BackgroundAccurate determination of tandem thymine-adenine (TA) repeat numbers in the UGT1A1 promoter region (rs3064744) is essential for diagnosing Gilbert’s syndrome and personalizing therapy with toxic agents like irinotecan and atazanavir. However, traditional polymerase chain reaction (PCR) assays face severe limitations due to the AT-rich sequence and overlapping melting temperatures (Tm) of the highly homologous 7TA and 8TA alleles. In this context, melting curve analysis (MCA) employing fluorophore-quencher systems has emerged as a promising alternative. The purpose of this study was to develop a novel genotyping approach combining optimized aPCR-MCA analysis with an automated classifier to overcome the limitations posed by the differentiation of highly homologous alleles and to demonstrate its practical application, providing the distribution of rs3064744 genotypes across four regional cohorts of the Russian population.MethodsA specialized Dual Head 1D-convolutional neural network (1D-CNN) ensemble with Test-Time Augmentation (TTA) was developed. The model was trained and internally validated on 1,620 engineered plasmid samples, and independently evaluated on an external clinical test set of 440 unique patient genomic DNA specimens. Real-time PCR was performed on CFX96 and DTprime platforms. Additionally, population-wide screening was conducted on 997 archival clinical samples from Moscow, Sakha (Yakutia), Dagestan, and Rostov regions.ResultsWhile 5TA and 6TA alleles were easily separated, absolute Tm distributions of 7TA and 8TA alleles overlapped significantly, and non-uniform Tm shifts of 0.8 °C–1.4 °C occurred across platforms. Conventional absolute Tm thresholding was therefore inadequate. By assessing relative morphological curve divergence against co-amplified 7TA/7TA and 7TA/8TA reference anchors, the 1D-CNN ensemble neutralized instrument noise. It achieved 100% accuracy on internal validation and 100% concordance (440/440) with clinical reference pyrosequencing. Population screening revealed that Dagestan, Yakutia, and Rostov cohorts closely align with the European population. Rare 5TA and 8TA alleles were detected at low frequencies in Yakutia and Moscow.ConclusionCombining LNA-modified aPCR-MCA with a comparative 1D-CNN model successfully circumvents thermodynamic limitations and eliminates human operator bias. This integrated system offers an accessible, high-throughput, and clinically valid solution for routine UGT1A1 pharmacogenetic testing.
Hyperhomocysteinemia in adolescence typically prompts investigation for classical inborn errors of sulfur amino acid metabolism, including cystathionine β-synthase deficiency and cobalamin-dependent remethylation disorders. However, persistent elevations may also arise from interactions between common genetic polymorphisms and acquired nutritional conditions that alter one-carbon metabolism.Case presentationWe report an 18-year-old male with type 1 diabetes mellitus, celiac disease on a strict gluten-free diet, congenital unilateral sensorineural hearing loss, and persistent isolated hyperhomocysteinemia. At age 16, he presented with an acute visual field disturbance and right occipital cortical MRI changes suggestive of ischemia. Plasma homocysteine was persistently between 50 and 65 μmol/L.Extensive metabolic and genetic investigations, including targeted gene panels, whole-exome and research whole-genome sequencing, mitochondrial DNA sequencing, mitochondrial complex activities in fibroblasts, and fibroblast complementation, excluded classical homocystinuria and remethylation defects. Sequential trials of pyridoxine, hydroxocobalamin, and high-dose betaine produced modest or transient improvement. Re-analysis of exome data showed homozygosity for the common MTHFR c.665C>T (p.Ala222Val) variant. Family testing revealed that his father (TT) and mother (CT) had normal homocysteine (10.9 and 10.4 μmol/L), indicating that MTHFR TT alone is insufficient to cause a biochemical phenotype and functions as a susceptibility factor. Combined oral methylfolate (1,000 µg daily) and vitamin B12 (cyanocobalamin 1,000 µg daily) reduced homocysteine from 66 to 24.6 μmol/L in 8 weeks.ConclusionThis case illustrates multifactorial hyperhomocysteinemia arising from interactions between celiac disease-related micronutrient vulnerability and reduced MTHFR activity. Recognition of gene-nutrient interactions is important when classical metabolic disorders are excluded and may guide targeted therapy.
BackgroundImmune checkpoint inhibitor (ICI) therapy for oral squamous cell carcinoma (OSCC) yields objective responses in fewer than 20% of patients, underscoring the urgent need for novel predictive biomarkers beyond PD-L1 expression and tumor mutational burden (TMB). Ferroptosis, an iron-dependent oxidative cell death program, has emerged as a dual-function regulator of tumor immunity. Whether ferroptotic dysregulation of the PDL stromal compartment and MT1/MT2 suppression constitute novel mechanistic determinants of ICI resistance in OSCC remains poorly understood and warrants mechanistic investigation.MethodsWe performed a single-cell RNA sequencing (scRNA-seq) analysis of a publicly available multi-regional OSCC dataset (GEO: GSE198315; adjacent non-tumor [NT], tumor core [TC], and metastatic lymph node [mLN]; 22,371 quality-controlled cells), encompassing dimensionality reduction, pseudotemporal trajectory reconstruction, immune checkpoint gene profiling (PD-1/PD-L1/CTLA-4/TIM-3/LAG-3), ferroptosis–immune crosstalk inference, and intercellular communication modeling. To experimentally validate key computational findings, we performed in vitro RT-qPCR experiments in primary human PDL fibroblasts exposed to oxidative conditioned medium (OCM), quantifying the expression of GPX4, ACSL4, MTNR1A (MT1), MTNR1B (MT2), and CD274 (PD-L1) at 24 h and 48 h.ResultsscRNA-seq revealed that OCM-exposed PDL cells exhibited a 3.2-fold elevation in the ferroptotic index, co-occurring with profound MT1/MT2 suppression and circadian axis disruption. Ferroptosis-susceptible PDL subpopulations showed coordinated upregulation of immunosuppressive ligands (PD-L1, CD47, and Galectin-9), reduced CD8+ T-cell infiltration scores, and enhanced myeloid-derived suppressor cell (MDSC) and tumor-associated macrophage (TAM) recruitment signals, suggesting a mechanistic association between PDL stromal ferroptosis and immune checkpoint-mediated immune evasion. In vitro RT-qPCR validation in primary human PDL fibroblasts (ATCC PCS-201-018) exposed to OCM confirmed significant downregulation of GPX4, SLC7A11 (xCT), MTNR1A (MT1), and MTNR1B (MT2), concurrent with the upregulation of ACSL4 and CD274 (PD-L1) at both 24 h and 48 h (all p < 0.05), directly corroborating the scRNA-seq-predicted ferroptosis–melatonin receptor–immune checkpoint co-regulatory axis.ConclusionWe establish a mechanistically grounded framework suggesting that PDL stromal ferroptosis and MT1 suppression constitute novel components of the OSCC tumor immune evasion landscape. In vitro RT-qPCR validation supports the ferroptosis–melatonin receptor–immune checkpoint co-regulatory axis as a candidate therapeutic target to overcome immunotherapy resistance in oral cancer, pending prospective clinical validation.
BackgroundSarcopenia is an emerging complication of type 2 diabetes mellitus (T2DM) characterized by progressive loss of skeletal muscle mass and function. Diabetic cardiomyopathy (DCM) is a distinct cardiac disease in T2DM patients independent of coronary artery disease and hypertension. Whether sarcopenia independently predicts DCM risk in T2DM patients, and whether shared molecular pathways including systemic inflammation and metabolic dysregulation underlie this association, remains unclear.MethodsThis retrospective cohort study enrolled 400 T2DM patients admitted to the First Affiliated Hospital of Chongqing Medical University between February 2022 and February 2026. Sarcopenia was diagnosed using AWGS 2019 criteria as the primary framework, with concurrent evaluation against the updated AWGS 2025 criteria. DCM was diagnosed by Doppler echocardiography in T2DM patients with myocardial dysfunction after excluding other cardiac etiologies, per clinically established criteria (2024 ESC DCM position statement); this echocardiographic approach, while standard practice, does not carry the tissue-characterization precision of cardiac MRI. Multivariate logistic regression (three sequentially adjusted models), propensity score matching, and prespecified subgroup analyses were performed.ResultsSarcopenia was identified in 137/400 patients (34.3%) and DCM in 113/400 (28.3%). DCM prevalence was significantly higher in sarcopenic versus non-sarcopenic patients (44.5% vs. 19.8%, p < 0.001). After full adjustment, sarcopenia remained independently associated with DCM risk (adjusted OR = 2.70, 95% CI: 1.72–4.24, p < 0.001; AUC-ROC = 0.812). The association was consistent across all subgroups (all p-interaction > 0.05). Sarcopenic patients exhibited elevated hs-CRP, NT-proBNP, ferritin, and uric acid, with lower vitamin D levels.ConclusionSarcopenia is independently associated with significantly elevated DCM risk in T2DM patients; the cross-sectional design precludes definitive causal inference and directionality requires prospective longitudinal confirmation. Shared mechanisms—including systemic inflammation, elevated ferritin and uric acid, and potentially common genetic regulatory pathways (hypothesized on the basis of existing literature)—may underlie the muscle–heart dysfunction axis. Routine sarcopenia screening using AWGS 2019 criteria—consistent with the updated AWGS 2025 framework—may facilitate early identification of T2DM patients at elevated DCM risk.
IntroductionFeed efficiency (FE) is a complex trait which determines livestock production profitability, yet the molecular mechanisms behind it remain unclear. This study investigated the blood transcriptomic profile of lambs, alongside genotype data with the aim to uncover the genetic basis of FE traits such as absolute dry matter intake (DMIabsolute), DMI adjusted for body size (DMIadjusted), average daily live weight gain (ADG), and residual feed intake (RFI).Materials and MethodsBulk RNA-Seq and genotype data were analysed using three complementary approaches: differential gene expression (DGE) analysis, weighted gene co-expression network analysis (WGCNA), and cis-expression Quantitative Trait Loci (cis-eQTL) mapping. These methods were used independently to identify genes and regulatory networks associated with FE traits and to investigate evidence supporting multi-trait candidate gene selection.ResultsDGE analysis revealed 2, 24, 85 and 4 differentially expressed genes for DMIabsolute, DMIadjusted, ADG, and RFI (Padjusted < 0.05), functionally enriched in sensory perception, ATP-dependent chromatin remodeling, Notch signaling and immune response pathways. 9 gene modules significantly associated with the FE traits (P ≤ 0.05) with correlations ranging from r = -0.56 to 0.49, were identified using WGCNA. Single nucleotide polymorphism (SNP)-level cis-eQTL analysis identified 93 eSNPs associated with 74 genes (false discovery rate (FDR) < 0.05), while permutation-derived gene level analysis identified 280 eGenes (FDR < 0.2, empirical P < 0.03). Across the three analyses, applying thresholds of DGE (Padjusted < 0.05), WGCNA (correlation, P ≤ 0.05), and cis-eQTL gene-level significance (empirical P < 0.05), multiple overlapping genes were identified including DNMT3A, KANSL1, NCOR1 for DMIadjusted, ACOX2, FANCF, CIMIP2B, LOC101115106, ARMH2, LOC132657496 for ADG, and LOC114114576 for RFI representing regulators of variations in FE.DiscussionThe integration of DGE, WGCNA, and cis-eQTL analyses identified key genes and regulatory mechanisms associated with variation in FE traits. These results highlight that integrated multi-trait candidate gene identification approaches can reveal key genes that lower feed intake while maintaining animal growth, supporting breeding strategies aimed at improving efficiency and long-term economic sustainability in sheep.
BackgroundNeutrophil extracellular trap-driven necrosis-related genes (NRGs) and inflammation-related genes (IRGs) are crucial in mitigating or inhibiting cancer progression in breast cancer patients. The interaction between NRGs and IRGs in breast cancer remains unclear. Thus, identifying prognostic genes associated with NETosis and inflammation in breast cancer may offer a novel approach to improving the outcome of breast cancer.MethodsGenes with statistically significant expression levels and correlations with IRGs and NRGs scores were selected as candidate genes, and the protein-protein interactions of the encoded proteins were explored. Subsequently, prognostic genes were further identified and build the risk model. Lastly, independent prognostic factors were determined through independent prognostic analysis, a prognostic model was established, and the immune microenvironment and drug sensitivity were analyzed.ResultsThe study identified ZMYND10, IL12B, CXCL13, TFF1, LTB, and SPIB as prognostic genes. Additionally, risk score and three clinical features, including age, were established as independent prognostic factors. A prognostic model with moderate predictive accuracy was developed. Further analysis revealed that six prognostic genes were considerably correlated with differential immune cells, among which CXCL13, IL12B, LTB, and SPIB were considerably positively correlated with most differential immune cells. Additionally, 18 drugs were considerably associated with the risk score, including six drugs such as Metformin and Thapsigargin, which could potentially be used to treat breast cancer.ConclusionThis study constructed a risk model and a nomogram for breast cancer prognosis using bioinformatics methods, and analyzed prognostic genes of breast cancer, which will be helpful to the improvement of breast cancer’s outcome and the development of clinical medicine.
Amyotrophic lateral sclerosis (ALS), the most common type of motor neuron disease, primarily manifests as progressive weakness, atrophy, fasciculations, bulbar palsy, and pyramidal tract symptoms. Accumulating evidence indicates that the pathological spectrum of ALS extends beyond the pyramidal and neuromuscular motor systems, involving additional brain regions, manifesting as ALS-plus syndrome. We present a case of an elderly woman with bulbar-onset ALS accompanied by cerebellar manifestations and an intermediate-length CACNA1A allele. Based on the Gold Coast criteria, ALS diagnosis was made. Notably, the patient exhibited cognitive impairment and a positive Romberg sign, suggesting a broader phenotypic spectrum. Genetic analysis showed a CAG repeat genotype of 10/20 in the CACNA1A gene. The patient’s son carried a 14/20 genotype and displayed isolated cerebellar ataxia without motor neuron features. We reviewed the literature on spinocerebellar ataxia (SCA) co-occurring with motor neuron disease and discussed the uncertain significance of the intermediate-length CACNA1A allele in this context, weighing coincidental co-occurrence against a potential causal link. To our knowledge, this case is the first reported instance of an intermediate-length CACNA1A allele co-occurring with ALS in Chinese population, although the association between the allele and ALS remains unclear.
ObjectiveTo characterize protein expression of NLRP3 inflammasome pathway components (NLRP3, TXNIP, ASC, IL-1β, IL-18, Caspase-1) in failing myocardium alongside exploratory mRNA profiling, elucidate their correlation with gut microbiota 16S rRNA gene profiles and the metabolite trimethylamine N-oxide (TMAO), and evaluate how dietary protein restriction and probiotic intervention modulate these pathways to influence heart failure progression.MethodsFive groups of male SD rats were established: Control, HF, HF + Pro, LHF, and LHF + Pro, using abdominal aortic constriction. Comprehensive genomic and molecular analyses included: (1) quantitative real-time PCR (qRT-PCR) profiling of six key inflammasome genes (NLRP3, TXNIP, ASC, IL-1β, IL-18, Caspase-1); (2) Western blot protein quantification of the NLRP3 pathway; (3) gut microbiota 16S rRNA gene sequencing (V3-V4 region, Illumina NovaSeq); (4) serum biomarker enzyme-linked immunosorbent assay (IL-18, IL-1β, TNF-α, brain natriuretic peptide, TMAO); and (5) histopathological and ultrastructural analysis of myocardial tissue.ResultsSerum IL-18 protein levels were significantly elevated in the LHF group compared to controls (P < 0.05) by ELISA, with the most pronounced increase observed under dietary protein restriction; however, IL-18 mRNA expression by qRT-PCR showed directionally consistent but statistically non-significant trends across groups (P = 0.929, n = 3 per group). TMAO levels were decreased in HF and HF + Pro groups but paradoxically elevated in the LHF group, a finding discussed in detail in the context of dietary substrate availability and hepatic FMO3 activity. Western blot results showed that the expression of NLRP3, TXNIP, ASC, IL-1β, and IL-18 proteins increased in all heart failure groups compared to the control group, with the most significant increase in the low-protein diet group. Pathological examination revealed increased myocardial fibrosis in heart failure groups, which was further aggravated by low-protein diet, while probiotic intervention partially improved these pathological changes.ConclusionHeart failure is associated with upregulation of NLRP3 inflammasome proteins (NLRP3-TXNIP-ASC-IL-1β/IL-18 axis) alongside gut microbiota dysbiosis; mRNA-level trends were directionally consistent but did not reach statistical significance. Low-protein diet markedly amplifies inflammasome protein expression and cardiac remodeling, while probiotic supplementation is associated with reduced NLRP3 pathway protein expression through microbiome restoration. These findings suggest NLRP3-related protein signatures as candidate biomarkers and potential therapeutic targets in heart failure, warranting further mechanistic investigation.
BackgroundDiffuse large B-cell lymphoma (DLBCL), a common type of non-Hodgkin lymphoma (NHL), is associated with heterogeneous clinical outcomes, with a subset of patients experiencing refractory disease or relapse, underscoring the need for novel biomarkers to refine risk stratification. This study aimed to investigate the biological role and clinical significance of synaptotagmin-like 4 (SYTL4) in DLBCL.MethodsRNA-seq data from TCGA and GTEx were normalized (TPM) and log2-transformed. Survival analysis stratified patients based on the median SYTL4 expression level (cutoff = 0.304), with Kaplan-Meier curves and Cox regression analysis performed. Differentially expressed genes (|log2FC|>1, FDR<0.05) underwent functional annotation (GOKEGG, GSEA) and PPI network constructed. Immune infiltration was assessed via ssGSEA. Formalin-fixed paraffin-embedded (FFPE) tissue blocks from testicular DLBCL patients were obtained. A tissue microarray was constructed. Immunohistochemistry with anti-SYTL4 antibody was performed, and digital images were scored semi-quantitatively (0–3+) by two pathologists.ResultsRNA-seq analysis revealed a significant upregulation of SYTL4 expression in DLBCL patients compared to healthy donors, observed in both tissue and peripheral blood samples, a finding further validated by immunohistochemical staining. Survival analysis revealed that elevated SYTL4 expression was correlated with an unfavorable prognosis (P = 0.037), and multivariate Cox regression confirmed that high SYTL4 expression was an independent prognostic factor (HR = 25.541, P = 0.017). Differential gene screening identified 1,074 differentially expressed genes, including 628 upregulated genes and 446 downregulated genes. Enrichment analysis revealed a significant association of SYTL4-related genes with pathways involved in cell–cell adhesion and the immune response. Protein‒protein interaction (PPI) network analysis revealed interactions between SYTL4 and key regulators such as phosphatase and actin regulator 2 (PHACTR2), suggesting its potential role in DLBCL progression.ConclusionThese findings highlight the potential of SYTL4 as a promising diagnostic marker, prognostic biomarker, and therapeutic target. Further exploration of its applicability in immunotherapy may lead to the development of personalized treatment strategies for DLBCL patients.
BackgroundThrough a more precise and safer means of diagnosing foetal aneuploidies, non-invasive prenatal testing (NIPT) with cell-free DNA (cfDNA) has revolutionized prenatal screening and removed the necessity of invasive diagnostic procedures. The aim of the systematic review was to determine the limits of, diagnostic accuracies, and clinical value of cfDNA-based NIPT in different foetal aneuploidies.MethodsWe conducted a systematic review of studies assessing the diagnostic performance of cfDNA-based NIPT for detecting Trisomy 21 (T21), Trisomy 18 (T18), Trisomy 13 (T13), sex chromosome aneuploidies (SCA), and copy number variations (CNVs)The studies included were prospective, retrospective, or diagnostic accuracy studies that compared cfDNA results with invasive prenatal diagnostic tests, including amniocentesis, CVS, karyotyping, and chromosomal microarray analysis (CMA).ResultsThe number of studies reviewed was 20, and it involved a total of more than 67,500 individuals. NIPT utilizing cfDNA has proven sensitive and specific in T21, T18, and T13 and an excellent accuracy level in most risk populations. In the case of T21 there was 100% sensitivity and 100% specificity of cfDNA in various studies. For Trisomy 18 the sensitivity was between 92.3% to 100% with a high mean specificity of 99.6%–100%. The sensitivity was also good, with Trisomy 13 diagnostic performance, as it lies between 78.6% and 100% and a specificity of 99.8 to 100 percent. However, SCA and CNVs showed more variable performance with a sensitivity of between 75 to 100 per cent in SCA and between 53.6 and 97.7 per cent, respectively. The presence of discordant outcomes, particularly in relation to SCA and microdeletions, was a problem area and underscored the importance of genetic counseling and standardized procedures.ConclusioncfDNA-based NIPT is a highly effective and non-invasive tool for screening common trisomies but has limitations in detecting SCA and CNVs. While the screening’s integration into clinical practice is beneficial, it is essential to address the limitations of discordant results and the psychological impacts on patients.Systematic Review Registrationhttps://www.crd.york.ac.uk/PROSPERO/view/CRD420261277611, identifier CRD420261277611.
The clinical adoption of pharmacogenetics has advanced unevenly despite rapid progress in genomic discovery. Genome-wide association studies and next-generation sequencing have substantially improved our understanding of the polygenic and regulatory architecture of complex diseases, yet translating these insights into clinically actionable pharmacogenetic strategies remains challenging. In this opinion article, we argue that targeted genetic approaches, traditionally represented by candidate gene association studies, should be reconsidered within a modern genomic framework. While such approaches proved limited as discovery tools for complex disease risk, they may retain translational value when integrated with genome-wide evidence and multi-omics prioritization. In pharmacogenetics, pathway-focused investigations and targeted validation studies can help bridge the gap between large-scale genomic discovery and clinical implementation. Within this framework, pharmacokinetic pharmacogenes (e.g., CYP2D6, CYP2C19) and pharmacodynamic phenotypes (e.g., treatment response, antipsychotic-induced weight gain) represent fundamentally different translational challenges, differing in effect size, biological complexity, and clinical readiness. We propose that the strategic integration of genome-wide analyses, sequencing, multi-omics data, and hypothesis-driven genetic studies may accelerate the clinical adoption of pharmacogenetics and contribute to more effective precision medicine in psychiatry.
Glioblastomas are aggressive, heterogeneous tumors that present significant challenges in both diagnosis and treatment. Despite advances in surgical resection, radiotherapy, and chemotherapy with temozolomide (TMZ), the prognosis for glioblastoma patients remains poor, largely due to tumor heterogeneity and resistance mechanisms, such as genetic mutations in DNA repair pathways. To address these specific heterogenous qualities of glioblastoma, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for characterizing glioblastoma tumors, enabling the identification of subpopulations that respond differently to treatment. However, utilizing the vast amount of data generated by scRNA-seq poses challenges in clinical applications. To overcome this challenge, computational models have been introduced to more effectively process patient scRNA-seq data into more digestible information for clinicians. More specifically, advanced deep learning approaches show promise for processing and analyzing patient scRNA-seq data, enhancing informed treatment approaches for highly heterogenous glioblastoma. This review aims to explain how scRNA-seq can be used to identify important areas of glioblastoma treatment resistance, evaluate current glioblastoma scRNA-seq-based deep learning models, and outline relevant training datasets to overcome patient scRNA-seq data availability limitations. Ultimately, these deep learning models can be utilized by researchers and clinicians to provide more informed and precise treatment to glioblastoma patients.
BackgroundWilms tumor (nephroblastoma) is a pediatric renal malignancy driven by disrupted nephrogenesis, yet its transcriptomic relationship with ferroptosis and immune remodeling remains poorly characterized.MethodsWe analyzed GSE66405 microarray data (28 Wilms tumor samples) together with an oral cancer 10X single-cell reference dataset to evaluate six biologically defined modules: developmental/nephrogenesis, Wnt/beta-catenin, ferroptosis/iron metabolism, immune/inflammatory, extracellular matrix, and cell-cycle. Module scores were calculated as mean z-scores across curated gene sets, and inter-module Pearson correlations, co-expression network analyses, and unsupervised clustering were performed in Python using scipy, scikit-learn, networkx, and matplotlib.ResultsDevelopmental and Wnt programs formed the central transcriptomic axis of Wilms tumor, with WT1, SIX1, SIX2, PAX2, and CTNNB1 as hub genes (Pearson r = 0.868 between module scores, P < 0.001). The developmental module showed the strongest correlation with ferroptosis (r = 0.920, P < 0.001), while ferroptosis and immune modules were also tightly linked (r = 0.851, P < 0.001). Ferroptosis-related genes (HMOX1, FTL, SLC40A1, TFRC, GPX4, SLC7A11) and immune markers (CD68, CD163, CD8A, GZMB) were detected as secondary remodeling modules associated with the developmental core. Cross-cancer comparison revealed partial conservation of ferroptosis and immune module architecture in the oral cancer reference, whereas the developmental-Wnt axis remained Wilms tumor-specific. In vitro qRT-PCR validation in WiT49 (Wilms tumor) and CAL-27 (oral squamous cell carcinoma) cell lines confirmed differential ferroptosis gene expression: HMOX1 and TFRC were significantly upregulated in WiT49 cells (p < 0.001), while GPX4 and SLC7A11 were relatively higher in CAL-27 cells (p < 0.01), corroborating lineage-specific iron metabolism remodeling.ConclusionThese results link developmental dysregulation, iron metabolism, and immune remodeling in Wilms tumor and identify candidate modules for future functional validation. The developmental-Wnt axis constitutes a Wilms tumor-specific transcriptomic core, while ferroptosis and immune programs represent partially conserved stress-response modules that may offer cross-lineage therapeutic relevance. In vitro qRT-PCR experiments in WiT49 and CAL-27 cells corroborated these transcriptomic findings, confirming lineage-differential expression of core ferroptosis regulators across the two cancer contexts.
BackgroundThe GRIA3 gene is located on the X chromosome and encodes a subunit (GluR3) of the a-amino-3- hydroxy-5-methylisoxazole-4-propionic acid receptor (AMPAR). The pathogenic variants of GRIA3 are mostly associated with neurodevelopmental disorders. Patients were overwhelmingly male and presented mainly with intellectual disability, dystonia, epilepsy and other symptoms.MethodsIn this study, we reported a pedigree that carried a novel splicing site variant of GRIA3 (c.268 + 1G>C) by whole exome sequencing (WES) and co-segregation analysis. Three affected family members (two males and one female) not only showed intellectual disability but also presented significant psychiatric symptoms and spatial memory deficits. The minigene assay further confirmed that this variant lead to exon 2 skipping.ResultsAccording to ACMG guidelines, We reclassified previously variant of unknown significance (VUS) into “likely pathogenic” through co-segregates analysis and minigene assay.ConclusionIt is worth noting that, unlike previous reports, our patients mainly manifested as intellectual disability combined with psychiatric symptoms, expanding the known phenotypic spectrum of GRIA3 gene. Moreover, this variant is the first reported, enriching the database and providing additional evidence to support genetic counselling and prenatal diagnosis.
Arthrobacter species are widely distributed in cold environments and are recognized for their ability to withstand multiple environmental stressors. Here, we report the whole-genome sequence of Arthrobacter sp. R5, a red-pigmented and UV-resistant bacterium isolated from shallow lake sediments collected at Edmonson Point, Antarctica. Whole-genome sequencing was performed using the Illumina NovaSeq 6000 platform, and the genome was assembled and annotated using the TORMES workflow. The assembled genome comprises 4,145,062 bp with a GC content of 67.78% and contains 3700 predicted coding sequences, 57 tRNAs, three rRNA genes, and one tmRNA gene. Functional classification based on Clusters of Orthologous Groups (COG) revealed a predominance of genes involved in transcription, amino acid and carbohydrate metabolism, signal transduction, and replication, recombination and repair. The genome harbours several genes associated with DNA damage repair, including photolyases, the UvrABC nucleotide excision repair system and the UmuCD SOS response system, which may contribute to the UV resistance phenotype of strain R5. Genome mining further identified multiple biosynthetic gene clusters, including terpene-associated regions containing genes related to carotenoid biosynthesis, supporting the genetic potential underlying the characteristic red pigmentation of this strain. The genomic dataset presented here provides a valuable resource for investigating the molecular mechanisms of environmental adaptation in Antarctic bacteria and for exploring the biotechnological potential of stress-protective metabolites produced by polar microorganisms.
Microbial phytases are crucial to organic phosphorus mineralization in marine phosphorus cycle, however, phytases from deep-sea bacteria remain poorly characterized. Here, we isolated and cultured a phytate-hydrolyzing Winogradskyella sp. 266wxhm from sponge Hymeniacidon sp. collected at a depth of 2435 m in the South Atlantic Ocean. The strain 266wxhm showed the highest similarity of 16S rRNA gene with Winogradskyella poriferorum UST030701-295ᵀ (96.61%), and the average nucleotide identity (ANI) was 76.90% with W. poriferorum UST030701-295ᵀ. These results suggest that strain 266wxhm represents a novel species of Winogradskyella. Whole-genome sequencing revealed a single circular chromosome of 3.96 Mb with a GC content of 33.33%, containing 3572 genes, including 3512 CDSs. Genes targeting phosphate uptake and regulation, organic phosphorus turnover, polyphosphate metabolism, and phosphonate-associated metabolism were identified. Notably, A.266wxhm_GM001357 was identified and annotated as a gene encoding 3-phytase (K01083/EC 3.1.3.8), containing conserved residues associated with Ca2+ coordination and structural stabilization, and belonged to the β-propeller phytase family. Finally, recombinant expression assays of A.266wxhm_GM001357 confirmed the phytase activity. This study provides microbial evidence for phytate-derived phosphorus mineralization in the deep sea.
While constructed treatment wetland systems (CTWS) and genomics have been identified as viable remediation options for oil sands processed-affected water, researchers have paid limited attention to the priorities of affected groups. To address this gap, we used focus groups to explore the perspectives on CTWS and genomics held by Indigenous Peoples, oil and gas industry employees, CTWS and genomics researchers, and government regulators and policymakers affected by oil sands remediation in northern Alberta. We identify six key concerns: confusion about the options themselves; challenges with communication about the options; differing perspectives on naturality; differing risk tolerances; questions about long term effects and who will maintain liability; and cultural impacts to Indigenous Peoples. Importantly, participants identified barriers related to ethical, legal, social, environmental, and governance implications, often referred to as ELSI, that affect their participation in decision-making about genomics-enhanced oil sands remediation. We recommend directions for improving meaningful engagement and participation.
Introduction:Major depressive disorder (MDD) and obesity are intersecting global crises. Despite observational links, a clinical paradox persists: antidepressants often improve metabolic status, while weight loss rarely alleviates core depressive symptoms. This prompts closer examination of whether the depression-obesity relationship reflects asymmetric genetic architecture, shared liability, or statistical constraints that obscure definitive conclusions. Methods:We developed an integrative multi-omics framework leveraging large-scale population data from the National Health and Nutrition Examination Survey (NHANES) and East Asian genetic data. Epidemiological regression was applied to NHANES to characterize real-world phenotypic cross-talk. We utilized bidirectional Mendelian randomization (MR) to explore the direction of association, targeted summary-data-based MR (SMR) with heterogeneity in dependent instruments (HEIDI) testing to prioritize candidate functional genes, and single-cell RNA sequencing (scRNA-seq) of regulatory T cells (Tregs). In silico cell composition adjustment and virtual knockout (VKO) simulations were implemented to distinguish intrinsic cellular remodeling from compositional shifts and to infer convergent downstream programs. Results:Bidirectional MR yielded a nominally significant association from MDD to obesity risk (β = 0.0458, P = 0.0209), whereas the reverse path was inconclusive due to low statistical power (<10%), precluding definitive conclusions about directionality. SMR/HEIDI identified multiple FDR-significant obesity-associated genes, including NT5C2, ACYP2, and TMEM180, whereas on the depression side only ACAT1 reached nominal significance, positioning it as a borderline hypothesis-generating candidate. Cell composition adjustment suggested that transcriptional signals reflected intrinsic remodeling, preserving up to 98% of effect sizes for top candidates. At the molecular level, the conditions diverged: obesity risk was dominated by immune-compartment inflammation and post-transcriptional splicing dysregulation, whereas MDD risk was characterized by ribosomal translation perturbations. Strikingly, VKO simulations revealed convergence on a shared downstream program anchored in cytoskeletal reorganization and E2F-target modulation. Exploratory druggability screening nominated FDFT1 (with a phase 3 inhibitor) and ADORA2A as potential repurposing candidates requiring experimental validation. Conclusion:Our findings provide a hypothesis-generating reframing of the traditional comorbidity model, suggesting that divergent molecular programs may converge on shared pathways. Although the full extent of bidirectional genetic relationships remains unconfirmed, these findings offer a preliminary foundation for exploring therapeutic strategies at the mood-metabolism interface.
