The Application of Organoids in the Study of Antiviral Innate Immunity.

Antiviral innate immunity plays a critical role in the defense against viral infections, yet its complex interactions with viruses have been challenging to study using traditional models. Organoids, three-dimensional (3D) tissue-like structures derived from stem cells, have emerged as powerful tools for modeling human tissues and studying the complex interactions between viruses and the host innate immune system. This chapter summarizes relevant applications of organoids in antiviral innate immunity studies and provides detailed information and experimental procedures for using organoids to study antiviral innate immunity.

Tumor-colonized Streptococcus mutans metabolically reprograms tumor microenvironment and promotes oral squamous cell carcinoma.

BACKGROUND: Oral squamous cell carcinoma (OSCC) remains a major death cause in head and neck cancers, but the exact pathogenesis mechanisms of OSCC are largely unclear. RESULTS: Saliva derived from OSCC patients but not healthy controls (HCs) significantly promotes OSCC development and progression in rat models, and metabolomic analyses reveal saliva of OSCC patients but not HCs and OSCC tissues but not adjacent non-tumor tissues contain higher levels of kynurenic acid (KYNA). Furthermore, large amounts of Streptococcus mutans (S. mutans) colonize in OSCC tumor tissues, and such intratumoral S. mutans mediates KYNA overproductions via utilizing its protein antigen c (PAc). KYNA shifts the cellular types in the tumor microenvironment (TME) of OSCC and predominantly expedites the expansions of S100a8highS100a9high neutrophils to produce more interleukin 1ß (IL-1ß), which further expands neutrophils and induces CD8 + T cell exhaustion in TME and therefore promotes OSCC. Also, KYNA compromises the therapeutic effects of programmed cell death ligand 1 (PD-L1) and IL-1ß blockades in oral carcinogenesis model. Moreover, KYNA-mediated immunosuppressive program and aryl hydrocarbon receptor (AHR) expression correlate with impaired anti-tumor immunity and poorer survival of OSCC patients. CONCLUSIONS: Thus, aberration of oral microbiota and intratumoral colonization of specific oral bacterium such as S. mutans may increase the production of onco-metabolites, exacerbate the oral mucosal carcinogenesis, reprogram a highly immunosuppressive TME, and promote OSCC, highlighting the potential of interfering with oral microbiota and microbial metabolism for OSCC preventions and therapeutics. Video Abstract.

Opportunistic infections changed before and after SARS-CoV-2 infection in inflammatory bowel disease patients: a retrospective single-center study in China.

Objective: SARS-CoV-2 transmission has become a serious worldwide public health concern. However, there is currently insufficient data to determine whether SARS-CoV-2 infection would affect opportunistic infections in inflammatory bowel disease (IBD) patients. Methods: A retrospective study included 451 IBD patients (294 UC and 157 CD). The IBD patients were divided into two groups: before SARS-CoV-2 infection and after SARS-CoV-2 infection, and outcomes were measured for these groups. The primary outcome was the presence and distribution of opportunistic infections. The secondary outcomes included factors associated with opportunistic infections, based on which a nomogram prediction model was developed and validated. Results: After SARS-CoV-2 infection, the proportion of IBD patients with opportunistic infections by Clostridium difficile (21.31% vs. 14.01%, p = 0.044) and Epstein-Barr virus (13.93% vs. 4.35%, p = 0.001) was significantly higher compared to that before. Conversely, the proportion of patients with hepatitis B virus (3.69% vs. 10.14%, p = 0.006) and herpes simplex virus type I (1.23% vs. 4.35%, p = 0.04) infections was significantly lower after the infection. Additionally, pre-SARS-CoV-2 infection factors associated with opportunistic infections in IBD include duration of illness, red blood cell count, the presence of comorbid chronic illnesses, and alcohol consumption, while post-SARS-CoV-2 infection, the primary risk factors involve corticosteroid use, red blood cell count, protein level, and high-sensitivity C-reactive protein. Conclusion: After the SARS-CoV-2 infection, there has been a shift in the occurrence of opportunistic infections among IBD patients. It might be attributed to the use of corticosteroids and also the strengthening of containment measures, heightened public health awareness, and widespread vaccination.

Carvedilol inhibits neuronal hyperexcitability caused by epilepsy-associated KCNT1 mutations.

BACKGROUND AND PURPOSE: KCNT1 encodes a sodium-activated potassium channel (Slack channel), and its mutation can cause several forms of epilepsy. Traditional antiepileptic medications have limited efficacy in treating patients with KCNT1 mutations. Here, we describe one heterozygous KCNT1 mutation, M267T, in a patient with EIMFS. The pathological channel properties of this mutation and its effect on neuronal excitability were investigated. Additionally, this study aimed to develop a medication for effective prevention of KCNT1 mutation-induced seizures. EXPERIMENTAL APPROACH: Wild-type or mutant KCNT1 plasmids were expressed heterologously in Xenopus laevis oocytes, and channel property assessment and drug screening were performed based on two-electrode voltage-clamp recordings. The single-channel properties were investigated using the excised inside-out patches from HEK293T cells. Through in utero electroporation, WT and M267T Slack channels were expressed in the hippocampal CA1 pyramidal neurons in male mice, followed by the examination of the electrical properties using the whole-cell current-clamp technique. The kainic acid-induced epilepsy model in male mice was used to evalute the antiseizure effects of carvedilol. KEY RESULTS: The KCNT1 M267T mutation enhanced Slack channel function by increasing single-channel open probability. Through screening 16 FDA-approved ion channel blockers, we found that carvedilol effectively reversed the mutation-induced gain-of-function channel properties. Notably, the KCNT1 M267T mutation in the mouse hippocampal CA1 pyramidal neurons affected afterhyperpolarization properties and induced neuronal hyperexcitability, which was inhibited by carvedilol. Additionally, carvedilol exhibited antiseizure effects in the kainic acid-induced epilepsy model. CONCLUSION AND IMPLICATION: Our findings suggest carvedilol as a new potential candidate for treatment of epilepsies.

Breast tumor segmentation using neural cellular automata and shape guided segmentation in mammography images.

PURPOSE: Using computer-aided design (CAD) systems, this research endeavors to enhance breast cancer segmentation by addressing data insufficiency and data complexity during model training. As perceived by computer vision models, the inherent symmetry and complexity of mammography images make segmentation difficult. The objective is to optimize the precision and effectiveness of medical imaging. METHODS: The study introduces a hybrid strategy combining shape-guided segmentation (SGS) and M3D-neural cellular automata (M3D-NCA), resulting in improved computational efficiency and performance. The implementation of Shape-guided segmentation (SGS) during the initialization phase, coupled with the elimination of convolutional layers, enables the model to effectively reduce computation time. The research proposes a novel loss function that combines segmentation losses from both components for effective training. RESULTS: The robust technique provided aims to improve the accuracy and consistency of breast tumor segmentation, leading to significant improvements in medical imaging and breast cancer detection and treatment. CONCLUSION: This study enhances breast cancer segmentation in medical imaging using CAD systems. Combining shape-guided segmentation (SGS) and M3D-neural cellular automata (M3D-NCA) is a hybrid approach that improves performance and computational efficiency by dealing with complex data and not having enough training data. The approach also reduces computing time and improves training efficiency. The study aims to improve breast cancer detection and treatment methods in medical imaging technology.

Repair and regeneration: ferroptosis in the process of remodeling and fibrosis in impaired organs.

As common clinical-pathological processes, wound healing and tissue remodelling following injury or stimulation are essential topics in medical research. Promoting the effective healing of prolonged wounds, improving tissue repair and regeneration, and preventing fibrosis are important and challenging issues in clinical practice. Ferroptosis, which is characterized by iron overload and lipid peroxidation, is a nontraditional form of regulated cell death. Emerging evidence indicates that dysregulated metabolic pathways and impaired iron homeostasis play important roles in various healing and regeneration processes via ferroptosis. Thus, we review the intrinsic mechanisms of tissue repair and remodeling via ferroptosis in different organs and systems under various conditions, including the inflammatory response in skin wounds, remodeling of joints and cartilage, and fibrosis in multiple organs. Additionally, we summarize the common underlying mechanisms, key molecules, and targeted drugs for ferroptosis in repair and regeneration. Finally, we discuss the potential of therapeutic agents, small molecules, and novel materials emerging for targeting ferroptosis to promote wound healing and tissue repair and attenuate fibrosis.

Notch-Driven Cholangiocarcinogenesis Involves the Hippo Pathway Effector TAZ via METTL3-m6A-YTHDF1.

BACKGROUND AND AIMS: Notch and TAZ are implicated in cholangiocarcinogenesis, but whether and how these oncogenic molecules interact remain unknown. METHODS: The development of CCA was induced by hydrodynamic tail vein (HDTV) injection of oncogenes (NICD/AKT) to the FVB/NJ mice. CCA xenograft was developed by inoculation of human CCA cells into the livers of SCID mice. Tissues and cells were analyzed using qRT-PCR, Western blotting analyses, Immunohistochemistry, ChIP-qPCR and WST-1 cell proliferation Assay. RESULTS: Our experimental findings show that TAZ is indispensable in NICD-driven cholangiocarcinogenesis. Notch activation induces the expression of METTL3 (Methyltransferase like-3) which catalyzes N6-methyladenosine (m6A) modification of TAZ mRNA and that this mechanism plays a central role in the crosstalk between Notch and TAZ in CCA cells. Mechanistically, Notch regulates the expression of METTL3 through the binding of NICD to its downstream transcription factor CSL in the promoter region of METTL3. METTL3 in turn mediates m6A modification of TAZ mRNA which is recognized by the m6A reader YTHDF1 to enhance TAZ protein translation. We observed that inhibition of Notch signaling decreased the protein levels of both MELLT3 and TAZ. Depletion of METTL3 by shRNAs or by the next generation GapmeR antisense oligonucleotides (ASOs) decreased the level of TAZ protein and inhibited the growth of human CCA cells in vitro and in mice. CONCLUSION: This study describes a novel Notch-METTL3-TAZ signaling cascade which is important in CCA development and progression. Our experimental results provide new insight into how the Notch pathway cooperates with TAZ signaling in CCA, and the findings may have important therapeutic implications.

53BP1 deficiency leads to hyperrecombination using break-induced replication (BIR).

Break-induced replication (BIR) is mutagenic, and thus its use requires tight regulation, yet the underlying mechanisms remain elusive. Here we uncover an important role of 53BP1 in suppressing BIR after end resection at double strand breaks (DSBs), distinct from its end protection activity, providing insight into the mechanisms governing BIR regulation and DSB repair pathway selection. We demonstrate that loss of 53BP1 induces BIR-like hyperrecombination, in a manner dependent on Polα-primase-mediated end fill-in DNA synthesis on single-stranded DNA (ssDNA) overhangs at DSBs, leading to PCNA ubiquitination and PIF1 recruitment to activate BIR. On broken replication forks, where BIR is required for repairing single-ended DSBs (seDSBs), SMARCAD1 displaces 53BP1 to facilitate the localization of ubiquitinated PCNA and PIF1 to DSBs for BIR activation. Hyper BIR associated with 53BP1 deficiency manifests template switching and large deletions, underscoring another aspect of 53BP1 in suppressing genome instability. The synthetic lethal interaction between the 53BP1 and BIR pathways provides opportunities for targeted cancer treatment.

Associations of five dietary indices with metabolic dysfunction-associated steatotic liver disease and liver fibrosis among the United States population.

Background and aims: The role of dietary factors in metabolic dysfunction-associated steatotic liver disease (MASLD)-which represents a new definition of liver steatosis and metabolic dysfunction- remains unclear. This study aimed to explore the relationships between dietary indices and MASLD. Methods: We analyzed data from the United States National Health and Nutrition Examination Survey (NHANES) 2017-2020 cycle, including 4,690 participants with complete vibration-controlled transient elastography (VCTE) data. Multivariate logistic regression models adjusted for covariates were used to assess the association between dietary indices, MASLD, and MASLD-associated liver fibrosis (MASLD-LF). Restricted cubic spline (RCS) models and subgroup analyses were also performed. Results: The Alternative Healthy Eating Index (AHEI), Healthy Eating Index-2020 (HEI-2020), Dietary Approaches to Stop Hypertension Index (DASHI), and Mediterranean Diet Index (MEDI) were found to be negatively associated with MASLD risk, while the Dietary Inflammatory Index (DII) had a positive association. The highest quartile of MEDI was linked to a 44% reduction in MASLD risk [Q1 vs. Q4 odds ratio (OR): 0.56; 95% confidence interval (CI): 0.34-0.94, P for trend: 0.012]. DASHI was uniquely associated with a reduced risk of MASLD-LF (continuous OR: 0.79; 95% CI: 0.64-0.97; p for trend: 0.003). Our RCS curves indicated a nonlinear association with DASHI-MASLD (p-overall: 0.0001, p-nonlinear: 0.0066). Subgroup analyses showed robust associations among the non-Hispanic White and highly educated populations. Conclusion: Specific dietary patterns were associated with reduced risks of MASLD and MASLD-LF. The DASHI, in particular, showed a significant protective effect against MASLD-LF. These findings suggest potential dietary interventions for managing MASLD and MASLD-LF, although large-scale randomized controlled trials are warranted to validate these findings.

Interactive effects of chlorothalonil and Varroa destructor on Apis mellifera during adult stage.

The interaction between environmental factors affecting honey bees is of growing concern due to their potential synergistic effects on bee health. Our study investigated the interactive impact of Varroa destructor and chlorothalonil on workers' survival, fat body morphology, and the expression of gene associated with detoxification, immunity, and nutrition metabolism during their adult stage. We found that both chlorothalonil and V. destructor significantly decreased workers' survival rates, with a synergistic effect observed when bees were exposed to both stressors simultaneously. Morphological analysis of fat body revealed significant alterations in trophocytes, particularly a reduction in vacuoles and granules after Day 12, coinciding with the transition of the bees from nursing to other in-hive work tasks. Gene expression analysis showed significant changes in detoxification, immunity, and nutrition metabolism over time. Detoxification genes, such as CYP9Q2, CYP9Q3, and GST-D1, were downregulated in response to stressor exposure, indicating a potential impairment in detoxification processes. Immune-related genes, including defensin-1, Dorsal-1, and Kayak, exhibited an initially upregulation followed by varied expression patterns, suggesting a complex immune response to stressors. Nutrition metabolism genes, such as hex 70a, AmIlp2, VGMC, AmFABP, and AmPTL, displayed dynamic expression changes, reflecting alterations in nutrient utilization and energy metabolism in response to stressors. Overall, these findings highlight the interactive and dynamic effects of environmental stressor on honey bees, providing insights into the mechanisms underlying honey bee decline. These results emphasize the need to consider the interactions between multiple stressors in honey bee research and to develop management strategies to mitigate their adverse effects on bee populations.

A novel fluorescent probe based on dicyanoisophorone derivatives for hypochlorite detection in living cells.

This study presents a long-wavelength fluorescent probe CNC for the detection of ClO- in vitro and in vivo. Upon interaction with ClO-, this probe exhibited a significant increase in fluorescence, with a significant Stokes shift (169 nm), lower detection limit (1.38 µM), high sensitivity and selectivity. Moreover, the probe demonstrated excellent cell permeability and minimal cytotoxicity, allowing for successful imaging of both endogenous and exogenous ClO- in living cells.

Complement C3 deposition restricts the proliferation of internalized Staphylococcus aureus by promoting autophagy.

Complement C3 (C3) is usually deposited spontaneously on the surfaces of invading bacteria prior to internalization, but the impact of C3 coating on cellular responses is largely unknown. Staphylococcus aureus (S. aureus) is a facultative intracellular pathogen that subverts autophagy and replicates in both phagocytic and nonphagocytic cells. In the present study, we deposited C3 components on the surface of S. aureus by complement opsonization before cell infection and confirmed that C3-coatings remained on the surface of the bacteria after they have invaded the cells, suggesting S. aureus cannot escape or degrade C3 labeling. We found that the C3 deposition on S. aureus notably enhanced cellular autophagic responses, and distinguished these responses as xenophagy, in contrast to LC3-associated phagocytosis (LAP). Furthermore, this upregulation was due to the recruitment of and direct interaction with autophagy-related 16-like 1 (ATG16L1), thereby resulting in autophagy-dependent resistance to bacterial growth within cells. Interestingly, this autophagic effect occurred only after C3 activation by enzymatic cleavage because full-length C3 without cleavage of the complement cascade reaction, although capable of binding to ATG16L1, failed to promote autophagy. These findings demonstrate the biological function of intracellular C3 upon bacterial infection in enhancing autophagy against internalized S. aureus.

Population pharmacokinetics and dosing simulations of meropenem in septic critically ill patients with complicated intra-abdominal infection or pneumonia.

OBJECTIVES: Meropenem pharmacokinetics (PK) may be altered in septic critically ill patients with complicated intra-abdominal infections (cIAI) and pneumonia. We aimed to evaluate the covariates affecting meropenem PK and the performance of different dosing regimens to optimize the PK/pharmacodynamic target. METHODS: Population PK analysis was performed using non-linear mixed-effects modeling. The final model was validated and used to simulate meropenem exposure to assess the probability of attaining the 100%ƒT>MIC target. RESULTS: Forty-six and 14 patients were respectively enrolled for PK analysis and external validation. A one-compartment linear model adequately described the data of 226 concentrations. The typical clearance (CL) and volume of distribution (Vd) were 9.69 L/h and 27.4 L, respectively. Septic shock from cIAI (cIASS) and actual body weight were significant covariates for meropenem Vd in addition to the influential covariates of creatinine clearance (CLCR-CG) and augmented renal clearance for CL. External validation showed the robustness and accuracy of this model. Simulation results proposed continuous infusion (CI) dosing regimens of meropenem against pathogens with MICs ≥ 2 mg/L in patients with cIASS and CLCR-CG ≥ 60 mL/min. CONCLUSIONS: For the patients with cIASS and CLCR-CG ≥ 60 mL/min, CI meropenem is proposed for treatment of less sensitive pathogens with MICs ≥ 2 mg/L.

Artificial intelligence strengthenes cervical cancer screening - present and future.

Cervical cancer is a severe threat to women's health. The majority of cervical cancer cases occur in developing countries. The WHO has proposed screening 70% of women with high-performance tests between 35 and 45 years of age by 2030 to accelerate the elimination of cervical cancer. Due to an inadequate health infrastructure and organized screening strategy, most low- and middle-income countries are still far from achieving this goal. As part of the efforts to increase performance of cervical cancer screening, it is necessary to investigate the most accurate, efficient, and effective methods and strategies. Artificial intelligence (AI) is rapidly expanding its application in cancer screening and diagnosis and deep learning algorithms have offered human-like interpretation capabilities on various medical images. AI will soon have a more significant role in improving the implementation of cervical cancer screening, management, and follow-up. This review aims to report the state of AI with respect to cervical cancer screening. We discuss the primary AI applications and development of AI technology for image recognition applied to detection of abnormal cytology and cervical neoplastic diseases, as well as the challenges that we anticipate in the future.

Benchmarking algorithms for single-cell multi-omics prediction and integration.

The development of single-cell multi-omics technology has greatly enhanced our understanding of biology, and in parallel, numerous algorithms have been proposed to predict the protein abundance and/or chromatin accessibility of cells from single-cell transcriptomic information and to integrate various types of single-cell multi-omics data. However, few studies have systematically compared and evaluated the performance of these algorithms. Here, we present a benchmark study of 14 protein abundance/chromatin accessibility prediction algorithms and 18 single-cell multi-omics integration algorithms using 47 single-cell multi-omics datasets. Our benchmark study showed overall totalVI and scArches outperformed the other algorithms for predicting protein abundance, and LS_Lab was the top-performing algorithm for the prediction of chromatin accessibility in most cases. Seurat, MOJITOO and scAI emerge as leading algorithms for vertical integration, whereas totalVI and UINMF excel beyond their counterparts in both horizontal and mosaic integration scenarios. Additionally, we provide a pipeline to assist researchers in selecting the optimal multi-omics prediction and integration algorithm.

Causal association between blood metabolites and vertigo: A Mendelian randomization study.

Metabolic disorders have been identified as an important factor causing nervous system diseases. However, due to the interference of confounding factors, the causal relationship between them has not been clearly elucidated, so it is necessary to study the causal relationship between them. To explore the causal relationship between blood metabolites and vertigo by Mendelian randomization. To assess causality, the inverse variance weighting method was employed as the primary analytical approach, complemented by additional sensitivity analyses. Metabolic pathway enrichment analysis and genetic correlation analysis were employed to further assess the metabolites. All statistical analyses were conducted using the R software. The study employed metabolite Genome Wide Association Study and vertigo diseases summary data sets to examine the causal relationship between 486 blood metabolites and 3 types of vertigo. A total of 55 potential metabolites associated with the 3 types of vertigo were identified, with 22, 16, and 13 candidate metabolites showing relatively reliable MR Evidence for Vestibular Dysfunction, Peripheral Vertigo, and Central Vertigo, respectively. Enrichment analysis was conducted to investigate the biological significance of these candidate metabolites, resulting in the identification of 7 key metabolic pathways across the 3 diseases, the metabolic pathway known as "Valine, leucine, and isoleucine biosynthesis" was found to be associated with all 3 types of vertigo, suggesting its potential influence on the vestibular system. Genetic correlation analysis revealed a genetic correlation between X-10510 and dodecanedioate with Vestibular Dysfunction. This study offers novel perspectives on the causal impact of blood metabolites on vertigo through the integration of genomics and metabolomics. Identifying metabolites that contribute to vertigo could serve as potential biomarkers and contribute to a better understanding of the underlying biological mechanisms associated with vertigo.

Drought and warming interaction cause substantial economic losses in the carbon market potential of China's northern grasslands.

Grasslands are being threatened by global drought and warming. Economic assessments of changing grassland carbon sequestration, a prerequisite for nature-based climate-change mitigation policies, are limited when researchers inadequate consider interactions between drought and warming. Here, we quantified the responses of 35 grass biomasses to combined drought and warming, based on manipulation experiments from 34 peer-reviewed papers; subsequently, we matched them with grasslands in northern China-the eastern range of the larger Eurasian Steppe-and further projected the economic implications for carbon market trading and carbon-sequestration costs. The results show that carbon sequestration in all grassland types, except for forbrich steppe, was significantly reduced by the synergistic interactions of drought and warming. Approximately 10 % of the grasslands in central Xinjiang, identified as forbrich steppe, showed resilience to these stressors. In contrast, the rest of northern China's grasslands suffered increased carbon losses due to drought and warming. The combined effects of drought and warming have caused a loss of 1.6 × 104 million Chinese yuan (CNY) in revenue and excess carbon-sequestration costs exceeding 1.1 × 105 million CNY. Overall, our study results indicate that the synergistic effects of drought and warming significantly undermine the economic viability of carbon sequestration in most of northern China's grasslands. As climate change intensifies, understanding and incorporating the complex interactions of drought and warming can aid in the sustainable management of grassland ecosystems and the development of effective climate-change mitigation policies in arenas, including carbon markets.

High-Performance Wearable Joule Heater Derived from Sea-Island Microfiber Nonwoven Fabric.

A three-dimensional (3D) hierarchical microfiber bundle-based scaffold integrated with silver nanowires (AgNWs) and porous polyurethane (PU) was designed for the Joule heater via a facile dip-coating method. The interconnected micrometer-sized voids and unique hierarchical structure benefit uniform AgNWs anchored and the formation of a high-efficiency 3D conductive network. As expected, this composite exhibits a superior electrical conductivity of 1586.4 S/m and the best electrothermal conversion performance of 118.6 °C at 2.0 V compared to reported wearable Joule heaters to date. Moreover, the durable microfiber bundle-PU network provides strong mechanical properties, allowing for the stable and durable electrothermal performance of such a composite to resist twisting, bending, abrasion, and washing. Application studies show that this kind of Joule heater is suitable for a wide range of applications, such as seat heating, a heating jacket, personal thermal management, etc.