Differentially Expressed Genes Research Articles

Integrated Transcriptomic and Metabolomic Analysis of Rat PASMCs Reveals the Underlying Mechanism for Pulmonary Arterial Hypertension.

Pulmonary arterial hypertension (PAH) is a kind of pulmonary vascular lesion characterized by vasoconstriction and reshaping of small pulmonary arteries, ultimately resulting in increased pulmonary artery pressure and pulmonary vascular resistance, and eventually leading to right ventricular failure and death. This study was aimed to construct a platelet-derived growth factor BB (PDGF-BB)-induced rat pulmonary artery smooth muscle cells (PASMCs) model and conduct a combined transcriptomic and metabolomic analysis to identify proliferation-related targets, thereby enhancing understanding of the pathogenesis underlying PAH. Rat PASMCs were isolated and cultured in the presence or absence of PDGF-BB for 24 hours. Cells were collected for transcriptomics and metabolomics investigations. A total of 1288 differentially expressed genes (572 up-regulated and 716 down-regulated) were identified in PDGF-BB-treated rat PASMCs compared to control cells. Subsequently, Gene ontology (GO) enrichment analysis revealed that 791 enriched GO terms were significantly enriched in PDGF-BB treated cells. Similarly, 294 differential metabolic pathways were enriched in PDGF-BB treated cells according to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, Gene Set Enrichment Analysis (GSEA) were performed on the differentially expressed genes (DEGs). It turned out that 7219 gene sets were more enriched in PDGF-BB treated cells. In addition, a total of 28 secondary differential metabolites were identified in PDGF-BB-treated rat PASMCs compared to control cells (p-value < 0.05 and VIP > 1). We speculate that Mylk, Pla2g4a, Gucy1b1, Adcy8, Adcy4, Gucy1a2, Col3a1, and Plcb4 are potential targets for the treatment of PAH.

Molecular Subtype Identification and Potential Drug Prediction Based on Anoikis-Related Genes Expression in Keratoconus.

Anoikis is a special apoptosis accompanied by the loss of extracellular matrix (ECM) environment and the decomposition of ECM is an important process in the occurrence of keratoconus (KC). This study aims to describe the expression profile of anoikis-related genes (ARGs) in KC samples, identify differentially expressed genes (DEGs), characterize the biological functions and immune characteristics of different molecular subtypes of KC and predict potential drugs based on the construction of a co-expression network. First, we identified molecular subtypes by optimal clustering K based on the expression profile of ARGs in the KC dataset and analyzed the differences of functional and immune characteristics. Then a weighted gene co-expression network was constructed based on cluster analysis to obtain hub genes and protein-protein interaction network was constructed to analyze hub nodes and predict potential node-targeting drugs. By comparing the expression profile between disease and normal samples, we found that there were significant differences in ARGs such as BCL2, CAV1, and CEACAM5. Consistent cluster analysis identified two definite clusters on the basis of ARGs expression difference. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment analysis showed that DEGs were enriched significantly in pathways like ECM receptor interaction, chemokine signal, notch signal, focal adhesion, and functional sets like proteolysis, anoikis, regulation of natural killer and T-cell proliferation. CIBERSORT calculation showed that there were significant differences between the two subtypes on immune cell infiltration (monocytes and plasma) and immune molecules (CCL11, CCL14, HLA-A, HLA-B, and so on). Then, co-expression network was constructed based on cluster phenotype, 5202 genes were selected as hub genes, and 321 HubDEGs were obtained after intersection with significant DEGs. Seven hub nodes, EIF4G1, KHSRP, PABPC1, POLR2A, PTBP1, RPS19, and SMARCA4, were identified and matched drugs or small molecular compounds. Insulin and dexamethasone were identified as potential target drugs. We revealed the differential expression of ARGs in KC samples, and identified two distinct subtypes that showed significant differences in biological function and immune infiltration. The identification of hub gene nodes elucidated their therapeutic value on predicted potential drugs.

The Effects of miR-22-3p on Differentiation of Human Dental Pulp Stem Cells into Neural Progenitor-Like Cells.

Stem cell treatment shows promise in treating conditions such as neurodegenerative disorders and spinal injuries, but its effectiveness is hampered by cell death and apoptosis. Improving the differentiation of MSCs into neural cells could enhance their therapeutic potential. The role of miR-22-3p in human dental pulp stem cells (HDPSCs), a superior alternative to treat neurodegenerative disorders, and its molecular mechanisms during neural differentiation remain elusive. Therefore, we investigated the miR-22-3p transfections during HDPSC differentiation into neural progenitor-like cells (NPCs) and elucidated the molecular processes through transcriptomic analysis. HDPSCs were differentiated into NPCs after transfection with a miR-22-3p mimic and inhibitor; the differentiation process was assessed by cell viability and expression of Nestin protein. mRNA sequencing on days 1, 3, and 7 of the differentiation process identified several differentially expressed genes (DEGs). Cytoscape and functional enrichment analysis pinpointed central hub genes among the DEGs and uniquely expressed genes. miR-22-3p mimic hindered HDPSC differentiation by reducing proliferation and increasing apoptosis. It downregulated genes linked to extracellular matrix, synaptic and vesicle functions, lipid metabolism, JAK-STAT, and cell cycle pathways across all days while activating proteasome and digestion pathways. In contrast, miR-22-3p inhibition boosts NPC proliferation and elevates Nestin neural marker protein expression. Altogether, miR-22-3p disrupts synapse functioning and lipid metabolism pathways, resulting in apoptosis and death. Conversely, inhibiting miR-22-3p enhances neural differentiation and proliferation of HDPSCs, suggesting its potential application in generating a greater quantity of NPCs and neurons.

Transcriptome Analysis Revealed the Regulatory Mechanism of DIMBOA Affecting Early Somatic Embryogenesis in Dimocarpus longan Lour.

Dimocarpus longan Lour. is an evergreen tree of the genus Longan in the Sapindaceae family, native to tropical and subtropical regions. Longan embryonic development is closely related to fruit set and fruit quality. An in-depth study of the mechanism of longan embryonic development could therefore contribute to the development of the longan industry. DIMBOA is the principal compound representing benzoxazinoids (BXs), and is closely linked to auxin biosynthesis and signal transduction. Auxin is one of the crucial hormones for inducing somatic embryogenesis (SE) in plants. Previous research has shown that DIMBOA promotes morphogenesis in the early somatic embryogenesis of longan, but the specific regulatory mechanism has not yet been clarified. To elucidate the molecular mechanism by which DIMBOA affects early somatic embryogenesis in longan, we chose longan embryogenic cultures grown under 0 mg/L DIMBOA as the control group (the check, CK), and longan embryogenic cultures grown under 0.1 mg/L DIMBOA as the treatment group (D) to be analyzed by transcriptomic sequencing. A total of 478 differentially expressed genes (DEGs) are detected in check vs. D, of which 193 are upregulated and 285 are downregulated. These DEGs are significantly enriched in the biosynthetic and metabolic functions of various substances such as vitamin B6 (VB6) biosynthesis, phenylpropanoid pathways, and carbohydrate metabolism. DIMBOA affects SE processes in longan via TFs, including MYB, ZF, bHLH, LBD, NAC, WRKY, etc. After DIMBOA treatment, the expression of most of the key genes for IAA synthesis was significantly downregulated, VB6 content was significantly reduced, and H2O2 content was significantly increased. Therefore, it is suggested that DIMBOA directly or indirectly affects the H2O2 content through the VB6 metabolic pathway, thereby regulating the endogenous IAA level to modulate the early SE morphogenesis of longan.

Mining differentially expressed genes in Fagus crenata seedlings in response to short‐term soil drought stress

AbstractWe analyzed the transcriptional response of current‐year Fagus crenata (beech) seedling leaves after exposure to short‐term drought. Following well‐watered and water‐stressed treatments, we mapped the RNA‐seq reads from the sampled leaves and identified 127 differentially expressed genes (DEGs), of which 89 were upregulated and 38 downregulated in water‐stressed plants. Several dozen upregulated DEGs were predicted to encode proteins that facilitate mitigating processes or help avoid the adverse effects caused by drought stress, including stomatal closure, reactive oxygen species (ROS) scavenging, abscisic acid (ABA) accumulation and response, and accumulation of osmoprotectants. The functional category of sulfate assimilation was enriched in upregulated DEGs, although there was also evidence of sulfur deficiency. These results suggest the existence of molecular mechanisms in beech that are common to other plant species, representing an acclimation response to drought stress as well as sulfur metabolism under drought stress conditions.

Peripheral Transcriptomics in Acute and Long-Term Kidney Dysfunction in SARS-CoV2 Infection.

Acute kidney injury (AKI) is common in SARS-CoV-2 infection and COVID-19, often leading to long-term kidney dysfunction. However, the transcriptomic features of AKI severity and its long-term effects are underexplored. We performed bulk RNA sequencing on peripheral blood mononuclear cells (PBMCs) from hospitalized SARS-CoV-2 patients and complemented these findings with proteomic data from the same cohort. We compared the functional enrichment findings with historical sepsis-AKI data and subsequently examined the association between molecular signatures and long-term kidney function changes. In 283 patients, 57 had mild AKI (stage 1) and 49 had severe AKI (stage 2 or 3). Following adjustments for age, sex, severity of infection, and pre-existing chronic kidney disease (CKD), we identified 6,432 differentially expressed genes (DEGs) in the severe AKI vs. control comparison, 840 in the mild AKI vs. control, and 1,213 in the severe vs. mild AKI comparison (FDR<0.05). Common pathways included unfolded protein response, cellular response to stress via eIF2, and IFN-g-mediated inflammatory response. Severe AKI was linked to pathways involved in mitochondrial dysfunction and endoplasmic reticulum stress. Proteomic analysis confirmed 40 established AKI and inflammation biomarkers, while gene-set enrichment of transcription regulators revealed additional biomarkers for severe AKI. Comparison with PBMC transcriptomics from sepsis-related AKI showed significant functional overlap (30%). Analysis of post-discharge eGFR data in 115 patients identified 177 DEGs for severe vs. control, 106 for mild vs. control, and 46 for severe vs. mild AKI. Key associations included kidney function decline related to carbohydrate and mitochondrial metabolism, inflammatory-response, and cardiovascular regulation. We demonstrate that severe AKI in SARS-CoV-2 infection is linked to mitochondrial dysfunction and ER stress. The functional overlap with sepsis-AKI suggests potential broader therapeutic applicability. Long-term kidney dysfunction is influenced by disruptions in cellular energy metabolism and immune response.

Identification of prognostic biomarker of non-small cell lung cancer based on mitochondrial permeability transition-driven necrosis-related genes and determination of anti-tumor effect of ARL14

BackgroundMitochondrial permeability transition (MPT)-driven necrosis (MPTDN) is a non-apoptotic mode of cell death triggered by oxidative stress and cytosolic Ca2+ overload. Recent evidence suggests that activation of MPTND can effectively induce cancer cell death and may represent a novel therapeutic strategy for cancer. Yet, the role of MPTDN-related genes in non-small cell lung cancer (NSCLC) remains unrevealed. This study aimed to identify MPTDN-related biomarkers for predicting prognosis and guiding treatment in NSCLC.MethodsGene expression profiles and clinical information of NSCLC were collected from public databases, and MPTDN-related genes were obtained from published article. Differential expressed MPTDN-related genes in NSCLC and control were screened, and molecular clusters were obtained. Based on the differentially expressed genes (DGEs) between clusters, univariate Cox and LASSO regression analyses were performed to screen biomarkers, followed by nomogram construction. Correlations between these biomarkers and immune cell infiltration, immune checkpoints, and chemotherapeutic agents were observed. Expression levels of MPTDN-related biomarkers were detected using RT-qPCR in NSCLC tissues and cells. Moreover, the biological function of ARL14 in NSLCL was verified in vitro.ResultsThirty-five differential MPTDN-related genes were identified, and two molecular clusters were obtained. Three biomarkers with prognostic values were finally screened, including ARL14, ZDHHC11B, and HLF. Among them, ARL14 was significantly upregulated in tumor samples, while ZDHHC11B and HLF were downregulated. Nomogram containing three genes exhibited predictive accuracy in 1, 3, and 5-year survival rates. Three gene were strongly associated with most immune cells, immune checkpoints, and drugs sensitivity. RT-qPCR confirmed that expression levels of three genes in tissues or cells were consistent with the results of bioinformatics analysis. Finally, ARL14 knockdown inhibited the malignant phenotype of NSCLC cells.ConclusionWe first performed the comprehensive analysis of MPTDN in NSCLC and screened three NSCLC-related biomarkers as promising biomarkers. ARL14 might be a new potential target for therapy of NSCLC.

A Phenotypically Distinct Human Th2 Cell Subpopulation Is Associated With Development of Allergic Disorders in Infancy.

Little is known about the ontogeny of T cell immunity during infancy in farming and urban lifestyles due to the lack of immunophenotyping in such birth cohorts. Two birth cohorts (farming and urban) at differing risks and rates of allergic diseases were compared. Blood mononuclear cells were collected from infants at birth, and 6 and 12 months of age. Full spectrum flow cytometry, followed by traditional gating and the Scalable Weighted Iterative Flow-clustering Technique (SWIFT) high-dimensional analysis, were used to identify cell populations that differed between farming and urban infants. Additionally, single-cell RNAseq and multiplex cytokine assays were used to assess the function of cell populations of interest. Several regulatory T cell (Treg) subpopulations were elevated in farming lifestyles and in non-atopic infants. A unique effector memory CD25+CD127+CD161-CD49d+CCR4+CRTH2+ Th2 population was elevated at 6 months in urban infants and in those who developed atopic dermatitis and/or food allergy and allergic sensitization. Although this population shared Th2 and IL-9 skewing with Th2A cells, the population uniquely failed to express CD161, produced more IL-2 and TNF-α, and upregulated the differentially expressed genes (DEGs), FOXP3 and the cytokine inducible SH2-containing protein gene (CISH) relative to Th2A cells. This population has been termed Th2B cells. We describe a unique effector memory Th2 population elevated in urban high-risk infants, potentially implicated in the development of allergic disease.

Potential biomarkers and immune infiltration linking endometriosis with recurrent pregnancy loss based on bioinformatics and machine learning

ObjectiveEndometriosis (EMs) is a chronic inflammatory disease characterized by the presence of endometrial tissue in the non-uterine cavity, resulting in dysmenorrhea, pelvic pain, and infertility. Epidemiologic data have suggested the correlation between EMs and recurrent pregnancy loss (RPL), but the pathological mechanism is unclear. This study aims to investigate the potential biomarkers and immune infiltration in EMs and RPL, providing a basis for early detection and treatment of the two diseases.MethodsTwo RPL and six EMs transcriptomic datasets from the Gene Expression Omnibus (GEO) database were used for differential analysis via limma package, followed by weighted gene co-expression network analysis (WGCNA) for key modules screening. Protein-protein interaction (PPI) network and two machine learning algorithms were applied to identify the common core genes in both diseases. The diagnostic capabilities of the core genes were assessed by receiver operating characteristic (ROC) curves. Moreover, immune cell infiltration was estimated using CIBERSORTx, and the Cancer Genome Atlas (TCGA) database was employed to elucidate the role of key genes in endometrial carcinoma (EC).Results26 common differentially expressed genes (DEGs) were screened in both diseases, three of which were identified as common core genes (MAN2A1, PAPSS1, RIBC2) through the combination of WGCNA, PPI network, and machine learning-based feature selection. The area under the curve (AUC) values generated by the ROC indicates excellent diagnostic powers in both EMs and RPL. The key genes were found to be significantly associated with the infiltration of several immune cells. Interestingly, MAN2A1 and RIBC2 may play a predominant role in the development and prognostic stratification of EC.ConclusionWe identified three key genes linking EMs and RPL, emphasizing the heterogeneity of immune infiltration in the occurrence of both diseases. These findings may provide new mechanistic insights or therapeutic targets for further research of EMs and RPL.

Integrative bioinformatics and experimental analyses identify U2SURP as a novel lactylation-related prognostic signature in esophageal carcinoma.

The lactylation modification has been implicated in several cancer types; however, the role of lactylation modification-related genes in esophageal carcinoma (EC) remains underexplored. Utilizing a set of 16 lactylation modification-related genes, cohorts of patients with EC were stratified into two distinct clusters, characterized by significant disparities in both survival outcomes and the immune microenvironment. An extensive bioinformatics analysis unveiled 382 differentially expressed genes (DEGs) between these two clusters. A subsequent univariate Cox regression analysis identified 24 DEGs specifically associated with lactylation, forming the basis of a constructed lactylation-related score. The resultant lactylation-related score exhibited notable predictive efficacy for survival and other clinicopathological traits, which was validated through calibration curves, Kaplan-Meier survival curves and the Wilcoxon test. Moreover, the lactylation-related score displayed a close correlation with immune cell infiltration in EC. Notable differential expressions of immune checkpoints and regulators were observed between groups stratified by low and high lactylation scores, with the latter exhibiting a more favorable response to anti-PD-1/PD-L1 therapy. Furthermore, the expression profile of U2 snRNP associated SURP domain containing (U2SURP), a constituent of the lactylation-related score, underwent both ex vivo and in vitro validation. The expression of U2SURP was significantly associated with lactylation levels, histological grade and tumor stage. Notably, knockdown of U2SURP expression inhibited the lactylation levels, immune genes IL-1A and IL-1B, proliferation, migration and invasion of EC cells. In conclusion, the lactylation-related score developed in the present study showed promise in predicting the prognosis and immunotherapeutic responses among patients with EC. Moreover, the identification of U2SUPR as a novel oncogene in EC suggests its potential as a prospective therapeutic target for EC treatment.

Genome-wide identification and characterization of WRKYs family involved in responses to Cylindrocarpon destructans in Panax notoginseng

BackgroundWRKY transcription factors (TFs) are key regulators of plant responses to biotic and abiotic stresses. Previous studies demonstrated that the role of WRKY TFs play in the disease resistance of Panax notoginseng, the causal agent of root rot disease. However, comprehensive genome-wide analyses of WRKY genes in this species remain scarce.ResultWe identified 79 WRKY genes in the P. notoginseng genome, classifing them into three groups based on structural features and phylogenetic relationships: Class I (14 genes), Class II (55 genes), and Class III (10 genes). Of these, 58 PnWRKY genes were mapped to the P. notoginseng chromosomes and showed collinearity with Arabidopsis thaliana, Daucus carota, and three Solanaceae species. Expression analysis revealed that 53 PnWRKY genes were actively transcribed across various tissues, including roots, flowers, stems, rhizomes, and different root parts. Furthermore, PnWRKY genes responded to Cylindrocarpon destructans infection and were induced by jasmonic acid (JA) and salicylic acid (SA). Notably, the ectopic expression of PnWRKY35 in tobacco enhanced resistance to C. destructans, accompanied by increased levels of gibberellins (GA24, GA3, GA8), JA, SA, and brassinolide. KEGG enrichment analysis of 547 differentially expressed genes (DEGs) indicated their involvement pathways related to disease resistance, including the biosynthesis of sesquiterpenes and triterpenes, JA biosynthesis, plant-pathogen interactions and the MAPK signaling pathway.ConclusionThis study demonstrated that the WRKY family in P. notoginseng plays a significant role in resistance to root rot disease. PnWRKY genes are responsive to MeJA and SA induction as well as C. destructans infection. Moreover, ectopic expression of PnWRKY35 activates multiple plant disease resistance pathways, increases phytohormone levels, and enhance resistance to C. destructans. These findings provide a foundation for future exploration of the mechanism underlying P. notoginseng resistance to root rot disease.

Transcriptomic and Phenotypic Responses of CucumberTrichome Density to Silver Nitrate and Sodium Thiosulfate Application

Cucumber (Cucumis sativus L.) is one of the most widely cultivated crops worldwide and is valued for its nutritional, economic, and ecological benefits. The regulation of defense mechanisms against herbivores, along with osmotic loss and environmental regulation, is greatly affected by trichomes in cucumbers. In this study, we attempted to characterize trichomes and examined fruit physiological and transcriptome profiles by RNA sequencing in cucumber breeding lines 6101-4 and 5634-1 at three stages of fruit development through foliar application with a combination of silver nitrate (AgNO3) and sodium thiosulfate (Na2S2O3) in comparison to non-treated controls. Notable increases in the number of trichomes and altered forms were observed for both inbred cultivars 6101-4 and 5634-1 against foliar application of chemical substances. RNA-seq analysis was performed to identify differentially expressed genes (DEGs) involved in multiple pathways in cucumber trichome formation. The enrichment of differentially expressed transcripts showed that foliar application upregulated the expression of many stress-responsive and trichome-associated genes including plant hormone signal transduction, sesquiterpenoid and triterpenoid biosynthesis, and the mitogen-activated protein kinase (MAPK) signaling pathway. The dominant regulatory genes, such as allene oxide synthase (AOS) and MYB1R1 transcription factor, exhibited significant modulations in their expression in response to chemical application. The RNA-seq results were further confirmed by RT-PCR-based analysis, which revealed that after chemical application, the dominant regulatory genes, such as allene oxide synthase (AOS), PTB 19, MYB1R1, bHLH62-like, MADS-box transcription factor, and salicylic acid-binding protein 2-like, were differentially expressed, implying that these DEGs involved in multiple pathways are involved the positive regulation of the initiation and development of trichomes in C. sativus. A comparison of trichome biology and associated gene expression regulation in other plant species has shown that silver nitrate (AgNO3) and sodium thiosulfate (Na2S2O3) are also responsible for hormonal and signaling pathway regulation. This study improves our knowledge of the molecular mechanisms involved in C. sativus trichome development. It also emphasizes the possibility of utilizing chemical composition to modulate C. sativus trichome-related characteristics of C. sativus, leading to the improvement of plant defense mechanisms as well as environmental adaptation.

Development of a prognostic model based on four genes related to exhausted CD8+ T cell in triple-negative breast cancer patients: a comprehensive analysis integrating scRNA-seq and bulk RNA-seq.

Low immune infiltration is closely associated with poor clinical results and an unfavorable response to therapy in triple-negative breast cancer (TNBC). T-cell exhaustion (TEX) is a significant risk factor for tumor immunosuppression and invasion. Although improving TEX and enhancing effector function are promising strategies for strengthening immunotherapy, their role in the pathogenesis of TNBC remains unclear. This study's objective was to develop a prognostic model for TNBC based on exhausted CD8+ T-cell (CD8+ Tex)-related differentially expressed genes(DEGs) and to investigate its clinical and immune relevance. Initially, 398 CD8+ Tex-related genes were screened utilizing single-cell RNA sequencing (scRNA-seq) data from TNBC patients. Pseudotime analysis confirmed that CD8+ Tex mainly clustered at the end of the differentiation pathways, making them a critical subset in TNBC progression. By analyzing the TCGA cohort, ten CD8+ Tex-related DEGs were identified assignificantly correlated with overall survival (OS) in TNBC patients, and a prognostic model containing four biomarkers (GBP1, CTSD, ABHD14B, andHLA-A) was constructed. The model demonstrated robust predictive capability in both the TCGA cohort and an external cohort, with the low-risk group exhibiting elevated expression of immunological checkpoint molecules and immune cell infiltration, as well as better responses to immunotherapy and chemotherapy. Furthermore, these four biomarkers were found to be highly expressed on CD8+ Tex and were associated with cellular communication efficiency. Therefore, this model is expected to be a new method for forecasting TNBC patients' prognosis and effectiveness of treatment, providing new insights for clinical decision-making.

Abstract TP346: Investigating Transcriptomic Profiles of Peripheral Blood Mononuclear Cells in Moyamoya Disease Using Single-Cell RNAseq

Objectives: Moyamoya Disease (MMD) is a complex cerebrovascular disease marked by progressive narrowing in the cerebral arteries. Previous studies have suggested that dysregulated genes in the peripheral blood of MMD patients are involved in extracellular matrix organization and immune responses. However, the mechanism by which the immune response contributes to MMD progression is unclear. In this study we investigated the immune landscape in the peripheral blood mononuclear cells (PBMCs) of MMD patients using single-cell RNA sequencing (scRNA-seq). Methods: Blood samples were collected from 3 bilateral MMD patients and 2 healthy controls. PBMCs were isolated and processed for 10x single-cell RNA sequencing. Immune cell heterogeneity and differentially expressed genes (DEGs) in each cell type were identified. Top biological pathways were determined using Ingenuity Pathway Analysis (IPA). Flow cytometry with an 11-fluorochrome panel was use to validate key immune populations and fluorescence-activated cell sorting (FACS) was used to isolate specific immune populations for transcriptome analysis. Results: Preliminary analysis revealed notable increase of cell percentages in certain cell types in MMD, such as CD8+T (9.21% vs 7.11%), B cells (6.94% vs 3.45%) and CD4+NKT (5.78% vs 3.22%), and decrease in CD8+NKT (9.59% vs 15.74%), compared to controls. Higher transcriptome dynamics were observed in certain cell type in MMD, with 2402 DEGs in classical monocytes, 1379 DEGs in CD4+T, 1312 DEGs in CD8+NKT and 997 DEGs in B cells. Interestingly, many cell types, except for classical and non-classical monocytes, displayed a higher number of downregulated DEGs in MMD, particularly in T cells, B cells, and NKT cells. Pathway analysis indicated that CD4+T, CD8+NKT, and B cells show predicted inhibition in several pathways, including T cell receptor and mTOR signaling, interleukins and CXCR4 signaling, as well as cell surface interactions at the vascular wall. Conclusion: These preliminary findings point to a distinct immunological profile in MMD, suggesting significant alterations in both immune cell activity and interaction within the vascular environment. Ongoing studies utilize FACS to validate specific immune populations and their transcriptomes in a larger cohort. These findings reveal unique transcriptomic signatures of peripheral blood immune cells in MMD and highlight key immune cell types that may contribute to its pathogenesis.

Identification of candidate biomarkers for gastric cancer by bioinformatics analysis of pooled microarray gene expression datasets in Gene Expression Omnibus.

467 Background: Gastric cancer (GC) remains one of the most prevalent malignant diseases worldwide. The high mortality rate is largely due to the limited treatment options and the challenges in diagnosing the cancer at an early stage. Understanding the genetic differences driving the proliferation of GC is crucial for advancing diagnostic methods and developing targeted treatments. This study aims to identify biomarkers involved in the pathogenesis of GC through integrated bioinformatics analysis. Methods: Extracted from the Geo Expression Omnibus, three DataSets (GSE118916, GSE79973, and GSE13861) were analyzed for differentially expressed genes (DEGs) using the R statistical language. The three data sets were then compared for common DEGs, which would serve as the focus of this study. These DEGs were functionally analyzed for pathways by Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). A protein–protein interaction (PPI) network was constructed to screen out candidate genes. Results: The results revealed that 123 DEGs of the three datasets containing 26 upregulated genes and 97 downregulated genes were ascertained in our study. The GO and KEGG enrichment analysis results showed that the functions of DEGs were mainly involved in the retinol metabolic process, xenobiotic metabolic process, collagen type I trimer, potassium: proton exchanging ATPase complex, benzaldehyde dehydrogenase (NAD+) activity, alcohol dehydrogenase (NADP+) activity, Collecting duct acid secretion, and Tyrosine metabolism. Through the PPI analysis network, the core genes with the highest degree of 7 nodes were selected: COL1A1, COL1A2, COL11A1, THBS2, ATP4A, COL10A1, and CXCL8. Conclusions: The 7 genes identified in this study may play a vital regulatory role in the occurrence and development of GC and may also be potential therapeutic targets. Further mechanistic studies of the pathogenesis and treatment of GC may be able to identify new targets using these shared pathways. These findings could contribute to a better understanding of the origins of gastric cancer and facilitate the development of early interventions. The bioinformatics analysis conducted in this study offers new insights and directions for further research on gastric cancer.

Repeated social defeat in male mice induced unique RNA profiles in projection neurons from the amygdala to the hippocampus

Chronic stress increases the incidence of psychiatric disorders including anxiety, depression, and posttraumatic stress disorder. Repeated Social Defeat (RSD) in mice recapitulates several key physiological, immune, and behavioral changes evident after chronic stress in humans. For instance, neurons in the prefrontal cortex, amygdala, and hippocampus are involved in the interpretation of and response to fear and threatful stimuli after RSD. Therefore, the purpose of this study was to determine how stress influenced the RNA profile of hippocampal neurons and neurons that project into the hippocampus from threat appraisal centers. Here, RSD increased anxiety-like behavior in the elevated plus maze and reduced hippocampal-dependent novel object location memory in male mice. Next, pan-neuronal (Baf53b-Cre) RiboTag mice were generated to capture ribosomal bound mRNA (i.e., active translation) activated by RSD in the hippocampus. RNAseq revealed that there were 1,694 differentially expressed genes (DEGs) in hippocampal neurons after RSD. These DEGs were associated with an increase in oxidative stress, synaptic long-term potentiation, and neuroinflammatory signaling. To further examine region-specific neural circuitry associated with fear and anxiety, a retrograde-adeno-associated-virus (AAV2rg) expressing Cre-recombinase was injected into the hippocampus of male RiboTag mice. This induced expression of a hemagglutinin epitope in neurons that project into the hippocampus. These AAV2rg-RiboTag mice were subjected to RSD and ribosomal-bound mRNA was collected from the amygdala for RNA-sequencing. RSD induced 677 DEGs from amygdala projections. Amygdala neurons that project into the hippocampus had RNA profiles associated with increased synaptogenesis, interleukin-1 signaling, nitric oxide, and reactive oxygen species production. Using a similar approach, there were 1,132 DEGs in neurons that project from the prefrontal cortex. These prefrontal cortex neurons had RNA profiles associated with increased synaptogenesis, integrin signaling, and dopamine feedback signaling after RSD. Collectively, there were unique RNA profiles of stress-influenced projection neurons and these profiles were associated with hippocampal-dependent behavioral and cognitive deficits.

Temporal transcriptome profiling in the response to Salmonella enterica serovar enteritidis infection in chicken cecum.

Salmonella enterica serovar Enteritidis (S. Enteritidis) is a common zoonotic pathogen that not only causes gastroenteritis or death of livestock and poultry but also poses a serious threat to human health, causing severe economic losses to the poultry industry and society. Herein, RNA-sequencing (RNA-seq) was used to analyze the transcriptome variation of chicken cecum at four different time points (1, 3, 7, and 14 days) following S. Enteritidis infection. There were 529, 1477, 476, and 432 differentially expressed genes (DEGs) in the cecum at four different days post-infection (dpi), respectively. The DEGs were significantly enriched in various immune-related pathways on 3 dpi and 7 dpi, such as cytokine-cytokine-receptor interaction and Toll-like receptor signaling pathway. DEGs were significantly enriched in several metabolic pathways on 14 dpi. Gene ontology (GO) enrichment of DEGs showed that up-regulated genes were significantly enriched in immune-related terms on 3 and 7 dpi. On 14 dpi, up-regulated genes were mainly enriched in the signaling-related terms, while the down-regulated genes were primarily enriched in the metabolic-related terms. Based on weighted gene co-expression network analysis (WGCNA), the key modules related to energy, non-coding processes, immunity, and development-related functions were identified at 1, 3, 7, and 14 dpi, respectively, and 5, 8, 6, and 5 hub genes were screened out, respectively. This study demonstrated that the chicken cecal transcriptome regulation responding to S. Enteritidis infection is time-dependent. The regulation of S. Enteritidis infection in chickens is coordinated by multiple systems, mainly involving immunity, metabolism, and signal transduction. Both 3 and 7 dpi are key time points for immune response. As the infection progresses, metabolism-related pathways were increasingly identified. This change reflects the dynamic adjustment between immune response and metabolism in Jining Bairi chickens following S. Enteritidis infection. These results suggested that starting from 3 dpi, the chickens gradually transition from an immune response triggered by S. Enteritidis infection to a state where they adapt to the infection by modulating their metabolism.

MRNA expression profile from whole blood revealed a cluster of 25 shared differentially expressed genes inversely related in multiple sclerosis and inflammatory bowel disease.

Multiple Sclerosis (MS) and Inflammatory Bowel Disease (IBD) are immune-mediated disorders with a significant concurrence among patients and share considerable genetic variations and environmental factors. This study aimed to identify shared differentially expressed genes (DEGs) between MS and IBD using mRNA expression data analysis to improve understanding of their co-occurrence and relationship between these two diseases and potentially achieve better disease management. Blood mRNA expression data from case-control studies on MS and IBD were retrieved from the NCBI-GEO database and analyzed using GEO2R to identify differentially expressed genes (DEGs) (p ≤ 0.05, fold change ≥ 1.5). Shared DEGs were studied for expression patterns, and protein-protein interaction (PPI) networks, biological processes, pathways, and hub genes were identified. DEGs and their single nucleotide variations (SNVs) from genome-wide association studies (GWAS) were further analyzed using in silico tools to explore functional implications. Five studies each for MS and IBD were included, following inclusion/exclusion criteria. Thirty-one shared DEGs were identified, with 25 showing inverse regulation patterns: up-regulated in MS and down-regulated in IBD. The intergenic SNV rs2688608 near PLAU was found to be functionally relevant to both the diseases. Pathway analysis revealed shared processes, including leukocyte extravasation, I-kappa B phosphorylation, viral protein interactions with cytokines, and NF-kappa B signalling. TNF, PLAU, VCAM1, and CX3CR1 were identified as hub genes, suggesting them as potential therapeutic targets. These findings highlight shared mechanisms in MS and IBD pathogenesis. This study identified shared molecular signatures between MS and IBD, supporting the concept of interconnected disease processes. The identified genes and pathways associated with inflammation and immune response offer valuable insights for further research into potential therapeutic targets for MS and IBD and their co-occurrence.

Potential molecular mechanisms of tobacco smoke exposure in Alzheimer's disease.

Smoking is detrimental to health, with tobacco use being a critical factor in the development of various neurodegenerative diseases, including Alzheimer's disease (AD), which progressively impairs brain function and poses a significant threat to public health. This study aims to examine the potential genetic alterations induced by smoking that are associated with AD and to investigate the underlying regulatory mechanisms. The research will provide theoretical foundations for targeted prevention and treatment strategies for AD. This study analyzed datasets from the Gene Expression Omnibus (GEO) and the Comparative Toxicogenomics Database (CTD) to identify genes affected by tobacco smoke exposure and those altered in patients with AD relative to normal controls. We conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses using OmicShare tools to screen for key pathways. Key genes were identified by constructing protein-protein interaction networks (PPI) in the STRING database with the aid of CytoHubba. Additionally, the binding activity of the proteins encoded by these key genes to nicotine, the main component of tobacco, was analyzed using molecular docking techniques. Finally, the analytical results were verified using Quantitative Real-Time Polymerase Chain Reaction. The CTD identified 12,164 CE-related genes affected by tobacco smoke exposure. A comparison of these datasets yielded 94 common genes that were both influenced by tobacco and differentially expressed across all brain regions. The GO and KEGG pathway enrichment analyses showed that these common differentially expressed genes (DEGs) were predominantly enriched in the Wnt/β-catenin and PI3K-AKT signaling pathways. The DEGs' PPI network, constructed using the STRING database, highlighted key genes such as HSP90AB1, SOS2, MAGI1, and YWHAZ. Molecular docking studies demonstrated that nicotine binds effectively to the protein structures of these key genes, primarily through amino acid residues such as Ser and Glu. Experimental validation showed that HSP90AB1 and YWHAZ exhibited notable expression discrepancies under varying concentrations of cigarette smoke extract (CSE) treatments, particularly demonstrating a pronounced down-regulation trend at elevated concentrations. The study indicates that tobacco may impact the function of transmembrane transporter proteins and contribute to the development of AD by affecting key genes such as HSP90AB1 and YWHAZ, as well as signaling pathways like PI3K-AKT.

Transcriptomic analysis of key genes and signaling pathways in sepsis-associated intestinal mucosal barrier damage

ObjectivesThe aim is to analyze differentially expressed genes (DEGs) in mice with sepsis-related intestinal mucosal barrier damage and to explore the diagnostic and protective mechanisms of this condition at the transcriptome level. MethodsSmall intestinal tissues from healthy male C57BL/6J mice subjected to Cecal ligation and puncture (CLP) and sham operation were collected. High-throughput sequencing was performed using the paired-end sequencing mode of the Illumina HiSeq platform. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted on the differentially expressed genes (DEGs). A protein–protein interaction (PPI) network was constructed using the STRING database, and hub genes were identified with Cytoscape. These hub genes were then validated using quantitative real-time polymerase chain reaction (RT-qPCR). ResultsA total of 239 DEGs were identified, with 49 upregulated and 130 downregulated genes. KEGG enrichment analysis showed that these DEGs were primarily involved in cytokine-cytokine receptor interaction, Th1 and Th2 cell differentiation, viral protein interactions with cytokines and their receptors, and the IL-17 signaling pathway. The top 10 hub genes were selected using the cytoHubba plugin. Experimental validation confirmed that the expression levels of TBX21, CSF3, IL-6, CXCR3, and CXCL9 matched the sequencing results. ConclusionTBX21, CSF3, IL-6,CXCR3, and CXCL9 may be potential biological markers for the diagnosis and treatment the sepsis-associated intestinal mucosal barrier.