Search Results (1,701)

Host microRNAs (miRNAs) are widely proposed as innate antiviral effectors against SARS-CoV-2, yet whether they actually restrict infection in lung epithelial cells remains unresolved. Two of the most-cited candidates, miR-29a-3p and miR-15b-5p, are predicted to bind both the viral genome and key entry/trafficking factors such as Furin and ATG9A, but functional evidence is fragmented and often contradictory. Here, we put both miRNAs to the test in human Calu-3 cells infected with the SARS-CoV-2 Beta and Omicron BA.1 variants, using parallel gain- and loss-of-function strategies coupled to RT-qPCR of viral and cellular transcripts and back-titration of infectious progeny on VeroE6/TMPRSS2 cells. Both miRNAs transiently suppressed viral gene expression at 6 hpi, but this early dampening was followed by a marked transcript rebound at 24 hpi, especially for Omicron, with virtually no impact on total extracellular viral RNA. More strikingly, miR-15b modulation enhanced infectious virus output during Beta infection, and miR-29a overexpression boosted Omicron BA.1 infectivity, while Furin, ATG9A, AKT3, and TFEB showed only modest, condition-dependent shifts. Rather than acting as clean antiviral effectors, miR-29a and miR-15b emerge as context-dependent modulators that can paradoxically favor SARS-CoV-2 replication—a cautionary signal for miRNA-based antiviral strategies. Full article

Background/Objectives: Fibronectin glomerulopathy (FNG) is a rare autosomal dominant inherited kidney disease. Approximately 40% of genetically confirmed FNG cases are associated with likely pathogenic variants in FN1. Patients with FNG have similar clinical features as those with chronic nephritis. Due to nonspecific clinical manifestations mimicking common childhood glomerular diseases, FNG poses significant diagnostic challenges in children, frequently resulting in delayed diagnosis. Case Description: A 9-year-old Chinese girl presented with manifestations suggestive of acute poststreptococcal glomerulonephritis (APSGN), including edema, hypertension, hypocomplementemia, nephrotic-range proteinuria (3.34 g/24 h), and microscopic hematuria (45–55 cells/HP). Despite resolution of edema and normalized complement C3 after initial therapy, proteinuria and hematuria persisted. Renal biopsy revealed prominent mesangial deposits extending to glomerular capillary walls, with strong fibronectin (FN) immunoreactivity and fibrillary electrondense deposits on electron microscopy. Genetic testing identified a heterozygous FN1 missense variant c.3051G>C (p.Trp1017Cys) in the proband and her asymptomatic father, classified as likely pathogenic per ACMG guidelines (supporting evidence: PS1, PM2, PP3, PP4). mRNA and cDNA sequencing confirmed the transcription of the mutant allele in the family members. Notably, these transcriptional analyses cannot provide direct evidence for the functional pathogenicity of the variant. The patient received combined angiotensin-converting enzyme inhibitor (ACEI) and angiotensin receptor blocker (ARB) therapy, and renal function remained stable during 3 years of follow-up. Conclusions: The FN1 c.3051G>C represents a novel nucleotide variant, while the corresponding amino acid alteration p.Trp1017Cys has been reported in the previous literature. This case expands the variant spectrum of FN1 and emphasizes the critical value of renal biopsy and genetic testing for diagnosing FNG in pediatric patients with persistent renal manifestations after suspected APSGN. Family screening is essential for identifying asymptomatic carriers. Our findings also highlight the phenotypic heterogeneity of FNG. Full article

FOXP3 is the master transcriptional regulator of regulatory T cells (Tregs) and is expressed in humans as two main alternatively spliced isoforms: full-length FOXP3 (FOXP3-FL) and the exon 2-deficient variant (FOXP3-Δ2). While the role of these isoforms has been mainly studied in CD4⁺ T cells, their distribution across peripheral blood leukocyte populations and their relationship with immune checkpoint expression remain incompletely defined. In this study, we used a multiparametric flow cytometry panel allowing isoform-specific detection of FOXP3-FL and FOXP3-Δ2, together with PD-1 and CTLA-4, to analyze peripheral blood samples from six healthy donors under basal conditions. Major leukocyte populations, including CD4⁺CD25⁺ and CD4⁺CD25⁻ T cells, CD8⁺ T cells, monocytes, and neutrophils, were evaluated. FOXP3-FL predominated in CD4⁺CD25⁺ T cells, whereas FOXP3-Δ2 was more frequently detected in CD8⁺ T cells, monocytes, and neutrophils. However, the absolute frequencies of these FOXP3-Δ2-positive populations were low, consistent with the overall low levels of FOXP3 expression observed in these cell types. In CD4⁺ T-cell subsets, PD-1 expression was generally higher than CTLA-4, regardless of FOXP3 isoform, and FOXP3-Δ2⁺ cells showed relatively higher PD-1 expression compared to FOXP3-FL⁺ cells. In contrast, checkpoint expression in non-CD4⁺ populations was limited. The observed FOXP3-FL⁺/FOXP3-Δ2⁺ ratios across immune cell populations were consistent with a predominant role of FOXP3-FL in maintaining immune tolerance under basal conditions; whether these patterns are preserved or altered in pathological settings warrants further investigation. These results provide a descriptive overview of FOXP3 isoform distribution and checkpoint expression across peripheral blood immune cell subsets in healthy individuals, which may serve as a reference for future studies in immune-mediated diseases. Full article

Sweet basil is a medicinal herb valued for its culinary and therapeutic applications, primarily due to its secondary metabolite content. Therefore, optimizing its cultivation is essential for growers seeking to improve both the quality and nutritional value of the plants. Two cultivars of Ocimum basilicum L., ‘Lettuce Leaf’ (LL) and ‘Purple Opal’ (PO), were evaluated under various nutritional regimes (mineral, organic, and organo-mineral). The assessment included measurements of total protein, fat, and ash content, as well as total polyphenol levels, phenolic acid content, and antioxidant activity. HPLC analysis was performed to evaluate the composition of selected phenolic and chlorogenic acids, flavonoids, and catechins. Additionally, mineral content was analyzed using OES-ICP. Gene expression of key genes involved in the phenylpropanoid pathway (PAL, C4H, 4Cl, CAD, and CVOMT) and the transcription factor OscWRKY1 was analyzed through RT-qPCR. The key findings indicated that the nutritional variants significantly impacted both primary and secondary metabolism in the assessed plants. Additionally, there was a significant (p < 0.05) cultivar-specific response to the different nutritional variants. The results suggest that the optimal nutritional strategy may vary depending on the target metabolite. Variant 4 was associated with the most favorable overall response in basil, including increased protein levels, higher total polyphenol content, and a balanced mineral composition. However, variant 5 showed the highest antioxidant activity for both cultivars. Rutin and protocatechuic acid were detected only in PO, and cryptochlorogenic acid was detected only in LL. A marked varietal difference was observed in gallocatechin content, with the LL variety containing more than fourfold higher levels than the PP variety. The results of RT-qPCR were fluctuating and strongly dependent on the cultivar. Full article

Endothelial dysfunction is an early event in the development of cardiovascular diseases and is characterized by impaired barrier function, inflammatory activation of endothelial cells (ECs), and alterations in lipid metabolism. In addition to typical (mononuclear) endothelial cells (TECs), multinucleated variant endothelial cells (MVECs) are present within the vascular wall; however, their functional role remains poorly understood. The aim of the present study was to investigate the molecular and functional characteristics of MVECs and their potential contribution to the development of endothelial dysfunction. Primary human umbilical vein endothelial cells (HUVECs) were used, and multinucleated cells were generated by polyethylene glycol-induced fusion. Cells were incubated under control conditions or exposed to low-density lipoproteins (LDL; 100 µg/mL, 24 h). A comprehensive analysis was performed, including transcriptomic and proteomic (secretome) profiling using gene set enrichment analysis (GSEA), as well as functional assays assessing transendothelial LDL transport, intracellular cholesterol accumulation, macrophage migration, and the expression and secretion of pro-inflammatory cytokines (IL-6, IL-8). MVECs exhibited pronounced differences compared to TECs. GSEA revealed reduced enrichment of pathways related to canonical nuclear factor kappa B (NF-κB) signaling and negative regulation of NF-κB transcription factor activity, actin cytoskeleton organization, focal adhesion assembly, basement membrane organization, and vesicle-mediated transport in MVECs relative to TECs, indicating impaired cytoskeletal integrity, altered cell–matrix interactions, dysregulated inflammatory signaling, and reduced vesicular trafficking activity. Functionally, MVECs demonstrated an increased capacity for cholesterol accumulation and enhanced transendothelial migration of macrophages. Notably, transendothelial LDL transport across the MVEC monolayer was not increased, suggesting a predominance of intracellular lipid accumulation. MVECs also exhibited a pronounced pro-inflammatory phenotype, characterized by elevated expression and secretion of IL-6 and IL-8. Taken together, these findings indicate that MVECs represent a functionally altered endothelial phenotype with impaired barrier function, dysregulated lipid metabolism, and enhanced inflammatory activity. Local accumulation of MVECs within the vascular wall may contribute to the formation of pro-atherogenic regions and play a role in the initiation and progression of endothelial dysfunction. Full article

Background/Aims: While pathogenic germline variants play a critical role in pediatric cancer susceptibility, traditional clinical genetics primarily focuses on single-gene interpretations. Transitioning to a systems-level analysis of inherited variation can uncover shared biological vulnerabilities, informing genetic counseling, surveillance, and targeted therapeutics. This study aims to implement an unsupervised machine learning framework to identify and characterize Germline Mutation Signatures (GMS) across diverse pediatric malignancies, elucidating latent genomic patterns that reveal shared oncogenic mechanisms. Methods: We analyzed germline whole-exome and whole-genome sequencing (WES/WGS) data from a retrospective cohort of 420 pediatric cancer patients and matched non-cancer controls. Variants were deeply annotated to capture multi-dimensional features, including predicted pathogenicity, splice-site disruption, regulatory impact, population frequency, and sequence context. To enable robust modeling, we integrated an augmented feature set encompassing evolutionary constraint, loss-of-function intolerance, and compositionally normalized substitution spectra. These high-dimensional annotations were processed using a deep autoencoder for non-linear representation learning, followed by Gaussian Mixture Modeling (GMM) of the latent space. Results: The framework delineated 13 signatures (GMS1–GMS13), yielding an optimal Davies–Bouldin index of 1.051. These signatures map to fundamental biological processes, including DNA repair deficiencies, transcription-coupled damage, replication stress, and aberrant RNA regulation. Crucially, these GMSs transcend traditional tissue-of-origin classifications, manifesting across multiple distinct cancer types. This observation indicates convergent germline etiologies and suggests potential shared susceptibilities to pathway-directed therapies. Conclusions: The discovery of these cross-cancer signatures provides a scalable, biologically interpretable framework for decoding inherited pediatric cancer risk. While the therapeutic mapping networks identified are currently exploratory and serve as a hypothesis-generating foundation, this deep learning-driven paradigm establishes a robust basis for stratified precision medicine. Pending prospective clinical validation, this approach holds significant translational potential to move beyond single-gene paradigms toward unified, systems-level precision oncology strategies. Full article

Background/Objectives: Managing bone diseases demands novel, natural compounds to bypass the heavy side effects of current therapies. Honey is well-known for its therapeutic traits, yet we know very little about how specific floral varieties impact bone tissue. This study confronts this gap by comparing how acacia, chestnut, and coriander honeys drive human osteoblast behavior in vitro. Methods: After mapping the phenolic/flavonoid profiles and antioxidant capacities of these honeys, we tested them on hFOB 1.19 human osteoblasts. We tracked cell migration via scratch assays and validated osteogenic maturation through Alkaline Phosphatase (ALP) activity and Alizarin Red (AR) mineralization over 7 days. Confocal time-lapse imaging with pharmacological inhibitors monitored intracellular calcium dynamics, while gene shifts were analyzed via qRT-PCR. Results: Coriander honey (CH) packed the highest polyphenol levels and antioxidant power. Biologically, while all honeys accelerated scratch closure, CH drove cell motility most potently. Remarkably, a 7-day treatment with these honeys sparked a significant and robust increase in ALP activity and mineralization, surpassing the osteogenic induction observed with standard osteoinductive media. Mechanistically, CH triggered a sharp [Ca²⁺] spike, relying on external calcium entry and IP3-dependent internal release via PLC activation. qRT-PCR confirmed this anabolic shift via OPG and OPN upregulation. Conclusions: Honey exerts pronounced multi-level osteopromotive effects at both the functional and transcriptional levels, tightly linked to its botanical source. Among the variants, coriander honey stands out for its exceptional ability to fast-track osteoblast migration, differentiation, and early mineral deposition. Therefore coriander honey represents a promising in vitro candidate that warrants further preclinical evaluation for bone repair applications. Full article

Background/Objectives: Immune surveillance is increasingly recognized as a modifier of myeloproliferative neoplasm (MPN) initiation and evolution, yet the contribution of the NKG2D receptor and its ligands MICA/MICB to CALR-mutated disease remains unclear. Methods: We performed high-resolution next-generation sequencing genotyping of MICA and MICB in 43 patients with CALR-mutated MPN (WHO 2022 criteria) and compared the allele and haplotype distributions with those of 156 healthy Bulgarian controls and 85 patients with JAK2 V617F-positive MPN. Associations were tested using age- and sex-adjusted additive generalized linear models; bi-locus haplotypes were evaluated using haplotype score methods. In a genotyped subgroup (35 CALR-mutated MPN patients and 105 controls), functional KLRK1 (NKG2D) polymorphisms were analyzed for haplotype-level associations. We also performed 700 ns molecular dynamics simulations of selected MICA variants in complex with NKG2D and reanalyzed publicly available single-cell RNA-sequencing data (GSE117826) and RNA-sequencing data from CRISPR/Cas9-edited CALR-mutant iPSC-derived megakaryocytes to evaluate MICA/MICB expression. Results: MICA*004:001 was significantly associated with CALR-mutated MPN versus controls (p = 0.004; Bonferroni-adjusted p = 0.047), while MICB*008:001 showed only nominal association. Exploratory haplotype analyses identified a MICA*009:01-MICB*004:001 haplotype associated with CALR-mutated status (p = 0.008) and a KLRK1 G-A-G-T haplotype (rs1049174-rs2617160-rs2246809-rs2617170) associated with increased CALR-mutated MPN risk (OR = 3.61; p = 0.029). Transcriptomic reanalysis indicated a higher fraction of CALR-mutant stem and progenitor cells expressing detectable MICA/MICB transcripts, and heterozygous CALR-mutant megakaryocytes exhibited higher MICA expression than the wild type. Conclusions: Together, these data support an exploratory immunogenetic and transcriptomic link between the NKG2D-MICA/MICB axis and CALR-mutated MPN, but direct protein-level and functional studies are required before mechanistic or therapeutic conclusions can be drawn. Full article

Background/Objectives: White–Sutton syndrome (WHSUS; OMIM 616364) is a rare neurodevelopmental disorder caused by pathogenic variants in the POGZ gene and characterized by developmental delay, intellectual disability, speech impairment, autism spectrum features, and dysmorphic traits. Although most reported cases are sporadic, inherited forms are exceptionally rare. We describe a familial case of WHSUS involving an affected mother and two children carrying a heterozygous POGZ nonsense variant, highlighting marked intra-familial phenotypic variability and expanding the clinical spectrum of the disorder. Methods: Clinical evaluation included multidisciplinary assessments. Genetic testing was performed using clinical exome sequencing (CES) with a virtual neurodevelopmental disorder (NDD) gene panel, followed by Sanger confirmation and segregation analysis in family members. The POGZ transcript reference NM_015100.3 was used for variant nomenclature and verified with the Mutalyzer tool. CNV detection from NGS data was performed using the Alissa CNV caller (Agilent) and visualized via IGV; the Xp11.22 microduplication was confirmed by chromosomal microarray (aCGH) and parental segregation analyses. Results: CES identified the heterozygous pathogenic POGZ variant c.1522C>T (p.Arg508*) in the female proband (III₆), an infant presenting with global developmental delay, hypotonia, speech impairment, gait abnormalities, and characteristic dysmorphic features. Segregation analysis demonstrated maternal inheritance and confirmed the presence of the variant in her affected brother (III₄), who also carries a de novo 1.79 kb microduplication at Xp11.22, while the maternal grandparents tested negative, indicating a de novo origin in the mother. The mother exhibited an attenuated phenotype, including mild neuropsychiatric and gastrointestinal manifestations. The variant is predicted to undergo nonsense-mediated decay (NMD), consistent with a moderate clinical presentation; however, experimental validation was not performed. Conclusions: This report documents a rare familial occurrence of WHSUS with highly variable expressivity. Our findings broaden the phenotypic and molecular characterization of POGZ-related disorders and emphasize the importance of comprehensive segregation studies and early genomic diagnosis. While experimental data link POGZ deficiency to DNA repair defects, no longitudinal clinical studies have demonstrated increased cancer risk in WHSUS; therefore, formal malignancy screening guidelines cannot be established at present, and this issue deserves future study in larger cohorts or registries. Full article

Objectives: This study investigated a variant, RPGR NM_001034853.2 c.1307G>A, p.[Gly436Asp, p?], in a large Irish pedigree with severe X-Linked Retinitis Pigmentosa (XLRP). The effect of the variant on RNA splicing was interrogated using in vitro functional analysis to provide evidence of disease causality. Methods: Three related individuals presenting with XLRP underwent target-capture sequencing, together with confirmatory Sanger sequencing and cascade analyses, to identify candidate variants. In silico investigations were undertaken using SpliceAI (version 1.3.1) and Alamut Visual software (version 2.13), among others. Functional analyses using in vitro midigene splice assays employing gateway expression vectors were undertaken. Variant and wildtype RNA were amplified by RT-PCR to investigate effects on splicing. RPGR c.1307G>A was subsequently reclassified using ACMG/AMP and ClinGen SVI recommendations. Results: Midigene investigation confirmed a cryptic acceptor site is being utilised together with the cryptic branchpoint motif to excise intron 10 and 90 bases of exon 11, leading to a frameshift and the creation of a premature stop codon. No functional RPGR transcript is predicted to remain. Given evidence of aberrant splicing, the variant classification was upgraded to pathogenic. Conclusions: RPGR c.1307G>A leads to creation of a cryptic branchpoint within an exon, resulting in protein truncation with deleterious effect(s). To the best of our knowledge, this is the first variant that leads to creation of a cryptic branchpoint within an exon associated with any IRD. The results illustrate the importance of investigating the functional consequences of both coding and non-coding variants with a predicted impact on splicing to understand their pathogenicity. Full article

Background/Objectives: As the most prevalent supraventricular arrhythmia, affecting around 1% of people worldwide, atrial fibrillation (AF) is implicated with a multitude of detrimental clinical sequelae, encompassing congestive failure, thromboembolic cerebral stroke, and premature death. Accumulating epidemiological evidence convincingly demonstrates genetic defects as a cornerstone in the pathogenesis of idiopathic AF. Despite significant genetic underpinnings responsible for AF, owing to substantial genetic heterogeneity, the predisposing genetic substrates for AF in most individuals remain to be ascertained. Methods: A four-generation pedigree suffering from familial AF and a cohort of 238 subjects affected with idiopathic AF, together with 266 healthy people, were enrolled prospectively. Pan-exome sequencing analysis was implemented on the chosen AF pedigree members, and Sanger sequencing assay was performed on all research subjects. The functional effects of the detected HAND2 variations were examined via an in vitro dual-reporter gene measurement. Results: Two novel heterozygous truncating HAND2 variations, NM_021973.3: c.138G>A; p.(Trp46*) and NM_021973.3: c.337C>T; p.(Gln113*), were discovered in the AF pedigree and one of the 238 AF cases, respectively. The two HAND2 variants co-segregated with the AF phenotype and were absent from the 532 control chromosomes of 266 healthy individuals. Quantitative reporter gene assays unveiled that both Trp46*- and Gln113*-mutant HAND2 failed to transcriptionally activate HCN4 and NPPA, two AF-causative genes. Additionally, the two variations nullified the synergistic transcriptional activation of NPPA by HAND2 and GATA4, another recognized gene predisposing to AF. Conclusions: These findings support HAND2 as a strong candidate gene contributing to AF susceptibility, which unravels novel etiopathogenesis underpinning the occurrence and perpetuation of AF and offers a potential molecular target for individualized medicine. Full article

Background: Reverse transcription is a key step in emerging RNA diagnostics, but reverse transcriptase (RT) enzymes often fail in the presence of inhibitors carried over from clinical samples or introduced during RNA extraction. Here, we dissect the molecular basis of inhibitor resistance in five engineered variants (V1 to V5) of Moloney Murine Leukemia Virus RT, originally optimized for thermostability and catalytic activity. Methods: Using a systematic framework that integrates structural analysis, thermal profiling, and diagnostic benchmarking, we evaluated cDNA synthesis from 40 to 70 °C under a panel of 11 clinically relevant inhibitors. Results: Across 30 mutations assessed, a recurrent set of substitutions (E69K, E302K/R, W313F, and N454K), present in RT V1 and V4, was associated with enhanced robustness, consistent with strengthened enzyme–nucleic acid engagement, while L435G likely contributes by modulating conformational flexibility. Notably, inhibitor tolerance was maximal at moderate reaction temperatures (≈40 °C), where productive enzyme–substrate interactions best offset inhibitory stress, while the wild-type enzyme was effectively inactivated by several inhibitors under the conditions tested. Although the engineered RTs remained catalytically competent at higher temperatures, increased thermal stress may destabilize productive enzyme–nucleic acid complexes, reducing resistance under inhibitory conditions. Conclusions: Together, these findings support substrate engagement as an important determinant of RT robustness and provide practical guidance for engineering inhibitor-resistant RTs for high-sensitivity RT-qPCR. Full article

Background/Objectives: IL23R encodes a pivotal component of the IL-23/Th17 signaling axis and represents a validated genetic susceptibility locus for inflammatory bowel disease (IBD), psoriasis, and ankylosing spondylitis. Despite extensive GWAS data, the functional consequences of the full spectrum of IL23R missense single-nucleotide variants (SNVs) have not been systematically characterized. This study aimed to identify high-risk missense SNVs through a multi-tool in silico pipeline. Methods: A total of 723 missense SNVs from NCBI dbSNP were verified against transcript NM_144701.3/Q5VWK5-1 (629 aa) using Ensembl VEP (GRCh38). Sequential filtering was performed using applied SIFT, PolyPhen-2, PROVEAN, E-SNPs&GO, MutPred2, and ConSurf (grade ≥ 7); AlphaMissense and FATHMM-MKL were used as independent annotation layers. Protein stability was assessed with MuPro and DynaMut2 (AlphaFold2 AF-Q5VWK5-F1-v6; pLDDT = 68.19); structural characterization was performed with Project HOPE, and interaction networks were constructed using STRING and GeneMANIA. Results: Sequential filtering identified 37 high-risk missense variants. MuPro predicted destabilizing effects for 36/37 variants, with concordant DynaMut2 results for 35/37. Project HOPE identified disulfide bond disruption in 11 variants, charge-altering substitutions in 8, and glycine/proline backbone conformational changes in 11. STRING analysis identified IL12RB1 (0.999), IL23A (0.999), JAK2 (0.995), IL12B (0.986), and STAT3 (0.980) as the leading IL23R interactors. The protective variant R381Q was appropriately characterized as neutral by PROVEAN (−1.16) and AlphaMissense (likely_benign), supporting the specificity of the pipeline. Conclusions: Comprehensive in silico analysis identified 37 high-risk IL23R missense candidates with convergent computational evidence of predicted deleteriousness, predominantly involving cysteine bridge disruption, charge alteration, and glycine/proline backbone conformational changes. These variants are presented as prioritized candidates for future functional validation and may inform subsequent investigations of IBD susceptibility and IL-23 pathway pharmacogenomics. Full article

Host genetic susceptibility to urogenital Chlamydia trachomatis (Ct) reinfection remains poorly understood. Coding variants identified in prior genome-wide association studies (GWAS) explained only a small fraction of the risk of reinfection. Our goal in this study was to characterize whether more risk would be captured by sequence variation that traditional GWAS insufficiently captures. Specifically, we evaluated the risk attributable to SNPs present in regulatory, non-coding regions; post-transcriptional regulation by microRNAs (miRNAs) that may depend on sequence variation in either the miRNA or the target mRNA; and copy number variants (CNVs). We analyzed GWAS data from African American women with or without documented urogenital Ct reinfection. Fine mapping and independent association analyses identified 30 unique index single-nucleotide polymorphisms (iSNPs), which were expanded to variants in linkage disequilibrium. Regulatory annotation was performed using HaploReg, RegulomeDB, FORGEdb, rSNPBase, and GTEx. We examined whether genes identified in the Ct reinfection GWAS are targeted by known Ct infection–associated microRNAs using curated databases. Genome-wide CNV calling was conducted using SNP intensity data, followed by stringent quality control and gene-level association testing. Functional annotation prioritized 7 SNPs with strong regulatory evidence, with stringent criteria for regulatory relevance, using HaploReg, RegulomeDB, FORGEdb, and rSNPBase. The strongest signals were observed at the CHIT1 locus, where multiple intronic variants (including rs2486963 and rs2244385) overlapped regulatory chromatin, altered transcription factor binding motifs, and acted as cis-expression quantitative trait loci for CHIT1 in whole blood. Additional regulatory variants were identified near TDRP, ERICH1, and DLGAP1, showing tissue-specific regulatory effects. MicroRNA analysis revealed extensive post-transcriptional targeting of SOCS6 and SULF1, while CHIT1 showed no curated Ct-associated miRNA interactions. CNV analysis identified 5775 high-confidence events, with nominal gene-level associations observed for ATAD3A, CARD14, TMEM240, and ZNF140. These results indicate that a greater fraction of the susceptibility to urogenital Ct reinfection may be driven by genetic variation affecting immune and epithelial pathways rather than protein-coding changes. Full article

Background: Salinity, which hampers wheat growth and development, is one of the major abiotic stresses. Plant-derived smoke (PDS) solution alleviates salt stress and promotes wheat growth and development; however, the underlying molecular mechanisms have not been completely clarified. Methods: In this study, nuclear proteomics was employed to reveal the promotive effect of PDS solution on salt-stressed wheat. Nuclear fractions were isolated from wheat roots, and their purity was confirmed via enrichment of histone H3 and reduction of cytosolic ascorbate peroxidase. Using this nuclear purification technique, label-free nano LC–MS/MS-based nuclear proteomics was performed to identify differentially abundant nuclear proteins in salt-stressed wheat with or without PDS solution treatment. Results: Salt stress decreased histone H2A and DNA polymerase levels, whereas PDS solution treatment of salt-stressed wheat increased levels of histone variants (H2A, H2B, H3, and H4), DNA polymerase, and DNA topoisomerase II. In addition, the PDS solution increased the levels of pre-mRNA cleavage factor Im 25 kDa subunit and RNA helicase in salt-stressed wheat. Immunoblot analysis further validated the increase in histone deacetylase levels triggered by the PDS solution treatment in the salt-stressed wheat. Conclusions: These results suggest that PDS solution alters nuclear proteins in a way that contributes to chromatin remodeling and transcription during salt stress. Full article