Expression Microarray Analysis Research Articles

Alleviation of Angiotensin II-Induced Vascular Endothelial Cell Injury through Long Non-coding RNA TUG1 Inhibition.

Hypertension damages endothelial cells, causing vascular remodelling. It is caused by Ang II-induced endothelial cell (EC) destruction. The long noncoding RNA (lncRNAs) are emerging regulators of endothelium homeostasis. Injured endothelium expresses lncRNA taurine-upregulated gene 1 (TUG1), which may mediate endothelial cell damage, proliferation, apoptosis, and autophagy and contribute to cardiovascular disease. However, uncertainty surrounds the function of lncRNA TUG1, on arterial endothelium cell damage. This research aimed to investigate the role and mechanism of lncRNA TUG1 in vascular endothelial cell injury. A microarray analysis of lncRNA human gene expression was used to identify differentially expressed lncRNAs in human umbilical vein endothelial cell (HUVEC) cultures. The viability, apoptosis, and migration of Ang II-treated HUVECs were then evaluated. In order to investigate the role of lncRNA TUG1 in hypertension, qRT-PCR, western blotting, and RNA-FISH were used to examine the expression of TUG1 in SHR mice. Ang II-activated HUVECs and SHR rats' abdominal aortas highly express the lncRNA TUG1. LncRNA TUG1 knockdown in HUVECs could increase cell viability, reduce apoptosis, and produce inflammatory factors. In SHR rat abdominal aortas, lncRNA TUG1 knockdown promoted proliferation and inhibited apoptosis. HE spotting showed that lncRNA TUG1 knockdown improved SHR rats' abdominal aorta shape. lncRNA TUG1 knockdown promotes miR-9- 5p, which inhibits CXCR4 following transcription. The lncRNA TUG1/miR-9-5p/CXCR4 axis and vascular cell injury were also examined. MiR-9-5p silencing or CXCR4 overexpression lowered cell survival, apoptosis, and lncRNA TUG1-induced IL-6 and NO expression. lncRNA TUG1 suppression could reduce Ang II-induced endothelial cell damage by regulating and targeting miR-9-5p to limit CXCR4 expression and open new vascular disease research pathways.

Microarray analysis of microrna expression in peripheral blood mononuclear cells of patients with polymyositis and dermatomyositis.

MicroRNAs (miRNAs) represent a new class of biomarkers in the context of connective tissue disorders. The miRNA expression profiles in peripheral blood mononuclear cells (PBMCs) of patients with polymyositis (PM) and dermatomyositis (DM) have not been fully elucidated. The objective is to investigate miRNAs expression profile in PBMCs of patients with PM/DM. Microarray technology was used to identify differentially expressed miRNAs in PBMCs obtained from 6 untreated PM/DM patients and 3 healthy controls (HCs). TaqMan-based stem-loop real-time PCR detection was used for validation in a cohort of 34 PM/DM patients and 20 HCs. Microarray analysis revealed 38 differentially expressed miRNAs (24 up-regulated and 14 down-regulated) in PM/DM patients compared to HCs. Four miRNAs (miR-320a, miR-335-3p, miR-34a-5p and miR-454-3p) were chosen for real-time PCR validation. The expression of miR-34a-5p was significantly upregulated in PM/DM group (P < 0.05). In subgroup analysis, miR-34a-5p was significantly upregulated in interstitial lung disease (ILD) group and DM group (P < 0.001). The level of SIRT1, a validated target of miR-34a, was significantly lower in PBMCs of PM/DM patients compared with HCs. MiR-34a-5p may potentially participate in the pathogenesis of PM/DM through SIRT1, and may serve as a potential new biomarker for PM/DM-ILD.

Downregulation of Serum PTEN Expression in Mercury-Exposed Population and PI3K/AKT Pathway-Induced Inflammation

ObjectiveThis study investigated the impact of occupational mercury (Hg) exposure on human gene transcription and expression, and its potential biological mechanisms. MethodsDifferentially expressed genes related to Hg exposure were identified and validated using gene expression microarray analysis and extended validation. Hg-exposed cell models and PTEN low-expression models were established in vitro using 293T cells. PTEN gene expression was assessed using qRT-PCR, and Western blotting was used to measure PTEN, AKT, and PI3K protein levels. IL-6 expression was determined by ELISA. ResultsCombined findings from gene expression microarray analysis, bioinformatics, and population expansion validation indicated significant downregulation of the PTEN gene in the high-concentration Hg exposure group. In the Hg-exposed cell model (25 and 10 μmol/L), a significant decrease in PTEN expression was observed, accompanied by a significant increase in PI3K, AKT, and IL-6 expression. Similarly, a low-expression cell model demonstrated that PTEN gene knockdown led to a significant decrease in PTEN protein expression and a substantial increase in PI3K, AKT, and IL-6 levels. ConclusionThis is the first study to report that Hg exposure downregulates the PTEN gene, activates the PI3K/AKT regulatory pathway, and increases the expression of inflammatory factors, ultimately resulting in kidney inflammation.

Abstract 5363: New targeted therapy on SOCS1-related immune-response in triple-negative breast cancer

Abstract Background: Triple-negative breast cancer (TNBC) is heterogenous, which includes basal-like, immunomodulatory, mesenchymal, mesenchymal stem cell and luminal androgen receptor subtypes. In addition to chemotherapy, PARP inhibitors and immune checkpoint inhibitors are effective for TNBC with BRCA-mutated and PD-L1-positive cases. However, overall survival of TNBC remains unfavorable. To explore new targeted therapy in TNBC, we reported previously that SOCS1 (suppressor of cytokine signaling 1), IL-13 and several genes were predicted as interactive targets of miRNA in TNBC from the microarray expression analysis (Agilent Technologies, Inc.) of small RNA extracted from 11 breast cancer specimens (AACR2020, #1709). Thus, we investigated SOCS1-related immune-response under co-culture of TNBC and monocyte cell lines with or without paclitaxel exposure. Materials and Methods: MDA-MB-231, MDA-MB-468, RAW264.7 cell lines were used with co-culture system (Falcon® Cell Culture Inserts, Corning, NY, USA). SOCS1-expression vector and siSOCS1 were transfected into TNBC cell lines with polyethylenimine (PEI Max; Polysciences, Inc., Warrington, PA). RAW264.7 was activated with lipopolysaccaride (5ug/ml) and IFNγ (10ng/ml) for 2 days before co-culture. Relative cell viability of TNBC cell lines with vehicle control (DMSO) or paclitaxel exposure was measured with WST-8 (Cell Counting Kit-8; Dojindo, Japan) using TC20 Automated cell counter (Bio-Rad Laboratories, Inc., Japan) after 2 days’ co-culture of TNBC and RAW264.7 cells under several conditions of SOCS1 overexpression and/or RAW264.7 activation. Results: First, paclitaxel inhibited cell growth of MDA-MB-231 and MDA-MB-468 in a dose-dependent manner (at 1nM~100nM). Second, at paclitaxel exposure of 10 nM and 50 nM, relative cell viability of MDA-MB-468 decreased with co-culture of activated RAW264.7. The tendency was enhanced with SOCS1 overexpression in breast cancer cell lines. Similar results were observed in MDA-MB-231 cells. Discussions: SOCS1 is well known as a negative regulator of JAK-STAT pathway. SOCS1 is also related to suppression of T cell activation and modulation of M1 macrophage. At AACR2020, we reported that SOCS1 gene amplification in cancer tissues after neoadjuvant chemotherapy was relatively lower in 6 cases with pathologically partial or complete response than in 11 cases with no pathological response. In vitro, paclitaxel-toxicity in TNBC cells was augmented by activated monocyte (M1 macrophage) and more sensitized with SOCS1 overexpression in TNBC cells. These results suggest that proinflammatory cytokines from M1 macrophage influence cell viability of TNBC. Conclusion: SOCS1 is a promising molecular target to modulate immune-response in TNBC. Citation Format: Shigeru Imoto, Tomohiro Chiba, Hirohito Seki, Yoshiharu Ishizaka, Ai Tsuchiya, Tomoko Kitaoka. New targeted therapy on SOCS1-related immune-response in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5363.

Abstract 3795: Possible role of miR-375-3p in cervical lymph node metastasis of oral squamous cell carcinoma

Abstract Latent cervical lymph node metastasis (LNM) is the most important prognostic factor in early oral squamous cell carcinoma (OSCC). However, no clinically useful predictors of LNM in early OSCC are available. In this study, we focused on the microRNAs (miRNAs) involved in the expression of numerous genes and explored those associated with latent cervical LNM in OSCC. Microarray analysis of miRNA expression showed that the expression levels of miR-375-3p were significantly reduced in primary OSCC tissues with latent cervical LNM. Subsequently, we quantified the expression of miR-375-3p by RT-qPCR and digital PCR. Similar to the results of miRNA microarray analysis, miR-375-3p was significantly downregulated in primary OSCC tissues with latent cervical LNM. The results of digital PCR showed a more significant difference than those of RT-qPCR. When the reference value for predicting latent cervical LNM was set to less than 57.85 copies based on the receiver operating characteristic curve, the sensitivity, specificity, accuracy, and area under the curve were 80%, 100%, 90%, and 0.942, respectively. Next, we examined the effects of miR-375-3p mimics on the growth and migration of four human OSCC cell lines (SAS-L1, HSC2, HSC3, and Ca9-22) that do not express miR-375-3p. When an miR-375-3p mimic was introduced into these cells, cell proliferation and migration were significantly suppressed. Total RNA was extracted from these cells reverse-transfected with miR-375-3p mimic for 48 hours. Microarray analysis and Ingenuity Pathway Analysis (IPA) miRNA target filter showed that miR-375-3p overexpression reduced the expression of 266 genes, of which 37 genes had the target sequences of miR-375-3p in their 3’-untranslated region. Among these target genes, CEPT1 and TIMM8A knockdown significantly inhibited the migration of all human OSCC cells, similar to miR-375-3p mimics. Furthermore, IPA core analysis revealed a decrease in expression of genes involved in the activation of PI3K-AKT pathways by miR-375-3p overexpression. These results indicated that downregulating miR-375-3p expression could promote cervical LNM by enhancing cell proliferation and migration in OSCC. We also found that CEPT1 and TIMM8A as novel target genes of miR-375-3p regulated the migration of human OSCC cells. The expression levels of miR-375-3p in primary OSCC tissues appear to be a useful biomarker for predicting latent cervical LNM. Citation Format: Masato Saika, Koh-ichi Nakashiro, Norihiko Tokuzen, Hiroyuki Shirai, Daisuke Uchida. Possible role of miR-375-3p in cervical lymph node metastasis of oral squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3795.

Abstract 6441: Discovery of ARID1A loss as a patient biomarker for NXP800 - A developmental activator of the integrated stress response (ISR) and inhibitor of the HSF1 pathway in ovarian cancer

Abstract Background. HSF1 helps cancer cells cope with multiple stresses caused by oncogene activation. Methods. See details below. Results. We discovered the bisamide NXP800 as an inhibitor of HSF1-mediated transcription through phenotypic screening and med chem optimization. Gene expression microarray analysis of human cancer cell lines and tumor xenografts treated with bisamide inhibitors indicated activation of the ATF4 axis of the ISR as a key mechanism of action. In SK-OV-3 ovarian cancer xenografts, NXP800 showed clear PK/PD relationships with increased expression of ATF4 transcriptional target genes alongside decreased expression of HSF1 transcriptional targets. NXP800 also caused tumor regressions in this model. Expanding in additional human ovarian cancer xenograft models, we observed efficacy in five and a complete lack of response in three others. The sensitive models all had homozygous deleterious mutations in the ARID1A gene, whereas the non-responding xenografts were all wild type (WT). ARID1A is a component of the SWI/SNF chromatin remodelling complex involved in repression and activation of target genes. Subsequent screening of the large Sanger human cancer cell line panel confirmed ARID1A as the most significant common disease-related alteration predicting sensitivity to NXP800 in ovarian cancer cell lines. This predictive relationship was confirmed in an ARID1A isogenic HCT-116 cell line pair; sensitivity was greater in the homozygous ARID1A mutant cells compared to WT, resulting in PARP cleavage in the mutant cells only. In vivo there was no effect in WT HCT-116 xenografts whereas growth inhibition was observed in the homozygous mutant cells, resulting in significantly smaller tumors. In addition, the induction of ATF4 target genes was stronger and more prolonged in the mutant cells. It is known that whereas short term ATF4 activation is adaptive, persistent activation can promote the induction of apoptosis. CHIP-seq analysis confirmed clear relationships between ARID1A status, ATF4 and HSF1 promoter occupancy, and the distribution of BRG1 and RNA pol II at target sites, although these were often gene-specific and complex. A relatively simple example is the regulation of the INHBE gene (expression of which is a PD biomarker). In untreated samples there is no binding of ATF4, BRG1 and RNA pol II at the INHBE promoter. NXP800 treatment results in the recruitment of BRG1, ATF4 and RNA pol II in ARID1A mutant TOV-21G cells but not in the RMGI WT cells, leading to increased expression in the mutant cells only. Conclusions. We propose that ARID1A loss alters the binding and recruitment of ATF4 and HSF1 leading to the altered and prolonged expression of ATF4 target genes and increased sensitivity to NXP800. NXP800 is currently in phase Ib for the treatment of ARID1A mutant platinum resistant ovarian cancer (NCT05226507). Citation Format: Robert H. te Poele, Marissa Powers, Swee Sharp, Emmanuel de Billy, Maria Taskinen, Loredana Pellegrino, Sharon Gowan, Asadh Miah, Angela Hayes, Matthew Cheeseman, Keith Jones, Suzanne Eccles, Florence Raynaud, Paul Clarke, Paul Workman. Discovery of ARID1A loss as a patient biomarker for NXP800 - A developmental activator of the integrated stress response (ISR) and inhibitor of the HSF1 pathway in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6441.

Androgen drives melanoma invasiveness and metastatic spread by inducing tumorigenic fucosylation

Melanoma incidence and mortality rates are historically higher for men than women. Although emerging studies have highlighted tumorigenic roles for the male sex hormone androgen and its receptor (AR) in melanoma, cellular and molecular mechanisms underlying these sex-associated discrepancies are poorly defined. Here, we delineate a previously undisclosed mechanism by which androgen-activated AR transcriptionally upregulates fucosyltransferase 4 (FUT4) expression, which drives melanoma invasiveness by interfering with adherens junctions (AJs). Global phosphoproteomic and fucoproteomic profiling, coupled with in vitro and in vivo functional validation, further reveal that AR-induced FUT4 fucosylates L1 cell adhesion molecule (L1CAM), which is required for FUT4-increased metastatic capacity. Tumor microarray and gene expression analyses demonstrate that AR-FUT4-L1CAM-AJs signaling correlates with pathological staging in melanoma patients. By delineating key androgen-triggered signaling that enhances metastatic aggressiveness, our findings help explain sex-associated clinical outcome disparities and highlight AR/FUT4 and its effectors as potential prognostic biomarkers and therapeutic targets in melanoma.

Pooled microarray expression analysis of failing left ventricles reveals extensive cellular-level dysregulation independent of age and sex

Existing cardiovascular studies tend to suffer from small sample sizes and unaddressed confounders. Re-profiling of 9 microarray datasets revealed significant global gene expression differences between 358 failing and 191 non-failing left ventricles independent of age and sex (p = 5.1e-10). Covariate-adjusted mixed-effect regression revealed 17 % (945/5553) genes with >1.5-fold changes. The extracellular matrix and integral membrane ontologies were significantly enriched and depleted in failing ventricles, respectively. Furthermore, MTSS1 implicated in cardiovascular dysfunction showed the greatest change in ischemic compared to dilated cardiomyopathy (Bonferroni p < 0.05 for all genes and ontologies). Transcriptomic meta-profiling here provided deeper insight into heart failure at the cellular level.

Genetic Discrimination of Grade 3 and Grade 4 Gliomas by Artificial Neural Network.

Gliomas, including anaplastic gliomas (AG; grade 3) and glioblastomas (GBM; grade 4), are malignant brain tumors associated with poor prognosis and low survival rates. Current classification systems based on histopathology have limitations due to intratumoral heterogeneity. The treatment and prognosis are distinctly different between grade 3 and grade 4 gliomas patients. Therefore, there is a need for molecular markers to differentiate these tumors accurately. In this study, we aimed to identify a gene expression signature using an artificial neural network (ANN) in application to microarray and serial analysis of gene expression (SAGE) data for grade 3 (AG) and grade 4 (GBM) gliomas discrimination. We acquired gene expression data from publicly available datasets on glial tumors of grades 3 and 4-a total of 93 grade 3 gliomas and 224 grade 4 gliomas. To select genes for classification, we implemented an artificial neural network-based method using a combination of self-organized maps (SOM) and perceptron. In general, we implemented a multi-stage procedure that involved multiple runs of a genetic algorithm to identify genes that provided optimal clusterization on the SOM. We performed this procedure multiple times, resulting in different sets of genes each time. Eventually, we selected several genes that appeared most frequently in the reduced sets and performed classification using them. Our analysis identified a set of seven genes (BCAS4, GLUD2, KCNJ10, KCND2, AKR7A2, FOLR1, and KIAA0319). The classification accuracy using this gene set was 87.5%. These findings suggest the potential of this gene set as a molecular marker for distinguishing grade 3 (AG) from grade 4 (GBM) gliomas.

Chronic Stress Blocks the Endometriosis Immune Response by Metabolic Reprogramming.

Studies have shown that the occurrence and development of endometriosis are closely linked to long-term psychological stress. The specific contribution of chronic stress to the metabolic adaptations in patients with endometriosis is still unknown. Lesions were removed from ten endometriosis patients during an operation, and the participants were divided into two groups using a psychological questionnaire. An mRNA Human Gene Expression Microarray analysis was applied to compare the mRNA expression profiles between the chronic stress group and the control group. In addition, the reliability of the mRNA Human Gene Expression Microarray analysis was verified by using research on metabolites based on both the liquid chromatography (LC-MS/MS) technique and quantitative reverse transcription polymerase chain reaction (RT-PCR). A microarray analysis of significantly up-regulated, differentially expressed genes between the chronic stress and the control groups showed genes that were principally related to metabolism-related processes and immune-related processes, such as the immune response process, negative regulation of T cell proliferation, the leucine metabolic process, and the L-cysteine metabolic process (p < 0.05). LC-MS showed that the differential metabolites were primarily concerned with arginine and proline metabolism, D-glutamine and D-glutamate metabolism, aspartate metabolism, glycine, serine metabolism, and tyrosine metabolism (p < 0.05). The possibility of chronic stress blocks the endometriosis immune response through metabolic reprogramming. Chronic stress reduces the supply of energy substrates such as arginine and serine, down-regulates T immune cell activation, and affects the anti-tumor immune response, thereby promoting the migration and invasion of endometriosis lesions in patients with chronic stress.

Exploring the hypoglycemic mechanism of chlorogenic acids from Pyrrosia petiolosa (Christ) Ching on type 2 diabetes mellitus based on network pharmacology and transcriptomics strategy

Ethnopharmacological relevancePyrrosia petiolosa (Christ) Ching (YBSW) is a Traditional Chinese medicine rich in chlorogenic acids. It is an important component in many Traditional Chinese medicinal hypoglycemic formulas and is commonly used by the Miao people to treat diabetes with good efficacy. Our previous research has suggested that chlorogenic acids may be the active ingredients in YBSW. Aim of the studyTo explore the mechanisms underlying the anti-type 2 diabetes mellitus (T2DM) hypoglycemic effects of chlorogenic acids contained in YBSW. Materials and methodsIn vivo experiments, hematoxylin-eosin staining (HE) staining, and immunohistochemistry (IHC) were used to determine the effects of chlorogenic acids contained in YBSW in rats. mRNA expression profiling, microarray analysis, and network pharmacology were used to analyze the underlying mechanisms of the effects. Finally, apoptosis and changes in the related pathways were evaluated in vitro using a 3-(4,5-dimethyl-2-thia-zolyl)-2,5-diphenyl-2-H-tetrazolium bromide assay, quantitative real-time polymerase chain reaction, immunofluorescence (IF) assessment, and flow cytometry. ResultsAfter the administration of isochlorogenic acid B, the levels of triglycerides, serum total cholesterol, and fasting blood glucose significantly decreased. HE and IHC staining revealed that isochlorogenic acid B significantly increased insulin expression in islet cells. Using network pharmacology and RNA-seq Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, we screened the advanced glycation end products–receptor for advanced glycation end products (AGE-RAGE) signaling pathway. We also verified that YBSW and its chlorogenic acid can inhibit apoptosis and downregulate the expression of related mRNA in the AGE-RAGE pathway in RIN-m5f cells. ConclusionsYBSW exhibits a significant hypoglycemic effect, with chlorogenic acid being an effective component. The therapeutic effect of chlorogenic acids contained in YBSW is mainly realized by promoting insulin secretion and pancreatic tissue repair. Moreover, YBSW substantially mitigates apoptosis via the AGE-RAGE pathway in T2DM.

Retracted: Microarray and Bioinformatics Analysis of Differential Gene and lncRNA Expression during Erythropoietin Treatment of Acute Spinal Cord Injury in Rats

Retracted: Microarray and Bioinformatics Analysis of Differential Gene and lncRNA Expression during Erythropoietin Treatment of Acute Spinal Cord Injury in Rats

Maternal diet during gestation affect prostatic tissue component in SHR/Izm offspring.

Numerous studies have investigated the associations between maternal nutritional status and various diseases, with the underlying mechanism often attributed to epigenetic changes. However, limited research has been conducted on the relationship between maternal nutrition and benign prostatic hyperplasia (BPH). In this study, we aimed to explore the potential association between maternal nutrition and BPH using an animal experiment and evaluating the findings through fluorescent immunostaining and genetic analysis. Female spontaneously hypertensive rats (SHR/Izm) were randomly assigned to three groups at the start of pregnancy: a standard diet group (SD; 17% protein, 7% fat), a low-protein diet group (LPD; 6% protein, 7% fat), and a high-fat diet group (HFD; 22% protein, 35% fat). The diets were maintained throughout gestation. After giving birth, both the mothers and their pups were exclusively fed a standard diet. Male pups were euthanized at 48 weeks, and their prostates were removed. The composition of the ventral prostate (VP) was evaluated using fluorescent immunostaining with antibodies for cytokeratin, vimentin, and Ki-67. Microarray analysis, real-time RT-PCR, and DNA methylation analysis using pyrosequencing were performed. Statistical analysis was conducted using one-way ANOVA and Tukey's multiple comparison test, with a significance level set at p < 0.05. Pups in the LPD group exhibited significant underweight from birth (1 day; SD vs.LPD vs.HFD: 4.46 vs. 4.08 vs. 4.35, p = 0.04) until weaning (21 days; SD vs.LPD vs.HFD: 30.8 vs. 27.4 vs. 29.2, p = 0.03). However, they exhibited catch-up growth, and there was no significant difference at 48 weeks (p = 0.84). The epithelial area in the ventral prostate was significantly increased in the LPD group (SD vs.LPD vs.HFD: 39% vs. 48% vs. 37%, p = 0.01), while the stromal area was significantly increased in the HFD group (SD vs.LPD vs.HFD: 11% vs. 11% vs. 15%, p < 0.01). Gene ontology analysis of the gene expression microarray showed increased activity in developmental processes (SD vs.LPD: p = 6.3E-03, SD vs.HFD: p = 7.2E-03), anatomical structure development (SD vs.LPD: p = 6.3E-03, SD vs.HFD: p = 5.3E-03), and cell differentiation (SD vs.LPD: p = 0.018, SD vs.HFD: p = 0.041) in both the LPD and HFD groups. Real-time RT-PCR revealed high expression levels of the transcription factors NFκB (p < 0.01) and Smad3 (p < 0.01) in both the LPD and HFD groups. XIAP, an apoptosis inhibitor, was increased in the LPD group (p = 0.02). The TGF beta pathway, associated with epithelial mesenchymal transition (EMT), and vimentin (p < 0.01) were upregulated in the HFD group. Pyrosequencing DNA methylation analysis of the TGF beta pathway indicated hypomethylation of TGFb1, TGFbR1, and Smad3 in all groups, although there were no significant differences. Our findings suggest that both maternal undernutrition and obesity influence the prostatic development of offspring. Maternal consumption of a low protein diet promotes epithelial hyperplasia through the upregulation of apoptosis inhibitors, while a high fat diet leads to increased stromal growth through the induction of EMT.

Circulating Total Extracellular Vesicles Cargo Are Associated with Age-Related Oxidative Stress and Susceptibility to Cardiovascular Diseases: Exploratory Results from Microarray Data.

Aging is a risk factor for many non-communicable diseases such as cardiovascular and neurodegenerative diseases. Extracellular vesicles and particles (EVP) carry microRNAs that may play a role in age-related diseases and may induce oxidative stress. We hypothesized that aging could impact EVP miRNA and impair redox homeostasis, contributing to chronic age-related diseases. Our aims were to investigate the microRNA profiles of circulating total EVPs from aged and young adult animals and to evaluate the pro- and antioxidant machinery in circulating total EVPs. Plasma from 3- and 21-month-old male Wistar rats were collected, and total EVPs were isolated. MicroRNA isolation and microarray expression analysis were performed on EVPs to determine the predicted regulation of targeted mRNAs. Thirty-one mature microRNAs in circulating EVPs were impacted by age and were predicted to target molecules in canonical pathways directly related to cardiovascular diseases and oxidative status. Circulating total EVPs from aged rats had significantly higher NADPH oxidase levels and myeloperoxidase activity, whereas catalase activity was significantly reduced in EVPs from aged animals. Our data shows that circulating total EVP cargo-specifically microRNAs and oxidative enzymes-are involved in redox imbalance in the aging process and can potentially drive cardiovascular aging and, consequently, cardiac disease.

Parvalbumin expression changes with retinal ganglion cell degeneration.

Glaucoma is one of the main causes of irreversible visual field loss and blindness worldwide. Vision loss in this multifactorial neurodegenerative disease results from progressive degeneration of retinal ganglion cells (RGCs) and their axons. Identifying molecular markers that can be measured objectively and quantitatively may provide essential insights into glaucoma diagnosis and enhance pathophysiology understanding. The chronic, progressive DBA/2J glaucomatous mouse model of glaucoma and C57BL6/J optic nerve crush (ONC) mouse model were used in this study. Changes in PVALB expression with RGC and optic nerve degeneration were assessed via gene expression microarray analysis, quantitative real-time polymerase chain reaction (qRT-PCR), Western blot and immunohistochemistry. Microarray analysis of the retinal gene expression in the DBA/2J mice at different ages showed that the expression of PVALB was downregulated as the mice aged and developed glaucoma with retinal ganglion cell loss. Analysis of qRT-PCR results demonstrated PVALB at the mRNA level was reduced in the retinas and optic nerves of old DBA/2J mice and in those after ONC compared to baseline young DBA2/J mice. PVALB protein expression measured by Western blot was also significantly reduced signal in the retinas and optic nerves of old DBA/2J mice and those eyes with crushed nerves. Immunohistochemical staining results demonstrated that there were fewer PVALB-positive cells in the ganglion cell layer (GCL) of the retina and staining pattern changed in the optic nerve from old DBA/2J mice as well as in mice eyes following ONC. PVALB is abundantly expressed both by RGCs' soma in the retinas and RGCs' axons in the optic nerves of C57BL/6J. Furthermore, the expression level of PVALB decreases with RGC degeneration in the glaucomatous DBA/2J mice and after ONC injury of C57BL6/6J, indicating that PVALB is a reliable RGC molecular marker that can be used to study retinal and optic nerve degeneration.

Cross-Comparison Individual Patient Level Analysis of Three Gene Expression Signatures in Localized Prostate in over 50,000 Men

Risk stratification guides the management of localized prostate cancer. Multiple commercial gene expression biomarkers have been developed to improve estimates of prognosis, however the 22-gene Decipher genomic classifier (22-GC) is the only test with level 1 evidence supporting its use per NCCN guidelines. It is unknown whether other commercial signatures, Oncotype (GPS) or Prolaris (CCP), are sufficiently correlated to negate the differences in evidence supporting these commercial tests. Herein, we aim to perform a cross-comparison of these signatures in a large cohort of patients diagnosed with localized prostate cancer. Patients diagnosed with localized prostate cancer who underwent whole transcriptome gene expression microarray analysis on their primary tumor biopsy specimen were included. The 22-GC score was calculated by Veracyte using a commercially locked model. Individual genes in each of the GPS and CCP gene signatures were identified, and the gene weights in each signature were retrained for prediction of metastasis in a multi-institutional cohort of 1,574 men with long-term outcome data. This was performed to improve correlation performance of GPS and CCP given only the 22-GC was trained for prediction of metastasis. For each of the three signatures, both continuous and categorical scores were calculated. Linear regression and spearman correlations were calculated both on univariable and multivariable analyses adjusting for age, grade group, PSA, and T-stage. A total of 50,881 patients were included (15,379 (30.2%) NCCN low-risk, 14,773 (29.0%) favorable intermediate-risk, 15,544 (30.5%) unfavorable intermediate-risk, and 5,185 (10.2%) high/very high-risk) with a median age of 68 years, and a median PSA of 6.2 ng/mL. On linear regression, the GPS model had poor goodness-of-fit to the 22-GC with an R2 of 0.36, as did the CCP model to the 22-GC with an R2 of 0.32. For CCP, the linear sum of the 31-genes was also tested but had inferior performance (R2 0.28) compared to the reoptimized CCP model. Results were similar on multivariable analysis adjusting for age, PSA, clinical stage and grade group. Spearman correlation between the continuous GPS model scores and the 22-GC was moderate at 0.59, as was the correlation between CCP model and the 22-GC of 0.54. CCP is a measure of proliferation, but in 22-GC high-risk patients, the majority (64.1%) of patients had low-average proliferation and only 35.9% had high proliferation, potentially explaining the lack of strong correlation. There is minimal to moderate correlation between the 22-GC and GPS or CCP gene expression signatures tested. Therefore, these tests should not be viewed as interchangeable, and utilization should be based on the level of evidence supporting each gene expression biomarker.

Genome-wide identification, characterization, and expression analysis of the Ovate family protein in Oryza sativa under biotic and abiotic stresses

The Ovate Family Proteins (OFPs) are plant-specific transcription factors with a conserved OVATE domain. The OFPs regulate organ shape in Arabidopsis and many crops, including rice, tomato, and melon. However, little is known regarding the OFPs' potential role in regulating plant immune response to biotic/abiotic stresses. Herein, we reported the identification, bioinformatic, and Insilco analysis of OFPs in rice (Oryza sativa L). Thirty-one OsOFP genes were identified from the rice genome database and further divided into six subgroups based on their sequence similarities. Gene expression analysis in developmental stages indicated that some members of the OsOFP gene family displayed tissue-specific patterns. Enrichment of hormonal-related cis-acting elements and varied expression under phytohormones further validated their participation in hormone-mediated plant growth. The microarray expression analysis showed their possible involvement against salinity, drought, brown planthopper (BPH)_striped rice stemborer (SSB) (OsOFP25), and rice leaf folder (RLF) (OsOFP26) infestations. The higher expression of OsOFP25 in the OsWRKY65-OE line implies their key role in reproductive biology. These results provide a systematic analysis of the OsOFPs and lay a foundation for the functional characterization of this gene family.

Genome-wide analysis reveals the TCP-miR159-miR319 module is crucial for rice (Oryza sativa L.) growth and response to drought and salinity.

The TCP are key plant-specific proteins responsible for regulating various developmental activities. Herein, we retrieved 21 OsTCP genes from the genome database of rice. The bioinformatics analysis, including conserved motif, domain, interactive proteins, gene ontology (GO) analysis, target micro-RNAs (miRNA) prediction, and the physiochemical properties, highlight the key aspects of OsTCP genes in Oryza sativa L. The phylogeny analysis disclosed that OsTCP was further clustered into five clades (Clade I - Clade V) based on the structural similarities and functional diversities. The GO analysis of OsTCP proteins showed they are primarily exercising the rice developmental processes, reproductive stages in particular. The microarray expression analysis showed transcription in twelve rice tissues, and the differential expression pattern of OsTCP genes revealed their possible involvement in auxin-mediated growth and response against salinity and drought. The predicted miRNA that includes miR159 and miR319 families further the engagement of OsTCP genes in the post-translational regulation of rice growth. Owing to the above-mentioned outcomes, we speculate that OsTCP genes in the O. sativa genome play an essential role in growth and development and fine-tuning the immune responses to various environmental stresses, thus providing major indications for further functional studies.

Genome-wide identification, characterization, and expression analysis of the Chalcone Synthase gene family in Oryza sativa under Abiotic Stresses

Chalcone synthase (CHS) is the pivotal enzyme that catalyzes the first committed step of the phenylpropanoid pathway leading to flavonoids. Herein, we identified twenty-seven OsCHS genes from the rice genome database. The bioinformatics analysis, including conserved motif, domain, interactive proteins, gene ontology (GO), target micro RNAs (miRNA) prediction, and the OsCHS physiochemical properties, highlight the key aspects of OsCHS genes in Oryza sativa L. The OsCHS proteins' phylogeny was further clustered into 4 sub-groups (Group I- Group IV) based on the structural similarities and functional diversities. The GO analysis of OsCHS proteins showed they are highly stress-responsive (biotic/abiotic) and involved in various growth and developmental processes. The microarray expression analysis showed transcription in twelve rice tissues, and the differential expression pattern of OsCHS genes revealed their possible involvement against salinity and drought. The higher expression of OsCHS15 in the OsWRKY65-OE line indicates its potential in hormonal-mediated stress response. The predicted miRNA that includes miR2260, miR167, miR11337, and miR2232 families further the engagement of OsCHS genes in the post-translational regulation of rice growth and stress-responsive. Owing to the above-mentioned outcomes, we speculate that OsCHS genes in the O. sativa genome play an essential role not only in growth and development but also in fine-tuning the immune responses to various environmental stresses and provide major indications for further functional studies.

Combination of Cefotaxime and Cisplatin Specifically and Selectively Enhances Anticancer Efficacy in Nasopharyngeal Carcinoma.

HMOX1 has a dual role in cancers, especially involving chemoresistance. We demonstrate that cephalosporin antibiotics exert strong anticancer activity in nasopharyngeal carcinoma mainly via drastic upregulation of HMOX1. Cephalosporin antibiotics are commonly used for the treatment or prophylaxis of bacterial infectious diseases in cancer patients. It is unknown whether they lead to chemoresistance in cancer patients, especially in nasopharyngeal carcinoma patients, who are being treated or required prophylaxis for an infectious syndrome with cephalosporin antibiotics. MTT and clonogenic colony formation assays assessed the viability and proliferation of cultured cancer cells. Flow cytometry was used to detect apoptosis. Tumor growth was assessed using a xenograft model. Microarray and RT-qPCR expression analyses investigated differential gene expression. Cefotaxime enhanced anticancer efficacy of cisplatin in nasopharyngeal carcinoma without enhancing the toxic side effects both in vitro and in vivo. However, cefotaxime significantly reduced the cytotoxicity of cisplatin in other cancer cell lines. Cefotaxime and cisplatin co-regulated 5 differential genes in CNE2 cells in a direction supporting the enhancement of anticancer efficacy, of which, THBS1 and LAPTM5 were further upregulated, STAG1, NCOA5, and PPP3CB were further downregulated. Out of the 18 apoptotic pathways significantly enriched in the combination group, THBS1 and HMOX1 overlapped in 14 and 12 pathways, respectively. Extrinsic apoptotic signaling pathway (GO: 2001236) was the only apoptotic pathway commonly enriched in cefotaxime group, cisplatin group and combination group, and THBS1 and HMOX1 were the overlapped genes of this pathway. THBS1 also overlapped in P53 signaling pathway and ECM-receptor interaction signaling pathway enriched by KEGG. Cephalosporin antibiotics are chemosensitizers of conventional chemotherapeutic drugs in the chemotherapy of nasopharyngeal carcinoma, but they may lead to chemoresistance by cytoprotection in other cancers. Cefotaxime and cisplatin co-regulate THBS1, LAPTM5, STAG1, NCOA5 and PPP3CB suggesting their involvement in the enhancement of anticancer efficacy in nasopharyngeal carcinoma. Targeting of P53 signaling pathway and ECM-receptor interaction signaling pathway was correlated to the enhancement. With additional benefit for treatment or prophylaxis of an infectious syndrome, cephalosporin antibiotics can benefit the therapy of nasopharyngeal carcinoma either as anticancer agents or as chemosensitizers of chemotherapeutic drugs in combination chemotherapy.