Changes In RNA Expression Research Articles

The antitumor effects of entinostat in ovarian cancer require adaptive immunity.

Ovarian cancer is poorly immunogenic; however, increased major histocompatibility complex class II (MHCII) expression correlates with improved immune response and prolonged survival in patients with ovarian cancer. The authors previously demonstrated that the histone deacetylase inhibitor entinostat increases MHCII expression on ovarian cancer cells. In the current study, they evaluated whether entinostat treatment and resultant MHCII expression would enhance beneficial immune responses and impair tumor growth in mice with ovarian cancer. C57BL/6 mice bearing intraperitoneal ID8 tumors were randomized to receive entinostat 20 mg/kg daily versus control. Changes in messenger RNA (mRNA) expression of 46 genes important for antitumor immunity were evaluated using NanoString analysis, and multicolor flow cytometry was used to measure changes in protein expression and tumor-infiltrating immune cells. Entinostat treatment decreased the growth of both subcutaneously and omental ID8 tumors and prolonged survival in immunocompetent C57BL/6 mice. NanoString analysis revealed significant changes in mRNA expression in 21 of 46 genes, including increased expression of the MHCI pathway, the MHCII transactivator (CIITA), interferon γ, and granzyme B. C57BL/6 mice that received entinostat had increased MHCII expression on omental tumor cells and a higher frequency of tumor-infiltrating, CD8-positive T cells by flow cytometry. In immunocompromised mice, treatment with entinostat had no effect on tumor size and did not increase MHCII expression. In the current murine ovarian cancer model, entinostat treatment enhances beneficial immune responses. Moreover, these antitumor effects of entinostat are dependent on an intact immune system. Future studies combining entinostat with checkpoint inhibitors or other immunomodulatory agents may achieve more durable antitumor responses in patients with ovarian cancer.

A genome-wide landscape of mRNAs, lncRNAs, and circRNAs during subcutaneous adipogenesis in pigs

BackgroundPreadipocyte differentiation plays a critical role in subcutaneous fat deposition in pigs. However, the roles of different RNAs, such as messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in the differentiation process of subcutaneous preadipocytes, are still largely unclear. In the present study, a transcriptome analysis, including the analysis of mRNAs, lncRNAs, and circRNAs, during different differentiation stages, namely, day 0 (D0), day 2 (D2), day 4 (D4), and day 8 (D8), of subcutaneous preadipocytes from Chinese Erhualian pigs was performed.ResultsA total of 1554, 470, 1344, 1777, and 676 differentially expressed (DE) mRNAs, 112, 58, 95, 136, and 93 DE lncRNAs, and 902, 787, 710, 932, and 850 DE circRNAs were identified between D2 and D0, between D4 and D2, between D8 and D4, between D4 and D0, and between D8 and D0, respectively. Furthermore, functional enrichment analysis showed that the common DE mRNAs during the entire differentiation process were mainly involved in lipid metabolic and cell differentiation processes. Additionally, co-expression network analysis identified the potential lncRNAs related to adipogenesis, e.g., MSTRG.131380 and MSTRG.62128.ConclusionsOur study provides new insights of the expression changes of RNAs during adipogenic differentiation, which might contribute to the phenotype of subcutaneous adipogenesis. These results greatly improve our understanding of the molecular mechanisms regulating subcutaneous fat deposition in pigs.

Diverse serotonin actions of vilazodone reduce l-3,4-dihidroxyphenylalanine-induced dyskinesia in hemi-parkinsonian rats.

The serotonergic system is a well-established modulator of l-dopa-induced dyskinesia. To date, targeting serotonin transporters or serotonin receptor subtype 1A (5-HT1A ) reduces l-dopa-induced dyskinesia in animal models; however, these strategies have failed to translate clinically. Ideally, a compound acting at both known antidyskinetic sites could optimize serotonin-mediated approaches. Vilazodone is a selective serotonin reuptake inhibitor and a partial 5-HT1A agonist approved by the U.S. Food and Drug Administration, situating Vilazodone in a unique position to reduce l-dopa-induced dyskinesia without compromising l-dopa-mediated motor improvements. The goal of the present study was to characterize Vilazodone's effects on l-dopa-induced behaviors, neurochemistry and gene expression in unilateral 6-hydroxydopamine-lesioned hemi-parkinsonian rats. In experiments 1 and 2, l-dopa-naïve and l-dopa-primed animals were coadministered Vilazodone and l-dopa daily for 3 weeks to model subchronic use, and behavioral, neurochemical, and messenger RNA (mRNA) expression changes were measured. In experiment 3, dyskinetic behavior was assessed following 5-HT1A or serotonin receptor subtype 1B blockade prior to Vilazodone-l-dopa coadministration. Vilazodone significantly suppressed developing and established l-dopa-induced dyskinesia without compromising the promotor effects of l-dopa therapy. In the dopamine-depleted striatum, Vilazodone-l-dopa cotreatment increased dopamine content, suggesting a normalization of dopamine kinetics in dyskinetic brain, and reduced l-dopa-induced c-Fos and preprodynorphin mRNA overexpression, indicative of attenuated dopamine D1 receptor-mediated direct pathway overactivity. Only 5-HT1A antagonism partially attenuated Vilazodone's antidyskinetic efficacy, suggesting both serotonin transporter-dependent effects and 5-HT1A receptors in Vilazodone's actions. Our findings show Vilazodone has a serotonin-dependent effect on rodent l-dopa-induced dyskinesia and implicate the potential for repositioning Vilazodone against l-dopa-induced dyskinesia development and expression in Parkinson's disease patients. © 2018 International Parkinson and Movement Disorder Society.

GW29-e0389 The Expression Changes of Plasma Long Non-coding RNAs on essential hypertension induced left ventricular hypertrophy

GW29-e0389 The Expression Changes of Plasma Long Non-coding RNAs on essential hypertension induced left ventricular hypertrophy

Genome-wide analysis of long non-coding RNAs in Catalpa bungei and their potential function in floral transition using high-throughput sequencing

BackgroundLong non-coding RNAs (lncRNAs) have crucial roles in various biological regulatory processes. However, the study of lncRNAs is limited in woody plants. Catalpa bungei is a valuable ornamental tree with a long cultivation history in China, and a deeper understanding of the floral transition mechanism in C. bungei would be interesting from both economic and scientific perspectives.ResultsIn this study, we categorized C. bungei buds from early flowering (EF) and normal flowering (NF) varieties into three consecutive developmental stages. These buds were used to systematically study lncRNAs during floral transition using high-throughput sequencing to identify molecular regulatory networks. Quantitative real-time PCR was performed to study RNA expression changes in different stages. In total, 12,532 lncRNAs and 26,936 messenger RNAs (mRNAs) were detected. Moreover, 680 differentially expressed genes and 817 differentially expressed lncRNAs were detected during the initiation of floral transition. The results highlight the mRNAs and lncRNAs that may be involved in floral transition, as well as the many lncRNAs serving as microRNA precursors. We predicted the functions of lncRNAs by analysing the relationships between lncRNAs and mRNAs. Seven lncRNA-mRNA interaction pairs may participate in floral transition.ConclusionsThis study is the first to identify lncRNAs and their potential functions in floral transition, providing a starting point for detailed determination of the functions of lncRNAs in C. bungei.

Global Long Noncoding RNA and mRNA Expression Changes between Prenatal and Neonatal Lung Tissue in Pigs.

Lung tissue plays an important role in the respiratory system of mammals after birth. Early lung development includes six key stages, of which the saccular stage spans the pre- and neonatal periods and prepares the distal lung for alveolarization and gas-exchange. However, little is known about the changes in gene expression between fetal and neonatal lungs. In this study, we performed transcriptomic analysis of messenger RNA (mRNA) and long noncoding RNA (lncRNA) expressed in the lung tissue of fetal and neonatal piglets. A total of 19,310 lncRNAs and 14,579 mRNAs were identified and substantially expressed. Furthermore, 3248 mRNAs were significantly (FDR-adjusted p value ≤ 0.05, FDR: False Discovery Rate) differentially expressed and were mainly enriched in categories related to cell proliferation, immune response, hypoxia response, and mitochondrial activation. For example, CCNA2, an important gene involved in the cell cycle and DNA replication, was upregulated in neonatal lungs. We also identified 452 significantly (FDR-adjusted p value ≤ 0.05) differentially expressed lncRNAs, which might function in cell proliferation, mitochondrial activation, and immune response, similar to the differentially expressed mRNAs. These results suggest that differentially expressed mRNAs and lncRNAs might co-regulate lung development in early postnatal pigs. Notably, the TU64359 lncRNA might promote distal lung development by up-regulating the heparin-binding epidermal growth factor-like (HB-EGF) expression. Our research provides basic lung development datasets and will accelerate clinical researches of newborn lung diseases with pig models.

SQ1274, a novel microtubule inhibitor, inhibits ovarian and uterine cancer cell growth

ObjectivePaclitaxel, a microtubule inhibitor, is subject to tumor resistance while treating high-grade serous ovarian and uterine cancer. This study aims to directly compare the effects of SQ1274, a novel microtubule inhibitor that binds to the colchicine-binding site on tubulin, and paclitaxel in high-grade serous ovarian and uterine cancer cell lines both in vitro and in vivo. MethodsWe assessed the sensitivity of ovarian (OVCAR8) and uterine (ARK1) cancer cell lines to SQ1274 and paclitaxel using XTT assays. We used western blot and quantitative real-time PCR to analyze changes in AXL RNA and protein expression by SQ1274 and paclitaxel. Differences in cell-cycle arrest and apoptosis were investigated using flow cytometry. Finally, we treated ovarian and uterine xenograft models with vehicle, paclitaxel, or SQ1274. ResultsFirst, we demonstrate that SQ1274 has a much lower IC50 than paclitaxel in both ARK1 (1.26 nM vs. 15.34 nM, respectively) and OVCAR8 (1.34 nM vs. 10.29 nM, respectively) cancer cell lines. Second, we show SQ1274 decreases both RNA and protein expression of AXL. Third, we show that SQ1274 causes increased cell-cycle arrest and apoptosis compared to paclitaxel. Finally, we report that SQ1274 more effectively inhibits tumor growth in vivo compared to paclitaxel. ConclusionsSQ1274 presents as a viable alternative to paclitaxel for treating ovarian and uterine cancer. This study supports the development of SQ1274 as a chemotherapeutic to treat ovarian and uterine cancer.

MiR-3075 Inhibited the Migration of Schwann Cells by Targeting Cntn2

Peripheral nerve injury is a complex biological process that involves the expression changes of various coding and non-coding RNAs. Previously, a number of novel miRNAs that were dysregulated in rat sciatic nerve stumps after peripheral nerve injury were identified and functionally annotated by Solexa sequencing. In the current study, we studied one of these identified novel miRNAs, miR-3075, in depth. Results of transwell-based cell migration assay showed that increased expression of miR-3075 suppressed the migration rate of Schwann cells while decreased expression of miR-3075 elevated the migration rate of Schwann cells, demonstrating that miR-3075 inhibited Schwann cell migration. Results of BrdU cell proliferation assay showed that neither miR-3075 mimic nor miR-3075 inhibitor would affect Schwann cell proliferation. We further studied candidate target genes of miR-3075 by using bioinformatic tools and analyzing gene expression patterns and found that miR-3075 might target contactin 2 (Cntn2). Previous study showed that Cntn2 regulated cell migration and myelination. Our current observation suggested that the biological effects of miR-3075 on Schwann cell phenotype might by through the negative regulation of Cntn2. Overall, our study revealed the function of a novel miRNA, miR-3075, and expanded our current understanding of the molecular mechanisms underlying peripheral nerve injury and regeneration.

Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer

Pancreatic neuroendocrine tumors (pNETs) are uncommon cancers arising from pancreatic islet cells. Here we report the analysis of gene mutation, copy number, and RNA expression of 57 sporadic well-differentiated pNETs. pNET genomes are dominated by aneuploidy, leading to concordant changes in RNA expression at the level of whole chromosomes and chromosome segments. We observed two distinct patterns of somatic pNET aneuploidy that are associated with tumor pathology and patient prognosis. Approximately 26% of the patients in this series had pNETs with genomes characterized by recurrent loss of heterozygosity (LoH) of 10 specific chromosomes, accompanied by bi-allelic MEN1 inactivation and generally poor clinical outcome. Another ~40% of patients had pNETs that lacked this recurrent LoH pattern but had chromosome 11 LoH, bi-allelic MEN1 inactivation, and universally good clinical outcome. The somatic aneuploidy allowed pathogenic germline variants (e.g., ATM) to be expressed unopposed, with RNA expression patterns showing inactivation of downstream tumor suppressor pathways. No prognostic associations were found with tumor morphology, single gene mutation, or expression of RNAs reflecting the activity of immune, differentiation, proliferative or tumor suppressor pathways. In pNETs, single gene mutations appear to be less important than aneuploidy, with MEN1 the only statistically significant recurrently mutated driver gene. In addition, only one pNET in the series had clearly actionable single nucleotide variants (SNVs) (in PTEN and FLCN) confirmed by corroborating RNA expression changes. The two clinically relevant patterns of LoH described here define a novel oncogenic mechanism and a plausible route to genomic precision oncology for this tumor type.

Nanosecond pulsed electric field exposure does not induce the unfolded protein response in adult human dermal fibroblasts.

Cell-circuit models have suggested that nanosecond pulsed electric fields (nsPEFs) can disrupt intracellular membranes including endoplasmic reticulum (ER), mitochondria, and/or nucleus thereby inducing intrinsic apoptotic pathways. Therefore, we hypothesized that the unfolded protein response (UPR) would be activated, due to the fluctuations of ionic concentrations, upon poration of the ER membrane. Quantitative real-time polymerase chain reaction was utilized to measure changes in messenger RNA (mRNA) expression of specific ER stress genes in adult human dermal fibroblast (HDFa) cells treated with tunicamycin (TM) (known ER stress inducer) and cells exposed to nsPEFs (100, 10-ns pulses at 150 kV/cm delivered at a repetition rate of 1 Hz). For HDFa cells, results showed time-dependent UPR activation to TM; however, when HDFa cells were exposed to nsPEFs, no significant changes in mRNA expression of ER stress genes, and/or caspase gene were observed. These results indicate that although cell death can be observed under these exposure parameters, it is most likely not initiated through activation of the UPR. Bioelectromagnetics. 2018;39:491-499, 2018. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

Abstract CT010: Pharmacodynamic (PD) changes in tumor RNA expression and the peripheral blood T cell receptor (TCR) repertoire in a phase I study of OX40 agonistic monoclonal antibody (mAb) PF-04518600 (PF-8600)

Abstract Introduction: PF-8600 is a fully human IgG2 agonistic mAb against the tumor necrosis factor superfamily receptor OX40. OX40 improves T cell survival, proliferation, and activation and may enhance anti-tumor immunity. In an ongoing phase I study (NCT02315066) of 52 patients (pts) with melanoma, hepatocellular carcinoma, head and neck carcinoma, or renal cell carcinoma treated with PF-8600 monotherapy in dose escalation, 2 pts had best overall response of partial response (PR) and 27 of stable disease. PF-8600 was well-tolerated at all doses. Peripheral blood flow cytometry had previously shown increased proliferation and activation of CD4 central memory T cells at certain dose levels, suggesting a PD effect. RNAseq analysis of tumor biopsy samples and TCR sequencing of peripheral blood were used to further support proof of mechanism. Methods: Biopsy samples at baseline and wk 6 were collected from 5 dose cohorts [0.1 (4), 0.3 (3), 1.5 (4), 3.0 (3) and 10.0 (2), dose in mg/kg (n)]. Biopsy tissue was analyzed by RNAseq and gene ranking-based gene set enrichment analysis (FGSEA) to identify immune pathways potentially up-regulated by OX40. CD4/CD8 cells were isolated from peripheral blood samples from 4 dose cohorts (0.1, 0.3, 1.5, and 3.0 mg/kg). DNA was extracted for sequencing of the TCR-β chain complementarity-determining region 3 (CDR3). Results: In a combined analysis of samples from pts dosed with ≥1.5 mg/kg, the top 3 gene sets showing enrichment at wk 6 of therapy were associated with inflammatory response, interferon-γ response and allograft rejection. These gene sets were identical to the top 3 most enriched in tumor from a syngeneic mouse tumor model exposed to a murine OX40 agonist. This pattern of enrichment was not observed if samples from lower doses were included in the analysis. TCR sequencing revealed clonal expansion of CD4/CD8 T cells at all dose levels at wk 6 [CD4: mean = 8 expanded clones per 100,000 clones (range = 1 - 80), CD8: mean = 56 (range = 1 - 500)]. The 2 patients with PR had among the lowest numbers of expanded CD4 and CD8 clones (CD4: 4 and 2; CD8: 7 and 4). Conclusion: Enrichment of gene sets associated with immune activation in tumor tissue from patients dosed with PF-8600 provides evidence supporting an active, immunomodulatory mechanism. Peripheral CD4/CD8 T cell populations exhibited clonal expansion in response to dosing with PF-8600 at all dose levels further suggesting a PD effect. However, clinical response did not necessarily correlate with a high number of expanded T cell clones, suggesting that clinical response to OX-40 agonism may be driven by the expansion of select anti-tumor T cell clones rather than a broad expansion of T cell clones in the peripheral blood. The phase I study will continue to evaluate PD changes in the tumor and peripheral blood in dose-expansion cohorts of PF-8600 ± utomilumab. Citation Format: Adi Diab, Omid Hamid, John A. Thompson, Willeke Ros, Fredericus A. L. M. Eskens, Toshihiko Doi, Siwen Hu-Lieskovan, Hua Long, Tenshang Joh, Shoba Potluri, Xiao Wang, Catherine Fleener, Carrie Turich Taylor, Bishu J. Ganguli, Jeffrey Chou, Anthony B. El-Khoueiry. Pharmacodynamic (PD) changes in tumor RNA expression and the peripheral blood T cell receptor (TCR) repertoire in a phase I study of OX40 agonistic monoclonal antibody (mAb) PF-04518600 (PF-8600) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr CT010.

Abstract 5904: Post-transcriptional regulation of androgen receptor by DDX3 in prostate cancer progression

Abstract Purpose Prostate cancer (CaP) driven by androgen receptor (AR) can be targeted therapeutically by androgen deprivation therapy (ADT); however, in 10-20% of cases, ADT fails, allowing disease recurrence. Mechanisms for recurrence include dysregulation of AR at the gene, RNA, and protein level. Recently, AR negative cell growth has been implicated as a mechanism of resistance. This study aims to identify mechanisms of drug resistance in castration-resistant prostate cancer (CRPC) that can be exploited therapeutically to reduce disease recurrence. Experimental Procedures Using the BCaP model, a novel series of cell lines derived from a single human prostate epithelial cell, we can study the progression of CaP from benign to metastasis. Additionally, using the LNCaP-C4 series we can study progression to CRPC. To determine the RNA binding capacity of DDX3, we utilized 1) RIP-qPRC for identification of mRNA targets and 2) RNAscope for visual colocalization. Changes in RNA and protein expression were determined using qPCR, Western blot, and IF. Results DDX3 is an ATP-dependent RNA helicase that can aid translation of target mRNAs, or in stress conditions, form ribonucleoprotein granules that prevent translation. While DDX3 is implicated in several cancers, its role as a translational regulator in CaP remains unstudied. In BCaP and LNCaP-C4, DDX3 protein expression increases through progression, concurrent with localization to cytoplasmic puncta. RIP-qPCR identified AR as an mRNA target of DDX3 in the metastatic and CRPC cell lines. Because of the dual role of DDX3 in translational control, AR expression in these models was investigated; while AR mRNA expression increased through progression, AR protein expression decreased. Treatments in vitro with RK33, a commercially available inhibitor of DDX3, restored the protein expression of AR and downstream AR signaling (PSA, Nkx3.1). These data suggest DDX3 acts as a translational repressor of AR in metastasis and CRPC. To confirm that increased DDX3 expression is sufficient to reduce AR protein expression, we overexpressed DDX3 using two models: induced cellular stress and a DDX3 expression vector. Here, we saw DDX3 localized to puncta, and subsequent reduction in AR and PSA protein. Because DDX3 is sufficient to reduce AR protein expression in metastases and CRPC, co-treatment of DDX3 inhibitors with anti-androgen therapy may prevent AR negative cell growth underlying recurrence. in vitro co-treatments with RK33 and bicalutamide, an AR antagonist, show decreased proliferation compared to either treatment alone, suggesting increased efficacy of bicalutamide with DDX3 inhibition. Conclusions DDX3 as a repressor of AR translation could have clinical implications as a mechanism of resistance to ADT. Based on preliminary data, DDX3 could be contributing to the regulation of AR post-transcriptionally, and targeting DDX3 could reduce resistance and disease recurrence. Citation Format: Jordan E. Vellky, William Ricke. Post-transcriptional regulation of androgen receptor by DDX3 in prostate cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5904.

Unique patterns of trimethylation of histone H3 lysine 4 are prone to changes during aging in Caenorhabditis elegans somatic cells

Tri-methylation on histone H3 lysine 4 (H3K4me3) is associated with active gene expression but its regulatory role in transcriptional activation is unclear. Here we used Caenorhabditis elegans to investigate the connection between H3K4me3 and gene expression regulation during aging. We uncovered around 30% of H3K4me3 enriched regions to show significant and reproducible changes with age. We further showed that these age-dynamic H3K4me3 regions largely mark gene-bodies and are acquired during adult stages. We found that these adult-specific age-dynamic H3K4me3 regions are correlated with gene expression changes with age. In contrast, H3K4me3 marking established during developmental stages remained largely stable with age, even when the H3K4me3 associated genes exhibited RNA expression changes during aging. Importantly, the genes associated with changes in H3K4me3 and RNA levels with age are enriched for functional groups commonly implicated in aging biology. Therefore, our findings suggested divergent roles of H3K4me3 in gene expression regulation during aging, with important implications on aging-dependent pathophysiologies.

Distance running alters peripheral microRNAs implicated in metabolism, fluid balance, and myosin regulation in a sex-specific manner.

Microribonucleic acids (miRNAs) mediate adaptive responses to exercise and may serve as biomarkers of exercise intensity/capacity. Expression of miRNAs is altered in skeletal muscle, plasma, and saliva following exertion. Women display unique physiologic responses to endurance exercise, and miRNAs respond to pathologic states in sex-specific patterns. However sex-specific miRNA responses to exercise remain unexplored. This study utilized high-throughput RNA sequencing to measure changes in salivary RNA expression among 25 collegiate runners following a single long-distance run. RNA concentrations in pre- and post-run saliva was assessed through alignment and quantification of 4,694 miRNAs and 27,687 mRNAs. Pair-wise Wilcoxon rank-sum test identified miRNAs with significant [false discovery rate (FDR) < 0.05] post-run changes. Associations between miRNA levels and predicted mRNA targets were explored with Pearson correlations. Differences in miRNA patterns between men ( n = 13) and women ( n = 12) were investigated with two-way analysis of variance. Results revealed 122 salivary miRNAs with post-run changes. The eight miRNAs with the largest changes were miR-3671, miR-5095 (downregulated); and miR-7154-3p, miR-200b-5p, miR-5582-3p, miR-6859-3p, miR-6751-5p, miR-4419a (upregulated). Predicted mRNA targets for these miRNAs represented 15 physiologic processes, including glycerophospholipid metabolism (FDR = 0.042), aldosterone-regulated sodium reabsorption (FDR = 0.049), and arrhythmogenic ventricular cardiomyopathy (FDR = 0.018). Twenty-six miRNA/mRNA pairs had associated changes in post-run levels. Three miRNAs (miR-4675, miR-6745, miR-6746-3p) demonstrated sex-specific responses to exercise. Numerous salivary miRNAs change in response to endurance running and target the expression of genes involved in metabolism, fluid balance, and musculoskeletal adaptations. A subset of miRNAs may differentiate the metabolic response to exercise in men and women.

MicroRNA 125a Regulates MHC-I Expression on Esophageal Adenocarcinoma Cells, Associated With Suppression of Antitumor Immune Response and Poor Outcomes of Patients

Immune checkpoint inhibition may affect growth or progression of highly aggressive cancers, such as esophageal adenocarcinoma (EAC). We investigated the regulation of expression of major histocompatibility complex, class 1 (MHC-I) proteins (encoded by HLA-A, HLA-B, and HLA-C) and the immune response to EACs in patient samples. We performed quantitative polymerase chain reaction array analyses of OE33 cells and OE19 cells, which express different levels of the ATP binding cassette subfamily B member 1 (TAP1) and TAP2, required for antigen presentation by MHC-I, to identify microRNAs (miRNAs) that regulate their expression. We performed luciferase assays to validate interactions between miRNAs and potential targets. We overexpressed candidate miRNAs in OE33, FLO-1, and OACP4 C cell lines and performed quantitative polymerase chain reaction, immunoblot, and flow cytometry analyses to identify changes in messenger RNA (mRNA) and protein expression; we studied the effects of cytotoxic T cells. We performed miRNA in situ hybridization, RNA-sequencing, and immunohistochemical analyses of tumor tissues from 51 untreated patients with EAC inthe Netherlands. Clinical and survival data were collected for patients, and EAC subtypes were determined. We found OE19 cells to have increased levels of 7 miRNAs. Of these, we found binding sites for miRNA 125a (MIR125a)-5p in the 3' untranslated region of the TAP2 mRNA and binding sites for MIR148a-3p in 3' untranslated regions of HLA-A, HLA-B, and HLA-C mRNAs. Overexpression of these miRNAs reduced expression of TAP2 in OE33, FLO-1, and OACP4 C cells, and reduced cell-surface levels of MHC-I. OE33 cells that expressed the viral peptide BZLF1 were killed by cytotoxic T cells, whereas OE33 that overexpressed MIR125a-5p or MIR 148a along with BZLF1 were not. In EAC and nontumor tissues, levels of MIR125a-5p correlated inversely with levels of TAP2 protein. High expression of TAP1 by EAC correlated with significantly shorter overall survival times of patients. EACs that expressed high levels of TAP1 and genes involved in antigen presentation also expressed high levels of genes that regulate the adaptive immune response, PD-L1, PD-L2, and IDO1; these EACs had a poor response to neoadjuvant chemoradiotherapy and associated with shorter overall survival times of patients. In studies of EAC cell lines andtumor tissues, we found increased levels of MIR125a-5p and MIR148a-3p to reduce levels of TAP2 and MHC-I, required for antigen presentation. High expression of MHC-I molecules by EAC correlated with markers of an adaptive immune response and significantly shorter overall survival times of patients.

Skeletal muscle-specific Sidt2 knockout in mice induced muscular dystrophy-like phenotype

BackgroundSidt2 is an integral lysosomal membrane protein. Previously, we generated a Sidt2 global knockout mouse and found impaired insulin secretion, along with skeletal muscle pathology. MethodsA mouse model with a muscle-specific knockout of the Sidt2 gene (Sidt2f/fCre) had been generated, to which extensive morphologic study as well as functional study was applied to investigate the direct role of Sidt2 on skeletal muscle tissue in vivo. Secondly, the autophagy-lysosomal pathway was examined by Western blot and immunostaining. Additionally, RNA expression changes in Sidt2f/fCre mice were analyzed by genechip. ResultsSidt2 deficiency in skeletal muscle results in pathognomonic hallmarks of muscular dystrophy, including muscle mass decrease, muscle weakness, fibrosis, central nucleation, fiber regeneration, mildly elevated serum creatine kinase, and dramatically elevated sarcolipin mRNA. Along with accumulation of autophagolysomes, LC3-II, adaptor protein p62, ubiquitinated aggregates, and Lamp2-positive vacuoles were increased significantly in Sidt2f/fCre skeletal muscle fibers. However, only lysosomal-related genes were upregulated, while the genes upstream of the autophagy pathway were unchanged. Simultaneously, the proteasome chymotryptic activity and the lysosomal soluble enzyme activity were unimpaired, which largely excluded the possibility of proteasome chymotryptic activity defect and the lysosomal soluble enzyme defect leading to ubiquitinated aggregates accumulation. ConclusionWe concluded that Sidt2 deficiency leads to muscular dystrophy-like phenotype in mice and Sidt2 plays a critical role in the late stage of autophagy.

Evaluating the Effects of Systemic, Exercise-Induced Skeletal Muscle Injury using Whole Transcriptome Sequencing

Abstract Recent advances in next generation sequencing have dramatically reduced the cost of whole transcriptome sequencing to measure differential gene expression. Extreme physical performances represent a unique model for investigating the combined effects of oxidative stress and eccentric muscle contraction on systemic skeletal muscle injury outcomes. Studying changes in whole transcriptome RNA expression may allow identification of specific potential treatment targets for a variety of disease states associated with chronic inflammation and oxidative stress. The purpose of this study was to investigate changes in whole transcriptome RNA expression in response to prolonged endurance running. The protocols were approved by the University IRB committee (in accordance with the latest Declaration of Helsinki) and subjects gave written informed consent to participate. Blood samples were collected in PAXgene RNA tubes at baseline, 4-h, and 24-h after performing a half-marathon race. After collection, tubes were frozen and total RNA was extracted and verified using accepted methods. RNAseq analysis was conducted using an Illumina NextSeq 500 sequencing platform. RNAseq analysis revealed distinct changes in injury, inflammation, anti-oxidant defense, and stress-associated RNA expression with responses appearing more pronounced at 24-h compared to 4-h post-race. These results confirm the systemic changes that occur following whole-body exercise-induced muscle injury in a human model. The next step in this research is to test potential therapeutic strategies to determine their effectiveness on altering the changes in the transcriptome.

Molecular Response to Neoadjuvant Chemotherapy in High-Grade Serous Ovarian Carcinoma.

While high-grade serous ovarian carcinoma (HGSOC) is the most common histologic subtype of ovarian cancer, significant tumor heterogeneity exists. In addition, chemotherapy induces changes in gene expression and alters the mutational profile. To evaluate the notion that patients with HGSOC could be better classified for optimal treatment based on gene expression, we compared genetic variants [by DNA next-generation sequencing (NGS) using a 50 gene Ion Torrent panel] and gene expression (using the NanoString PanCancer 770 gene Panel) in the tumor from 20 patients with HGSOC before and after neoadjuvant chemotherapy (NACT). NGS was performed on plasma cell free DNA (cfDNA) on a select group of patients (n = 14) to assess the utility of using cfDNA to monitor these changes. A total of 86 genes had significant changes in RNA expression after NACT. Thirty-eight genetic variants (including SNPs) from 6 genes were identified in tumors pre-NACT, while 59 variants from 19 genes were detected in the cfDNA. The number of DNA variants were similar after NACT. Of the 59 variants in the plasma pre-NACT, only 6 persisted, whereas 33 of 38 specific variants in the tumor DNA remained unchanged. Pathway analysis showed the most significant alterations in the cell cycle and DNA damage pathways.Implications: Gene expression profiles at the time of interval debulking provide additional genetic information that could help impact treatment decisions after NACT; although, continued collection and analysis of matched tumor and cfDNA from multiple time points are needed to determine the role of cfDNA in the management of HGSOC. Mol Cancer Res; 16(5); 813-24. ©2018 AACR.

Combinatory RNA-Sequencing Analyses Reveal a Dual Mode of Gene Regulation by ADAR1 in Gastric Cancer.

Adenosine deaminase acting on RNA 1 (ADAR1) is known to mediate deamination of adenosine-to-inosine through binding to double-stranded RNA, the phenomenon known as RNA editing. Currently, the function of ADAR1 in gastric cancer is unclear. This study was aimed at investigating RNA editing-dependent and editing-independent functions of ADAR1 in gastric cancer, especially focusing on its influence on editing of 3' untranslated regions (UTRs) and subsequent changes in expression of messenger RNAs (mRNAs) as well as microRNAs (miRNAs). RNA-sequencing and small RNA-sequencing were performed on AGS and MKN-45 cells with a stable ADAR1 knockdown. Changed frequencies of editing and mRNA and miRNA expression were then identified by bioinformatic analyses. Targets of RNA editing were further validated in patients' samples. In the Alu region of both gastric cell lines, editing was most commonly of the A-to-I type in 3'-UTR or intron. mRNA and protein levels of PHACTR4 increased in ADAR1 knockdown cells, because of the loss of seed sequences in 3'-UTR of PHACTR4 mRNA that are required for miRNA-196a-3p binding. Immunohistochemical analyses of tumor and paired normal samples from 16 gastric cancer patients showed that ADAR1 expression was higher in tumors than in normal tissues and inversely correlated with PHACTR4 staining. On the other hand, decreased miRNA-148a-3p expression in ADAR1 knockdown cells led to increased mRNA and protein expression of NFYA, demonstrating ADAR1's editing-independent function. ADAR1 regulates post-transcriptional gene expression in gastric cancer through both RNA editing-dependent and editing-independent mechanisms.

Changes in the Messenger RNA Expression of Toll-Like Receptors 2 and 4 in Healthy Infants According to Age.

Toll-like receptors (TLRs) are potentially useful indicators of several pediatric disease states. Here, we explore the mechanisms by which inflammation is regulated by interactions between microbiota and the host. Little data are available regarding the expression of TLRs in postnatal healthy infants. TLR 2 and TLR4 are extracellular TLRs that act as innate immune receptors by recognizing a wide range of endogenous ligands and microorganisms. The aim of this study was to use real-time polymerase chain reaction to investigate the expression of the messenger RNAs (mRNAs) of TLR2 and TLR4 in blood samples obtained from healthy full-term infants and toddlers. We analyzed the mRNA expression levels of TLRs in 88 healthy term children separated according to age. The median expression level of TLR2 was 1.49 ± 1.10 arbitrary units (AU) (n = 25) in infants younger than 3 months, 0.67 ± 0.72 AU (n = 25) in infants aged between 3 and 12 months, and 0.03 ± 0.02 AU (n= 38) in infants older than 12 months. The median expression level of TLR4 was 1.25 ± 0.79 AU (n = 25) in infants younger than 3 months, 0.75 ± 0.54 AU (n = 25) in infants aged 3 to 12 months, and 0.44 ± 0.28 AU (n = 38) in infants older than 12 months. There was difference in the mRNA expression level of TLR2 and TLR4 between infants aged 0 to 3 and 3 to 12 months and those aged more than 1 year (p < 0.0001 and p < 0.0001, respectively) CONCLUSION: We found that the expression levels of TLR2 and TLR4 were associated with age. In particular, we observed that their expression increased during the suckling period and then clearly decreased once the infants reached 1 year of age (p < 0.001). These findings could be related to microbial colonization and the immune system.