Search Results (336)

Background: Prenatal detection of fetal structural anomalies often prompts chromosomal analysis; however, chromosomal microarray analysis (CMA) has limited diagnostic yield for monogenic disorders. Whole-exome sequencing (WES) has emerged as a powerful tool for identifying single-gene etiologies, particularly in cases with complex neurodevelopmental phenotypes. Case Presentation: We report a female infant presenting with prenatally detected ventriculomegaly and inconclusive chromosomal testing. Prenatal investigations, including karyotyping and genome-wide chromosomal sequencing, identified several copy number variants classified as variants of uncertain significance but failed to establish a definitive diagnosis. Postnatally, the patient developed progressive neurological abnormalities, including microcephaly, facial dysmorphism, dystonic movements, and severe global developmental delay. Trio-based whole-exome sequencing identified a heterozygous de novo pathogenic missense variant in the DDX3X gene (c.976C>T; p.Arg326Cys), establishing the diagnosis of DDX3X-related neurodevelopmental disorder. Conclusions: This case highlights the diagnostic limitations of standard prenatal chromosomal testing in detecting monogenic neurodevelopmental disorders and underscores the critical role of timely genetic counseling and exome sequencing. Earlier selective implementation of WES during pregnancy could have enabled an earlier diagnosis, improved prognostic counseling, and optimized clinical decision-making. Full article

Background/Objectives: Parasporin PS2Aa1, recently designated as Mpp46Aa1, is recognized for its selective anticancer activity against various human cell lines. In this study, specific regions of the native protein were fragmented, and targeted amino acid substitutions were introduced to improve cytotoxic selectivity and potency. Methods: The modified fragments were evaluated individually and in combination with curcumin, a polyphenol with well-documented anticancer properties, and Sacha inchi-derived matrices, known for their antioxidant and antiproliferative activities. Results: Experimental results demonstrated that the substituted variant designated T104L-G108W exhibited superior anticancer activity compared to the native peptide P102-K11. Synergism assays revealed that curcumin-bioconjugated peptides were more effective against the tested cell lines, whereas combinations with Sacha inchi reduced cytotoxicity, suggesting possible interference in the mechanisms of action. Functional assays, including caspase 3/7 and 9 activation, Annexin V-Cy3 staining, and cell viability analysis with 6-CFDA, confirmed increased sensitivity in SiHa and HeLa cell lines, particularly for peptide T104L-G108W. Conclusions: Collectively, these findings support the effectiveness of a substitution-based strategy in improving parasporin fragments and underscore the therapeutic potential of peptide T104L-G108W as a novel anticancer candidate. Furthermore, this study provides preliminary evidence that natural biomolecules can be optimized through targeted modifications and rational combinations, establishing a framework for the development of sustainable and selective therapeutic approaches in cancer treatment. Full article

Nucleotide-binding and leucine-rich repeat receptors (NLRs) play an important role in plant innate immunity. Previous reports indicate that SUT1 (SUPPRESSOR OF TOPP4 1) is required for the autoimmune response mediated by TYPE ONE PROTEIN PHOSPHATASE 4 (TOPP4) mutation topp4-1 (namely TOPP4^T246M) in Arabidopsis. We observed that co-expression of SUT1 with TOPP4 mutant versions, instead of wild-type TOPP4, produced robust cell death in N. benthamiana. The YFP-labeled SUT1 was localized on the plasma membrane (PM), and Gly2, Cys4, and Ser6 are crucial amino acid sites for its PM localization and function. Further dissection proclaimed that the function and localization of SUT1 are influenced by mutations in conserved specific residues. These findings may provide a new perspective for elucidating the activation mechanism of SUT1. Full article

Ischemic stroke is a major cause of long-term disability and death, with oxidative stress contributing substantially to post-ischemic injury. Reperfusion restores oxygen supply but simultaneously increases reactive oxygen species (ROS), amplifying secondary neuronal damage. This study examined time-dependent changes in systemic thiol redox status following transient middle cerebral artery occlusion (tMCAO) in rats. Plasma concentrations of cysteine (CySH), cystine (CySS), glutathione (GSH), and glutathione disulfide (GSSG), along with corresponding CySS/CySH and GSSG/GSH ratios and redox potentials (Eh), were evaluated 24 and 48 h after occlusion. At 24 h, thiol concentrations and redox ratios showed no significant differences between sham and tMCAO groups. By 48 h, a marked oxidative shift emerged, characterized by reduced CySH, elevated GSSG, and significant increases in both CySS/CySH and GSSG/GSH ratios. Redox potentials also demonstrated substantial oxidation at this time point. These findings indicate that prolonged ischemia–reperfusion induces systemic oxidative stress, with plasma redox status serving as a sensitive indicator of reperfusion-related injury. The results underscore the plasma redox status as a potentially sensitive biomarker of reperfusion-induced oxidative injury and support the therapeutic value of targeting redox imbalance to mitigate oxidative damage following stroke. Full article

Background and Clinical Significance: Adams–Oliver syndrome type 3 (AOS3) is a rare congenital disorder typically characterised by terminal transverse limb defects and variable involvement of other organ systems. Although pathogenic variants in RBPJ are well established in AOS3, associated neurodevelopmental or psychiatric features have been only sporadically documented. Case Presentation: We describe a male patient first evaluated at the age of 10 years and subsequently re-evaluated at 14 years, with AOS3 presenting terminal limb defects together with autistic-like behaviour, cognitive difficulties, dyslexia, and recurrent depressive symptoms. Whole-exome sequencing (WES) identified a heterozygous pathogenic variant in RBPJ (c.505A>G; p.Lys169Glu), confirming the molecular diagnosis of autosomal dominant AOS3. Additional findings included a heterozygous missense variant in CACNA1A (p.Arg1678Cys), a gene linked to neurological disorders with broad phenotypic variability. Because of elevated homocysteine levels, the patient was also tested for MTHFR variants and was found to be heterozygous for C677T and A1298C. Conclusions: This case illustrates a rare combination of a validated AOS3-associated RBPJ variant, along with additional CACNA1A and MTHFR variants that may influence the patient’s neurocognitive and psychiatric characteristics. The results underscore the importance of comprehensive genetic testing in atypical AOS presentations and highlight the complexity of interpreting overlapping genetic factors. Full article

The maximum protein or nitrogen deposition is commonly used as the basis for modeling the amino acid intake in growing birds. In previous studies, the exponential functions of the nitrogen balance data were used to estimate the theoretical maximum for nitrogen deposition (ND_maxT) as a reference model for the amino acid intake. However, this amino acid intake value is only valid for the period in which the ND_maxT was estimated. Additionally, physiological changes, such as the rapid development of reproductive organs and associated increases in protein deposition that occur in the period before the first egg is laid, should be considered in the models. Thus, this study was conducted to model the daily ND_maxT of pullets and integrate this value into the factorial model to estimate the daily methionine + cysteine (Met+Cys) intake. Our results showed that, up to 63 days of age, the values of ND_maxT obtained via the modeling procedure were 11% higher than the values predicted using the Gompertz function. At 105 days, there was a protein deposition peak from the growth of the reproductive organs, which contributed 14% of the variation in the model in this age. Alongside these factors, the integration of the models enabled daily Met+Cys estimates consistent with the literature; however, the recommendations varied according to the targeted daily protein deposition (50% or 60% of ND_maxT), daily feed intake, and amino acid utilization efficiency. The modeling approach demonstrated here for Met+Cys can be used to model other amino acid requirements and can be extended to other species. Full article

Background and Aims: Gastric cancer (GC) remains a leading cause of cancer-related mortality, frequently diagnosed at advanced stages. High-risk features—tumor size ≥ 40 mm, cT3/cT4, nodal involvement, diffuse histology, and Borrmann type III/IV—are associated with peritoneal metastasis (PM). Staging laparoscopy with peritoneal washing (PW) is superior to conventional preoperative imaging modalities, including contrast-enhanced CT, MRI, PET/CT and endoscopic ultrasound, in detecting occult peritoneal disease. In this era of personalized medicine and expanding loco-regional strategies such as cytoreductive surgery (CRS)/Hyperthermic IntraPEritoneal Chemotherapy (HIPEC) and Pressurized IntraPeritoneal Aerosol Chemotherapy (PIPAC), accurate staging is crucial. This study assessed the impact of SL and PW in high-risk GC. Methods: We retrospectively analyzed 113 consecutive high-risk GC patients who underwent SL and PW between 2014 and 2024 at our institution. The primary endpoint was detection of PM or positive cytology (CY+). Secondary endpoints were treatment modification, eligibility for loco-regional therapy, and safety. Results: SL/PW identified PM or CY+ in 26 patients (23%), including 16 with CY+ only. None had radiologic signs of peritoneal disease. SL findings altered treatment in all cases: 21 patients (81%) with Peritoneal Cancer Index (PCI) < 6 underwent induction chemotherapy followed by CRS + HIPEC; 5 patients (PCI > 6) were spared non-therapeutic laparotomy and treated with bidirectional systemic chemotherapy and PIPAC. In 10 patients, systemic therapy was shifted from FLOT (fluorouracil, leucovorin, oxaliplatin, and docetaxel) to FOLFOX (fluorouracil, leucovorin, and oxaliplatin) ± nivolumab. No perioperative complications occurred; all patients were discharged within 24 h without delay in systemic treatment. Conclusions: SL with PW is safe and significantly improves staging accuracy in high-risk GC, enabling personalized therapeutic planning. Routine integration of SL should be considered essential in treatment algorithms to guide systemic and loco-regional strategies. Full article

Background/Objectives: Thyroid hormones (THs) regulate almost all physiological processes in vertebrates via specific mechanisms exercised spatiotemporally throughout the lifespan. The TH signalling can be impaired by thyroid-disrupting chemicals (TDCs) capable of disrupting the hypothalamic–pituitary–thyroid (HPT) axis. Octyl methoxycinnamate (OMC) (also designated octinoxate), one of the most widely used ultraviolet (UV) filters, has emerged as an environmental contaminant and has raised significant concerns recently due to its disruptive effects as TDC on humans and animals. Although the disruption of TH homeostasis has been reported, its exact modes of action (MoA) remain largely unknown. Our study aimed to provide a comparative information on the molecular interactions of OMC on TH signalling in humans and zebrafish. Methods: In silico approaches were performed comparing OMC with endogenous thyroid hormone T3 and the anti-thyroid drug propylthiouracil (PTU). Results: Our findings suggested a key role of OMC on the corticotrophin-releasing hormone receptor (crhr2), thyrotropin receptor (TSHR/tshr), and thyroid nuclear receptors (TR/tr-α and -β). At the hypothalamic level, a favourable binding of OMC to zebrafish crhr2 was found, involving ALA86, CYS44, HIS89, ILE63, ILE64, LEU92, PRO87, PRO88, SER48, and THR47. At the pituitary level, OMC was bound to human TSHR by the amino acid residues ASN590, GLU506, ILE583, ILE640, LEU570, MET572, PRO571, SER505, TYR667, VAL502, VAL586, ALA644, LEU587, MET637, SER641, and TYR582 and to zebrafish tsrh by ASN589, ILE639, MET636, ILE582, LEU569, LEU586, VAL501, and VAL585. Concerning nuclear receptors, OMC showed a more favourable binding energy of T3, involving the shared residues PHE218 and MET259 with T3 in both species. For human TRβ, OMC shared T3 with residues ILE 275, ILE276, LEU346, PHE269, PHE272, THR273, ALA279, ASN331, HIS435, LEU330, MET310, MET313, and PHE455. No similar residues were obtained for zebrafish trβ compared with the humans. Conclusions: Overall, the action of OMC seems to agree with primary hypothyroidism (anti-thyroid action) mimicking the T3 hormone. This investigation demonstrates that OMC acts as a potential TDC and provides new insights into its disruptive action on the HPT axis. Full article

Objective: This study investigated whether rapamycin could modulate the polarisation of CD4+ T cells towards T_H1, T_H2, T_H17, and Treg cells using peripheral blood mononuclear cell (PBMC) obtained from patients with granulomatosis with polyangiitis and microscopic polyangiitis (GPA/MPA). Methods: Twenty patients with GPA/MPA were included in this study. Their stored PBMCs were cultured and stimulated with anti-CD3 and anti-CD28 antibodies for 72 h in the presence or absence of rapamycin (10 nM). The cells were stained for surface markers with anti-CD4-FITC and anti-CD25-APC, followed by intracellular staining using anti-interferon (IFN)-γ-PE, anti-IL-4-PerCP-Cy5, anti-IL17A-APC, and anti-Foxp3-PE. The stained cells were analysed using a flow cytometer. Results: The median age of the 20 GPA/MPA patients (10 men and 10 women) was 65.5 years. Rapamycin treatment significantly modulated the polarisation of CD4+IFN-γ+ T (T_H1) cells compared to no treatment among GPA/MPA patients. In addition, the polarisation of CD4+IFN-γ+ T (T_H1) cells was also significantly reduced in rapamycin-treated PBMC obtained from active patients compared to untreated PBMC from the same patients; however, these alterations were not observed in inactive patients. Conversely, rapamycin treatment did not affect the polarisation of CD4+IL-4+ T (T_H2), CD4+IL-17+ T (T_H17), or CD4+FoxP3+CD25+ T (Treg) cells, regardless of GPA/MPA activity. Conclusions: This study was the first pilot study to demonstrate that rapamycin modulates the polarisation of CD4+ T cells towards CD4+IFN-γ+ T cells in active GPA/MPA. Full article

Cholangiocarcinoma is a rare but highly lethal cancer of the biliary epithelium, marked by heterogeneous molecular subtypes, unclear etiology, and poor five-year survival, highlighting the need for new diagnostic and therapeutic strategies; therefore, this study integrates genomic, transcriptomic, single-cell, methylomic, and molecular-dynamics data to pinpoint pathogenic variants. We performed an integrative multi-omics analysis of publicly available datasets. Somatic variants from 23 tumor samples in The Cancer Genome Atlas were annotated with 11 pathogenicity tools (AUC ≥ 0.86 across EVE, REVEL, SIFT, AlphaMissense, DEOGEN2 were the most stringent). Differential gene expression was assessed in matched bulk RNA-seq (tumor vs. non-tumor) using DESeq2 with Benjamini–Hochberg FDR correction. A single-cell RNA-seq dataset comprising 23,782 cells from an intrahepatic cholangiocarcinoma was clustered with marker genes identified by Wilcoxon rank-sum tests. Illumina 450 K methylation arrays (52 tumors, 12 normal livers) were analyzed with limma and DMRcate to detect differentially methylated probes and regions. AlphaFold3 models of wild-type and MAP2K1^R49C were subjected to 50 ns all-atom molecular-dynamics simulations in GROMACS; conformational shifts were quantified by RMSD/RMSF and stability tested with FoldX5. Twenty-four tumor-specific missense variants were detected. The four highest-confidence pathogenic substitutions (EVE, REVEL, SIFT, AlphaMissense, DEOGEN2) occurred in TUBB3, FLNC, ABCA1, and MAP2K1. Bulk RNA-seq confirmed significant dysregulation of these genes and enrichment of extracellular-matrix organization, cytoskeletal remodeling, MAPK signaling, and cholesterol-efflux pathways. Single-cell analysis resolved 23 transcriptionally distinct clusters; proliferative malignant cholangiocytes selectively over-expressed ABCA1 and MAP2K1, indicating tumor-cell specificity. Methylome profiling identified 148,928 DMPs and 7040 DMRs; promoter hypomethylation of TUBB3 and ABCA1 correlated with their transcriptional activation. Substituting Arg-49 with Cys in MAP2K1 dismantles the Arg-centred hydrogen-bond/salt-bridge cluster, reduces hydrophobic packing, and, corroborated by 50 ns MD (Welch’s t = −58.06, p = 3.17 × 10⁻²³⁰) and FoldX5 ($\mathrm{\Delta }\mathrm{\Delta }$G = +2.3 kcal mol⁻¹), significantly destabilises the protein, manifesting as higher backbone RMSD and increased local flexibility relative to wild type. This multi-omics, public data-driven synthesis delineates a coherent network of genomic, epigenomic, transcriptomic, and structural vulnerabilities, offering a rational framework for therapeutic targeting of cholangiocarcinoma. This study reveals novel bile duct-associated variations that expand our understanding of cholangiocarcinoma pathogenesis and provide potential targets for precision medicine approaches. Full article

Capillary-driven microfluidic chips have emerged as promising platforms for point-of-care diagnostics, offering portable, inexpensive, and pump-free operation. Accurate tracking of cell flow in these systems is vital for quantitative applications such as on-chip cytometry, cell counting, and biomechanical analysis. However, tracking in capillary-driven devices is challenging due to rapid cell displacements, flow instabilities, and visually similar cells. Under these conditions, conventional tracking algorithms such as TrackPy, TrackMate, SORT, and DeepSORT exhibit frequent identity switches and trajectory fragmentation. Here, we introduce FloCyT, a robust, high-speed centroid tracking tool specifically designed for capillary-driven and microfluidic flow. FloCyT leverages microchannel geometry for tracking and uses anisotropic gating for association, global flow-aware track initialisation, and channel-specific association. This enables precise tracking even under challenging conditions of capillary-driven flow. FloCyT was evaluated on 12 simulated and 4 real patient datasets using standard multi-object tracking metrics, including IDF1 and MOTA, ID switches, and the percentage of mostly tracked objects. The results demonstrate that FloCyT outperforms both standard and flow-aware-modified versions of TrackPy and SORT, achieving higher accuracy, more complete trajectories, and fewer identity switches. By enabling accurate and automated cell tracking in capillary-driven microfluidic devices, FloCyT enhances the quantitative sensing capability of image-based microfluidic diagnostics, supporting novel, low-cost, and portable cytometry applications. Full article

Cornelia de Lange Syndrome (CdLS) is a rare multisystem developmental disorder caused primarily by mutations in cohesin complex genes, including RAD21. Psoriasis is a chronic inflammatory skin disease linked to immune dysregulation, notably involving TNFAIP3 (A20), a negative regulator of NF-κB signaling. Although case reports have suggested a possible coexistence of CdLS and psoriasis, the underlying molecular basis has remained unexplored. Here we report the first case of molecular co-occurrence of CdLS and generalized pustular psoriasis in a patient with novel heterozygous nonsense variant in RAD21 (c.1306C>T, p.Gln436*), pathogenic for CdLS type 4, and a previously unreported truncating variant in TNFAIP3 (c.2199C>A, p.Cys733*), predicted to disrupt NF-κB regulation and classified as a variant of uncertain significance. Structural protein modeling showed significant conformational disruption in RAD21 and partial truncation of the ZnF domains of TNFAIP3, supporting their functional impact. This study is the first to suggest a possible molecular mechanism that may explain the rare co-occurrence of CdLS and psoriasis: RAD21 deficiency disrupts chromatin architecture and immune gene regulation, while TNFAIP3 loss-of-function removes critical NF-κB inhibition, resulting in synergistic developmental and inflammatory phenotypes. Secondary transcriptomic data analysis further suggests that RAD21 knockdown may downregulate TNFAIP3 expression, providing a possible mechanistic intersection. Our findings provide the first molecular evidence linking RAD21 and TNFAIP3, introducing a novel pathogenic hypothesis connecting cohesin dysfunction and immune dysregulation. This work expands the mutational spectrum of both genes and opens a new avenue for understanding developmental-inflammatory disease overlap. Full article

Background: Multiple Sclerosis (MS) is a chronic, autoimmune, multifactorial, and complex disorder of the central nervous system (CNS), affecting more than 2 million individuals globally. Genome-wide association studies (GWAS) have explained only a small fraction of its high heritability, highlighting the need for alternative approaches to identify rare genetic variants that contribute to its etiology. To address this, we performed whole-exome sequencing (WES) in a multi-affected family. Methods: WES was performed in a MS multigenerational family comprising two affected sisters, their two healthy brothers, and one affected son. Results: Bioinformatics analysis identified 47 co-segregating rare variants. Three missense variants in genes involved in inflammation, autoimmunity, and demyelinization were identified as the most promising candidates: c.443 C>T, p.Pro148Leu in the RTN4 gene, c.1678 T>G, p.Phe560Val in the JAK2 gene, and c.3449 A>G, p.Tyr1150Cys in the DUOX2 gene. Protein modeling and in silico tools suggest that the three selected variants may have a significant impact on protein function. Conclusions: We identified novel candidate genes for MS in a multiplex family, providing evidence for an oligogenic model of disease susceptibility. Further replication and functional studies are required to validate these preliminary results. Full article

Industrial Internet of Things (IIoT) systems are increasingly exposed to sophisticated and rapidly evolving cyber threats. In response, this work proposes a proactive threat detection framework that leverages pretrained transformer-based language models to identify emerging attack patterns within IIoT ecosystems. This work introduces a transformer-based framework that fine-tunes domain-specific pretrained models (SecBERT, SecRoBERTa, CyBERT), derives potential attack-path patterns from vulnerability–tactic mappings, and incorporates a retrieval-based fallback mechanism. The fallback not only improves robustness under uncertainty, but also provides a practical solution to the absence of labeled datasets linking ICS-specific MITRE ATT&CK tactics with vulnerabilities, thereby filling a key research gap. Experiments show that the fine-tuned models substantially outperform traditional machine learning baselines; SecBERT achieves the best balance while maintaining high inference efficiency. Overall, the framework advances vulnerability-driven threat modeling in IIoT and offers a foundation for the proactive identification of attack patterns. Full article

People with HIV (PWH) are at an increased risk for AIDS-associated non-Hodgkin lymphoma (AIDS-NHL); however, the immune signatures underlying this risk are not well understood. In this study, we utilized mass cytometry by time-of-flight (CyTOF) to analyze T-cells and monocytes in the PBMCs of treatment-naïve PWH, including those 3 to 36 months before an AIDS-NHL diagnosis (HIV-positive pre-NHL), as well as people without HIV (PWoH). Mass cytometry is an advanced single-cell analysis platform that combines flow cytometry principles with mass spectrometry. Unlike conventional flow cytometry, this technology employs antibodies conjugated to unique metal isotopes instead of fluorescent markers, enabling simultaneous measurement of over 40 distinct cellular markers per individual cell without spectral overlap limitations. Participants were enrolled at the Los Angeles site of the MACS/WIHS Combined Cohort Study (MWCCS). Unsupervised clustering and Uniform Manifold Approximation and Projection (UMAP) analysis identified CD3⁺ T-cell and CD14⁺ monocyte metaclusters, and Spearman’s rank correlation assessed their relationships with B-cell subsets exhibiting aberrant phenotypes. We observed elevated levels of CD8⁺CD20⁺ T-cells, CD8⁺CD14⁺ T-cells, and M2-like CD14⁺CD163⁺ monocytes in HIV-positive pre-NHL individuals compared to HIV-negative controls. Positive correlations were found between CD19⁺ AICDA⁺ cMYC⁺ B-cells and M1-like CD14⁺cMYC⁺ monocytes (metacluster, MC02), and between metaclusters of CD8⁺PD-1⁺CD27⁺CXCR4⁻ T-cells (MC05) and CD4⁺FoxP3⁺PD-1⁺CD27⁺CD28⁺CXCR4⁻ ICOS⁺ T-cells (MC08). In addition, a different CD19⁺ B-cell metacluster (FoxP3⁺AICDA⁺cMYC⁺) was positively associated with a metacluster of CD8⁺PD-1⁺CD27⁺CD28⁺CXCR4⁺ T-cells (MC03). Moreover, the metacluster of CD8⁺PD-1⁺CD27⁺CXCR4⁻ T-cells (MC05) negatively correlated with M2-like CD14⁺CD163⁺ monocytes (MC06), while CD8⁺CD14⁺ T-cells positively correlated with AICDA⁺ Bregs and IL-10⁺ B-regs in HIV-positive pre-NHL individuals. Unsupervised analysis revealed increased frequencies of CD8⁺CD20⁺ T-cells in HIV-positive individuals compared to HIV-negative controls. These immune alterations provide valuable insights into potential biomarkers for early detection, monitoring, and therapeutic strategies for AIDS-NHL. Full article