CD63 + tumor-associated macrophages drive the progression of hepatocellular carcinoma through the induction of epithelial-mesenchymal transition and lipid reprogramming.

BACKGROUND: Tumor-associated macrophages (TAMs) constitute a substantial part of human hepatocellular carcinoma (HCC). The present study was devised to explore TAM diversity and their roles in HCC progression. METHODS: Through the integration of multiple 10 × single-cell transcriptomic data derived from HCC samples and the use of consensus nonnegative matrix factorization (an unsupervised clustering algorithm), TAM molecular subtypes and expression programs were evaluated in detail. The roles played by these TAM subtypes in HCC were further probed through pseudotime, enrichment, and intercellular communication analyses. Lastly, vitro experiments were performed to validate the relationship between CD63, which is an inflammatory TAM expression program marker, and tumor cell lines. RESULTS: We found that the inflammatory expression program in TAMs had a more obvious interaction with HCC cells, and CD63, as a marker gene of the inflammatory expression program, was associated with poor prognosis of HCC patients. Both bulk RNA-seq and vitro experiments confirmed that higher TAM CD63 expression was associated with the growth of HCC cells as well as their epithelial-mesenchymal transition, metastasis, invasion, and the reprogramming of lipid metabolism. CONCLUSIONS: These analyses revealed that the TAM inflammatory expression program in HCC is closely associated with malignant tumor cells, with the hub gene CD63 thus representing an ideal target for therapeutic intervention in this cancer type.

SLC25A19 is a novel prognostic biomarker related to immune invasion and ferroptosis in HCC.

SLC25A19 is a mitochondrial thiamine pyrophosphate (TPP) carrier that mediates TPP entry into the mitochondria. SLC25A19 has been recognized to play a crucial role in many metabolic diseases, but its role in cancer has not been clearly reported. Based on clinical data from The Cancer Genome Atlas (TCGA), the following parameters were analyzed among HCC patients: SLC25A19 expression, enrichment analyses, immune infiltration, ferroptosis and prognosis analyses. In vitro, the SLC25A19 high expression was validated by qRT-PCR and Immunohistochemistry. Subsequently, a series of cell function experiments, including CCK8, EdU, clone formation, trans-well and scratch assays, were conducted to illustrate the effect of SLC25A19 on the growth and metastasis of cancer cells. Meanwhile, indicators related to ferroptosis were also detected. SCL25A19 is highly expressed in HCC and predicts a poor prognosis. Elevated SLC25A19 expression in HCC patients was markedly associated with T stage, pathological status (PS), tumor status (TS), histologic grade (HG), and AFP. Our results indicate that SLC25A19 has a generally good prognosis predictive and diagnostic ability. The results of gene enrichment analyses showed that SLC25A19 is significantly correlated with immune infiltration, fatty acid metabolism, and ferroptosis marker genes. In vitro experiments have confirmed that silencing SLC25A19 can significantly inhibit the proliferation and migration ability of cancer cells and induce ferroptosis in HCC. In conclusion, these findings indicate that SLC25A19 is novel prognostic biomarker related to immune invasion and ferroptosis in HCC, and it is an excellent candidate for therapeutic target against HCC.

Polyprodrug nanomedicine for chemiexcitation-triggered self-augmented cancer chemotherapy and gas therapy.

Carbon monoxide (CO) has emerged as a potential antitumor agent by inducing the dysfunction of mitochondria and the apoptosis of cancer cells. However, it remains challenging to deliver appropriate amount of CO into tumor to ensure efficient tumor growth suppression with minimum side effects. Herein we developed a CO prodrug-loaded nanomedicine based on the self-assembly of camptothecin (CPT) polyprodrug amphiphiles. The polyprodrug nanoparticles readily dissociate upon exposure to endogenous H2O2 in the tumor, resulting in rapid release of CPT and generation of high-energy intermediate dioxetanedione. The latter can transfer the energy to neighboring CO prodrugs to activate CO production by chemiexcitation, while CPT promotes the generation of H2O2 in tumors, which in turn facilitates cascade CPT and CO release. As a result, the polyprodrug nanoparticles display remarkable tumor suppression in both subcutaneous and orthotopic breast tumor-bearing mice owing to the self-augmented CPT release and CO generation. In addition, no obvious systemic toxicity was observed in mice treated with the metal-free CO prodrug-loaded nanomedicine, suggesting the good biocompatibility of the polyprodrug nanoparticles. Our work provides new insights into the design and construction of polyprodrug nanomedicines for synergistic chemo/gas therapy.

Otitis media with effusion in adults during the SARS-CoV-2 epidemic.

OBJECTIVES: The purpose of this study was to investigate the fluctuations in the prevalence of individuals diagnosed with otitis media with effusion (OME) during the SARS-CoV-2 pandemic, while also evaluating the persistence of SARS-CoV-2 in middle ear effusion (MEE) and assessing the effectiveness of tympanocentesis as a treatment modality for OME in this specific period. METHODS: The total number of outpatients and patients diagnosed with OME in our department was recorded for January 2022 and January 2023. Thirty patients (aged 15-86 years) were categorized into two groups: group A (n = 12), who developed OME during their SARS-CoV-2 infection and group B (n = 18), who experienced OME after the resolution of SARS-CoV-2 infection. All patients underwent otoendoscopic tympanocentesis (without a ventilation tube), where MEE and nasopharyngeal secretions were simultaneously collected for SARS-CoV-2 detection by polymerase chain reaction. The time interval from SARS-CoV-2 infection to tympanocentesis, results of SARS-CoV-2 detection, preoperative and postoperative average hearing threshold, and Eustachian Tube Dysfunction Questionnaire (ETDQ-7) scores were documented. RESULTS: The proportion of outpatients with OME in January 2023 was higher than that in January 2022. There were five patients who had positive test results for SARS-CoV-2 on MEE after tympanocentesis. These 5 patients underwent tympanocentesis at a mean of 28 ± 7.28 days following confirmation of SARS-CoV-2 infection. The ETDQ-7 scores of group A exhibited a reduction from 21.85 ± 4.8 to 10.00 ± 4.07 following tympanocentesis, while the ETDQ-7 scores of group B also demonstrated a decrease from 21.22 ± 4.65 to 10.11 ± 3.68 after undergoing tympanocentesis. The tympanocentesis was effective in both groups. CONCLUSIONS: The study confirmed that the proportion of outpatients with OME in the Clinics of Otolaryngology during the SARS-CoV-2 epidemic increased significantly. SARS-CoV-2 RNA was detectable in MEE of COVID-19-related OME patients. Tympanocentesis was therapeutic for OME during SARS-CoV-2 infection, which facilitated viral clearance in MEE.

Structural and molecular investigation of the impact of S30L and D88N substitutions in G9R protein on coupling with E4R from Monkeypox virus (MPXV).

Understanding the pathogenesis mechanism of the Monkeypox virus (MPXV) is essential to guide therapeutic development against the Monkeypox virus. In the current study, we investigated the impact of the only two reported substitutions, S30L, D88N, and S30L-D88N on the G9R of the replication complex in 2022 with E4R using structural modeling, simulation, and free energy calculation methods. From the molecular docking and dissociation constant (KD) results, it was observed that the binding affinity did not increase in the mutants, but the interaction paradigm was altered by these substitutions. Molecular simulation data revealed that these mutations are responsible for destabilization, changes in protein packing, and internal residue fluctuations, which can cause functional variance. Additionally, hydrogen bonding analysis revealed that the estimated number of hydrogen bonds are almost equal among the wild-type G9R and each mutant. The total binding free energy for the wild-type G9R with E4R was -85.00 kcal/mol while for the mutants the TBE was -42.75 kcal/mol, -43.68 kcal/mol, and -48.65 kcal/mol respectively. This shows that there is no direct impact of these two reported mutations on the binding with E4R, or it may affect the whole replication complex or any other mechanism involved in pathogenesis. To explore these variations further, we conducted PCA and FEL analyses. Based on our findings, we speculate that within the context of interaction with E4R, the mutations in the G9R protein might be benign, potentially leading to functional diversity associated with other proteins.Communicated by Ramaswamy H. Sarma.

IL-22-Induced Ubiquitin-Specific Protease 15 Promotes Proliferation and Inflammation of Keratinocytes through Stabilization of Squamous Cell Carcinoma Antigen 2.

Ubiquitin-specific protease 15 (USP15) plays a significant role in regulating various biological processes in several autoimmune diseases and cancers. However, its role in psoriatic keratinocytes (KCs) has not been extensively studied. In this study, we described that USP15 promotes proliferation and inflammation in KCs by stabilizing squamous cell carcinoma antigen 2. We discovered that the expression of USP15 and squamous cell carcinoma antigen 2 was elevated in lesions from patients with clinical psoriasis and an imiquimod-induced psoriatic dermatitis mouse model. USP15 was able to bind, deubiquitinate, and stabilize squamous cell carcinoma antigen 2. Knocking down USP15 resulted in reduced KC inflammation and impaired KC viability and clonogenicity. Topically applying USP15 small interfering RNA significantly ameliorated imiquimod-induced psoriatic dermatitis and reduced the infiltration of T cells and neutrophils. In addition, we determined that IL-22 was a key cytokine that upregulated the expression of USP15. These findings provide insights regarding the mechanisms involved in the proliferation and inflammation of KCs mediated by IL-22, suggesting a potential IL-22-USP15-squamous cell carcinoma antigen 2 axis in the pathogenesis of psoriatic KCs.

Incorporation of Epoxy Carbon onto CeO2-Supported Pt to Tackle the CO Self-Poisoning Issue.

The catalytic oxidation of carbon monoxide (CO) under ambient conditions plays a crucial role in the abatement of indoor CO, which poses risks to human health. Despite the notable activity exhibited by Pt-based catalysts in CO oxidation, their efficacy is usually diminished by the CO self-poisoning issue. In this work, three different Pt/CeO2-based catalysts, which have distinct coordinative environments of Pt but an identical Pt/CeO2 substrate structure, were synthesized by activating the catalyst with CO using different temperatures and durations. Compared with clean and graphite-covered Pt on CeO2, the one modified by epoxy carbon showed higher activity and stability. The combination of characterizations and density functional theory modeling demonstrated that the clean Pt on CeO2 rapidly deactivated due to the CO self-poisoning albeit high initial activity, and conversely, low initial activity was observed for the more stable graphite-covered catalyst due to the obstruction of the Pt site. In contrast, epoxy carbon species on Pt shifted the d-band of Pt to lower energy, weakening the Pt-CO binding strength. Such a modification mitigated the self-poisoning effect while maintaining ample active sites and enabling the complete oxidative removal of CO under ambient conditions. This work may provide a general approach to tackling the self-poisoning issue.

Establishment and validation of a callus tissue transformation system for German chamomile (Matricaria chamomilla L.).

BACKGROUND: German chamomile (Matricaria chamomilla L.) is an important medicinal plant, and the essential oils in the flowers have various biological activities. Genetic transformation systems are important for plant quality improvement and molecular research. To the best of our knowledge, a genetic transformation system has not yet been reported for German chamomile. RESULTS: In this study, we developed Agrobacterium-mediated transformation protocols for German chamomile callus tissues. This involved optimizing key parameters, such as hygromycin and cefotaxime concentrations, bacterial density, and infection and co-culture durations. We also performed gas chromatography-mass spectrometry analysis to identify volatile compounds in non-transgenic and transgenic callus and hairy root tissues. Furthermore, to compare and verify the callus transformation system of German chamomile, we transferred McFPS to the hairy roots of German chamomile. The results showed that the optimal conditions for Agrobacterium-mediated callus tissue transformation were as follows: explant, petiole; cefotaxime concentration, 300 mg/L; hygromycin concentration, 10 mg/L; and bacterial solution concentration, OD600 = 0.6; callus transformation efficiency was the highest when the co-culture time was 3 days. CONCLUSIONS: Establishment of a high-efficiency callus transformation system will lay the foundation for gene function identification in German chamomile.

The solution surface of the Li-Stephens haplotype copying model.

The Li-Stephens (LS) haplotype copying model forms the basis of a number of important statistical inference procedures in genetics. LS is a probabilistic generative model which supposes that a sampled chromosome is an imperfect mosaic of other chromosomes found in a population. In the frequentist setting which is the focus of this paper, the output of LS is a "copying path" through chromosome space. The behavior of LS depends crucially on two user-specified parameters, [Formula: see text] and [Formula: see text], which are respectively interpreted as the rates of mutation and recombination. However, because LS is not based on a realistic model of ancestry, the precise connection between these parameters and the biological phenomena they represent is unclear. Here, we offer an alternative perspective, which considers [Formula: see text] and [Formula: see text] as tuning parameters, and seeks to understand their impact on the LS output. We derive an algorithm which, for a given dataset, efficiently partitions the [Formula: see text] plane into regions where the output of the algorithm is constant, thereby enumerating all possible solutions to the LS model in one go. We extend this approach to the "diploid LS" model commonly used for phasing. We demonstrate the usefulness of our method by studying the effects of changing [Formula: see text] and [Formula: see text] when using LS for common bioinformatic tasks. Our findings indicate that using the conventional (i.e., population-scaled) values for [Formula: see text] and [Formula: see text] produces near optimal results for imputation, but may systematically inflate switch error in the case of phasing diploid genotypes.

Government regulation strategy, leading firms' innovation strategy, and following firms imitation strategy: An analysis based on evolutionary game theory.

In the innovation ecosystem, the knowledge-based game behavior of each subject not only pertains to its own survival and development but also affects evolution of the innovation ecosystem. The present study investigates the choice of government's regulation strategy, leading firms' innovation protection strategy and following firms' imitation strategy from the perspective of group evolutionary game. Based on the cost-benefit perspective, an asymmetric tripartite evolutionary game model and a simulation model are constructed to analyze the strategies and stability of the evolutionary equilibrium of each subject. We focus mainly on the protection intensity of innovation achievements by leading enterprises and the difficulty of imitation and substitution by following enterprises. The cost of patent operation and maintenance, government subsidies, and the relative difficulty of technology substitution and imitation were identified as the key factors affecting the evolutionary equilibrium of the system. Based on different scenarios resulting from the aforementioned factors, four equilibrium states are observed in the system, namely {no government regulation, technology secrecy, substitution}, {no government regulation, technology secrecy, imitation}, {no government regulation, patent application, imitation}, and {government regulation, patent application, imitation}. Finally, the study suggests corresponding recommendations for the three parties, which can help governments as well as the leading and following firms to choose appropriate behavioral strategies. At the same time, this study offers positive insights to participants in the global innovation ecosystem.

Proteomics-based vaccine targets annotation and design of subunit and mRNA-based vaccines for Monkeypox virus (MPXV) against the recent outbreak.

Monkeypox Virus (MPXV) is a growing public health threat with increasing cases and fatalities globally. To date, no specific vaccine or small molecule therapeutic choices are available for the treatment of MPXV disease. In this work, we employed proteomics and structural vaccinology approaches to design mRNA and multi-epitopes-based vaccines (MVC) against MPXV. We first identified ten proteins from the whole proteome of MPXV as potential vaccine targets. We then employed structural vaccinology approaches to map potential epitopes of these proteins for B cell, cytotoxic T lymphocytes (CTL), and Helper T lymphocytes (HTL). Finally, 9 CTL, 6 B cell, and 5 HTL epitopes were joined together through suitable linkers to construct MVC (multi-epitope vaccine) and mRNA-based vaccines. Molecular docking, binding free energy calculation, and in silico cloning revealed robust interaction of the designed MVC with toll-like receptor 2 (TLR2) and efficient expression in E. Coli K12 strain. The immune simulation results revealed that the antigen titer after the injection reached to the maximum level on the 5th day and an abrupt decline in the antigen titer was observed upon the production of IgM, IgG and IgM + IgG, dendritic cells, IFN-gamma, and IL (interleukins), which suggested the potential of our designed vaccine candidate for inducing an immune response against MPXV.

Identification and characterization of bone/cartilage-associated signatures in common fibrotic skin diseases.

Background: Fibrotic skin diseases are characterized by excessive accumulation of the extracellular matrix (ECM) and activation of fibroblasts, leading to a global healthcare burden. However, effective treatments of fibrotic skin diseases remain limited, and their pathological mechanisms require further investigation. This study aims to investigate the common biomarkers and therapeutic targets in two major fibrotic skin diseases, namely, keloid and systemic sclerosis (SSc), by bioinformatics analysis. Methods: The keloid (GSE92566) and SSc (GSE95065) datasets were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified, followed by functional enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We then constructed a protein-protein interaction (PPI) network for the identification of hub genes. We explored the possibility of further functional enrichment analysis of hub genes on the Metascape, GeneMANIA, and TissueNexus platforms. Transcription factor (TF)-hub gene and miRNA-hub gene networks were established using NetworkAnalyst. We fixed GSE90051 and GSE76855 as the external validation datasets. Student's t-test and receiver operating characteristic (ROC) curve were used for candidate hub gene validation. Hub gene expression was assessed in vitro by quantitative real-time PCR. Results: A total of 157 overlapping DEGs (ODEGs) were retrieved from the GSE92566 and GSE95065 datasets, and five hub genes (COL11A1, COL5A2, ASPN, COL10A1, and COMP) were identified and validated. Functional studies revealed that hub genes were predominantly enriched in bone/cartilage-related and collagen-related processes. FOXC1 and miR-335-5p were predicted to be master regulators at both transcriptional and post-transcriptional levels. Conclusion: COL11A1, COL5A2, ASPN, COL10A1, and COMP may help understand the pathological mechanism of the major fibrotic skin diseases; moreover, FOXC1 and miR-355-5p could build a regulatory network in keloid and SSc.

Experimental and Kinetic Study of the Effect of Nitrogen Dioxide on Ethanol Autoignition.

The contribution of NO2 to the ethanol ignition delay time was investigated behind reflected shock waves. The experiments were performed at a pressure of 0.20 MPa, temperature range of 1050-1650 K, equivalence ratio of 0.5/1.0/1.5, and ethanol/NO2 mixing ratios of 100/0, 90/10, and 50/50. The experimental results showed that the addition of NO2 decreased the ignition delay time and promoted the reactivity of ethanol under all equivalence ratios. With an increase in NO2 blending, the effect of equivalence ratio on the ethanol ignition delay time decreased, and with an increase in temperature, the effect of NO2 in promoting ethanol ignition weakened. An updated mechanism was proposed to quantify NO2-promoted ethanol ignition. The mechanism was validated based on available experimental data, and the results were in line with the experimental trends under all conditions. Chemical kinetic analyses were performed to interpret the interactions between NO2 and ethanol for fuel ignition. The numerical analysis indicated that the promotion effect of NO2 is primarily due to an increase of the rate of production and concentration of the radical pool, especially the OH radical pool. The reaction NO + HO2 ⇔ NO2 + OH is key to generating chain-initiating OH radicals.

Anlotinib dramatically improved pulmonary hypertension and hypoxia caused by Pulmonary Tumor Thrombotic Microangiopathy (PTTM) associated with gastric carcinoma: a case report.

BACKGROUND: Pulmonary tumor thrombotic microangiopathy (PTTM) is a rare malignancy-related respiratory complication, demonstrating rapid progression of pulmonary hypertension (PH) and respiratory failure. Although a number of treatments have been attempted for patients diagnosed with or suspected of having PTTM, successful-treated cases of PTTM were mainly from imatinib therapy, which was a PDGF receptor inhibitor. Anlotinib was a novel tyrosine kinase inhibitor that targets VEGFR, FGFR, PDGFR, and c-kit. CASE PRESENTATION: We reported a patient of PTTM associated with gastric carcinoma, whom were treated with anlotinib, thereby exhibiting significant improvement of PH and respiratory dysfunction. CONCLUSION: Our case provides a new understanding of therapy to PTTM, with implications for defining anlotinib as candidate drug for PTTM. Clinical diagnosis and prompt initiation of anlotinib might be one of the strategies in patients with unstable PTTM.

Ranking Breast Cancer Drugs and Biomarkers Identification Using Machine Learning and Pharmacogenomics.

Breast cancer is one of the major causes of death in women worldwide. It is a diverse illness with substantial intersubject heterogeneity, even among individuals with the same type of tumor, and customized therapy has become increasingly important in this sector. Because of the clinical and physical variability of different kinds of breast cancers, multiple staging and classification systems have been developed. As a result, these tumors exhibit a wide range of gene expression and prognostic indicators. To date, no comprehensive investigation of model training procedures on information from numerous cell line screenings has been conducted together with radiation data. We used human breast cancer cell lines and drug sensitivity information from Cancer Cell Line Encyclopedia (CCLE) and Genomics of Drug Sensitivity in Cancer (GDSC) databases to scan for potential drugs using cell line data. The results are further validated through three machine learning approaches: Elastic Net, LASSO, and Ridge. Next, we selected top-ranked biomarkers based on their role in breast cancer and tested them further for their resistance to radiation using the data from the Cleveland database. We have identified six drugs named Palbociclib, Panobinostat, PD-0325901, PLX4720, Selumetinib, and Tanespimycin that significantly perform on breast cancer cell lines. Also, five biomarkers named TNFSF15, DCAF6, KDM6A, PHETA2, and IFNGR1 are sensitive to all six shortlisted drugs and show sensitivity to the radiations. The proposed biomarkers and drug sensitivity analysis are helpful in translational cancer studies and provide valuable insights for clinical trial design.

Mutational Impacts on the N and C Terminal Domains of the MUC5B Protein: A Transcriptomics and Structural Biology Study.

Cholangiocarcinoma (CCA) involves various epithelial tumors historically linked with poor prognosis because of its aggressive sickness course, delayed diagnosis, and limited efficacy of typical chemotherapy in its advanced stages. In-depth molecular profiling has exposed a varied scenery of genomic alterations as CCA's oncogenic drivers. Previous studies have mainly focused on commonly occurring TP53 and KRAS alterations, but there is limited research conducted to explore other vital genes involved in CCA. We retrieved data from The Cancer Genome Atlas (TCGA) to hunt for additional CCA targets and plotted a mutational landscape, identifying key genes and their frequently expressed variants. Next, we performed a survival analysis for all of the top genes to shortlist the ones with better significance. Among those genes, we observed that MUC5B has the most significant p-value of 0.0061. Finally, we chose two missense mutations at different positions in the vicinity of MUC5B N and C terminal domains. These mutations were further subjected to molecular dynamics (MD) simulation, which revealed noticeable impacts on the protein structure. Our study not only reveals one of the highly mutated genes with enhanced significance in CCA but also gives insights into the influence of its variants. We believe these findings are a good asset for understanding CCA from genomics and structural biology perspectives.