IntroductionThe proliferation of biobanks and the collection of gender identity data have created opportunities to conduct transgender identity genetic research (TIGR), which explores possible genetic contributions to gender identity. However, without meaningfully engaging trans communities, researchers may struggle to understand and prevent potential harms while maximizing potential benefits, particularly when research fails to incorporate the social, medical, and political factors and environments shaping transgender peoples’ lives. This study explored factors associated with transgender individuals’ perspectives on and willingness to participate in TIGR.MethodsBetween January and May 2025, we recruited a nationwide sample (n = 495) of transgender adults. Participants completed a cross-sectional survey assessing sociodemographics, policy safety, health, TIGR perspectives, and willingness to participate in TIGR. Regression models assessed correlates of TIGR perspectives and willingness to participate.ResultsParticipants’ median age was 29 years (IQR = 25–34); 38.4% were people of color. While 62.2% would be willing to participate, 68.9% agreed TIGR could harm transgender communities. More positive TIGR perspectives were observed among people of color (aβ = 0.48, 95% CI = 0.18 to 0.56) and those experiencing food insecurity (aβ = 0.21, 95% CI = 0.02 to 0.40). Less favorable perspectives were associated with disability (aβ = –0.20, 95% CI = –0.38 to –0.02), medical gender affirmation (aβ = –0.30, 95% CI = –0.54 to –0.06), mixed vs. negative transgender policy environment (aβ = –0.32, 95% CI = –0.59 to –0.05), and high medical mistrust (aβ = –0.24, 95% CI = –0.46 to –0.03). Positive perspectives were strongly associated with willingness to participate in TIGR (aOR = 14.48, 95% CI = 7.30 to 28.70).DiscussionAlthough most participants were willing to participate in TIGR, a substantial minority were unsure or unwilling, reflecting concerns about trust, risk, and benefits. Future genomics research involving transgender people must prioritize trust-building efforts, particularly those that ensure participant safety, to encourage future research participation.
BackgroundIsolated lissencephaly sequence (ILS) is a severe neurodevelopmental disorder associated with 17p13.3 microdeletion. This 6-year longitudinal study aimed to systematically characterize physical and neurodevelopmental trajectories of a Chinese ILS patient and offer evidence for early diagnosis and clinical intervention.MethodsFrom April 2021 to April 2026, a child with severe developmental delay and his family members (parents and elder brother) were recruited in Lianyungang, eastern China. Trio whole-exome sequencing (trio-WES) and copy number variation sequencing (CNV-seq) were used to identify the pathogenic variant. Serial physical growth and neurodevelopmental assessments were conducted during the 6-year longitudinal follow-up. Bioinformatics analysis was used to explore potential molecular pathogenic mechanisms.ResultsA de novo 2.06 Mb heterozygous deletion at 17p13.3p13.2 (chr17:1707883_3765621del, GRCh37) was identified in the proband, which included PAFAH1B1 but spared YWHAE and CRK. Longitudinal data showed a progressive decline in both height and weight. Height Z score decreased from −0.37 at 2 months to −1.92 at 57 months. Weight Z score decreased from −1.25 at 2 months to −1.79 at 57 months. Gesell developmental quotients (DQ) showed significant progressive declines in five domains with a decelerating trajectory: adaptive behavior (B2 = 0.019, 95% CI: 0.002–0.036, RQ2= 0.978), gross motor (B2 = 0.013, 95% CI: -0.004 – 0.030, RQ2= 0.944), fine motor (B2 = 0.017, 95% CI: -0.012 – 0.047, RQ2= 0.870), language (B2 = 0.021, 95% CI: -0.006 – 0.049, RQ2= 0.905), personal social behavior (B2 = 0.020, 95% CI: -0.014 - 0.054, RQ2= 0.847). Bioinformatics analysis confirmed that haploinsufficiency of the PAFAH1B1 gene was the primary pathogenic cause. Furthermore, genes in the deleted region were significantly enriched in olfactory perception and calcium ion transmembrane transport pathways.ConclusionThis study reports a 6-year longitudinal follow-up of ILS in a Chinese patient. PAFAH1B1 haploinsufficiency causes the core lissencephaly phenotype, while co-deletion of olfactory and calcium-regulatory genes may exert synergistic effects. These findings expand the phenotypic spectrum of ILS in Chinese populations and provide insights for mechanistic studies and genetic counseling.
IntroductionTobacco smoking remains a leading cause of many life-threatening diseases, particularly lung cancer. Waterpipe smoking has rapidly gained popularity worldwide, while research on this tobacco form remains limited. Tobacco smoking has been linked to the shortening of telomeres and activation of telomerase, important regulators of genomic stability and cancer progression. However, the direct impact of whole-smoke exposure on telomere dynamics and its relationship with cancer progression remains minimally explored, and this requires suitable experimental systems.MethodsThis study aims to demonstrate an experimental procedure to enable prolonged exposure of lung cancer cells (A549) to sub-toxic concentrations of cigarette and waterpipe smoke extracts, and to investigate in those cells the effects on telomere length, telomerase activity, and cancer progression. We also checked telomere length, epithelial-to-mesenchymal transition (EMT) markers, and migration in two other colon (HCT116) and breast cancer (MCF7) cell lines.ResultsAfter 12 weeks of exposure, there was a significant decrease in relative telomere length in heterogeneous/parents of A549 cells with waterpipe exposure, and a significant increase in telomerase activity with cigarette exposure. Chronic exposure to both smoke extracts also led to a significant upregulation in the expression of the SNAI2 mesenchymal marker in both heterogeneous populations and single-cell-derived colonies. Additionally, chronic exposure to cigarette smoke extract significantly enhanced migration in single-cell-derived colonies. Comparable results were seen in the colonies of colon and breast cancer cell lines.DiscussionOur findings revealed that chronic smoke exposure disrupts telomere dynamics particularly in lung cancer cells and triggers transcriptional EMT changes that might contribute to cancer progression in lung, breast, and colon cancer cells, offering new insights into a potential link between tobacco smoke, telomere dysfunction, and cancer progression.
Comprehensive, well-structured databases are critical for storing, integrating, and analyzing genomics data. This manuscript presents a hybrid methodology combining the traditional Database Development Life Cycle (DDLC) with agile principles to build a comprehensive genome database for Boesenbergia rotunda, known as Fingerroot ginger. Boesenbergia rotunda (L.) Mansf., also recognized as Fingerroot ginger or Chinese keys, is a perennial herb from the Zingiberaceae family in the order Zingiberales. Fingerroot ginger is widely used in Asian cuisine, especially the rhizome, and is recognized for its potent bioactive compounds, including panduratin A, 4-hydroxypanduratin, and cardamonin, which are reported to have notable anti-inflammatory, anti-tumor, and antimicrobial, especially antiviral, effects. The Fingerroot Genome Database incorporates genome, transcriptome, coding sequences, and functional annotations in a relational schema of 27 tables. Using iterative refinement during modular development, we integrated tools such as BLAST+ and JBrowse2 to support sequence search and genome visualization. This case study illustrates how a structured DDLC approach can be combined with Agile-inspired refinement to guide the development of a species-specific bioinformatics database for an underexplored medicinal plant.
Background15q11.2–q13 duplication syndrome (Dup15q; OMIM #608636) is a rare neurodevelopmental disorder. While interstitial duplications (copy number = 3) are relatively well characterized, contiguous rearrangements comprising both tetrasomic (copy number = 4) and adjacent trisomic (copy number = 3) segments are rare. We report a Chinese girl with a de novo contiguous 15q11.1–q13.3 duplication, whose underlying genetic diagnosis was initially delayed because her early neurodevelopmental abnormalities were partly attributed to prematurity.Case PresentationThe patient was born at 35+2 weeks of gestation and presented with global developmental delay, severe autism spectrum disorder (CARS: 44), and profound cognitive and language impairment (GQ 30, GMQ 57 at 2 years 4 months). Brain MRI demonstrated delayed myelination, and magnetic resonance spectroscopy showed metabolic abnormalities in the left frontal lobe. Video-electroencephalography at 3 years of age revealed sleep-activated frontocentral epileptiform discharges without clinical seizures. Trio whole-genome sequencing with copy number variation analysis identified a de novo contiguous duplication consisting of a ∼10.34 Mb tetrasomic segment (15q11.1–q13.2; CN = 4) and an adjacent ∼2.40 Mb trisomic segment (15q13.2–q13.3; CN = 3). Despite long-term rehabilitation, the patient remained nonverbal and exhibited persistent severe neurodevelopmental impairment.ConclusionThis case expands the genomic spectrum of complex proximal 15q rearrangements and highlights the value of high-resolution genomic testing for resolving complex neurodevelopmental disorders. It also emphasizes that severe genetic etiologies may be overlooked when developmental abnormalities are initially attributed to prematurity. These findings support early comprehensive genomic evaluation in children with profound developmental delay, autism spectrum disorder, or persistent developmental impairment despite conventional rehabilitation.
BackgroundRetinoblastoma (RB) is the most common ocular malignancy in children, but the relationship between environmental pollutants and RB-related molecular alterations remains unclear. This study aimed to identify candidate targets and pathways potentially linking 2.3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) with RB.MethodsNetwork toxicology, computational toxicology, and integrated RB transcriptomic analyses were used to identify candidate TCDD-RB targets. WGCNA, eight machine-learning algorithms, and SHAP analysis were applied to screen hub genes and evaluate their contributions to model prediction. Functional enrichment analysis, GSEA/GSVA, immune microenvironment analysis, molecular docking, and expression validation in RB cell lines were subsequently performed to assess the potential biological relevance of the hub genes.ResultsA total of 18 candidate TCDD-RB targets were identified and were mainly enriched in cell-cycle regulation, G2/M transition, DNA replication, and the p53 signaling pathway. Machine learning further identified five hub genes, namely, CA14, PIP5K1B, GRIA2, KDR, and CDK1. Among them, CDK1 was significantly upregulated in RB and was associated with proliferation-related pathways, including the cell cycle, DNA replication, and mismatch repair. The other four genes were significantly downregulated and may be involved in metabolic homeostasis and immune microenvironment regulation. Molecular docking predicted potential structural compatibility between TCDD and all five hub proteins, with CDK1 showing the most favorable predicted docking energy. qRT-PCR analysis in RB cell lines supported the differential expression patterns of the five hub genes, and qRT-PCR and Western blotting confirmed the efficiency of CDK1 overexpression and knockdown.ConclusionThis study delineated a candidate molecular network at the intersection of TCDD-associated toxic This study delineated a candidate molecular network at the intersection of TCDD-associated toxicological targets and RB-related transcriptomic alterations. CDK1 emerged as a candidate hub associated with cell-cycle dysregulation, whereas CA14, PIP5K1B, GRIA2, and KDR were linked to broader disturbances in cellular homeostasis and microenvironmental regulation. Because these findings are based primarily on computational analyses and preliminary expression validation, they should be regarded as hypothesis-generating. Direct TCDD exposure and functional studies are required to determine whether TCDD functionally affects these genes or RB-related cellular phenotypes.
BackgroundAedes aegypti is the primary arboviral vector globally, and its affinity to feed on human hosts is a key determinant of transmission intensity. Despite the epidemiological importance of anthropophily, the genomic architecture underlying the molecular basis of host-feeding behavior remains understudied.MethodsHere, we present an integrated genome-wide association study (GWAS) and structural variant analysis of host-feeding behavior in 21 field-collected Ae. aegypti females phenotyped as human-blood-fed (HF; n = 11) or non-human-blood-fed (NHF; n = 10). Whole-genome sequencing yielded 661,519 high-quality SNPs distributed across all three chromosomes. Principal component analysis on a linkage disequilibrium-pruned dataset revealed modest population structure (PC1 = 11.69%, PC2 = 10.98%).ResultsGWAS using a general linear model with five PC covariates (λ = 1.05) identified 11 suggestive SNPs in genes including an actin binding protein on chromosome 2 and G-protein coupled receptor 39 on chromosome 3. Chromosomal inversion analysis using Delly identified an HF-specific inversion on chromosome 2 harboring 13 genes across three functionally coherent chemosensory categories: the sensory developmental regulator tap, odorant receptors (Or6, Or31, Or33) and an odorant-binding protein (Gp68), and eight gustatory receptor genes (Gr15–Gr19a, Gr35, Gr36, Gr66).ConclusionThe concentration of co-adapted chemosensory genes within a single non-recombining chromosomal unit is consistent with a possible supergene model of anthropophily, paralleling inversion-mediated behavioral divergence in Anopheles gambiae. These exploratory findings provide a preliminary genomic framework for host-seeking behavior in Ae. aegypti and identify probable candidate loci warranting functional validation before application to vector surveillance.
BackgroundImmune checkpoint inhibitors (ICIs) have transformed cutaneous melanoma therapy, yet 50% of patients show primary or acquired resistance, and current biomarkers (PD-L1 and tumor mutational burden) lack precision. High-frequency ultrasound (HFUS), contrast-enhanced ultrasound (CEUS), and shear-wave elastography (SWE) are inexpensive and repeatable, but their relationship to the immune transcriptome and ICI outcomes is unknown.MethodsIn this single-center retrospective study, 218 patients with cutaneous melanoma who received first-line anti-PD-1-based ICIs and pretreatment ultrasound were divided into training (n = 153) and internal validation (n = 65) sets. HFUS/CEUS/SWE radiomic features were filtered for reproducibility and selected by LASSO to construct an ultrasound radiomic score (US-score). Across three public transcriptomic cohorts (TCGA-SKCM, GSE91061, and GSE78220) and a melanoma single-cell dataset (GSE115978), we combined differential expression, WGCNA, immune deconvolution, and LASSO-Cox to derive an IRGS. Four core genes (CXCL10, CD8A, IFNG, and CXCL9) were validated in vitro by RT-PCR in three ATCC melanoma cell lines after IFN-γ stimulation.ResultsThe objective response rate was 42.7% (median follow-up 28.4 months). The US-score independently predicted response (adjusted OR: 2.6; 95% CI: 1.7–3.9; validation AUC: 0.78). The IRGS stratified public cohorts into immune-hot/cold groups with distinct outcomes (TCGA-SKCM overall-survival HR: 2.14; 95% CI: 1.56–2.93; response AUC: 0.79). The US-score correlated with the IRGS (r = 0.58) and with CD8+ T-cell density on multiplex immunohistochemistry (r = 0.62). The combined nomogram outperformed any single biomarker (validation AUC: 0.88 vs. 0.78 [US], 0.76 [IRGS], and 0.68 [clinical]) with good calibration and net benefit and separated progression-free survival (median: 18.6 vs. 6.3 months; HR: 3.12, 95% CI: 2.08–4.68). In vitro, all four genes were significantly induced by IFN-γ (CXCL10 up to 8.3-fold; all p < 0.05).ConclusionUltrasound radiomics encodes information about the melanoma tumor-immune microenvironment; combined with an immune-related gene signature, it provides a non-invasive, biologically anchored tool for stratifying ICI response and resistance.
BackgroundSpinal muscular atrophy (SMA) and tuberous sclerosis complex (TSC) are both rare genetic disorders, and their co-occurrence is expected to be exceptionally uncommon. Although risdiplam has demonstrated efficacy in SMA, evidence regarding its use in preterm infants with complex genetic comorbidities remains limited.ResultsWe report preterm monozygotic twins born at 32+5 weeks of gestation with genetically confirmed SMA caused by homozygous deletion of SMN1 exons 7–8, with two copies of SMN2. During baseline evaluation prior to presymptomatic treatment, brain magnetic resonance imaging revealed incidental abnormalities, including cortical dysplasia and subependymal nodules, which prompted further genetic testing and led to the diagnosis of TSC with a TSC1 c.1041G>A variant. Presymptomatic risdiplam was initiated at a corrected gestational age of 38+5 weeks. Both twins showed marked improvement in motor function. By 12 months of age, they had achieved independent rolling, unsupported sitting, crawling, and pulling to stand, accompanied by substantial improvements in CHOP INTEND and HINE-2 scores. Risdiplam was well tolerated, and no commonly reported adverse events were observed during follow-up.ConclusionThis report describes the first documented co-occurrence of SMA and TSC in preterm monozygotic twins and suggests that presymptomatic risdiplam may be effective and well tolerated in this complex clinical setting over 1 year of follow-up. These findings also highlight the importance of comprehensive genetic evaluation in infants with SMA who present with atypical neuroimaging or neurological features. Longer-term follow-up is needed to clarify safety, efficacy, and optimal integrated management strategies in patients with complex genetic comorbidities.
BackgroundInflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) often present with overlapping gastrointestinal symptoms despite distinct pathophysiological mechanisms. Colonoscopy remains the diagnostic gold standard but is invasive, costly and frequently overutilized. Single biomarkers have limited diagnostic value because they do not fully reflect the complex metabolic and inflammatory alterations underlying intestinal diseases. We aimed to develop and validate an interpretable machine learning-based scoring system integrating multidimensional metabolism-related biomarkers for invasive examination triage.MethodsThis retrospective single-center study included 729 participants (313 healthy controls, 210 IBS, 100 ulcerative colitis and 106 Crohn’s disease patients) enrolled between July 2021 and November 2025. Demographic, clinical, and metabolism-related laboratory biomarkers reflecting inflammatory metabolism, nutritional metabolism, hepatic metabolic function, and renal metabolic homeostasis were collected. Correlation network analysis, least absolute shrinkage and selection operator (LASSO) regression, extreme gradient boosting (XGBoost), and a simplified nomogram-based scoring system were applied to differentiate IBD from non-IBD conditions.ResultsSignificant differences were observed across all clinical and metabolism-related variables (P < 0.001). IBD patients exhibited elevated inflammatory-metabolic-related biomarkers and dense inflammation-driven metabolic correlation networks, whereas IBS patients showed metabolic profiles similar to healthy controls. XGBoost achieved the best diagnostic performance (AUC = 0.992), followed by LASSO (AUC = 0.978). A simplified scoring system incorporating sex, age, log-transformed fecal calprotectin (LogFC), log-transformed C-reactive protein (LogCRP), hemoglobin (HB), albumin (ALB), white blood cell count (WBC) and platelet count (PLT) achieved an AUC of 0.910, outperforming fecal calprotectin (FC) alone (AUC = 0.844) and the FC-CRP combination (AUC = 0.855). The scoring system demonstrated substantial clinical net benefit and correlated with colonoscopic inflammation severity (AUC = 0.761). Inflammatory and metabolism-related biomarkers were the strongest predictors of IBD.ConclusionIBD is characterized by distinct multidimensional metabolism-related biomarker signatures. The proposed machine learning-based scoring system integrates these metabolism-related biomarkers into a reliable, non-invasive tool for invasive examination triage, potentially reducing unnecessary colonoscopies and improving clinical resource utilization.
Clarifying gene regulatory networks (GRNs) remains one of the central challenges of systems biology and is crucial for elucidating pathogenesis and curing diseases. Various machine learning techniques have been developed for gene regulatory network inference, but identifying intricate interactions is still a fundamental problem. Here, we propose a network structure refinement scheme, termed HSTXGB (a hyperparameter self-tuning XGBoost method integrating pre- and post-processing), to infer GRNs from time-course expression data by leveraging the nonlinear modeling capability of XGBoost while integrating prior knowledge (e.g., knockout data) and posterior statistics (e.g., regulation probabilities). Specifically, HSTXGB first calculates regulation relationship confidences using a self-tuning XGBoost model, which accounts for temporal dependencies in gene expression. Then, two novel strategies are designed to integrate information from prior data and to incorporate statistical information, which correspond to fluctuations in knockout experiments and to regulatory frequency and intensity, respectively. The confirmatory experiments on the benchmark datasets from the DREAM challenge as well as the E. coli datasets (8 networks in total) demonstrated that our HSTXGB scheme achieves significantly better performance compared with eight other state-of-the-art methods.
BackgroundThird-generation epidermal growth factor receptor tyrosine kinase inhibitor osimertinib serves as the gold standard therapy for treating NSCLC patients harboring EGFR T790M mutations. The clinical utility of this agent, however, faces considerable constraints due to the unavoidable emergence of acquired resistance mechanisms. Understanding the molecular basis of osimertinib resistance holds paramount importance for determining optimal follow-up treatment approaches.MethodsClinical information from 86 lung adenocarcinoma patients carrying EGFR T790M mutations who showed disease advancement following osimertinib therapy was examined retrospectively, spanning the period from January 2018 through December 2023. Genomic characterization was conducted via next-generation sequencing on tissue or liquid biopsy specimens collected after resistance developed. Protein expression alterations were assessed through immunohistochemical staining, while critical resistance pathways underwent validation using cell line models.ResultsAmong the 86-patient cohort, the median duration before disease progression reached 14.2 months. Genomic characterization identified these predominant resistance pathways: C797S mutations in EGFR (23.3%), amplification of MET (15.1%), amplification of HER2 (8.1%), mutations in PIK3CA (7.0%), transformation to small cell lung cancer (9.3%), and epithelial-mesenchymal transition (12.8%). Concurrent presence of multiple resistance mechanisms was detected in 24.4% of the patient population. Within the C797S mutation subset, 65.0% exhibited C797S/T790M in cis arrangement, 30.0% demonstrated trans arrangement, and 5.0% showed mixed configurations. Laboratory validation established that MET amplification confers resistance via bypass activation of both ERK and AKT signaling cascades. The poorest clinical outcomes were observed among patients undergoing histological transformation (median overall survival from confirmed progression: 8.3 months).ConclusionRemarkable heterogeneity characterizes the resistance mechanisms emerging against osimertinib in EGFR T790M-positive lung adenocarcinoma, with EGFR secondary mutations, bypass signaling pathway activation, and histological transformation representing the primary categories. Detection of specific resistance mechanisms enables tailored subsequent therapeutic approaches, with potential outcome improvements achievable through combination strategies incorporating targeted agents or immunotherapy.
Sound scientific sample diversity will require attention to cultivating trust among populations underrepresented as biobank participants. While no particular group is the focus of this report, the observations presented may be particularly helpful for cultivating trust necessary for enrollment of underrepresented populations. Community engagement strategies indicate that such trust is built through relationships extending across the spectrum of biomedicine rather than focused exclusively on a particular research project. Central to these relationships are communication behaviors reflected in both research and clinical encounters. This ‘brief research report’ presents preliminary clinical research findings from a pilot analysis of return of genetic results conversations relevant to the cultivation of trust.
IntroductionAnterior cruciate ligament (ACL) rupture is a common orthopaedic disease in dogs, with varying prevalence and genetic susceptibility across different breeds. Here we investigate the association between genomic structural variation (SV) and ACL rupture risk in the Labrador Retriever and Rottweiler breeds.MethodsWe used 1,058 Labrador Retrievers (464 cases, 594 controls) and 108 Rottweilers (83 cases, 25 controls). Using breed‐specific de novo genome assemblies, we first characterized SV between Labrador Retriever and Rottweiler genomes to provide genomic context for breed-level differences. We then quantified runs of homozygosity (ROH) and evaluated the association between homozygosity measures (nROH, AVGROH, and FROH) and ACL rupture risk using breed‐specific and combined‐breed logistic regression models.ResultsThe association between homozygosity parameters and ACL rupture in the Labrador Retriever was not significant (P > 0.05 for all models). In contrast, inbreeding coefficient (FROH) was significantly associated with increased ACL rupture risk (OR = 2.011, 95% CI:1.120‐3.98, P‐value = 0.026) in the Rottweiler when sex and interaction effects were included in the model.ConclusionThese findings suggest a potential association between inbreeding and ACL rupture risk in Rottweilers. In addition, joint analysis of Labrador Retriever and Rottweiler data revealed multicollinearity between breed and homozygosity content, which highlights the heterogeneity of genetic risk factors across breeds. Our findings suggest that breed‐specific genetic models are crucial for understanding the genetic contribution to ACL rupture and for developing accurate genetic risk prediction tools. Given the relatively small and imbalanced Rottweiler dataset, independent validation in larger populations is warranted to further explore the potential breed‐specific genetic loci contributing to ACL rupture in the Rottweiler.
BackgroundDuchenne muscular dystrophy (DMD) is an X-linked recessive disorder caused by mutations in the DMD gene. Understanding the carrier frequency and mutation spectrum in specific populations is critical for genetic counseling and early intervention. However, data on DMD carrier frequency among women of childbearing age and early pregnancy in Yueyang City, China, remain limited. This study aimed to characterize the carrier rate and mutation profile to support preventive strategies and reduce disease incidence.MethodsA total of 25,611 women of childbearing age or early pregnancy from Yueyang City were enrolled. Combined next-generation sequencing and multiplex ligation-dependent probe amplification were used to detect pathogenic/likely pathogenic (P/LP) variants, copy number variants (CNVs), and small indels. Variants were classified per established guidelines. Carrier rates and geographical distribution were analyzed. Prenatal diagnosis was offered to identified carriers with follow-up to assess outcomes.ResultsTwenty-eight women were identified as P/LP carriers (0.11%), representing 25 distinct variants. CNVs constituted the majority (71.43%), with exon 45–55 deletions (64.29%) predominating over duplications (7.14%); notably, 13/18 CNVs clustered in this hotspot. SNVs and small indels accounted for the remaining 28.57%. Intra-regional variation was marked, with the highest rate in Yunxi District (0.74%). Additionally, 81 VUSs (51 distinct types) were detected, 66.67% being missense. One male fetus inheriting a maternal VUS developed DMD-like features postpartum. Overall, 12 variants (1 LP, 11 VUSs) were previously unreported, including a nonsense variant c.3502G>T (p.E1168*) classified as LP.ConclusionThis first population-based study in Yueyang City, China, characterized the DMD carrier frequency (0.11%) and mutation spectrum among women of childbearing age or in early pregnancy. It revealed geographical heterogeneity and a high prevalence of CNVs, especially exon 45–55 deletions. Crucially, it highlights the underappreciated screening value of VUS. We recommend focused attention on VUS, particularly those with Bayesian scores ≥3, in genetic counseling and prenatal diagnosis to improve preventive strategies and reduce DMD incidence.
Thyroid cancer is the most common type of endocrine malignancy, and its aggressive types are diagnosed at advanced stage due to limited treatment options. This study aimed to identify upregulated SLC7A5 across thyroid cancer cell types using an integrated transcriptomics approach. Total RNA was extracted from different samples. Differential expression analysis was performed through DESeq2. Functional enrichment analyses were performed to explore key pathways. The PPI network was built using the STRING database to investigate the functional relationships among significantly differentially expressed genes. Differential expression analysis revealed that SLC7A5 was significantly upregulated in KTC-1. GO and KEGG analyses were enriched with cell adhesion, protein binding, extracellular exosome, RNA processing, ECM-receptor interactions, and focal adhesion. The PPI network analysis showed the interaction of SLC7A5 with TERF1, CARD10, PSAT1, SIRPA, and MYC. Western blot analysis revealed that expression of mTOR was not elevated in KTC-1. Overall, these results could provide valuable insights for further validation in thyroid cancer therapy.
Glycogen storage disease type VII (GSD-VII), or Tarui disease, is a rare autosomal recessive disorder caused by biallelic loss-of-function variants in the PFKM gene encoding the muscle isoform of phosphofructokinase (PFK), a key enzyme of the glycolytic pathway. PFK deficiency impairs glycogen and glucose metabolism in skeletal muscle and erythrocytes, causing exercise intolerance, exertional myalgia, and myoglobinuria, and, in some cases, fixed proximal muscle weakness, as well as haemolytic anaemia. We report the case of an Italian woman with genetically confirmed GSD-VII harbouring a homozygous missense variant in PFKM (NM_000289.6:c.550C>T, p.Arg184Trp). This variant was previously identified in Wachtelhund dogs, a spontaneous animal model of PFK deficiency, but never reported in patients so far. PFK activity in skeletal muscle (PFKM) was found severely decreased and ultrastructural analysis revealed glycogen accumulation and mitochondrial alteration, supporting the pathogenetic role of the identified variant.
BackgroundHypoxia-driven vascular, immune, and metabolic remodeling is a key biological process involved in cardiovascular diseases, cancer, and other complex systemic disorders. Acute mountain sickness (AMS) is an acute manifestation of hypobaric hypoxia, but its systemic molecular features remain incompletely defined.MethodsWe performed integrated plasma proteomic and metabolomic profiling in 81 healthy Han Chinese male participants after rapid high-altitude exposure. Differential analysis, weighted gene co-expression network analysis (WGCNA), tissue-specific protein mapping, regulatory network reconstruction, machine learning, and druggability assessment were applied to characterize AMS-associated molecular alterations and identify candidate biomarkers and targets.ResultsMulti-omics profiling identified 3,137 proteins and 4,104 metabolites and showed clear separation between AMS and non-AMS participants. AMS was characterized by coordinated thrombo-inflammatory activation, coagulation-related disturbance, and metabolic reprogramming, including suppression of oxidative phosphorylation-related signatures. WGCNA identified symptom associated proteomic and metabolomic modules linked to headache severity, oxygen saturation, and hemodynamic traits. Tissue-specific protein mapping revealed a liver-centered but multi-organ circulating proteomic architecture, suggesting hepatic secretory remodeling with additional neural and immune-system contributions. Regulatory network analysis highlighted NOTCH1 as a candidate upstream regulatory hub, whereas druggability analysis prioritized NOTCH1 and the antioxidant-related protein GSTA1 as translational candidates. An mRMR plus logistic regression classifier integrating 15 proteomic features and SpO2 achieved good discriminatory performance, with an AUC of 0.968 in the training cohort and 0.913 in the test cohort.ConclusionThis study defines a multi-layer molecular framework of human acute hypoxic stress, linking vascular regulation, inflammation, coagulation, metabolic remodeling, tissue origin, and biomarker prioritization. These findings provide mechanistic insight into AMS and support multi-omics-based biomarker discovery and target prioritization in hypoxia-associated systemic diseases.
BackgroundFrequent intravitreal administration of antivascular endothelial growth factor Vascular endothelial growth factor agents remains a major limitation in the management of wet age-related macular degeneration (wAMD). This study evaluated whether suprachoroidal delivery of an engineered recombinant adeno-associated viral (rAAV)-aflibercept vector could achieve sustained, targeted expression with improved efficacy and safety compared with intravitreal administration.MethodsAL-001, an engineered rAAV vector expressing aflibercept, was developed and characterized. Its expression profile was first assessed in New Zealand white rabbits following suprachoroidal space (SCS) injection. Efficacy, pharmacokinetics, and safety were then evaluated in a nonhuman primate model of laser-induced choroidal neovascularization (CNV), comparing SCS and intravitreal (IVT) administration routes.ResultsAL-001 efficiently expressed aflibercept in relevant ocular cells in vitro. In rabbits, SCS administration produced sustained aflibercept levels in ocular tissues. In the nonhuman primate CNV model, a single SCS injection of AL-001 showed favorable efficacy to IVT injection and a notable mild inflammatory response. At week 4, grade IV lesion incidence was 0% (0/48) after SCS administration versus 14.3% (6/42) after IVT administration (absolute difference, −14.3 percentage points; 95% CI, 3.7%–27.8%; P = 0.0258). Throughout follow-up, mean leakage area and grade IV lesion incidence remained 0 with SCS, versus IVT peaks of approximately 0.3 mm2 and 33.0%, respectively, declining to 0.03 mm2 and 2.0% by day 100. Both the medium and high doses decreased pathological vascular leakage and subretinal hyperreflective material. Vector administration preceded laser-induced CNV modeling, demonstrating that sustained intraocular aflibercept expression in the retina and choroid provided durable antiangiogenic protection. Pharmacokinetic analysis confirmed distinct ocular exposure profiles between routes, with viral genomes confined predominantly to the injected eye and no significant systemic accumulation. AL-001 was well tolerated, without sustained intraocular pressure elevation or severe ocular inflammation, and only mild-to-moderate treatment-emergent adverse events. Low pre-existing anti-AAV2 immunity and time-dependent neutralizing antibody responses postdosing, informing a translational model for patient stratification and redosing feasibility.ConclusionSuprachoroidal administration of AL-001 is well tolerated and provides durable, targeted aflibercept expression with pronounced antiangiogenic efficacy. These results support AL-001 as a promising, long-acting therapeutic candidate for wAMD.
ObjectiveThis study aimed to assess the diagnostic yield, clinical indications, and utility of next-generation sequencing (NGS) testing since its implementation through collaboration between the University of Rijeka Faculty of Medicine and the Clinical Hospital Centre Rijeka.Materials and MethodsThis retrospective study included patients referred between 2018 and 2023 from the Clinical Hospital Centre Rijeka to the University of Rijeka Faculty of Medicine for genetic testing, primarily using exome sequencing.ResultsBetween April 2018 and December 2023, 412 patients were referred for exome sequencing, of whom 353 (85.7%) underwent diagnostic genetic testing. A notable increase in tests ordered was observed over time. Patients were most frequently referred from Pediatrics (55.0%), Neurology (29.5%), Cardiology (7.4%), Ophthalmology (3.4%), and others (4.7%). A diagnosis was confirmed in 103/353 patients, corresponding to an overall diagnostic yield of 29.2%, and an adjusted diagnostic yield of 27.2% after collapsing related individuals into single family units. In these confirmed cases, 83 distinct disorders involving 71 unique genes were identified, with most patients showing heterozygous variants and several recurrent disorders and genes. Variants of uncertain significance were reported in 35/353 (9.9%) patients.ConclusionThe 27.2% diagnostic yield demonstrates effective integration of NGS into tertiary clinical practice. The recent introduction of medical genetics specialization is expected to further improve referral quality, variant interpretation, and overall diagnostic outcomes.
