Search Results (180)

Breast cancer remains a leading cause of global mortality. According to international cancer data, significant progress has been made in treating breast cancer; however, metastasis and drug resistance continue to be the primary causes of mortality for many patients. This study investigated the modulation of apoptosis-related genes in response to ionizing radiation and estrogen exposure based on a human breast epithelial cell model (MCF-10F and its transformed variants: Estrogen, Alpha3, Alpha5, Tumor2) previously established, where cells were treated with high linear energy transfer alpha particles, with or without 17β-estradiol. Gene expression profiling was performed using an Affymetrix U133A microarray, and bioinformatic analyses assessed differential expression, estrogen receptor status, and correlations with overall survival. Distinct gene expression patterns emerged across cell lines and tumor subtypes. TP53 expression correlated positively with TP63, BIK, CFLAR, BIRC3, and BCLAF1. TP63, PERP, CFLAR, BCLAF1, GULP1, and BIRC3 were elevated in normal tissue, whereas BIK, PHLDA2, and BBC3 were upregulated in tumors. ER-positive tumors exhibited higher TP63, BIK, BCLAF1, and BBC3 expression, while ER-negative tumors showed increased PERP, CFLAR, BIRC3, and PHLDA2. Notably, elevated BCLAF1 expression was associated with poorer survival in Luminal A patients, and high PHLDA2 expression correlated with reduced survival in Luminal B cases. These findings indicate that resistance to apoptosis is a fundamental mechanism in breast cancer progression and therapeutic evasion. Breast tumors selectively alter the expression of key genes to promote growth, evade apoptosis, and develop therapeutic resistance. The differential expression and correlations of these apoptosis-related genes highlight their potential as molecular targets for future personalized cancer therapies and as valuable biomarkers for prognostic stratification and predicting therapeutic response. Full article

Background: Personalizing adjuvant chemotherapy (ACT) after curative resection in early-stage NSCLC remains unmet because prior ACT-biomarker findings rarely reproduce across studies. Key barriers are platform and preprocessing heterogeneity, dominant batch effects, and incomplete ACT annotations. As a result, many signatures that perform well in a single cohort fail during external validation. We created an open, harmonized meta-database linking gene expression with curated ACT exposure and survival to enable fair benchmarking and modeling. Methods: A PRISMA-guided search of 999 GEO studies (through January 2025) used LLM-assisted triage of titles, clinical tables, and free text to identify datasets with explicit ACT status and patient-level survival. Eight Affymetrix microarray cohorts (GPL570/GPL96) met eligibility. Raw CEL files underwent robust multi-array average; probes were re-annotated to Entrez IDs and collapsed by median. Covariate-preserving ComBat adjusted platform/study while retaining several clinical factors. Batch structure was quantified by principal-component analysis (PCA) variance, silhouette width, and UMAP. Two quality-control (QC) filters, median M-score deviation and PCA leverage, flagged and removed technical outliers. Results: The final meta-database comprises 1340 patients (223 (16.6%) ACT; 1117 (83.4%) observation), 13,039 intersecting genes, and 594 overall-survival events. Batch-associated variance (PC1 + PC2) decreased from 63.1% to 20.1%, and mean silhouette width shifted from 0.82 to −0.19 post-correction. Seven arrays (0.5%) were excluded by QC. Event depth supports high-dimensional survival and heterogeneity-of-treatment modeling, and the multi-cohort design enables internal–external validation. Conclusions: This first open, rigorously harmonized NSCLC transcriptomic database provides the sample size, demographic diversity, and technical consistency required to benchmark ACT-benefit markers. By making these data openly available, it will accelerate equitable precision-oncology research and enable data-driven treatment decisions in early-stage NSCLC. Full article

Dipeptidyl-peptidase IV (DPP4) inhibitors have shown potential anti-tumor properties. This study investigates the therapeutic potential of evogliptin, a DPP4 inhibitor, both as a single agent and in combination with temozolomide (TMZ), in glioma models. In vitro studies were performed using U87 and U373 glioma cell lines exposed to different concentrations of TMZ (250, 500 μM) and evogliptin (250, 500 ng/mL), either alone or together, for 24, 48, and 72 h. Cell viability was determined with the MTT assay. In vivo effectiveness was tested in a xenograft mouse model treated with intraperitoneal injections of evogliptin (60 mg/k g/day), TMZ (15 mg/kg/day), or their combination over 3 weeks. The combination of TMZ and evogliptin markedly reduced cell viability compared to single-agent treatments. DPP4 mRNA levels decreased more substantially with combination therapy. miRNA expression profiling with Affymetrix arrays indicated that certain miRNAs, such as miR-4440 and miR-6780b-5p, were upregulated after treatment with evogliptin or the combination regimen, whereas others were downregulated. These miRNAs could play a role in limiting glioma growth through DPP4 regulation. In the animal model, evogliptin alone did not provide a survival advantage. Analysis of TCGA data showed that glioma patients with decreased DPP4 expression had improved survival rates. The co-administration of evogliptin and temozolomide resulted in distinct miRNA profile changes. Nevertheless, both in vitro and in vivo, the added cytotoxicity from the combination was minimal. Full article

Obesity is a risk factor associated with cardiovascular diseases that may lead to heart failure (HF). However, in HF, overweight and obese patients have longer survival than underweight patients, a phenomenon known as the obesity paradox. MiRNAs play a fundamental role in gene regulation involved in obesity and HF. The main objective of this study was to identify and validate differentially expressed circulating miRNAs in HF–obese and HF–lean patients. This case–control study was carried out in two phases: discovery and validation. In the discovery phase, plasma samples from 20 HF patients and from 10 healthy controls were analyzed using the miRNA 4.0 Affymetrix GeneChip array. Differentially expressed miRNAs were ranked and selected for validation. In this phase, plasma miRNAs -451a, -22-3p, and -548ac from 80 patients and controls were analyzed by qPCR. Target analysis and functional enrichment analysis were performed. When comparing HF–lean and HF–obese groups compared to controls, miRNAs -451a and -22-3p were up-regulated in both discovery and validation phases, while -548ac was down-regulated in the discovery phase and up-regulated in the validation phase, indicating that miRNA changes are independent of obesity. These miRNAs regulate genes and different biological processes associated with metabolic, morphological, and functional outcomes. Full article

Grapevine cultivars (Vitis vinifera L.) generally exhibit relatively high tolerance to drought stress. In contrast, the drought tolerance of other Vitis species and their hybrids used as rootstocks differs considerably. In order to attain a better understanding of the molecular basis of drought tolerance in grapevine, we conducted a comparative transcriptomic analysis of roots of drought-stressed Cabernet Sauvignon (CS, Vitis vinifera L.) and rootstock of Kober 5BB (V. berlandieri × V. riparia) using the Affymetrix Vitis Genome Array Version 2.0. We identified 1279 (745 upregulated and 534 downregulated) and 1925 (807 upregulated and 118 downregulated) differentially expressed genes in 5BB and CS. Numerous genes that are putatively involved in aquaporins, proline-rich protein, reactive oxygen species, osmoprotection, and lipid transfer were differentially expressed in response to drought stress in both genotypes. When gene ontology analyses were examined, it was observed that CS and 5BB genotypes were associated with the highest number of similar genes in both the molecular function (protein binding, catalytic activity, and DNA binding) and the biological process (metabolic process and translation) categories. The identification of different regulated genes between 5BB and CS roots is expected to help advance our understanding of molecular mechanisms operating during drought stress in grapevine roots. Full article

Subclinical coronary atherosclerosis (SCA) is an early stage of coronary artery disease (CAD) that often goes unrecognized until clinical events occur. Identifying circulating molecular biomarkers could improve early diagnosis and risk assessment in asymptomatic individuals. This study employed a two-phase approach to identify plasma extracellular vesicle (EV)-derived microRNAs (miRNAs) associated with SCA. In the discovery phase, plasma samples from male participants were analyzed using Affymetrix GeneChip miRNA 4.0 microarrays. Differentially expressed miRNAs were refined through bioinformatic analysis, cross-species comparison with murine data, and target gene prediction. In the validation phase, six candidate miRNAs were quantified by RT-qPCR in an independent cohort. Six miRNAs were differentially expressed between individuals with SCA and controls. Among these, the combination of miR-146b-5p, miR-4701-3p, and miR-1180-3p demonstrated a high discriminative capacity for SCA (AUC = 0.8281; sensitivity = 93.75%; specificity = 93.75%). Functional enrichment analysis revealed that predicted target genes are involved in key atherosclerosis-related pathways, including inflammation, lipid metabolism, and vascular remodeling. EV-derived miRNAs may serve as non-invasive biomarkers for the early detection of coronary atherosclerosis. These findings provide insight into the molecular processes underlying subclinical vascular disease and support the integration of EV-associated miRNAs into preventive cardiology strategies. Full article

Background: Glucose intolerance (GI) is a metabolic disorder that is a consequence of hyperglycemia. Glucose intolerance can, under some conditions, progress to type 2 diabetes mellitus (T2D), where insulin is insufficiently utilized. As a result of genetic and lifestyle effects, the incidence of T2D has increased worldwide. Pathophysiological consequences of the disease may include retinopathy, nephropathy, and neuropathy. Skeletal muscle is one of the major organs that regulates blood sugar homeostasis, both at rest and during exercise. Thus, understanding the molecular and genetic perspectives on the contribution of skeletal muscles to the predisposition to diabetes is a hot topic in diabetes research. In this study, we conducted a differential analysis of gene expression and compared the expression profiles of all the genes in the skeletal muscles of normal, glucose-intolerant, and diabetic individuals via the Affymetrix HGU133plus2 platform. Data were collected from the Gene-Expression Omnibus (GEO) series GSE18732. Gene Ontology enrichment and perturbed pathways were thoroughly analyzed. Results: We found that genes that were significantly differentially expressed between the different tissues contribute to metabolic pathways related to glucose homeostasis, as well as several signaling pathways related to insulin signaling, e.g., the MAPK, mTOR, Toll-like receptor (TLR), p53, WNT and neurotrophin signaling pathways. Furthermore, some genes related to several malignancies were also differentially expressed across the different clinical groups. Additionally, some of these genes are related to epigenetic regulation. Furthermore, other differentially expressed genes were connected to several myopathies. Conclusions: This study may serve as a gene-based analysis that contributes as a basis for further analysis. This investigation may include gene and protein networks that serve in understanding diabetes, the mechanism of action of the involved proteins, and pharmacology and drug design targeting T2D. Full article

Osteoporosis is a common disease characterized by a reduction in bone mineral density (BMD), leading to an increased risk of pathological fractures and even mortality. Although menopause is a major risk factor, osteoporosis can also occur in premenopausal women. The aim of this study was to identify genetic variants associated with the development of osteoporosis in Korean premenopausal women. Subjects were recruited from the Anseong and Ansan cohorts of the Korean Genome and Epidemiology Study (KoGES). Clinical and epidemiological characteristics were assessed, and participants were classified based on BMD values measured at the distal radius and mid-shaft tibia. Individuals with confounding risk factors such as low body weight, smoking, high alcohol consumption, steroid/hormone therapy, or relevant medical history were excluded. A total of 247 healthy controls and 57 osteoporosis patients were included. Genotyping was performed using the Illumina Infinium HumanExome BeadChip and the Affymetrix Axiom Exome Array. Data were analyzed using the SNP and Variation Suite and PLINK, with quality control thresholds set at MAF ≥ 0.05 and HWE p ≥ 0.01. Functional annotation and protein structure predictions were performed using PolyPhen-2, SIFT, and PROVEAN. Genome-wide association analyses identified 113 single-nucleotide polymorphisms (SNPs) in 69 genes significantly associated with osteoporosis (p < 0.05) in both platforms, with 18 SNPs showing high cross-platform consistency (p < 0.01). Several of these genes were implicated in bone metabolism (e.g., ESRRG, PECAM1, COL6A5), vitamin D metabolism (e.g., NADSYN1, EFTUD1), skeletal muscle function (e.g., PACSIN2, ESRRG), and reproductive processes (e.g., CPEB1, EFCAB6, ASXL3). Notably, the CPEB1 rs783540 SNP exhibited the strongest association (p < 0.001) in both analyses. Our findings suggest that genetic polymorphisms in pathways related to bone metabolism, vitamin D signaling, muscle–bone interaction, and reproductive hormone regulation may contribute to the development of osteoporosis in Korean premenopausal women. These results provide a genetic basis for early identification of at-risk individuals and warrant further functional studies to elucidate the underlying mechanisms. Full article

Astrocytic tumors are a heterogeneous group of glial neoplasms characterized by marked differences in biological behavior and patient prognosis. Transforming growth factor-beta (TGF-β) signaling plays a pivotal role in astrocytoma pathogenesis; however, the extent and mechanisms of its epigenetic regulation remain poorly understood. This study aimed to investigate how promoter methylation and microRNA-mediated mechanisms regulate key genes within the TGF-β signaling pathway across various astrocytoma grades. Tumor tissue samples from 65 patients with WHO grade II–IV astrocytomas were analyzed using Affymetrix gene expression and microRNA microarrays. Promoter methylation of TGF-β signaling genes was assessed using methylation-specific polymerase chain reaction (MSP). Gene expression was validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR), and protein levels were quantified using enzyme-linked immunosorbent assay (ELISA). MicroRNA targets were predicted using bioinformatic tools, and survival analyses were conducted using Kaplan–Meier and Cox regression models. Six genes—SMAD1, SMAD3, SKIL, BMP2, SMAD4, and MAPK1—showed significant upregulation in high-grade tumors (fold change > 5.0, p < 0.05), supported by RT-qPCR and protein-level data. Promoter hypomethylation and reduced expression of regulatory microRNAs (e.g., hsa-miR-145-5p targeting SMAD3) were more common in higher-grade tumors. Protein–protein interaction analysis indicated strong functional interconnectivity among the overexpressed genes. High protein levels of SMAD1, SMAD3, and SKIL were significantly associated with shorter overall survival (p < 0.001). This multi-level analysis reveals that astrocytic tumor progression involves epigenetic derepression and microRNA-mediated dysregulation of TGF-β signaling. Elevated expression of SMAD1, SMAD3, and SKIL emerged as strong prognostic indicators, underscoring their potential as biomarkers and therapeutic targets in astrocytic tumors. Full article

The etiology of women with gestational diabetes mellitus (GDM) and a greater risk of developing type 2 diabetes (T2D) after delivery remains unknown. This study aimed to investigate the global gene expression in four postpartum women with previous GDM (pGDM), three with T2D, and three with a history of normoglycemic pregnancy (controls). Total RNA was extracted from whole blood between March and May 2020. Global mRNA expression was determined using an Affymetrix Human Gene 2.0 ST Array. The expression of the selected focused genes was validated by RT-PCR. The microarray revealed 140 transcripts (p < 0.05, fold change cut-off ≥ 2) in patients with pGDM compared to controls. We identified 583 gene-altered transcripts between patients with T2D and controls. Interestingly, 60 transcripts had genes shared by pGDM or T2D versus the controls. The selected upregulated genes involved in inflammatory response, glycosylation, and death-like domains, according to the functional network analysis of pGDM (TNFAIP6, PDK3) and T2D (MMP9 and CARD6), showed similar trends to those obtained via microarray. Thus, these differentially expressed genes and their corresponding network and pathway analyses in women with pGDM and T2D offer valuable insights into the possible biological mechanisms of the progression of GDM to T2D. Full article

Sepsis is a life-threatening condition characterized by dysregulated immune responses to infection. To elucidate early transcriptional changes in sepsis, we conducted a case–control study profiling gene expression in whole blood from 20 early-stage sepsis patients and 9 healthy controls. Using Affymetrix Clariom D Human Arrays and robust preprocessing, we identified differentially expressed genes (DEGs) using standard bioinformatic pipelines. A total of 344 genes were significantly upregulated, while 9703 were significantly downregulated in sepsis patients (|log2FC| > 1, adjusted p < 0.05). Pathway enrichment and Gene Ontology analysis revealed activation of innate immune pathways, neutrophil degranulation, and cytokine signaling, alongside suppression of lymphocyte differentiation and antigen presentation. These results suggest a shift toward an innately driven inflammatory state in early sepsis. Our findings provide transcriptomic insights that may support the development of early diagnostic biomarkers and therapeutic targets. Full article

Introduction: The interface between T cells and the tumor microenvironment, termed the ‘immunological synapse’, consists of multiple checkpoint protein pairs co-expressed on both sides of the synapse. mir-16, a microRNA from a widely known tumor-suppressor family of miRNAs, was previously shown by us to be downregulated in melanoma. As other miRNAs from this family have been shown to directly target checkpoint proteins, here we investigated whether miR-16 influences the expression patterns of checkpoint proteins in melanoma. Methods: Single-cell gene expression data from the melanoma microenvironment were retrieved from a public database. Melanoma cell lines were established from metastatic lesions and transiently transfected with an hsa-miR-16-5p-mimic RNA or a mir-16-expressing plasmid. The mRNA expression profiles were analyzed using an Affymetrix microarray. Direct targets of miR-16 were identified by luciferase reporter assays. Protein levels were assessed by Western blotting. Results: Bioinformatic analysis revealed that the expression levels of eight checkpoint mRNAs, known to be present on the melanoma side of the immunological synapse, were highly correlated. Four of these mRNAs contained putative binding sites for the miR-15/16 family. miR-16 expression was significantly reduced in melanoma cells, compared to normal melanocytes. Luciferase reporter assays demonstrated that miR-16 directly targets the 3′ untranslated regions (3′UTRs) of CD40, CD80. The mRNAs downregulated following miR-16 overexpression were highly enriched for genes involved in autophagy, vesicle-mediated transport, and the regulation of protein membrane localization. Among these, VTI1B and SMPD1 were confirmed to be direct targets of miR-16. Transient overexpression of miR-16 resulted in a significant reduction in SMPD1 and VTI1B levels in melanoma cell lines. Conclusions: Our findings suggest that miR-16 potentially modulates melanoma tumorigenesis, metastasis and immunogenicity by altering the composition of checkpoint proteins at the immunological synapse and by regulating cellular pathways associated with intracellular trafficking and transmembrane protein presentation. Full article

Aquaculture has become a crucial component of global food production, yet catfish (10.8% of global finfish production) breeding programs often lack sufficient genetic data to fully utilize their production potential. In the last 15 years, there have been improvements in this field as two high-density (HD) single nucleotide polymorphism (SNP) arrays (250K and 690K) and low-density panels have been developed for North American channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus). This lack of genomic tools hinders genetic improvement efforts in other commercially relevant catfish species besides them. Therefore, this review investigated the reason behind the lack of SNP chip usage in genetic-based selections in most catfish breeding programs and the cross-species applicability of the already existing high-density SNP arrays for genotyping members of the Clariidae, African catfish (Clarias gariepinu), and Siluridae, European catfish (Silurus glanis), families. This paper systematically reviews the literature of more than 16 SNP arrays, with 66 non-target species, and assesses the possibility of adapting catfish SNP arrays to the catfish families of interest. With lowered filtering (e.g., MAF > 0) thresholds, the Affymetrix Axiom 250K and Axiom Catfish 690K Genotyping Array could potentially be used on important market species like African and European catfishes. In the long term, chip development would be the solution for these species, but, until then, cross-application is a viable alternative. Despite low polymorphic SNPs (~1%) and call rates (~0%), this SNP array could aid researchers and breeders, improving catfish aquaculture and management. Full article

Patients with end-stage renal disease (ESRD) are at increased risk of cardiovascular disease (CVD), such as myocardial infarction (MI). Uremic toxins and endothelial dysfunction are central to this process. In this exploratory study, we used the Affymetrix GeneChip microarray to investigate the gene expression profile in uremic serum-induced human coronary arterial endothelial cells (HCAECs) from ESRD patients with and without MI (UWI and UWOI groups) as an approach to its underlying mechanism. We also explored which pathways are involved in this process. We found 100 differentially expressed genes (DEGs) among the conditions of interest by supervised principal component analysis and hierarchical cluster analysis. The expressions of four major DEGs were validated by quantitative RT-PCR. Pathway analysis and molecular network were used to analyze the interaction and expression patterns. Ten pathways were identified as the main enriched metabolic pathways according to the transcriptome profiling analysis, which were, among others, positive regulation of inflammatory response, positive regulation of extracellular signal-regulated kinases 1 and 2 (ERK1/2) cascade, cardiac muscle cell development, highlighting positive regulation of mitogen-activated protein kinase (MAPK) activity (p = 0.00016). Up- and down-regulation of genes from HCAECs exposed to uremic serum could contribute to increased endothelial dysfunction and CVD in ESRD patients. Our study suggests that inflammation and the ERK-MAPK pathway are highly enriched in kidney disease patients with MI, suggesting their role in ESRD pathology. Further studies and approaches based on MAPK pathway interfering strategies are needed to confirm these data. Full article

Aging, marked by a decline in cellular function and increased risk of diseases, involves the accumulation of senescent cells. This study aims to develop and characterize 3D senescent skin models to understand cellular senescence mechanisms’ implications in cutaneous aging. Normal human epidermal keratinocytes (NHEKs) were cultured from early to late passages (p2 to p7) to induce replicative senescence or sourced from both young and aged donors to reconstruct 3D models. Histological analyses assessed tissue morphology and integrity, while permeability assays evaluated epidermal barrier function. Analyses using immunostaining, RT-PCR, Affymetrix™ GeneChip™ Microarrays identified key markers of cellular senescence, epidermal homeostasis, and other related processes. Results showed that NHEKs at p5 and beyond, and those from aged donors, exhibited significant morphological disruptions, decreased expression of differentiation-associated genes, and impaired barrier function. Increased p16ink4a-positive cells indicated enhanced senescence. Transcriptome analysis revealed significant changes in keratinocyte differentiation, cell–cell interaction, cell cycle regulation, extracellular matrix homeostasis, and inflammation. These findings underscore the relevance of addressing cellular senescence for enhancing skin health and promoting skin longevity. These 3D senescent skin models, validated by consistent results from both passage-induced senescence and aged donor keratinocytes, are valuable for understanding skin aging and developing anti-aging treatments, positioning them as essential tools in the pursuit of skin longevity-focused innovations. Full article