Enriched Terms Research Articles

Transcriptomic alterations in the ovine caruncular endometrium due to imbalanced nutrition and FSH-induced ovarian hyperstimulation

BackgroundImbalanced diet and exogenous gonadotrophins affect uterine function and morphology. In sheep, FSH-induced superovulation alters implantation-related gene expression, influenced by both treatment and diet. In this study, we used deep RNA sequencing (NGS, RNA-Seq) to expand our understanding of these effects on the caruncular endometrium.MethodsEwes (n = 3–5/group) were separated into control fed (CF), overfed (OF), and underfed (UF) groups, with each group subdivided between FSH (superovulated; SOV) or saline (negative controls; CONT) treatment. Caruncular samples were collected on day 10 of diestrus of the subsequent estrous cycle, with samples from CF_CONT also collected on day 5 to assess time-dependent changes.ResultsThe 1484 differentially expressed genes (DEGs, P < 0.01, FDR < 0.05) identified between CF_CONT animals at days 5 and 10 were predominantly associated with increased immune activity and cellular metabolic processes and cellular proliferation. In CONT animals, imbalanced nutrition (i.e., both OF and UF) was associated with enrichment of terms associated with cell adhesion and differentiation, immune response and angiogenesis. The FSH carry-over effects resulted in a higher number of DEGs in CF animals (1374), than in OF (168) or UF (18), mostly associated with dysregulation of cell cycle and hormonal sensitivity.ConclusionThe absence of genes concurrently affected by superovulation (SOV) in all feeding regimes indicates that the effects of FSH on the caruncular transcriptome are multidirectional and dependent upon body condition. Therefore, the homeostasis of ovine caruncles is influenced by both body condition and superovulation (SOV), potentially affecting uterine receptivity.Graphical

DNA Imprinting and Differentially Expressed Genes in Longissimus thoracis Muscle of Bos indicus Submitted to Early Weaning Management

Background/Objectives: Early weaning management followed by energy supplementation can lead to metabolic alterations in the calf that exert long-term effects on the animal’s health and performance. It is believed that the main molecular basis underlying these metabolic adaptations are epigenetic mechanisms that regulate, activate, or silence genes at different stages of development and/or in response to different environmental stimuli. However, little is known about postnatal metabolic programming in Bos indicus. Therefore, this study aimed to compare the DNA methylation profile of Nellore animals submitted to conventional and early weaning and to correlate the findings with genes differentially expressed in the Longissimus thoracis skeletal muscle of Bos indicus cattle. Methods: For this, we used Reduced Representation Bisulfite Sequencing (RRBS) and RNA-Sequencing techniques to prospect differentially methylated genes (DMGs). Results: A total of 481 differentially methylated regions were identified, with 52% (250) being hypermethylated and 48% (231) hypomethylated. Functional enrichment analysis of 53 differentially methylated and differentially expressed genes was performed. The main enriched terms and pathways were associated with 3′-5′-cyclic adenosine monophosphate (cAMP) signaling, which presents the upregulated adenylate cyclase 3 (ADCY3) gene and significatively hypomethylated in the promoter region. Alterations in cAMP signaling are involved in numerous processes, many of them related to lipid metabolism. The relative differential expression of key genes of this pathway demonstrates the relationship between cAMP signaling and de novo lipogenesis. Conclusions: These findings suggest an important role of postnatal metabolic programming through DNA methylation mechanisms in determining fat deposition in beef.

A nested case-control study of circular ribonucleic acid expression profiles in the peripheral blood of pregnant women with pre-eclampsia.

To examine the expression of circular ribonucleic acid (circRNA) in the peripheral blood of pregnant women with preeclampsia (PE) prior to the onset of the disease. A prospective nested case-control study included pregnant women who delivered at Fujian Maternal and Child Health Hospitals between November 2021 and October 2022. The study included three women diagnosed with PE (the PE group) and three healthy pregnant women (the control group). The expression of circRNAs in the peripheral blood before clinical diagnosis at 20 weeks gestation was analyzed by microarray technology, and the functional analysis and regulatory network prediction were done. There were 162 circRNAs with differentially expressed multiplicity of > 2.0 in the PE group compared to the control group. Out of them, 30 circRNAs were up-regulated and 132 were down-regulated. Gene ontology (GO) analysis revealed that the host genes of the differentially expressed circRNAs mainly participated in protein localization to plasma membrane, insemination, etc. Most enriched terms were related to cytoplasmic dynein complex, microtubule cytoskeleton, etc. In terms of molecular function, the enriched terms were related to dynein light intermediate chain binding, polyubiquitin modification-dependent protein binding, etc. Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway enrichment analysis revealed that differentially expressed circRNAs were involved in vasopressin-regulated water reabsorption, cyclic guanosine monophosphate-protein kinase G (cGMP-PKG), calcium- and other signaling pathways. CircRNAs are involved in a variety of biological processes and regulatory network related to the pathogenesis of PE.

Development of a deep learning-based 1D convolutional neural network model for cross-species natural killer T cell identification using peripheral blood mononuclear cell single-cell RNA sequencing data

Background and Aim: Natural killer T (NKT) cells exhibit the traits of both T and NK cells. Although their roles have been well studied in humans and mice, limited knowledge is available regarding their roles in dogs and pigs, which serve as models for human immunology. Single-cell RNA sequencing (scRNA-Seq) can elucidate NKT cell functions. However, identifying cells in mixed populations, like peripheral blood mononuclear cells (PBMCs) is challenging using this technique. This study presented the application of one-dimensional convolutional neural network (1DCNN) for the identification of NKT cells within scRNA-seq data derived from PBMCs. Materials and Methods: We used human scRNA-Seq data to train a 1DCNN model for cross-species identification of NKT cells in canine and porcine PBMC datasets. K-means clustering was used to isolate human NKT cells for training the 1DCNN model. The trained model predicted NKT cell subpopulations in PBMCs from all species. We performed Differential gene expression and Gene Ontology (GO) enrichment analyses to assess shared gene functions across species. Results: We successfully trained the 1DCNN model on human scRNA-Seq data, achieving 99.3% accuracy, and successfully identified NKT cell candidates in human, canine, and porcine PBMC datasets using the model. Across species, these NKT cells shared 344 genes with significantly elevated expression (FDR ≤ 0.001). GO term enrichment analyses confirmed the association of these genes with the immunoactivity of NKT cells. Conclusion: This study developed a 1DCNN model for cross-species NKT cell identification and identified conserved immune function genes. The approach has broad implications for identifying other cell types in comparative immunology, and future studies are needed to validate these findings. Keywords: 1D convolutional neural network, K-means clustering, natural killer T cell, peripheral blood mononuclear cells, single-cell RNA sequencing.

UG0712, A Ginsenoside Complex, Improved Endurance Performance and Changed Hepatic and Muscular Transcriptomic Signatures in C57BL/6N Male Mice.

Ginsenosides, active compounds derived from Panax ginseng, exhibit promising potential in enhancing physical performance. This study investigates the impact of UG0712 (UG), a novel ginsenoside compound, on endurance capacity, body weight, organ weights, blood parameters, and specific transcriptomic changes in liver and muscle tissues using a C57BL/6N mouse model. The mice received UGs orally at three doses: UG50 (50 mg/kg), UG100 (100 mg/kg), and UG200 (200 mg/kg) for a specified duration. Endurance capacity, physiological parameters, and transcriptome signatures in liver and muscle tissues were assessed. UG administration significantly improved time to exhaustion, with UG50 and UG200 showing substantial enhancements. Body and organ weights exhibited no notable differences, suggesting a lack of adverse effects. Biochemical markers, except for decreased creatine kinase levels in the UG100 group, showed no significant variations. Transcriptome analysis revealed limited group separation and dose-dependent patterns. The UG100 group displayed significant enrichment in lipid metabolism and muscle-related terms. Identified dose-dependent improvements in endurance capacity highlight UGs' potential as supplements. The absence of adverse effects on body and organ weights, along with positive effects on biochemical markers, supports their safety. Despite limited dose-dependent patterns in transcriptomic analyses, the UG100 group showcased significant enrichment in pathways related to muscle and lipid metabolism. These findings offer valuable insights for athletes and aging individuals seeking to enhance physical performance, warranting further exploration into UG effects' on molecular mechanisms.

Gene expression meta-analysis identifies novel pathways of the avian influenza virus disease

Humans and other animals are both susceptible to avian influenza virus. The avian influenza (AI) pandemic could be brought on by the appearance of a new, radical AI virus capable of spreading disease and maintaining prolonged human-to-human transmissions. The possibility of an AI pandemic makes it important for public health. Despite efforts to identify a linkage between them, the hierarchical relationship between all the factors that influence the pathophysiology of this disease, the shared biological pathways, and the exact identities of its important triggers are yet unknown. To find shared gene expression profiles and overlapping biological processes, an integrated gene expression meta-analysis was carried out for three independent microarray data of the avian influenza virus. This study found 1284 common differentially expressed genes (DEGs), of which 73 were overexpressed and 119 were under-expressed, analyzed using various packages in the R tool. The extensive biological, functional enrichment and pathway analysis was performed using the EnrichR tool and identified the defence response to the symbiont (GO:0140546), Interferon Alpha/Beta Signaling (R-HSA-909733), and spliceosome as the most enriched terms of biological process and pathways respectively. In a network meta-analysis, ISG15 and RELA were pinpointed as the top hub genes for over and under-expression, respectively. This meta-analysis technique for avian influenza infection highlights important gene profiles and their linked pathways. These findings highlight the value of using meta-analysis to detect novel gene markers that may offer key insight into disease pathogenesis and perhaps pave the way for creating more effective therapeutic approaches.

Abstract A017: IGF2BP1 is essential for ETO2/GLIS2 leukemogenesis via stabilization of primitive myeloid transcriptional programs

Abstract Certain subtypes of pediatric leukemia continue to have dismal cure rates despite advances in targeted therapy. One such disease is acute megakaryoblastic leukemia (AMKL) with a rearrangement of ETO2/GLIS2 (also known as CBFA2T3/GLIS2.) Based on our preliminary data utilizing CRISPR/Cas9 screens in vivo in patient-derived xenografts, we have nominated IGF2BP1 as a potential vulnerability in ETO2/GLIS2-rearranged AMKL. For our discovery phase, we utilized a patient-derived E2G2r AMKL which successfully engrafts in NSGS mice. We created a stable Cas9-expressing subclone using lentiviral transduction followed by FACS enrichment and limiting dilution transplants. We then generated a custom library targeting the top 100 overexpressed genes between E2G2r leukemias versus other leukemia PDXs which we previously characterized, including eight transcription factors with motifs enriched in differentially expressed genes, as well as eight pan-essential positive controls. Mice were sacrificed at humane endpoints, and spleens and bone marrow underwent PCR amplification for gRNA sequences followed by sequencing and analysis with MAGeCK-VISPR (Wei L, et al. Genome Biol 2015). We observed the dropout of 38 genes with a false discovery rate &amp;lt; 0.25, including all positive control gRNAs. Among the most significantly depleted genes was the RNA binding protein IGF2BP1. We subsequently characterized phenotypic changes using shRNAs in the E2G2r cell line M07e and ETO2/GLIS2-transformed CD34+ umbilical cord blood cells. Notably, we observed impaired cell growth with IGF2BP1 knockdown in both cell lines as well as the parent xenograft. We also generated M07e lines expressing a degron (FKBPF36V, aka “dTAG”, Nabet et al. Nat Chem Biol 2018) knocked in at the endogenous IGF2BP1 locus and observed similar phenomena. Through flow cytometry of M07e following IGF2BP1 depletion, we observed changes in the leukemic immunophenotype as well, suggesting perturbation of megakaryocyte differentiation potential. To determine the mechanism underlying our observations, we performed enhanced UV crosslinking with IP and sequencing (Blue SM et al. Nat Protoc 2022) against both IGF2BP1 and m6A residues based on the putative role of IGF2BP1 as an m6A reader. We observed binding of IGF2BP1 predominantly in 3’UTRs, as well as the presence of m6A-modified bases at IGF2BP1 binding sites. Gene ontology (GO) analysis of IGF2BP1-bound transcripts demonstrated enrichment for GO terms pertaining to embryonic hematopoiesis and megakaryocyte maturation/development. We further evaluated global changes in gene expression following IGF2BP1 loss, and performed RNAseq 72 hours following shRNA-mediated knockdown. GO analysis showed that downregulated genes were highly enriched for E2F-mediated transcriptional programs. We hypothesize that IGF2BP1 regulates myeloid developmental transcripts essential for E2G2r leukemogenesis, likely via stabilization in an m6A-dependent fashion, and thus may represent a selective therapeutic target. Work is ongoing to further elucidate this proposed mechanism. Citation Format: Jason Clark, Mark Wunderlich, Jing Chen, Daniel Starczynowski, Lynn Lee. IGF2BP1 is essential for ETO2/GLIS2 leukemogenesis via stabilization of primitive myeloid transcriptional programs [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr A017.

Exploring mechanisms of gene expression control during Ustilago maydis teliospore germination

Fungal plant pathogens produce spores for survival and dispersion. Developing an understanding of the mechanisms involved in spore dormancy and germination will aid in mitigating the impact of diseases they cause. The thick-walled diploid teliospores of Ustilago maydis were used as a model for studying fungal spore dormancy and germination. These spores develop only in infected maize tissue and can remain dormant for long periods of time. Teliospores germinate under favourable conditions, resume meiosis, and produce basidiospores to initiate new rounds of infection. Previous research identified changing gene transcripts during teliospore germination, but analysis was hampered by asynchronous germination. The more comprehensive RNA-seq analysis of U. maydis teliospore germination presented here aimed to identify gene altered transcript levels detectable above the background of fluctuating changes resulting from asynchronous germination. The analyses identified 18 different patterns of gene transcript level changes. It also indicated that gene expression is controlled at the transcriptional and post-transcriptional levels. Gene ontology term enrichment analyses of these patterns revealed genes that are involved in cell morphogenesis, metabolism, and RNA metabolism.

Oxidative Stress and Inflammation-Related mRNAs Are Elevated in Serum of a Finnish Wet AMD Cohort.

Localized diseases can be affected by and affect the systemic environment via blood circulation. In this study, we explored the differences in circulating serum mRNAs between patients with wet AMD (wAMD) and controls. Blood samples were obtained from 60 Finnish patients with wAMD and 64 controls. After serum preparation and RNA sequencing, the count data was examined for differentially expressed genes (DEGs) and further checked for enriched molecular pathways and ontology terms as well as links to clinical data. We found many DEGs and some enriched pathways, including the inflammation and cell survival-associated pathway tumour necrosis factor alpha (TNF-α) signaling via nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). The related DEGs were oxidized low-density lipoprotein receptor 1 (OLR1), salt inducible kinase 1 (SIK1), and coagulation factor III (F3). DEGs from degradative macular and retinal processes were also examined, many of which were also related to cardiovascular disease and maintenance. Additionally, DEG counts were inspected in relation to clinical and anti-VEGF treatment parameters, and glutamine amidotransferase-like class 1 domain-containing 3A (GATD3A) levels were found to be significantly lower in patients with wAMD treated with anti-VEGF. Differentially expressed systemic mRNAs that are linked to mitochondrial function, oxidative stress, and inflammation may have a role in the pathology of wAMD. Our observations provide new data for the understanding of the progression of wAMD.

YAP1 and WWTR1 are required for murine pregnancy initiation.

Endometrial stromal cell decidualization is required for pregnancy success. Although this process is integral to fertility, many of the intricate molecular mechanisms contributing to decidualization remain undefined. One pathway that has been implicated in endometrial stromal cell decidualization in humans in vitro, is the Hippo signaling pathway. Two previously conducted studies showed that the effectors of the Hippo signaling pathway, YAP1 and WWTR1, are required for decidualization of primary endometrial stromal cells in vitro. To investigate the in vivo role of YAP1 and WWTR1 in decidualization and pregnancy initiation, we generated Progesterone receptor Cre mediated mutation of a combination of Yap1 and Wwtr1 alleles. Female Yap1 and Wwtr1 triple allele mutants exhibited subfertility, a compromised decidualization response, decreased endometrial receptivity, delayed embryonic development, and a unique transcriptional profile at 7.5 days post coitus. Bulk mRNA sequencing revealed aberrant maternal remodeling evidenced by significant alterations in extracellular matrix encoding genes at 7.5 days post-coitus in mutant dams and enrichment for terms associated with fertility-compromising diseases like pre-eclampsia and endometriosis. In addition, differentially expressed genes overlapped directionally with Estrogen receptor and Epidermal growth factor receptor regulated genes as identified by microarray. Our results indicate that Yap1 and Wwtr1 are necessary for successful mammalian pregnancy initiation.

The heterogeneity of breast cancer metastasis: a bioinformatics analysis utilizing single-cell RNA sequencing data.

Breast cancer is a common malignancy in women, and its metastasis is a leading cause of cancer-related deaths. Single-cell RNA sequencing (scRNA-seq) can distinguish the molecular characteristics of metastasis and identify predictor genes for patient prognosis. This article explores gene expression in primary breast cancer tumor tissue against metastatic cells in the lymph node and liver using scRNA-seq. Breast cancer scRNA-seq data from the Gene Expression Omnibus were used. The data were processed using R and the Seurat package. The cells were clustered and identified using Metascape. InferCNV is used to analyze the variation in copy number. Differential expression analysis was conducted for the cancer cells using Seurat and was enriched using Metascape. We identified 18 distinct cell clusters, 6 of which were epithelial. CNV analysis identified significant alterations with duplication of chromosomes 1, 8, and 19. Differential gene analysis resulted in 17 upregulated and 171 downregulated genes for the primary tumor in the primary tumor vs. liver metastasis comparison and 43 upregulated and 4 downregulated genes in the primary tumor in the primary tumor vs lymph node metastasis comparison. Several enriched terms include Ribosome biogenesis, NTP synthesis, Epithelial dedifferentiation, Autophagy, and genes associated with epithelial-to-mesenchymal transitions. No single gene or pathway can clearly explain the mechanisms behind tumor metastasis. Several mechanisms contribute to lymph node and liver metastasis, such as the loss of differentiation, epithelial-to-mesenchymal transition, and autophagy. These findings necessitate further study of metastatic tissue for effective drug development.

Mechanisms of Amomum villosum essential oil in enhancing tilapia (Oreochromis niloticus) intestinal health

Amomum villosum is a member of the ginger family to treat gastrointestinal diseases in humans. Supplementing the diet of tilapia (Oreochromis niloticus) with essential oil (EOA) can enhance digestive and intestinal antioxidant capacity. We conducted a comparative experiment using tilapia to further understand the potential molecular response mechanism to dietary EOA. Fish were divided into four groups with different feeding doses of EOA: L (2 g/Kg) group, M (4 g/Kg) group, and H (8 g/Kg) group, along with a control group without EOA supplementation. The level of inflammatory factors (TNF-α, IL-1) declined significantly in the EOA group. Comparative transcriptome of the intestines revealed differentially expressed genes (DEGs) in each group, which further revealed that enriched terms were closely related to important pathways such as PI3K-Akt signaling, cell adhesion molecules, regulation of actin cytoskeleton, and autoimmune thyroid disease. These pathways play significant roles in regulating various cellular processes and immune responses of intestines. Intestine metabolomic analysis indicated that dietary EOA caused changes in metabolic processes, particularly in nucleotide metabolism, indicating the potential impact of EOA on these processes. To identify key factors regulating the molecular response to EOA supplementation, a weighted gene co-expression network analysis combined with transcriptome and differential metabolites to identify key genes and metabolites. Glycitein and genistein are substances related to the metabolism of soybean meal were identified. Hmgb2, Parp11, Bcoll is considered to be the key genes, and has the immune regulation function. This study provides new insights into the molecular basis underlying the protective effects of dietary EOA in tilapia. The results can benefit the aquaculture industry by developing dietary strategies to improve the health and welfare of tilapia in intensive farming.

The STRIPAK associated kinase MST4 is a novel mediator in heart failure pathogenesis

Abstract Heart failure still poses substantial challenges in understanding its underlying molecular pathways. We recently found the mammalian STE20-like kinase 4 (MST4) significantly upregulated in human failing hearts (5.7-fold in DCM and 3.8-fold ICM) as well as in heart failure animal models (i.e. 2.5-fold in Calsarcin-1-KO, 2.5-fold in MLP-KO). MST4 is a member of striatin interacting phosphatases and kinases complexes (STRIPAK), an emerging group of multiprotein complexes responsible for integrating cellular signalling pathways. We provide the first evidence of functional STRIPAK complexes containing MST4 by co-immunoprecipitation and interactomics experiments in cardiomyocytes. Moreover, we found MST4 to interact with several intercalated disc proteins like beta-Catenin or Desmin. Adenoviral overexpression of MST4 in neonatal rat ventricular cardiomyocytes (NRVCM) results in a significant increase in cell size (+13%). This was not accompanied by the activation of fetal genes such as NPPA, NPPB or RCAN1.4, but rather by an increase in phosphorylation of Protein kinase B (PKB/Akt, 3.3-fold). Akt is usually associated with physiological hypertrophy, indicating that MST4 may be involved in protective pathways in cardiomyocytes. In support of this notion, MST4 overexpression reduced apoptotic activity (cleavage of Caspase 3 -69%, Caspase 7 -80%, Parp1 -27%) and improved both contractility (fractional shortening cell +23%, fractional shortening sarcomere +30%, time to max. contraction cell -10%, time to max. contraction sarcomere -12%) and relaxation parameters (time to max. relaxation velocity cell -12%) in isolated adult rat ventricular cardiomyocytes. In order to identify cardiac targets of MST4, we performed a comprehensive analysis of the phosphoproteome of NRVCM overexpressing MST4 compared with control-virus +/- pharmacological inhibitor at two time points. We identified more than 70,000 peptides including more than 20,000 phosphopeptides in more than 4,000 protein groups. Using linear modelling with a reduced data set containing regulated features selected by thresholds for p-value and fold change, we observed a consistent MST4 effect and a number of enriched gene ontology terms. Here, we found several potential MST4 targets and effects on protein expression levels associated with intercalated disc proteins. In human heart samples, MST4 was also localized to the intercalated disc region by immunostaining. Interesting proteins in that context that might help explain some of the observed cardioprotective MST4 effects are Connexin 43, Desmin, Ryanodine receptor, Phospholemman, Junctophilin2, Myozap or Frizzled 1. Taken together, our data imply that MST4 upregulation in human heart failure serves an adaptive role which may offer translational opportunities.Graphical Abstract

Investigating the Role of Hub Calcification Proteins in Atherosclerosis via Integrated Transcriptomics and Network-Based Approach.

Atherosclerosis (AS) is a chronic inflammatory condition of the arteries, characterized by plaque formation that can restrict blood flow and lead to potentially fatal cardiovascular events. Given that AS is responsible for a quarter of global deaths, this study aimed to develop a systematic bioinformatics approach to identify biomarkers and regulatory targets involved in plaque development, with the goal of reducing cardiovascular disease risk. AS-specific mRNA expression profiles were retrieved from a publicly accessible database, followed by differentially expressed genes (DEGs) identification and AS-specific weighted gene co-expression network (WGCN) construction. Thereafter, calcification and atherosclerosis-specific (CASS) DEGs were utilized for protein-protein interaction network (PPIN) formation, followed by gene ontology (GO) term and pathway enrichment analyses. Lastly, AS-specific 3-node miRNA feed-forward loop (FFL) construction and analysis was performed. Microarray datasets GSE43292 and GSE28829 were obtained from gene expression omnibus (GEO). A total of 3785 and 6176 DEGs were obtained in case of GSE28829 and GSE43292; 3256 and 5962 module DEGs corresponding to GSE28829 and GSE43292 were obtained from WGCN. From a total of 54 vascular calcification (VC) genes, 20 and 29 CASS-DEGs corresponding to GSE28829 and GSE43292 were overlapped. As observed from FFL centrality measures, the highest-order subnetwork motif comprised one TF (SOX7), one miRNA (miR-484), and one mRNA (SPARC) in the case of GSE28829. Also, in the case of GSE43292, the highest-order subnetwork motif comprised one TF (ESR2), one miRNA (miR-214-3p), and one mRNA (MEF2C). These findings have important implications for developing new therapeutic strategies for AS. The identified TFs and miRNAs may serve as potential therapeutic targets for treating atherosclerotic plaques, offering insights into the molecular mechanisms underlying the pathogenesis and highlighting new avenues for research and treatment.

Effect and mechanism of allergen-specific immunotherapy on small airway dysfunction in children with asthma.

The purpose of this study was to investigate the effectiveness of allergen-specific immunotherapy (AIT) on small airway dysfunction (SAD) and the underlying mechanism with a special focus on basophils. Sixty-five children with mild to moderate asthma who were under regular inhaled corticosteroid (ICS) treatment for more than 1 year but whose FEF75 remained below 65% of the predicted value and had positive results for serum Der p or Der f were enrolled. Children with asthma underwent house dust mite (HDM) subcutaneous immunotherapy (SCIT) treatment for 1 year. Clinical symptoms and lung function were evaluated every 3 months during HDM SCIT treatment. Basophil activation test (BAT) was carried out before and after HDM SCIT treatment. RNA sequencing was performed in isolated basophils from peripheral blood after 6 months of HDM SCIT treatment, followed by GO term and KEGG pathway enrichment analysis between patients with and without HDM SCIT treatment. HDM AIT treatment ameliorated clinical symptoms while concurrently improved lung function parameters, such as FEV1/FVC, FEF75, FEF50 and MMEF (p < .05). It is worth noting that FEF75 values showed a highly significant, gradual and persistent increase (from 49.55 ± 1.27% at baseline to 71.89 ± 2.64% after 1 year of therapy) and 22 of 35 patients no longer had SAD after 1 year of treatment. BAT results revealed that AIT treatment significantly reduced basophil activity to the inhalant allergen mixtures containing HDM in vitro challenge from baseline. GO term and KEGG pathway enrichment analysis of basophils revealed that downregulated genes were mainly involved in immune cell activation, antigen presentation, and Th2 cell differentiation. Our study demonstrated that HDM AIT not only improved SAD related lung function parameters, but also reduced basophil activity. RNA sequencing revealed the inhibition of phagocytosis and the phagosome pathway in basophils which may affect the polarization of Th2 cell differentiation after HDM AIT.

Autism Spectrum Disorder and Atypical Brain Connectivity: Novel Insights from Brain Connectivity-Associated Genes by Combining Random Forest and Support Vector Machine Algorithm.

It is estimated that approximately one in every 100 children is diagnosed with autism spectrum disorder (ASD) around the globe. Currently, there are no curative pharmacological treatments for ASD. Discoveries on key molecular mechanisms of ASD are essential for precision medicine strategies. Considering that atypical brain connectivity patterns have been observed in individuals with ASD, this study examined the brain connectivity-associated genes and their putatively distinct expression patterns in brain samples from individuals diagnosed with ASD and using an iterative strategy based on random forest and support vector machine algorithms. We discovered a potential gene signature capable of differentiating ASD from control samples with a 92% accuracy. This gene signature comprised 14 brain connectivity-associated genes exhibiting enrichment in synapse-related terms. Of these genes, 11 were previously associated with ASD in varying degrees of evidence. Notably, NFKBIA, WNT10B, and IFT22 genes were identified as ASD-related for the first time in this study. Subsequent clustering analysis revealed the existence of two distinct ASD subtypes based on our gene signature. The expression levels of signature genes have the potential to influence brain connectivity patterns, potentially contributing to the manifestation of ASD. Further studies on the omics of ASD are called for so as to elucidate the molecular basis of ASD and for diagnostic and therapeutic innovations. Finally, we underscore that advances in ASD research can benefit from integrative bioinformatics and data science approaches.

Exploring the detrimental effects of microplastics on Asian seabass (Lates calcarifer) fingerlings survival and health

Microplastics (MPs) are widely used and disposed of indiscriminately, posing a potential threat to aquatic life. Herein, Asian seabass (Lates calcarifer) fingerlings were exposed to various concentrations (1, 10 and 100 ppt or g/kg) of dietary polyethylene MPs for 16 days. The results indicated a significant increase in mortality among the fish fed with dietary MPs compared to the control. Furthermore, histological analysis of the liver revealed moderate-to-severe morphological alterations, hepatocyte necrosis and vacuolisation as the concentration gradient of MPs increased. The severity of the alterations was highest at a concentration of 100 ppt, indicating a direct correlation between MP and liver damage. In addition, RNA sequencing and Gene Ontology term enrichment analysis revealed that a total of 4137 genes were significantly differentially expressed, with 1958 upregulated and 2179 downregulated genes. The significantly enriched terms included ‘oxidoreductase activity’, ‘endocytosis’, ‘mitochondrial’, ‘immune system process’ and ‘lipid catabolic process’. Moreover, the Kyoto Encyclopaedia of Genes and Genomes enrichment analysis demonstrated that dietary MPs triggered oxidative stress, immune response and adaptive mechanism pathways in fish. Thus, MPs can induce metabolic disorders in L. calcarifer, highlighting their potential threat to aquatic organisms.

Screening and identification of microRNAs mediating cartilage endplate degeneration in human intervertebral disks.

This study aimed to discover micro-ribonucleic acids (microRNAs) involved in the degeneration of cartilage endplates through next-generation sequencing and lay the foundation for further research. The cartilage endplate was obtained from patients who underwent interbody fusion surgery at the Department of Spine Surgery, Shanghai East Hospital Affiliated to Tongji University, from 1 January 2020 to 1 January 2023. Total RNA was extracted from the cartilage endplate tissue. Discover differential genes through NGS. To annotate gene functions, all target genes were aligned against the Kyoto Encyclopedia of Genes (KEGG) and Gene Ontology (GO) databases. The GO enrichment and KEGG enrichment analyses of target genes were performed using phyper, a function of R. The p-value was corrected using the Bonferroni method, and a corrected p-value of ≤0.05 was taken as the threshold. GO terms or KEGG terms fulfilling this condition were defined as significantly enriched terms. The screened miRNAs and their target protein were verified in vitro using quantitative polymerase chain reaction (qPCR) and Western blotting (WB). RNA was extracted from normal and degenerated cartilage endplate tissues for NGS. Eight downregulated differentially expressed genes (DEGs) and 22 upregulated DEGs were found. The KEGG pathway analysis of these target genes revealed that differential microRNAs and target genes were enriched in different signaling pathways, and the regulated signaling pathways were mainly mitochondrial autophagy and autophagy. The qPCR results demonstrated a significant upregulation of miR-25-3p and miR-345-5p in degenerative cartilage endplate tissues (p ≤ 0.001). Western blot analysis revealed that BRD4 exhibited a marked increase in protein expression levels in degenerative cartilage endplate tissues (p ≤ 0.0001), while BECN1 showed a significant decrease in protein expression levels within these samples (p ≤ 0.0001). We found that DEG hsa-miR-25-3p and hsa-miR-345-5p can be used as diagnostic and therapeutic targets for IDD. The significant target proteins of miR-25-3p and miR-345-5p were BRD4 and BECN1, respectively.

Mapping transcriptomic profiles of seminal vesiculitis and experimental verification

ObjectiveSeminal vesiculitis is a prevalent infectious disease in the genitourinary system, but its intrinsic pathogenesis and molecular features remain unclear. MethodsIn this study, we utilized next-generation sequencing technology to demonstrate the transcriptomic landscapes of clinical specimens from seminal vesiculitis patients. We identified enriched Go Ontology terms, pathway maps, processes, toxicity, and metabolic networks. ResultsGlutathione transferase activity is highly enriched, indicating its essential role in the disease's development. Furthermore, we established inflammation models of the seminal vesicle and validated the crucial function of glutathione transferase activity in these models ConclusionsOur results provide a robust platform for further intensive studies of seminal vesiculitis.

Transcriptomic Profiles of Male Thai Ricefish (Oryzias minutillus) after Encountering Two Related Species of Males (Oryzias latipes or Oryzias woworae).

&lt;b&gt;Background and Objective:&lt;/b&gt; The Thai ricefish (&lt;i&gt;Oryzias minutillus&lt;/i&gt;) is the smallest &lt;i&gt;Oryzias&lt;/i&gt; spp. and is important in the trophic structure of freshwater ecological systems. However, interactions with related species via gene expression profiles are unknown in this species. Here, this study reports on the first attempt to investigate the transcriptome profiles of male Thai ricefish induced by the males of two &lt;i&gt;Oryzias&lt;/i&gt;. Japanese ricefish (&lt;i&gt;O. latipes&lt;/i&gt;) and Daisy's ricefish (&lt;i&gt;O. woworae&lt;/i&gt;, a remarkably colourful &lt;i&gt;Oryzias&lt;/i&gt;) were used in the experiments. &lt;b&gt;Materials and Methods:&lt;/b&gt; &lt;i&gt;Oryzias minutillus&lt;/i&gt; was put in the presence of &lt;i&gt;O. latipes&lt;/i&gt; (as group 1) or &lt;i&gt;O. woworae&lt;/i&gt; (as group 2) for 7 days in aquaria divided by a transparent partition wall. Thai ricefish faced the same species as control group. Fish in each group were measured the distance between fish individuals of &lt;i&gt;O. minutillus&lt;/i&gt; to &lt;i&gt;O. latipes&lt;/i&gt; or &lt;i&gt;O. woworae&lt;/i&gt;. One-way ANOVA with &lt;i&gt;post hoc&lt;/i&gt; Tukey's test was used to analyse the significant differences among groups. &lt;i&gt;Oryzias minutillus&lt;/i&gt; from groups 1 and 2 on day 7 were subjected to RNA-sequencing analysis via next-generation sequencing. &lt;b&gt;Results:&lt;/b&gt; Long-distance encounters of fish appeared in group 2 on day 7, but there were no significant differences between fish distances. Among the differentially expressed genes, the up-and downregulated genes were more highly expressed in group 2 than in group 1. According to gene ontology term enrichment analysis, genes downregulated in the "locomotion" pathway were detected in group 1 but not in group 2. Conversely, downregulation of "pigmentation" and "reproductive process" was detected only in group 2. &lt;b&gt;Conclusion:&lt;/b&gt; These results suggested that the different patterns of gene expression in &lt;i&gt;O. minutillus&lt;/i&gt; may be affected by the presence of &lt;i&gt;O. latipes&lt;/i&gt; and &lt;i&gt;O. woworae&lt;/i&gt;.