SEPPA-mAb: spatial epitope prediction of protein antigens for mAbs.

Identifying the exact epitope positions for a monoclonal antibody (mAb) is of critical importance yet highly challenging to the Ab design of biomedical research. Based on previous versions of SEPPA 3.0, we present SEPPA-mAb for the above purpose with high accuracy and low false positive rate (FPR), suitable for both experimental and modelled structures. In practice, SEPPA-mAb appended a fingerprints-based patch model to SEPPA 3.0, considering the structural and physic-chemical complementarity between a possible epitope patch and the complementarity-determining region of mAb and trained on 860 representative antigen-antibody complexes. On independent testing of 193 antigen-antibody pairs, SEPPA-mAb achieved an accuracy of 0.873 with an FPR of 0.097 in classifying epitope and non-epitope residues under the default threshold, while docking-based methods gave the best AUC of 0.691, and the top epitope prediction tool gave AUC of 0.730 with balanced accuracy of 0.635. A study on 36 independent HIV glycoproteins displayed a high accuracy of 0.918 and a low FPR of 0.058. Further testing illustrated outstanding robustness on new antigens and modelled antibodies. Being the first online tool predicting mAb-specific epitopes, SEPPA-mAb may help to discover new epitopes and design better mAbs for therapeutic and diagnostic purposes. SEPPA-mAb can be accessed at http://www.badd-cao.net/seppa-mab/.

HIT 2.0: an enhanced platform for Herbal Ingredients' Targets.

Literature-described targets of herbal ingredients have been explored to facilitate the mechanistic study of herbs, as well as the new drug discovery. Though several databases provided similar information, the majority of them are limited to literatures before 2010 and need to be updated urgently. HIT 2.0 was here constructed as the latest curated dataset focusing on Herbal Ingredients' Targets covering PubMed literatures 2000-2020. Currently, HIT 2.0 hosts 10 031 compound-target activity pairs with quality indicators between 2208 targets and 1237 ingredients from more than 1250 reputable herbs. The molecular targets cover those genes/proteins being directly/indirectly activated/inhibited, protein binders, and enzymes substrates or products. Also included are those genes regulated under the treatment of individual ingredient. Crosslinks were made to databases of TTD, DrugBank, KEGG, PDB, UniProt, Pfam, NCBI, TCM-ID and others. More importantly, HIT enables automatic Target-mining and My-target curation from daily released PubMed literatures. Thus, users can retrieve and download the latest abstracts containing potential targets for interested compounds, even for those not yet covered in HIT. Further, users can log into 'My-target' system, to curate personal target-profiling on line based on retrieved abstracts. HIT can be accessible at http://hit2.badd-cao.net.

A study on related factors affecting dental fear in preschool children.

This study aims to examine the manifestations of dental anxiety (DA) and its influencing factors during dental visits among preschool children. The data of 166 preschool children who visited the Department of Dentistry of our hospital from April 2021 to April 2023 with oral problems were retrieved. Their DA performance was investigated using the Children's Fear Survey Schedule-Dental Subscale (CFSS-DS). In addition, based on their general data and potential risk factor information, we performed logistic regression analysis to identify the factors influencing DA. Of the 166 questionnaires distributed, a total of 160 valid questionnaires were retrieved. The average CFSS-DS score was 35.57 ± 3.51 points. Sixty-six children had DA, resulting in an incidence rate of 41.25%. The top 5 items with the highest CFSS-DS scores were fear of needles, dentists, tooth extraction, drilling and oral anesthesia. When the 66 children with DA were classified into a DA group and a non-DA group, we observed significant differences in age distribution, dental experience, only child status, general anxiety symptoms, dental condition, family income and specific dental treatment procedures, particularly tooth extraction, between them (p < 0.05). Multivariate logistic regression analysis revealed that preschool children aged ≤4 years, those with prior dental experiences, single-child status, general anxiety symptoms, suboptimal dental health, family incomes below 100,000 yuan/year, and those undergoing specific dental procedures, such as tooth extractions, were independently associated with a higher risk of DA (p < 0.05). The incidence of DA in preschool children is high, and they exhibit substantial fear of needles, dentists, tooth extraction, drilling and oral anesthesia. Preschool children aged ≤4 years, with prior dental experiences, single-child status, the presence of general anxiety symptoms, suboptimal dental health, family incomes below 100,000 yuan/year, and those undergoing dental procedures, particularly tooth extraction, could be more predisposed to DA.

SEPPA 3.0-enhanced spatial epitope prediction enabling glycoprotein antigens.

B-cell epitope information is critical to immune therapy and vaccine design. Protein epitopes can be significantly affected by glycosylation, while no methods have considered this till now. Based on previous versions of Spatial Epitope Prediction of Protein Antigens (SEPPA), we here present an enhanced tool SEPPA 3.0, enabling glycoprotein antigens. Parameters were updated based on the latest and largest dataset. Then, additional micro-environmental features of glycosylation triangles and glycosylation-related amino acid indexes were added as important classifiers, coupled with final calibration based on neighboring antigenicity. Logistic regression model was retained as SEPPA 2.0. The AUC value of 0.794 was obtained through 10-fold cross-validation on internal validation. Independent testing on general protein antigens resulted in AUC of 0.740 with BA (balanced accuracy) of 0.657 as baseline of SEPPA 3.0. Most importantly, when tested on independent glycoprotein antigens only, SEPPA 3.0 gave an AUC of 0.749 and BA of 0.665, leading the top performance among peers. As the first server enabling accurate epitope prediction for glycoproteins, SEPPA 3.0 shows significant advantages over popular peers on both general protein and glycoprotein antigens. It can be accessed at http://bidd2.nus.edu.sg/SEPPA3/ or at http://www.badd-cao.net/seppa3/index.html. Batch query is supported.

pH and effects on Streptococcus mutans growth of denture adhesives: an in vitro study.

OBJECTIVES: To evaluate the pH and effects on Streptococcus mutans growth of denture adhesives. BACKGROUND: There is little information regarding the pH of contemporary adhesives and their influences on S. mutans growth. MATERIALS AND METHODS: The adhesives tested were Polident® cream, Protefix® cream and Protefix® powder. Samples of each adhesive were added to deionized water to produce solutions of 10.0, 5.0, 2.5 and 1.0% w/v (cream formulations) or 5.0, 2.5,1.0 and 0.5% (powder formulation). The pH values were measured immediately after preparation and at 1-, 2-, 3-, 6-, 12-, and 24-h intervals using a digital pH meter. Streptococcus mutans UA159 was inoculated in the Brain Heart Infusion medium with or without the adhesive extracts (control). Bacterial growth was observed by measuring absorption at 600 nm every 1 h for 12 h using a spectrophotometer. RESULTS: The tested adhesives generally remained relatively pH-stable over 24 h, ranging from 5.5 to 7.0. There were no statistically significant differences in S. mutans growth rates between the extract-treated and control cultures (p>0.5). CONCLUSIONS: Some adhesives produce a pH below the critical pH of hydroxyapatite and may not be suitable for patients with natural teeth. None of the tested adhesives significantly affect S. mutans growth.

Multi-omic profiling reveals potential biomarkers of hepatocellular carcinoma prognosis and therapy response among mitochondria-associated cell death genes in the context of 3P medicine.

Background: Cancer cell growth, metastasis, and drug resistance are major challenges in treating liver hepatocellular carcinoma (LIHC). However, the lack of comprehensive and reliable models hamper the effectiveness of the predictive, preventive, and personalized medicine (PPPM/3PM) strategy in managing LIHC. Methods: Leveraging seven distinct patterns of mitochondrial cell death (MCD), we conducted a multi-omic screening of MCD-related genes. A novel machine learning framework was developed, integrating 10 machine learning algorithms with 67 different combinations to establish a consensus mitochondrial cell death index (MCDI). This index underwent rigorous evaluation across training, validation, and in-house clinical cohorts. A comprehensive multi-omics analysis encompassing bulk, single-cell, and spatial transcriptomics was employed to achieve a deeper insight into the constructed signature. The response of risk subgroups to immunotherapy and targeted therapy was evaluated and validated. RT-qPCR, western blotting, and immunohistochemical staining were utilized for findings validation. Results: Nine critical differentially expressed MCD-related genes were identified in LIHC. A consensus MCDI was constructed based on a 67-combination machine learning computational framework, demonstrating outstanding performance in predicting prognosis and clinical translation. MCDI correlated with immune infiltration, Tumor Immune Dysfunction and Exclusion (TIDE) score and sorafenib sensitivity. Findings were validated experimentally. Moreover, we identified PAK1IP1 as the most important gene for predicting LIHC prognosis and validated its potential as an indicator of prognosis and sorafenib response in our in-house clinical cohorts. Conclusion: This study developed a novel predictive model for LIHC, namely MCDI. Incorporating MCDI into the PPPM framework will enhance clinical decision-making processes and optimize individualized treatment strategies for LIHC patients. Supplementary Information: The online version contains supplementary material available at 10.1007/s13167-024-00362-8.

Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination.

The current SARS-CoV-2 variants strikingly evade all authorized monoclonal antibodies and threaten the efficacy of serum-neutralizing activity elicited by vaccination or prior infection, urging the need to develop antivirals against SARS-CoV-2 and related sarbecoviruses. Here, we identified both potent and broadly neutralizing antibodies from a five-dose vaccinated donor who exhibited cross-reactive serum-neutralizing activity against diverse coronaviruses. Through single B-cell sorting and sequencing followed by a tailor-made computational pipeline, we successfully selected 86 antibodies with potential cross-neutralizing ability from 684 antibody sequences. Among them, PW5-570 potently neutralized all SARS-CoV-2 variants that arose prior to Omicron BA.5, and the other three could broadly neutralize all current SARS-CoV-2 variants of concern, SARS-CoV and their related sarbecoviruses (Pangolin-GD, RaTG13, WIV-1, and SHC014). Cryo-EM analysis demonstrates that these antibodies have diverse neutralization mechanisms, such as disassembling spike trimers, or binding to RBM or SD1 to affect ACE2 binding. In addition, prophylactic administration of these antibodies significantly protects nasal turbinate and lung infections against BA.1, XBB.1, and SARS-CoV viral challenge in golden Syrian hamsters, respectively. Importantly, post-exposure treatment with PW5-5 and PW5-535 also markedly protects against XBB.1 challenge in these models. This study reveals the potential utility of computational process to assist screening cross-reactive antibodies, as well as the potency of vaccine-induced broadly neutralizing antibodies against current SARS-CoV-2 variants and related sarbecoviruses, offering promising avenues for the development of broad therapeutic antibody drugs.

A new gcrR-deficient Streptococcus mutans mutant for replacement therapy of dental caries.

BACKGROUND: gcrR gene acts as a negative regulator related to sucrose-dependent adherence in S. mutans. It is constructive to test the potential capacity of mutans with gcrR gene deficient in bacteria replacement therapy. METHODS: In this study, we constructed the mutant by homologous recombination. The morphological characteristics of biofilms were analyzed by confocal laser scanning microscopy. S. mutans UA159 and the mutant MS-gcrR-def were inoculated, respectively, or together for competitive testing in vitro and in rat model. RESULTS: Adhesion assay showed that the adhesion ability of the mutant increased relative to the wild type, especially in the early stage. MS-gcrR-def out-competed S. mutans UA159 in vitro biofilm, and correspondingly coinfection displayed significantly fewer caries in vivo. The former possessed both a lower level of acid production and a stronger colonization potential than S. mutans UA159. CONCLUSION: These findings demonstrate that MS-gcrR-def appears to be a good candidate for replacement therapy.

The molecular mechanism of propionate-regulating gluconeogenesis in bovine hepatocytes.

OBJECTIVE: Cows that are nursing get around 80% of their glucose from liver gluconeogenesis. Propionate, a significant precursor of liver gluconeogenesis, can regulate the key genes involved in hepatic gluconeogenesis expression, but its precise effects on the activity of enzymes have not yet been fully elucidated. Therefore, the aim of this study was to investigate the effects of propionate on the activity, gene expression, and protein abundance of the key enzymes involved in the gluconeogenesis of dairy cow hepatocytes. METHODS: The hepatocytes were cultured and treated with various concentrations of sodium propionate (0, 1.25, 2.50, 3.75, and 5.00 mM) for 12 h. Glucose content in the culture media was determined by an enzymatic coloring method. The activities of gluconeogenesis related enzymes were determined by enzyme linked immunosorbent assay kits, and the levels of gene expression and protein abundance of the enzymes were detected by real-time quantitative polymerase chain reaction and Western blot, respectively. RESULTS: Propionate supplementation considerably increased the amount of glucose in the culture medium compared to the control (p<0.05); while there was no discernible difference among the various treatment concentrations (p>0.05). The activities of cytoplasmic phosphoenolpyruvate carboxylase (PEPCK1), mitochondrial phosphoenolpyruvate carboxylase (PEPCK2), pyruvate carboxylase (PC), and glucose-6-phosphatase (G6PC) were increased with the addition of 2.50 and 3.75 mM propionate; the gene expressions and protein abundances of PEPCK1, PEPCK2, PC, and G6PC were increased by 3.75 mM propionate addition. CONCLUSION: Propionate encouraged glucose synthesis in bovine hepatocytes, and 3.75 mM propionate directly increased the activities, gene expressions and protein abundances of PC, PEPCK1, PEPCK2, and G6PC in bovine hepatocytes, providing a theoretical basis of propionate-regulating gluconeogenesis in bovine hepatocytes.

Exosomes combined with biomaterials in the treatment of spinal cord injury.

Spinal cord injury (SCI) is a serious and disabling disease with a high mortality rate. It often leads to complete or partial sensory and motor dysfunction and is accompanied by a series of secondary outcomes, such as pressure sores, pulmonary infections, deep vein thrombosis in the lower extremities, urinary tract infections, and autonomic dysfunction. Currently, the main treatments for SCI include surgical decompression, drug therapy, and postoperative rehabilitation. Studies have shown that cell therapy plays a beneficial role in the treatment of SCI. Nonetheless, there is controversy regarding the therapeutic effect of cell transplantation in SCI models. Meanwhile exosomes, as a new therapeutic medium for regenerative medicine, possess the advantages of small size, low immunogenicity, and the ability to cross the blood-spinal cord barrier. Certain studies have shown that stem cell-derived exosomes have anti-inflammatory effects and can play an irreplaceable role in the treatment of SCI. In this case, it is difficult for a single treatment method to play an effective role in the repair of neural tissue after SCI. The combination of biomaterial scaffolds and exosomes can better transfer and fix exosomes to the injury site and improve their survival rate. This paper first reviews the current research status of stem cell-derived exosomes and biomaterial scaffolds in the treatment of SCI respectively, and then describes the application of exosomes combined with biomaterial scaffolds in the treatment of SCI, as well as the challenges and prospects.

Influence of continuous renal replacement therapy on the plasma concentration of tigecycline in patients with septic shock: A prospective observational study.

Objective: The influence of continuous renal replacement therapy (CRRT) on the steady-state plasma concentration of high-dose tigecycline was investigated in septic shock patients to provide references for drug dosing. Methods: In this prospective observational study, 17 septic shock patients presenting with severe infections needing a broad-spectrum antibiotic therapy with high-dose tigecycline (100 mg per 12 h) in the intensive care unit were included and divided into CRRT group (n = 6) or non-CRRT group (n = 11). The blood samples were collected and plasma drug concentration was determined by SHIMADZU LC-20A and SHIMADZU LCMS 8040. The steady-state plasma concentration was compared between groups using unpaired t-test. Furthermore, between-groups comparisons adjusted for baseline value was also done using multivariate linear regression model. Results: Peak concentration (Cmax) of tigecycline was increased in CRRT group compared to non-CRRT group, but there were no statistical differences (505.11 ± 143.84 vs. 406.29 ± 108.00 ng/mL, p-value: 0.129). Trough concentration (Cmin) of tigecycline was significantly higher in CRRT group than in non-CRRT group, with statistical differences (287.92 ± 41.91 vs. 174.79 ± 33.15 ng/mL, p-value: 0.000, adjusted p-value: 0.000). In safety, Cmin was reported to be a useful predictor of hepatotoxicity with a cut-off of 474.8 ng/mL. In our studies, Cmin of all patients in CRRT group was lower than 474.8 ng/mL. Conclusion: The plasma concentration of tigecycline was increased in septic shock patients with CRRT treatment and only Cmin shown statistical differences. No dose adjustment seems needed in the view of hepatotoxicity. Clinical Trial Registration: https://www.chictr.org.cn/, identifier ChiCTR2000037475.

A decellularized spinal cord extracellular matrix-gel/GelMA hydrogel three-dimensional composite scaffold promotes recovery from spinal cord injury via synergism with human menstrual blood-derived stem cells.

Spinal cord injury (SCI), as a serious disabling disease, is still haunted by lacking of effective treatments. We previously found that transplantation of menstrual blood-derived mesenchymal stem cells (MenSCs) promoted axon regeneration in rats with SCI, while the abominable microenvironment after the SCI inhibited the survival of stem cells after transplantation. Biomaterials can support the activity of stem cells and accelerate the functional reconstruction of the injured spinal cord. In this study, we constructed a novel composite scaffold consisting of the decellularized spinal cord extracellular matrix-gel (DSCG) and the GelMA hydrogel, which harbored high water retention, wettability, degradability and soft mechanical property. In vitro, the DSCG/GelMA composite scaffold provided a dual bionic microenvironment with optimized bioactive components and favorable microstructures for the adhesion, proliferation and differentiation of MenSCs. After that, we prepared MenSC-encapsulated DSCG/GelMA composite scaffolds to bridge the 2 mm gap in rats with completely transected SCI. The in vivo results showed that the combined use of the DSCG/GelMA composite scaffold with MenSCs improved the motor function, reduced the inflammatory response, promoted neuronal differentiation, and inhibited the proliferation of reactive astrocytes after spinal cord injury. Altogether, our study provided a promising novel therapeutic option of using bioactive materials synergistic with stem cells for the treatment of SCI.

Construction of a decellularized spinal cord matrix/GelMA composite scaffold and its effects on neuronal differentiation of neural stem cells.

Spinal cord injury (SCI) leads to severe loss of motor and sensory functions, and the rehabilitation of SCI is a worldwide problem. Tissue-engineered scaffolds offer new hope for SCI patients, while the newly developed materials encountered a challenge in modeling the microenvironment around the lesion site. We constructed a new composite scaffold by mixing decellularized spinal cord extracellular matrix (dECM) with gelatin methacryloyl (GelMA). The dECM, as a natural biological material, retained a large number of proteins and growth factors related to neurogenesis. GelMA was a photopolymerizable material, harbored a polymer network structure, soft texture, certain shape and plenty of water. The viability, proliferation, and differentiation of neural stem cells (NSCs) on the composite scaffold were evaluated by cell count kit-8 (CCK8), Live/Dead assay, phalloidin staining, 5-Ethynyl-2'-deoxyurdine (EdU), immunofluorescence staining and western blot. The Live/Dead assay, phalloidin staining, EdU, and CCK8 assay showed that the composite scaffold had good biocompatibility and provided better support for proliferation of NSCs. Results of immunocytochemistry and western blot showed that the composite scaffolds promoted the specific differentiation of NSCs into neuron cells. Together, this dECM/GelMA composite scaffold can be used as a cell culture coating, the isolated NSCs seeded on the surface of composite scaffold expressed neuronal markers and assumed neuronal morphology. Our work provided a new method that would be widely used in tissue engineering of SCI.

SAS: A Platform of Spike Antigenicity for SARS-CoV-2.

Since the outbreak of SARS-CoV-2, antigenicity concerns continue to linger with emerging mutants. As recent variants have shown decreased reactivity to previously determined monoclonal antibodies (mAbs) or sera, monitoring the antigenicity change of circulating mutants is urgently needed for vaccine effectiveness. Currently, antigenic comparison is mainly carried out by immuno-binding assays. Yet, an online predicting system is highly desirable to complement the targeted experimental tests from the perspective of time and cost. Here, we provided a platform of SAS (Spike protein Antigenicity for SARS-CoV-2), enabling predicting the resistant effect of emerging variants and the dynamic coverage of SARS-CoV-2 antibodies among circulating strains. When being compared to experimental results, SAS prediction obtained the consistency of 100% on 8 mAb-binding tests with detailed epitope covering mutational sites, and 80.3% on 223 anti-serum tests. Moreover, on the latest South Africa escaping strain (B.1.351), SAS predicted a significant resistance to reference strain at multiple mutated epitopes, agreeing well with the vaccine evaluation results. SAS enables auto-updating from GISAID, and the current version collects 867K GISAID strains, 15.4K unique spike (S) variants, and 28 validated and predicted epitope regions that include 339 antigenic sites. Together with the targeted immune-binding experiments, SAS may be helpful to reduce the experimental searching space, indicate the emergence and expansion of antigenic variants, and suggest the dynamic coverage of representative mAbs/vaccines among the latest circulating strains. SAS can be accessed at https://www.biosino.org/sas.

A benchmark dataset of protein antigens for antigenicity measurement.

Antigenicity measurement plays a fundamental role in vaccine design, which requires antigen selection from a large number of mutants. To augment traditional cross-reactivity experiments, computational approaches for predicting the antigenic distance between multiple protein antigens are highly valuable. The performance of in silico models relies heavily on large-scale benchmark datasets, which are scattered among public databases and published articles or reports. Here, we present the first benchmark dataset of protein antigens with experimental evidence to guide in silico antigenicity calculations. This dataset includes (1) standard haemagglutination-inhibition (HI) tests for 3,867 influenza A/H3N2 strain pairs, (2) standard HI tests for 559 influenza virus B strain pairs, and (3) neutralization titres derived from 1,073 Dengue virus strain pairs. All of these datasets were collated and annotated with experimentally validated antigenicity relationships as well as sequence information for the corresponding protein antigens. We anticipate that this work will provide a benchmark dataset for in silico antigenicity prediction that could be further used to assist in epidemic surveillance and therapeutic vaccine design for viruses with variable antigenicity.

A novel gene mutation of Runx2 in cleidocranial dysplasia.

Haploinsufficiency of the runt-related transcription factor 2 (Runx2) gene is widely known to be responsible for cleidocranial dysplasia (CCD). To date, more than 190 mutations in Runx2 gene have been reported to be related to CCD. In this study, a novel mutation of Runx2 gene was observed in a female with CCD. Genomic DNA was extracted from peripheral venous blood of the proband and eleven members of her family. Genetic testing on these twelve people identified a novel missense mutation (c.895 T>C, Y299H) in exon 5 of the RUNX2 gene in the proband. This mutation results in an amino acid change at codon 895 (P.Tyr 299 His.) from a tryptophan codon (TAT) to a histidine codon (CAT). Our finding may further extend the known mutation spectrum of the RUNX2 gene, and facilitate prenatal genetic diagnosis of CCD in the future.

MicroRNA-92b promotes tumor growth and activation of NF-κB signaling via regulation of NLK in oral squamous cell carcinoma.

miR-92b has been reported to be dysregulated in many types of human cancers. However, the role of miR-92b in oral squamous cell carcinoma (OSCC) is unknown. The aim of the present study was to investigate the function and mechanism of miR-92b in human OSCC. Using quantitative reverse­transcription PCR (qRT-PCR), we found that the miR-92b level in primary tumors (n=85) was significantly elevated compared with that in the adjacent normal tissues (p<0.001). A high level of miR-92b was significantly associated with a large tumor size (p=0.005), advanced tumor stage (p<0.001) and poorer prognosis (p=0.04). Functionally, miR-92b was shown to not only promote the proliferation of OSCC cells in MTT and colony formation and xenograft assays, but also to inhibit cell apoptosis in a flow cytometric assay. In western blotting and luciferase assay, NLK was identified as a direct and functional target of miR-92b. We also found that NLK was involved in miR-92b-induced cell proliferation, and its protein level was obviously downregulated in the miR-92b-overexpressing xenograft tumors. Finally, luciferase reporter assay and fluorescent immunostaining revealed that miR-92b activated the NF-κB signaling pathway, which may be responsible for the effects of miR-92b on cell proliferation. Taken together, our results indicate that miR-92b upregulation accelerates tumor growth and present a novel mechanism of miRNA­mediated NF-κB activation in OSCC.