International Journal of Molecular Sciences最新文献

Genetics strongly impacts the course of metabolic dysfunction-associated steatotic liver disease (MASLD), with the I148M Patatin like phospholipase domain containing 3 (PNPLA3) variant representing the main modifier. Fat accumulation in the hepatic lobule, strongly enhanced by this SNP, may be influenced by the liver's zonation. Therefore, we applied spatial transcriptomics to investigate the metabolic processes across portal (PZ)-central (CZ) zones in I148M PNPLA3 carriers. Visium CytAssist technology was applied to liver biopsies from MASLD patients sharing similar disease severity, who were wild-type (WT) or homozygous for the I148M variant (Discovery cohort, n = 4). The distribution of steatosis, inflammation, and fibrosis was assessed in the liver biopsies of MASLD patients, stratified according to the I148M variant (validation cohort, n = 100). At the Visium-LOUPE browser, we spatially mapped PZ and CZ hepatocytes (HEPs), revealing higher lipid turnover, glucose signaling, and lower mitochondrial activity in I148M-PZ-HEPs compared to 148M-CZ-HEPs. Thus, the I148M variant could unbalance the physiological hepatic zonation boosting steatosis development in PZ, consequently inducing mitochondrial dysfunction. The unsupervised analysis confirmed the altered metabolic pattern among CZ and PZ in patients carrying the variant. Interestingly, PNPLA3 expression was higher in I148M-PZ, which also showed an enrichment of non-parenchymal cells, thus possibly explaining the more severe injury in this area. Finally, in the validation cohort, we observed a pronounced PZ distribution of steatosis, inflammation, and fibrosis in I148M PNPLA3 subjects compared to WT, confirming the spatial data. The I148M variant contributes to the metabolic switching across different hepatic zones and represents a new clinical perspective by defining a specific histological pattern of MASLD.

Cystic fibrosis (CF) is characterized by neutrophil-driven airway inflammation and acute respiratory events (AREs) that contribute to progressive lung damage. AREs are clinically heterogeneous and often occur without measurable changes in lung function. This study aimed to evaluate the utility of molecular airway inflammatory markers for detecting AREs in school-age children with CF. We performed a secondary analysis of a prospective observational study of children with CF (ages 6.7-16.8 years) followed for two years. Sputum samples were collected from 50 participants during stable visits and AREs. Concentrations of 14 inflammatory cytokines were measured using ELISA and multiplex assays. Associations with lung function (ppFEV₁ and lung clearance index [LCI]) and time to next ARE were assessed. A total of 179 sputum samples were analyzed, including 64 collected during AREs. Calprotectin, interleukin-8 (IL-8), and IL-1β were increased during AREs compared with stable visits, although concentrations frequently remained within ranges observed at stable visits. Other cytokines, including GM-CSF, IL-17A, IL-1α, TNF-α, and SPLUNC-1, were predictive of shorter time to subsequent AREs. No biomarker correlated with lung function measures. These findings indicate that airway inflammatory cytokine changes are associated with clinically diagnosed AREs but not with pulmonary function, supporting their potential role as complementary biomarkers in CF care.

High-grade serous ovarian carcinoma (HGSOC) is characterised by profound genomic instability and limited durable responses to standard therapy, leading to poor prognosis. The use of next-generation sequencing technologies has improved understanding of its molecular landscape, revealing consistent Tumour Protein p53 (TP53) mutations, homologous recombination defects, pathway alterations, and epigenetic dysregulation. Such genomic profiling now underpins the classification criteria between the ovarian cancer subtypes described by the Cancer Genome Atlas. Widespread chromosomal instability and pathogenic variants in multiple genes distinguish HGSOC from other subtypes of ovarian cancer and, further, from low-grade serous ovarian cancer. Importantly, the new-found understanding of the genomic landscape of HGSOC guides the use of platinum-based chemotherapies and Poly(ADP-ribose) Polymerase (PARP) inhibitors, with homologous recombination deficiency emerging as a cancer vulnerability that enhances treatment response. A combined multi-omics approach integrates transcriptomics, proteomics, metabolomics, and epigenomics to further the understanding of the characteristics, therapeutic targets and treatment resistance within HGSOC. Despite these advances, major challenges persist, including intratumoural heterogeneity and the poor diversity of genomic datasets. Artificial Intelligence (AI) technology, Clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing, neoantigen-guided immunotherapy and ovarian cancer vaccination indicate a promising future for genomics-guided interventions and support the integration of genomics within multi-omic approaches to improve HGSOC outcomes.

Pathogenic variants in the thyroid-stimulating hormone receptor gene (TSHR) contribute to a wide spectrum of thyroid dysfunctions, ranging from congenital hypothyroidism to thyrotropin resistance. With the advancement of bioinformatics algorithms for variant effect prediction, assessing the pathogenic potential of variants has become increasingly important. This study aimed to investigate the pathogenic effects of TSHR variants classified as variants of uncertain significance (VUSs) in the gnomAD v4.1.0 database. TSHR variants listed in gnomAD v4.1.0 were retrieved and filtered to select missense VUSs based on ClinVar classifications. Multiple bioinformatics tools were used to assess the secondary and three-dimensional structures of the TSHR, as well as protein stability, evolutionary conservation, and molecular dynamics simulations. A total of 2760 TSHR variants were found in gnomAD v4.1.0, including 75 frameshifts, 80 splice-sites, 265 in the 3' and 5' untranslated regions, 422 synonymous, 892 others, and 1026 missense variants. Among these, 68 missense VUSs were identified and selected for bioinformatics analysis. Three variants (p.Cys29Trp, p.Leu57Pro, and p.Phe97Ser) were consistently predicted to be pathogenic by all the bioinformatics tools used. All three variants were located within the leucin-rich repeat domain extracellular region of the TSHR and within a highly conserved region across species. Molecular dynamics simulations for mutant proteins (p.Cys29Trp, p.Leu57Pro, and p.Phe97Ser) reveal structural instability in comparison to the wild protein. Comprehensive bioinformatics analysis revealed that three TSHR missense VUSs exhibited pathogenic potential. These variants may contribute to thyroid dysfunction by affecting the receptor's structural and signalling integrity.

Drought stress induces pronounced metabolic and transcriptional reprogramming of glucosinolate (GLS) biosynthesis in Brassica oleracea. An integrative approach combining HPLC-based quantification of individual GLSs, quantitative real-time PCR of core biosynthetic and regulatory genes, correlation-based network analysis, and in silico promoter characterization was applied to evaluate drought responses across genetically diverse accessions. Drought triggered strong, accession-specific shifts in GLS composition, with sinigrin content increasing from 35.9% to 55.1% in BR1 and glucoerucin reaching up to 80.2% in CCP1, while indolic GLSs such as glucobrassicin and neoglucobrassicin accounted for >75% of total GLSs in CV2 and CCP3. Hierarchical clustering separated accessions into four distinct drought response clusters independent of morphotype. Correlation analysis revealed drought-induced rewiring of GLS interdependencies, characterized by strengthened positive associations among aliphatic GLSs (r > 0.75). Gene expression profiling identified conserved MYB-centered regulatory modules (MYB28, MYB29, MYB34, MYB122) alongside strong accession-specific induction of CYP79F1 (up to 6.3-fold), FMOGS-OX5 (up to 4.8-fold), and ST5a (up to 5.1-fold). Promoter analysis revealed enrichment of ABA- and stress-responsive cis-regulatory elements. These findings delineate a genotype-dependent regulatory framework underlying GLS plasticity and identify quantitative metabolic and transcriptional markers relevant for breeding drought-resilient Brassica cultivars.

Alzheimer's disease (AD) is the most common cause of dementia and is characterized by progressive cognitive decline, β-amyloid accumulation, tau pathology, oxidative stress, and neuroinflammation. Increasing evidence suggests that metabolic dysregulation may contribute to AD pathogenesis. Glucagon-like peptide-2 (GLP-2), an intestinal peptide hormone, has demonstrated neuroprotective effects in preclinical models, potentially through anti-inflammatory and anti-apoptotic mechanisms. However, its role in human neurodegenerative disorders remains insufficiently understood. This study aimed to compare plasma GLP-2 concentrations between individuals with AD and cognitively healthy controls and to examine associations between GLP-2 levels, cognitive impairment severity, and metabolic parameters. Sixty-one patients with clinically diagnosed AD and twenty-three cognitively unimpaired controls were recruited. Plasma total GLP-2 concentrations were assessed at baseline in all participants and additionally at 6 and 12 months in a subgroup of 34 AD patients. Cognitive function was evaluated using the Mini-Mental State Examination (MMSE) and the Clinical Dementia Rating (CDR) scale. Group comparisons, subgroup analyses based on AD severity, repeated-measures analyses, Spearman correlations, and multivariable linear regression models (including age and clinical group) were performed. Plasma GLP-2 concentrations were significantly higher in AD patients than in controls, with a moderate effect size (Cohen's d ≈ 0.60). In severity-based subgroup analyses, both the mild and moderate-to-severe AD groups showed significantly higher GLP-2 levels than controls. Longitudinal analyses in AD patients (n = 34) showed no significant changes in GLP-2 concentrations over 12 months. Cognitive performance declined over time, with a significant reduction in MMSE from baseline to 6 months, whereas GLP-2 levels were not correlated with MMSE or CDR at any time point. GLP-2 levels correlated positively with body mass index (BMI), body weight, insulin, and HOMA-IR. In multivariable regression analysis, neither age nor clinical group independently predicted GLP-2 concentrations (both p > 0.05). Plasma GLP-2 concentrations were higher in patients with AD than in cognitively healthy controls; however, GLP-2 levels were not associated with cognitive performance or its progression over 12 months. GLP-2 was positively related to markers of adiposity and insulin resistance, suggesting stronger links to metabolic status than to cognitive severity. Further studies are needed to clarify whether GLP-2 alterations in AD reflect compensatory mechanisms, metabolic factors, or disease-related pathophysiology.

The incidence of early-onset colorectal cancer (EOCRC; <50 years) continues to increase, with the most rapid rises occurring among Hispanic/Latino (H/L) populations who remain underrepresented in molecular research. Because the TP53 signaling pathway is a key driver of colorectal tumorigenesis, this study aimed to clarify its prognostic significance in FOLFOX-treated EOCRC across ancestry groups. We analyzed 2515 colorectal cancer (CRC) cases (266 H/L, 2249 non-Hispanic White [NHW]) stratified by ancestry, age at onset, and FOLFOX exposure. Fisher's exact, chi-square, and Kaplan-Meier's analyses were applied, and multi-dimensional data integration was performed using AI-HOPE and AI-HOPE-TP53, conversational artificial intelligence platforms enabling natural language-driven exploration of clinical, genomic, and therapeutic features. TP53 pathway alterations were common in both H/L (85%) and NHW (83%) FOLFOX-treated patients. Among late-onset NHW cases, FOLFOX treatment was associated with higher TP53 mutation frequencies and lower ATM and CDKN2A mutation rates compared with untreated counterparts, while CHEK2 alterations were significantly less frequent in late-onset H/L patients. Missense mutations were the predominant alteration type across groups. These findings suggest that TP53 pathway alterations may be associated with ancestry- and treatment-specific clinical patterns in EOCRC and illustrate how AI-enabled integrative analytic frameworks can facilitate hypothesis generation and prioritize candidate biomarkers for future validation in precision oncology.

Alcohol use disorder (AUD) is highly comorbid with psychiatric conditions and is increasingly recognized as a modifiable factor associated with cognitive decline and dementia, including Alzheimer's disease (AD). While epidemiological and experimental studies consistently demonstrate that chronic alcohol exposure exacerbates neurodegenerative vulnerability rather than implying a single dominant causal pathway, accumulating evidence supports a multifactorial and context-dependent framework in which alcohol acts as a disease-modifying stressor that perturbs endogenous adaptive and resilience mechanisms. Hydrogen sulfide (H₂S), involved in redox regulation, mitochondrial function, neuroinflammatory control, and vascular homeostasis, has emerged as a candidate pathway that may be indirectly affected by alcohol exposure and relevant to neurodegenerative processes. This narrative mechanistic review synthesizes preclinical and clinical data examining alcohol-induced perturbations and H₂S-related signaling pathways in the context of AD. We analyzed studies on the effects of acute and chronic alcohol exposure, as well as on cellular processes influenced by H₂S bioavailability and signaling. Across experimental models and human studies, alcohol exposure was consistently associated with oxidative and mitochondrial stress, neuroinflammation, and vascular dysfunction-processes that overlap with biological domains normally regulated by H₂S. Alcohol-related cognitive impairment frequently occurs in the absence of proportional increases in classical AD pathology, suggesting that alcohol may accelerate disease progression through non-canonical mechanisms. H₂S signaling confers resilience against oxidative, inflammatory, and mitochondrial stress, whereas reduced H₂S bioavailability or disrupted sulfide-dependent signaling increases neuronal vulnerability and cognitive impairment. However, the available data do not support a unidirectional or exclusive role for H₂S as an integrative driver of alcohol-related AD pathology. H₂S signaling represents a biologically plausible convergent and modulatory pathway linking alcohol exposure to AD risk.

Reliable and disease-specific blood biomarkers are critically needed for Alzheimer's disease (AD), particularly in early stages when interventions are most effective. Although phosphorylated tau and neurofilament light chain (NfL) are widely used, their diagnostic specificity has been reported to decrease in elderly populations with multimorbidities. Syndecan-3 (SDC3), a heparan sulfate proteoglycan implicated in amyloid and tau aggregation, has recently emerged as a mechanistically relevant biomarker candidate. In this clinically realistic cohort study, we examined 46 participants, including 23 clinically diagnosed AD patients and 23 age-matched non-AD individuals with psychiatric and/or metabolic comorbidities. SDC3 expression was quantified in peripheral blood mononuclear cells (PBMCs), while soluble SDC3 and NfL were measured in plasma. Both PBMC-expressed and plasma SDC3 levels were elevated in AD compared with non-AD participants and showed a strong intercorrelation, whereas plasma NfL was likewise increased in AD. Individually, PBMC-SDC3, plasma SDC3, and NfL demonstrated moderate discriminatory performance. However, multivariable models integrating SDC3 (PBMC or plasma), NfL, and age achieved substantially improved discrimination (AUC > 0.8). SDC3 did not correlate with NfL, consistent with a biological signal distinct from neuroaxonal injury and reflective of peripheral immune-metabolic remodeling. Together, these findings identify SDC3 as a blood-based biomarker associated with systemic immune remodeling that complements established neuronal markers in a clinically realistic AD versus non-AD comparison. While exploratory, this study supports further investigation of SDC3 within integrated, multi-domain biomarker strategies in larger and independent cohorts.

The purpose of this study was to investigate whether quercetin, a flavonoid abundantly found in onion leaves and other plant foods, induces the dilation of retinal blood vessels in rats. The time-course changes in retinal arteriolar diameter were measured using a retinal circulation evaluation system based on a high-resolution digital fundus camera developed in our laboratory. The intravenous administration of quercetin (10-100 µg/kg/min) increased the retinal arteriolar diameter in a dose-dependent manner. This vasodilatory effect of quercetin was almost completely suppressed through an intravitreal pretreatment with N_ω-nitro-l-arginine methyl ester (l-NAME), a nitric oxide (NO) synthase inhibitor. In contrast, the systemic intravenous infusion of quercetin did not cause significant changes in the systemic blood pressure and heart rate. These results suggest that NO production plays an important role in the quercetin-induced dilation of retinal arterioles. Quercetin, which is abundantly present in several plant foods and possesses antioxidant properties, may be a useful agent for the prevention of various ocular diseases associated with visual impairment caused by reduced retinal blood flow.