Microarray-based Expression Profiling Research Articles

Pioglitazone Identifies a New Target for Aneurysm Treatment: Role of Egr1 in an Experimental Murine Model of Aortic Aneurysm

Peroxisome proliferator-activated receptor γ agonists have been shown to inhibit angiotensin II (AngII)-induced experimental abdominal aortic aneurysms. Macrophage infiltration to the vascular wall is an early event in this pathology, and therefore we explored the effects of the peroxisome proliferator-activated receptor γ agonist pioglitazone on AngII-treated macrophages. Using microarray-based expression profiling of phorbol ester-stimulated THP-1 cells, we found that a number of aneurysm-related gene changes effected by AngII were modulated following the addition of pioglitazone. Among those genes, polycystic kidney disease 1 (PKD1) was significantly up-regulated (multiple testing corrected p < 0.05). The analysis of the PKD1 proximal promoter revealed a putative early growth response 1 (EGR1) binding site, which was confirmed by chromatin immunoprecipitation (ChIP) and quantitative PCR. Further analysis of publicly available ChIP-sequencing data revealed that this putative binding site overlapped with a conserved EGR1 binding peak present in 5 other cell lines. Quantitative real-time PCR showed that EGR1 suppressed PKD1, while AngII significantly up-regulated PKD1, an effect counteracted by pioglitazone. Conversely, in EGR1 short hairpin RNA lentivirally transduced THP-1 cells, reduced EGR1 led to a significant up-regulation of PKD1, especially after treatment with pioglitazone. In vivo, deficiency of Egr1 in the haematopoietic compartment of mice completely abolished the incidence of CaCl₂-induced aneurysm formation.

Abstract 313: Perinatal Growth Restriction Decreases Hepatic RNA Editing of Apolipoprotein B in Male Rat Offspring

Introduction: Individuals born with intrauterine growth restriction develop cardiovascular disease. We employed hepatic microarray-based expression profiling of male rat offspring born to mothers subjected to combined intrauterine and postnatal calorie restriction (IPCR) as a discovery driven experiment to interrogate intrauterine growth restriction. These studies identified that the expression of Apobec1 and Apobec1 complementation factor (A1CF), genes known to edit apolipoprotein B (ApoB) mRNA through the epigenetic process of cytosine deamination, are decreased in IPCR. Editing of ApoB mRNA at position 666 changes the ribonucleotide base from a cytosine to a uracil (U) and controls the production of ApoB100 and ApoB48 lipoproteins. Hypothesis: IPCR decreases hepatic ApoB mRNA editing in male offspring through transcriptional regulation of Apobec1 and A1CF. Methods: Pyrosequencing designed to interrogate ApoB mRNA editing was used to quantify hepatic ApoB100 and ApoB48 transcripts in an experiment employing the male offspring (litters culled to 6 male offspring for each mother) from 4 control fed mothers and 4 mothers subjected to 50% calorie restriction from embryonic day 11 to postnatal day 21 (IPCR). RT-qPCR and western blotting were employed to quantify the hepatic expression of Apobec1 and A1CF. Serum ApoB100 and Apo48 were quantified by ELISA. Results: ApoB transcripts in the control fed offspring were edited, with a U base call of 55 ± 2% at position 666, whereas IPCR offspring possessed decreased editing with a U base call of 12 ± 1% (n=12 for each group; F=368; p&lt;0.0001). The RT-qPCR relative quotient (RQ) in the IPCR group was 0.2 ± 0.1 (F=107;p&lt;0.0001) and 0.4 ± 0.1 (F=25;p&lt;0.0001) for Apobec1 and A1CF, respectively (RQ=1 in the control fed offspring for both Apobec1 and A1CF). Relative to control, IPCR treatment significantly decreased hepatic Apobec1 and A1CF proteins by 45% ± 10 and 27 % ± 9.2 respectively. IPCR treatment increased serum ApoB100 by 1.5 fold ± 0.43 (p= 0.051) and significantly decreased ApoB48 by 0.8 fold ± 0.1 (n=6) compared to control. Conclusion: These data define a novel association of IPCR and ApoB editing through a nutritionally controlled epigenetic process working through transcriptional control of Apobec1 and A1CF.

The Histamine H4 Receptor Regulates Chemokine Production in Human Natural Killer Cells

Background: Natural killer (NK) cells have been detected in the lesional skin of patients with inflammatory skin diseases, where high levels of histamine are also present. Therefore, we investigated the effect of histamine, in particular via the histamine H4 receptor (H4R), on gene expression levels in human NK cells. Methods: Comprehensive microarray-based mRNA expression profiling was performed to assess the gene expression levels in human NK cells in response to H4R stimulation in an unbiased approach. The expression of selected cytokines and chemokines was quantified by real-time PCR and enzyme-linked immunosorbent assay. Results: The microarray analysis identified only few genes which were differentially regulated upon H4R stimulation. In follow-up studies, a significant upregulation of CCL3 and CCL4 at the mRNA level and in addition for CCL3 also at the protein level via the H4R was observed. Conclusion: The elevated expression levels of chemokines in response to H4R stimulation might foster the inflammation in allergic skin diseases and characterize the H4R as a promising therapeutic target.

Compound mouse mutants of bZIP transcription factors Mafg and Mafk reveal a regulatory network of non-crystallin genes associated with cataract.

Although majority of the genes linked to early-onset cataract exhibit lens fiber cell-enriched expression, our understanding of gene regulation in these cells is limited to function of just eight transcription factors and largely in the context of crystallins. We report on small Maf transcription factors Mafg and Mafk as regulators of several non-crystallin human cataract-associated genes in fiber cells and establish their significance to this disease. We applied a bioinformatics tool for cataract gene discovery iSyTE to identify Mafg and its co-regulators in the lens, and generated various null-allelic combinations of Mafg:Mafk mouse mutants for phenotypic and molecular analysis. By age 4 months, Mafg-/-:Mafk+/- mutants exhibit lens defects that progressively develop into cataract. High-resolution phenotypic characterization of Mafg-/-:Mafk+/- mouse lens reveals severely disorganized fiber cells, while microarray-based expression profiling identifies 97 differentially regulated genes (DRGs). Integrative analysis of Mafg-/-:Mafk+/- lens-DRGs with (1) binding motifs and genomic targets of small Mafs and their regulatory partners, (2) iSyTE lens expression data, and (3) interactions between DRGs in the String database, unravel a detailed small Maf regulatory network in the lens, several nodes of which are linked to cataract. This approach identifies 36 high-priority candidates from the original 97 DRGs. Significantly, 8/36 (22%) DRGs are associated with cataracts in human (GSTO1, MGST1, SC4MOL, UCHL1) or mouse (Aldh3a1, Crygf, Hspb1, Pcbd1), suggesting a multifactorial etiology that includes oxidative stress and misregulation of sterol synthesis. These data identify Mafg and Mafk as new cataract-associated candidates and define their function in regulating largely non-crystallin genes linked to human cataract.

MicroRNAs as potential biomarkers for noninvasive detection of fetal trisomy 21.

The objective of this study was to discover a panel of microRNAs (miRNAs) as potential biomarkers for noninvasive prenatal testing (NIPT) of trisomy 21 (T21) and to predict the biological functions of identified biomarkers using bioinformatics tools. Using microarray-based genome-wide expression profiling, we compared the expression levels of miRNAs in whole blood samples from non-pregnant women, whole blood samples from pregnant women with euploid or T21 fetuses, and placenta samples from euploid or T21 fetuses. We analyzed the differentially expressed miRNAs according to disease and tissue type (P value <0.05 and two-fold expression change). To predict functions of target genes of miRNAs, the functional annotation tools were used. We identified 299 miRNAs which reasonably separate the whole blood from the placenta. Among the identified miRNAs, 150 miRNAs were up-regulated in the placenta, and 149 miRNAs were down-regulated. Most of the up-regulated miRNAs in the placenta were members of the mir-498, mir-379, and mir-127 clusters. Among the up-regulated miRNAs in the placenta, mir-1973 and mir-3196 were expressed at higher levels in the T21 placenta than in the euploid placenta. The two miRNAs potentially regulate 203 target genes that are involved in development of brain, central nervous system, and nervous system. The genes are significantly associated with T21-related disorder such as congenital abnormalities, mental disorders, and nervous system diseases. Our study indicates placenta-specific miRNAs that may be potential biomarkers for NIPT of fetal T21 and provides new insights into the molecular mechanisms of T21 via regulation of miRNAs.

TRPM7 maintains progenitor-like features of neuroblastoma cells: implications for metastasis formation.

Neuroblastoma is an embryonal tumor derived from poorly differentiated neural crest cells. Current research is aimed at identifying the molecular mechanisms that maintain the progenitor state of neuroblastoma cells and to develop novel therapeutic strategies that induce neuroblastoma cell differentiation. Mechanisms controlling neural crest development are typically dysregulated during neuroblastoma progression, and provide an appealing starting point for drug target discovery. Transcriptional programs involved in neural crest development act as a context dependent gene regulatory network. In addition to BMP, Wnt and Notch signaling, activation of developmental gene expression programs depends on the physical characteristics of the tissue microenvironment. TRPM7, a mechanically regulated TRP channel with kinase activity, was previously found essential for embryogenesis and the maintenance of undifferentiated neural crest progenitors. Hence, we hypothesized that TRPM7 may preserve progenitor-like, metastatic features of neuroblastoma cells. Using multiple neuroblastoma cell models, we demonstrate that TRPM7 expression closely associates with the migratory and metastatic properties of neuroblastoma cells in vitro and in vivo. Moreover, microarray-based expression profiling on control and TRPM7 shRNA transduced neuroblastoma cells indicates that TRPM7 controls a developmental transcriptional program involving the transcription factor SNAI2. Overall, our data indicate that TRPM7 contributes to neuroblastoma progression by maintaining progenitor-like features.

The hepatic transcriptome of young suckling and aging intrauterine growth restricted male rats.

Intrauterine growth restriction leads to the development of adult onset obesity/metabolic syndrome, diabetes mellitus, cardiovascular disease, hypertension, stroke, dyslipidemia, and non-alcoholic fatty liver disease/steatohepatitis. Continued postnatal growth restriction has been shown to ameliorate many of these sequelae. To further our understanding of the mechanism of how intrauterine and early postnatal growth affects adult health we have employed Affymetrix microarray-based expression profiling to characterize hepatic gene expression of male offspring in a rat model of maternal nutrient restriction in early and late life. At day 21 of life (p21) combined intrauterine and postnatal calorie restriction treatment led to expression changes in circadian, metabolic, and insulin-like growth factor genes as part of a larger transcriptional response that encompasses 144 genes. Independent and controlled experiments at p21 confirm the early life circadian, metabolic, and growth factor perturbations. In contrast to the p21 transcriptional response, at day 450 of life (d450) only seven genes, largely uncharacterized, were differentially expressed. This lack of a transcriptional response identifies non-transcriptional mechanisms mediating the adult sequelae of intrauterine growth restriction. Independent experiments at d450 identify a circadian defect as well as validate expression changes to four of the genes identified by the microarray screen which have a novel association with growth restriction. Emerging from this rich dataset is a portrait of how the liver responds to growth restriction through circadian dysregulation, energy/substrate management, and growth factor modulation.

Identification of a bona fide microRNA biomarker in serum exosomes that predicts hepatocellular carcinoma recurrence after liver transplantation.

BackgroundPredictive biomarkers for the recurrence of hepatocellular carcinoma (HCC) have great benefit in the selection of treatment options, including liver transplantation (LT), for HCC. The purpose of this study was to identify specific microRNAs (miRs) in exosomes from the serum of patients with recurrent HCC and to validate these molecules as novel biomarkers for HCC recurrence.MethodsWe employed microarray-based expression profiling of miRs derived from exosomes in the serum of HCC patients to identify a biomarker that distinguishes between patients with and without HCC recurrence after LT. This was followed by the validation in a separate cohort of 59 HCC patients who underwent living related LT. The functions and potential gene targets of the recurrence-specific miRs were analysed using a database, clinical samples and HCC cell lines.ResultsWe found that miR-718 showed significantly different expression in the serum exosomes of HCC cases with recurrence after LT compared with those without recurrence. Decreased expression of miR-718 was associated with HCC tumour aggressiveness in the validated cohort series. We identified HOXB8 as a potential target gene of miR-718, and its upregulation was associated with poor prognosis.ConclusionCirculating miRs in serum exosomes have potential as novel biomarkers for predicting HCC recurrence.

Changes in gene expression in liver tissue from patients with fulminant hepatitis E.

To study host gene expression and number of immune cells in liver tissues from patients with fulminant hepatitis E (FH-E). Microarray-based expression profiling was done using Illumina Human WG-6_v3_BeadChip arrays on post-mortem liver tissue from 5 patients with FH-E, and compared with similar tissue from 6 patients with fulminant hepatitis B (FH-B; disease controls) and normal liver tissue from 6 persons. Differential expression was defined as ≥ 2.0-fold change with Benjamini-Hochberg false discovery rate below 0.05 using t-test in liver tissue from FH-B and FH-E, than healthy liver tissue. For some genes that showed differential expression in FH-E, microarray data were validated using quantitative reverse transcription PCR. Differentially expressed gene lists were then subjected to "Gene Ontology" analysis for biological processes, and pathway analysis using BioCarta database on the DAVID server. In addition, tissue sections were stained for CD4(+), CD8(+) and CD56(+) cells using indirect immunohistochemistry; cells staining positive for each of these markers were counted and compared between groups. Compared to normal livers, those from patients with FH-E and FH-B showed differential expression of 3377 entities (up-regulated 1703, downregulated 1674) and 2572 entities (up 1164, down 1408), respectively. This included 2142 (up 896, down 1246) entities that were common between the two sets; most of these belonged to metabolic, hemostatic and complement pathways, which are active in normal livers. Gene expression data from livers of patients with FH-E but not those of FH-B showed activation of several immune response pathways, particularly those involving cytotoxic T cells. The fold-change values of mRNA for selected genes in livers from FH-E than in normal liver tissue determined using quantitative reverse transcription PCR showed excellent concordance with microarray analysis. At immunohistochemistry, CD8(+) T cells showed an increase in liver biopsies from both FH-E [median 53.4 per arbitrary unit area (range 31.2-99.9)] and FH-B [median 49.3 (19.3-51.0); P = 0.005] compared to control liver tissue [median 6.9 (3.1-14.9)]. FH-E patients show CD8(+) T cell infiltration and increased gene expression of cytotoxic T cell pathways in liver, suggesting a possible pathogenetic role for these cells.

Bioimaging of microRNA124a-independent neuronal differentiation of human G2 neural stem cells

Evaluation of the function of microRNAs (miRNAs or miRs) through miRNA expression profiles during neuronal differentiation plays a critical role not only in identifying unique miRNAs relevant to cellular development but also in understanding regulatory functions of the cell-specific miRNAs in living organisms. Here, we examined the microarray-based miRNA expression profiles of G2 cells (recently developed human neural stem cells) and monitored the expression pattern of known neuron-specific miR-9 and miR-124a during neuronal differentiation of G2 cells in vitro and in vivo. Of 500 miRNAs analyzed by microarray of G2 cells, the expression of 90 miRNAs was significantly increased during doxycycline-dependent neuronal differentiation of G2 cells and about 60 miRNAs showed a gradual enhancement of gene expression as neuronal differentiation progressed. Real-time PCR showed that expression of endogenous mature miR-9 was continuously and gradually increased in a pattern dependent on the period of neuronal differentiation of G2 cells while the increased expression of neuron-specific mature miR-124a was barely observed during neurogenesis. Our recently developed miRNA reporter imaging vectors (CMV/Gluc/3×PT_miR-9 and CMV/Gluc/3×PT_miR-124a) containing Gaussia luciferase, CMV promoter and three copies of complementary nucleotides of each corresponding miRNA showed that luciferase activity from CMV/Gluc/3×PT_miR-9 was gradually decreased both in vitro and in vivo in G2 cells induced to differentiate into neurons. However, in vitro and in vivo bioluminescence signals for CMV/Gluc/3×PT_miR-124a were not significantly different between undifferentiated and differentiated G2 cells. Our results demonstrate that biogenesis of neuron-specific miR-124a is not necessary for doxycycline-dependent neurogenesis of G2 cells.

Gene Expression Profiling and Pathway Network Analysis Predicts a Novel Antitumor Function for a Botanical-Derived Drug, PG2.

PG2 is a botanical drug that is mostly composed of Astragalus polysaccharides (APS). Its role in hematopoiesis and relieving cancer-related fatigue has recently been clinically investigated in cancer patients. However, systematic analyses of its functions are still limited. The aim of this study was to use microarray-based expression profiling to evaluate the quality and consistency of PG2 from three different product batches and to study biological mechanisms of PG2. An integrative molecular analysis approach has been designed to examine significant PG2-induced signatures in HL-60 leukemia cells. A quantitative analysis of gene expression signatures was conducted for PG2 by hierarchical clustering of correlation coefficients. The results showed that PG2 product batches were consistent and of high quality. These batches were also functionally equivalent to each other with regard to how they modulated the immune and hematopoietic systems. Within the PG2 signature, there were five genes associated with doxorubicin: IL-8, MDM4, BCL2, PRODH2, and BIRC5. Moreover, the combination of PG2 and doxorubicin had a synergistic effect on induced cell death in HL-60 cells. Together with the bioinformatics-based approach, gene expression profiling provided a quantitative measurement for the quality and consistency of herbal medicines and revealed new roles (e.g., immune modulation) for PG2 in cancer treatment.

Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes.

The eukaryotic cell division cycle is a highly regulated process that consists of a complex series of events and involves thousands of proteins. Researchers have studied the regulation of the cell cycle in several organisms, employing a wide range of high-throughput technologies, such as microarray-based mRNA expression profiling and quantitative proteomics. Due to its complexity, the cell cycle can also fail or otherwise change in many different ways if important genes are knocked out, which has been studied in several microscopy-based knockdown screens. The data from these many large-scale efforts are not easily accessed, analyzed and combined due to their inherent heterogeneity. To address this, we have created Cyclebase—available at http://www.cyclebase.org—an online database that allows users to easily visualize and download results from genome-wide cell-cycle-related experiments. In Cyclebase version 3.0, we have updated the content of the database to reflect changes to genome annotation, added new mRNA and protein expression data, and integrated cell-cycle phenotype information from high-content screens and model-organism databases. The new version of Cyclebase also features a new web interface, designed around an overview figure that summarizes all the cell-cycle-related data for a gene.

E4BP4 is a repressor of epigenetically regulated SOSTDC1 expression in breast cancer cells.

We and others show that SOSTDC1 is down-regulated in breast cancer tissues compared to matched normal tissues. Previously, we found that epigenetic mechanisms underlie the down-regulation of SOSTDC1 in gastric cancer cells. The aim of this study was to assess the putative epigenetic regulation of SOSTDC1 expression in breast cancer cells. Microarray-based expression profiling was performed in a series of primary breast cancers and matched normal tissues. Real-time PCR was performed to assess SOSTDC1 and E4BP4 mRNA levels in MCF7, BT549, MBMDA231, T47D (breast cancer) and HEK293T (normal kidney) cell lines. Methylation-specific PCR (MSP) and bisulfite sequencing PCR (BSP) were performed to assess the methylation level of the SOSTDC1 gene promoter, and 5-Aza 2-deoxycytidine (5'-Aza-dC) treatment was used to induce its demethylation. A luciferase assay was used to measure SOSTDC1 promoter activity in vitro. Stable shRNA-mediated knockdown of E4BP4 was carried out in MCF7 cells and confirmed by Western blotting. Finally, MCF7 cell proliferation and survival were measured by MTS assay. We found that SOSTDC1 is frequently down-regulated in primary breast cancers (98.2%) and in all breast cancer cell lines tested. MSP and BSP analyses revealed SOSTC1 promoter hypermethylation at CpG sites. 5'-Aza-dC treatment induced a striking down-regulation of SOSTDC1 gene expression, whereas BSP analysis showed demethylation of its promoter. Subsequent in silico SOSTDC1 promoter analysis indicated the presence of putative transcriptional repressor E4BP4 binding sites, and promoter deletion studies indeed revealed repressor binding regions encompassing these E4BP4 binding sites. Relative quantification of E4BP4 expression showed an inverse correlation to SOSTDC1 expression in the breast cancer cell lines tested. Exogenous over-expression of E4BP4 in HEK-293 and BT549 cells reduced SOSTDC1 expression and its promoter activity, respectively. Stable shRNA-mediated E4BP4 BT549 and MCF7 knock-down cells treated with 5'-Aza-dC exhibited up-regulation of SOSTDC1 expression and a concomitant inhibition of cell proliferation and survival. From our results we conclude that the transcriptional repressor E4BP4 plays a role in repressing epigenetically regulated SOSTDC1 expression in breast cancer cells, which can be reverted by E4BP4 silencing.

Gene expression profiling of mononuclear cells from patients with sepsis secondary to community-acquired pneumonia

Mechanisms governing the inflammatory response during sepsis involve crosstalk between diverse signaling pathways, but current knowledge provides an incomplete picture of the syndrome. Microarray-based expression profiling is a powerful approach for the investigation of complex clinical conditions such as sepsis. In this study, we investigated whole-genome expression profiles in mononuclear cells from septic patients admitted in intensive care units with community-acquired pneumonia. Blood samples were collected at the time of sepsis diagnosis and seven days later since we aimed to evaluate the role of biological processes or genes possibly involved in patient recovery. Here we provide a detailed description of the study design, including clinical information, experimental methods and procedures regarding data analysis. Metadata corresponding to microarray results deposited in the database Gene Expression Omnibus (GEO) under the accession number GSE48080 are also described in this report. Our dataset allows the identification of genes possibly associated with host defense to infection as well as gene expression patterns associated with patient outcome.

Abstract 3549: miRNAs and androgen receptor interplay in prostate cancer

Abstract Background In the treatment of advanced prostate cancer (PCa) a common strategy is to interfere with androgen receptor (AR) transcriptional activity by means of androgen deprivation. Despite an initial good response, the majority of tumors eventually progress to an androgen-independent phenotype, known as castrate-resistant prostate cancer (CRPC) which retains enhanced AR signaling and for which effective long-term treatment is currently not available. The discovery of miRNAs as novel members of the AR transcriptome disclosed the existence of an intricate network between AR, miRNAs and down-stream target genes that needs to be further investigated. Materials and Methods A list of potential AR regulated miRNAs and/or their host genes (HGs) was generated through microarray-based expression profiling and chromatin-immunoprecipitation coupled with deep sequencing (ChIP-seq) in prostate cancer cells. AR binding sites in the candidate miRNAs and HGs were verified after 1 h of androgen stimulation using androgen receptor chromatin immunoprecipitation followed by PCR detection of the binding sites. Real-time PCR was performed to analyze the changes of expression after 24 h and 48 h of androgen treatment. As experimental models, AR positive DUCaP and LNCaP cell lines were chosen. Results Overall, 29 miRNAs and/or miRNA-HGs were detected to be significantly regulated upon 8 h and 24 h of androgen treatment and to harbor single or multiple putative AR binding sites. A direct association of AR with miR22, miR29a and the miR17-92 cluster was validated along with their regulation after androgen stimulation. For the miR17-92 cluster and miR22, it was additionally confirmed that the expression of the HGs and the corresponding resident miRNAs are affected similarly by androgen exposure. Interestingly, the basal levels of the miRNAs under study appear reduced in AR positive cell lines when compared with AR negative ones. Conclusions The AR transcriptome includes specific miRNAs whose aberrant expression is associated with well known pro- or anti-oncogenic effects. Further information on the complex regulatory machinery that guides miRNAs activity and role in prostate cancer cells are provided with this work, highlighting the importance of the interplay between miRNAs and AR. Indeed, the selected miRNAs are differentially expressed in various prostate cancer cell lines depending on AR presence or absence and are also regulated upon androgen stimulation. Hence, this class of miRNAs may represent new promising biomarkers for prostate cancer or novel potential therapeutic targets for treatment of castrate-resistant prostate cancer. Supported by the PhD Program MCBO of FWF Citation Format: Lorenza Pasqualini, Huajie Bu, Narisu Narisu, Johannes Rainer, Michal R. Schweiger, Peter S. Chines, Christian Fuchsberger, Helmut Klocker. miRNAs and androgen receptor interplay in prostate cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3549. doi:10.1158/1538-7445.AM2014-3549

Identification and clinical implications of circulating microRNAs for estrogen receptor-positive breast cancer.

Cancer-associated microRNAs have been stably detected in blood. The objective of this study was to identify a panel of circulating microRNAs with the potential to serve as biomarkers for estrogen receptor-positive (ER+)/human epidermal growth factor receptor 2 (HER2)- breast cancer. We used microarray-based expression profiling to compare the levels of circulating microRNAs in blood samples from 11 ER+/HER2- advanced breast cancer patients plus 5 age-matched controls. MicroRNA levels were validated by reverse transcription quantitative polymerase chain reaction in 40 control subjects, 187 early breast cancer patients, and 45 metastatic breast cancer patients. Then, we assessed the association between the levels of microRNA and clinical outcomes of ER+/HER2- metastatic breast cancer. Initially, we found that miR-1280, miR-1260, and miR-720 were up-regulated in blood from breast cancer patients (P < 0.05). In validation, miR-1280 levels significantly increased in breast cancer patients and reflected tumor status (control<<early cancer<metastatic cancer). Among 37 metastatic breast cancer patients, miR-1280 levels significantly decreased after treatment in patients who responded to systemic treatment (P < 0.001). We confirmed that miR-1280 was not a classic microRNA, but a tRNA(Leu)-derived fragment. These findings suggest that a circulating tRNA-derived microRNA, miR-1280, is differently expressed in breast cancer patients and may serve as a biomarker for ER-positive breast cancer.

G.P.213: Investigating the molecular mechanisms underlying the progression of collagen VI-related muscular dystrophies

Ullrich congenital muscular dystrophy (UCMD) presents at birth or in infancy with progressive muscle weakness, joint contractures and respiratory failure, and is caused by mutations in the three genes coding for collagen VI. Dysfunction of the collagen VI microfibrills in the extracellular matrix perturbs the normal extracellular matrix/muscle interface, leading to yet incompletely characterized downstream effects. Review of muscle biopsies from UCMD patients show that the histological appearance changes with disease progression, suggesting changing disease-driving pathways throughout the progression of the disease. In preparation for a molecular investigation of such pathways, we analyzed 39 UCMD patient muscle biopsies with an automated image analysis algorithm using the degree of atrophy, fibrosis, and regeneration as criteria to group the biopsies. We performed microarray-based expression profiling on the grouped patient biopsies and age-matched controls. Expression profiling results correlated with staging obtained from the automated image analysis algorithm. Further studies will establish the involvement of specific molecules in different stages of UCMD to identify suitable targets for therapeutic intervention. (NIH).

An integrative analysis of the tumorigenic role of TAZ in human non-small cell lung cancer.

TAZ, also known as WWTR1, has recently been suggested as an oncogene in non-small cell lung cancer (NSCLC). We investigated the clinical relevance of TAZ expression and its functional role in NSCLC tumorigenesis. We characterized TAZ at the DNA (n=192), mRNA (n=196), and protein levels (n=345) in an NSCLC patient cohort. Gene expression analysis was complemented by a meta-analysis of public datasets (n=1,382). The effects of TAZ on cell proliferation and cell cycle were analyzed in cell cultures and on tumor growth in mice. TAZ-dependent microarray-based expression profiles in NSCLC cells were combined with molecular profiles in human NSCLC tissues for in silico analysis. Higher TAZ mRNA and protein levels were associated with shorter patient survival. Transduction of TAZ enhanced cell proliferation and tumorigenesis in bronchial epithelial cells, whereas TAZ silencing suppressed cell proliferation and induced cell cycle arrest in NSCLC cells. Microarray and cell culture experiments showed that ErbB ligands (amphiregulin, epiregulin, and neuregulin 1) are downstream targets of TAZ. Our in silico analysis revealed a TAZ signature that substantiated the clinical impact of TAZ and confirmed its relationship to the epidermal growth factor receptor signaling pathway. TAZ expression defines a clinically distinct subgroup of patients with NSCLC. ErbB ligands are suggested to mediate the effects of TAZ on lung cancer progression. Our findings emphasize the tumorigenic role of TAZ and may serve as the basis for new treatment strategies.

MicroRNA-26a-5p and microRNA-23b-3p up-regulate peroxiredoxin III in acute myeloid leukemia

MicroRNAs (miRNAs) are small RNAs that regulate target gene expression. Using microarray-based miRNA expression profiling, we compared the miRNA expression in granulocytes from four patients with acute myeloid leukemia and four healthy controls. Thirty-four miRNAs were found to be differentially expressed, including 20 miRNAs that were up-regulated and 14 miRNAs that were down-regulated. The expression of selected miRNAs (miR-26a-5p and miR-23b-3p) was independently validated in 20 patients and 12 healthy controls. Notably, we demonstrated that peroxiredoxin III (PrxIII) is a common direct target of both miR-26a-5p and miR-23b-3p. Furthermore, these results indicate that the two decreased miRNAs could scavenge cellular reactive oxygen species (ROS) by targeting the PrxIII gene. These findings are discussed with regard to the known function of PrxIII as a ROS scavenger and the high endogenous ROS levels required for hematopoietic stem cell differentiation. These findings may potentially offer insights into the pathological relationships between miR-26a-5p, miR-23b-3p and leukemogenesis.

Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing

Eosinophilic esophagitis (EoE) is an allergic inflammatory disorder of the esophagus that is compounded by genetic predisposition and hypersensitivity to environmental antigens. Using high-density oligonucleotide expression chips, a disease-specific esophageal transcript signature was identified and shown to be largely reversible with therapy. In an effort to expand the molecular signature of EoE, we performed RNA sequencing on esophageal biopsies from healthy controls and patients with active EoE and identified a total of 1 607 significantly dysregulated transcripts (1 096 upregulated, 511 downregulated). When clustered by raw expression levels, an abundance of immune-cell specific transcripts that are highly induced in EoE are expressed at low (or undetectable) levels in healthy controls. Moreover, 66% of the gene signature identified by RNA sequencing was previously unrecognized in the EoE transcript signature by microarray-based expression profiling and included several long non-coding RNAs (lncRNA), an emerging class of transcriptional regulators. The lncRNA BANCR was upregulated in EoE and induced in IL-13–treated primary esophageal epithelial cells. Repression of BANCR significantly altered the expression of IL-13–induced pro-inflammatory genes. Together, these data comprise new potential biomarkers of EoE and demonstrate a novel role for lncRNAs in EoE and IL-13–associated responses.