Systemic lupus erythematosus (SLE) is biologically heterogeneous, motivating development of reproducible molecular subtypes that can track change over time. The aim of this study was to establish a reproducible molecular stratification of SLE across cohorts and platforms and connect the resulting subtypes to clinical activity, serology, and serum proteomics. We computed Gene Set Variation Analysis scores for eight immune gene modules from baseline transcriptomes (ILLUMINATE whole-blood microarray [N = 1,756], LOTUS whole-blood RNA sequencing [RNA-seq; N = 585], and Genuity peripheral blood mononuclear cell (PBMC) RNA-seq [N = 812]). We clustered ILLUMINATE patients (K = 2-8) and selected K = 6, then used a random forest classifier to assign subtypes in LOTUS and Genuity. We analyzed serum proteomics (SomaScan in LOTUS; Olink in Genuity), assessed glucocorticoid associations with neutrophil modules, and quantified baseline to week 24 stability in LOTUS. Six molecular subtypes replicated across cohorts and corresponded to different levels of disease activity and serology (P < 0.001). Proteomic patterns converged with transcriptomics, with concordant differential proteins across Olink and SomaScan among shared targets. Neutrophils were a key axis: one neutrophil module tracked glucocorticoid use, whereas a second was glucocorticoid independent. In LOTUS, subtype assignments were mostly stable to week 24; when patients moved, transitions were nonrandom, occurred between adjacent subtypes, and were similar in the placebo group. We demonstrated reproducible SLE molecular subtypes (interferon, plasmablast/B cell, neutrophil) supported by independent proteomics. In LOTUS, subtypes were largely stable through week 24. When patients changed subtypes, transitions followed preferential trajectories, supporting longitudinal tracking and trial design utility.
Yeast molecular display is a convenient tool for developing and improving recombinant proteins and assessing their functions. Molecular display using Saccharomyces cerevisiae has been applied for screening valuable biochemical molecules, including antigens and antibodies. In this chapter, we describe the genetic construction of a yeast molecular display system for a nanobody and its evaluation using fluorescence microscopy and flow cytometry.
Unlike in hematologic malignancies like acute promyelocytic leukemia (APL), the tumorigenic role of RARA fusions in solid tumors, including melanomas, remains largely unknown. Here, we present a comprehensive clinicopathologic and molecular analysis of two cutaneous melanomas harboring RARA fusions. Both melanomas were of the acral subtype, affecting the feet of adults (median age: 60.5 years) without sex predilection. At diagnosis, Breslow thickness ranged from 1.2 to 5.5 mm, ulceration was present in one case, and the median mitotic rate was 4/mm2. Tumor cells exhibited variable cytomorphology, including spindled and epithelioid features, with occasional rhabdoid morphology. Molecular analysis revealed a consistently low tumor mutational burden (median: 4.5 mutations/Mb). One acral melanoma was triple wild-type (lacking mutations in BRAF, NRAS, and NF1) and showed no gene amplifications, but harbored a LOC107984974::RARA fusion. The other acral melanoma carried an NF1 loss-of-function mutation and multiple gene amplifications involving 11q13.3 (CCND1, FGF3, FGF4, FGF19), 11q13.5-q14.1 (PAK1), 12q15 (MDM2), and 6q24.3 (SHPRH), along with two RARA fusions: RARA::LRP5 and RARA::RNF169. Over a median follow-up of 23 months, one patient developed a distant metastasis involving the brain approximately 20 months after the initial diagnosis. At last follow-up, one patient was alive with disease, while the other remained alive without clinical or radiological evidence of recurrence. These findings expand the current understanding of the molecular landscape of acral melanomas and may provide insights into the potential utility of targeted therapies against RARA fusions in a subset of melanomas, analogous to their therapeutic role in APL.
Systemic lupus erythematosus (SLE) is an autoimmune disease driven by immune dysregulation. Parabens, commonly used preservatives, are potential environmental factors that may influence immune function and contribute to autoimmune diseases like SLE, although the underlying mechanisms remain unclear. A network toxicology approach was used to investigate potential associations between parabens and SLE-related genes. Paraben target genes were identified from ChEMBL, STITCH, and SwissTargetPrediction, while SLE-related genes were obtained from GeneCards, OMIM, and TTD. Shared paraben-SLE genes were subjected using gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses. Hub genes were identified via network analysis with Cytoscape and further evaluated using three gene expression omnibus datasets. Molecular docking simulations were performed to predict potential interactions between parabens and proteins encoded by the identified hub genes. 56 shared paraben-SLE genes were identified and were enriched in immune-related processes, including leukocyte proliferation, T cell activation, and cytokine receptor binding. KEGG analysis highlighted enrichment in immune response pathways, including Toll-like receptor (TLR) signaling. Candidate hub genes, including TLR4, cytotoxic T-lymphocyte associated protein 4 (CTLA4), and CD86, were differentially expressed across three independent SLE gene expression datasets. Molecular docking simulations predicted potential binding interactions between parabens and these hub gene proteins. This study identified candidate genes and pathways potentially associated with both paraben exposure and immune dysregulation in SLE, particularly TLR4, CTLA4, and CD86. These findings are based on computational predictions and require further experimental and clinical studies to determine their biological relevance and potential implications for autoimmune diseases.
Memory B cells underpin the capacity of the immune system to confer durable protective immunity by mounting rapid and enhanced secondary antibody responses. Hence, they are central to vaccine efficacy and to limiting long-term tissue damage after reinfection. Despite their importance, the cellular origins, molecular programs, and tissue-specific specialization of memory B cells remain incompletely understood. Here, we review recent advances in memory B cell development and regulation, with a particular focus on tissue-resident memory B cells. We discuss how memory B cells arise from distinct developmental precursors as well as the extrinsic regulators and molecular programs that govern memory B cell identity and function. We further examine emerging evidence for tissue-resident memory B cell populations in the respiratory airways and their implications for mucosal vaccination strategies against airborne pathogens. Together, these findings provide a framework for leveraging memory B cell biology in clinical applications.
The global prevalence of metabolic diseases, including obesity, type 2 diabetes mellitus (T2DM), and metabolic dysfunction-associated steatotic liver disease (MASLD), continues to rise, representing a major global health threat and economic burden. Dihydroberberine (DHB), a reduced derivative of berberine (BBR), has recently garnered attention due to its superior lipophilicity and intestinal absorption. Pharmacokinetic studies suggested that DHB achieves significantly higher blood concentrations compared to BBR at equivalent doses. This review systematically synthesized the current preclinical evidence regarding the metabolic regulatory mechanisms of DHB. Key pharmacological targets identified in cell and animal models included the activation of AMP-activated protein kinase (AMPK) and glucokinase (GCK), modulation of lipid metabolism, and attenuation of inflammatory and oxidative stress pathways. Furthermore, DHB interacted extensively with the gut microbiota, acting both as a microbial metabolite of BBR and a modulator of microbial composition. Toxicological assessments indicated a favorable safety profile, although potential risks such as hERG channel inhibition required careful evaluation. Importantly, while in vitro and animal studies demonstrated significant metabolic benefits, human clinical trials assessing direct disease outcomes remained highly limited. This review highlighted the pharmacokinetic advantages of DHB and outlined the critical translational gaps that must be addressed in future research.
Immune dysregulation (ID), defined as aberrant immune activation or suppression, may result in autoimmune or inflammatory disorders, lymphoproliferative malignancies, and allergic diseases. Apoptosis, nuclear factor-κB (NFκB), and phosphoinositide 3-kinase (PI3K) pathways are major pathways involved in ID. This study aimed to assess ID using targeted inflammatory gene-expression profiles in comparison with controls. We grouped patients according to presenting features: autoimmune lymphoproliferative syndrome (ALPS) (group 1), immune cytopenia (group 2), and EBV-associated lymphoproliferation (group 3). We established real-time quantitative polymerase chain reaction (RT-qPCR) analysis for selected genes (CASP8, CASP10, FAS, FASL, AKT, MAP3K7, MAP3K14, mTOR, NFKB1, NFKB2, NFKBIA, and TRAF3) involved in inflammatory pathways, and calculated gene expression fold changes using the logarithmic Delta-Delta Ct (2^(-delta delta CT)) method. The median age of symptom onset in group 1 (n=10), group 2 (n=12), and group 3 (n=10) was 9.3 (0.5-38.7), 5.7 (0.7-19), 22.5 (0.7-45) years, respectively (p=0.181). The median age at hospital admission was 12 (1.9-38.7), 9.4 (2.3-35), and 34.8 (0.9-54.7) years in groups 1, 2, and 3, respectively (p=0.152). There was a significant difference between patient and control groups (p<0.05), but none among patient groups regarding targeted gene expression (relative quantification values). According to ROC curve analysis, the most discriminative target genes are NFKB2, MAP3K7, AKT, mTOR, NFKB1, and FAS. We propose an ID signature that includes targeted gene expression profiles (NFKB1, NFKB2, MAP3K7, AKT, mTOR, and FAS) and suggest using these specific gene expressions as a biomarker for diagnosis and therapy response in ID.
The liver is a central immunological organ. Liver resident macrophages, Kupffer cells (KC), but also sinusoidal endothelial cells, dendritic cells (DC) and other immune cells are involved in balancing immunity and tolerance against pathogens, commensals or food antigens. Hepatic stellate cells (HSCs) have been primarily characterized as the main effector cells in liver fibrosis, due to their capacity to transdifferentiate into collagen-producing myofibroblasts (MFB). More recent studies elucidated the fundamental role of HSC in liver immunology. HSC are not only the major storage site for dietary vitamin A (Vit A) (retinol, retinoic acid), which is essential for proper function of the immune system. This pericyte further represents a versatile source of many soluble immunological active factors including cytokines [e.g., interleukin 17 (IL-17)] and chemokines [C-C motif chemokine (ligand) 2 (CCL2)], may act as an antigen presenting cell (APC), and has autophagy activity. Additionally, it responds to many immunological triggers via toll-like receptors (TLR) (e.g., TLR4, TLR9) and transduces signals through pathways and mediators traditionally found in immune cells, including the Hedgehog (Hh) pathway or inflammasome activation. Overall, HSC promote rather immune-suppressive responses in homeostasis, like induction of regulatory T cells (Treg), T cell apoptosis (via B7-H1, PDL-1) or inhibition of cytotoxic CD8 T cells. In conditions of liver injury, HSC are important sensors of altered tissue integrity and initiators of innate immune cell activation. Vice versa, several immune cell subtypes interact directly or via soluble mediators with HSC. Such interactions include the mutual activation of HSC (towards MFB) and macrophages or pro-apoptotic signals from natural killer (NK), natural killer T (NKT) and gamma-delta T cells (γδ T-cells) on activated HSC. Current directions of research investigate the immune-modulating functions of HSC in the environment of liver tumors, cellular heterogeneity or interactions promoting HSC deactivation during resolution of liver fibrosis. Understanding the role of HSC as central regulators of liver immunology may lead to novel therapeutic strategies for chronic liver diseases.
Accurate liquid chromatography retention time (RT) prediction is a critical component of compound identification in metabolomics and lipidomics. However, existing RT prediction approaches are often limited by the scarcity of experimental RT measurements for many molecular classes, restricting model generalization and the construction of comprehensive RT libraries. Transfer learning from data-rich chemical domains offers a potential strategy to overcome these limitations, but its effectiveness for metabolite RT prediction remains insufficiently explored. We developed a transfer learning framework based on ChemBERTa that leverages large peptide datasets to improve metabolite RT prediction under data-sparse conditions. A peptide-pretrained model was trained using a multi-task objective that jointly predicted RT and seven RDKit-derived molecular descriptors. Compared with an RT-only model, the multi-task approach learned more robust chemical representations and demonstrated superior generalization to metabolites, achieving a median test R² of 0.842 versus 0.820. When transferred to metabolite RT prediction, the multi-task pretrained model substantially outperformed models trained from scratch at low-data regimes. Using only 3% of metabolite training data (2,129 compounds), transfer learning achieved a median test R² of 0.322 compared with 0.216 for the baseline model, while reducing MAE from 131.7 to 114.9. Significant improvements were also observed at 5% and 10% training fractions, with benefits gradually diminishing as larger metabolite datasets became available. In contrast, a peptide-pretrained single-task RT model showed performance comparable to the baseline, indicating that the observed gains arise primarily from multi-task molecular property learning rather than peptide pretraining alone. These findings demonstrate that multi-task transfer learning provides an effective and scalable strategy for improving RT prediction in metabolomics, particularly when experimental training data are limited. Freely available on https://github.com/uchealex/CHEMBEDDING. Supplementary data are available at Bioinformatics online.
Tumor-induced immune evasion is a critical mechanism that promotes resistance to anticancer therapies and facilitates cancer progression. Notwithstanding the emergence of immunotherapies, especially immune checkpoint inhibitors (ICIs) and adoptive cell therapies, several cancers show resistance against such therapeutic interventions by adopting various methods of immune evasion. These include alterations to the tumor microenvironment (TME), infiltration of immunosuppressive cells, overexpression of inhibitory checkpoint molecules, and modified antigen presentation. This study provides a comprehensive assessment of the cellular and molecular principles behind immune evasion, as well as novel and established strategies for its prevention. The mechanisms, clinical implications, and limitations of significant therapeutic modalities, including checkpoint blockade, CAR-T cell therapy, cancer vaccines, and oncolytic virotherapy, are addressed. Particular emphasis is placed on combinatorial approaches, TME reprogramming, and next-generation targets like LAG-3, TIM-3, and TIGIT. The research examines the potential of predictive biomarkers, including PD-L1, Tumor Mutational Burden (TMB), Microsatellite Instability (MSI), and the microbiome, to guide personalized immunotherapy. Overcoming resistance and achieving enduring responses requires the integration of immunological insights with high-throughput molecular profiling and adaptive clinical trial design as the subject develops. The efficacy of immunotherapies across many cancer types may be enhanced by adopting a systems-level perspectives on tumor-immune interactions. Ultimately, restoring effective antitumor immunity with new, customized therapies is a crucial advancement in current oncology.
Resistance training has been shown to activate the protein synthesis pathway, leading to muscle growth in humans. However, this type of exercise has shown equivocal results in animal studies due to the difficulty of mimicking muscle overload in vivo. This study aimed to determine whether ladder-based exercise in mice induces canonical molecular, cellular, and functional adaptations to training. Mice performed a single exercise session or 6 weeks of training in the ladder climb. Acute responses included mTOR phosphorylation, puromycin incorporation, and mRNA levels of myogenic regulatory factors (MRF). Chronic adaptations were assessed by strength, fat-free mass, physical performance, and blood lactate levels to confirm the training load. Sarcomeric proteins were analyzed using Western blot, while histology measured muscle fiber diameter and satellite cell (SC) fusion. The SC amount was quantified by flow cytometry. After a single exercise bout, mTOR phosphorylation increased at one and 3 h, with puromycin incorporation and MRF mRNA levels elevated at 8 h. After 6 weeks of training, the mice showed increased skeletal muscle strength and fat-free mass, with no changes in physical performance. Muscle-specific adaptations included increases in sarcomeric proteins and fiber diameters. SC adaptations were associated with an increased pool and enhanced capacity to fuse with muscle fibers. Our results demonstrate that ladder-based resistance exercise in mice induces molecular, cellular, and functional responses that are directionally consistent with adaptations reported after human resistance training, supporting its value for investigating the molecular and cellular mechanisms underlying this training.
Bladder cancer (BC) is the sixth most common cancer among men worldwide and represents a significant cause of morbidity and mortality. High-grade BC is associated with an increased risk of progression to muscle-invasive and metastatic disease, negatively impacting patient prognosis. Despite advances in molecular characterization, therapeutic strategies remain limited, and the identification of novel molecular targets is essential. MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation and play critical roles in tumor development and progression. Among them, miRNA-23b and miRNA-27b have been implicated in several malignancies; however, their functional role in high-grade BC remains incompletely understood. This study aimed to evaluate the expression levels of miRNAs-23b and 27b in a high-grade BC cell line and to investigate their effects on cell migration, invasion, and proliferation, exploring their potential therapeutic relevance. The high-grade BC T24 cell line was used. Cells were divided into four groups: Control (no transfection), negative control (Scramble), miRNA-23b mimic, and miRNA-27b mimic. Relative miRNA expression levels were determined by quantitative polymerase chain reaction (qPCR). Functional assays included wound healing (migration), Matrigel invasion assay, and colony formation assay (proliferation). Statistical analyses were performed to compare groups, and p-values < 0.05 were considered statistically significant. Transfection resulted in significant overexpression of miRNA-23b and miRNA-27b compared to both Scramble (p = 0.0344 and p = 0.0386, respectively) and Control groups (p = 0.0343 and p = 0.0390, respectively). Both miRNA-23b and miRNA-27b significantly reduced cell migration compared to Scramble (p = 0.0286). Additionally, miRNA-23b significantly decreased invasion compared to Scramble and Control (p < 0.0001), with similar findings observed for miRNA-27b (p < 0.0001). No statistically significant differences were observed in colony formation among groups. Overexpression of miRNA-23b and miRNA-27b significantly reduced migration and invasion in a high-grade BC cell line, without affecting proliferation. These findings suggest that both miRNAs may act as tumor suppressors in high-grade BC and represent promising candidates for future therapeutic development in bladder cancer.
The importance of HLA mismatch in haploidentical hematopoietic cell transplantation (HaploHCT) with post-transplant cyclophosphamide (PTCy) is debated. If HLA mismatch does impact outcomes, a molecular mismatch model could predict transplant outcomes more effectively than allele mismatch. In this retrospective study, we quantified molecular HLA disparity using eplet mismatch for 265 patient-donor pairs undergoing HaploHCT with PTCy for hematologic malignancy. We discovered an interaction among eplet mismatch (EpMM), HLA class, and mismatch vector that was associated with clinical outcomes. This interaction was termed Class-wise HLA Imbalance of Mismatched Eplets (CHIME), which comprised risk scores of 0, 1, and 2. The CHIME score retained association with non-relapse mortality (CHIME 1 vs. 0, HR 2.85 (1.10-7.37); CHIME 2 vs. 0, HR 3.63 (1.36-9.68), adjusted p = 0.046) and severe aGvHD grade III-IV (CHIME 1 HR 7.82 (1.03-59.22); CHIME 2 HR 8.08 (1.01-64.63), adjusted p = 0.046) after adjustment for transplant-related variables. The CHIME score, when combined with CD3 cell dose, correlated with higher rates of cytokine release syndrome (CRS). The CHIME model may improve clinical outcome prediction over HLA antigen or allele mismatch.
Precise quantification of the causative agent of syphilis, Treponema pallidum (T. pallidum) is critical for advancing research in pathogenesis, treatment response, and vaccine development. However, current methods have certain limitations. Dark-field microscopy (DFM) suffers from low sensitivity, poor reproducibility, and strong operator dependence, while quantitative PCR (qPCR) offers high precision but is time-consuming, technically demanding, and reliant on high-quality, consistent commercial reagents. This methodological bottleneck highlights the urgent need for a technique that integrates the speed and simplicity of direct detection with the precision, objectivity, and throughput of an automated assay. Herein, to bridge this gap, we propose a strategy for rapid, high-throughput quantification of T. pallidum using a novel, fluorescence-based flow cytometric assay implemented on an automated urine analyzer (the Sysmex UF-5000 analyzer). The assay demonstrated a limit of detection of 7.02 × 10³T. pallidum/mL and excellent precision (all coefficients of variation < 20%). It showed strong quantitative agreement with qPCR across a wide dynamic range (4.98 × 103-2.10 × 107T. pallidum/mL), with an excellent correlation (r = 0.9967), without significant proportional or constant bias (Passing-Bablok slope = 1.003). Bland-Altman analysis confirmed a close agreement (mean difference: -1.14 × 105T.pallidum/mL). In contrast, DFM exhibited substantially higher variability (CVs 15.19-83.52%) and failed to detect low-concentration samples. Operationally, the flow cytometric assay provides results within 30 s per sample at a low consumable cost (approximately $0.35 per test), outperforming DFM in objectivity and throughput and qPCR in both speed and cost-effectiveness. In summary, this novel flow cytometric assay effectively overcomes the historical challenges associated with T.pallidum quantification. This automated, precise, and rapid assay integrates the simplicity of direct detection with the accuracy of molecular quantification, offering a standardized and practical tool to enhance research in syphilis microbiology, pharmacology, and immunology, paving the way for more reproducible and translatable scientific discoveries.
Salmonella enterica remains a leading foodborne zoonotic pathogen worldwide, with poultry serving as a major reservoir and vehicle for antimicrobial resistance dissemination to humans. This study investigated the genotypic basis and distribution of multidrug resistance (MDR) among 29 S. enterica isolates from broiler farms in Egypt, emphasizing the role of mobile genetic elements as integrons and the assessment of genetic relatedness using ERIC-PCR. Molecular screening revealed high prevalence of resistance determinants, including floR (93.1%), tetA (86.2%), aphA1 (82.8%), cmlA (75.9%), ereA (75.9%), sulI (62.1%), aadA1 (51.7%), dfrA1 (48.3%), aac(3)-IV (44.8%), tetB (41.4%), sulII (31.0%), aac(6')-Ib-cr (24.1%), catA1 (20.7%), fosA3 (20.7%), and qnrA (10.3%). High-risk serovars, including S. Jerusalem, S. Colorado, and S. Kentucky, harbored multiple resistance genes and exhibited pronounced XDR profiles. Notably, this study reports the detection of aphA1 and fosA3 in Salmonella isolates derived from broiler chickens, which may represent an early or uncommon finding in Egypt. Many resistance genes were associated with horizontally transferable class 1 integron, underscoring its key role in the dissemination of multidrug resistance (MDR) within poultry systems and along the food chain. ERIC-PCR genotyping segregated isolates into two major genetic groups with seven sub-clusters, reflecting clustering patterns and genetic diversity among the isolates, alongside notable heterogeneity in resistance, virulence, and biofilm-associated genes.Overall, poultry in Egypt represents a significant reservoir of genetically diverse and potentially transmissible MDR S. enterica, highlighting the need for enhanced antimicrobial stewardship and genomic surveillance to mitigate public health risks.
Lung cancer is the leading cause of cancer-related mortality worldwide, and non-small cell lung cancer (NSCLC) accounts for approximately 85% of all lung cases with limited therapeutic options and poor clinical outcomes. Bromodomain-containing protein 8 (BRD8), an epigenetic regulator, has been reported to exert oncogenic roles in multiple solid tumors. Nevertheless, its biological functions and molecular mechanisms in NSCLC remain largely uncharacterized, which motivates us to explore its role in NSCLC progression. The mitogen-activated protein kinase (MAPK) pathway is a well-recognized core oncogenic cascade driving NSCLC malignant phenotypes. Our transcriptome profiling further revealed that the MAPK pathway was the most significantly enriched signaling pathway downstream of BRD (Bromodomain-containing protein), thus we selected it as the key pathway for in-depth mechanistic investigation. In the present study, we found that BRD8 (Bromodomain-containing protein8) was markedly overexpressed in clinical NSCLC tissues and cell lines. Functional assays demonstrated that BRD8 prominently promoted the proliferation, migration and invasion of NSCLC cells. Co-immunoprecipitation combined with mass spectrometry confirmed the direct interaction between BRD8 and MBD2 (methyl-CpG-binding domain protein 2), and their binding was located at the methyl-CpG-binding domain of MBD2. Ubiquitination assays showed that BRD8 enhanced the total and K63 (Lysine63)-linked polyubiquitin chains of MBD2. As a typical post-translational modification, K63-linked ubiquitination generally does not trigger proteasomal degradation but maintains protein stability. Cycloheximide chase assays verified that BRD8 prolonged the half-life of MBD2 and enhanced its stability. Subsequent rescue experiments using the MBD2 K63 mutant demonstrated that mutation at this lysine residue of MBD2 abolishes BRD8-mediated assembly of K63-linked polyubiquitin chains and impairs MBD2 stability. Mechanically, MBD2 acted as a critical downstream effector to mediate BRD8-induced activation of the MAPK pathway. In vivo nude mouse xenograft experiments indicated that knockdown of BRD8 or MBD2 dramatically suppressed tumor growth and decreased MAPK pathway activity. In conclusion, BRD8 facilitates NSCLC progression by interacting with MBD2 to enhance its K63-linked ubiquitination and protein stability, thereby activating the MAPK signaling pathway. This preclinical investigation elucidates the BRD8/MBD2 oncogenic mechanism and provides evidence for subsequent NSCLC research.
We developed and internally cross-validated an integrated circulating tumor DNA assay incorporating single nucleotide variants (SNVs), insertions/deletions (indels), copy number alterations (CNAs), and structural variants (SVs) to distinguish neurofibromatosis type 1 patients with malignant peripheral nerve sheath tumors (MPNST) from those with benign plexiform neurofibromas and tumor-free controls. Among 82 participants, the assay achieved an AUC of 0.917 versus 0.737 for off-target genome-wide CNA analysis. We detected disease-specific alterations, relapse eighty days before diagnosis, and molecular clearance consistent with remission.
Fifteen years after the initial description of type I interferonopathies, this review aims to provide an updated overview of the field by integrating recent genetic and mechanistic advances. It also seeks to outline practical diagnostic approaches and highlight current and emerging targeted therapeutic strategies. Type I interferonopathies are a group of monogenic autoinflammatory diseases caused by inappropriate activation of type I interferon signaling. Multiple pathogenic mechanisms have been identified, including abnormalities in nucleic acid metabolism or sensing, constitutive activation of innate immune pathways, proteasome dysfunction, endosomal Toll-like receptor hyperactivation, and impaired negative regulation of IFNAR signaling. These mechanisms result in overlapping neuroinflammatory, cutaneous, and systemic manifestations, with variable severity and often significant morbidity and mortality. Advances in the understanding of the molecular basis of type I interferonopathies have refined their classification and improved diagnostic strategies. These insights are paving the way for more precise, mechanism-based treatments, offering promising perspectives for patient management despite the persistent severity of these disorders.
The cotton bollworm Helicoverpa armigera is a major global pest controlled by genetically engineered crops expressing Bacillus thuringiensis (Bt) toxins, including Vip3Aa. While Vip3Aa is widely deployed, the genetic basis of resistance remains poorly understood. Previous work identified disruption of a thyroglobulin-like gene (HaVipR1) as one mechanism of resistance, suggesting additional loci may be involved. Using linkage analysis, transcriptomics, long-read sequencing, and CRISPR-Cas9 gene editing, we identify a second thyroglobulin-like gene, HaVipR2, as a novel mediator of Vip3Aa resistance. Resistance in a field-derived H. armigera line was shown to be monogenic, recessive, and autosomal, mapping to chromosome 29. Long-read sequencing revealed a ~ 16 kb transposable element insertion disrupting HaVipR2, which was undetectable using standard short-read approaches. CRISPR-Cas9 knockout of HaVipR2 conferred > 900-fold resistance, confirming its causal role. Comparative analyses show that HaVipR1 and HaVipR2 share conserved domain architecture, indicating that thyroglobulin-domain proteins represent a recurrent target of resistance evolution. Our findings establish thyroglobulin-domain proteins as a new class of Bt resistance genes in Lepidoptera and demonstrate that transposable element insertions can drive adaptive resistance while evading detection by conventional methods. These results highlight the importance of long-read sequencing and accurate genome annotation for resistance monitoring and provide new insights into the molecular basis and evolution of Vip3Aa resistance.
Chronic inflammatory lung diseases are associated with elevated levels of neutrophil elastase (NE), leading to epithelial damage and dysregulated cellular responses. However, the molecular mechanisms underlying NE-mediated disruption of epithelial anti-protease defenses, including the regulation of SERPINB1, remain poorly defined. In this study, we investigated NE-induced responses in bronchial epithelial cells cultured at air-liquid interface (ALI) focusing on epithelial cell death, inflammation, and SERPINB1 dynamics. NE exposure induced dose- and time-dependent cytotoxicity, accompanied by morphological alterations, mitochondrial membrane depolarization, and modest changes in caspase-3, -8, and -9 activity. In ALI cultures, NE was applied either apically, basolaterally or to both compartments simultaneously to evaluate exposure-side-dependent epithelial responses. NE differentially modulated apoptosis-related gene expression, including changes in BCL2, BAX, CASP3, CASP8, CASP9, PARP1, and AIF, depending on NE concentration and exposure side. Cytokine profiling revealed dose-, exposure-side-, and sampling-compartment-dependent changes in IL-6, IL-8, and GM-CSF secretion. Importantly, SERPINB1 expression was markedly reduced at both mRNA and protein levels, while domain-specific immunofluorescence suggested altered SERPINB1 localization and epitope accessibility, suggesting functional alterations beyond transcriptional loss. siRNA-mediated SERPINB1 knockdown further modified NE-associated apoptosis-related gene expression, supporting a functional link between NE exposure and epithelial SERPINB1 regulation. Collectively, these findings establish the NE-SERPINB1 axis as a critical determinant of epithelial cell fate, contributing to epithelial apoptosis, inflammatory mediator release, and protease-antiprotease imbalance. This study provides a systematic analysis of dose- and exposure-side-dependent epithelial responses to NE under ALI culture conditions. Our results highlight the NE-SERPINB1 axis as a contributor to epithelial dysfunction in chronic airway inflammation and support the exploration of SERPINB1-modulating strategies for preserving epithelial integrity and mitigating neutrophil-driven pathology in lung diseases.