enhanced clonogenic and differentiation abilities compared with controls. Mechanistically, GSDMD knockdown promoted self-renewal and granulocyte differentiation by restricting calcium influx, contributing to granulopoiesis. Functionally, GSDMD deficiency led to increased pathogenic neutrophil extracellular traps (NETs) in lupus peripheral blood and bone marrow-derived neutrophils. Taken together, our data establish that GSDMD deletion accelerates LN development by promoting granulopoiesis in a calcium influx-regulated manner, unraveling its unrecognized critical role in LN pathogenesis.

The Spermine Oxidase/Spermine Axis Coordinates ATG5-Mediated Autophagy to Orchestrate Renal Senescence and Fibrosis.

Decreased plasma spermine levels are associated with kidney dysfunction. However, the role of spermine in kidney disease remains largely unknown. Herein, it is demonstrated that spermine oxidase (SMOX), a key enzyme governing polyamine metabolism, is predominantly induced in tubular epithelium of human and mouse fibrotic kidneys, alongside a reduction in renal spermine content in mice. Moreover, renal SMOX expression is positively correlated with kidney fibrosis and function decline in patients with chronic kidney disease. Importantly, supplementation with exogenous spermine or genetically deficient SMOX markedly improves autophagy, reduces senescence, and attenuates fibrosis in mouse kidneys. Further, downregulation of ATG5, a critical component of autophagy, in tubular epithelial cells enhances SMOX expression and reduces spermine in TGF-ß1-induced fibrogenesis in vitro and kidney fibrosis in vivo. Mechanically, ATG5 readily interacts with SMOX under physiological conditions and in TGF-ß1-induced fibrogenic responses to preserve cellular spermine levels. Collectively, the findings suggest SMOX/spermine axis is a potential novel therapy to antagonize renal fibrosis, possibly by coordinating autophagy and suppressing senescence.

The glycolytic enzyme PFKFB3 drives kidney fibrosis through promoting histone lactylation-mediated NF-κB family activation.

Persistently elevated glycolysis in kidney has been demonstrated to promote chronic kidney disease (CKD). However, the underlying mechanism remains largely unclear. Here, we observed that 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3), a key glycolytic enzyme, was remarkably induced in kidney proximal tubular cells (PTCs) following ischemia-reperfusion injury (IRI) in mice, as well as in multiple etiologies of patients with CKD. PFKFB3 expression was positively correlated with the severity of kidney fibrosis. Moreover, patients with CKD and mice exhibited increased urinary lactate/creatine levels and kidney lactate, respectively. PTC-specific deletion of PFKFB3 significantly reduced kidney lactate levels, mitigated inflammation and fibrosis, and preserved kidney function in the IRI mouse model. Similar protective effects were observed in mice with heterozygous deficiency of PFKFB3 or those treated with a PFKFB3 inhibitor. Mechanistically, lactate derived from PFKFB3-mediated tubular glycolytic reprogramming markedly enhanced histone lactylation, particularly H4K12la, which was enriched at the promoter of NF-κB signaling genes like Ikbkb, Rela, and Relb, activating their transcription and facilitating the inflammatory response. Further, PTC-specific deletion of PFKFB3 inhibited the activation of IKKß, I κ B α, and p65 in the IRI kidneys. Moreover, increased H4K12la levels were positively correlated with kidney inflammation and fibrosis in patients with CKD. These findings suggest that tubular PFKFB3 may play a dual role in enhancing NF-κB signaling by promoting both H4K12la-mediated gene transcription and its activation. Thus, targeting the PFKFB3-mediated NF-κB signaling pathway in kidney tubular cells could be a novel strategy for CKD therapy.

Preparation of Ultrafine Co- and Ni-Coated (Ti,W,Mo,Ta)(C,N) Powders and Their Influence on the Microstructure of Ti(C,N)-Based Cermets.

The use of metal-coated ceramic powders not only effectively enhances the wettability of the metal-ceramic interface but also promotes a more uniform microstructure in Ti(C,N)-based cermets, which is advantageous for improving their mechanical properties. In this study, ultrafine Co- and Ni-coated (Ti,W,Mo,Ta)(C,N) powders were synthesized via the spray-drying-in-situ carbothermal reduction method. Subsequently, Ti(C,N)-based cermets were effectively fabricated using the as-prepared ultrafine Co- and Ni-coated (Ti,W,Mo,Ta)(C,N) powders. The impact of reaction temperature, heating rate, and isothermal time on the phase and microstructure of prepared powders was analyzed using X-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Additionally, the microstructure of the as-sintered cermets was experimentally investigated. The findings reveal that the complete reduction of Co and Ni metal salts, pre-coated on the surface of (Ti,W,Mo,Ta)(C,N) particles, can be achieved through rapid heating (10 °C/min) in a specific temperature range (600-1000 °C) with an isothermal time of 3 h at a lower reduction temperature (1000 °C). The synthesized powders have only two phases: the (Ti,W,Mo,Ta)(C,N) phase and Co/Ni phase, and no other heterogeneous phases were observed with an oxygen content of 0.261 wt.%. Notably, the conventional core-rim structure was not dominant in the cermets obtained from the prepared Co- and Ni-coated (Ti,W,Mo,Ta)(C,N) powders. Moreover, the heterogeneous segregation effect of the Co/Ni coating on the ultrafine powder particles resulted in a finer microstructure than the traditional cermets with the same composition. However, the grain size is mainly in the range of 0.5-0.8 µm. The weaker residual stresses at the core and rim interfaces and the finer particle distributions could theoretically enhance the toughness of Ti(C,N)-based cermets, simultaneously.

COVID-19 Rebound After VV116 vs Nirmatrelvir-Ritonavir Treatment: A Randomized Clinical Trial.

Importance: With the widespread use of anti-SARS-CoV-2 drugs, accumulating data have revealed potential viral load rebound after treatment. Objective: To compare COVID-19 rebound after a standard 5-day course of antiviral treatment with VV116 vs nirmatrelvir-ritonavir. Design, Setting, and Participants: This is a single-center, investigator-blinded, randomized clinical trial conducted in Shanghai, China. Adult patients with mild-to-moderate COVID-19 and within 5 days of SARS-CoV-2 infection were enrolled between December 20, 2022, and January 19, 2023, and randomly allocated to receive either VV116 or nirmatrelvir-ritonavir. Interventions: Participants in the VV116 treatment group received oral 600-mg VV116 tablets every 12 hours on day 1 and 300 mg every 12 hours on days 2 through 5. Participants in the nirmatrelvir-ritonavir treatment group received oral nirmatrelvir-ritonavir tablets with 300 mg of nirmatrelvir plus 100 mg of ritonavir every 12 hours for 5 days. Participants were followed up every other day until day 28 and every week until day 60. Main Outcomes and Measures: The primary outcome was viral load rebound (VLR), defined as a half-log increase in viral RNA copies per milliliter compared with treatment completion. Secondary outcomes included a reduction in the cycle threshold value of 1.5 or more, time until VLR, and symptom rebound, defined as an increase of more than 2 points in symptom score compared with treatment completion. The primary outcome and secondary outcomes were analyzed using the full analysis set. Sensitivity analyses were conducted using the per protocol set. Adverse events were analyzed using the safety analysis set. Results: The full analysis set included 345 participants (mean [SD] age, 53.2 [16.8] years; 175 [50.7%] were men) who received VV116 (n = 165) or nirmatrelvir-ritonavir (n = 180). Viral load rebound occurred in 33 patients (20.0%) in the VV116 group and 39 patients (21.7%) in the nirmatrelvir-ritonavir group (P = .70). Symptom rebound occurred in 41 of 160 patients (25.6%) in the VV116 group and 40 of 163 patients (24.5%) in the nirmatrelvir-ritonavir group (P = .82). Viral whole-genome sequencing of 24 rebound cases revealed the same lineage at baseline and at viral load rebound in each case. Conclusions and Relevance: In this randomized clinical trial of patients with mild-to-moderate COVID-19, viral load rebound and symptom rebound were both common after a standard 5-day course of treatment with either VV116 or nirmatrelvir-ritonavir. Prolongation of treatment duration might be investigated to reduce COVID-19 rebound. Trial Registration: Chinese Clinical Trial Registry Identifier: ChiCTR2200066811.

Water temperature governs organophosphate ester dynamics in the aquatic food chain of Poyang Lake.

Organophosphate esters (OPEs) are increasingly recognized as pervasive environmental contaminants, primarily from their extensive application in flame retardants and plasticizers. Despite their widespread presence, the intricacies of OPE bioaccumulation within aquatic ecosystems remain poorly understood, particularly the environmental determinants influencing their distribution and the bioaccumulation dynamics across aquatic food chains. Here we show that water temperature plays a crucial role in modulating the dispersion of OPE in the aquatic environment of Poyang Lake. We quantified OPE concentrations across various matrices, uncovering levels ranging from 0.198 to 912.622 ng L-1 in water, 0.013-493.36 ng per g dry weight (dw) in sediment, 0.026-41.92 ng per g wet weight (ww) in plankton, 0.13-2100.72 ng per g dw in benthic invertebrates, and 0.31-3956.49 ng per g dw in wild fish, highlighting a pronounced bioaccumulation gradient. Notably, the intestines emerged as the principal site for OPE absorption, displaying the highest concentrations among the seven tissues examined. Among the various OPEs, tris(chloroethyl) phosphate was distinguished by its significant bioaccumulation potential within the aquatic food web, suggesting a need for heightened scrutiny. The propensity for OPE accumulation was markedly higher in benthic invertebrates than wild fish, indicating a differential vulnerability within aquatic biota. This study lays a foundational basis for the risk assessment of OPEs as emerging contaminants and underscores the imperative to prioritize the examination of bioaccumulation effects, particularly in benthic invertebrates, to inform future environmental safeguarding strategies.

[Effect of No-tillage on Soil Aggregates in Farmland：A Meta Analysis].

In order to clarify the impact of no-tillage on the quality of farmland soil aggregates in China and promote the adaptive application of no-tillage practices， a Meta-analysis was conducted by collecting data from 116 published studies. The effects of no-tillage on aggregate size distribution， mean weight diameter （MWD）， and aggregate-associated C were studied. The results showed that compared with that under tillage， no-tillage significantly increased the proportion of macroaggregates （10.9%） and MWD （12.8%） and decreased the proportion of clay and silt （-15.5%） but had no significant effect on soil microaggregate and aggregate-associated C. The subgroup and Meta regression analysis showed that no-tillage significantly increased the proportion of macroaggregates in Northwest China （17.6%） and MWD in North China （15.4%）. In upland and clay loam， no-tillage increased MWD by 12.6% and 18.4%， respectively. The effect of no-tillage on increasing the proportion of macroaggregates increased with the soil pH. When straw returned， no-tillage significantly increased the proportion of macroaggregates （9.6%） and MWD （11.6%）， but no significant effect of no-tillage on aggregates was found after straw removal. Regarding test duration， short-term （ < 5 a） no-tillage could significantly increase the proportion of macroaggregates， whereas long-term （ > 10 a） no-tillage could improve the MWD. In different soil layers， no-tillage could only significantly improve the aggregate size distribution and MWD in topsoil （0-20 cm） but had no effect in subsoil （ > 20 cm）. In summary， no-tillage could improve aggregate size distribution and stability but had no effect on aggregate-associated C. Production region， soil properties， field management methods， and other factors should be fully considered in production practice to effectively improve the quality of soil aggregates.

GANSamples-ac4C: Enhancing ac4C site prediction via generative adversarial networks and transfer learning.

RNA modification, N4-acetylcytidine (ac4C), is enzymatically catalyzed by N-acetyltransferase 10 (NAT10) and plays an essential role across tRNA, rRNA, and mRNA. It influences various cellular functions, including mRNA stability and rRNA biosynthesis. Wet-lab detection of ac4C modification sites is highly resource-intensive and costly. Therefore, various machine learning and deep learning techniques have been employed for computational detection of ac4C modification sites. The known ac4C modification sites are limited for training an accurate and stable prediction model. This study introduces GANSamples-ac4C, a novel framework that synergizes transfer learning and generative adversarial network (GAN) to generate synthetic RNA sequences to train a better ac4C modification site prediction model. Comparative analysis reveals that GANSamples-ac4C outperforms existing state-of-the-art methods in identifying ac4C sites. Moreover, our result underscores the potential of synthetic data in mitigating the issue of data scarcity for biological sequence prediction tasks. Another major advantage of GANSamples-ac4C is its interpretable decision logic. Multi-faceted interpretability analyses detect key regions in the ac4C sequences influencing the discriminating decision between positive and negative samples, a pronounced enrichment of G in this region, and ac4C-associated motifs. These findings may offer novel insights for ac4C research. The GANSamples-ac4C framework and its source code are publicly accessible at http://www.healthinformaticslab.org/supp/.

Do the same chlorinated organophosphorus flame retardants that cause cytotoxicity and DNA damage share the same pathway?

Organophosphorus flame retardants (OPFRs) have been frequently detected with relatively high concentrations in various environmental media and are considered emerging environmental pollutants. However, their biological effect and underlying mechanism is still unclear, and whether chlorinated OPFRs (Cl-OPFRs) cause adverse outcomes with the same molecular initial events or share the same key events (KEs) remains unknown. In this study, in vitro bioassays were conducted to analyze the cytotoxicity, mitochondrial impairment, DNA damage and molecular mechanisms of two Cl-OPFRs. The results showed that these two Cl-OPFRs, which have similar structures, induced severe cellular and molecular damages via different underlying mechanisms. Both tris(2-chloroethyl) phosphate (TCEP) and tris(1-chloro-2-propyl) (TCPP) induced oxidative stress-mediated mitochondrial impairment and DNA damage, as shown by the overproduction of intracellular reactive oxygen species (ROS) and mitochondrial superoxide. Furthermore, the DNA damage caused by TCPP resulted in p53/p21-mediated cell cycle arrest, as evidenced by flow cytometry and real-time PCR. At the cellular and molecular levels, TCPP increased the sub-G1 apoptotic peak and upregulated the p53/Bax apoptosis pathway, possibly resulted in apoptosis associated with its stronger cytotoxicity. Although structurally similar to TCPP, TCEP did not induce mitochondrial impairment and DNA damage by the same KEs. These results provide insight into the toxicity of Cl-OPFRs with similar structures but different mechanisms, which is of great significance for constructing adverse outcome pathways or determining intermediate KEs.

Fish Physiologically Based Toxicokinetic Modeling Approach for In Vitro-In Vivo and Cross-Species Extrapolation of Endocrine-Disrupting Chemicals in Risk Assessment.

High-throughput in vitro assays combined with in vitro-in vivo extrapolation (IVIVE) leverage in vitro responses to predict the corresponding in vivo exposures and thresholds of concern. The integrated approach is also expected to offer the potential for efficient tools to provide estimates of chemical toxicity to various wildlife species instead of animal testing. However, developing fish physiologically based toxicokinetic (PBTK) models for IVIVE in ecological applications is challenging, especially for plausible estimation of an internal effective dose, such as fish equivalent concentration (FEC). Here, a fish PBTK model linked with the IVIVE approach was established, with parameter optimization of chemical unbound fraction, pH-dependent ionization and hepatic clearance, and integration of temperature effect and growth dilution. The fish PBTK-IVIVE approach provides not only a more precise estimation of tissue-specific concentrations but also a reasonable approximation of FEC targeting the estrogenic potency of endocrine-disrupting chemicals. Both predictions were compared with in vivo data and were accurate for most indissociable/dissociable chemicals. Furthermore, the model can help determine cross-species variability and sensitivity among the five fish species. Using the available IVIVE-derived FEC with target pathways is helpful to develop predicted no-effect concentration for chemicals with similar mode of action and support screening-level ecological risk assessment.

Small-molecule anti-COVID-19 drugs and a focus on China's homegrown mindeudesivir (VV116).

The coronavirus disease 2019 (COVID-19) pandemic has stimulated tremendous efforts to develop therapeutic agents that target severe acute respiratory syndrome coronavirus 2 to control viral infection. So far, a few small-molecule antiviral drugs, including nirmatrelvir-ritonavir (Paxlovid), remdesivir, and molnupiravir have been marketed for the treatment of COVID-19. Nirmatrelvir-ritonavir has been recommended by the World Health Organization as an early treatment for outpatients with mild-to-moderate COVID-19. However, the existing treatment options have limitations, and effective treatment strategies that are cost-effective and convenient for tackling COVID-19 are still needed. To date, four domestically developed oral anti-COVID-19 drugs have been granted conditional market approval in China. These drugs include azvudine, simnotrelvir-ritonavir (Xiannuoxin), leritrelvir, and mindeudesivir (VV116). Preclinical and clinical studies have explored the efficacy and tolerability of mindeudesivir and supported its early use in mild-to-moderate COVID-19 cases at high risk for progression. In this review, we discuss the most recent findings regarding the pharmacological mechanism and therapeutic effects focusing on mindeudesivir and other small-molecule antiviral agents for COVID-19. These findings will expand our understanding and highlight the potential widespread application of China's homegrown anti-COVID-19 drugs.