Gene Ontology Pathway Research Articles

Role of intraperitoneal paclitaxel in eosinophil activation and recruitment in the peritoneal cavity and anti-tumor effects against peritoneal metastasis from gastric cancer.

471 Background: Recent studies indicate that the efficacy of chemotherapy is significantly influenced by the tumor immune microenvironment. Peritoneal cavity contains many immune cells, however, the relationship between immune response within the peritoneal cavity and tumor response remains poorly understood. Methods: Single cell suspensions were obtained from ascites or peritoneal lavages from 41 patients with PM from GC. In 28 patients, cells were collected both before and after 1-3 courses of IP chemotherapy. These samples were immunestained with mAbs targeting to specific lymphoid or myeloid subsets, and their proportions in CD45(+) leukocytes were analyzed using flowcytometry. Eosinophils were purified by magnetic cell sorting for subsequent RNA-Seq analysis. Results: Among 41 patients with PM, tumor leukocyte ratio (TLR) calculated as CD326(+) tumor cells divided by CD45(+) leukocytes varied from 0.002% to 58.1%. TLR was not correlated with any ratios of immune cells, however, the ratios of CD8(+) T cells, NK cells and CD16(-) CD193(+) eosinophils tended to decrease with the increase in TLR. Conversely, the ratios of CD19(+) B cell, CD14(+) macrophages and CD16(+) neutrophils increased with elevated TLR. Mean survival time of these patients was 17.7 months. None of the leukocyte subsets showed significant association with patient outcome. In 28 patients, the ratios of lymphocytes mostly decreased with significant difference in CD4(+) T cells and CD19(+) B cells after IP treatment. In contrast, the ratio of CD11b(+) myeloid cells increased in peritoneal cavity after IP treatment. Among the myeloid cells, the ratio of CD16(-) CD193(+) eosinophils significantly increased. The change was particularly prominent in in post-treatment negative peritoneal lavage cytology (CY0) patients (M=0.47% vs M=10.0%, p<0.0001), while the difference was not significant in post-treatment positive peritoneal lavage cytology (CY1) patients (M=0.93% vs M=0.97%, p=0.84). Patients with eosinophil ratio of ≥2% after IP chemotherapy in peritoneal cavity had significantly longer overall survival compared to those with lower eosinophil ratios (17.3 mo vs 26.7 mo, p=0.034; HR =0.23[0.06-0.89]). The peritoneal eosinophils after IP treatment exhibited elevated levels of CD11b and CD63 expression compared to circulating eosinophils (p<0.01), while SSC-A levels tended to be lower. Gene ontology pathways revealed enrichment of cytokine-mediated signaling pathway, extracellular matrix organization and response to interferon-gamma in peritoneal eosinophils (p<0.0001). Conclusions: IP-PTX induces eosinophil activation and recruitment in the peritoneal cavity, while also affecting other types of immune cells. These effects may potentially contribute to the anti-tumor response against peritoneal metastases.

Systemic Changes in Early Pregnancy in the Mare: An Integrated Proteomic Analysis of Blood Plasma, Histotroph, and Yolk Sac Fluid at Day 14 Post‐Ovulation

ABSTRACTPurposeEmbryo‐maternal signaling during the establishment of pregnancy in horses remains one of the biggest mysteries in large animal physiology. Early pregnancy loss represents a major source of economic loss to the breeding industry. This study aimed to investigate the systemic changes associated with early pregnancy by mapping the proteome of blood plasma at 14 days in pregnant and non‐pregnant mares.Experimental DesignPlasma proteomes were analysed in commercially bred pregnant (n = 17) and non‐pregnant (n = 17) Thoroughbred mares at 14 days after ovulation, using high‐resolution mass spectrometry. Day 14 histotroph and yolk sac fluid were also profiled and datasets were integrated through pathway analysis.ResultsWe identified 229 total protein IDs, with 12 increased and 10 decreased significantly in pregnant versus non‐pregnant plasma. To gain functional insight, these data were aligned with proteomes of 14‐day pregnant mare uterine fluid (n = 4; 1358 IDs) and conceptus fluid (soluble proteins within the yolk sac fluid; n = 4; 1152 IDs), and further interrogated using gene ontology databases and pathway analysis.Conclusions and Clinical RelevanceThese analyses identified consistent systemic changes in the mare's proteome that indicate a profound and specific immune response to early pregnancy, which appears to precede the systemic endocrine response to pregnancy. Integrated pathway analysis suggests that embryo‐maternal interactions in early pregnancy may mimic elements of the virus‐host interaction to modulate the maternal immune response. Transthyretin (TTR) and uteroglobin (SCGB1A1) were respectively down‐ and upregulated in plasma while also present in uterine fluid, and are proposed to be key proteins in early pregnancy establishment. These findings contribute significantly to our knowledge of early pregnancy in the mare and identify potential new avenues for developing clinical approaches to reduce early embryo loss.

Pathological and Molecular Characterization of Grass Carp Co-Infected with Two Aeromonas Species.

The grass carp (Ctenopharyngodon idella) is highly susceptible to infections caused by Aeromonas species, particularly A. hydrophila and A. veronii. However, the immunological mechanisms underlying co-infection by these pathogens remain largely uncharted. This study investigated the pathogenesis and host immune response in grass carp following concurrent infection with A. hydrophila and A. veronii. Mortality was observed as early as 24 h post-infection, with cumulative mortality reaching 68%. Quantitative analysis demonstrated significantly elevated bacterial loads in hepatic tissue at 3 days post-infection (dpi). Histopathological evaluation revealed severe hepatic lesions characterized by cellular necrosis, cytoplasmic vacuolization, and hemorrhagic manifestations. Comparative transcriptomic analysis of hepatic tissues between co-infected and control specimens identified 868 and 411 differentially expressed genes (DEGs) at 1 and 5 dpi, respectively. Gene ontology and KEGG pathway analyses revealed significant enrichment of immune-related genes primarily associated with Toll-like receptor signaling and TNF signaling cascades. Notably, metabolic pathways showed substantial suppression while immune responses were significantly activated after infected. These findings provide novel insights into the host-pathogen interactions during Aeromonas co-infection in grass carp, which may facilitate the development of effective prevention and control strategies.

MicroRNA-130b Is a Unique Autophagy-Related Epigenetic Predictor of FLOT-Chemotherapy in Gastric Cancers.

Liquid biopsies have great potential for precision medicine as they provide information about primary and metastatic tumors using minimally invasive techniques. MicroRNAs (miRNAs) are promising biomarkers for detecting gastric cancer (GC). The aim of the study was to identify miR molecules associated with autophagy in gastric cancer (GC) cells, determine their expression levels in GC and FLOT-treated patients, and assess the efficacy of FLOT therapy in GC patients. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathways were used to analyze cellular pathways. MicroRNAs were isolated from the tissues. The study found a connection between the expression of the let-7a-5p gene and the size of primary tumors. Bioinformatics analysis identified multiple targets and signaling pathways associated with this phenomenon. We observed an increase in the levels of miR-21-3p and hsa-miR-130b-3p with lymph node involvement. miR-21-3p is associated with the activation of molecular pathways induced by H. pylori in cases of coinfection. Patients with complete regression had higher levels of expression of hsamir- 130b-3p. The bioinformatics analysis allowed us to identify the most significant targets among microRNAs. Based on the presented data, it becomes clear that GC is heterogeneous and that the process of autophagy is complex. The association between hsa-miR-130b-3p and tumor response to therapy is particularly interesting.

Brain RNA profiling highlights multiple disease pathways in persons with HAND: uncovering determinants of biotype diversity.

To discover microRNA (miRNA)-RNA transcript interactions dysregulated in brains from persons with HIV-associated neurocognitive disorder (HAND), we investigated RNA expression using machine learning tools. Brain-derived host RNA transcript and miRNA expression was examined from persons with or without HAND using bioinformatics platforms. By combining next generation sequencing, droplet digital (dd)PCR quantitation of HIV-1 genomes, with bioinformatics and statistical tools, we investigated differential RNA expression in frontal cortex from persons without HIV (HIV[-]), with HIV without brain disease (HIV[+]), with HIV-associated neurocognitive disorder (HAND), or HAND with encephalitis (HIVE). Expression levels for 147 transcripts and 43 miRNAs showed a minimum 4-fold difference between clinical groups with a predominance of antiviral (Type I interferon) signaling-, neural cell maintenance-, and neurodevelopmental disorder-related genes that was validated by gene ontology and molecular pathway inferences. Scale of signal-to-noise ratio (SSNR) and biweight midcorrelation (bicor) analyses identified 14 miRNAs and 45 RNA transcripts, which were highly correlated and differentially expressed (p ≤ 0.05). Machine learning applications compared regression models predicated on HIV-1 DNA, or RNA viral quantities that disclosed miR-4683 and miR-154-5p were dominant variables associated with differential expression of host RNAs. These miRNAs were also associated with antiviral-, cell maintenance-, and neurodevelopmental disorder-related genes. Antiviral as well as neurodevelopmental disorder-related pathways in brain were associated with HAND, based on correlated RNA transcripts and miRNAs. Integrated molecular methods with machine learning offer insights into disease mechanisms, underpinning brain-related biotypes among persons with HIV that could direct clinical care.

Insights of cellular and molecular changes in sugarcane response to oxidative signaling

Main conclusionSignificant changes in the proteome highlight essential metabolic adaptations for development and oxidative signaling induced by the treatment of young sugarcane plants with hydrogen peroxide. These adaptations suggest that hydrogen peroxide acts not only as a stressor but primarily as a signaling molecule, triggering specific metabolic pathways that regulate growth and plant resilience.Sugarcane is a crucial crop for sugar and ethanol production, often influenced by environmental signals. Hydrogen peroxide (H2O2) is increasingly recognized as an important signaling molecule that regulates plant development and adaptation. In this study, two-month-old sugarcane plants were treated with varying concentrations of H2O2 to investigate how this molecule acts as a signal at the cellular, biochemical, and proteomic levels. Antioxidant enzyme activity exhibited fluctuations, suggesting a dynamic response to oxidative signaling. Lipid peroxidation, observed through TBARs and scanning electron microscopy, highlighted early membrane modifications. Proteomic analysis (ProteomeXchange PXD048142) identified 2,699 proteins, with 155 showing significant expression changes in response to H2O2 signaling. Bioinformatics, including Principal Component Analysis, revealed distinct proteomic profiles in roots and leaves, indicating tissue-specific metabolic reprogramming. Functional annotation through Gene Ontology and KEGG pathway enrichment showed that oxidative signaling led to the repression of photosynthesis-related pathways in leaves, while promoting pathways related to protein processing, glycolysis, and carbon metabolism in roots. Additionally, bioinformatic tools identified proteins involved in amino acid metabolism, the TCA cycle, and carbohydrate metabolism as critical components of sugarcane's adaptive signaling response. The data suggest that sugarcane plants responded to oxidative signals by adjusting their metabolic networks, promoting sustained development and potential pathways for targeted plant breeding.

Integrative Analysis of Whole-Genome and Transcriptomic Data Reveals Novel Variants in Differentially Expressed Long Noncoding RNAs Associated with Asthenozoospermia.

Background/Objectives: Asthenozoospermia, characterized by reduced sperm motility, is a common cause of male infertility. Emerging evidence suggests that noncoding RNAs, particularly long noncoding RNAs (lncRNAs), play a critical role in the regulation of spermatogenesis and sperm function. Coding regions have a well-characterized role and established predictive value in asthenozoospermia. However, this study was designed to complement previous findings and provide a more holistic understanding of asthenozoospermia, this time focusing on noncoding regions. This study aimed to identify and prioritize variants in differentially expressed (DE) lncRNAs found exclusively in asthenozoospermic men, focusing on their impact on lncRNA structure and lncRNA-miRNA-mRNA interactions. Methods: Whole-genome sequencing (WGS) was performed on samples from asthenozoospermic and normozoospermic men. Additionally, an RNA-seq dataset from normozoospermic and asthenozoospermic individuals was analyzed to identify DE lncRNAs. Bioinformatics analyses were conducted to map unique variants on DE lncRNAs, followed by prioritization based on predicted functional impact. The structural impact of the variants and their effects on lncRNA-miRNA interactions were assessed using computational tools. Gene ontology (GO) and KEGG pathway analyses were employed to investigate the affected biological processes and pathways. Results: We identified 4173 unique variants mapped to 258 DE lncRNAs. After prioritization, 5 unique variants in 5 lncRNAs were found to affect lncRNA structure, while 20 variants in 17 lncRNAs were predicted to disrupt miRNA-lncRNA interactions. Enriched pathways included Wnt signaling, phosphatase binding, and cell proliferation, all previously implicated in reproductive health. Conclusions: This study identifies specific variants in DE lncRNAs that may play a role in asthenozoospermia. Given the limited research utilizing WGS to explore the role of noncoding RNAs in male infertility, our findings provide valuable insights and a foundation for future studies.

The role of microRNA in the regulation of hepatic metabolism and energy-expensive processes in the hibernating dormouse.

The garden dormouse (Eliomys quercinus) is a fat-storing mammal that undergoes annual periods of hibernation to mitigate the effects of food scarcity, low ambient temperatures, and reduced photoperiod that characterize winter. Like other hibernating species, this animal suppresses its metabolic rate by downregulating nonessential genes and processes in order to prolong available energy stores and limit waste accumulation throughout the season. MicroRNAs (miRNAs) are short, single-stranded, noncoding RNAs that bind to mRNA and mediate post-transcriptional suppression, making miRNA ideal for modulating widespread changes in gene expression, including global downregulation typified by metabolic rate depression. Using next-generation sequencing, we analyzed an RNA-seq dataset to determine which miRNAs are differentially regulated during hibernation in the dormouse liver. We found that the expression of 19 miRNAs was altered during hibernation; however, only one major miRNA (miR-34a-5p) remained significantly downregulated after correcting for false discovery rate. Gene Ontology and KEGG Pathway Analysis predicted that energy metabolism, nuclear-related functions such as histone binding, chromatin- and chromosomal binding, and the cell cycle are processes that may be differentially regulated during hibernation due to miRNA regulation. Taken together, our data suggest that miRNA influence appears to be strongly directed toward suppressing energy-intensive processes in the nucleus hence contributing to extend the animal's endogenous fuel reserves for the duration of hibernation.

Trained Immunity Enhances Host Resistance to Infection in Aged Mice.

Aging significantly increases the incidence and severity of infections, with individuals aged 65 and above accounting for 65% of sepsis cases. Innate immune training, known as "trained immunity" or "innate immune memory", has emerged as a potential strategy to enhance infection resistance by modulating the aging immune system. We investigated the impact of β-glucan-induced trained immunity on aged mice (18-20 months old) compared to young adult mice (10-12 weeks old). Our findings showed that β-glucan equally augmented the host resistance to infection in both young and aged mice. This enhancement was characterized by augmented bacterial clearance, enhanced leukocyte recruitment and decreased cytokine production in response to Pseudomonas aeruginosa infection. Furthermore, young and aged trained macrophages displayed heightened metabolic capacity and improved antimicrobial functions, including enhanced phagocytosis and respiratory burst. RNA-seq analysis showed a distinctive gene expression pattern induced by trained immunity in macrophages characterized by activation of pathways regulating inflammation and the host response to infection and suppression of pathways regulating cell division, which was consistently observed in both young and aged groups. As compared to macrophages from young mice, aged macrophages showed increased activation of gene ontology pathways regulating angiogenesis, connective tissue deposition and wound healing. Our results indicate that immune training can be effectively induced in aging mice, providing valuable insights into potential strategies for enhancing infection resistance in the elderly.

Understanding the Molecular Mechanisms of Incomptine A in Treating Non-Hodgkin Lymphoma Associated with U-937 Cells: Bioinformatics Approaches, Part I.

Background: Incomptine A (IA) has been reported to have cytotoxic activity in non-Hodgkin lymphoma cancer cell lines and have effects on U-937 cells, including the induction of apoptosis, the production of reactive oxygen species, and the inhibition of glycolytic enzymes. Also, IA has cytotoxic activity in the triple-negative subtypes, HER2+, and luminal A of breast cancer cells, with its properties being associated with an effect on the antiapoptotic function of Hexokinase II (HKII). Objectives: In this research, we reviewed the altered levels of proteins present in the lymph nodes of male Balb/c mice inoculated with U-937 cells and treated with IA or methotrexate, as well as mice only inoculated with cancer cells. Methods: Five approaches, including Tandem Mass Tag (TMT), Gene ontology (GO), Reactome, KEGG pathway analysis, and molecular docking, were used. Results: TMT showed that 74 proteins were differentially expressed, out of which 12 presented overexpression (FC ≥ 1.5) and 62 were under expressed (FC ≤ 0.67). In general, the TMT approach showed that IA had a better effect on proteins than methotrexate. Gene ontology, Reactome, and KEGG pathway analysis showed that proteins with altered levels may be implicated in several processes, including gene silencing by RNA, oxidative phosphorylation, glycolysis/gluconeogenesis, cytoskeleton organization, and ATP metabolic and energetic processes. The molecular docking analysis, which used 23 altered proteins as targets, revealed that IA interacted with all the proteins used. Conclusions: The results obtained using the five bioinformatic approaches provide information and show that IA could be used to treat non-Hodgkin lymphoma induced with the U-937 cell line. Also, it could provide a basis for future research and the development of clinical trials.

MicroRNA Screening Reveals Upregulation of FoxO-Signaling in Relapsed Acute Myeloid Leukemia Patients.

Background/Objectives: AML is an aggressive malignant disease characterized by aberrant proliferation and accumulation of immature blast cells in the patient's bone marrow. Chemotherapeutic treatment can effectively induce remission and re-establish functional hematopoiesis. However, many patients experience chemoresistance-associated relapse and disease progression with a poor prognosis. The identification of molecular determinants of chemoresistance that could serve as potential targets for the therapeutic restoration of chemosensitivity has proven to be challenging. Methods: To address this, we have analyzed longitudinal changes in the expression of microRNAs during disease progression in a small set of four AML patients, combined with gene ontology (GO) pathway analysis and evaluation of gene expression data in patient databases. Results: MicroRNA profiling of bone marrow samples at diagnosis and after relapse revealed significant differential expression of a large number of microRNAs between the two time points. Subsequent GO pathway analysis identified 11 signal transduction pathways likely to be affected by the differential miRNA signatures. Exemplary validation of the FoxO signaling pathway by gene expression analysis confirmed significant upregulation of FOXO1 and the target genes GADD45 and SOD2. Conclusions: Here, we show how a microRNA-based pathway prediction strategy can be used to identify differentially regulated signaling pathways that represent potential targets for therapeutic intervention.

Identification of a pyroptosis-related prognostic model for colorectal cancer and validation of the core gene SPTBN5

BackgroundPyroptosis, an emerging type of programmed cell death. The mechanisms of pyroptosis mainly include inflammasome-activated pyroptosis and non-inflammasome-activated pyroptosis. Multiple prognostic scoring systems that utilize pyroptosis-related gene expression have been validated as effective predictors of patient outcomes. But the relationship between pyroptosis and colorectal cancer remains unclear. This study has established a gene signature associated with pyroptosis to forecast the prognosis of CRC patients. MethodsAn analysis of 52 pyroptosis genes was conducted in both CRC and normal colorectal tissues, leading to the discovery of differentially expressed genes (DEGs). Core pyroptosis-related genes were identified using least absolute shrinkage and selection operator (LASSO) Cox regression to establish a prognostic risk score (PRS) for predicting CRC patient outcomes. The TCGA cohort was split into high-risk and low-risk groups based on the PRS, followed by Gene Ontology (GO) and KEGG pathway analyses. Additionally, differences in the enrichment scores of 16 immune cell types and the activity of 13 immune-related pathways were compared. The role of SPTBN5, a core pyroptosis-related gene, was validated through functional experiments on human colorectal adenocarcinoma cells (SW480).Results40 differentially expressed genes were identified from 52 pyroptosis genes. A risk model was subsequently developed using 25 core pyroptosis-related genes identified through LASSO Cox regression analysis, and this model was validated in GEO cohorts. GO and KEGG pathway analyses showed that the DEGs are predominantly associated with mineral absorption, thyroid hormone synthesis, and pancreatic secretion. Functional experiments demonstrated that down-regulation of SPTBN5 expression through transfection led to significant decreases in the proliferation, migration, and clonogenicity of SW480 cells.ConclusionThe PRS can identify high-risk CRC patient groups and predict patient prognosis. SPTBN5 may present a potential therapeutic target for CRC.

Magnesium Supplementation Modifies Arthritis Synovial and Splenic Transcriptomic Signatures Including Ferroptosis and Cell Senescence Biological Pathways.

Rheumatoid arthritis (RA) is a common systemic autoimmune inflammatory disease that can cause joint damage. We have recently reported that oral magnesium supplementation significantly reduces disease severity and joint damage in models of RA. In the present study, we analyzed the transcriptome of spleens and synovial tissues obtained from mice with KRN serum-induced arthritis (KSIA) consuming either a high Mg supplemented diet (Mg2800; n = 7) or a normal diet (Mg500; n = 7). Tissues were collected at the end of a 15-day KSIA experiment. RNA was extracted and used for sequencing and analyses. There was an enrichment of differentially expressed genes (DEGs) belonging to Reactome and Gene Ontology (GO) pathways implicated in RA pathogenesis such as RHO GTPases, the RUNX1 pathway, oxidative stress-induced senescence, and the senescence-associated secretory phenotype. Actc1 and Nr4a3 were among the genes with the highest expression, while Krt79 and Ffar2 were among the genes with the lowest expression in synovial tissues of the Mg2800 group compared with the Mg500 group. Spleens had an enrichment for the metabolism of folate and pterines and the HSP90 chaperone cycle for the steroid hormone receptor. We describe the tissue transcriptomic consequences of arthritis-protecting Mg supplementation in KSIA mice. These results show that oral Mg supplementation may interfere with the response to oxidative stress and senescence and other processes known to participate in RA pathogenesis. We provide new evidence supporting the disease-suppressing effect of increased Mg intake in arthritis and its potential to become a new addition to the therapeutic options for RA and other autoimmune and inflammatory diseases.

Genomic Insights into Rheumatoid Arthritis through computational Profiling for Hub Genes

Rheumatoid arthritis (RA) is a complex autoimmune disorder predominantly affecting joints, with its etiology and response to treatment still not fully understood despite extensive historical documentation. This study aims to shed light on the differentially expressed genes (DEGs) associated with RA progression, potentially identifying new drug targets and management strategies. This study analyzed gene expression data (GSE193193) from the Gene Expression Omnibus (GEO) database, identifying 3672 significant DEGs out of 36107 initially retrieved genes. Among these, 283 genes were up-regulated and 360 were down-regulated. Gene enrichment analysis was performed to uncover relevant gene ontology terms and pathways. Subsequently, network construction and analysis, along with hub gene prediction using Cytoscape's MCODE and CytoHubba plugins, were conducted. Key genes identified in this study include HBB, ALAS2, GATA1, AHSP, HBG1, HBG2, HBD, KLF1, SLC4A1, EPB42, ZMYND10, DNAJC7, HYDIN, LRRC6, FN1, NCAM1, FASLG, CTCF, SMAD4, and STAT1. These genes are implicated not only in RA but also in other diseases, presenting them as potential therapeutic targets. Additionally, three transcription factors (GATA1, NFKB1, and RELA) and one miRNA (has-mir-27a-3p) were identified as key regulators of these hub genes. In conclusion, this study not only enhances our understanding of the molecular mechanisms underlying RA but also identifies several critical DEGs and regulatory factors that could serve as promising targets for therapeutic intervention. The identification of these genes and regulatory elements paves the way for the development of targeted treatments, which could significantly improve disease management and patient outcomes. Future research focusing on these identified targets may lead to innovative strategies for combating RA and potentially other autoimmune disorders, thereby offering new hope to patients affected by these conditions.

Transcriptomic Profiling Reveals Altered Expression of Genes Involved in Metabolic and Immune Processes in NDV-Infected Chicken Embryos.

The poultry industry is significantly impacted by viral infections, particularly Newcastle Disease Virus (NDV), which leads to substantial economic losses. It is essential to comprehend how the sequence of development affects biological pathways and how early exposure to infections might affect immune responses. This study employed transcriptome analysis to investigate host-pathogen interactions by analyzing gene expression changes in NDV-infected chicken embryos' lungs. RNA-Seq reads were aligned with the chicken reference genome (Galgal7), revealing 594 differentially expressed genes: 264 upregulated and 330 downregulated. The most overexpressed genes, with logFC between 8.15 and 8.75, included C8A, FGG, PIT54, FETUB, APOC3, and FGA. Notably, downregulated genes included BPIFB3 (-4.46 logFC) and TRIM39.1 (-4.26 logFC). The analysis also identified 29 novel transcripts and 20 lncRNAs that were upregulated. Gene Ontology and KEGG pathways' analyses revealed significant alterations in gene expression related to immune function, metabolism, cell cycle, nucleic acid processes, and mitochondrial activity due to NDV infection. Key metabolic genes, such as ALDOB (3.27 logFC), PRPS2 (2.66 logFC), and XDH (2.15 logFC), exhibited altered expression patterns, while DCK2 (-1.99 logFC) and TK1 (-2.11 logFC) were also affected. Several immune-related genes showed significant upregulation in infected lung samples, including ALB (6.15 logFC), TLR4 (1.86 logFC), TLR2 (2.79 logFC), and interleukin receptors, such as IL1R2 (3.15 logFC) and IL22RA2 (1.37 logFC). Conversely, genes such as CXCR4 (-1.49 logFC), CXCL14 (-2.57 logFC), GATA3 (-1.51 logFC), and IL17REL (-2.93 logFC) were downregulated. The higher expression of HSP genes underscores their vital role in immune responses. Comprehension of these genes' interactions is essential for regulating viral replication and immune responses during infections, potentially aiding in the identification of candidate genes for poultry breed improvement amidst NDV challenges.

Proteomic Alterations in Retinal Müller Glial Cells Lacking Interleukin-6 Receptor: A Comprehensive Analysis.

Interleukin-6 (IL-6) is an inflammatory cytokine implicated in various retinal pathologies and functions primarily through two signaling pathways: cis-signaling via IL-6 binding to its membrane-bound receptor (IL-6Rα), and trans-signaling via IL-6 binding to soluble IL-6 receptor (sIL-6R). Because the differential effects of IL-6 signaling in retinal Müller glial cells (MGCs) remain unclear, we generated an MGC-specific Il6ra-/- knockout (KO) mouse to eliminate IL-6Rα and, consequently, IL-6 cis-signaling in MGCs. In this study, we examined the proteomic changes in MGCs isolated from KO mice lacking a functional IL-6Rα. The proteomes of MGCs isolated from wild-type (WT) and KO mice were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and validated by parallel reaction monitoring (PRM). Relevant biological functions and pathways were examined using Gene Ontology and Ingenuity Pathway Analysis. LC-MS/MS detected 1866 proteins, of which 81 were significantly altered (41 upregulated, 40 downregulated). PRM analysis confirmed differential expression of Ptgis (fold change [FC] = 3.63), Dpep1 (FC = 2.79), Fmo1 (FC = 2.77), Igfbp7 (FC = 2.07), Rpb1 (FC = 1.73), Pygp (FC = 1.46), Niban 1 (FC = 0.58), Mest (FC = 0.48), and Aldh3a1 (FC = 0.30). The significantly altered proteins are involved in oxidative stress balance, inflammation, mitochondrial dysfunction, and regulation of vascular endothelial growth factor (VEGF) signaling. The absence of IL-6Rα in KO MGCs corresponded to significant changes in their proteomic profile, highlighting the impact of autocrine IL-6 signaling on MGC function. This study provides a basis for future research evaluating distinct roles of IL-6 in MGCs and subsequent effects on retinal pathology.

Exploration of the key active ingredients and mechanisms of Sparganii Rhizoma-Curcumae Rhizoma compatible formulation against human colorectal cancer through network pharmacology and in vitro experiments

IntroductionSparganii Rhizoma-Curcumae Rhizoma (SR-CR) formulation may offer an effective treatment for human colorectal cancer (CRC). However, the active ingredients and underlying mechanisms of this herbal formulation remain unclear. MethodsThis study integrates network pharmacology, molecular docking and experimental verification to identify key active ingredients and elucidate the mechanisms of SR-CR in CRC treatment. ResultsTwenty-three active components of SR-CR were identified using the TCMSP, UniProt and Gene Cards databases. These components were associated with 178 targets, of which 118 are directly related to CRC. Protein-protein interaction (PPI) network analysis identified protein kinase B (AKT) 1, epidermal growth factor receptor (EGFR), SRC, Bcl2 and CASP3 as core anti-CRC targets. Gene Ontology (GO) and KEGG pathway analyses were performed on these 178 intersecting targets, and the results showed that these targets are involved in EGFR tyrosine kinase inhibitor resistance and AGE-RAGE signaling pathway in diabetic complications. At the same time, five compounds, including bisdemethoxycurcumin, formononetin, β-sitosterol, stigmasterol and hederagenin, were selected based on the target number of effective components and tested for cytotoxicity against human CRC cell lines HT-29, HCT-8 and HCT-116 in vitro. The results showed that bisdemethoxycurcumin exhibited significant anti-proliferative activity against HCT-116 cells. Molecular docking results indicated that bisdemethoxycurcumin effectively binds with AKT, EGFR, Bcl-2 and CASP3. Further pharmacological experiments demonstrated that bisdemethoxycurcumin inhibits HCT-116 cell proliferation and migration via inhibiting EGFR-AKT pathway, and induces apoptosis by up-regulating Bcl-2 expression. DiscussionBased on our study, inhibiting the EGFR-AKT pathway and upregulating Bcl2 may be one of the mechanisms by which SR-CR inhibits the growth of CRC. The main active ingredients of SR-CR include bisdemethoxycurcumin, formononetin, β-sitosterol, stigmasterol and hederagenin, which may exert anti-colon cancer activity by targeting the regulation of AKT, EGFR, Bcl-2 and CASP3. However, we need more in vitro and in vivo evidence to confirm this conclusion. This study lays the foundation for further research on the pharmacological mechanism of SR-CR in the treatment of CRC.

The identification of key genes and pathways in polycystic ovary syndrome by bioinformatics analysis of next-generation sequencing data

BackgroundPolycystic ovary syndrome (PCOS) is a reproductive endocrine disorder. The specific molecular mechanism of PCOS remains unclear. The aim of this study was to apply a bioinformatics approach to reveal related pathways or genes involved in the development of PCOS.MethodsThe next-generation sequencing (NGS) dataset GSE199225 was downloaded from the gene expression omnibus (GEO) database and NGS dataset analyzed is obtained from in vitro culture of PCOS patients’ muscle cells and muscle cells of healthy lean control women. Differentially expressed gene (DEG) analysis was performed using DESeq2. The g:Profiler was utilized to analyze the gene ontology (GO) and REACTOME pathways of the differentially expressed genes. A protein–protein interaction (PPI) network was constructed and module analysis was performed using HiPPIE and cytoscape. The miRNA-hub gene regulatory network and TF-hub gene regulatory network were constructed. The hub genes were validated by using receiver operating characteristic (ROC) curve analysis.ResultsWe have identified 957 DEG in total, including 478 upregulated genes and 479 downregulated gene. GO terms and REACTOME pathways illustrated that DEG were significantly enriched in regulation of molecular function, developmental process, interferon signaling and platelet activation, signaling, and aggregation. The top 5 upregulated hub genes including HSPA5, PLK1, RIN3, DBN1, and CCDC85B and top 5 downregulated hub genes including DISC1, AR, MTUS2, LYN, and TCF4 might be associated with PCOS. The hub gens of HSPA5 and KMT2A, together with corresponding predicted miRNAs (e.g., hsa-mir-34b-5p and hsa-mir-378a-5p), and HSPA5 and TCF4 together with corresponding predicted TF (e.g., RCOR3 and TEAD4) were found to be significantly correlated with PCOS.ConclusionsThese study uses of bioinformatics analysis of NGS data to obtain hub genes and key signaling pathways related to PCOS and its associated complications. Also provides novel ideas for finding biomarkers and treatment methods for PCOS and its associated complications.

Comprehensive prognostic gene identification and functional characterization of GRAMD1A in Wilms tumor: development of risk prediction models and therapeutic implications.

Wilms tumor (WT) is the most common pediatric kidney cancer, with survival rates exceeding 90% in localized cases. However, advanced or recurrent WT remains difficult to treat due to poor prognosis and limited knowledge of its molecular mechanisms. Gene expression profiling has shown promise in identifying prognostic markers and therapeutic targets. This study aimed to identify key prognostic genes and pathways in WT, construct risk prediction models, and validate their role in tumor progression. RNA sequencing and clinical data from 136 WT patients were obtained from the TARGET database. Differential gene expression analysis was conducted using GEO datasets GSE11024 and GSE66405 to compare WT and normal kidney tissues. Identified differentially expressed genes (DEGs) underwent Gene Ontology (GO) and KEGG pathway enrichment analysis to explore biological functions and pathways associated with WT progression. Univariate Cox regression was used to assess the association between DEGs and overall survival (OS) and progression-free survival (PFS). LASSO regression models were developed for risk stratification, and model accuracy was evaluated using time-dependent ROC curves. External validation confirmed key hub genes, while functional assays in WT cell lines (WiT-49) assessed the role of GRAMD1A in tumor behavior. A total of 3,395 DEGs were identified, with 1,564 upregulated and 1,831 downregulated genes. Enrichment analyses revealed significant pathways involved in cell cycle regulation and metabolic reprogramming. Six key genes (GRAMD1A, PLXNA3, SPR, EBAG9, RBM47, and RIDA) were associated with both OS and PFS. LASSO models demonstrated strong predictive performance, with GRAMD1A identified as a major risk factor. External validation confirmed differential expression, and functional assays showed that GRAMD1A silencing significantly inhibited WT cell viability, proliferation, migration, and invasion. This study identifies novel prognostic genes and potential therapeutic targets in WT. GRAMD1A, SPR, EBAG9, RBM47, and RIDA play critical roles in WT progression, with GRAMD1A as a key oncogenic factor, offering potential for risk stratification and future therapeutic intervention.

Identification of gastric cancer biomarkers through in-silico analysis of microarray based datasets

Gastric cancer is among the most prevalent cancers worldwide including in Pakistan. Late diagnosis of gastric cancer leads to reduced survival. The present study aimed to investigate biomarkers for early diagnosis and prognosis of gastric cancer. For this purpose, the ten microarray-based gene expression datasets (GSE54129, GSE79973, GSE161533, GSE103236, GSE33651, GSE19826, GSE118916, GSE112369, GSE13911, and GSE81948) were retrieved from GEO database and analyzed by GEO2R to identify differentially expressed genes. Datasets were arranged in subsets of different dataset combinations to identify common DEGs. The gene ontology and functional pathway enrichment analysis of common DEGs was performed by DAVID tool. Pan-cancer analysis was conducted by UALCAN database. Survival analysis of common DEGs was done by Kaplan-Meier plotter. A total of 71 common DEGs were identified in different combinations of datasets. Among them, only 5 DEGs namely ATP4B, ATP4A, CCKBR, KCNJ15, and KCNJ16 were detected to be common in all the datasets. The GO and pathway analysis represented that the identified DEGs are involved in gastric acid secretion and collecting duct acid secretion pathways. Further expression validation of these five genes using three additional datasets (GSE31811, GSE26899, and GSE26272) confirmed their differential expression in gastric cancer samples. The pan-cancer analysis also revealed aberrant expression of DEGs in various cancers. The survival analysis showed the association of these 5 DEGs with poor survival of gastric cancer patients. To conclude, this study revealed a panel of 5 genes, which can be employed as diagnostic and prognostic biomarkers of gastric cancer patients.