Previous Microarray Studies Research Articles

Differential Expressions of microRNAs and Transfer RNA-derived Small RNAs: Potential Targets of Choroidal Neovascularization

ABSTRACTPurpose: Choroidal neovascularization (CNV) is one of the major clinical characteristics of neovascular age-related macular degeneration (AMD). Small non-coding RNAs, such as microRNAs (miRNAs) and transfer RNA-derived small RNAs (tsRNAs) play key roles in diverse biological functions. The purpose of the study was to investigate the roles and possible functions of the miRNAs and tsRNAs in CNV.Methods: The mouse model of laser-induced CNV was conducted by laser photocoagulation. The expression profiles of miRNAs and tsRNAs were accessed by small RNA sequencing (RNA-Seq) in RPE-choroid-sclera complexes of mice in CNV group and control group. Selected altered miRNAs and tsRNAs were validated by qRT-PCR. Target genes were predicted by informatics analysis and intersected with the previous microarray study of altered mRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted to reveal the biological functions and signaling pathways with which these target genes are most enriched.Results: The results revealed that 79 miRNAs and 72 tsRNAs in total were significantly altered in the RPE-choroid-sclera complexes of CNV mice. GO analysis revealed that the altered target genes of the selected miRNAs most enriched in immune response, integral component of membrane and peptide binding, while the altered target genes of tsRNAs most enriched in regulation of immune system process, extracellular region, and core promoter binding. Moreover, KEGG pathway analysis demonstrated that altered target genes of miRNAs and tsRNAs most enriched in hematopoietic cell lineage and nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway, respectively.Conclusions: Our study identified differential expressions of miRNAs and tsRNAs in CNV model, and these altered miRNAs and tsRNAs might be novel potential targets in treating CNVs in patients with neovascular AMD.

Non-coding and Coding Transcriptional Profiles Are Significantly Altered in Pediatric Retinoblastoma Tumors

Retinoblastoma is a rare pediatric tumor of the retina, caused by the homozygous loss of the Retinoblastoma 1 (RB1) tumor suppressor gene. Previous microarray studies have identified changes in the expression profiles of coding genes; however, our understanding of how non-coding genes change in this tumor is absent. This is an important area of research, as in many adult malignancies, non-coding genes including LNC-RNAs are used as biomarkers to predict outcome and/or relapse. To establish a complete and in-depth RNA profile, of both coding and non-coding genes, in Retinoblastoma tumors, we conducted RNA-seq from a cohort of tumors and normal retina controls. This analysis identified widespread transcriptional changes in the levels of both coding and non-coding genes. Unexpectedly, we also found rare RNA fusion products resulting from genomic alterations, specific to Retinoblastoma tumor samples. We then determined whether these gene expression changes, of both coding and non-coding genes, were also found in a completely independent Retinoblastoma cohort. Using our dataset, we then profiled the potential effects of deregulated LNC-RNAs on the expression of neighboring genes, the entire genome, and on mRNAs that contain a putative area of homology. This analysis showed that most deregulated LNC-RNAs do not act locally to change the transcriptional environment, but potentially function to modulate genes at distant sites. From this analysis, we selected a strongly down-regulated LNC-RNA in Retinoblastoma, DRAIC, and found that restoring DRAIC RNA levels significantly slowed the growth of the Y79 Retinoblastoma cell line. Collectively, our work has generated the first non-coding RNA profile of Retinoblastoma tumors and has found that these tumors show widespread transcriptional deregulation.

SNPs in LncRNA genes are associated with non-small cell lung cancer in a Chinese population.

BackgroundIt has indicated that single nuclear polymorphisms (SNPs) in the regions encoding non‐coding transcripts are associated with lung cancer susceptibility. In a previous microarray study, we identified 13 differentially expressed long non‐coding RNAs (lncRNAs) in non‐small cell lung cancer (NSCLC) and associations of SNPs in these lncRNA genes with lung cancer were unknown. We conducted a case‐control study to address this issue.MethodsUsing the TaqMan method, we genotyped 17 SNPs located in the 13 lncRNA genes in 1294 cases with NSCLC and 1729 healthy controls. Unconditional logistic regression and Cox proportional hazards regression were used to analyze the associations of these SNPs with NSCLC risk and patient survival, respectively. These analyses were also repeated in subgroups of cases and controls stratified by gender, age group, smoking status, disease stage, and histological type.ResultsWe identified three SNPs associated with NSCLC risk. For SNP rs498238, CC genotype was associated with lower risk compared to TT genotype (adjusted OR = 0.33, 95%CI: 0.11‐0.97, P = 0.043). For rs16901995, CT/TT genotypes were associated with lower risk compared to CC genotype in non‐smokers (adjusted OR = 0.78, 95%CI: 0.62‐0.98, P = 0.035). Variant genotypes in rs219741 were associated with NSCLC risk in young patients, and the adjusted OR was 1.47 (95%CI: 1.03‐2.10, P = 0.033) when compared to the wild genotype. No SNPs were found to be associated with patient overall survival in the study.ConclusionThe study suggests that some genetic polymorphisms in the lncRNA genes may influence the risk of NSCLC among Chinese.

Early growth response-1 regulates acetylcholinesterase and its relation with the course of Alzheimer's disease.

Our previous studies showed that the transcription factor early growth response-1 (EGR1) may play a role in keeping the brain cholinergic function intact in the preclinical stages of Alzheimer's disease (AD). In order to elucidate the mechanisms involved, we first performed data mining on our previous microarray study on postmortem human prefrontal cortex (PFC) for the changes in the expression of EGR1 and acetylcholinesterase (AChE) and the relationship between them during the course of AD. The study contained 49 patients, ranging from non-demented controls (Braak stage 0) to late AD patients (Braak stage VI). We found EGR1-mRNA was high in early AD and decreased in late AD stages, while AChE-mRNA was stable in preclinical AD and slightly decreased in late AD stages. A significant positive correlation was found between the mRNA levels of these two molecules. In addition, we studied the relationship between EGR1 and AChE mRNA levels in the frontal cortex of 3-12-months old triple-transgenic AD (3xTg-AD) mice. EGR1- and AChE-mRNA were lower in 3xTg-AD mice compared with wild-type (WT) mice. A significant positive correlation between these two molecules was present in the entire group and in each age group of either WT or 3xTg-AD mice. Subsequently, AChE expression was determined following up- or down-regulating EGR1 in cell lines and the EGR1 levels were found to regulate AChE at both the mRNA and protein levels. Dual-luciferase assay and electrophoretic mobility shift assay in the EGR1-overexpressing cells were performed to determine the functionally effective binding sites of the EGR1 on the AChE gene promoter. We conclude that the EGR1 can upregulate AChE expression by a direct effect on its gene promoter, which may contribute significantly to the changes in cholinergic function in the course of AD. The 3xTg-AD mouse model only reflects later stage AD.

Developmental Dioxin Exposure Alters the Methylome of Adult Male Zebrafish Gonads.

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a persistent environmental toxicant and endocrine disrupting compound with reproductive and developmental effects in humans and model organisms, including zebrafish. Our previous microarray and histological studies found defects in spermatogenesis and fertility of zebrafish in response to acute developmental TCDD exposure. These effects are apparent following exposure during reproductive development, modeling fetal basis of adult-onset disease. Some outcomes of these previous studies (reduced fertility, changes in sex ratio, transcriptomic alterations) are also transgenerational – persisting to unexposed generations – through the male germline. We hypothesized that DNA methylation could be a possible mechanism for these reproductive effects and performed whole genome bisulfite sequencing (WGBS), which identifies whole genome DNA methylation status at the base pair level, on testes of adult zebrafish exposed to TCDD (two separate hour-long exposures to 50 pg/mL TCDD at 3 and 7 weeks post fertilization). In response to TCDD exposure, multiple genes were differentially methylated; many of which are involved in reproductive processes or epigenetic modifications, suggesting a role of DNA methylation in later-life health outcomes. Additionally, several differentially methylated genes corresponded with gene expression changes identified in TCDD-exposed zebrafish testes, indicating a potential link between DNA methylation and gene expression. Ingenuity pathway analysis of WGBS and microarray data revealed genes involved in reproductive processes and development, RNA regulation, the cell cycle, and cellular morphology and development. We conclude that site-specific changes in DNA methylation of adult zebrafish testes occur in response to acute developmental TCDD exposure.

Neospora caninum cytoplasmic dynein LC8 light chain 2 (NcDYNLL2) is differentially produced by pathogenically distinct isolates and regulates the host immune response.

Neospora caninum is the causative agent of bovine neosporosis. A N. caninum cytoplasmic dynein LC8 light chain (NcDYNLL) protein was characterized in this study. Cytoplasmic dyneins, including DYNLLs, belong to the microtubule minus-end-directed motor proteins and are involved in many cellular processes. Previous microarray studies revealed that NcDYNLL was downregulated in the non-pathogenic clone, Ncts-8, when compared with the wild-type NC1 isolate. The present study showed that DYNLLs from different species are highly conserved (>85% identity), and the NcDYNLL belongs to the DYNLL2 family. NcDYNLL2 and Toxoplasma gondii DYNLL2 have identical amino acid sequences, although they are slightly divergent at the genetic level (89% identity). NcDYNLL2 was cloned and expressed in Escherichia coli and purified. NcDYNLL2 was identified in soluble and insoluble fractions of tachyzoite lysate. As expected, soluble NcDYNLL2 was lower in the Ncts-8 lysate when compared with that of NC1 isolate. NcDYNLL2 release by the tachyzoites was low; however, it was increased when tachyzoites were treated with either calcium ionophore or ethanol. The data indicate that NcDYNLL2 may be actively secreted at low levels, but the secretion was upregulated by agents that also augment microneme protein secretions. Immunostaining of NcDYNLL2 in isolated and intracellular Neospora tachyzoites showed a diffuse distribution pattern. Furthermore, rNcDYNLL2 was internalized by the host immune cells and stimulated tumour necrosis factor-α) and interleukin-12 (IL-12) production by murine dendritic cells. Taken together, these results suggest that NcDYNLL2 is a secretory protein that cross-regulates host immunity.

Gap junction β‑2 expression is negatively associated with the estrogen receptor status in breast cancer tissues and is a regulator of breast tumorigenesis.

Gap junction β‑2 gene (GJB2, also known as connexin26) is a member of the connexin family which forms gap junction channels. Many connexin genes have been considered to be tumor suppressor genes. However, the overexpression of GJB2 has been found to be associated with a poor prognosis in several human cancers. In our previous microarray study, we revealed the overexpression of GJB2 in breast cancer tissues. Hence, in this study, we investigated the expression of GJB2 in human breast cancer and its role in breast cancer cell proliferation and migration. The RT‑qPCR results revealed the upregulation of the GJB2 gene in invasive ductal carcinoma (P<0.001) of the breast. Immunohistochemical analysis revealed an intense cytoplasmic and membrane staining. We observed that the staining for GJB2 was more intense in the majority of the estrogen receptor (ER)‑negative breast cancer tissues compared to the normal breast tissues (P<0.0001). By contrast, the majority of the ER‑positive breast cancer samples exhibited weak to moderate staining; however, this difference was not statistically significant compared to the normal tisues. The knockdown of GJB2 in human breast cancer cell lines using shRNA led to a significant decrease in the proliferative ability and an increase in the migratory ability of breast cancer cells. In addition, the knockdown of GJB‑2 led to a significant reduction in tumor volume and proliferation (as demonstrated by MIB‑1 staining) in orthotopic xenografts in immunocompromised mice. On the whole, the findings of this study indicate that GJB2 may be an important regulator of breast tumorigenesis.

The expression of ubiquitin-specific peptidase 8 and its prognostic role in patients with breast cancer.

To clarify the clinical relevance of ubiquitin-specific protease 8 (USP8) for patients with breast cancer (BC). Previous BC microarray studies GSE37751, GSE7390, and GSE21653 were reanalyzed to determine the USP8 levels between BC patients and the corresponding normal breast tissues and the correlation between USP8 expression and clinical features and clinical outcomes of patients with BC. Gene set enrichment analysis (GSEA) was conducted to investigate the potential mechanisms. USP8 was downregulated in BC cells compared with that in normal breast tissues (P < 0.0001). The Χ2 test and logistic regression analysis demonstrated that patients in USP8 high-expression group were correlated with better clinical features (including histopathological grading, estrogen receptors, clinical risk group according to Nottingham prognostic index [NPI] criteria and clinical risk group according to Veridex signature) compared with patients in USP8 low-expression group. Kaplan-Meier survival and Cox proportional regression analysis suggested that USP8 predicted better survivals of BC patients in terms of distant metastasis-free survival, time to distant metastasis, disease-free survival, and overall survival. GSEA suggested that USP8 might impact the proliferation of BC cells through several biological processes associated tumorigenesis of BC. USP8 was significantly downregulated in BC patients (P < 0.0001). Our results demonstrated that USP8 might predict better clinical characteristics and might be a protective factor for patients with BC.

PO-235 Integrin beta-like 1 overexpression stimulates invasiveness of ovarian cancer cells in vitro

IntroductionIn our previous microarray study we analysed gene expression profile of over 100 ovarian cancer samples.1 We identified two molecular subgroups of high grade serous ovarian cancers (HG-SOC) with distinct gene expression profiles and survival.2 Among differentially expressed genes was an Integrin beta-like1 gene (ITGBL1). ITGBL1 is a poorly characterised protein, structurally cognate with integrin β. Our aim was to study whether and how ITGBL1 can influence the phenotype of ovarian cancer cells.Material and methodsITGBL1 coding sequence was PCR-amplified from cDNA and cloned into pLNCX2 vector. Retroviral system was used to obtain two ovarian cancer cell lines: OAW42/ITGBL1(+) and SKOV3/ITGBL1(+) with overexpression of ITGBL1. Control cell lines were obtained by transduction with empty vector. A Matrigel cell invasion assay was performed using 24-well transwell inserts (coated with fibronectin and matrigel). Crystal violet staining of invaded cells was performed, then the dye was solubilized with 10% acetic acid and the absorbance was measured at a wavelength of 595 nm.Results and discussionsWe compared invasion rate of control OAW42 and SKOV3 cells with that of isogenic cell lines containing ITGBL1 construct. The results indicate that ITGBL1 overexpression increases invasiveness of ovarian cancer cells.ConclusionOur results indicate that ITGBL1 may increase ovarian cancer cell invasion rate. Along with our previous reported results that overexpression of ITGBL1 may increase migration, decrease adhesion3 and has no effect on proliferation rate,4 this results suggests that ITGBL1 may play an important role in ovarian cancer progression enabling easier spreading of the cells within peritoneal cavity.ReferencesKM Lisowska, et al. Front. Oncol2014. doi:10.3389/fonc.2014.00006KM Lisowska,et al. J. Cancer Res. Clin. Oncol2016. doi:10.1007/s00432-016-2147-yAJ Cortez, et al. Int. J. Gynecol. Cancer2016; 26(3):665.AJ Cortez, et al. Int. J. Gynecol. Cancer2017;27(4):1931.

Transcription Factor Binding Site Enrichment Analysis in Co-Expression Modules in Celiac Disease.

The aim of this study was to construct celiac co-expression patterns at a whole genome level and to identify transcription factors (TFs) that could drive the gliadin-related changes in coordination of gene expression observed in celiac disease (CD). Differential co-expression modules were identified in the acute and chronic responses to gliadin using expression data from a previous microarray study in duodenal biopsies. Transcription factor binding site (TFBS) and Gene Ontology (GO) annotation enrichment analyses were performed in differentially co-expressed genes (DCGs) and selection of candidate regulators was performed. Expression of candidates was measured in clinical samples and the activation of the TFs was further characterized in C2BBe1 cells upon gliadin challenge. Enrichment analyses of the DCGs identified 10 TFs and five were selected for further investigation. Expression changes related to active CD were detected in four TFs, as well as in several of their in silico predicted targets. The activation of TFs was further characterized in C2BBe1 cells upon gliadin challenge, and an increase in nuclear translocation of CAMP Responsive Element Binding Protein 1 (CREB1) and IFN regulatory factor-1 (IRF1) in response to gliadin was observed. Using transcriptome-wide co-expression analyses we are able to propose novel genes involved in CD pathogenesis that respond upon gliadin stimulation, also in non-celiac models.

MiR‑3147 serves as an oncomiR in vulvar squamous cell cancer via Smad4 suppression.

The incidence of vulvar squamous cell carcinoma (VSCC) has increased annually over the last decade. MicroRNAs (miRNAs/miRs) serve an important role in tumor progression and development. Our previous microarray studies have revealed that miR-3147 was overexpressed in VSCC. However, its function and underlying mechanism in VSCC remain unknown. In the present study, it was confirmed by reverse transcription-quantitative polymerase chain reaction that the expression of miR-3147 was markedly upregulated in VSCC tissues. The increased expression of miR-3147 was positively associated with the depth of invasion. The overexpression of miR-3147 resulted in the promotion of vulvar cancer cell proliferation, migration, invasion, G1/S progression and invasion-associated gene expression. miR-3147 may participate in the process of epithelial-mesenchymal transition and reduce the expressions of downstream target genes in the transforming growth factor-β/Smad signaling pathway in A431 cells. The knockdown of Smad4 by small interfering RNA promoted malignant behaviours in A431 cells. In addition, miR-3147 regulated Smad4 by directly binding to its 3′ untranslated region. In conclusion, the results indicated that miR-3147 may serve an oncogenic role in VSCC by targeting Smad4. miR-3147 may represent a novel potential therapeutic target marker for VSCC.

Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection

BackgroundAvian influenza A H5N1 virus can cause lethal disease in humans. The virus can trigger severe pneumonia and lead to acute respiratory distress syndrome. Data from clinical, in vitro and in vivo suggest that virus-induced cytokine dysregulation could be a contributory factor to the pathogenesis of human H5N1 disease. However, the precise mechanism of H5N1 infection eliciting the unique host response are still not well understood.MethodsTo obtain a better understanding of the molecular events at the earliest time points, we used RNA-Seq to quantify and compare the host mRNA and miRNA transcriptomes induced by the highly pathogenic influenza A H5N1 (A/Vietnam/3212/04) or low virulent H1N1 (A/Hong Kong/54/98) viruses in human monocyte-derived macrophages at 1-, 3-, and 6-h post infection.ResultsOur data reveals that two macrophage populations corresponding to M1 (classically activated) and M2 (alternatively activated) macrophage subtypes respond distinctly to H5N1 virus infection when compared to H1N1 virus or mock infection, a distinction that could not be made from previous microarray studies. When this confounding variable is considered in our statistical model, a clear set of dysregulated genes and pathways emerges specifically in H5N1 virus-infected macrophages at 6-h post infection, whilst was not found with H1N1 virus infection. Furthermore, altered expression of genes in these pathways, which have been previously implicated in viral host response, occurs specifically in the M1 subtype. We observe a significant up-regulation of genes in the RIG-I-like receptor signaling pathway. In particular, interferons, and interferon-stimulated genes are broadly affected. The negative regulators of interferon signaling, the suppressors of cytokine signaling, SOCS-1 and SOCS-3, were found to be markedly up-regulated in the initial round of H5N1 virus replication. Elevated levels of these suppressors could lead to the eventual suppression of cellular antiviral genes, contributing to pathophysiology of H5N1 virus infection.ConclusionsOur study provides important mechanistic insights into the understanding of H5N1 viral pathogenesis and the multi-faceted host immune responses. The dysregulated genes could be potential candidates as therapeutic targets for treating H5N1 disease.

Increase of Serum Kallikrein-8 Level After Long-term Telbivudine Treatment.

Our previous cDNA microarray study revealed increased cellular mRNA levels of a panel of genes, including kallikrein-8 (KLK8), after long-term telbivudine treatment in chronic hepatitis B patients. The aim of this study was to verify whether serum protein levels of KLK8, a cancer-related enzyme, are indeed increased after telbivudine treatment. A total of 83 chronic hepatitis B patients receiving telbivudine for >2 years were retrospectively analyzed. Serum KLK8 protein and estimated glomerular filtration rate (eGFR) changes were compared before and after treatment. Both serum KLK8 protein and eGFR increased significantly after long-term telbivudine treatment (paired t-test: KLK8, p<0.001; eGFR, p=0.001). No direct correlation was found between KLK8 increase and eGFR change. However, eGFR change was positively associated with post-treatment KLK8 levels following adjustment for body height (p<0.001). Telbivudine treatment resulted in increased levels of serum KLK8 protein. Furthermore, eGFR increase was associated with body height-adjusted, post-treatment KLK8 levels.

MiR-302b Suppresses Osteosarcoma Cell Migration and Invasion by Targeting Runx2

Osteosarcoma patients with lung metastasis and local invasion remain challenging to treat despite the significant contribution of the combination of surgery and neo-adjuvant chemotherapy. Our previous microarray study demonstrated that miR-302b had significantly lower expression in osteosarcoma cell lines than in osteoblast cell lines. In the present study, we further elucidated the role of miR-302b in regulating the migration and invasiveness of osteosarcoma. MiR-302b expression was markedly down-regulated in osteosarcoma cell lines and clinical tumour tissues. Lower levels of miR-302b expression were significantly associated with metastasis and high pathological grades. A functional study demonstrated that over-expression of miR-302b suppressed tumour cell proliferation, invasion and migration in vitro and in vivo. Runx2 was identified as a direct target gene for miR-302b by bioinformatics analysis and dual-luciferase reporter gene assay. Moreover, over-expression of miR-302b induced down-regulation of Runx2, OPN, MMP-2, MMP-9, MMP-12, MMP-14, and VEGF in 143B cells. Exogenous expression of Runx2 partially rescued the inhibitory effect of miR-302b on the invasion and migration activity of 143B osteosarcoma cells. Taken together, our results indicate that miR-302b functions as a tumour repressor in the invasion and migration of osteosarcoma by directly downregulating Runx2 expression and may be a potential therapeutic target for osteosarcoma.

LEF1, TFE3, and AR are putative diagnostic markers of solid pseudopapillary neoplasms.

The diagnosis of solid pseudopapillary neoplasms (SPNs) is challenging because some SPNs share many similar morphological and immunohistochemical features with other pancreatic neoplasms. In this study, we investigated potential diagnostic markers of SPN.Based on the SPN-specific upregulated genes from a previous DNA microarray and proteome study, we selected six immunohistochemical markers [beta-catenin, androgen receptor (AR), lymphoid enhancer-binding factor 1 (LEF1), transcription factor for immunoglobulin heavy-chain enhancer 3 (TFE3), fused in sarcoma (FUS), and WNT inhibitory factor 1 (WIF-1)]. We also evaluated the Ki-67 proliferative index to investigate its associations with prognosis. To validate these markers, we studied 91 SPNs as well as 51 pancreatic ductal carcinomas (PDC) and 48 neuroendocrine tumors (NET) as controls.We found frequent and diffuse nuclear expressions of β-catenin (98.9%), AR (81.3%), LEF1 (93.4%), TFE3 (74.7%), FUS (84.6%), and cytoplasmic expression of WIF-1 (96.7%) in SPNs. In contrast, PDCs and NETs showed no expression. (P < 0.001). When beta-catenin, LEF1, and TFE3 staining were combined, the sensitivity and specificity were 100% and 91.9%, respectively. Four (4.4%) SPNs showed distant metastasis and these tumors were associated with a relatively high Ki-67 proliferative index (≥ 5%; P = 0.013).We identified LEF1, TFE3, and AR as putative diagnostic markers of SPN, auxiliary to β-catenin. Incorporated into an immunohistochemical panel, these markers could be beneficial to distinguish SPN from PDC and NET. In addition, we suggest that the Ki-67 proliferative index can be a predictive marker of metastasis in SPNs.

Is cardiovascular disease in patients with diabetes associated with serum levels of MMP-2, LOX, and the elastin degradation products ELM and ELM-2?

Background: Diabetes mellitus type 2 (T2DM) is a significant risk factor for the development of cardiovascular diseases (CVDs). In a previous microarray study of internal mammary arteries from patients with and without T2DM, we observed several elastin-related genes with altered mRNA-expression in diabetic patients, namely matrix metalloproteinase 2 (MMP-2), lysyl oxidase (LOX) and elastin itself. In this study we investigate whether the serum concentrations of elastin-related proteins correlate to signs of CVD in patients with T2DM.Methods: Blood samples from 302 type 2 diabetic patients were analysed for MMP-2, LOX, and the elastin degradation products ELM and ELM2. The results were investigated for correlations to signs of CVD in different vascular territories, as determined by myocardial perfusion scintigraphy, carotid artery thickness and ankle-brachial blood pressure index.Results: T2DM patients with peripheral arterial disease (low ankle-brachial index) (PAD) display higher levels of MMP-2 and ELM compared to patients without PAD. However, none of the proteins or degradation products correlated with myocardial ischemia or a combined measure of CVD-signs, including myocardial ischemia, increased carotid thickness and decreased ankle-brachial blood pressure.Conclusions: Our results suggest that the diabetic environment affects the circulating amounts of MMP-2 and ELM in patients with PAD. However, the same connection could not be seen in diabetic patients with CVD broadly identified in three vascular territories. LOX and ELM-2 did not correlate to any type of CVD. Overall, serum levels of elastin-related molecules are only remotely related to CVD in type 2 diabetes.

Abstract 3577: Splice expression variation analysis (SEVA) for differential gene isoform usage in cancer

Abstract Alternative splicing events (ASE) are a significant component of expression alterations in cancer, and have been demonstrated to be critically important in the development of malignant phenotypes in a variety of tumors. These alternative gene isoforms alter cell-signaling networks and serve as a hidden source of tumor-driving alterations not identified in multi-omics analyses. Recent studies have demonstrated that reads from RNA-seq data can infer gene isoforms expressed in a single sample. Therefore, RNA-seq data of tumors offers the opportunity to systematically evaluate expressed gene isoforms and identify splicing events in cancer samples. To characterize a cancer specific ASEs landscape, it is essential to perform differential splice variant expression analysis to identify isoform variants that are unique to tumor samples compared to normal tissue. In spite of the breadth of ASE algorithms, few have been validated in primary tumor samples. Current methods for differential splice variant analysis compare mean expression of gene isoforms in sample groups. Because these variants are tumor-specific, ASEs are expected to have more variable exon junction expression than normal samples. Therefore, current differential ASE analysis algorithms from RNA-seq may not account for heterogeneous gene isoform usage in tumors. To address this, we introduce Splice Expression Variability Analysis (SEVA) to detect differential splice variation usage in tumor and normal samples and accounts for tumor heterogeneity. This algorithm compares the degree of variability of junction expression profiles within a population of normal samples relative to that in tumor samples. The performance of SEVA was compared with two existing algorithms, EBSeq and DiffSplice, in simulated and real RNA-seq data. Simulated data suggest that SEVA is robust and computationally efficient relative to EBSeq and DiffSplice. In contrast to EBSeq and DiffSplice, SEVA was able to identify alternative splicing events independent of overall gene expression differences. Finally, additional validation was performed using RNA-seq data for primary tumor data from HPV-positive oropharynx squamous cell carcinoma (OPSCC) tumors and normal samples from both TCGA and an independent tumor cohort of 46 OPSCC tumors and 25 normal samples. In these tumor samples, SEVA finds cancer-specific ASEs in genes that are independent of their differential expression status. Moreover, SEVA finds approximately hundreds of splice variant candidates, manageable for experimental validation in contrast to the thousands of candidates found with EBSeq or DiffSplice. These candidates include experimentally validated splice variants in HNSCC from a previous microarray study. Based on performance in both simulated and real data, SEVA represents a robust algorithm that is well suited for differential ASE analysis, particularly in RNA-sequencing data from heterogeneous primary tumor samples. Citation Format: Bahman Afsari, Theresa Guo, Michael Considine, Dylan Kelley, Emily Flam, Liliana Florea, Patrick Ha, Donald Geman, Michael F. Ochs, Joseph A. Califano, Daria A. Gaykalova, Alexander V. Favorov, Elana J. Fertig. Splice expression variation analysis (SEVA) for differential gene isoform usage in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3577. doi:10.1158/1538-7445.AM2017-3577

Abdominal Aortic Aneurysm–Associated MicroRNA-516a-5p Regulates Expressions of Methylenetetrahydrofolate Reductase, Matrix Metalloproteinase-2, and Tissue Inhibitor of Matrix Metalloproteinase-1 in Human Abdominal Aortic Vascular Smooth Muscle Cells

MicroRNAs (miRNAs or miRs) have been highlighted to be involved in abdominal aortic aneurysm (AAA) with the emergence of recent miRNA microarray profiling studies. miR-516a-5p has been shown to be significantly overexpressed in vascular smooth muscle cells (VSMCs) from human AAA tissues from our previous microarray study, suggesting its crucial association with AAA. In addition, further bioinformatics analysis predicted methylenetetrahydrofolate reductase (MTHFR), which regulates homocysteine (Hcy) metabolism and is proposed to be a risk gene for AAA formation and to be the downregulation target of miR-516a-5p. However, the pathogenic role of miR-516a-5p in VSMCs for AAA formation remains unresolved. This study aims to investigate the role of miR-516a-5p in human VSMCs for AAA pathogenesis. miR-516a-5p was stably overexpressed and knocked down in VSMCs explant cultured from human abdominal aortic tissues by means of lentiviral system. The MTHFR protein expression was first examined by Western blotting. In addition, the protein expressions of several key components involved in AAA pathogenic features are as follows: matrix metalloproteinase (MMP)-2, MMP-9, tissue inhibitor of matrix metalloproteinase (TIMP)-1 and TIMP-2 for elastin degradation; collagen type 1 alpha 1 for compensatory collagen synthesis; monocyte chemoattractant protein-1 for inflammation, were also evaluated. Apoptotic level of VSMCs was examined by terminal deoxynucleotidyl transferase dUTP nick end labeling assay. Results showed that protein expression of MTHFR was significantly downregulated on miR-516a-5p overexpression (P<0.05) in VSMCs, whereas it was significantly upregulated on miR-516a-5p knockdown (P<0.05). Of all the AAA key components investigated, only MMP-2 and TIMP-1 protein expressions were found altered. A significant increase in MMP-2 (P<0.05) and decrease in TIMP-1 (P<0.05) expressions were observed on miR-516a-5p overexpression in VSMCs. Apoptosis was not promoted on miR-516a-5p overexpression or knockdown in VSMCs. Our findings suggested that miR-516a-5p may regulate MTHFR, MMP-2, and TIMP-1 expressions in human VSMCs, possibly promoting the disruption of Hcy metabolism and proteolytic degradation of elastin for AAA formation.

α-amanitin resistance in Drosophila melanogaster: A genome-wide association approach.

We investigated the mechanisms of mushroom toxin resistance in the Drosophila Genetic Reference Panel (DGRP) fly lines, using genome-wide association studies (GWAS). While Drosophila melanogaster avoids mushrooms in nature, some lines are surprisingly resistant to α-amanitin—a toxin found solely in mushrooms. This resistance may represent a pre-adaptation, which might enable this species to invade the mushroom niche in the future. Although our previous microarray study had strongly suggested that pesticide-metabolizing detoxification genes confer α-amanitin resistance in a Taiwanese D. melanogaster line Ama-KTT, none of the traditional detoxification genes were among the top candidate genes resulting from the GWAS in the current study. Instead, we identified Megalin, Tequila, and widerborst as candidate genes underlying the α-amanitin resistance phenotype in the North American DGRP lines, all three of which are connected to the Target of Rapamycin (TOR) pathway. Both widerborst and Tequila are upstream regulators of TOR, and TOR is a key regulator of autophagy and Megalin-mediated endocytosis. We suggest that endocytosis and autophagy of α-amanitin, followed by lysosomal degradation of the toxin, is one of the mechanisms that confer α-amanitin resistance in the DGRP lines.

Downregulation of miR-214-3p May Contribute to Pathogenesis of Ulcerative Colitis via Targeting STAT6.

MicroRNAs (miRs) are small noncoding RNA molecules and recently have demonstrated that altered expression and functions are their tight association with ulcerative colitis (UC). Previous microarray study reported that miR-214 was downregulated in the sigmoid colon of patients with active UC, but the roles of miR-214 in the pathogenesis of UC remain to be elucidated. In this study, significant lower level of miR-214-3p and higher level of STAT6 in the intestinal mucosa of active UC patients compared with the health controls were confirmed by quantitative real-time PCR. Results of luciferase reporter assays and western blot demonstrated that miR-214-3p directly targets STAT6 and negatively regulates the expression of STAT6 at the posttranscriptional level. Furthermore, the expression of miR-214-3p was decreased in TNF-α treated HT29 cells and STAT6 protein level was increased in a time-dependent manner. Silenced STAT6 and upregulation of miR-214-3p could decrease the level of INF-γ in TNF-α treated HT29 cells. Additionally, the results of the present study indicate that miR-214-3p and STAT6 axis may be a novel therapeutic target for intestinal inflammation of patients with active UC.