Search Results (187)

Maternal undernutrition (MUN) causes severe metabolic disruption in the offspring of mammals. Here we determined the role of histone modification in hepatic gene expression in late-gestation fetuses of nutritionally restricted cows, an established model using low-nutrition (LN) and high-nutrition (HN) conditions. The chromatin immunoprecipitation sequencing results show that genes with an altered trimethylation of histone 3 lysine 4 (H3K4me3) are associated with cortisol synthesis and secretion, the PPAR signaling pathway, and aldosterone synthesis and secretion. Genes with the H3K27me3 alteration were associated with glutamatergic synapse and gastric acid secretion. Compared to HN fetuses, promoter H3K4me3 levels in LN fetuses were higher in GDF15, IRF2BP2, PPP1R3B, and QRFPR but lower in ANGPTL4 and APOA5. Intriguingly, genes with the greatest expression changes (>1.5-fold) exhibited the anticipated up-/downregulation from elevated or reduced H3K4me3 levels; however, a significant relationship was not observed between promoter CpG methylation or H3K27me3 and the gene set with the greatest expression changes. Furthermore, the stress response genes EIF2A, ATF4, DDIT3, and TRIB3 were upregulated in the MUN fetal liver, suggesting activation by upregulated GDF15. Thus, H3K4me3 likely plays a crucial role in MUN-induced physiological adaptation, altering the hepatic gene expression responsible for the integrated stress response and systemic energy metabolism, especially circulating lipoprotein lipase regulation. Full article

Endometrial cancer (EC) is the most common gynecological malignancy in developed countries. Risk factors for EC include metabolic alterations (obesity, metabolic syndrome, insulin resistance), hormonal imbalance, age at menopause, reproductive factors, and inherited conditions, such as Lynch syndrome. For the inherited forms, several genes had been implicated in EC occurrence and development, such as POLE, MLH1, TP53, PTEN, PIK3CA, PIK3R1, CTNNB1, ARID1A, PPP2R1A, and FBXW7, all mutated at high frequency in EC patients. However, gene function impairment is not necessarily caused by mutations in the coding sequence of these and other genes. Gene function alteration may also occur through post-transcriptional control of messenger RNA translation, frequently caused by microRNA action, but transcriptional impairment also has a profound impact. Here, we review how chromatin modifications change the expression of genes whose impaired function is directly related to EC etiopathogenesis. Chromatin modification plays a central role in EC. The modification of chromatin structure alters the accessibility of genes to transcription factors and other regulatory proteins, thus altering the intracellular protein amount. Thus, DNA structural alterations may impair gene function as profoundly as mutations in the coding sequences. Hence, its central importance is in the diagnostic and prognostic evaluation of EC patients, with the caveat that chromatin alteration is often difficult to identify and needs investigations that are specific and not broadly used in common clinical practice. The different phases of the healthy endometrium menstrual cycle are characterized by differential gene expression, which, in turn, is also regulated through epigenetic mechanisms involving DNA methylation, histone post-translational modifications, and non-coding RNA action. From a medicolegal and policy-making perspective, the implications of using epigenetics in cancer care are briefly explored as well. Epigenetics in endometrial cancer is not only a topic of biomedical interest but also a crossroads between science, ethics, law, and public health, requiring integrated approaches and careful regulation. Full article

Transcriptomic profiling has shown that exposure to PM_2.5, a common air pollutant, can modulate gene expression, which has been linked to negative health effects and diseases. However, there are few population-based cohort studies on the association between PM_2.5 exposure and specific gene set expression. In this study, we used an unbiased transcriptomic profiling approach to examine gene expression in a mouse model exposed to PM_2.5 and to identify PM_2.5-responsive genes. The gene expressions were further validated in both the human cell lines and a population-based cohort study. Two cohorts of healthy older adults (aged ≥ 65 years) were recruited from regions characterized by differing levels of PM_2.5. Logistic regression and decision tree algorithms were then utilized to construct predictive models for PM_2.5 exposure based on these gene expression profiles. Our results indicated that the expression of five genes (FAM102B, PPP2R1B, OXR1, ITGAM, and PRP38B) increased with PM_2.5 exposure in both cell-based assay and population-based cohort studies. Furthermore, the predictive models demonstrated high accuracy in classifying high-and-low PM_2.5 exposure, potentially supporting the integration of gene biomarkers into public health practices. Full article

Rectal carcinoma (RC) represents approximately 30% of all colorectal carcinomas (CRC) and is considered a distinct clinical entity. Vascular invasion (VI) is recognized as an independent predictor of poor outcomes in RC. In this study, we applied bioinformatics methods to identify gene pathways most likely associated with VI in rectal carcinoma. As ADAMTS8 showed statistically significant negative relations with the VI in RC patients, we further analyzed its top co-dependent genes—DNAL4, EVI2B, PPP1R35, PTGR3, RPL21, SOX4, and ZNF3—for the experimentally proven molecular modulators. We identified a total of 23 compounds from the Comparative Toxicogenomics Database based on previously reported data for all eight target genes. The search was expanded to include additional chemical agents by structure similarity using the PubChem database, which revealed 9661 additional compounds. These were subsequently used for molecular interaction analysis against target proteins co-expressed with, or associated with, ADAMTS8 in RC with VI. Ultimately, we identified four high-affinity compounds—cyanoginosin LR, doxorubicin, benzo[a]pyrene, and dibenzo(a,e)pyrene—that interacted with all target proteins. These compounds show potential for further assessment of their role in modulating processes related to vascular invasion, which is a strong negative predictor of RC outcomes. Full article

Coronary atherosclerosis (CAS) is a major cause of cardiovascular morbidity worldwide. The understanding of atherosclerosis has shifted from a cholesterol deposition disorder to an inflammation-driven disease, with anti-inflammatory therapies demonstrating clinical efficacy. Identifying inflammatory protein targets is crucial for developing targeted therapies. A proteome-wide Mendelian randomization (MR) analysis was performed to explore therapeutic targets for CAS by integrating inflammatory proteomics data from the UK-PPP (54,219 participants, 2923 proteins) and Iceland cohorts (35,559 participants, 4907 proteins) as exposures and outcome data for CAS, atherosclerosis, and carotid atherosclerosis from FinnGen. Replication MR employed meta-analysis of six proteomics datasets and CAS data from three sources, while the impact of the identified proteins on four cardiovascular diseases was also investigated. Colocalization analysis (PPH₄ > 0.9), reverse MR, and SMR were used to ensure robust causal inference. Proteome-wide MR identified 11 proteins significantly associated with CAS (p < 3.52 × 10⁻⁵), with all but CD4 linked to cardiovascular disease risk. Notably, colocalization confirmed the causal roles of PCSK9, IL6R, CELSR2, FN1, and SPARCL1 in CAS, and single-cell RNA-seq analysis revealed that five genes (TGFB1, SPARCL1, IL6R, FN1, and CELSR2) were exclusively expressed in smooth muscle cells of either coronary plaques or healthy vasculature. Druggability assessments were subsequently conducted for these targets. The three most promising targets (CELSR2, FN1, and SPARCL1), along with the other identified proteins and their biological functions, exhibit robust causal associations with CAS. FN1 and TGFB1 have the potential for drug repurposing in atherosclerosis treatment. Full article

With the availability of multi-frequency, multi-constellation global navigation satellite system (GNSS) modules, precise transportation applications have become attainable. For transportation applications, GNSS geodetic-grade receivers can achieve an accuracy of a few centimeters to a few decimeters through differential, precise point positioning (PPP), real-time kinematic (RTK), and PPP-RTK solutions in both post-processing and real-time modes; however, these receivers are costly. Therefore, this research aims to assess the accuracy of a cost-effective multi-GNSS real-time PPP solution for transportation applications. For this purpose, the U-blox ZED-F9P module is utilized to collect dual-frequency multi-GNSS observations through a moving vehicle in a suburban area in New Aswan City, Egypt; thereafter, datasets involving different multi-GNSS combination scenarios are processed, including GPS, GPS/GLONASS, GPS/Galileo, and GPS/GLONASS/Galileo, using both RT-PPP and RTK solutions. For the RT-PPP solution, the satellite clock and orbit correction products from Bundesamt für Kartographie und Geodäsie (BKG), Centre National d’Etudes Spatiales (CNES), and the GNSS research center of Wuhan University (WHU) are applied to account for the real-time mode. Moreover, GNSS datasets from two geodetic-grade Trimble R4s receivers are collected; hence, the datasets are processed using the traditional kinematic differential solution to provide a reference solution. The results indicate that this cost-effective multi-GNSS RT-PPP solution can attain positioning accuracy within 1–3 dm, and is thus suitable for a variety of transportation applications, including intelligent transportation system (ITS), self-driving cars, and automobile navigation applications. Full article

With the increasing demand for near real-time atmospheric water vapor monitoring, this study evaluates the performance of the open-source PRIDE PPP-AR software (version 3.0.5) for retrieving Zenith Total Delay (ZTD) and Integrated Water Vapor (IWV) over the African continent over a one-year period. PRIDE PPP-AR is compared with established PPP-AR and PPP solutions, including CSRS-PPP, IGN-PPP, and NGL and using GipsyX, ERA5, and IGS products as references. A robust methodology combining time series processing and statistical evaluation was adopted. Multiple tools were leveraged to ensure a comprehensive performance analysis of GNSS data from seven stations in Africa, where such studies remain scarce. The results show that PRIDE PPP-AR achieves ZTD accuracy comparable to GipsyX (RMSE < 6 mm, R² ≈ 0.99) and performs at a similar level to NGL and CSRS-PPP. Compared to the other solutions, PRIDE PPP-AR has an accuracy similar to CSRS-PPP and NGL, but slightly better than IGN-PPP, in line with ERA5 and IGS references. For IWV retrieval, comparisons with ERA5 indicate RMSE values of about 1.5 to 2.7 kg/m², depending on station location and climatic conditions. IWV variability tends to increase towards the equator, where the recorded fluctuations are higher than in subtropical zones. In addition, collocated radiosonde (RS) measurements in Abidjan confirm good agreement, further validating the reliability of the software. This study highlights the potential of GNSS meteorology, in providing reliable spatiotemporal IWV monitoring and indicates that the PRIDE PPP-AR is ready for the high precision meteorological applications in African regions. These results offer promising prospects for spatiotemporal studies through African multi-GNSS networks and the PRIDE PPP-AR approach. Full article

Runs of homozygosity (ROHs) are continuous homozygous segments of genomes that can be used to infer the historical development of the population. ROH studies allow us to analyze the genetic structure of a population and identify signs of selection. The present study searched for ROH regions in the Faverolle chicken breed. DNA samples from modern individuals and museum Faverolle specimens were obtained and sent for whole-genome sequencing (WGS) with 30× coverage. The results were aligned to the reference genome and subjected to additional filtering. ROH segments were then analyzed using PLINK 1.9. As a result, 10 regions on GGA1, 2, 3, 4, and 13 were identified. A total of 19 genes associated with fat deposition and lipid metabolism (GBE1, CACNA2D1, STON1, PPP1R21, RPL21L1, ATP6V0E1, CREBRF, NKX2-2, COMMD1), fertility (LHCGR, GTF2A1L, SAMD5), muscle development and body weight (VGLL3, CACNA2D1, FOXN2, ERGIC1, RPL26L1), the shape and relative size of the skeleton (FAT4), and autophagy and apoptosis (BNIP1) were found. Developmental protein genes (PAX1, NKX2-2, NKX2-4, NKX2-5) formed a separate cluster. Probably, selection for the preservation of high flavor characteristics contributed to the consolidation of these ROH regions. The present research enhances our knowledge on the Faverolle breed’s genome and pinpoints their ROH segments that are also specific «selection traces». Full article

Background: Colonic diverticulosis is a common condition, particularly in the elderly population. While dietary habits, obesity, smoking, and physical inactivity contribute to its pathogenesis, emerging evidence highlights a genetic predisposition affecting extracellular matrix (ECM) remodeling, inflammation, and connective tissue integrity. The aim of this systematic review was to summarize genetic determinants of colonic diverticulosis. Methods: The PubMed^® database was searched for original studies in humans. The inclusion criteria were named genetic factor and confirmed diverticulosis. Patients with diverticulitis and diverticular diseases were excluded from this review. Results: Out of 137 publications, 10 articles met the inclusion criteria: six large association studies (GWAS) and four cross-sectional studies. The genes regulating ECM turnover, including TIMP1, MMP3, and MMP9, are involved in diverticulosis development. The TIMP1 (rs4898) T allele has been associated with increased susceptibility, potentially due to its role in ECM remodeling. Similarly, MMP3 (rs3025058) and MMP9 (rs3918242) polymorphisms contribute to altered collagen degradation. The COL3A1 (rs3134646) variant coding modified collagen type III may promote diverticular formation. Other genes, such as ARHGAP15 (rs4662344, rs6736741), affect cytoskeletal dynamics. Identified in GWAS studies, gene candidates may be grouped into blood group and immune system-related genes (ABO, HLA-DQA1, HLA-H, OAS1, TNFSF13, FADD), extracellular matrix and connective tissue genes (COL6A1, COLQ, EFEMP1, ELN, HAS2, TIMP2), signaling and cell communication (BMPR1B, WNT4, RHOU, PHGR1, PCSK5), nervous system and neurodevelopment (BDNF, CACNB2, GPR158, SIRT1, SCAPER, TRPS1), metabolism and transporters (SLC25A28, SLC35F3, RBKS, PPP1R14A, PPP1R16B), lipids and cholesterol (LDAH, LYPLAL1, STARD13), transcription and gene regulation (ZBTB4, UBTF, TNRC6B), apoptosis (FADD, PIAS1), and poorly characterized genes (C1TNF7, ENSG00000224849, ENSG00000251283, LINC01082, DISP2, SNX24, THEM4, UBL4B, UNC50, WDR70, SREK1IP1). Conclusions: There are a number of gene variants that probably predispose to colonic diverticulosis. Detailed characterization of the multigene background of diverticulosis will enable appropriate therapeutic or preventive interventions in the future. Full article

Background: Macrocephaly can be a component manifestation of several monogenic conditions, in association with intellectual disability/developmental delay (ID/DD) behaviour abnormalities, including autism spectrum disorders (ASD), and variable additional features. On the other hand, idiopathic ASD can present with developmental delay and macrocephaly. Methods: We carried out a retrospective analysis of a cohort of 78 patients who were tested from February 2017 to December 2024 by high-throughput sequencing of a panel of 27 genes (ABCC9, AKT1, AKT2, AKT3, BRWD3, DIS3L2, DNMT3A, EZH2, GPC3, GPC4, HERC1, MED12, MTOR, NFIA, NFIX, NSD1, PDGFRB, PIK3CA, PIK3R1, PIK3R2, PPP2R1A, PPP2R5D, PTEN, RAB39B, RNF135, SETD2, and TBC1D7) because of neurodevelopmental impairment, including ID/DD, ASD/behaviour abnormalities associated with macrocephaly, mimicking to a large extent idiopathic ASD. Results: Pathogenic variants leading to the diagnosis of monogenic conditions were detected in 22 patients (28%), including NSD1 (2), PTEN (16), and PPP2R5D (4). Distinctive of the PTEN-associated phenotype were true macrocephaly (100%), ASD or behaviour abnormalities (92%), mild/borderline ID (79%), and no facial dysmorphisms. Typical of the PPP2R5D-associated phenotype were relative macrocephaly (75%), a few unspecific peculiar facial characteristics (50%), and a more variable presentation of the neurodevelopmental phenotype. Conclusions: Pathogenic variants in PTEN and PPP2R5D are the most recurrent gene mutations in a patient-oriented procedure for the genetic diagnosis of apparently idiopathic ASD and behaviour abnormalities associated with macrocephaly. The clinical applicability of the presented diagnostic strategy is discussed. Full article

The epigenetic regulation of gene expression through the covalent modification of histones is crucial for developing germline cells. To study the regulatory role of alternative splicing (AS) of euchromatic histone lysine methyltransferase 2 (EHMT2/G9A) in spermatogenesis in Mongolian horses, this study first examines the localization of the EHMT2 gene in testicular support cells and then predicts the higher-order structures of sequences with and without AS. Two types of lentiviral vectors for overexpression were subsequently constructed for the EHMT2 gene, one with AS and one without, to infect support cells. The proliferation and activity of infected cells were measured using CCK8, and the differential expression of spermatogenesis-related genes in the two types of support cells was analyzed via qRT–PCR. We analyzed the expression of EHMT2 by immunofluorescence staining. EHMT2 was expressed in the nuclei of Sertoli cells. The expression of spermatogenesis-related genes was measured in the two types of cells. The results reveal that the expression levels of the FSH, Stra8, CCNB2, CDC27, NRG1, PPP2R5C, CCNB2, and YWHAZ genes in the AS group were greater than those in the control group. These results indicate that AS events in EHMT2 affect gene expression and thus affect spermatogenesis. Full article

Congenital developmental abnormalities in piglets, such as intersex and aproctia, adversely affect survival rates, growth performance, and genetic breeding efficiency in pig populations. To elucidate their genetic basis, we performed a genome-wide association study (GWAS) on 1030 Large White pigs. We combined 50 K SNP chip data with SWIM-based genotype imputation to enhance the resolution of genetic variation detection, followed by MLM analysis. Our results identified 53 significant SNPs, with 52 associated with intersex and 1 with aproctia. Key candidate genes included MAD1L1, ID4, EFNA5, and PPP1R16B for intersex and ARNT2 for aproctia. Functional enrichment analysis highlighted pathways related to gonadal development (e.g., progesterone-mediated oocyte maturation) and embryonic morphogenesis. Collectively, the identification of these SNPs and candidate genes advances our understanding of the genetic architecture of intersex and aproctia in piglets. These findings provide actionable insights for optimizing genetic breeding strategies and improving health management in Large White pig production, with potential implications for reducing economic losses caused by congenital disorders. Full article

This article aims to examine the real-time precise point positioning (PPP) solution’s accuracy utilizing the low-cost dual-frequency multi-constellation U-blox ZED-F9P module and real-time GNSS orbit and clock products from five analysis centers, including Bundesamt für Kartographie und Geodäsie (BKG), Centre National d’Etudes Spatiales (CNES), International GNSS Service (IGS), Geo Forschungs Zentrum (GFZ), and GNSS research center of Wuhan University (WHU). Three-hour static quad-constellation GNSS measurements are collected from ZED-F9P modules and geodetic grade Trimble R4s receivers over a reference station in Aswan City, Egypt, for a period of three consecutive days. Since a multi-GNSS PPP processing model is applied in the majority of the previous studies, this study employs the single-constellation GNSS PPP solution to process the acquired datasets. Different single-constellation GNSS PPP scenarios are adopted, namely, GPS PPP, GLONASS PPP, Galileo PPP, and BeiDou PPP models. The obtained PPP solutions from the low-cost module are validated for the positioning and precipitable water vapor (PWV) domains. To provide a reference positioning solution, the post-processed dual-frequency geodetic-grade GNSS PPP solution is applied; additionally, as the station under investigation is not a part of the IGS reference station network, a new technique is proposed to estimate reference PWV values. The findings reveal that the GPS and Galileo 3D position’s accuracy is within the decimeter level, while it is within the meter level for both the GLONASS and BeiDou models. Additionally, millimeter-level PWV precision is obtained from the four PPP models. Full article

Heart failure (HF) remains a major cause of mortality worldwide. While novel approaches, including gene and cell therapies, show promise, efficient delivery methods for such biologics to the heart are critically needed. One emerging strategy is lung-to-heart delivery using nanoparticle (NP)-encapsulated biologics. This study examines the efficiency of delivering a therapeutic peptide conjugated to a cell-penetrating peptide (CPP) to the heart via the lung-to-heart route through intratracheal (IT) injection in mice. The CPP, a tandem repeat of NP2 (dNP2) derived from the human novel LZAP-binding protein (NLBP), facilitates intracellular delivery of the therapeutic payload. The therapeutic peptide, SE, is a decoy peptide designed to inhibit protein phosphatase 1 (PP1)-mediated dephosphorylation of phospholamban (PLN). Our results demonstrated that IT injection of dNP2-SE facilitated efficient delivery to the heart, with peak accumulation at 3 h post-injection. The administration of dNP2-SE significantly ameliorated morphological and functional deterioration of the heart under myocardial infarction. At the molecular level, dNP2-SE effectively prevented PLN dephosphorylation in the heart. Immunoprecipitation experiments further revealed that dNP2-SE binds strongly to PP1 and disrupts its interaction with PLN. Collectively, our findings suggest that lung-to-heart delivery of a CPP-conjugated therapeutic peptide, dNP2-SE, represents a promising approach for the treatment of HF. Full article

Cutaneous lupus erythematosus (CLE) is a chronic autoimmune skin disorder with limited therapeutic options, particularly for refractory discoid lupus (DLE), which often results in scarring and atrophy. Recent studies have identified miR-31, miR-485-3p, and miR-885-5p as key regulators of inflammation, apoptosis, and fibrosis in CLE skin lesions. This research investigates a novel topical miRNA therapy using DDC642 elastic liposomes to target these pathways in CLE. DDC642 liposomes were complexed with miRNAs (anti-miR-31, anti-miR-485-3p, pre-miR-885-5p) and characterized through dynamic light scattering and Cryo-TEM. Cytotoxicity, cellular penetration, and therapeutic efficacy were evaluated in primary keratinocytes, PBMCs, and immune 3D-skin organoids. miRNA lipoplexes were successfully synthesized with optimized particle size, surface charge, and encapsulation efficiency. These lipoplexes exhibited effective cellular penetration and low cytotoxicity. Anti-miR-31 lipoplexes reduced miR-31 and NF-κB levels while increasing STK40 and PPP6C expression. Pre-miR-885-5p lipoplexes elevated miR-885-5p levels and downregulated PSMB5 and NF-κB in keratinocytes. While anti-miR-485-3p lipoplexes reduced T-cell activation markers. Anti-miR-31 and pre-miR-885-5p lipoplexes successfully modulated inflammatory pathways in 3D-skin CLE models. miRNA lipoplexes represent promising candidates for pioneering topical genetic therapies for CLE. Further studies, including animal models, are necessary to validate and optimize these findings. Full article