Search Results (88)

Alzheimer’s disease (AD) involves not only the neural parenchyma but also brain-border interfaces in which border-associated macrophages (BAMs) regulate amyloid-β (Aβ) handling, vascular function, and immune surveillance. This review focuses on a pathological axis in which persistent vascular Aβ40 and aging-related stress shift clearance-competent BAMs toward oxidative-stress and senescent-like states. Two experimentally supported but incompletely connected branches are emphasized. In one, Aβ engages macrophage CD36–NOX2 signaling and generates reactive oxygen species that impair neurovascular function. In the other, Aβ40 internalization promotes TSPAN4-dependent migrasome formation and enrichment of CD5L/AIM; vascularly deposited CD5L/AIM lowers endothelial CD59, facilitates C5b–9 formation, and damages the blood–brain barrier. A separate aging study indicates that CD5L/AIM-rich BAM migrasomes can transmit apoptosis resistance and senescence-like dysfunction to microglia. Human evidence is currently strongest for CAA rather than parenchymal AD: a small CAA cohort showed increased circulating CD14-positive migrasomes and monocyte TSPAN4, with an exploratory area under the ROC curve of approximately 0.91 for TSPAN4-positive monocytes versus healthy controls, whereas AD patients selected to lack imaging evidence of CAA did not show increased circulating migrasome counts. Accordingly, the Aβ40–TSPAN4–CD5L/AIM vascular branch should presently be regarded as a CAA-enriched mechanism that may be especially relevant to AD with prominent CAA, not as a universal mechanism of Aβ42-dominant sporadic AD without substantial vascular amyloid. Direct demonstration of BAM-derived migrasomes in human AD brain tissue is still lacking, and neither TSPAN4 nor CD5L/AIM is sufficiently specific to serve as a stand-alone biomarker. We therefore distinguish peer-reviewed human observations, experimental causal evidence, preprint findings, and proposed cross-pathway interactions and outline biomarker validation and pathway-selective therapeutic strategies that preserve beneficial BAM functions. Full article

Background: Facioscapulohumeral muscular dystrophy (FSHD) is a progressive and heterogeneous disorder lacking reliable circulating biomarkers for disease monitoring and therapeutic response. We hypothesized that metabolic dysregulation, lipotoxicity, and endoplasmic reticulum (ER) stress induce sphingolipid remodeling that is reflected in serum and correlates with disease severity. Methods: We performed RNA sequencing, differential expression, and pathway analyses on biceps brachii muscle biopsies from mild (n = 9) and severe (n = 5) FSHD patients and healthy controls (n = 6). Selected transcripts were validated by OpenArray quantitative PCR. Serum samples from mild (n = 9), severe (n = 13), and control subjects (n = 10) were analyzed by targeted and untargeted LC-MS/MS sphingolipidomics. Results: Severe FSHD exhibited transcriptomic signatures of mitochondrial dysfunction, ER stress, inflammation, and extracellular vesicle biogenesis. RNA-seq revealed activation of the de novo ceramide synthesis pathway, with increased SPTLC1–3, CERS2, CERS5, and DEGS1, reduced SMPD1/4 and SMPDL3A, and dysregulation of cerebroside metabolism. Migrasome/extracellular vesicle markers (TSPAN4, TM4SF1, PIGK, CPQ, ITGA5, and ITGB1) were predominantly upregulated in patients with severe disease. Serum lipidomics showed severity-dependent increases in dihydroceramides, ceramides, sphingomyelins, and dihydrosphingomyelins, while the Cer/HexCer d18:1/18:0 ratio progressively increased with disease severity. Conclusions: Integrated transcriptomic and lipidomic analyses identify sphingolipid dysregulation and extracellular vesicle biogenesis as hallmarks of severe FSHD and support circulating sphingolipids as candidate biomarkers for disease severity and therapeutic monitoring. Full article

Microphthalmia, anophthalmia and ocular coloboma (MAC) are rare developmental eye disorders. Although over 100 causative genes have been identified, the molecular spectrum and genotype–phenotype correlations remain incompletely understood, particularly in genetically diverse populations. We set out to molecularly characterize MAC in the Israeli population. Forty-seven MAC-affected individuals from 43 unrelated families were enrolled. DNA of all probands was subjected to whole exome sequencing. The most common phenotype was microphthalmia (64% of patients). Definite or possible molecular diagnoses were achieved in 13/43 probands (30%) and involved 10 different genes (MFRP, SMO, GJA8, SOX2, RARB, TSPAN12, SHH, PTPN11, BEST1, and TP63). An in vitro splicing assay was used to explore the pathogenicity of a variant in the SMO gene. Following stringent filtering of exome data, 226 rare possibly pathogenic variants were identified in 218 genes not previously associated with MAC. The rate of molecular diagnosis achieved in this Israeli MAC cohort is similar to the reported range in other studies. The results further demonstrate the genetic heterogeneity of MAC, while supporting the involvement of complex inheritance and/or environmental factors in many of the cases. Further studies are required to reveal these underlying etiological factors, and to support the novel genotype–phenotype associations suggested here. Full article

Background/Objectives: This study engineered and evaluated a targeted, folate-functionalized chitosan nanoparticle (CS-FA NP) delivery system to enhance the therapeutic efficacy of standard quercetin and Coriandrum sativum seed extract against breast cancer. Methods: Phytochemical profiling confirmed a 14% crude yield for the methanolic extract, with gas chromatography–mass spectrometry (GC-MS) and high-performance liquid chromatography (HPLC) identifying quercetin as the principal bioactive agent. The synthesized CS-FA NPs exhibited a core size of 7–20 nm, an average hydrodynamic diameter of 150–160 nm, a stable zeta potential of −55 mV, and high encapsulation efficiencies (87.2% for quercetin and 80.5% for coriander). Kinetic assessments confirmed a biphasic, diffusion-controlled release matching Higuchi matrix kinetics. Anticancer activity was evaluated in vitro using MTT cytotoxicity, Annexin V-FITC/PI apoptosis analysis, RT-qPCR, and ex vivo rat aortic ring assays, followed by validation in a syngeneic 4T1 mammary tumor mouse model. Results: In vitro, folate-receptor-targeted quercetin nanoparticles (T4) demonstrated superior, selective cytotoxicity, particularly against triple-negative MDA-MB-231 cells, while sparing normal fibroblasts. Annexin V-FITC/PI apoptosis profiling and ex vivo aortic ring assays revealed profound, cell-line-dependent programmed cell death and up to 90% inhibition of microvessel sprout outgrowth. Mechanistically, RT-qPCR verified that nano-formulations induced complete transcriptional silencing of NANOG, MMP-1, VEGFA, TSPAN8, TWIST, EMMPRIN, and CDK1, alongside marked upregulation of P27^KIP1 and P21^CIP1. In vivo, these nano-formulations successfully improved tumor-associated pathological features, reduced aggressive tumor spindle-cell proliferation, and suppressed elevated serum CA15-3 and arginase biomarkers. Conclusions: Folate-functionalized chitosan nano-formulations significantly enhanced the anticancer efficacy of quercetin and Coriandrum sativum seed extract through improved targeted delivery, potent antiproliferative, anti-angiogenic, and pro-apoptotic activities, together with favorable modulation of multiple molecular pathways associated with breast cancer progression. These findings support their potential as promising targeted nanotherapeutic strategies for breast cancer treatment. Full article

Background/Objectives: Acute lymphoblastic leukaemia (ALL) is a biologically heterogeneous disease in which transcriptional dysregulation contributes to disease onset and progression. Despite survival rates exceeding 90% in high-income countries, relapsed and high-risk cases remain a major clinical challenge, highlighting the need for improved molecular stratification, namely the classification of patients based on genetic and transcriptomic features associated with prognosis, therapeutic response, and disease biology, as well as for the identification of novel therapeutic targets. Methods: We performed an integrative cross-platform analysis to investigate the expression and potential relevance of three candidate genes: PXDN, TCF4, and TSPAN7 in ALL. Gene expression was interrogated across the MILE microarray cohort and the St. Jude Cloud PeCan paediatric RNA-sequencing dataset. Results: Differential expression analyses consistently showed significant upregulation of TCF4 and PXDN in B-cell ALL (B-ALL) across both platforms (adjusted p < 0.001), while TSPAN7 displayed higher expression in T-cell ALL (T-ALL) and variable upregulation in B-ALL. These findings were supported by preliminary validation using quantitative PCR in paediatric B-ALL samples. To explore potential functional associations, we performed gene regulatory network inference using scGraphVerse, identifying differentially expressed genes putatively linked to PXDN, TCF4, and TSPAN7. Structural modelling using AlphaFold suggested candidate protein–protein interaction interfaces for a subset of these genes, although these predictions require experimental validation. Functional enrichment analysis indicated an over-representation of developmental pathways associated with PXDN- and TCF4-related networks, whereas TSPAN7-associated genes were enriched in processes linked to neuronal lineage development. Conclusions: Collectively, our results identify, for the first time, PXDN, TCF4 and TSPAN7 as differentially expressed genes in ALL and highlight the usefulness of integrative transcriptomic analyses across independent datasets. While limited by small-scale experimental validation and reliance on computational predictions, this study provides a framework for prioritising candidate genes and generates testable hypotheses regarding their potential involvement in leukaemia-associated molecular pathways. Full article

In genetics and evolutionary biology, selection signatures refer to distinct genomic patterns that reflect the action of natural and artificial selection on populations over time. Detecting such signatures provides critical insights into adaptive evolution and breed differentiation, especially in livestock populations subjected to diverse production environments and breeding objectives. In this study, a total of 96 samples were collected from four different cattle breeds, namely, South African indigenous Nguni (n = 28), Bonsmara (n = 21), Angus (n = 22), and Simmental (n = 25). The samples were genotyped using the Illumina Bovine SNP 150K BeadChip and subjected to quality control. Selection signatures were identified using the integrated haplotype score (iHS) method and the fixation index (Fst) method to assess the genetic differences between breeds. The complementary application of within-population and cross-population approaches enabled the detection of both recent and divergent selective pressures. A total of twelve regions were found to be under selection, with Bos taurus autosome (BTA) 12 being common between Nguni and Bonsmara. Gene annotation analyses identified several genes, including FAM110B, CDK8, and FLT1 in Bonsmara cattle, whereas Nguni cattle indicated potential genes such as CRB1, PLA2G4A, and VASH2, with CDK8 common between Bonsmara and Nguni on BTA 12. Cross-population analyses further identified PLCXD3, FAM149B1, and GRIK2 as candidate genes differentiating Bonsmara from Nguni cattle, and TSPAN9 distinguishing Simmental from Angus cattle. These results indicated breed-specific adaptive divergence. The study revealed genomic regions that are under selection in South African Nguni, Bonsmara, and Simmental cattle, with less information for Angus cattle breeds. Several candidate genes were found to be associated with reproductive traits (such as sperm count and inseminations per conception), disease resistance (such as bovine respiratory disease), and calving ease. This study identifies breed-specific and shared genomic regions under selection across diverse cattle breeds, providing novel insights into the genetic basis of adaptation and production-related traits. These findings explain the potential application of selection signature analyses in genomic-assisted breeding programmes aimed at improving productivity, resilience, and sustainability of cattle populations. Full article

Stress-induced premature senescence (SIPS) of endothelial cells can cause endothelial dysfunction. As a first-line antidiabetic agent, the specific role of metformin in SIPS has not yet been clarified. In this study, an in vitro SIPS model was induced by exposing human umbilical vein endothelial cells (HUVECs) to hydrogen peroxide (H₂O₂), and the effects of metformin on cell senescence, proliferation, migration, tube formation, and mitochondrial function were evaluated. Gene expressions altered by metformin were profiled via transcriptome sequencing. Specifically, the potential involvement of migrasome-mediated mitocytosis in metformin-driven effects was examined using confocal microscopy and siRNA-mediated silencing. The results showed that metformin significantly reduced SA-β-gal activity and restored the migration and tube-forming capacities of H₂O₂-induced senescent HUVECs. Moreover, metformin regulated mitochondrial dynamics, restored mitochondrial membrane potential, and attenuated intracellular oxidative stress. Notably, transcriptomic and functional analyses suggested that metformin enhanced migrasome formation and migrasome-mediated mitocytosis. Inhibition of migrasome formation by siTSPAN4 abolished the protective effect of metformin against SIPS. Collectively, these findings demonstrate that metformin alleviates early SIPS-associated changes in HUVECs and suggest that migrasome-mediated mitocytosis contributes to this protection by ameliorating mitochondrial dysfunction. This provides novel mechanistic insight into the vascular protective effects of metformin. Full article

To compare the genetic causes, prevalence, and clinical characteristics of syndromic and non-syndromic familial exudative vitreoretinopathy (FEVR). A total of 281 patients with FEVR who underwent clinical and genetic evaluation at five ophthalmological institutions in Japan between 2010 and 2023 were included. Whole-exome sequencing, Sanger sequencing, or karyotype analysis was performed using blood samples from probands and available family members. Clinical characteristics of FEVR probands were assessed according to the presence or absence of systemic abnormalities. Among the 281 FEVR probands, 42 (15%) had syndromic FEVR and 239 (85%) had non-syndromic FEVR. Syndromic FEVR was more frequently diagnosed during infancy (95% vs. 57%, p < 0.0001) and occurred more often in sporadic cases (69% vs. 50%, p = 0.028). Variants in Norrin/β-catenin signaling genes were less common in syndromic FEVR (29% vs. 54%, p = 0.0026), whereas symmetrical retinal severity was more frequently observed (67% vs. 39%, p = 0.001). Sex distribution did not differ between groups. Pathogenic variants were identified in 71% of syndromic cases, most commonly in KIF11, NDP, CTNNB1, DOCK6, TSPAN12, and LRP5. Syndromic FEVR exhibits distinct and heterogeneous genetic and clinical features compared with non-syndromic FEVR. Genotype–phenotype characterization may enable earlier diagnosis. Full article

Glioblastoma (GBM) shows extensive epigenetic heterogeneity. In IDH-wildtype (IDH-WT) GBM, promoter DNA methylation may regulate lineage programs influencing tumor evolution and prognosis; here, we systematically profiled promoter-level methylation dynamics across longitudinal tumors. Genome-wide DNA methylation data were obtained from the publicly available Gene Expression Omnibus (GEO; GSE279073) dataset, comprising a longitudinal cohort of 226 IDH-wildtype glioblastomas profiled on the Illumina Infinium EPIC 850K array across primary and recurrent stages at the University of California, San Francisco. From 333 Gene Ontology gliogenesis-annotated genes (GO:0042063), a 48-gene promoter panel was derived, with ≥2 probes per gene. Promoter methylation was summarized as the median β-value and tested using one-sample Wilcoxon with FDR correction. Functional enrichment, longitudinal variation, and patient-level methylation burden were assessed. Validation analyses were performed using independent IDH-wildtype GBM datasets from The Cancer Genome Atlas (RNA-seq and 450K methylation; n = 347). Promoter hypomethylation predominated across all stages, with 25 genes consistently hypomethylated and 7 hypermethylated. Functional enrichment highlighted gliogenesis, glial cell differentiation, neurogenesis, and Notch-related signaling. In TCGA, promoter methylation inversely correlated with expression for 11 of 33 genes (FDR < 0.05). An Expression Score contrasting hypomethylated and hypermethylated genes was positively associated with improved overall survival, where higher scores predicted better outcome (HR = 0.87, p = 0.016; Q4 vs. Q1 HR = 0.68, p = 0.025), and a complementary Methylation Score showed that higher promoter hypermethylation predicted poorer outcome (HR = 1.73, p < 0.001). CNTN2 and TSPAN2 were adverse prognostic genes (FDR < 0.05). The Expression Score was highest in Proneural tumors and lowest in Mesenchymal tumors (p < 0.001), reflecting a proneural-like state associated with better prognosis. Promoter methylation within gliogenesis genes defines a stable yet prognostically informative epigenetic signature in IDH-WT GBM. Hypomethylation promotes transcriptional activation and a favorable outcome, whereas hypermethylation represses lineage programs and predicts poorer survival. Full article

Dorper sheep (DOR) are a commercially important mutton breed renowned for their high growth rate, favorable carcass composition, environmental adaptability, and natural wool shedding. In China, they are widely utilized as terminal sires to enhance growth and carcass yield in local breeds. To elucidate the genetic basis of these traits, we sequenced the genomes of 20 DOR and integrated the data with whole-genome sequences from 73 individuals representing four Chinese indigenous breeds. Analyses of genetic diversity, inbreeding coefficients, and population structure revealed reduced genomic diversity, elevated inbreeding levels, and clear genetic separation for DOR from other indigenous breeds. Selective sweep scans using F_ST, pi, and XP-EHH identified candidate genes involved in five major trait categories: growth performance and development (COL2A1, DAB2IP, EPYC, TSPAN18, WNT1, CTPS1, FBXW7, INSR, S100A6, SOCS2), energy metabolism (ACSS3, ADGRE3, CPT2, GCGR, PRKAA1), fat deposition and adipocyte differentiation (EHBP1, FOXP1, KLF12, PDGFD, RALGAPA2), immune response (CXCR6, IL17RB, NFKBIZ, TMEM154), and wool traits (CERS4, MITF). These results will provide novel insights into the genomic architecture of economically important traits in DOR and support their genetic improvement through informed crossbreeding with Chinese local breeds. Full article

Background: Breast ductal carcinoma in situ (DCIS), a common precursor of breast cancer, has poorly understood susceptible driver genes. This study aimed to identify genes influencing DCIS progression by integrating Mendelian randomization (MR) and Gene Expression Omnibus (GEO) datasets. Methods: The GEO database was searched for DCIS-related datasets to extract differentially expressed genes (DEGs). MR was employed to find exposure single-nucleotide polymorphisms (SNPs) of expression quantitative trait locus (eQTL) gene expression from Genome-Wide Association Study database (GWAS) (IEU openGWAS project). DCIS was designated as the outcome variable. The intersection of genes was used for GO, KEGG and CIBERSORT analyses. The functional validation of selected DEGs was performed using Transwell invasion assays. Results: Four datasets (GSE7782, GSE16873, GSE21422, and GSE59246) and 19,943 eQTL exposure data were obtained from GEO and the IEU openGWAS project, respectively. By intersecting DEGs, 13 genes (LGALS8, PTPN12, YTHDC2, RNGTT, CYB5R2, KLHDC4, APOBEC3G, GPX3, RASA3, TSPAN4, MAPKAPK3, ZFP37, and RAB3IL1) were incorporated into subsequent KEGG and GO analyses. Functional assays confirmed that silencing PTPN12, YTHDC2 and MAPKAPK3, or overexpressing GPX3, RASA3 and TSPAN4, significantly suppressed DCIS cell invasion. These DEGs were linked to immune functions, such as antigen processing and presentation and the tumor microenvironment (TME), and they showed associations with dendritic cell activation differences. Conclusions: Thirteen genes were associated with DCIS progression, and six genes were validated in the cell experiments. KEGG and GO analyses highlight TME’s role in early breast cancer, enhancing understanding of DCIS occurrence and aiding identification of high-risk tumors. Full article

Background/Objectives: Triple-negative breast cancer (TNBC) is an aggressive subtype lacking ER, PR, and HER2 expression, with limited targeted therapies and poor outcomes. Epigenetic dysregulation, particularly aberrant DNA methylation, is a key driver. Decitabine, a DNA methyltransferase inhibitor (DNMTi), shows promise by reactivating silenced tumor suppressor genes and modulating immune responses. This systematic review evaluates preclinical and clinical evidence on decitabine’s efficacy, mechanisms, and translational potential in TNBC. Methods: A PRISMA-2020 compliant search of PubMed, EBSCO, Web of Science, and Semantic Scholar was conducted up to April 2025. Included studies assessed decitabine alone or in combination in TNBC preclinical or clinical settings. Risk of bias was assessed using QUIPS and RoB 2.0 tools. Results: Twenty-five studies were included. In vitro, decitabine-induced growth inhibition, apoptosis, and re-expression of silenced genes (such as BRCA1 and CDH1). In vivo, it reduced tumor burden and enhanced anti-tumor immunity through MHC-I, PD-L1, and STING pathway upregulation. Synergy was noted with anti-PD-1, HDAC inhibitors, and chemotherapy. Resistance mechanisms included persistent DNMT activity, low DCK, and miRNA-driven escape (miR-155–TSPAN5). Conclusions: Decitabine demonstrates strong preclinical and early clinical potential in TNBC via epigenetic reprogramming and immune activation. Future strategies should focus on biomarker-based selection and resistance mitigation. Full article

AMOG/β₂, the β₂ isoform of the sodium pump (Na⁺/K⁺-ATPase), functions as an adhesion molecule on glial cells, mediating critical neuron–astrocyte interactions during central nervous system (CNS) development. Despite its established role in glial adhesion, the neuronal receptor that partners with AMOG/β₂ remains unknown. This review examines the structural and functional properties of AMOG/β₂, including its capacity to form trans-dimers, both homophilic and potentially heterophilic—drawing comparisons with the β₁ subunit, a well-characterized adhesion molecule. By integrating computational modeling, in vitro data, and structural predictions, we explore how factors such as N-glycosylation and cis-membrane interactions influence β₂-mediated adhesion. We further consider candidate neuronal partners, including TSPAN31 and RTN4, and speculate on their potential roles in mediating heterophilic AMOG/β₂ interactions. Finally, we discuss the broader implications of AMOG/β₂ in neuron–glia communication, synaptic organization, neurodevelopment, and CNS disorders such as glioblastoma. Identifying the binding partner of AMOG/β₂ holds promise not only for understanding the molecular basis of CNS adhesion but also for uncovering novel mechanisms of neuroglial regulation in health and disease. Full article

Background: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy of immature T cells, driven by dysregulated transcriptional networks and oncogenic signaling pathways. Here, we present the first comprehensive analysis of the expression and regulation of TSPAN32, a tetraspanin implicated in lymphocyte homeostasis, in T-ALL. Methods: Transcriptomic data from the Leukemia MILE study (GSE13159) were analyzed to assess TSPAN32 expression across leukemic subtypes. Gene Set Enrichment Analysis (GSEA) was performed to explore biological pathways associated with TSPAN32-correlated genes. For mechanistic validation, HPB-ALL cells were used as a model, with NOTCH signaling inhibited by γ-secretase inhibitor (GSI) treatment and TAL1–LMO1 overexpression induced through doxycycline-inducible lentiviral vectors. Gene expression changes were quantified by RT-qPCR. Results: TSPAN32 was frequently downregulated in T-ALL compared to healthy bone marrow, although expression was retained in a subset of cases. GSEA revealed that TSPAN32-correlated genes were inversely associated with cell cycle–related programs, consistent with its established role as a negative regulator of T cell proliferation. Mechanistically, TAL1–LMO1 overexpression strongly induced TSPAN32, while GSI-mediated NOTCH inhibition partially reactivated its expression. Interestingly, GSI treatment also increased TAL1 levels despite downregulating LMO1. Conversely, TAL1–LMO1 overexpression suppressed NOTCH1 and NOTCH3, highlighting a reciprocal regulatory interplay between NOTCH and TAL1/LMO1 oncogenic circuits that shapes TSPAN32 expression dynamics in T-ALL. Conclusions: This study identifies TSPAN32 as a novel transcriptional target under the influence of key leukemogenic pathways and suggests its potential role as a modulator of leukemic T cell proliferation, with implications for therapeutic strategies targeting TAL1 and NOTCH signaling. Full article

This investigation examines the function of the mouse Mycn gene in regulating and activating quiescent mammary stem cells, which are vital for mammary gland development. The mammary gland, consisting of luminal and basal cells, progresses through complex developmental stages from embryonic development through puberty, adulthood, pregnancy, lactation, and involution. Quiescent stem cells, existing in a reversible non-proliferative state, are essential for gland maintenance, yet their activation mechanisms remain poorly understood. Mycn, a member of the Myc/MYC oncogene family, is recognized for its roles in embryonic development and cancer, notably aggressive neuroblastoma and triple-negative breast cancer. Through single-cell RNA sequencing (scRNA-seq), CRISPR knockout, and overexpression experiments, this study demonstrates that Mycn is highly enriched in the terminal end buds (TEBs) of the pubertal mammary gland, particularly in basal cells, and is critical for ductal development. Both deletion and overexpression of Mycn diminish the stemness and regenerative capacity of mammary stem cells. Mycn enhances cell proliferation while downregulating quiescent stem cell markers and regulators, including Bcl11b and Tspan8, affecting stem cell maintenance and differentiation. This research clarifies the regulatory role of Bcl11b in controlling Tspan8 expression and demonstrates that Mycn indirectly targets both under normal conditions. Maintaining appropriate levels of Mycn expression is essential for normal development and cancer prevention. These insights contribute to understanding diseases and aggressive cancers, including triple-negative breast cancer (TNBC), and suggest potential therapeutic approaches. Full article