Pathway Analysis Of Differentially Expressed Genes Research Articles

Upregulation of Neuroinflammation-Associated Genes in the Brain of SARS-CoV-2-Infected Mice

Neurological manifestations are a significant complication of coronavirus disease 2019 (COVID-19), but the underlying mechanisms are yet to be understood. Recently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced neuroinvasion and encephalitis were observed in K18-hACE2 mice, leading to mortality. Our goal in this study was to gain insights into the molecular pathogenesis of neurological manifestations in this mouse model. To analyze differentially expressed genes (DEGs) in the brains of mice following SARS-CoV-2 infection, we performed NanoString gene expression analysis using three individual animal samples at 1, 3, and 6 days post-infection. We identified the DEGs by comparing them to animals that were not infected with the virus. We found that genes upregulated at day 6 post-infection were mainly associated with Toll-like receptor (TLR) signaling, RIG-I-like receptor (RLR) signaling, and cell death pathways. However, downregulated genes were associated with neurodegeneration and synaptic signaling pathways. In correlation with gene expression profiles, a multiplexed immunoassay showed the upregulation of multiple cytokines and chemokines involved in inflammation and cell death in SARS-CoV-2-infected brains. Furthermore, the pathway analysis of DEGs indicated a possible link between TLR2-mediated signaling pathways and neuroinflammation, as well as pyroptosis and necroptosis in the brain. In conclusion, our work demonstrates neuroinflammation-associated gene expression profiles, which can provide key insight into the severe disease observed in COVID-19 patients.

Differential transcriptomic alterations in nasal versus lung tissue of acrolein-exposed rats

Introduction: Acrolein is a significant component of anthropogenic and wildfire emissions, as well as cigarette smoke. Although acrolein primarily deposits in the upper respiratory tract upon inhalation, patterns of site-specific injury in nasal versus pulmonary tissues are not well characterized. This assessment is critical in the design of in vitro and in vivo studies performed for assessing health risk of irritant air pollutants.Methods: In this study, male and female Wistar-Kyoto rats were exposed nose-only to air or acrolein. Rats in the acrolein exposure group were exposed to incremental concentrations of acrolein (0, 0.1, 0.316, 1 ppm) for the first 30 min, followed by a 3.5 h exposure at 3.16 ppm. In the first cohort of male and female rats, nasal and bronchoalveolar lavage fluids were analyzed for markers of inflammation, and in a second cohort of males, nasal airway and left lung tissues were used for mRNA sequencing.Results: Protein leakage in nasal airways of acrolein-exposed rats was similar in both sexes; however, inflammatory cells and cytokine increases were more pronounced in males when compared to females. No consistent changes were noted in bronchoalveolar lavage fluid of males or females except for increases in total cells and IL-6. Acrolein-exposed male rats had 452 differentially expressed genes (DEGs) in nasal tissue versus only 95 in the lung. Pathway analysis of DEGs in the nose indicated acute phase response signaling, Nrf2-mediated oxidative stress, unfolded protein response, and other inflammatory pathways, whereas in the lung, xenobiotic metabolism pathways were changed. Genes associated with glucocorticoid and GPCR signaling were also changed in the nose but not in the lung.Discussion: These data provide insights into inhaled acrolein-mediated sex-specific injury/inflammation in the nasal and pulmonary airways. The transcriptional response in the nose reflects acrolein-induced acute oxidative and cytokine signaling changes, which might have implications for upper airway inflammatory disease susceptibility.

Evidence for increased DNA damage repair in the postmortem brain of the high stress-response group of schizophrenia.

Schizophrenia (SZ) is a disorder diagnosed by specific symptoms and duration and is highly heterogeneous, clinically and pathologically. Although there are an increasing number of studies on the association between genetic and environmental factors in the development of SZ, the actual distribution of the population with different levels of influence of these factors has not yet been fully elucidated. In this study, we focused on stress as an environmental factor and stratified SZ based on the expression levels of stress-responsive molecules in the postmortem prefrontal cortex. We selected the following stress-responsive molecules: interleukin (IL) -1β, IL-6, IL-10, tumor necrosis factor-α, interferon-γ, glucocorticoid receptor, brain-derived neurotrophic factor, synaptophysin, S100 calcium-binding protein B, superoxide dismutase, postsynaptic density protein 95, synuclein, apolipoprotein A1 (ApoA1), ApoA2, and solute carrier family 6 member 4. We performed RNA sequencing in the prefrontal gray matter of 25 SZ cases and 21 healthy controls and conducted a hierarchical cluster analysis of SZ based on the gene expression levels of stress-responsive molecules, which yielded two clusters. After assessing the validity of the clusters, they were designated as the high stress-response SZ group and the low stress-response SZ group, respectively. Ingenuity Pathway Analysis of differentially expressed genes (DEGs) between clusters was performed, and Terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) staining was conducted on four cases each in the high and low stress-response SZ groups to validate DNA damage. We found higher prevalence of family history of SZ in the low stress-response SZ group (0/3 vs. 5/4, p = 0.04). Pathway analysis of DEGs between clusters showed the highest enrichment for DNA double-strand break repair. TUNEL staining showed a trend toward a lower percentage of TUNEL-positive cells in the high stress-response SZ group. Our results suggest that there are subgroups of SZ with different degrees of stress impact. Furthermore, the pathophysiology of these subgroups may be associated with DNA damage repair. These results provide new insights into the interactions and heterogeneity between genetic and environmental factors.

Identification of key genes and the pathophysiology associated with allergen-specific immunotherapy for allergic rhinitis

BackgroundAllergen-specific immunotherapy (AIT) is a causative treatment in allergic rhinitis (AR), comprising long-term allergen administration and over three years of treatment. This study is carried out for revealing the mechanisms and key genes of AIT in AR.MethodsThe present study utilized online Gene Expression Omnibus (GEO) microarray expression profiling dataset GSE37157 and GSE29521 to analyze the hub genes changes related to AIT in AR. Based on limma package, differential expression analysis for the two groups (samples of allergic patients prior to AIT and samples of allergic patients undergoing AIT) was performed to obtain differentially expressed genes (DEGs). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs were conducted using DAVID database. A Protein-Protein Interaction network (PPI) was built and a significant network module was acquired by using Cytoscape software (Cytoscape, 3.7.2). Utilizing the miRWalk database, we identified potential gene biomarkers, constructed interaction networks of target genes and microRNAs (miRNAs) using Cytoscape software, and explore the cell type-specific expression patterns of these genes in peripheral blood using publicly available single-cell RNA sequencing data (GSE200107). Finally, we are using PCR to detect changes in the hub genes that are screened using the above method in peripheral blood before and after AIT treatment.ResultsGSE37157 and GSE29521 included 28 and 13 samples, respectively. A total of 119 significantly co-upregulated DEGs and 33 co-downregulated DEGs were obtained from two datasets. The GO and KEGG analyses demonstrated that protein transport, positive regulation of apoptotic process, Natural killer cell mediated cytotoxicity, T cell receptor signaling pathway, TNF signaling pathway, B cell receptor signaling pathway and Apoptosis may be potential candidate therapeutic targets for AIT of AR. From the PPI network, 20 hub genes were obtained. Among them, the PPI sub-networks of CASP3, FOXO3, PIK3R1, PIK3R3, ATF4, and POLD3 screened out from our study have been identified as reliable predictors of AIT in AR, especially the PIK3R1.ConclusionOur analysis has identified novel gene signatures, thereby contributing to a more comprehensive understanding of the molecular mechanisms underlying AIT in the treatment of AR.

Molecular mechanisms underlying equine endometrial cup regression: a transcriptomic analysis

The gonadotropin-secreting equine endometrial cups (EC) have a major role in pregnancy maintenance, but an intriguingly short lifespan. First seen in the maternal endometrium at days (d) 38-40 post-ovulation, the EC undergo degeneration via poorly understood mechanisms starting around d 60-70, with complete dehiscence at approximately 120-150 d of gestation. Pregnancy losses during the EC physiological lifespan and EC pathological persistence after abortion or uncomplicated parturition usually lead to irregular estrous cyclicity and subfertility, with only anecdotal and inconsistent therapeutic options currently available. A holistic understanding of the cellular signaling leading to EC regression may provide insight for development of effective therapies for retained or persistent EC. We therefore hypothesized that comparing the transcriptome of EC during development and regression could elucidate key regulators and molecular pathways leading to EC trophoblast cell demise. Samples of EC were dissected from the adjacent endometrium of pregnant pony mares during early development (DEC, 42-47 d post-ovulation, n = 5), and regression (REC, 96 – 120 d, n = 5). Next generation RNA sequencing was performed with Illumina NovaSeq6000 and reads mapped to EquCab3.0 (STAR-2.5.2b). Differentially expressed genes (DEGs) were identified with Cuffdiff-2.2.1 (FDR < 0.05). A total of 2,504 DEG were identified, being 1,648 upregulated and 856 downregulated in REC when compared to DEC. Pathway Analysis of DEGs was also performed (IPA, Qiagen). Interestingly, the main pathways affected in REC included oxidative phosphorylation (P = 1.08e-38);mitochondrial dysfunction (P = 2e-25); estrogen receptor signaling (P = 2.2e-10); Sirtuin signaling pathway (P = 9.64e-16), which has central regulatory roles in cell senescence and apoptosis; and Granzyme A Signaling (3.29e-15), associated with Cytotoxic T Lymphocyte and Natural Killer-mediated apoptosis via caspase-independent pathways. Upstream regulator analysis highlighted the roles of mitochondrial protein ubiquinol-cytochrome c reductase complex-3; rapamycin-insensitive companion of mTOR, an essential molecule in cellular homeostasis; Torin-1, a potent mTOR inhibitor; dead box protein 5, which may act as a co-activator of estrogen receptor signaling; and transducing-like enhancer protein-3, a member of a family of proteins that regulate cell fate through the Notch signaling pathway. Importantly, the main upstream regulators and downstream molecules are also involved in cancer cell biology (P = 1.32e-07 – 1.71e-122), including the downstream effectors of neoplastic and epithelial cell death secreted phosphoprotein 1 (Spp1), and secreted protein acidic and cysteine rich (Sparc). Along with aromatase, Spp1 and Sparc were upregulated in REC in comparison to DEC. In summary, we have highlighted key molecular pathways and regulators of EC regression, which merit further molecular and functional investigations. Since multiple identified molecules have also been targeted in human oncological treatments, further investigation of their effectiveness in hastening EC demise is warranted.

Distinct Adipogenic and Fibrogenic Differentiation Capacities of Mesenchymal Stromal Cells from Pancreas and White Adipose Tissue.

Pancreatic steatosis associates with β-cell failure and may participate in the development of type-2-diabetes. Our previous studies have shown that diabetes-susceptible mice accumulate more adipocytes in the pancreas than diabetes-resistant mice. In addition, we have demonstrated that the co-culture of pancreatic islets and adipocytes affect insulin secretion. The aim of this current study was to elucidate if and to what extent pancreas-resident mesenchymal stromal cells (MSCs) with adipogenic progenitor potential differ from the corresponding stromal-type cells of the inguinal white adipose tissue (iWAT). miRNA (miRNome) and mRNA expression (transcriptome) analyses of MSCs isolated by flow cytometry of both tissues revealed 121 differentially expressed miRNAs and 1227 differentially expressed genes (DEGs). Target prediction analysis estimated 510 DEGs to be regulated by 58 differentially expressed miRNAs. Pathway analyses of DEGs and miRNA target genes showed unique transcriptional and miRNA signatures in pancreas (pMSCs) and iWAT MSCs (iwatMSCs), for instance fibrogenic and adipogenic differentiation, respectively. Accordingly, iwatMSCs revealed a higher adipogenic lineage commitment, whereas pMSCs showed an elevated fibrogenesis. As a low degree of adipogenesis was also observed in pMSCs of diabetes-susceptible mice, we conclude that the development of pancreatic steatosis has to be induced by other factors not related to cell-autonomous transcriptomic changes and miRNA-based signals.

Pre-Operative Physical Function Predicts Post-Operative Skeletal Muscle Gene Expression in Old Mice

In older adults, pre-operative physical function predicts post-operative outcomes. The biological mechanisms underlying vulnerability to physical decline remain poorly understood. Using a mouse model of laparotomy, we sought to identify biological correlates of post-operative function. 24-month-old male C57BL/6N mice were categorized as high functioning (HF) or low functioning (LF) based on pre-operative performance on the accelerating rotarod. On post-operative days (POD) 2 and 4, LF mice had lower rotarod latency to fall times than HF mice did. Forelimb grip strength was reduced after laparotomy in both HF and LF groups on POD 1 and 3 and did not differ significantly between these groups. Whole transcriptome sequencing analysis (RNAseq) of soleus muscles collected on POD 5 showed 224 and 228 differentially expressed genes (DEGs) for HF and LF, respectively, compared to their respective controls. Only 21 DEGs were observed in both groups, including Pparα, Fst and Pla2g15. Such changes may be hallmarks of the post-surgical response in aging. Pathway analysis of DEGs using Ingenuity Pathway Analysis software (Qiagen) revealed one pathway common to HF and LF (osteoarthritis) whereas activation of GP6 signaling and apoptosis signaling was observed in HF and inhibition of PPARα/RXR activation and PPARα signaling was noted in LF. We conclude that pre-operative performance on the accelerating rotarod correlates with differences in skeletal muscle gene expression, which may contribute to the differences in functional outcomes post-operatively in HF and LF mice. Further studies are needed to delineate the roles of these signaling pathways in physical resilience to surgery.

Abstract 2333: EMT programs ovarian cancer cells to survive the adipocyte-rich microenvironment

Abstract Background: Metabolic pathways are non-canonical targets of the EMT program. The relevance of re-programming metabolism during the metastasis cascade is underscored in ovarian cancer cells, which primarily metastasizes to the adipocyte-rich omentum. Ovarian cancer-adipocyte interaction has been shown to promote fatty acid (FA) uptake into the cancer cells. These FA are then catabolized via β-oxidation thus providing the energy required for rapid tumor growth. β-oxidation of FA requires efficient mitochondria and oxygen processing. The objective of this study is to determine if E/M status determine adaptation and survival in adipocyte-rich microenvironment. Materials and Methods: RNA seq was performed in Ck18+/Twist- epithelial and Ck18-/Twist+ mesenchymal human ovarian cancer cells. Pathway and Gene Ontology analyses were performed on differentially expressed (DEX) genes (FC&amp;gt;2 and p&amp;lt;0.05) using iPathway Guide. Protein levels were determined by western blot. Oxygen consumption rate was measured using Seahorse XF Analyzer. Cell viability was quantified using CelltoxTM Green viability dye. Results: Pathway analysis of DEX genes with focus on metabolic pathways showed the following DEX pathways: glycolysis/gluconeogenesis (p=0.008); pyruvate metabolism (0.019); fatty acid degradation (p=0.01); fatty acid elongation (0.008). Gene ontology analysis showed significant difference in GO:0006979: response to oxidative stress (p=0.007). Further analysis of DEX genes within these pathways showed upregulation in mesenchymal cancer cells of both pyruvate dehydrogenase subunits, PDHA1 (p = 0.011) and PDHB (p=0.014) and upregulation of carnitine palmitoyltransferase (CPT1; p=0.011), the rate limiting enzyme in FA β-oxidation. The upregulation of these genes was validated at the protein level by western blot analysis, which also showed increased levels of COX-IV in mesenchymal cancer cells compared to epithelial cancer cells. Moreover, mesenchymal cells exhibited enhanced maximal respiration and enhanced spare respiratory capacity. Finally, viability studies conclusively demonstrate the metabolic flexibility in mesenchymal cancer cells, which maintained viability upon nutrient deprivation suggesting metabolic plasticity. In contrast, cell death was observed epithelial cancer cells upon nutrient deprivation, which was rescued by the addition of glucose but not the FA, oleic acid. Conclusion: Ovarian cancer cells acquire enhanced pyruvate shuttling to the TCA cycle, a more efficient FA β-oxidation machinery, as well as more efficient oxygen processing during EMT. These phenotypes are relevant in supporting survival in the adipocyte microenvironment. Further elucidation of EMT related pathways that re-program lipid metabolism may lead to better control of carcinomatosis in ovarian cancer patients. Citation Format: Hussein Chehade, Alexandra Fox, Roslyn Tedja, Radhika Gogoi, Gil Mor, Ayesha B. Alvero. EMT programs ovarian cancer cells to survive the adipocyte-rich microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2333.

Identification of key candidate genes in local dorsal root ganglion inflammation by integrated bioinformatics analysis.

The purpose of the present study was to identify potential markers of local dorsal root ganglion (DRG) inflammation to aid diagnosis, treatment and prognosis evaluation of DRG pain. A localized inflammation of the DRG (LID) rat model was used to study the contribution of inflammation to pain. The dataset GSE38859 was obtained from the Gene Expression Omnibus database. Pre-treatment standardization of gene expression data for each experiment was performed using the R/Bioconductor Limma package. Differentially expressed genes (DEGs) were identified between a LID model and a sham surgery control group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of DEGs and gene set enrichment analysis (GSEA) were carried out using the ‘clusterProfiler’ package in R. Using the Search Tool for Retrieval of Interacting Genes, a protein-protein interaction network was constructed and visualized. Candidate genes with the highest potential validity were validated using reverse transcription-quantitative PCR and western blotting. In total, 66 DEGs were enriched in GO terms related to inflammation and the immune response processes. KEGG analysis revealed 14 associated signaling pathway terms. Protein-protein interaction network analysis revealed 9 node genes, 3 of which were among the top 10 DEGs. Matrix metallopeptidase 9, chemokine CXCL9, and complement component 3 were identified as key regulators of DRG inflammatory pain progression.

Transcriptomic analysis reveals a role of phenylpropanoid pathway in the enhancement of chilling tolerance by pre-storage cold acclimation in cucumber fruit

Cucumber fruits are susceptible to chilling injury, which can cause severe quality losses. In this study, pre-storage cold acclimation (PsCA, 10°C for 72 h) significantly induced chilling tolerance in cucumber fruits. To gain insight into the induction mechanisms of PsCA, comparative transcriptome analysis of fruit samples at 0 h, 12 h and 72 h during cold treatments were conducted. High-throughput transcriptome sequences were de novo assembled into 24878 unique transcripts. A total of 10164 differentially expressed genes (DEGs) were identified during cold stress, and 6205 DEGs were identified during cold acclimation, and 7976 DEGs were identified in cold acclimation compared to cold stress. Large numbers of DEGs were commonly detected between cold stress and cold acclimation, suggesting that these DEGs are related to cold response. Twelve DEGs were selected for qRT-PCR validation, and confirmed the credibility and accuracy of transcriptome data. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs indicated that biological processes or pathways such as plant hormone signal transduction, carbon metabolism, and biosynthesis of amino acids were commonly affected by cold stress and acclimation treatments when compared to fruits just harvested. However, compared with cold stress, cold acclimation-affected DEGs were most enriched in phenylpropanoid pathway. Moreover, PsCA upregulated the expression of six DEGs in phenylpropanoid pathway in cold-stored cucumbers. These results suggest that phenylpropanoid pathway may play a role in PsCA-enhanced chilling tolerance. These findings provide novel insights into understand the induction mechanisms underlying PsCA-induced chilling tolerance in cold-stored cucumbers.

Ulcerative colitis immune cell landscapes and differentially expressed gene signatures determine novel regulators and predict clinical response to biologic therapy

The heterogeneous pathobiology underlying Ulcerative Colitis (UC) is not fully understood. Using publicly available transcriptomes from adult UC patients, we identified the immune cell landscape, molecular pathways, and differentially expressed genes (DEGs) across patient cohorts and their association with treatment outcomes. The global immune cell landscape of UC tissue included increased neutrophils, T CD4 memory activated cells, active dendritic cells (DC), and M0 macrophages, as well as reduced trends in T CD8, Tregs, B memory, resting DC, and M2 macrophages. Pathway analysis of DEGs across UC cohorts demonstrated activated bacterial, inflammatory, growth, and cellular signaling. We identified a specific transcriptional signature of one hundred DEGs (UC100) that distinctly separated UC inflamed from uninflamed transcriptomes. Several UC100 DEGs, with unidentified roles in UC, were validated in primary tissue. Additionally, non-responders to anti-TNFα and anti-α4β7 therapy displayed distinct profiles of immune cells and pathways pertaining to inflammation, growth, and metabolism. We identified twenty resistant DEGs in UC non-responders to both therapies of which four had significant predictive power to treatment outcome. We demonstrated the global immune landscape and pathways in UC tissue, highlighting a unique UC signature across cohorts and a UC resistant signature with predictive performance to biologic therapy outcome.

CT23 knockdown attenuating malignant behaviors of hepatocellular carcinoma cell is associated with upregulation of metallothionein 1.

The cancer-testis antigen 23 (CT23) gene has been reported in association with the pathogenesis and progressof hepatocellular carcinoma (HCC). However, the alterations of gene expression profiling induced by CT23 knockdown in HCC cells remains largely unknown. In this study, theRNA interfering (RNAi) method was used to silence CT23 expression in BEL-7404 cells. Microarray analysis was performed on mRNAextracted from the CT23 knockdown cells and the control cells to determine the alterations of gene expression profiles. The result showed a total of 1051 genes expressed differentially (two-fold change), including 470 genes upregulated and 581 gene downregulated in the CT23 knockdown cells. A bioinformaticanalysis showed that the functional differentially expressed genes (DEGs) were linked to cell proliferation, migration, and apoptosis, and metallothionein 1 (MT1) attainedthe maximum enrichment scores in functional annotation, classification, and pathway analysis of DEGs. Furthermore, Western blot analysis and cell behaviors assays verified that CT23 modulates cell proliferation, migration, and apoptosis by regulating MT1 expression in HCC cells and non-neoplastic hepatocytes. In summary, downregulated CT23 gene in BEL-7404 cells might change the expressions of carcinogenesis and progression related genes in HCC by upregulating MT1 expression, which would provide insight intosearching for a novel therapeutic target for HCC.

Homologous recombination repair rathway and RAD54L in early-stage lung adenocarcinoma.

ObjectiveThe current study aims to identify the dysregulated pathway involved in carcinogenesis and the essential survival-related dysregulated genes among this pathway in the early stage of lung adenocarcinoma (LUAD).Patients and MethodsData from The Cancer Genome Atlas (TCGA) including 526 tumor tissues of LUAD and 59 healthy lung tissues were analyzed to gain differentially expressed genes (DEGs). Gene ontology (GO) analysis was conducted with DAVID, while the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs was performed, followed by gene set enrichment analysis (GSEA) methods. Survival analysis was implemented in TCGA dataset and validated in Gene Expression Omnibus (GEO) cohort GSE50081, which includes 127 patients with stage I LUAD.ResultsGSEA enrichment analysis suggested that homologous recombination repair (HRR) pathway was significantly enriched. Subsequent KEGG pathway enrichment analysis indicated the significant up-regulation of HRR pathway in patients with T1 stage LUAD. Retrieved in Gene database, RAD54L is involved in HRR pathway and were recognized to be significantly differentially expressed in T1 stage LUAD in our study. The survival analysis indicated that high expression of RAD54L was significantly related to worse overall survival in patients with T1 stage LUAD (TCGA cohort: HR=2.10, 95% CI [1.47–2.98], P = 0.001; GSE50081 validation cohort: HR = 2.61, 95% CI [1.51–4.52], P = 0.002). Multivariate cox regression analysis indicated that RAD54L is an independent prognostic factor in the early-stage LUAD.ConclusionHRR pathway is up-regulated in LUAD, among which the expression of RAD54L was found to be significantly differentially expressed in T1 stage tumor tissue. Patients with high expression of RAD54L were associated with worse overall survival in the TCGA cohort and validation cohort. This study suggests a potential mechanism of lung cancer progression and provide a budding prognostic factor and treatment target in early-stage LUAD.

Identification of biomarkers, pathways and potential therapeutic target for docetaxel resistant prostate cancer

ABSTRACT Docetaxel has been proved to provide survival benefit for advanced prostate cancer (PCa) patients. Resistance to docetaxel further reduces the survival of these patients. Herein, we performed a comprehensive bioinformatic analysis to identify differentially expressed genes (DEGs) between docetaxel sensitive and resistant PCa (DRPC) cell based on Gene Expression Omnibus (GEO) database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were applied for functional and pathway analysis of DEGs. The STRING database, cytoscape software and plug-in ‘cytoHubba’ were used to construct protein–protein interaction (PPI) networks and identify hub genes. Survival analysis were performed via GEPIA database. Finally, we conducted immune infiltration analysis by TIMER. A total of 460 DEGs were identified. GO functional analysis showed that these DEGs are mainly enriched in chemotaxis, negative regulation of intracellular signal transduction, and regulation of cell adhesion, positive regulation of inflammatory response, regulation of response to cytokine stimulus. According to the results of KEGG pathway analysis, these DEGs are mainly involved in signaling by Rho GTPases, Miro GTPases and RHOBTB3; interferon Signaling; arginine biosynthesis; PI3K-Akt signaling pathway; cytokine-cytokine receptor interaction; MAPK signaling pathway. Finally, CCNB1 and EZH2 were identified as prognostic hub genes and the expression of these two genes were associated with immune infiltration. The present study may helps to improve the understanding of the molecular mechanisms of DRPC and facilitate the selection of therapeutic and prognostic biomarkers for DRPC.

Effects of Tamoxifen on the Mutant Allele Burden and Disease Course in Patients with Myeloproliferative Neoplasms - Results of the Tamarin Study

Effects of Tamoxifen on the Mutant Allele Burden and Disease Course in Patients with Myeloproliferative Neoplasms - Results of the Tamarin Study

Comprehensive transcriptome profiling of Caragana microphylla in response to salt condition using de novo assembly.

To investigate the response of Caragana microphylla in salt condition, transcriptome analysis, differentially expressed genes (DEGs) comparison with Arabidopsis thaliana, and the chlorophyll content analysis were performed. Gene Ontology (GO) term, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of DEGs indicated that salt condition affected photosynthesis and chlorophyll in C. microphylla. The DEGs compared with salt responsive genes of A. thaliana indicated that C. microphylla's responses to salt differed greatly from those of the model plant and that the results also indicated up-regulated genes related to photosynthesis and chlorophyll in C. microphylla. Moreover, we confirmed that salt-treated C. microphylla increased chlorophyll content, and the genes of protoporphyrin IX downstream in chlorophyll biosynthesis were induced in the heatmap analysis. These results showed a similar pattern to some halophytes plants with increased chlorophyll at a certain salt concentration, and we assumed that C. microphylla also has a mechanism to adapt or tolerate moderate salt conditions.

Understanding salt tolerance mechanism using transcriptome profiling and de novo assembly of wild tomato Solanum chilense.

Soil salinity affects the plant growth and productivity detrimentally, but Solanum chilense, a wild relative of cultivated tomato (Solanum lycopersicum L.), is known to have exceptional salt tolerance. It has precise adaptations against direct exposure to salt stress conditions. Hence, a better understanding of the mechanism to salinity stress tolerance by S. chilense can be accomplished by comprehensive gene expression studies. In this study 1-month-old seedlings of S. chilense and S. lycopersicum were subjected to salinity stress through application of sodium chloride (NaCl) solution. Through RNA-sequencing here we have studied the differences in the gene expression patterns. A total of 386 million clean reads were obtained through RNAseq analysis using the Illumina HiSeq 2000 platform. Clean reads were further assembled de novo into a transcriptome dataset comprising of 514,747 unigenes with N50 length of 578 bp and were further aligned to the public databases. Genebank non-redundant (Nr), Viridiplantae, Gene Ontology (GO), KOG, and KEGG databases classification suggested enrichment of these unigenes in 30 GO categories, 26 KOG, and 127 pathways, respectively. Out of 265,158 genes that were differentially expressed in response to salt treatment, 134,566 and 130,592 genes were significantly up and down-regulated, respectively. Upon placing all the differentially expressed genes (DEG) in known signaling pathways, it was evident that most of the DEGs involved in cytokinin, ethylene, auxin, abscisic acid, gibberellin, and Ca2+ mediated signaling pathways were up-regulated. Furthermore, GO enrichment analysis was performed using REVIGO and up-regulation of multiple genes involved in various biological processes in chilense under salinity were identified. Through pathway analysis of DEGs, “Wnt signaling pathway” was identified as a novel pathway for the response to the salinity stress. Moreover, key genes for salinity tolerance, such as genes encoding proline and arginine metabolism, ROS scavenging system, transporters, osmotic regulation, defense and stress response, homeostasis and transcription factors were not only salt-induced but also showed higher expression in S. chilense as compared to S. lycopersicum. Thus indicating that these genes may have an important role in salinity tolerance in S. chilense. Overall, the results of this study improve our understanding on possible molecular mechanisms underlying salt tolerance in plants in general and tomato in particular.

Mechanisms of Maintenance of Foot-and-Mouth Disease Virus Persistence Inferred From Genes Differentially Expressed in Nasopharyngeal Epithelia of Virus Carriers and Non-carriers.

Foot-and-mouth disease virus (FMDV) causes persistent infection of nasopharyngeal epithelial cells in ~50% of infected ruminants. The mechanisms involved are not clear. This study provides a continued investigation of differentially expressed genes (DEG) identified in a previously published transcriptomic study analyzing micro-dissected epithelial samples from FMDV carriers and non-carriers. Pathway analysis of DEG indicated that immune cell trafficking, cell death and hematological system could be affected by the differential gene expression. Further examination of the DEG identified five downregulated (chemerin, CCL23, CXCL15, CXCL16, and CXCL17) and one upregulated (CCL2) chemokines in carriers compared to non-carriers. The differential expression could reduce the recruitment of neutrophils, antigen-experienced T cells and dendritic cells and increase the migration of macrophages and NK cells to the epithelia in carriers, which was supported by DEG expressed in these immune cells. Downregulated chemokine expression could be mainly due to the inhibition of canonical NFκB signaling based on DEG in the signaling pathways and transcription factor binding sites predicted from the proximal promoters. Additionally, upregulated CD69, IL33, and NID1 and downregulated CASP3, IL17RA, NCR3LG1, TP53BP1, TRAF3, and TRAF6 in carriers could inhibit the Th17 response, NK cell cytotoxicity and apoptosis. Based on our findings, we hypothesize that (1) under-expression of chemokines that recruit neutrophils, antigen-experienced T cells and dendritic cells, (2) blocking NK cell binding to target cells and (3) suppression of apoptosis induced by death receptor signaling, viral RNA, and cell-mediated cytotoxicity in the epithelia compromised virus clearance and allowed FMDV to persist. These hypothesized mechanisms provide novel information for further investigation of persistent FMDV infection.

Abstract B050: Identification of differentially expressed and spliced genes between breast, colon, lung, and prostate cancer from African American and white patients

Abstract Racial/ethnic disparity in cancer refers to the disproportionate incidence of and/or mortality from various cancers among population groups. In addition to differences in social, lifestyle and structural determinants of health, there is accumulating evidence for a biologic contribution to racial/ethnic disparity in cancer. To understand further the biologic mechanisms underlying racial/ethnic disparity in cancer, the analysis of differential aggregate gene expression and mutation among cancer patients of different population groups is important. Our recently published work reported differential RNA splicing as a critical mechanism underlying prostate cancer aggressiveness and drug response in African American (AA) patients. Here, we use R to analyze the Genomic Data Commons for differential aggregate gene expression (2-fold mean change, p &amp;lt; 0.001, Wilcoxon rank sum test) and TCGASpliceSeq to analyze TCGA for differential RNA splicing (20% median change, percent spliced in) between breast (BRCA, 183 AA and 761 white), colon (COAD, 56 AA and 194 white), squamous and adenocarcinoma lung (LUSC and LUAD, 34 and 57 AA and 392 and 444 white, respectively), and prostate (PRAD, 49 AA and 307 white) cancer specimens from AA and white patients. Our analysis identified 698 differentially expressed genes (DEGs) and 114 alternative RNA splicing events (ARSs) in BRCA, 107 DEGs and 57 ARSs in COAD, 25 and 117 DEGs and 115 and 53 ARSs in LUSC and LUAD, respectively, and 25 DEGs and 71 ARSs in PRAD from AA and white patients. Notably, comparing the lists of DEGs or ARSs from each cancer type with each of the other cancer types yields a minority of overlapping DEGs or ARSs among cancer types, indicating that race-related DEGs and ARSs are largely specific to cancer type. Pathway analysis of DEGs and ARSs reveals that the majority of these genes function in pathways relevant to cancer development and progression, such as programmed cell death, DNA repair, signal transduction, gene expression and metabolism. These analyses increase understanding of molecular mechanisms underlying racial/ethnic disparity in cancer. Upon further study of the function of these variants, such DEGs and ARSs have the potential to become candidates for development of new precision medicine interventions. Citation Format: Muthana Al Abo, Daniel J. George, Jennifer A. Freedman, Steven R. Patierno. Identification of differentially expressed and spliced genes between breast, colon, lung, and prostate cancer from African American and white patients [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr B050.

Identification of Differentially Expressed Genes and Key Pathways in the Dorsal Root Ganglion After Chronic Compression.

Neuropathic pain (NP) is caused by primary or secondary impairment of the peripheral or central nervous systems. Its etiology is complex and involves abnormal patterns of gene expression and pathway activation. Using bioinformatics analysis, we aimed to identify NP-associated changes in genes and pathways in L4 and L5 dorsal root ganglia (DRG) in a rat model of NP induced by chronic compression of the DRG (CCD). Genome-wide transcriptional analyses were used to elucidate the molecular mechanisms underlying NP. We screened differentially expressed genes (DEGs) 7 days after CCD in comparison with sham-operated controls. Quantitative real-time polymerase chain reaction (RT-qPCR) and western blotting were used to confirm the presence of key DEGs. Kyoto Encyclopedia of Genes and Genomes (KEGG)-pathway analysis of DEGs and global signal transduction network analysis of DEGs were also conducted. The CCD group developed clear mechanical and thermal allodynia in the ipsilateral hind paw compared with the sham group. This comparison identified 1,887 DEGs, with 1156 upregulated and 731 downregulated DEGs, and 123 DEG-enriched pathways. We identified the key candidate genes that might play a role in the development of NP, namely syndecan 1 (Sdc1), phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma (Pi3k), Janus kinase 2 (Jak2), jun proto-oncogene, AP-1 transcription factor subunit (Jun), and interleukin 6 (IL-6) by analyzing the global signal transduction network. RT-qPCR and western blot analysis confirmed the microarray results. The DEGs Sdc1, Pi3k, Jak2, Jun, and IL-6, and the cytokine signaling pathway, the neuroactive ligand-receptor interaction, the toll-like receptor signaling pathway, and the PI3K-Akt signaling pathway may have decisive modulatory roles in both nerve regeneration and NP. These results provide deeper insight into the mechanism underlying NP and promising therapeutic targets for its treatment.