Background: Secondary hair germ (SHG)-associated epithelial cells are a key progenitor population that contribute to hair follicle regeneration during early anagen. Although SHG-associated cells become activated during early anagen and contribute to the formation of regenerating follicular structures, the morphologically recognizable SHG compartment becomes less apparent as lower hair follicle structures develop during mid-anagen. However, the transcriptional changes accompanying the transition from SHG-associated states toward lower hair follicle-associated states remain poorly characterized. This study aimed to characterize the transcriptional changes associated with this transition and identify a proliferative intermediate transcriptional state during early anagen. By integrating single-cell transcriptomic analysis with regulatory and cell–cell communication analyses, we sought to improve the understanding of cellular state transitions and microenvironmental changes during early hair follicle regeneration. Methods: Hematoxylin and eosin staining (H&E) was performed to examine histological changes in mouse dorsal skin on days 0, 5, 10, 15, 20, 25, and 30 of the hair cycle. In parallel, previously published single-cell RNA sequencing data from mouse dorsal skin during early anagen were reanalyzed. Hair follicle epithelial cells were extracted and reclustered to identify cell subpopulations with distinct transcriptional characteristics. Cell types were annotated based on canonical marker genes and subpopulation-specific expression patterns. Differential expression analysis, functional enrichment analysis, cell-cycle analysis, developmental potential assessment, trajectory inference, transcription factor regulon analysis, and cell–cell communication analysis were further performed to characterize the relationships among hair germ cells, proliferative lower hair follicle-like cells (PR-loHF), and lower hair follicle cells. Results: Proliferative lower hair follicle-like cells (PR-loHF) were identified as a transcriptionally defined intermediate state associated with the transition from secondary hair germ (SHG)-associated cells toward lower hair follicle-associated cells. PR-loHF exhibited enrichment of biological programs associated with cell-cycle activity, epithelial remodeling, extracellular matrix organization, and developmental regulation. Moreover, compared with SHG-associated and lower hair follicle-associated states, PR-loHF exhibited distinct transcription factor regulon activity and cell–cell communication patterns, further supporting its characterization as a transcriptionally distinguishable intermediate state. Conclusions: PR-loHF represents a proliferative intermediate transcriptional state emerging during the transition from secondary hair germ (SHG)-associated cells toward lower hair follicle-associated states, providing new insights into transcriptional transitions and microenvironmental regulation during early hair follicle regeneration.
Background/Objectives: Acomys cahirinus exhibits more favorable cardiac remodeling after ischemic injury than Mus musculus, yet the molecular organization of the intact myocardium remains poorly characterized. This study aimed to identify baseline interspecies differences in the adult left ventricle, with particular emphasis on ventricular cardiomyocyte transcriptional states. Methods: Intact left ventricles from adult male A. cahirinus and M. musculus were analyzed by single-nucleus RNA sequencing using three biological samples per species. Cross-species integration was followed by cell type annotation, pseudobulk differential expression analysis, Augur-based assessment of interspecies separability, coexpression module analysis, and focused reintegration analysis of ventricular cardiomyocytes. Cardiomyocyte profiles were further compared with published embryonic and early postnatal M. musculus heart datasets. Results: Both species contained comparable major myocardial cell populations, whereas marked interspecies transcriptional differences persisted within individual cell types. Ventricular cardiomyocytes exhibited the largest number of differentially expressed genes and were classified into three transcriptional states: contractile, matrix-associated, and alternative. Adult A. cahirinus cardiomyocytes retained a mature cardiomyocyte phenotype but showed greater enrichment of developmental, morphogenetic, and Hippo-associated gene programs than adult M. musculus cardiomyocytes. Their transcriptional profile did not correspond to embryonic or early postnatal mouse states. The integrated atlas further identified interspecies differences in fibroblast-associated and extracellular matrix-related programs. Conclusions: The intact myocardium of A. cahirinus exhibits cell type-specific transcriptional differences relative to M. musculus. Ventricular cardiomyocytes display a distinct mature transcriptional configuration rather than a direct immature state, which may contribute to the favorable response of A. cahirinus to myocardial injury.
Background: Small-molecule-regulated gene switches are important tools for programmable mammalian cell engineering, and compact switches responsive to clinically familiar ligands that can be administered locally are particularly attractive for externally regulated transgene expression. Methods: Here, we developed ZF10–ΔVDR, a compact zinc-finger–VDR transcriptional switch, by fusing an orthogonal human-derived zinc-finger array, ZF10, to the hinge and ligand-binding domain of the vitamin D receptor. The resulting switch enabled transgene regulation by calcipotriol, a clinically used topical vitamin D analog and VDR agonist. Results: ZF10–ΔVDR maintained low basal activity, showed limited activation by the tested vitamin D species at physiologically relevant reference concentrations, and was robustly activated by calcipotriol. The system functioned across multiple human cell types. In vivo, topical calcipotriol increased serum reporter output in mice bearing subcutaneous microencapsulated-cell implants, whereas oral vitamin D3 did not measurably activate this system under the tested conditions. In a separate HaCaT implantation model, topical calcipotriol increased bioluminescence at wound-adjacent implantation sites. ZF10–ΔVDR also supported reversible ON/OFF cycling under the tested conditions and inducible secreted protein output in vitro. Conclusions: These findings establish ZF10–ΔVDR as a calcipotriol-responsive switch with limited activation by endogenous vitamin D species, activity across multiple mammalian cell types, reversible regulation under the tested conditions, and compatibility with topical induction in vivo.
Pediatric nephrology is shifting from broad phenotype-based labels toward molecularly defined, genotype-guided diagnosis and management. Childhood kidney disorders are enriched for monogenic causes, yet persistent microscopic hematuria, bilateral kidney cysts, steroid-resistant nephrotic syndrome, and thrombotic microangiopathy may represent shared endpoints of biologically distinct mechanisms. Using these four scenarios, this narrative review illustrates how structured phenotyping, pedigree analysis, biochemical evaluation, and appropriately selected genomic testing can establish etiology, revise diagnoses, and guide clinical decision-making. Molecular diagnosis may support early nephroprotection, prevent ineffective immunosuppression, reveal tumor or extrarenal risks, enable mechanism-based therapy, and optimize transplantation planning. It also enables cascade testing, reproductive counseling, presymptomatic evaluation of relatives, and safer assessment of living-related donors. Genomic findings, however, require clinical context. Variants must be evaluated against gene–disease validity, inheritance, segregation, molecular mechanism, and phenotype, while variants of uncertain significance should not independently determine treatment or donor eligibility. Negative or inconclusive findings should prompt phenotypic reassessment, evaluation of analytical limitations, targeted studies, and periodic genomic reanalysis. Emerging genome and long-read sequencing, multiomics, artificial intelligence, and RNA-based therapeutics may further expand precision care, but rigorous interpretation, equitable access, appropriate counseling, and multidisciplinary collaboration remain essential. Precision nephrology derives value not from identifying variants alone, but from converting molecular etiology into safer, anticipatory, and individualized care.
Background/Objectives: Individuals with 46,XY disorders of sexual development (DSD) present with incomplete genital masculinization, aberrant gonadal development, and occasional retention of Müllerian duct remnants. Genetic factors play a substantial role in DSD pathogenesis, and whole-exome sequencing has expanded the catalog of candidate variants in recent years. However, the underlying molecular pathways remain incompletely characterized, and the functional relevance of most isolated genetic findings has not been systematically determined. This study aimed to identify and functionally characterize novel NR5A1 variants in DSD. Methods: A heterozygous missense variant NR5A1 c.88T>A (p.Cys30Ser) was identified in two patients with DSD, and initial functional characterization of the variant was performed via immunofluorescence analysis, Western Blotting, RNA sequencing, and quantitative real-time PCR analysis. Results: Wildtype NR5A1 protein localized predominantly to the nucleus, whereas the p.Cys30Ser mutant exhibited dual nuclear and cytoplasmic distribution. Compared with the wildtype, the p.Cys30Ser variant altered the expression of 642 genes, with differentially expressed genes primarily enriched in the neuroactive ligand–receptor interaction pathway. The variant impaired the transactivation of canonical NR5A1 downstream targets, resulting in the marked downregulation of 560 genes including key regulators such as KISS1R, CYP11A1, STAR, GABRP, and GRAMD1D. Conclusions: This study is the first to identify and functionally characterize the NR5A1 p.Cys30Ser variant in the context of DSD. Our findings broaden the mutational spectrum of NR5A1-related DSD and provide new insights into the molecular genetic basis of sexual development disorders.
Background/Objectives: The black grouse (Lyrurus tetrix) is experiencing a rapid decline across much of Europe. In Poland, the Carpathians and Sudetes constitute two of the last important strongholds of this endangered species; however, the genetic relationships between populations inhabiting these mountain systems remain poorly understood. Methods: A total of 579 non-invasive samples were collected in the Jizera Mountains and Giant Mountains (Sudetes), as well as in the Tatra Mountains and the Orava–Nowy Targ Basin (Carpathians). Microsatellite genotyping at nine loci identified 122 individuals. Genetic diversity and population genetic structure were assessed using F-statistics, AMOVA, STRUCTURE, PCoA and DAPC. Results: Significant genetic differentiation was detected among populations, with substantially lower differentiation within the mountain regions than between the Sudetes and Carpathians. Analyses consistently identified two major genetic groups corresponding to the Sudetes and Carpathians. The highest genetic diversity was recorded in the Tatra Mountains. Some individuals from this population displayed genetic signatures consistent with possible connectivity to neighbouring populations outside the study area, although this hypothesis requires testing with additional reference samples from these populations. Conclusions: The results demonstrate strong genetic structuring of black grouse populations in southern Poland and suggest limited contemporary gene flow between the Sudetes and Carpathians mountain ranges. The observed differentiation supports treating the Sudeten and Carpathian populations as separate Management Units. The Tatra Mountains constitute an important reservoir of genetic diversity and may play a key role in maintaining genetic connectivity within the Carpathian population.
Background/Objectives: Tryporyza intacta is a stem-boring pest that readily causes dead hearts in sugarcane seedlings and dead tops in mature plants, leading to large-scale yield reduction. Reverse chemical ecology studies of this pest contribute to its field biological control. During olfactory recognition, odor molecules are integrated by the olfactory nervous system after interacting with odorant-binding proteins (OBPs) and chemosensory proteins (CSPs), thereby regulating insect behavior. Methods: Two novel full-length general odorant-binding protein (GOBP) genes were cloned from antennal tissues using reverse transcription PCR. Protein sequence analysis was conducted to determine sequence similarity and conserved structural features. The recombinant GOBP1-2 protein was expressed in Escherichia coli and purified via Ni-ion affinity chromatography. Fluorescence binding assays were performed to evaluate the binding affinities of GOBP1-2 with various volatile odorant molecules. Results: Protein sequence analysis revealed that the two identified GOBPs shared high sequence similarity with other insect GOBPs and contained the characteristic six-cysteine motif. Fluorescence binding assays demonstrated that GOBP1-2 proteins exhibited differential binding affinities to distinct volatile odorant molecules, indicating selective ligand recognition. Conclusions: These findings suggest that GOBPs and effective volatile odorants likely play a functional role in the olfactory behavioral responses of this moth. This research provides valuable insights for developing field attractants targeting this sugar borer.
Rind color is an important quality trait in zucchini (Cucurbita pepo). As a core transcription factor in plant pigment biosynthesis, APRR2 plays a conserved yet mechanistically diverse regulatory role in the formation of rind color in various vegetables. However, the APRR2 transcription factor regulates rind color but has not been systematically identified in C. pepo. In this study, 50 APRR2 genes were defined by the presence of the conserved REC domain verified. These genes were identified and found to be unevenly distributed across the 20 chromosomes, primarily expanded through tandem duplication events. Phylogenetic and structural analysis classified these genes into three distinct subgroups, all featuring the conserved REC domain essential for pigment regulation but exhibiting variations in motifs and intron–exon structures. Promoter analysis revealed abundant light-responsive, hormone-responsive and stress-responsive elements that may contribute to environmental adaptation and photomorphogenesis. Crucially, transcriptome analysis during rind development (0 and 10 days after pollination) in green (GR) and white (WR) rind lines demonstrated profound functional divergence. Expression clusters indicated temporal shifts in metabolism and enriched “circadian rhythm-plant” and “photosynthesis” pathways in WR at 0 DAP. Specific APRR2 genes were tightly correlated with rind color. qPCR validation of the 24 selected APRR2 genes classified them into four trend groups based on the direction of expression change at 10 DAP. In total, 14 genes were upregulated in both GR and WR, 6 were downregulated in both lines, 1 was upregulated in GR but downregulated in WR, and 3 were downregulated in GR but upregulated in WR. Furthermore, protein–protein interaction prediction and yeast two-hybrid (Y2H) assays detected a physical interaction in yeast between a core APRR2 protein and a bHLH62 transcription factor, suggesting a potential interaction that may be involved in rind color regulation, pending in planta validation. The study first identified the members of the APRR2 gene family in C. pepo and conducted a bioinformatics analysis on them. The study establishes the molecular basis of APRR2 function and offers valuable resources for breeding improved C. pepo varieties.
Background/Objectives: Genetic overlap between any ischaemic stroke (AIS) and coronary artery disease (CAD) can obscure associations less closely tied to coronary risk. We aimed to separate coronary-shared from residual AIS genetic effects. Methods: We applied GWAS-by-subtraction to GIGASTROKE AIS and UK Biobank/CARDIoGRAMplusC4D CAD summary statistics. A Cholesky model separated a CAD-related shared component (F1) from a model-defined residual AIS component (F2). We tested model order, factor covariance, population prevalence, CAD input, LD reference and sample-size parameter then characterised loci using FUMA, SuSiE-RSS, genetic correlation, MAGMA, SMR/HEIDI and targeted colocalisation. Results: AIS and CAD had a genetic correlation of 0.490. F1 and F2 had SNP heritabilities of 0.0251 and 0.00414, and F2 contained 14 FUMA loci. F2 Z scores remained correlated across covariance (minimum r = 0.994), prevalence (minimum r = 0.998) and alternative-CAD analyses (r = 0.984). Reverse ordering produced reallocation of source-trait signal. At rs974819, the T allele was associated positively with CAD and negatively with marginal AIS, producing a model-derived CAD-AIS-discordant F2 association. Source-trait colocalisation showed that NBEAL1, PHACTR1 and PDGFD signals were present in one or both input-trait analyses, whereas the F11 protein signal aligned with AIS and F2. In a potentially overlapping FinnGen cross-implementation analysis, all 13 F2 lead variants showed concordant directions. Within overlapping stroke-subtype analyses, F2 showed stronger alignment with cardioembolic stroke. Conclusions: GWAS-by-subtraction resolved a model-defined residual AIS component that was stable across covariance, prevalence and CAD-input specifications, supporting a component-based view of AIS genetic effects after modelling shared coronary architecture.
Background: PRKD1-related congenital heart defects and ectodermal dysplasia syndrome (CHDED) is a rare multisystem developmental disorder caused by heterozygous gain-of-function variants in PRKD1. Reported phenotypes include congenital heart defects, ectodermal abnormalities, limb anomalies, and neurodevelopmental impairment, while vascular manifestations remain poorly characterized. We report an adult patient with a de novo PRKD1 variant and bilateral carotid artery dissections. Methods: Clinical, cardiovascular, neurological, and genetic evaluations were performed, including SNP-microarray and trio whole-exome sequencing with additional analysis of genes associated with heritable thoracic aortic and connective tissue disorders. Results: The patient was diagnosed at 35 years of age with a de novo PRKD1 c.1808G>A p.(Arg603His) variant. He had childhood-onset congenital heart disease, ectodermal and skeletal abnormalities, hearing impairment, infertility, and learning difficulties. In adulthood, he developed bilateral carotid artery dissections and mild aortic dilatation. No additional pathogenic or likely pathogenic variants were identified in the evaluated connective tissue and heritable aortic disease genes. The PRKD1 variant was absent or extremely rare in population databases and had supporting functional evidence for a gain-of-function effect. Conclusions: This case raises the possibility of a previously unrecognized vascular manifestation of PRKD1-related CHDED. Although a biological association is plausible, causality cannot be established from a single case. Further clinical and functional studies are needed to determine whether vascular fragility is a recurrent feature of PRKD1-related disease. This case also highlights the importance of considering rare genetic syndromes in patients with unexplained arteriopathy and congenital heart disease.
Background/Objectives: Promoter DNA methylation is conventionally summarised as a regional mean. Two alternatives have been proposed to capture information the mean discards: the concurrence ratio derived from partially methylated bisulfite reads (CAMDA) and single-CpG Shannon (β-) entropy. Benchmarks of such metrics typically report one coefficient per metric on a single gene set at a single aggregation scale. We asked how far that comparison depends on analytical choices that are rarely reported. Methods: Matched whole-genome bisulfite sequencing (WGBS) and RNA-seq from one donor of human CD3+ T cells were analysed. Promoter windows spanning −1000 to +500 bp around the transcription start site (TSS) were divided into fifteen 100 bp bins; all three metrics were computed on an identical CpG set and correlated with log2(FPKM) by Spearman’s ρ. The comparison was repeated across annotation source, quantification level, coverage threshold, aggregation scheme, the treatment of zero-expression transcripts and CpG island status, with metric differences assessed by paired bootstrap over promoters and over chromosomes. Results: Across a grid of five analytical choices, the mean methylation coefficient ranged from −0.145 to −0.593 and the ordering of the metrics reversed between configurations. At the 100 bp bin scale, the largest difference between metrics was 0.037; aggregating the same CpGs to the whole promoter opened differences of up to 0.31, so the apparent superiority of a metric is itself a function of the aggregation scale. CAMDA exceeded the regional mean consistently but modestly, with the advantage largest in distal upstream bins and indistinguishable from zero adjacent to the TSS. β-Entropy is a strictly monotone function of the folded measure 1 − 2|β − 0.5|; at the 100 bp scale, the mean of per-CpG entropy tracked the folding transform of regional mean methylation to within 0.002 in every bin, while at the whole-promoter scale, the two separated by 0.041. Within CpG islands, the regional mean weakened (ρ = −0.246) while CAMDA did not (−0.494). Conclusions: In this single-donor dataset, analytical design affected the estimated coupling more than the choice of summary metric. The observed range is dataset-specific and should not be interpreted as a transferable numerical estimate. Rather, these results show that evaluating plausible analytical configurations can provide important context when comparing promoter methylation summary metrics.
Background/Objectives: Alternative splicing (AS) contributes substantially to transcriptomic diversity and has emerged as an important regulator of cancer progression. However, the genome-wide characterization of AS events specific to estrogen receptor (ER)-positive breast cancer remains limited. This study aims to comprehensively profile AS in ER-positive breast cancer and identify a prognostic AS signature associated with patient outcome. Methods: Clinical and splicing data (Percent Spliced In values) were obtained from The Cancer Genome Atlas (TCGA) for 737 ER-positive samples. Prognostic AS events were identified using Cox regression analysis. The Least Absolute Shrinkage Selection Operator (LASSO) model was used to construct an AS-based prognostic signature, and a standardized risk score was calculated for each sample. The signature was then evaluated by Kaplan–Meier (KM) analysis and receiver operating characteristic (ROC) curves, in addition to other methods to validate model performance. Furthermore, transcript-level annotation and RNA expression correlation were performed to evaluate biological relevance. Results: Profiling identified 6276 AS events across 4457 genes, with exon skipping (ES) representing the most prevalent class (34.4%). Model analysis established a novel five-event AS prognostic signature (comprising DNAJC14, BAZ2B, PCDHAC1, PCDHA7, and DAPL1). The signature significantly stratified patients into high-risk and low-risk groups for both disease-free survival (DFS; p < 0.001) and overall survival (OS; p < 0.001). HER2-specific analysis demonstrated more consistent performance in HER2-negative patients for both DFS (p < 0.001) and OS (p = 0.018). The model achieved area under the curve (AUC) of 0.804 for 60-month follow-up supporting long-term prognostic performance. Additionally, the signature demonstrated stable and reliable discrimination with a concordance index (C-index) of approximately 0.73 across multiple validation methods. Conclusions: The study identified AS signature with promising prognostic value in ER-positive breast cancer. This highlights the potential of splicing-based models to refine risk stratification beyond conventional gene expression analysis.
Background: Enteroviruses (EVs) have been proposed as environmental triggers in type 1 diabetes (T1D), potentially through activation of innate immune pathways and type I interferon (IFN) responses. However, the relationship between detectable viral infection and IFN-related transcriptional responses remains unclear. Methods: In this cross-sectional, exploratory study, peripheral blood samples from individuals with new-onset T1D, established T1D, and healthy controls were analyzed by an enterovirus 5′NCR-targeted RT-PCR assay and for the expression of innate immune receptors (TLR3, TLR7, TLR8), interferon-stimulated genes (IFI27, IFIT1, ISG15, IFI44L, RSAD2, SIGLEC1), and FOXP3, assessed as an exploratory marker related to regulatory T-cell biology potentially influenced by type I interferon signaling. Gene expression was assessed by quantitative RT-PCR, and comparisons were performed between groups. Results: Enterovirus-targeted amplification was observed in only one T1D sample under the applied assay conditions. In the setting of limited enterovirus-targeted amplification under the applied assay conditions, TLR3 was significantly increased in established T1D, while TLR7 was increased in both new-onset and established T1D, with the highest levels in established disease; these differences remained significant after correction for multiple comparisons across the full gene panel. TLR8 was unchanged. Several of the selected interferon-stimulated genes showed group-specific expression patterns: IFI27 and RSAD2 were significantly increased in new-onset T1D, whereas IFIT1 and ISG15 were more evident in established T1D. SIGLEC1 and IFI44L showed no significant differences. FOXP3 transcript abundance was also increased in both diabetic groups, a finding that correlated with lymphocyte proportion and is interpreted with caution. Conclusions: These findings indicate group-specific differences in whole-blood transcript expression of selected RNA-sensing and IFN-related genes in T1D under conditions in which enterovirus-targeted amplification was observed in only one sample. Given the cross-sectional whole-blood design and the analytical limitations of the EV assay, these results are hypothesis-generating and do not establish the presence or absence of systemic enterovirus infection or functional pathway activation.
Tobacco use disorder (TUD) is a complex multifactorial condition resulting from the interplay between nicotine-induced neurobiological adaptations, behavioral and learning processes, environmental influences, and individual genetic susceptibility. Genetic research has progressively evolved from twin and family studies through candidate-gene approaches to large-scale genome-wide association studies (GWAS), substantially improving our understanding of the genetic architecture of tobacco use and nicotine dependence. This review summarizes the current evidence on the genetic basis of TUD, with particular emphasis on major biological pathways. We also discuss the limitations of early candidate-gene studies and the paradigm shift introduced by large GWAS and meta-analyses, and polygenic risk scores, which indicate that tobacco use and nicotine dependence have a highly polygenic and pleiotropic architecture. Finally, we review the potential clinical applications of genetic information in smoking-cessation treatment, while highlighting current limitations in clinical translation. In the future, it is clear that a multidisciplinary approach—combining genetics, clinical practice, and social sciences—will be necessary to transform tobacco use management into a precision-based model and reduce its impact on public health.
Background/Objectives: The population genetic structure of Albania remains insufficiently characterized at both regional and broader European scales. This study investigated genetic variation within Albania and its relationship with neighboring and European populations using autosomal short tandem repeats (STRs). Methods: Sixteen autosomal STR loci were analyzed in 2000 unrelated individuals from 12 Albanian counties, grouped into Northern, Central, and Southern regions. Population structure was assessed using principal component analysis (PCA), pairwise Weir–Cockerham FST, hierarchical AMOVA, and Bayesian clustering (STRUCTURE Version 2.3.4). Population affinities were further evaluated using Nei’s standard genetic distance, multidimensional scaling, and neighbor-joining analysis of European reference populations. Results: PCA revealed extensive regional overlap, with PC1 and PC2 explaining 2.64% and 2.61% of variation, respectively. Pairwise FST values were close to zero, with confidence intervals overlapping zero, while AMOVA indicated negligible regional differentiation. STRUCTURE identified K = 3 as the strongest relative solution, but ancestry coefficients showed extensive admixture without discrete regional clustering. European comparisons revealed low Nei distances (approximately 0.004–0.014), with Albania showing particularly close affinity to Greece and other Southeastern European populations. Conclusions: Albanian autosomal STR variation demonstrates high regional homogeneity and limited population substructure, while broader affinities are consistent with geographic patterns across Southeastern Europe.
Background/Objectives: Epidemiological studies link autoimmune diseases (AIDs) to follicular lymphoma (FL) risk, but their shared genetic architecture and causal mechanisms remain unclear. Methods: A two-sample Mendelian randomization (MR) analysis was employed to assess causal relationships between 15 AIDs and FL. Pleiotropic loci were identified through the Pleiotropy Analysis under Composite Null (PLACO). Bayesian colocalization analysis, functional mapping, and Multi-marker Analysis of GenoMic Annotation were applied to fine-map shared genetic variants and identify their target genes. Summary data-based MR was used with multitissue expression quantitative trait locus data to infer causal effects of gene expression. HyPrColoc analysis was applied to decipher shared genetic regulation of immune cell phenotypes. Results: MR revealed that rheumatoid arthritis increased FL risk (ORIVW = 1.55, nominal p = 7.16 × 10−5, FDR-corrected p = 1.07 × 10−3), whereas composite autoimmune disease reduced FL risk (ORIVW = 0.70, nominal p = 4.61 × 10−5, FDR-corrected p = 6.92 × 10−4). Hypothyroidism showed only a nominally suggestive protective trend (ORIVW = 0.88, nominal p = 0.015), which did not survive Benjamini–Hochberg multiple-testing correction (FDR-corrected p = 0.075). Fifty-five pleiotropic loci shared between FL and AIDs were identified, among which key loci such as 1p36.32, 6p21.32, 17p13.1, and 11q23.3 exhibited strong colocalization evidence. Core pleiotropic genes (e.g., TNFRSF14, MMEL1, CXCR5, and RNASET2) were prioritized, which implicated pathways related to MHC class II antigen presentation, interferon signaling, and T cell activation. HyPrColoc analysis demonstrated that these loci colocalized with the expression of immune receptors, including BAFF-R on B cells and HVEM (TNFRSF14) on naïve CD8+ T cells. Conclusions: Our study identifies divergent causal effects of selected AIDs on FL risk and demonstrates localized pleiotropy at key loci, providing novel insights into shared immunogenetic mechanisms.
Chalcone synthase (CHS) is a key enzyme in flavonoid biosynthesis, and its activity strongly influences the efficiency of flavonoid production in plants. By controlling the biosynthesis of secondary metabolites, CHS contributes to plant adaptation to diverse environmental stresses. Here, we identified CHS members across the Phoebe zhennan genome and systematically examined their gene structures, phylogenetic relationships, and potential roles in golden-thread wood color formation and drought response. Genome-wide screening resolved 11 putatively functional PzCHSs, which were unevenly distributed across six chromosomes. Physicochemical analyses indicated that most PzCHS proteins were hydrophilic. Phylogenetic reconstruction divided the PzCHS family into three groups, whose members generally shared similar gene structures. One tandem duplication event and five segmental duplication events were detected. Synteny analysis revealed extensive collinearity between the CHS families of P. zhennan, Phoebe bournei and Cinnamomum camphora, consistent with their close evolutionary relationships. Promoter regions of PzCHS genes were enriched for phytohormone-responsive and growth-related cis-elements, suggesting roles in development and hormonal regulation. Transcriptome profiling showed that PzCHS6 was upregulated in the transition zone of wood and under drought stress, suggesting that this gene may be associated with both golden-thread wood color formation and drought response. These results provide a framework for functional dissection of the CHS members and offer candidate genes for golden-thread wood color improvement and drought response breeding.
The height of the first fruiting branch node (HFFBN) is a core indicator for mechanical harvesting of cotton, and the development of molecular markers for this trait is important for accelerating the breeding process. In this study, using bulked segregant analysis coupled with whole-genome sequencing (BSA-seq), one quantitative trait locus (QTL) associated with the HFFBN was mapped; a molecular marker, qFBH7, associated with the HFFBN of cotton was developed; and its application value was systematically evaluated. A total of 20 lines with extreme phenotypes were selected from the recombinant inbred lines constructed using upland cotton Z3-146 and Z3-147 as parental lines. The screened lines with extreme phenotypes were used to construct the extreme high-HFFBN pool and the extreme low-HFFBN pool, which were subsequently used for BSA-seq. Using the upland cotton genome as a reference, relevant QTLs were mapped by BSA-seq. One relevant candidate region was identified, with a total length of 2.25 Mb. The validation experiments revealed that the genotyping results of the KASP_FBH7_03 molecular marker in the parental lines Z3-146 and Z3-147 were completely consistent with the BSA-seq data: Z3-146 had the TT genotype, and Z3-147 had the CC genotype. Among the 66 samples from the natural population, there was a significant difference (p < 0.05) in the HFFBN between the CC and TT genotypes, and the mean HFFBN of the TT genotype was greater than that of the CC genotype. In summary, the KASP_FBH7_03 molecular marker can be effectively used for selective breeding for the HFFBN of cotton, and the TT genotype has a positive regulatory effect on the HFFBN. This study not only provides resources for breeding cotton varieties suited to mechanical harvesting but also offers a robust tool for molecular marker-assisted selection.
Colorectal cancer (CRC) remains a major cause of cancer morbidity and mortality. Immune checkpoint inhibitors (ICIs) have transformed the treatment of microsatellite instability-high/mismatch repair-deficient (MSI-H/dMMR) CRC, yet most CRCs are microsatellite-stable/mismatch repair-proficient (MSS/pMMR) and remain poorly responsive to immunotherapy. MicroRNAs (miRNAs) are well positioned to influence this biology because individual miRNAs can coordinate multiple tumor-intrinsic and microenvironmental programs that shape antitumor immunity. Rather than cataloging miRNAs one by one, this review organizes the evidence around the major barriers that sustain an immune-cold CRC microenvironment: altered checkpoint and costimulatory signaling, defective antigen presentation, impaired effector T-cell access and function, suppressive myeloid and stromal compartments, and extracellular vesicle (EV)-mediated intercellular communication. We also critically assess tissue and circulating miRNA signatures as candidate biomarkers of ICI response and discuss therapeutic approaches based on miRNA mimics, inhibitors, and targeted delivery platforms. The available evidence supports a biologically compelling role for miRNA networks in CRC immune regulation, but clinical translation remains limited by context dependence, delivery, off-target effects, and the lack of treatment-linked validation in CRC cohorts.
Background: Pathogenic variants in SLC6A1, which encodes the γ-aminobutyric acid (GABA) transporter GAT-1, cause developmental and epileptic encephalopathies (DEEs) through reduced GABA uptake, impaired transporter trafficking, and functional haploinsufficiency. 4-phenylbutyrate (PBA) is a clinically available small molecule with chemical-chaperone and histone-deacetylase-inhibitor activities that can rescue misfolded GABAergic proteins, but variant-level rescue data are needed to guide precision treatment. Methods: We report a novel de novo missense mutation p.Ala305Val in GAT-1 encoding SLC6A1, in a patient with myoclonic-atonic epilepsy and a developmental and epileptic encephalopathy phenotype. Ala305Val was compared with the residue-matched comparator p.Ala305Thr (Ala305Thr). Variant effects were evaluated by (i) protein-structure prediction across nine stability-prediction algorithms using the cryo-EM-derived human GAT-1 template (PDB 7Y7W); (ii) 3H-GABA uptake assays in HEK293T cells and in human iPSC-derived astrocytes and cortical neurons; (iii) live-cell confocal microscopy of ER colocalization; (iv) pharmacologic rescue with PBA, TUDCA and salubrinal (v) and GAT-1 cDNA gene-augmentation, alone and in combination with PBA. Results: AI-based stability predictors uniformly indicated destabilization of GAT-1 p.Ala305Val and GAT-1 p.Ala305Thr. GAT-1 p.Ala305Val reduced 3H GABA uptake across HEK293Ts, astrocytes, and neurons. The mutant transporter accumulated within the endoplasmic reticulum (ER), with ER colocalization rising from approximately 30% in wildtype to ~80% in GAT-1 p.Ala305Val; PBA reduced ER retention to approximately ~40% and restored total GAT-1 fluorescence toward wildtype levels. Pharmacochaperones (PBA, TUDCA) restored GABA uptake for the mutant transporters. Wildtype GAT-1 gene augmentation improved GABA uptake in the heterozygous condition but combined PBA plus wildtype allele augmentation produced rescue greater than either intervention alone in the available dose-response ranges. Conclusions: GAT-1 p.Ala305Val is a trafficking-impaired, loss-of-function variant whose dysfunction is amenable to two convergent therapeutic axes: pharmacologic correction of folding and trafficking, and augmentation of functional transporter expression. These findings support a two-pronged precision-medicine framework for SLC6A1-related DEEs in which PBA increased the transporter function augmented by genetic approaches.
