Determine Differentially Expressed Genes Research Articles

A comparison of the TempO-Seq and Affymetrix microarray platform using RTqPCR validation

Next-generation risk assessment relies on mechanistic data from new approach methods, including transcriptome data. Various technologies, such as high-throughput targeted sequencing methods and microarray technologies based on hybridization with complementary probes, are used to determine differentially expressed genes (DEGs). The integration of data from different technologies requires a good understanding of the differences arising from the use of various technologies.To better understand the differences between the TempO-Seq platform and Affymetrix chip technology, whole-genome data for the volatile compound dimethylamine were compared. Selected DEGs were also confirmed using RTqPCR validation. Although the overlap of DEGs between TempO-Seq and Affymetrix was no higher than 37%, a comparison of the gene regulation in terms of log2fold changes revealed a very high concordance. RTqPCR confirmed the majority of DEGs from either platform in the examined dataset. Only a few conflicts were found (11%), while 22% were not confirmed, and 3% were not detected.Despite the observed differences between the two platforms, both can be validated using RTqPCR. Here we highlight some of the differences between the two platforms and discuss their applications in toxicology.

Identification of potential inhibitors for drug resistance in acute lymphoblastic leukemia through differentially expressed gene analysis and in silico screening

Acute lymphoblastic leukemia (ALL) is a disease of lymphocyte origin predominantly diagnosed in children. While its 5-year survival rate is high, resistance to chemotherapy drugs is still an obstacle. Our aim is to determine differentially expressed genes (DEGs) related to Asparaginase, Daunorubicin, Prednisolone, and Vincristine resistance and identify potential inhibitors via docking. Three datasets were accessed from the Gene Expression Omnibus database; GSE635, GSE19143, and GSE22529. The microarray data was analyzed using R4.2.0 and Bioconductor packages, and pathway and protein-protein interaction analysis were performed. We identified 1294 upregulated DEGs, with 12 genes consistently upregulated in all four resistant groups. KEGG analysis revealed an association with the PI3K-Akt pathway. Among DEGs, 33 hub genes including MDM2 and USP7 were pinpointed. Within common genes, CLDN9 and HS3ST3A1 were subjected to molecular docking against 3556 molecules. Following ADMET analysis, three drugs emerged as potential inhibitors: Flunarizine, Talniflumate, and Eltrombopag. Molecular dynamics analysis for HS3ST3A1 indicated all candidates had the potential to overcome drug resistance, Eltrombopag displaying particularly promising results. This study promotes a further understanding of drug resistance in ALL, introducing novel genes for consideration in diagnostic screening. It also presents potential inhibitor candidates to tackle drug resistance through repurposing.

EXTH-06. GLIOBLASTOMA PATIENT SPECIFIC TRANSCRIPTOME REMODELING IN RESPONSE TO MDM2 ANTAGONIST TREATMENT OF WILD-TYPE P53 CANCER STEM CELLS IS ASSOCIATED WITH SENSITIVITY AND STRATEGIES FOR COMBINATION THERAPY

Abstract Over 70% of glioblastomas are p53 wild-type and these patients could benefit from p53 reactivation treatment. Here we determined the sensitivity of a glioblastoma patient-derived cancer stem cells (CSCs) panel to three MDM2 antagonists (MDM2a) to test to what extent transcriptional reprogramming is affected by genomic background and correlates to response to acute treatment with MDM2 antagonists. IC50 concentrations and area above the curve (AAC) were measured from dose response curves obtained from 4 and 7-day treatment. The inhibitors were specific to wt-p53 CSCs, but these presented a wide range of sensitivity. Seven wt-p53 CSCs were treated RG7112 IC50 concentrations or DMSO control for 24h (n=4). RNA was isolated for Illumina Truseq stranded mRNA libraries sequenced at 30M depth. Quantified raw counts were processed using NOISeq R package to determine differentially expressed genes (DEG) between control and treated samples. In addition to the expected high representation of upregulated p53 targets in all cell lines, we observed significan cell specific transcriptome alterations, including enrichment of survival pathways, such as mTOR, ERK and NFkB in the less sensitive CSC lines, which did not readily correlate with the individual genomic landscapes. E2F targets, G2-M cell cycle check point and DNA-repair pathways were highly enriched in the downregulated genes. Combination of MDM2a with radiation treatment (RT) was synergistic to a subset of CSCs. As validation we found that MDM2a treatment was effective in sensitizing a resistant orthotopic mouse glioblastoma PDX to fractionated RT, with maximum efficacy when treatment started 24h prior to RT vs simultaneously (Log-rank Mantel-Cox test: p=0.0006 vs 0.0277). The integration of the treatment-mediated transcriptional patterns with differential sensibility to MDM2 antagonists and genomic landscape of the CSC panel provides a platform to identify targets for combination therapies, which is the most promising clinical application of the reactivation of wt-p53 in GBMs.

Maternal obesity and high leptin levels prime pro-inflammatory pathways in human cord blood leukocytes

IntroductionMaternal obesity alters the immune function in the offspring. We hypothesize that maternal obesity and pro-inflammatory pathways induce leptin-related genes in neonatal monocytes, whereby high leptin levels enhance their inflammatory response. MethodsTranscriptional profiles of cord blood leukocytes (CBL) in basal and pro-inflammatory conditions were studied to determine differentially expressed genes (DEG). The DNA methylation profile of CB monocytes (CBM) of neonates born to control BMI mothers and women with obesity was assayed to identify differentially methylated probes (DMP). CBM-derived macrophages were cultured with or without leptin (10–100 ng/ml) and then stimulated with lipopolysaccharide (LPS, 100 ng/ml) and interferon-gamma (20 ng/ml) to assess the induction of TNF-α and IL-10 transcripts. ResultsCBL from pregnancies with obesity (CBL-Ob) showed 12,183 DEG, affecting 49 out of 78 from the leptin pathway. Control CBM exposed to LPS showed 45 leptin-related DEG, an effect prevented by the co-exposure to LPS and IL-10. Conversely, CBM-Ob showed 5279 DMP enriched in insulin- and leptin-related genes, and Lasso regression of leptin-related DMP showed high predictive value for plasma leptin levels (r2 = 0.9897) and maternal BMI categories (AUC = 1). Chronic exposure to leptin increased TNF-α and decreased IL-10 levels in control BMI samples but not in Ob-CBM. Enhanced TNF-α induction after proinflammatory stimulation was observed in leptin-treated control BMI samples. DiscussionObesity in pregnancy is associated with a distinctive expression and DNA methylation profile of leptin-related genes in cord blood monocytes, meanwhile, leptin enhances the expression of pro-inflammatory cytokines upon stimulation with M1-skewing agents.

Idiopathic Pulmonary Fibrosis Molecular Substrates Revealed by Competing Endogenous RNA Regulatory Networks.

Idiopathic pulmonary fibrosis (IPF) is a chronic progressive fibrotic disease of the lung with poor prognosis. Fibrosis results from remodeling of the interstitial tissue. A wide range of gene expression changes are observed, but the role of micro RNAs (miRNAs) and circular RNAs (circRNA) is still unclear. Therefore, this study aimed to establish an messenger RNA (mRNA)-miRNA-circRNA competing endogenous RNA (ceRNA) regulatory network to uncover novel molecular signatures using systems biology tools. Six datasets were used to determine differentially expressed genes (DEGs) and miRNAs (DEmiRNA). Accordingly, protein-protein, mRNA-miRNA, and miRNA-circRNA interactions were constructed. Modules were determined and further analyzed in the Drug Gene Budger platform to identify potential therapeutic compounds. We uncovered common 724 DEGs and 278 DEmiRNAs. In the protein-protein interaction network, TMPRSS4, ESR2, TP73, CLEC4E, and TP63 were identified as hub protein coding genes. The mRNA-miRNA interaction network revealed two modules composed of ADRA1A, ADRA1B, hsa-miR-484 and CDH2, TMPRSS4, and hsa-miR-543. The DEmiRNAs in the modules further analyzed to propose potential circRNA regulators in the ceRNA network. These results help deepen the understanding of the mechanisms of IPF. In addition, the molecular leads reported herein might inform future innovations in diagnostics and therapeutics research and development for IPF.

MCM10 as a novel prognostic biomarker and its relevance to immune infiltration in gliomas.

Gliomas are one of the most common malignancies in the central nervous system (CNS). Members of the minichromosomal maintenance protein (MCM) family play an essential role in diagnosing and prognosis of malignant tumors. MCM10 is found in gliomas, but the prognosis and immune infiltration of gliomas has not been elucidated. To explore the biological function and immune infiltration of MCM10 in gliomas and provide a reference for the diagnosis, treatment, and prognostic evaluation. The MCM10 expression profile and the clinical information database of glioma patients were obtained from the China Glioma Genome Atlas (CGGA) and Cancer Genome Atlas (TCGA) glioma data. We analyzed the MCM10 expression levels in various cancers from The TCGA.RNA sequencing data were analyzed using the R packages to determine differentially expressed genes (DEGs) between high- and low MCM10 expressing GBM tissues from the TCGA-GBM database. The Wilcoxon rank sum test was used to compare MCM10 expression levels in glioma and normal brain tissue. To evaluate the value of MCM10 expressions in the prognosis of glioma patients by the Kaplan-Meier survival analysis, a univariate Cox analysis, multivariate Cox analysis, and a ROC curve analysis were used to analyze the correlation of MCM10 expression and the clinicopathological features of glioma patients using the TCGA database data. Subsequently, a functional enrichment analysis was performed to explore its potential signaling pathways and biological functions. Moreover, a single-sample gene set enrichment analysis was used to assess the extent of immune cell infiltration. Lastly, the authors constructed a nomogram to predict the overall survival rate (OS) of gliomas at 1, 3 and 5 years after diagnosis. MCM10 is highly expressed in 20 cancer types including gliomas, and MCM10 expression was an independent adverse prognostic factor in glioma patients. Similarly, high expression of MCM10 was associated with advanced age (60 years), increased tumor grade, tumor recurrence or development of a secondary tumor, IDH wild-type, and non-codeletion of 1p19q (p< 0.01). The OS nomogram generated a consistency index of 0.821. The results of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and Gene Ontology (GO) functional analysis showed that the cell-cycle-related and tumor-related signaling pathways were significantly enriched in the MCM10 high expression phenotype. Moreover, signaling pathways were significantly enriched in Gene Set Enrichment Analysis (GSEA), including Rho GTPases, M phase, DNA repair, extracellular matrix organization, and nuclear receptors. Furthermore, MCM10 over expression was negatively correlated with the level of immune cell infiltration in natural killer CD56 bright cells, follicular helper T cells, plasmacytoma dendritic cells, and dendritic cells. MCM10 is an independent prognostic index of glioma patients, and the high expression of MCM10 suggests a poor prognosis; MCM10 expression is closely related to the immune cell infiltration of gliomas, and MCM10 may be related to drug resistance and development of gliomas.

Transcriptomic Analysis of the Developing Testis and Spermatogenesis in Qianbei Ma Goats.

Reproductive competence in male mammals depends on testicular function. Testicular development and spermatogenesis in goats involve highly complex physiological processes. In this study, six testes were, respectively, obtained from each age group, immature (1 month), sexually mature (6 months) and physically mature (12 months old) Qianbei Ma goats. RNA-Seq was performed to assess testicular mRNA expression in Qianbei Ma goats at different developmental stages. Totally, 18 libraries were constructed to screen genes and pathways involved in testis development and spermatogenesis. Totally, 9724 upregulated and 4153 downregulated DEGs were found between immature (I) and sexually mature (S) samples; 7 upregulated and 3 downregulated DEGs were found between sexually mature (S) and physically mature (P) samples, and about 4% of the DEGs underwent alternative splicing events between I and S. Select genes were assessed by qRT-PCR, corroborating RNA-Seq findings. The detected genes have key roles in multiple developmental stages of goat testicular development and spermatogenesis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to determine differentially expressed genes (DEGs). GO analysis revealed DEGs between S and P contributed to "reproduction process", "channel activity" and "cell periphery part" between I and S, and in "ion transport process", "channel activity" and "transporter complex part". KEGG analysis suggested the involvement of "glycerolipid metabolism", "steroid hormone biosynthesis" and "MAPK signaling pathway" in testis development and spermatogenesis. Genes including IGF1, TGFB1, TGFBR1 and EGFR may control the development of the testis from immature to sexually mature, which might be important candidate genes for the development of goat testis. The current study provides novel insights into goat testicular development and spermatogenesis.

Regulation of host gene expression by gastrointestinal tract microbiota in Chinook Salmon (Oncorhynchus tshawytscha).

Differences in gut microbiome composition are linked with health, disease and ultimately host fitness; however, the molecular mechanisms underlying that relationship are not well characterized. Here, we modified the fish gut microbiota using antibiotic and probiotic feed treatments to address the effect of host microbiome on gene expression patterns. Chinook salmon (Oncorhynchus tshawytscha) gut gene expression was evaluated using whole transcriptome sequencing (RNA-Seq) on hindgut mucosa samples from individuals treated with antibiotic, probiotic and control diets to determine differentially expressed (DE) host genes. Fifty DE host genes were selected for further characterization using nanofluidic qPCR chips. We used 16S rRNA gene metabarcoding to characterize the rearing water and host gut microbiome (bacterial) communities. Daily administration of antibiotics and probiotics resulted in significant changes in fish gut and aquatic microbiota as well as more than 100 DE genes in the antibiotic and probiotic treatment fish, relative to healthy controls. Normal microbiota depletion by antibiotics mostly led to downregulation of different aspects of immunity and upregulation of apoptotic process. In the probiotic treatment, genes related to post-translation modification and inflammatory responses were up-regulated relative to controls. Our qPCR results revealed significant effects of treatment (antibiotic and probiotic) on rabep2, aifm3, manf, prmt3 gene transcription. Moreover, we found significant associations between members of Lactobacillaceae and Bifidobacteriaceae with host gene expression patterns. Overall, our analysis showed that the microbiota had significant impacts on many host signalling pathways, specifically targeting immune, developmental and metabolic processes. Our characterization of some of the molecular mechanisms involved in microbiome-host interactions will help develop new strategies for preventing/ treating microbiome disruption-related diseases.

Effects of NUCB2/nesfatin-1 on lipid metabolism in the hepatopancreas of largemouth bass (Micropterus salmoides)

Although nucleobindin-2 (NUCB2)/nesfatin-1 has multiple biological functions, there is a scarcity of information regarding the regulatory effect of NUCB2/nesfatin-1 on lipid metabolism in mammals and fish. In order to investigate the mechanism underlying the effect of nesfatin-1 on lipid metabolism in largemouth bass (Micropterus salmoides), the sequence of NUCB2 was cloned and nesfatin-1 was expressed in prokaryotic system. Intraperitoneal injection of 5, 50 or 500 ng/g nesfatin-1 protein to determine differentially expressed genes (DEGs) in largemouth bass by transcriptomic profiling. The triglyceride and total cholesterol levels in the hepatopancreas and plasma were subsequently determined. The results showed that the NUCB2 cDNA sequence was 2015 bp in length and analyzed that NUCB2 mRNA was abundantly expressed in the hepatopancreas. RNA-seq analysis revealed that 385, 1647, and 750 genes were differentially expressed in the three groups, respectively, of which 33, 69, and 61 DEGs, respectively, were involved in lipid metabolism. GO and KEGG analysis showed that the DEGs were enriched in 24 signaling pathways related to lipid metabolism. The PPAR signaling pathway was significantly enriched following treatment with nesfatin-1. The fatty acid transport genes (ACSL, FABP3, FATP, ACBP) were significantly downregulated in the pathway (p < 0.05). Additionally, the TG (p < 0.01) and T-CHO (p < 0.05) levels in the hepatopancreas were significantly down-regulated at 50 ng/g nesfatin-1 protein injection dose, while TG and T-CHO levels in plasma were not significantly altered (p > 0.05). The present study demonstrated that at an optimal concentration, nesfatin-1 affected lipid metabolism in the hepatopancreas of largemouth bass primarily via the PPAR signaling pathway, to down-regulate the expression of fatty acid transport genes, which in turn decreased lipid synthesis in the hepatopancreas. The findings provide useful insights for further analysis of the mechanism underlying the effect of nesfatin-1, and for elucidating the regulation of lipid metabolism homeostasis in the aquaculture production of largemouth bass.

A Systems Biology Approach to Identify Novel Biomarkers in Progression from Crohn's Disease to Colorectal Cancer.

This study aimed to find the key genes and miRNAs as potential biomarkers related to the progression of colorectal cancer (CRC) from Crohn's disease (CD). CD is widely accepted as one of the main risk factors leading to CRC. So, Identifying the novel molecular pathways involved in the development of CRC from CD can provide potential solutions for therapeutic interventions. By implementing a systematic approach, we have analyzed mRNA and miRNA datasets containing CRC and CD samples to determine differentially expressed genes (DEGs) and miRNAs (DEmiRNA). Then by selecting common genes involved in the progression from CD to CRC, different downstream analyses including mRNA-miRNA network, functional enrichment analysis, gene set enrichment analysis, and survival analysis were performed. Finally, quantitative real-time PCR (RT-PCR) analysis of tissue samples obtained from Normal/CRC samples was used to confirm the differential expression of selected genes and miRNA. There were 10 DE miRNA and 181 genes DEGs common between progression from CD to CRC. The genes obtained for each of the 10 miRNAs were considered as the final target for downstream analyzes. In addition, analysis of RT-PCR indicated that miR-195-5p, PHLPP2, and LITAF were downregulated in the cancer group compared to the control group. This study showed that PHLPP2, LITAF, and miR-195-5p may have key roles in the tumorigenesis of CRC and they can be used as therapeutic targets and diagnostic biomarkers after further in-vitro and in-vivo evaluation.

The whole-cell proteome shows the characteristics of macrolides-resistant Bordetella pertussis in China linked to the biofilm formation

The macrolides-resistant Bordetella pertussis (MR-Bp) isolates in China evolved from the ptxP1/fhaB3 allele and rapidly became predominant, suggestive of an adaptive transmission ability. This was different from the global prevalent ptxP3 strains, in which MR-Bp was rarely reported. The study aimed to determine the underlying mechanism responsible for fitness and resistance in these two strains. We identify proteomic differences between ptxP1/fhaB3 and ptxP3/fhaB1 strains using tandem mass tag (TMT)-based proteomics. We then performed in-depth bioinformatic analysis to determine differentially expressed genes (DEGs), followed by gene ontology (GO), and protein–protein interaction (PPI) network analysis. Further parallel reaction monitoring (PRM) analysis confirmed the expression of four target proteins. Finally, the crystal violet method was used to determine biofilm-forming ability. The results showed that the main significantly different proteins between the two represent isolates were related to biofilm formation. Furthermore, we have confirmed that ptxP1/fhaB3 showed hyperbiofilm formation in comparison with ptxP3/fhaB1. It is suggested that the resistance and adaptability of ptxP1/fhaB3 strains may be related to the formation of biofilm through proteomics. In a word, we determined the significantly different proteins between the ptxP1/fhaB3 and ptxP3/fhaB1 strains through whole-cell proteome, which were related to biofilm formation.

Hedgehog signaling is a potential therapeutic target for vascular calcification

BackgroundPatients with chronic kidney disease (CKD) suffered from vascular calcification (VC), one major contributor for their increased mortality rate. Hedgehog (Hh) signaling plays a crucial role in physiological bone mineralization and is associated with several cardiovascular diseases. However, the molecular changes underlying VC is ill defined and it remains unclear whether Hh signaling intervention affects VC. MethodsWe constructed human primary vascular smooth muscle cell (VSMC) calcification model and performed RNA sequencing. Alizarin red staining and calcium content assay were conducted to identify the occurrence of VC. Three different R packages were applied to determine differentially expressed genes (DEGs). Enrichment analysis and protein–protein interaction (PPI) network analysis were carried out to explore the biological roles of DEGs. qRT-PCR assay was then applied to validate the expression of key genes. By using Connectivity Map (CMAP) analysis, several small molecular drugs targeting these key genes were obtained, including SAG (Hedgehog signaling activator) and cyclopamine (CPN) (Hedgehog signaling inhibitor), which were subsequently used to treat VSMC. ResultsObvious Alizarin red staining and increased calcium content identified the occurrence of VC. By integrating results from three R packages, we totally obtained 166 DEGs (86 up-regulated and 80 down-regulated), which were significantly enriched in ossification, osteoblast differentiation, and Hh signaling. PPI network analysis identified 10 key genes and CMAP analysis predicted several small molecular drugs targeting these key genes including chlorphenamine, isoeugenol, CPN and phenazopyridine. Notably, our in vitro experiment showed that SAG markedly alleviated VSMC calcification, whereas CPN significantly exacerbated VC. ConclusionsOur research provided deeper insight to the pathogenesis of VC and indicated that targeting Hh signaling pathway may represent a potential and effective therapy for VC.

Transcriptomic analysis of adipose, hepatic, and mammary gland tissues in lactating cows with elevated peripheral serotonin

Lactation is a highly energy intensive state, particularly for dairy cattle, which have been genetically selected for copious milk secretion. Blood serotonin content is greatly increased during lactation, at least in part because of increased production by the lactating mammary glands. We hypothesized that increasing peripheral serotonin in lactating cows, by infusion of the serotonin precursor 5-hydroxytryptophan (5-HTP), would alter gene expression in metabolically active tissues to support energy partitioning towards lactation.To test this hypothesis, multiparous midlactation Holstein cows (n=8/treatment) were intravenously infused with 5-HTP (1mg/kg bodyweight) or saline over two 10-day treatment periods. Treatments were infused via jugular catheters for 1h/day starting at 0700, on days 1–3 and 8–10, with no infusions on days 4–7. On day 10, 6h after the last infusion, biopsies of subcutaneous white adipose (WAT), hepatic, and mammary tissues were performed. Total RNAs were extracted from these tissues, and followed by whole transcriptome sequencing. Adapter-trimmed sequences were mapped to the cattle reference genome (ARS-UCD 1.2) using STAR. Differential gene expression analysis was done using DEseq2. A combinatory cutoff of mean read count≥5, fold-change≥2, and p-value&lt;0.01 was used to determine differentially expressed genes (DEG). Relative to saline-infused cows, 5-HTP cows had 152 genes downregulated and 38 upregulated in WAT, 117 genes downregulated and 141 upregulated in hepatic tissue, and 79 genes downregulated and 86 upregulated in mammary tissue.DEG from each tissue were then analyzed by QIAGEN Ingenuity Pathway Analysis (IPA) to identify enriched pathways and functions impacted by 5-HTP. In WAT, downregulated genes were enriched in triacylglycerol biosynthesis and upregulated genes were enriched in PPAR signaling, with upregulated gene enrichment in several apoptosis-related pathways as well. Decreased biological function categories in WAT included carbohydrate metabolism and lipid metabolism. In hepatic tissue, downregulated genes were enriched in superpathway of cholesterol biosynthesis while upregulated genes were enriched in cAMP-mediated signaling and citrulline biosynthesis. In mammary tissue, 5-HTP infusion exclusively upregulated genes involved in lipid metabolism, including functions in transport, export, flux and efflux of lipids and cholesterol. In conclusion, lactating cows with elevated peripheral serotonin developed a systemic response, altering the expression of genes in energy metabolic pathways, including reduced lipid synthesis and cell survival in WAT, reduced cholesterol synthesis in the liver, and increased lipid trafficking in the mammary tissue. Together, these changes may function to shift energy partitioning towards milk synthesis. This work was supported by USDA-NIFA Predoctoral Fellowship grant #2021-67034-35172 and research funding provided by Adisseo Bluestar Co. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Construction of Metastasis-Specific Regulation Network in Ovarian Cancer Based on Prognostic Stemness-Related Signatures.

WE aimed to reveal the correlation between ovarian cancer (OV) metastasis and cancer stemness in OV. RNA-seq data and clinical information of 591 OV samples (551 without metastasis and 40 with metastasis) were obtained from TCGA. The edgeR method was used to determine differentially expressed genes (DEGs) and transcription factors (DETFs). Then, mRNA expression-based stemness index was calculated using one-class logistic regression (OCLR). Weighted gene co-expression network analysis (WGCNA) was used to define stemness-related genes (SRGs). Univariate and multivariate Cox proportional hazard regression were conducted to identify the prognostic SRGs (PSRGs). PSRGs, DETFs, and 50 hallmark pathways quantified by gene set variation analysis (GSVA) were integrated into Pearson co-expression analysis. Significant co-expression interactions were utilized to construct an OV metastasis-specific regulation network. Cell communication analysis was carried out based on single cell RNA sequencing data to explore the molecular regulation mechanism of OV. Eventually, assay for targeting accessible-chromatin with high throughout sequencing (ATAC), chromatin immunoprecipitation sequencing (ChIP-seq) validation, and multiple data sets were used to validate the expression levels and prognostic values of key stemness-related signatures. Moreover, connectivity map (CMap) was used to identify potential inhibitors of stemness-related signatures. Based on edgeR, WGCNA, and Cox proportional hazard regression, 22 PSRGs were defined to construct a prognostic prediction model for metastatic OV. In the metastasis-specific regulation network, key TF-PSRS interaction pair was NR4A1-EGR3 (correlation coefficient = 0.81, p < 0.05, positive), and key PSRG-hallmark pathway interaction pair was EGR3-TNFα signaling via NFκB (correlation coefficient = 0.44, p < 0.05, positive), which were validated in multi-omics databases. Thioridazine was postulated to be the most significant compound in treatment of OV metastasis. PSRGs played critical roles in OV metastasis. Specifically, EGR3 was the most significant PSRG, which was positively regulated by DETF NR4A1, inducing metastasis via TNFα signaling.

Influence of the At-Arrival Host Transcriptome on Bovine Respiratory Disease Incidence during Backgrounding

Bovine respiratory disease (BRD) remains the leading disease within the U.S. beef cattle industry. Marketing decisions made prior to backgrounding may shift BRD incidence into a different phase of production, and the importance of host gene expression on BRD incidence as it relates to marketing strategy is poorly understood. Our objective was to compare the influence of marketing on host transcriptomes measured on arrival at a backgrounding facility on the subsequent probability of being treated for BRD during a 45-day backgrounding phase. This study, through RNA-Seq analysis of blood samples collected on arrival, evaluated gene expression differences between cattle which experienced a commercial auction setting (AUCTION) versus cattle directly shipped to backgrounding from the cow-calf phase (DIRECT); further analyses were conducted to determine differentially expressed genes (DEGs) between cattle which remained clinically healthy during backgrounding (HEALTHY) versus those that required treatment for clinical BRD within 45 days of arrival (BRD). A profound difference in DEGs (n = 2961) was identified between AUCTION cattle compared to DIRECT cattle, regardless of BRD development; these DEGs encoded for proteins involved in antiviral defense (increased in AUCTION), cell growth regulation (decreased in AUCTION), and inflammatory mediation (decreased in AUCTION). Nine and four DEGs were identified between BRD and HEALTHY cohorts in the AUCTION and DIRECT groups, respectively; DEGs between disease cohorts in the AUCTION group encoded for proteins involved in collagen synthesis and platelet aggregation (increased in HEALTHY). Our work demonstrates the clear influence marketing has on host expression and identified genes and mechanisms which may predict BRD risk.

Evaluation of Genes and Molecular Pathways Involved in the Progression of Monoclonal Gammopathy of Undetermined Significance (MGUS) to Multiple Myeloma: A Systems Biology Approach.

Today, Monoclonal Gammopathy of Undetermined Significance (MGUS) is known as a plasma cell malignancy susceptible to evolving into the life-threatening stage, multiple myeloma (MM), without prominent clinical manifestations. Despite the discovery of advanced therapies and multiple pathogenic markers, the complexity of MM development has made it an incurable malignancy. In this study, the microarray dataset was downloaded from the Gene Expression Omnibus (GEO) database and analyzed using the LIMMA package of R-software to determine differentially expressed genes (DEGs) in MGUS and MM compared to the control samples. Enrichment analysis of DEGs was evaluated using the GeneCodis4 software. Protein-protein interaction (PPI) networks were constructed via the GeneMANIA database, and Cytoscape visualized them. The Molecular Complex Detection (MCODE) plugin from Cytoscape was used to identify the key modules from the PPI network. Afterward, the hub genes were recognized using the cytoHubba plug-in in Cytoscape. Eventually, the correlation between hub-DEGs and MM-specific survival was evaluated via the PrognoScan database. A total of 138 (MM-normal) and 136 (MGUS-normal) DEGs were obtained from the datasets, and 62 common DEGs between MGUS and MM diseases (26 up-regulated and 36 down-regulated genes) were screened out for subsequent analyses. Following enrichment analyses and the PPI network's evaluation, FOS, FOSB, JUN, MAFF, and PPP1R15A involved in the progression of MGUS to MM were detected as the hub genes. The survival analysis revealed that FOS, FOSB, and JUN among hub genes were significantly associated with disease-specific survival (DSS) in MM. Identifying the genes involved in the progression of MGUS to MM can help in the design of preventive strategies as well as the treatment of patients. In addition, their evaluation can be effective in the survival of patients.

Left ventricular assist device bioinformatics identify possible hubgenes and regulatory networks involved in the myocardium of patients with left ventricular assist device.

ObjectiveThe aim of this study was to clarify the changes of myocardial gene expression profile after left ventricular assist device (LVAD) implantation and the related molecular biological significance.MethodsA thorough bioinformatic analysis to evaluate the changes in gene expression profile in patients pre-LVAD and post-LVAD was conducted. Four relevant gene expression datasets—GSE430, GSE974, GSE21610, and GSE52601 from Gene Expression Omnibus (GEO) database were downloaded. Analysis of GEO2R, Gene Ontology (GO), protein-protein interaction (PPI) were used to determine differentially expressed genes (DEGs) and their function, respectively.ResultsA total of 37 DEGs were identified, including 26 down-regulated and 11 up-regulated genes. The molecular function of DEGs were enriched in “cytokine activity,” “neurotransmitter binding,” “receptor ligand activity.” The gene set enrichment analysis (GSEA) revealed an overall marked increase of neutrophil degranulation signaling, closely correlated with the G protein coupled receptor (GPCR)—ligand binding process after LVAD assistance. 16 hubgenes in these DEGs were further selected and the biological process involved is mainly related to positive regulation of leukocyte chemotaxis mediated by chemokines.ConclusionInflammatory signaling pathway is crucial for the pathophysiology after LVAD implantation. Chemokines mediate cardiac inflammatory response and tissue remodeling after LVAD implantation through GPCR—ligand binding.

Interactions between the soil bacterial community assembly and gene regulation in salt‐sensitive and salt‐tolerant sweet sorghum cultivars

AbstractComplex bacterial communities in the rhizosphere play a crucial role in plant growth and stress tolerance. These communities vary across cultivars and external environments. However, the influences of salt stress on the structural composition of bacterial microbiome and gene expression of salt‐sensitive and salt‐tolerant sweet sorghum (Sorghum bicolor L. Moench) cultivars have not been studied sufficiently. Here, we employed a combination of 16S rRNA gene profiling and RNA‐seq analysis to characterize changes in root‐associated microbiomes and determine differentially expressed genes (DEG) in the roots of salt‐tolerant M‐81E and salt‐sensitive 'Roma' var. sweet sorghum cultivars under soil conditions with/without salinity. Results revealed that the two contrasting sweet sorghum genotypes selectively filtered and recruited distinct root microbiota in response to salt stress. M‐81E‐enriched bacterial taxa were more diverse and exhibited a higher abundance of metabolic functions than Roma‐enriched taxa. M‐81E‐associated bacterial co‐occurrence networks were more complex and harboured more positive links than Roma‐associated bacterial networks. Furthermore, nine DEG were identified as core salt‐responsive genes and were central to the salt tolerance of sweet sorghum. Correlation analysis revealed that the expression of HSP70, a molecular chaperone, is linked to the recruitment of numerous M‐81E‐enriched bacteria; their relationship needs further exploration. The study supplements the comprehension of the potential role of host–microbe interactions in the response of sweet sorghum to salt stress.

Key molecules associated with thyroid carcinoma prognosis: A study based on transcriptome sequencing and GEO datasets.

BackgroundThyroid carcinoma (THCA) has a low mortality rate, but its incidence has been rising over the years. We need to pay attention to its progression and prognosis. In this study, a transcriptome sequencing analysis and bioinformatics methods were used to screen key genes associated with THCA development and analyse their clinical significance and diagnostic value.MethodsWe collected 10 pairs of THCA tissues and noncancerous tissues, these samples were used for transcriptome sequencing to identify disordered genes. The gene expression profiles were obtained from the Gene Expression Omnibus (GEO) database. Comprehensive analysis of thyroid clinicopathological data using The Cancer Genome Atlas (TCGA). R software was used to carry out background correction, normalization and log2 conversion. We used quantitative real-time PCR (qRT–PCR) and Western blot to determine differentially expressed genes (DEGs) expression in samples. We integrated the DEGs expression, clinical features and progression-free interval (PFI). The related functions and immune infiltration degree were established by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), and single-sample Gene Set Enrichment Analysis (ssGSEA). The UALCAN database was used to analyse the methylation level.ResultsWe evaluated DEGs between normal tissue and cancer. Three genes were identified: regulator of G protein signaling 8 (RGS8), diacylglycerol kinase iota (DGKI) and oculocutaneous albinism II (OCA2). The mRNA and protein expression levels of RGS8, DGKI and OCA2 in normal tissues were higher than those in THCA tissues. Better survival outcomes were associated with higher expression of RGS8 (HR=0.38, P=0.001), DGKI (HR=0.52, P=0.022), and OCA2 (HR=0.41, P=0.003). The GO analysis, KEGG analysis and GSEA proved that the coexpressed genes of RGS8, DGKI and OCA2 were related to thyroid hormone production and peripheral downstream signal transduction effects. The expression levels of RGS8, DGKI and OCA2 were linked to the infiltration of immune cells such as DC cells. The DNA methylation level of OCA2 in cancer tissues was higher than that in the normal samples.ConclusionsRGS8, DGKI and OCA2 might be promising prognostic molecular markers in patients with THCA and reveal the clinical significance of RGS8, DGKI and OCA2 in THCA.

Identification of key genes and infiltrating immune cells among acetaminophen-induced acute liver failure and HBV-associated acute liver failure

BackgroundAcute liver failure (ALF) is a life-threatening complication that is relatively uncommon. ALF causes severe hepatocyte damage and necrosis, which can lead to liver dysfunction and even multi-organ failure. A growing body of evidence suggests that immune cell infiltration and some abnormally expressed genes are associated with ALF development. However, in ALF, they have yet to be thoroughly investigated.MethodsThe Gene Expression Omnibus (GEO) database was used to obtain microarray datasets such as GSE74000, GSE120652, GSE38941, and GSE14668, which were then examined via GEO2R to determine differentially expressed genes (DEGs) associated with ALF. Metascape was employed to annotate the underlined genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The mechanism of IGF1 in 2 different kinds of ALF including acetaminophen-induced ALF and hepatitis B virus (HBV)-induced ALF was studied using gene set enrichment analysis (GSEA). Next, immune cell infiltration was investigated and differentiated in ALF using CIBERSORT.ResultsSix genes (HAO2, IGF1, PLA2G7, SC5D, GNE, SLC1A1) were found to be abnormally expressed in the 2 distinct types of ALF i.e., acetaminophen-induced ALF and HBV-induced ALF. IGF1 was identified as a hub gene in ALF and was found to be associated with several developmental cascades including immune responses, inflammatory responses, and intracellular calcium homeostasis. Additionally, the number of CD4 naive T cells, CD8 T cells, and follicular helper T cells was increased in acetaminophen-induced ALF, whereas the number of activated NK cells, resting NK cells, and plasma cells was increased in HBV-induced ALF.ConclusionsThe present study determined a potential molecular target, namely IGF1, in acetaminophen-induced ALF and HBV-induced ALF, which may provide novel insights into the pathophysiology and management of ALF. Concurrently, the putative immunological pathways have been found.