Single-cell RNA sequencing and spatial transcriptomics of bladder Ewing sarcoma.

Bladder Ewing sarcoma/primitive neuroectodermal tumor (bladder ES/PNET) is a rare and highly malignant tumor associated with a poor prognosis, yet its underlying mechanisms remain poorly understood. Here, we employed a combination of single-cell RNA sequencing (scRNA-seq), spatial transcriptomics (ST), and functional analyses to delve into the pathogenesis of bladder ES/PNET. The investigation revealed the presence of specialized types of epithelial cells (referred to as bladder ES-Epi) and mast cells (referred to as bladder ES-Mast) within bladder ES/PNET in comparison to urothelial carcinoma. Notably, TNFRSF12A exhibited significant upregulation in bladder ES/PNET. Furthermore, mast cells possessed the ability to activate epithelial cells through the TNFSF12-TNFRSF12A ligand-receptor signaling pattern. In addition, Enavatuzumab can significantly inhibit the migratory ability of the Ewing sarcoma cell line RD-ES. This groundbreaking study provides unprecedented mechanistic insights into the progression of bladder ES/PNET and introduces a potential therapeutic avenue for treating this challenging malignancy.

Radiographic features and subtypes of congenital thumb duplication type C3 according to Wu et al. and their potential implications for surgical management: new classification and preliminary results.

BACKGROUND: Wu et al. introduced a modified radiographic system that allows classification of all forms of CTD with excellent interobserver and intraobserver reliability. No study to date has evaluated the radiographic characteristics of Wu et al. type C3 CTD with osseous attachment at the level of the metacarpal. OBJECTIVE: This study aimed to evaluate the radiographic features of type C3 CTD according to the system of Wu et al., to describe the different anatomical subtypes of the duplication, and to propose a categorization approach to distinguish diverse surgical strategies based on the radiographic anatomy of this specific subtype of duplication. METHODS: We performed a retrospective analysis of 215 patients (221 thumbs) diagnosed with Wu et al. type C3 CTD at our Institution between 2015 and 2021. We evaluated all CTDs by examining the alignment of the interphalangeal (IP) and metacarpophalangeal (MP) joints and by assessing the presence of abnormal hypertrophic epiphysis of the primary thumb on posteroanterior (PA) radiographs. The proposed classification system has four types: Type I with good alignment of both MP and IP joints, Type II with ulnar deviation of the MP joint, Type III with radial deviation in the MP joint and Type IV with abnormal hypertrophic epiphysis of the distal phalanx of the main thumb with ulnar deviation of the IP joint with or without ulnar deviation of the MP joint. RESULTS: There were 140 male and 75 female patients with CTD (221 thumbs). There were 65 left, 144 right and 6 bilateral forms. The right-to-left, male-to-female and unilateral-to-bilateral ratios were 2.2:1, 1.9:1 and 35.8:1 respectively. The mean age at surgery was 22.3 ± 11.8 months (range, 8-80). The proposed classification system allowed the classification of all CTDs (n = 221). Specifically, 53 fingers were classified as Type I (24%), 136 as Type II (61.5%), 21 as Type III (9.5%), and 11 as Type IV (5%). CONCLUSION: The proposed system is based on radiographic pathoanatomy and complements that of Wu et al. by identifying four distinct subtypes of deformity. It has the potential to improve inter-professional communication and guide surgery in patients with Wu et al. type C3 CTD. However, our results are preliminary and further research is needed to validate them. LEVEL OF EVIDENCE: III.

Research Progress on Food-Derived Bioactive Peptides: An Overview of the 3rd International Symposium on Bioactive Peptides.

Interest in food-derived bioactive peptides is on the rise. In 2023, the 3rd International Symposium on Bioactive Peptides (ISBP) was held in Niagara Falls, Canada, to provide a platform for knowledge exchange, networking, and collaboration among researchers in this field. This article aims to provide a high-level overview of the key progress and emerging trends in bioactive peptides based on the 3rd ISBP. This review highlights the production of bioactive peptides from sustainable sources through the integration of artificial intelligence and wet-lab research, the emerging roles of bioactive peptides in cognitive function, and the ability of peptides to act as taste modifiers. The emerging research trend in bioactive peptides focuses on utilizing novel processing technologies, understanding peptide-receptor interactions, applying omics in mechanistic studies, conducting clinical trials, and facilitating product development and commercialization.

Screening and characterization of an antifreeze peptide from sea cucumber intestinal protein hydrolysates.

Protein deterioration caused by ice crystals is an important factors affecting the frozen storage of fish. In this study, antifreeze peptides extracted from hydrolysates of sea cucumber intestinal protein with inhibition of protein denaturation were screened and characterized. The peptide Leu-Pro-Glu-Phe-Thr-Glu-Glu-Glu-Lys (LPEFTEEEK), derived from neutral protease hydrolysates of sea cucumber intestinal protein, was investigated for its potential to enhance the quality of salmon fillets during three freeze-thaw cycles. The results showed that the application of LPEFTEEEK effectively maintained the texture of fish fillets, as well as the oxidative and conformation stability of myofibrillar protein during the freezing process. Additionally, molecular dynamics simulations verified that LPEFTEEEK could bind to ice crystals and inhibit their recrystallization, thus preventing organisms from being damaged by freezing. This suggests that LPEFTEEEK holds significant promise as a novel cryoprotective agent for marine-derived antifreeze peptides.

AIM2 Deficiency Alleviates Cardiac Inflammation and Hypertrophy in HFD/STZ-Induced Diabetic Mice by Inhibiting the NLRC4/IRF1 Signaling Pathway.

Absent in melanoma 2(AIM2) exacerbates atherosclerosis by inflammasome assembly. However, AIM2-mediated inflammation in diabetic cardiomyopathy remains incompletely understood. Here we investigate the role of AIM2 in high glucose (HG)- and diabetes-induced inflammatory cardiomyopathy. By RNA-seq, we found that AIM2 were significantly upregulated in HG-induced macrophages, upregulation of AIM2 in cardiac infiltrating macrophages was confirmed in a high-fat diet (HFD)/streptozotocin (STZ)-induceddiabetic mouse model . Therefore, AIM2 knockout mice were constructed. Compared to WT mice, HFD/STZ-induced cardiac hypertrophy and dysfunction were significantly improved in AIM2-/- mice, despite no changes in blood glucose and body weight. Further, AIM2 deficiency inhibited cardiac recruitment of M1-macrophages and cytokine production. Mechanistically, AIM2-deficient macrophgaes reduced IL-1ß and TNF-α secretion, which impaired the NLRC4/IRF1 signaling in cardiomyocytes, and reduced further recruitment of macrophages, attenuated cardiac inflammation and hypertrophy, these effects were confirmed by silencing IRF1 in WT mice, and significantly reversed by overexpression of IRF1 in AIM2-/- mice. Taken together, our findings suggest that AIM2 serves as a novel target for the treatment of diabetic cardiomyopathy.

Antioxidant and anti-inflammatory peptides in dry-fermented sausages fermented with Staphylococcus simulans QB7.

This study focused on investigating the impacts of Staphylococcus simulans QB7 (S. simulans QB7) on the generation of antioxidant and anti-inflammatory peptides in dry-fermented sausages and the associated mechanisms by in silico. S. simulans QB7 remarkably increased (P < 0.05) the peptide concentration, antioxidant, and anti-inflammatory capacity of peptide extracts. There were 29 peptide sequences with potential activities of antioxidation and anti-inflammation according to BIOPEP-UWM prediction. Molecular docking results indicated that peptide GPGPWG can bind to Kelch-like ECH-associated protein 1 (Keap1) with highest interaction energy, while peptide ANPILEAFG showed highest interaction energy towards p65, I kappa B kinase 2 (IKK-ß), c-Jun N-terminal kinases (JNK), and p38 kinases (p38) due to form salt bridge, h-bond, and pi-alkyl. These results suggested that S. simulans QB7 promoted antioxidant and anti-inflammatory peptide generation within dry-fermented sausages.

Zinc finger protein LjRSDL regulates arbuscule degeneration of arbuscular mycorrhizal fungi in Lotus japonicus.

In arbuscular mycorrhizal (AM) symbiosis, appropriate regulation of the formation, maintenance, and degeneration of the arbuscule are essential for plants and fungi. In this study, we identified a Cysteine-2/Histidine-2 zinc finger protein (C2H2-ZFP)-encoding gene in Lotus japonicus named Regulator of Symbiosome Differentiation-Like (LjRSDL) that is required for arbuscule degeneration. Evolutionary analysis showed that homologs of LjRSDL exist in mycorrhizal flowering plants. We obtained ProLjRSDL::GUS transgenic hairy roots and showed that LjRSDL was strongly upregulated upon AM colonization, particularly at 18 days post AM fungi inoculation and specifically expressed in arbuscular-containing cells. The mycorrhization rate increased in the ljrsdl mutant but decreased in LjRSDL overexpressed L. japonicus. Interestingly, we observed higher proportions of large arbuscule in the ljrsdl mutant but lower proportions of larger arbuscule in LjRSDL overexpressing plants. Transcriptome analyses indicated that genes involved in arbuscule degeneration were significantly changed upon the dysregulation of LjRSDL and that LjRSDL-dependent regulation in AM symbiosis is mainly via the hormone signal transduction pathway. LjRSDL, therefore, represents a C2H2-ZFP that negatively regulates AM symbiosis. Our study provides insight into understanding plant-AM fungal communication and AM symbiosis development.

Insights into the biocorrosion of Q235A steel influenced by the electron transfer process between iron and methanogenic microbiota.

Anaerobic microbiologically influenced corrosion (MIC) of Fe (0) metals causes great harm to the environment and economy, which depends on the key electron transfer process between anaerobic microorganisms and Fe (0) metals. However, the key electron transfer process in microbiota dominating MIC remains unclear, especially for methanogenic microbiota wildly distributed in the environment. Herein, three different methanogenic microbiota (Methanothrix, Methanospirillum, and Methanobacterium) were acclimated to systematically investigate electron transfer pathways on corroding Q235A steel coupons. Results indicated that microbiota dominated by Methanothrix, Methanospirillum, or Methanobacterium accelerated the steel corrosion mainly through direct electron transfer (DET) pathway, H2 mediated electron transfer (HMET) pathway, and combined DET and HMET pathways, respectively. Compared with Methanospirillum dominant microbiota, Methanothrix or Methanobacterium dominant microbiota caused more methane production, higher weight loss, corrosion pits with larger areas, higher corrosion depth, and smaller corrosion pits density. Such results reflected that the DET process between microbiota and Fe (0) metals decided the biocorrosion degree and behavior of Fe (0) metals. This study insightfully elucidates the mechanisms of methanogenic microbiota on corroding steels, in turn providing new insights for anti-corrosion motives.

Thermostability and activity improvement in l-threonine aldolase through targeted mutations in V-shaped subunit.

l-threonine aldolase (LTA) catalyzes the synthesis of ß-hydroxy-α-amino acids, which are important chiral intermediates widely used in the fields of pharmaceuticals and pesticides. However, the limited thermostability of LTA hinders its industrial application. Furthermore, the trade-off between thermostability and activity presents a challenge in the thermostability engineering of this enzyme. This study proposes a strategy to regulate the rigidity of LTA's V-shaped subunit by modifying its opening and hinge regions, distant from the active center, aiming to mitigate the trade-off. With LTA from Bacillus nealsonii as targeted enzyme, a total of 25 residues in these two regions were investigated by directed evolution. Finally, mutant G85A/M207L/A12C was obtained, showing significantly enhanced thermostability with a 20 °C increase in T5060 to 66 °C, and specific activity elevated by 34 % at the optimum temperature. Molecular dynamics simulations showed that the newly formed hydrophobicity and hydrogen bonds improved the thermostability and boosted proton transfer efficiency. This work enhances the thermostability of LTA while preventing the loss of activity. It opens new avenues for the thermostability engineering of other industrially relevant enzymes with active center located at the interface of subunits or domains.

Conservation and specialization of the Ycf2-FtsHi chloroplast protein import motor in green algae.

The protein import motor in chloroplasts plays a pivotal role in their biogenesis and homeostasis by driving the translocation of preproteins into chloroplasts. While the Ycf2-FtsHi complex serves as the import motor in land plants, its evolutionary conservation, specialization, and mechanisms across photosynthetic organisms are largely unexplored. Here, we isolated and determined the cryogenic electron microscopy (cryo-EM) structures of the native Ycf2-FtsHi complex from Chlamydomonas reinhardtii, uncovering a complex composed of up to 19 subunits, including multiple green-algae-specific components. The heterohexameric AAA+ ATPase motor module is tilted, potentially facilitating preprotein handover from the translocon at the inner chloroplast membrane (TIC) complex. Preprotein interacts with Ycf2-FtsHi and enhances its ATPase activity in vitro. Integrating Ycf2-FtsHi and translocon at the outer chloroplast membrane (TOC)-TIC supercomplex structures reveals insights into their physical and functional interplay during preprotein translocation. By comparing these findings with those from land plants, our study establishes a structural foundation for understanding the assembly, function, evolutionary conservation, and diversity of chloroplast protein import motors.

Structural insights into the chloroplast protein import in land plants.

Chloroplast proteins are imported via the translocon at the outer chloroplast membrane (TOC)-translocon at the inner chloroplast membrane (TIC) supercomplex, driven by an ATPase motor. The Ycf2-FtsHi complex has been identified as the chloroplast import motor. However, its assembly and cooperation with the TIC complex during preprotein translocation remain unclear. Here, we present the structures of the Ycf2-FtsHi and TIC complexes from Arabidopsis and an ultracomplex formed between them from Pisum. The Ycf2-FtsHi structure reveals a heterohexameric AAA+ ATPase motor module with characteristic features. Four previously uncharacterized components of Ycf2-FtsHi were identified, which aid in complex assembly and anchoring of the motor module at a tilted angle relative to the membrane. When considering the structures of the TIC complex and the TIC-Ycf2-FtsHi ultracomplex together, it becomes evident that the tilted motor module of Ycf2-FtsHi enables its close contact with the TIC complex, thereby facilitating efficient preprotein translocation. Our study provides valuable structural insights into the chloroplast protein import process in land plants.

Interplay of Food-Derived Bioactive Peptides with Gut Microbiota: Implications for Health and Disease Management.

Bioactive peptides (BPs) are protein fragments with beneficial effects on metabolism, physiology, and diseases. This review focuses on proteolytic BPs, which are produced by the action of gut microbiota on proteins in food and have demonstrated to influence the composition of gut microbes. And gut microbiota are candidate targets of BPs to alleviate oxidative stress, enhance immunity, and control diseases, including diabetes, hypertension, obesity, cancer, and immune and neurodegenerative diseases. Despite promising results, further research is needed to understand the mechanisms underlying the interactions between BPs and gut microbes, and to identify and screen more BPs for industrial applications. Overall, BPs offer potential as therapeutic agents for various diseases through their interactions with gut microbes, highlighting the importance of continued research in this area.

RAS-Selective Lethal 3-Induced Ferroptosis Promotes the Antitumor Efficiency of Anti-Programmed Cell Death Protein 1 Treatment in Colorectal Cancer.

BACKGROUND/AIMS:  Anti-programmed cell death protein 1 (PD-1) treatment has exhibited clinical benefits in colorectal cancer (CRC). However, the low response rate of CRC to immunotherapy is an urgent problem that needs to be solved. MATERIALS AND METHODS:  MC-38 tumor cells was challenged subcutaneously in the flank of 7-week-old male C57BL/6 mice. The mice were randomly divided into 3 groups, and 200µg/mouse anti-PD-1 antibody and 100 mg/kg RAS-Seletive Lethal 3 (RSL) or phosphate buffer saline (PBS) were intraperitoneally injected every 2 days. The expression of oxidative stress and ferroptosis-related genes was measured by Western blotting, real-time reverse transcription-polymerase chain reaction, Prussian blue staining, and enzyme-linked immunosorbent assay. RESULTS:  Anti-PD-1 treatment-unresponsive tumors showed stronger immunosuppression than responsive tumors. Notably, the responsive tumors showed higher levels of H2O2 and reactive oxygen species, both of which could impair the antitumor effect of cytotoxic CD8+ T cells. The anti-PD-1 treatment-responsive tumors showed a higher expression of pro-ferroptosis genes and Fe2+ accumulation than those of anti-PD-1 nonresponsive tumors, indicating the potential role of ferroptosis in the efficacy of anti-PD-1 treatment. In MC-38 syngeneic tumor model, (1S, 3R)-RSL3 (RSL), a glutathione peroxidase 4 inhibitor, effectively promoted the antitumor effect of anti-PD-1 treatment in vivo. However, anti-PD-1 treatment did not affect the levels of ferroptosis-related genes in tumor model. Mechanistically, RSL treatment significantly upregulated the frequency of proliferating (ki67+) and cytotoxic (GZMB+) CD8+ T cells. Furthermore, the frequency of tumor neoantigen-specific interferon (IFN)-γ CD8+ T cells showed a significant increase after RSL plus anti-PD-1 treatment. CONCLUSION:  RSL may be a promising drug for potentiating the antitumor efficiency of anti-PD-1 treatment in CRC.

Crystal structure of lipase from Pseudomonas aeruginosa reveals an unusual catalytic triad conformation.

The Pseudomonas aeruginosa lipase PaL catalyzes the stereoselective hydrolysis of menthyl propionate to produce L-menthol. The lack of a three-dimensional structure of PaL has so far prevented a detailed understanding of its stereoselective reaction mechanism. Here, the crystal structure of PaL was determined at a resolution of 1.80 Å by single-wavelength anomalous diffraction. In the apo-PaL structure, the catalytic His302 is located in a long loop on the surface that is solvent exposed. His302 is distant from the other two catalytic residues, Asp274 and Ser164. This configuration of catalytic residues is unusual for lipases. Using metadynamics simulations, we observed that the enzyme undergoes a significant conformational change upon ligand binding. We also explored the catalytic and stereoselectivity mechanisms of PaL by all-atom molecular dynamics simulations. These findings could guide the engineering of PaL with an improved diastereoselectivity for L-menthol production.

Combined deep learning and radiomics in pretreatment radiation esophagitis prediction for patients with esophageal cancer underwent volumetric modulated arc therapy.

PURPOSE: To develop a combined radiomics and deep learning (DL) model in predicting radiation esophagitis (RE) of a grade ≥ 2 for patients with esophageal cancer (EC) underwent volumetric modulated arc therapy (VMAT) based on computed tomography (CT) and radiation dose (RD) distribution images. MATERIALS AND METHODS: A total of 273 EC patients underwent VMAT were retrospectively reviewed and enrolled from two centers and divided into training (n = 152), internal validation (n = 66), and external validation (n = 55) cohorts, respectively. Radiomic and dosiomic features along with DL features using convolutional neural networks were extracted and screened from CT and RD images to predict RE. The performance of these models was evaluated and compared using the area under curve (AUC) of the receiver operating characteristic curves (ROC). RESULTS: There were 5 and 10 radiomic and dosiomic features were screened, respectively. XGBoost achieved a best AUC of 0.703, 0.694 and 0.801, 0.729 with radiomic and dosiomic features in the internal and external validation cohorts, respectively. ResNet34 achieved a best prediction AUC of 0.642, 0.657 and 0.762, 0.737 for radiomics based DL model (DLR) and RD based DL model (DLD) in the internal and external validation cohorts, respectively. Combined model of DLD + Dosiomics + clinical factors achieved a best AUC of 0.913, 0.821 and 0.805 in the training, internal, and external validation cohorts, respectively. CONCLUSION: Although the dose was not responsible for the prediction accuracy, the combination of various feature extraction methods was a factor in improving the RE prediction accuracy. Combining DLD with dosiomic features was promising in the pretreatment prediction of RE for EC patients underwent VMAT.

Deoxycholic acid inducing chronic atrophic gastritis with colonic mucosal lesion correlated to mucosal immune dysfunction in rats.

The present study aimed to explore the underlying mechanism of bile reflux-inducing chronic atrophic gastritis (CAG) with colonic mucosal lesion. The rat model of CAG with colonic mucosal lesion was induced by free-drinking 20 mmol/L sodium deoxycholate to simulate bile reflux and 2% cold sodium salicylate for 12 weeks. In comparison to the control group, the model rats had increased abundances of Bacteroidetes and Firmicutes but had decreased abundances of Proteobacteria and Fusobacterium. Several gut bacteria with bile acids transformation ability were enriched in the model group, such as Blautia, Phascolarctobacter, and Enterococcus. The cytotoxic deoxycholic acid and lithocholic acid were significantly increased in the model group. Transcriptome analysis of colonic tissues presented that the down-regulated genes enriched in T cell receptor signaling pathway, antigen processing and presentation, Th17 cell differentiation, Th1 and Th2 cell differentiation, and intestinal immune network for IgA production in the model group. These results suggest that bile reflux-inducing CAG with colonic mucosal lesion accompanied by gut dysbacteriosis, mucosal immunocompromise, and increased gene expressions related to repair of intestinal mucosal injury.

Ovomucin and its hydrolysates differentially influenced colitis severity in Citrobacter rodentium-infected mice.

Egg white protein ovomucin and its hydrolysates were previously reported to exhibit anti-inflammatory and anti-adhesive activities. However, their potential to regulate pathogen colonization and disease severity has not been fully characterized. To investigate the effects of ovomucin (OVM) and its hydrolysates including ovomucin-Protex 26L (OP) and -pepsin/pancreatin (OPP) on host resistance to pathogen infection, a well-documented colitis model in mice for attaching and effacing E. coli pathogens, Citrobacter rodentium, was used in the current study. C57Bl/6J female mice were fed on a basal diet supplemented with OVM or its hydrolysates for 3 weeks prior to the C. rodentium challenge, with the dietary treatments continued for seven days. Body weight was not affected throughout the experimental period. OP supplementation resulted in lower (P < 0.05) pathogen loads at 7 dpi. Attenuated colitis severity was observed in mice that received OVM and OP, as indicated by reduced colonic pathological scores and pro-inflammatory responses compared with the infected control group. In contrast, OPP consumption resulted in enhanced C. rodentium colonization and disease severity. Notably, reduced microbial diversity indices of the gut microbiota were observed in the OPP-supplemented mice compared with the OVM- and OP-supplemented groups. This study showed the potential of OVM and OP to alleviate the severity of colitis induced by infection while also suggesting the opposite outcome of OPP in mitigating enteric infection.

Multi-omics deep learning for radiation pneumonitis prediction in lung cancer patients underwent volumetric modulated arc therapy.

BACKGROUND AND OBJECTIVE: To evaluate the feasibility and accuracy of radiomics, dosiomics, and deep learning (DL) in predicting Radiation Pneumonitis (RP) in lung cancer patients underwent volumetric modulated arc therapy (VMAT) to improve radiotherapy safety and management. METHODS: Total of 318 and 31 lung cancer patients underwent VMAT from First Affiliated Hospital of Wenzhou Medical University (WMU) and Quzhou Affiliated Hospital of WMU were enrolled for training and external validation, respectively. Models based on radiomics (R), dosiomics (D), and combined radiomics and dosiomics features (R+D) were constructed and validated using three machine learning (ML) methods. DL models trained with CT (DLR), dose distribution (DLD), and combined CT and dose distribution (DL(R+D)) images were constructed. DL features were then extracted from the fully connected layers of the best-performing DL model to combine with features of the ML model with the best performance to construct models of R+DLR, D+DLD, R+D+DL(R+D)) for RP prediction. RESULTS: The R+D model achieved a best area under curve (AUC) of 0.84, 0.73, and 0.73 in the internal validation cohorts with Support Vector Machine (SVM), XGBoost, and Logistic Regression (LR), respectively. The DL(R+D) model achieved a best AUC of 0.89 and 0.86 using ResNet-34 in training and internal validation cohorts, respectively. The R+D+DL(R+D) model achieved a best performance in the external validation cohorts with an AUC, accuracy, sensitivity, and specificity of 0.81(0.62-0.99), 0.81, 0.84, and 0.67, respectively. CONCLUSIONS: The integration of radiomics, dosiomics, and DL features is feasible and accurate for the RP prediction to improve the management of lung cancer patients underwent VMAT.