AGAT-PPIS: a novel protein-protein interaction site predictor based on augmented graph attention network with initial residual and identity mapping.

Identifying protein-protein interaction (PPI) site is an important step in understanding biological activity, apprehending pathological mechanism and designing novel drugs. Developing reliable computational methods for predicting PPI site as screening tools contributes to reduce lots of time and expensive costs for conventional experiments, but how to improve the accuracy is still challenging. We propose a PPI site predictor, called Augmented Graph Attention Network Protein-Protein Interacting Site (AGAT-PPIS), based on AGAT with initial residual and identity mapping, in which eight AGAT layers are connected to mine node embedding representation deeply. AGAT is our augmented version of graph attention network, with added edge features. Besides, extra node features and edge features are introduced to provide more structural information and increase the translation and rotation invariance of the model. On the benchmark test set, AGAT-PPIS significantly surpasses the state-of-the-art method by 8% in Accuracy, 17.1% in Precision, 11.8% in F1-score, 15.1% in Matthews Correlation Coefficient (MCC), 8.1% in Area Under the Receiver Operating Characteristic curve (AUROC), 14.5% in Area Under the Precision-Recall curve (AUPRC), respectively.

Long-acting anti-inflammatory injectable DEX-Gel with sustained release and self-healing properties regulates TH1/TH2 immune balance for minimally invasive treatment of allergic rhinitis.

BACKGROUND: Allergic rhinitis (AR) is a prevalent immune-related allergic disease, and corticosteroid nasal sprays serve as the primary treatment for this patient population. However, their short duration of efficacy and frequent administration pose challenges, leading to drug wastage and potential adverse effects. To overcome these limitations, we devised a novel approach to formulate DEX-Gel by incorporating dexamethasone (DEX) into a blend of Pluronic F127, stearic acid (SA), and polyethylene glycol 400 (PEG400) to achieve sustained-release treatment for AR. RESULTS: Following endoscopic injection into the nasal mucosa of AR rats, DEX-Gel exhibited sustained release over a 14-day period. In vivo trials employing various assays, such as flow cytometry (FC), demonstrated that DEX-Gel not only effectively managed allergic symptoms but also significantly downregulated helper T-cells (TH) 2 and TH2-type inflammatory cytokines (e.g., interleukins 4, 5, and 13). Additionally, the TH1/TH2 cell ratio was increased. CONCLUSION: This innovative long-acting anti-inflammatory sustained-release therapy addresses the TH1/TH2 immune imbalance, offering a promising and valuable approach for the treatment of AR and other inflammatory nasal diseases.

Identification of BRAF, CCND1, and MYC mutations in a patient with multiple primary malignant tumors: a case report and review of the literature.

BACKGROUND: Multiple primary malignant tumors (MPMTs), usually associated with worse malignant behavior and prognosis comparing to a single primary tumor, and have recently been found to have an increasing incidence globally. However, the pathogenesis of MPMTs remains to be clarified. Here, we report a unique case of the coexistence of malignant melanoma (MM), papillary thyroid carcinoma (PTC), and clear-cell renal cell carcinoma (ccRCC) along with our perceptions on its pathogenesis. CASE PRESENTATION: The case reported is of a 59-year-old male patient with unilateral nasal obstruction as well as a renal occupying lesion. Positron emission tomography-computed tomography (PET-CT) revealed a palpable mass of 32 × 30 mm on the posterior and left walls of the nasopharynx. In addition, an isodense nodule was observed in the right superior renal pole, approximately 25 mm in diameter, as well as a slightly hypodense shadow in the right leaf of the thyroid, approximately 13 mm in diameter. Nasal endoscopy and magnetic resonance imaging (MRI) confirmed the existence of a nasopharyngeal neoplasm. Afterward, biopsies of the nasopharyngeal neoplasm, thyroid gland and kidney were performed, and the patient was diagnosed with MM, PTC, and ccRCC according to the pathological and immunohistochemical results. Moreover, mutation of BRAFV600E was detected in bilateral thyroid tissues, and amplification of both CCND1 and MYC oncogenes were detected in the nasopharyngeal melanoma. After chemotherapy, the patient is now in good overall condition. CONCLUSIONS: This is the first reported case of a patient with the co-existence of MM, PTC and ccRCC undergoing chemotherapy with a favorable prognosis. Herein, we suggest that such a combination may be non-random, as for mutation of BRAFV600E might account for the co-occurrence of PTC and MM, while mutations of CCND1 and MYC cause the coexistence of MM and ccRCC. This finding may provide valuable guidance on the diagnosis and treatment of such disease, as well as the prevention of developing a second or third tumor for patients with a single primary.

OmeDDG: Improved Protein Mutation Stability Prediction Based on Predicted 3D Structures.

Determining changes in the protein's thermal stability following mutations is critical in protein engineering and understanding pathogenic missense mutations. Despite the development of various computational methods to predict the effects of single-point mutations, their accuracy remains limited. In this study, we propose a new computational method, OmeDDG, that more accurately predicts mutation-induced Gibbs free energy changes in protein folding (ΔΔG). OmeDDG takes the sequences of wild-type and mutant proteins as input, utilizes OmegaFold to obtain the 3D structure, employs a convolutional neural network to extract structural features, and combines them with protein mutation features and pretraining features to predict the stability of single-point mutations in proteins. We performed a comprehensive comparison between OmeDDG and other available prediction methods on four blind test datasets, confirming that OmeDDG can effectively enhance protein mutation prediction performance. Notably, on the antisymmetric dataset Ssym, OmeDDG achieves the best performance, demonstrating favorable antisymmetry with PCC = 0.79 and RMSE = 0.96 for forward mutations and PCC = 0.77 and RMSE = 0.97 for reverse mutant types.

A Novel Multi-Scale Graph Neural Network for Metabolic Pathway Prediction.

Predicting the metabolic pathway classes of compounds in the human body is an important problem in drug research and development. For this purpose, we propose a Multi-Scale Graph Neural Network framework, named MSGNN. The framework includes a subgraph encoder, a feature encoder and a global feature processor, and a graph augmentation strategy is adopted. The subgraph encoder is responsible for extracting the local structural features of the compound, the feature encoder learns the characteristics of the atoms, and the global feature processor processes the information from the pre-training model and the two molecular fingerprints, while the graph augmentation strategy is to expand the train set through a scientific and reasonable method. The experiment result illustrates that the accuracy, precision, recall and F1 metrics of MSGNN reach 98.17%, 94.18%, 94.43% and 94.30%, respectively, which is superior to the similar models we have known. In addition, the ablation experiment demonstrates the indispensability of MSGNN modules.

TNF-α Regulates the Glucocorticoid Receptor Alpha Expression in Human Nasal Epithelial Cells Via p65-NF-κb and p38-MAPK Signaling Pathways.

Background: Tumor necrosis factor (TNF)-α induces changes in the glucocorticoid receptor (GR) isoforms' expression in human nasal epithelial cells (HNECs) in chronic rhinosinusitis (CRS). Objective: However, the underlying mechanism of TNF-α induced GR isoforms' expression in HNECs remains unclear. Here, we explored changes in inflammatory cytokines and glucocorticoid receptor alpha isoform (GRα) expression in HNECs. Materials and Methods: To explore the expression of TNF-α in nasal polyps and nasal mucosa of CRS, fluorescence immunohistochemical analysis was employed. To investigate changes in inflammatory cytokines and GRα expression in HNECs, RT-PCR and western blotting were performed following the cells' incubation with TNF-α. Cells were pretreated with the nuclear factor-κB gene binding (NF-κB) inhibitor QNZ, the p38 inhibitor SB203580, and dexamethasone for one hour, then a TNF-α. Western blotting, RT-PCR, and immunofluorescence had been utilized for the cells' analysis and the ANOVA for the data analysis. Results: The TNF-α fluorescence intensity was mainly distributed in nasal epithelial cells of nasal tissues. TNF-α prominently inhibited the expression of GRα mRNA from 6 to 24 h in HNECs. GRα protein was decreased from 12 to 24 h. Treatment with QNZ, SB203580, or dexamethasone inhibited the TNF-α and interleukin (IL)-6 mRNA expression and increased the GRα levels. Conclusion: TNF-α induced changes in the GR isoforms' expression in HNECs, and it was mediated through p65-NF-κB and p38-MAPK signal transduction pathways, which could be considered a promising neutrophilic CRS treatment.

Loss of SENP3 mediated the formation of nasal polyps in nasal mucosal inflammation by increasing alternative activated macrophage.

BACKGROUND AND AIM: Small ubiquitin-like modifier (SUMO)-specific protease (SENP)3 is a protease molecule that responds to reactive oxygen species (ROS) with high sensitivity. However, the role of ROS and SENP3 in the formation of nasal polyps (NPs) remains unclear. This study aimed to explore how SENP3 influenced the outcome of chronic rhinosinusitis (CRS) by altering macrophage function, that is, the formation of NPs. METHODS: The alternative activation of macrophage (M2) was detected with CD68+ CD206+ in humans and CD206+ in mice. The nasal mucosa of patients with CRS was tested using flow cytometry (CD68, CD80, and CD206) and triple-color immunofluorescence staining (CD68, CD206, and SENP3). The bone marrow-derived macrophages from SENP3 knockout and control mice were stimulated with interleukin (IL)-4 and IL-13 to analyze alternative macrophage polarization in vitro. An animal model of allergic rhinitis was constructed using SENP3 knockout mice. CD206 was detected by immunofluorescence staining. The thickening of eosinophil-infiltrated mucosa was detected by Luna staining. RESULTS: The number of CD68+ CD206+ M2 increased in the nasal mucosa of patients with CRS with NP (CRSwNP) compared with patients with CRS without NP (CRSsNP), but with no significant difference between the groups. SENP3 knockout increased the polarization of F4/80+ CD206+ M2. Meanwhile, the number of CD206+ M2 significantly increased in the allergic rhinitis model constructed using SENP3 knockout mice and controls, with a more obvious proliferation of the nasal mucosa. CONCLUSION: Downregulation of SENP3 promotes the formation of nasal polyps mediated by increasing alternative activated macrophage in nasal mucosal inflammation.

Post-Surgery Subcutaneous Seeding of Laryngeal Squamous Cell Carcinoma: A Rare Case.

Laryngeal squamous cell carcinoma (LSCC) is the most common malignant head and neck cancer, with a 40% recurrence rate in the first 3 years after radical treatment. Recurrence of LSCC mostly comprises lymphogenous metastasis, hematogenic metastasis, and locoregional recurrence, while LSCC seeding is rarest: there are only 4 cases reported in PubMed, and none of them is one of subcutaneous seeding. We report a case with post-surgery subcutaneous seeding of LSCC. The final biopsy demonstrated that the subcutaneous seeding of the LSCC was 2 cm away from the primary lesion, with no recurrent foci observed in the larynx and tracheostoma and little relation to the primary lesion. Thus, we drew the conclusion that LSCC surgeries should stick to the principle of the non-tumor technique to prevent subcutaneous seeding.

Heterogeneity in subcutaneous adipose tissue morphology and metabolic complications in overweight and obese women.

OBJECTIVE: The aim of this study was to assess morphological features of intact adipose tissue (AT) ex vivo from both subcutaneous (s.c.) abdominal and gluteal areas using a novel approach of multiphoton autofluorescence microscopy (MPAM) combined with second harmonic generation microscopy (SHGM), and to assess the relationship between morphological features in the two AT sites and insulin resistance to peripheral glucose disposal. METHOD: This study was a cross-sectional evaluation of AT morphology feature and peripheral insulin resistance. SUBJECTS: Fourteen overweight/obese premenopausal women underwent body composition studies, hyperinsulinemic-euglycemic clamps, and needle biopsy of both the s.c. abdominal and gluteal AT areas. MPAM combined with SHGM was used to measure adipocyte maximal diameter and collagen fiber bundle thickness within a sampled image volume after three-dimensional visualization. RESULTS: Higher body mass index (BMI) was associated with larger adipocyte diameter in s.c. abdominal, but not gluteal, AT. Higher adipocyte diameter was associated with higher pericellular collagen thickness. Adipocyte diameter in s.c. abdominal, but not gluteal, AT was associated positively with leptin and negatively with adiponectin plasma levels and peripheral glucose disposal rate. The latter correlation was no longer significant after adjustment for collagen thickness. CONCLUSION: In overweight/obese premenopausal women, larger adipocyte diameter in s.c. abdominal, but not gluteal, AT associates with low plasma adiponectin and systemic insulin resistance, and suggests that increased collagen thickness (obesity-related scarring) could contribute to these findings.

Obligate intracellular bacterium Ehrlichia inhibiting mitochondrial activity.

Ehrlichia are obligately intracellular bacteria that reside in a vacuole in the cytoplasm of phagocytes. We determined by confocal microscopy the interaction between Ehrlichia and mitochondria in DH82 cells to investigate the mechanism of Ehrlichia survival inside the phagocyte. The most remarkable finding of our study was that Ehrlichia morulae interacted with mitochondria and inhibited mitochondrial metabolism. We showed that in Ehrlichia chaffeensis-infected DH82 cells, mitochondria did not incorporate BrdU and transcriptional level of the mitochondrial gene NADPH2 was significantly reduced, indicating the inhibition of mitochondrial metabolism. This study demonstrates that Ehrlichia are able to inhibit mitochondrial activities, and it opens up a new avenue for the study of Ehrlichia pathogenesis.