Search Results (111)

Background and objectives: Adducins are cytoskeletal proteins essential for membrane stability, actin–spectrin network organization, and cell signaling. Mutations in the genes ADD1, ADD2, and ADD3 have been linked to hypertension, neurodevelopmental disorders, and cancer. However, no comprehensive in silico saturation mutagenesis study has systematically evaluated the pathogenic potential and structural consequences of all possible missense mutations in adducins. This study aimed to identify high-risk variants and their potential impact on protein stability and function. Methods: We performed computational saturation mutagenesis for all possible single amino acid substitutions across the adducin proteins family. Pathogenicity predictions were conducted using four independent tools: AlphaMissense, Rhapsody, PolyPhen-2, and PMut. Predictions were validated against UniProt-annotated pathogenic variants. Predictive performance was assessed using Cohen’s Kappa, sensitivity, and precision. Mutations with a prediction probability ≥ 0.8 were further analyzed for structural stability using mCSM, DynaMut2, MutPred2, and Missense3D, with particular focus on functionally relevant domains such as phosphorylation and calmodulin-binding sites. Results: PMut identified the highest number of pathogenic mutations, while PolyPhen-2 yielded more conservative predictions. Several high-risk mutations clustered in known regulatory and binding regions. Substitutions involving glycine were consistently among the most destabilizing due to increased backbone flexibility. Validated variants showed strong agreement across multiple tools, supporting the robustness of the analysis. Conclusions: This study highlights the utility of multi-tool bioinformatic strategies for comprehensive mutation profiling. The results provide a prioritized list of high-impact adducin variants for future experimental validation and offer insights into potential therapeutic targets for disorders involving ADD1, ADD2, and ADD3 mutations. Full article

Therapeutic antibodies with lambda light chains (λ-Abs) are underrepresented compared to kappa light chains (κ-Abs). Here, we evaluated two SARS-CoV-2-specific monoclonal antibodies (mAbs) that exhibit high (P5C3) and low (H4) antigen binding as κ and λ variants. mAbs expressed in glycoengineered Nicotiana benthamiana did not show differences in expression levels, glycosylation, and antigen binding, while κ-Abs exhibited slightly increased thermodynamic stability over λ-Abs. SARS-CoV-2 neutralization and IgG-FcγR immune complex studies revealed increased activities of H4 IgG1κ compared to H4 IgG1λ, with no differences observed between P5C3 variants. Our results indicate that constant light chain variability and Ab specificity contribute to Ab features, a fact that should be considered in engineering therapeutics. Full article

Background: Patients suffering from a new variant of endemic pemphigus foliaceus in El Bagre, Colombia, South America (El Bagre-EPF) produce autoantibodies (Abs) to different proteins in the skin (frustre form), as well as to those in other organs (Senear–Usher-like and systemic forms). Here, we hypothesize whether patients’ autoantibodies play a role in triggering epicardium and pericardium autoimmunity and pathogenicity. We based this hypothesis on knowing that these patients frequently show clinical symptoms of the chest and heart, and we hypothesize that the autoantibodies of this disease are the main contributors to the base of the pericardial conditions of these patients. Materials and Methods: A case-control study for testing the sera of patients affected by El Bagre-EPF (n = 45) and matched controls from the endemic area (n = 45) was conducted to evaluate reactivity with the pericardial tissue. Patients’ necropsies were tested by immunohistochemistry (IHC), in El Bagre-EPF patients (n = 7) and matched controls. Results: The sera from most El Bagre-EPF patients displayed polyclonal autoreactivity with both layers of the pericardium, i.e., fibrous pericardium and serous pericardium (mainly to cell junctions and sensory nerve formations), as well as with the neurovascular cell junction branches. Controls were negative (p < 0.1). These reactivities were detected by IIF, CM, and IHC using secondary Abs against total IgG, IgM, Kappa and lambda, C3C of the complement, fibrinogen, and albumin. Furthermore, Abs against MIZAP, ARVCF, desmoplakin I-II, and p0071 colocalized with the Abs of El Bagre-EPF (p < 0.1). Conclusions: Patients affected by El Bagre-EPF produce autoantibodies directed against molecules present in the cell junctions of the pericardium and adnexal structures. Further studies will focus on the clinical significance of these findings. Full article

Background: The radiological evaluation of the carotid sinus (CS) anatomy and its morphometry is essentially important for various surgical procedures involving the carotid bifurcation and the CS itself. Despite its tremendous clinical significance, studies dealing with the CS anatomy are seldom reported. Hence, the present study aimed to evaluate the frequencies of the CS positional variants and their morphometry and correlate them with age and body mass index (BMI). Methods: In this retrospective cross-sectional study, a total of 754 disease-free carotid arteries were examined using computed tomography angiography scans to determine the CS positional variations (such as types I to III) and its morphometry, including the CS diameter and length. Additionally, the association between these parameters and factors such as sex, age, and body mass index were explored using appropriate statistical tests. The inter-rater agreement of the collected dataset was evaluated using Cohen’s Kappa. Results: The CS type I was observed in 87.67% of the cases, and type II and type III were observed at lower frequencies with 9.02% and 3.32%, respectively. There were statistically significant (p < 0.001) differences observed in the mean diameter and length of the sinus between the sex and the type I CS variations. However, there was no significant and strong correlation between the age and BMI factors with sinus length and sinus diameter. The kappa values for inter-rater agreement ranged from 0.77 to 0.99 for all parameters. Conclusions: In type I, the CS length and carotid vessel’s diameter is significantly different between the sexes. However, age and BMI do not affect the CS anatomy in radiologically disease-free carotid arteries. Knowledge of the CS variant anatomy is clinically significant as it influences the patients’ surgical and physiological outcomes. Full article

Background: Chemoresistance is an existing challenge faced in the treatment of the hairy cell leukemia variant (HCL-v). Classical hairy cell leukemia (HCL-c) is very sensitive to the standard of care with purine nucleoside analogs (PNAs) cladribine (cDa) and pentostatin. However, almost half of these patients eventually become less sensitive to chemotherapy and relapse. HCL-variant (HCL-v) is a biologically distinct entity from HCL-c that is not sensitive to frontline PNA therapy, and this treatment is not recommended for these patients. To address these treatment challenges, we investigated the role of B-cell activating factor (BAFF) in promoting HCL-v cell chemoresistance. Methods: Flow cytometry and quantitative PCR were used to measure the levels of BAFF and its receptors. To determine BAFF activated pathways in HCL-c and HCL-v, the Bonna-12 HCL-c cell line or HCL-v patient-derived cancer cells were stimulated with recombinat BAFF and activation of common BAFF-activated pathways, including the nonclassical nuclear factor kappa B (NF-κB) pathway, the Extracellular Signal-Regulated Kinase (Erk) and phosphatidylinositol-3 (PI-3) kinase (PI3K)/AKT serine/threonine kinase (AKT) pathways were measured by western blotting. To test whether BAFF signaling promotes chemoresistance in HCL-v, we stimulated patient-derived HCL-v cells with BAFF and performed RNA sequencing. Lastly, to confirm the functional implications of BAFF signaling in HCL-v, we treated patient-derived HCL-v cells with exogenous BAFF before treatment with cladribine. Results: We found that HCL-v patient-derived cancer cells express receptors of BAFF at varying degrees and express relatively lower levels of membrane-bound BAFF ligand expression. BAFF stimulation of these cells resulted in substantial activation of the nonclassical NF-κB pathway, which is known to promote anti-apoptotic and pro-survival effects in B-cell cancers. Conversely, in the Bonna-12 cell line, we observed constitutive activation of the nonclassical NF-κB pathway. Through RNA sequencing, we found that BAFF upregulates a myriad of genes that are known to promote chemoresistance in various cancers, including IL1, CXCL1/2, CXCL5, CXCL8, TRAF3, and PTGS2. Lastly, we found that BAFF protects these cells from cladribine-induced cell death in vitro. Conclusions: We conclude that BAFF provides chemo-protection in HCL-v cells by activating nonclassical NF-κB signaling, which results in the upregulation of multiple pro-survival or anti-apoptotic genes. Our results highlight an important role of BAFF in HCL-v resistance to chemotherapy and suggest that the BAFF blockade may enhance the chemosensitivity to PNAs in drug-resistant HCL-v patients. Full article

SARS-CoV-2 virus and its variants remain a global health threat, due to their capacity for rapid evolution. Variants throughout the COVID-19 pandemic exhibited variations in virulence, impacting vaccine protection and disease severity. Investigating nonstructural protein variants is critical to understanding viral evolution and manipulation of host protein interactions. We focus on nonstructural protein 3 (nsp3), with multiple domains with different activities, including viral polyprotein cleavage, host deubiquitylation, de-ISGylation, and double-membrane vesicle formation. Using affinity purification–mass spectrometry (AP-MS), we identify differential protein interactions in nsp3 caused by mutations found in variants identified between 2019 and 2024: Alpha 20I, Beta 20H, Delta 21I, Delta 21J, Gamma 20J, Kappa 21B, Lambda 21G, Omicron 21K, and Omicron 21L. A small set of amino acid substitutions in the N-terminal region of nsp3 (nsp3.1) could be traced to increased interactions with RNA-binding proteins, which are vital in viral replication. Meanwhile, variants of the central region of nsp3 (nsp3.2) were found to share interactions with protein quality control machinery, including ER-associated degradation. In this construct, shared trends in interactor enrichment are observed between Omicron 21K and Delta 21I. These results underscore how minor mutations reshape host interactions, emphasizing the evolutionary arms race between the host and virus. We provide a roadmap to track the interaction changes driven by SARS-CoV-2 variant evolution. Full article

Background/Objectives: The growing use of artificial intelligence (AI) in musculoskeletal radiographs presents significant potential to improve diagnostic accuracy and optimize clinical workflow. However, assessing its performance in clinical environments is essential for successful implementation. We hypothesized that our AI applied to urgent bone X-rays could detect fractures, joint dislocations, and effusion with high sensitivity (Sens) and specificity (Spec). The specific objectives of our study were as follows: 1. To determine the Sens and Spec rates of AI in detecting bone fractures, dislocations, and elbow joint effusion compared to the gold standard (GS). 2. To evaluate the concordance rate between AI and radiology residents (RR). 3. To compare the proportion of doubtful results identified by AI and the RR, and the rates confirmed by GS. Methods: We conducted an observational, double-blind, retrospective study on adult bone X-rays (BXRs) referred from the emergency department at our center between October and November 2022, with a final sample of 792 BXRs, categorized into three groups: large joints, small joints, and long-flat bones. Our AI system detects fractures, dislocations, and elbow effusions, providing results as positive, negative, or doubtful. We compared the diagnostic performance of AI and the RR against a senior radiologist (GS). Results: The study population’s median age was 48 years; 48.6% were male. Statistical analysis showed Sens = 90.6% and Spec = 98% for fracture detection by the RR, and 95.8% and 97.6% by AI. The RR achieved higher Sens (77.8%) and Spec (100%) for dislocation detection compared to AI. The Kappa coefficient between RR and AI was 0.797 for fractures in large joints, and concordance was considered acceptable for all other variables. We also analyzed doubtful cases and their confirmation by GS. Additionally, we analyzed findings not detected by AI, such as chronic fractures, arthropathy, focal lesions, and anatomical variants. Conclusions: This study assessed the impact of AI in a real-world clinical setting, comparing its performance with that of radiologists (both in training and senior). AI achieved high Sens, Spec, and AUC in bone fracture detection and showed strong concordance with the RR. In conclusion, AI has the potential to be a valuable screening tool, helping reduce missed diagnoses in clinical practice. Full article

Background/Objectives: The accurate detection of EGFR mutations, particularly the rare S768I variant, is crucial for guiding treatment decisions in non-small cell lung cancer (NSCLC) patients. This study investigated the incidence of false positives in S768I mutation detection using the Idylla^TM qPCR system and compared results with next-generation sequencing (NGS). Methods: A prospective observational study was conducted at the Dr. Negrín University Hospital between July 2023 and July 2024. Six NSCLC patient samples with S768I variant detection by Idylla^TM were analyzed from all NSCLC cases tested during the study period. Initial testing was performed on tissue samples (Idylla1), followed by replicate analysis using extracted DNA (Idylla2). Results were compared with NGS as the reference method. Statistical analysis included the calculation of sensitivity, specificity, accuracy, and Kappa concordance index. Results: Initial Idylla testing showed an 80% false positive rate, with only one of five positive results confirmed by NGS. The first analysis demonstrated high sensitivity (100%) but low specificity (20%), with an accuracy of 0.333 and poor concordance with NGS (Kappa = 0.077). Repeat testing using extracted DNA showed improved performance, with increased accuracy (0.833) and better agreement with NGS (Kappa = 0.571). Analysis of amplification curves revealed that false positives typically showed normalized fluorescence values below 12 points, with no clear correlation between false positives and factors such as sample quantity or tumor content. Conclusions: While the Idylla^TM system shows high sensitivity for S768I detection, its initial specificity is problematic, leading to frequent false positives. These findings emphasize the importance of confirming positive S768I results through alternative methods like NGS, particularly when these results could influence therapeutic decisions. Results suggest the need to refine the system’s interpretation algorithms to improve specificity. Full article

Snakebite is a critical global public health issue, causing substantial mortality and morbidity, particularly in tropical and subtropical regions. The development of innovative antivenoms targeting snake venom toxins is therefore of paramount importance. In this study, we adopted an epitope-directed approach to design three degenerate 15-mer peptides based on amino acid sequence alignments of snake venom phospholipase A₂s (PLA₂s) and snake venom serine proteases (SVSPs) from snake (Crotalus atrox). By leveraging their immunogenic and inhibitory profiles, these peptides were specifically designed to target the Asp49 and Lys49 variants of PLA₂ and SVSP toxins. Groups of five mice were immunized with each peptide, and IgG mRNA was subsequently extracted from peripheral blood mononuclear cells (PBMCs) and spleen lymphocytes of the top three responders. The extracted mRNA was reverse-transcribed into complementary DNA (cDNA), and the variable regions of the IgG heavy and kappa chains were amplified using polymerase chain reaction (PCR). These amplified regions were then linked with a 66-nucleotide spacer to construct single-chain variable fragments (scFvs). Sequence analysis of 48 randomly selected plasmids from each PLA₂ and SVSP scFv library revealed that over 80% contained scFv sequences with notable diversity observed in the complementarity-determining regions (CDRs), particularly CDR3. Enzyme-linked immunosorbent assay (ELISA) results demonstrated that the SP peptide elicited a broader immune response in mice compared to the Asp49 peptide, implying the strong immunogenicity of the SP peptide. These scFvs represent a promising foundation for the development of recombinant human monoclonal antibodies targeting snake PLA₂ and SVSP toxins, providing a potential therapeutic strategy for the treatment of snakebites. Full article

Pulmonary and extrapulmonary manifestations have been reported following infection with SARS-CoV-2, the causative agent of COVID-19. The virus persists in multiple organs due to its tropism for various tissues, including the skeletal system. This study investigates the effects of SARS-CoV-2 infection, including both ancestral and Omicron viral strains, on differentiating mesenchymal stem cells (MSCs), the precursor cells, into osteoblasts. Although both viral strains can productively infect osteoblasts, precursor cell infection remained abortive. Viral exposure during osteoblast differentiation demonstrates that both variants inhibit mineral and organic matrix deposition. This is accompanied by reduced expression of runt-related transcription factor 2 (RUNX2) and increased levels of interleukin-6 (IL-6), a cytokine that negatively regulates osteoblast differentiation. Furthermore, the upregulation of receptor activator of nuclear factor kappa B ligand (RANKL) strongly suggests that the ancestral and Omicron variants may disrupt bone homeostasis by promoting osteoclast differentiation, ultimately leading to the formation of bone-resorbing cells. This process is dependent of spike glycoprotein since its neutralization significantly reduced the effect of infective SARS-CoV-2 and UV-C inactivated virus. This study underscores the capacity of ancestral and Omicron SARS-CoV-2 variants to disrupt osteoblast differentiation, a process essential for preserving the homeostasis and functionality of bone tissue. Full article

Even though COVID-19 is no longer the primary focus of the global scientific community, its high mutation rate (nearly 30 substitutions per year) poses a threat of a potential comeback. Effective vaccines have been developed and administered to the population, ending the pandemic. Nonetheless, reinfection by newly emerging subvariants, particularly the latest JN.1 strain, remains common. The rapid mutation of this virus demands a fast response from the scientific community in case of an emergency. While the immune escape of earlier variants was extensively investigated, one still needs a comprehensive understanding of how specific mutations, especially in the newest subvariants, influence the antigenic escape of the pathogen. Here, we tested comprehensive in silico approaches to identify methods for fast and accurate prediction of antibody neutralization by various mutants. As a benchmark, we modeled the complexes of the murine antibody 2B04, which neutralizes infection by preventing the SARS-CoV-2 spike glycoprotein’s association with angiotensin-converting enzyme (ACE2). Complexes with the wild-type, B.1.1.7 Alpha, and B.1.427/429 Epsilon SARS-CoV-2 variants were used as positive controls, while complexes with the B.1.351 Beta, P.1 Gamma, B.1.617.2 Delta, B.1.617.1 Kappa, BA.1 Omicron, and the newest JN.1 Omicron variants were used as decoys. Three essentially different algorithms were employed: forced placement based on a template, followed by two steps of extended molecular dynamics simulations; protein–protein docking utilizing PIPER (an FFT-based method extended for use with pairwise interaction potentials); and the AlphaFold 3.0 model for complex structure prediction. Homology modeling was used to assess the 3D structure of the newly emerged JN.1 Omicron subvariant, whose crystallographic structure is not yet available in the Protein Database. After a careful comparison of these three approaches, we were able to identify the pros and cons of each method. Protein–protein docking yielded two false-positive results, while manual placement reinforced by molecular dynamics produced one false positive and one false negative. In contrast, AlphaFold resulted in only one doubtful result and a higher overall accuracy-to-time ratio. The reasons for inaccuracies and potential pitfalls of various approaches are carefully explained. In addition to a comparative analysis of methods, some mechanisms of immune escape are elucidated herein. This provides a critical foundation for improving the predictive accuracy of vaccine efficacy against new viral subvariants, introducing accurate methodologies, and pinpointing potential challenges. Full article

Bipolar disorder’s etiology involves genetics, environmental factors, and gene–environment interactions, underlying its heterogeneous nature and treatment complexity. In 2020, Forstner and colleagues catalogued 378 sequence variants co-segregating with familial bipolar disorder. A notable candidate was an R59Q missense mutation in the PDZ (PSD-95/Dlg1/ZO-1) domain of RGS12. We previously demonstrated that RGS12 loss removes negative regulation on the kappa opioid receptor, disrupting basal ganglia dopamine homeostasis and dampening responses to dopamine-eliciting psychostimulants. Here, we investigated the R59Q variation in the context of potential PDZ domain functional alterations. We first validated a new target for the wildtype RGS12 PDZ domain—the SAPAP3 C-terminus—by molecular docking, surface plasmon resonance (SPR), and co-immunoprecipitation. While initial molecular dynamics (MD) studies predicted negligible effects of the R59Q variation on ligand binding, SPR showed a significant reduction in binding affinity for the three peptide targets tested. AlphaFold2-generated models predicted a modest reduction in protein–peptide interactions, which is consistent with the reduced binding affinity observed by SPR, suggesting that the substituted glutamine side chain may weaken the affinity of RGS12 for its in vivo binding targets, likely through allosteric changes. This difference may adversely affect the CNS signaling related to dynorphin and dopamine in individuals with this R59Q variation, potentially impacting bipolar disorder pathophysiology. Full article

Ground filtering is crucial for airborne Light Detection and Ranging (LiDAR) data post-processing. The progressive triangulated irregular network densification (PTD) algorithm and its variants outperform others in accuracy, stability, and robustness, using grid-based seed point selection, TIN construction, and iterative rules for ground point identification. However, these methods still face limitations in removing low points and accurately preserving terrain details, primarily due to their sensitivity to grid size. To overcome this issue, a novel PTD filtering algorithm based on an adaptive grid (AGPTD) was proposed. The main contributions of the proposed method include an outlier removal method using a radius outlier removal algorithm and Kd-tree, a method for establishing an adaptive two-level grid based on point cloud density and terrain slope, and an adaptive selection method for angle and distance thresholds in the iterative densification processing. The performance of the AGPTD algorithm was assessed based on widely used benchmark datasets. Results show that the AGPTD algorithm outperforms the classical PTD algorithm in retaining ground feature points, especially in reducing Type I error and average total error significantly. In comparison with other advanced algorithms developed in recent years, the novel algorithm showed the lowest average Type I error, the minimal average total error, and the greatest average Kappa coefficient, which were 1.11%, 2.28%, and 90.86%, respectively. Additionally, the average accuracy, precision, and recall of AGPTD were 97.69%, 97.52%, and 98.98%, respectively. Full article

Background: The coronavirus, SARS-CoV-2, is the causative agent for COVID-19, first registered in Wuhan, China and responsible for more than 6 million deaths worldwide. Currently, RT-PCR is the gold-standard method for diagnosing COVID-19. However, serological tests are needed for screening acute disease diagnosis and screening large populations during the COVID-19 outbreak. Objectives: Herein, we described the development and validation of an in-house enzyme-linked immunosorbent assay (ELISA) for detecting the levels of anti-spike-1-RBD IgM antibody (CovIgM-ELISA) in well-defined serum/plasma panel for screening and identifying subjects infected with SARS-CoV-2 in a Latin population. Method: In-house CovIgM-ELISA has the format of an indirect ELISA. It was optimized by checkerboard titration using recombinant SARS-CoV-2 spike-S1-RBD protein as an antigen. Results: We found that, compared to the RT-PCR as the standard method, the in-house CovIgM-ELISA displayed sensitivities of 96.15% and 93.22% for samples collected up to 30 or 60 days after infection, respectively, as well as 95.59% specificity with 97.3% accuracy. The agreement kappa value (κ) of our CovIgM-ELISA was substantial when compared to RT-PCR ($\kappa$ = 0.873) and the anti-SARS-CoV-2 IgM ELISA (InBios Int) ($\kappa$ = 0.684). The IgM levels detected in the population positively correlated with the neutralizing activity against the wild-type, Alpha and Delta variants of concern, but failed to neutralize Omicron. Conclusions: These data indicate that our in-house CovIgM-ELISA is a compatible performing assay for the detection of SARS-CoV-2 infection. Full article

CD44 regulates cell adhesion, proliferation, survival, and stemness and has been considered a tumor therapy target. CD44 possesses the shortest CD44 standard (CD44s) and a variety of CD44 variant (CD44v) isoforms. Since the expression of CD44v is restricted in epithelial cells and carcinomas compared to CD44s, CD44v has been considered a promising target for monoclonal antibody (mAb) therapy. We previously developed an anti-CD44v10 mAb, C₄₄Mab-18 (IgM, kappa), to recognize the variant exon 10-encoded region. In the present study, a mouse IgG_2a version of C₄₄Mab-18 (C₄₄Mab-18-mG_2a) was generated to evaluate the antitumor activities against CD44-positive cells compared with the previously established anti-pan CD44 mAb, C₄₄Mab-46-mG_2a. C₄₄Mab-18-mG_2a exhibited higher reactivity compared with C₄₄Mab-46-mG_2a to CD44v3–10-overexpressed CHO-K1 (CHO/CD44v3–10) and oral squamous cell carcinoma cell lines (HSC-2 and SAS) in flow cytometry. C₄₄Mab-18-mG_2a exerted a superior antibody-dependent cellular cytotoxicity (ADCC) against CHO/CD44v3–10. In contrast, C₄₄Mab-46-mG_2a showed a superior complement-dependent cytotoxicity (CDC) against CHO/CD44v3–10. A similar tendency was observed in ADCC and CDC against HSC-2 and SAS. Furthermore, administering C₄₄Mab-18-mG_2a or C₄₄Mab-46-mG_2a significantly suppressed CHO/CD44v3–10, HSC-2, and SAS xenograft tumor growth compared with the control mouse IgG_2a. These results indicate that C₄₄Mab-18-mG_2a could be a promising therapeutic regimen for CD44v10-positive tumors. Full article