Genes Overlapped Research Articles

Estrogen receptor β exerts tumor suppressive effects in prostate cancer through repression of androgen receptor activity.

Estrogen receptor β (ERβ) was first identified in the rodent prostate and is abundantly expressed in human and rodent prostate epithelium, stroma, immune cells and endothelium of the blood vessels. In the prostates of mice with inactivated ERβ, mutant phenotypes include epithelial hyperplasia and increased expression of androgen receptor (AR)-regulated genes, most of which are also upregulated in prostate cancer (PCa). ERβ is expressed in both basal and luminal cells in the prostate while AR is expressed in luminal but not in the basal cell layer which harbors the prostate stem cells. To investigate the mechanisms of action of ERβ and its potential cross-talk with AR, we used RNA-seq to study the effects of estradiol or the synthetic ligand, LY3201, in AR-positive LNCaP PCa cells which had been engineered to express ERβ. Transcriptomic analysis indicated relatively few changes in gene expression with ERβ overexpression, but robust responses following ligand treatments. There is significant overlap of responsive genes between the two ligands, estradiol and LY3201 as well as ligand-specific alterations. Gene set analysis of down-regulated genes identified an enrichment of androgen-responsive genes, such as FKBP5, CAMKK2, and TBC1D4. Consistently, AR transcript, protein levels, and transcriptional activity were down-regulated following ERβ activation. In agreement with this, we find that the phosphorylation of the CAMKK2 target, AMPK, was repressed by ligand-activated ERβ. These findings suggest that ERβ-mediated signaling pathways are involved in the negative regulation of AR expression and activity, thus supporting a tumor suppressive role for ERβ in PCa.

Transcriptome profiling of differentiated lenses through RNA sequencing

Objective: To gain insight into the transcriptional landscape including mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) of the differentiated lens. Methods: Experiment research. The total RNAs of the differentiated lenses were extracted and purified. Total RNAs of 16-week, 23-week, and 25-week differentiated lenses were then sequenced using Illumina HiSeq 2500, and analyzed using bioinformatics tools. The top expressed and differentially expressed mRNAs and lncRNAs were screened. The expressions of overlap genes among the 16-week, 23-week, and 25-week lenses were analyzed by Venn diagram. The expression tendency of lens-specific genes was obtained and verified with real-time polymerase chain reaction. Results: A total of 67 518 311 mapped reads were obtained from differentiated lenses at 16 weeks, 99 440 160 at 23 weeks, and 67 262 320 at 25 weeks. The gene overlap expression analysis showed 740 of the top 1 000 highly expressed mRNAs, 170 of the top 300 highly expressed lncRNAs, and 69 of the top 100 highly expressed circRNAs overlapping expressed in lenses at 16, 23, and 25 weeks, respectively. Lens specific gene expression analysis revealed that the expression of crystallin (CRY) AA, CRYGA, CRYGB, CRYGC, CRYGD, CRYGEP, and CRYGS was upregulated, while the expression of gap junction (GJ) A3 and GJA8 was downregulated with the differentiation of lenses. Conclusion: The lens transcriptome profile shows that more than half of the high expressed mRNA, lncRNA and circRNA at different differentiation stages are overlapping expressed, and all of them have high expression of lens specific protein genes, such as CRY, GJ etc. (Chin J Ophthalmol, 2020, 56: 356-363).

Reference genome and annotation updates lead to contradictory prognostic predictions in gene expression signatures: a case study of resected stage I lung adenocarcinoma.

RNA-sequencing enables accurate and low-cost transcriptome-wide detection. However, expression estimates vary as reference genomes and gene annotations are updated, confounding existing expression-based prognostic signatures. Herein, prognostic 9-gene pair signature (GPS) was applied to 197 patients with stage I lung adenocarcinoma derived from previous and latest data from The Cancer Genome Atlas (TCGA) processed with different reference genomes and annotations. For 9-GPS, 6.6% of patients exhibited discordant risk classifications between the two TCGA versions. Similar results were observed for other prognostic signatures, including IRGPI, 15-gene and ORACLE. We found that conflicting annotations for gene length and overlap were the major cause of their discordant risk classification. Therefore, we constructed a prognostic 40-GPS based on stable genes across GENCODE v20-v30 and validated it using public data of 471 stage I samples (log-rank P < 0.0010). Risk classification was still stable in RNA-sequencing data processed with the newest GENCODE v32 versus GENCODE v20-v30. Specifically, 40-GPS could predict survival for 30 stage I samples with formalin-fixed paraffin-embedded tissues (log-rank P = 0.0177). In conclusion, this method overcomes the vulnerability of existing prognostic signatures due to reference genome and annotation updates. 40-GPS may offer individualized clinical applications due to its prognostic accuracy and classification stability.

Phylogenetic relationships of Limacodidae and insights into the higher phylogeny of Lepidoptera

To determine the systematic status of family Limacodidae within Lepidoptera, the complete mitochondrial genome (mitogenome) of Thosea sinensis (Lepidoptera: Zygaenoidea: Limacodidae) was sequenced. The genome is 15,544 base pairs (bp), including 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and an AT-rich region. These characteristics are similar to of other lepidopterans. The gene order of T. sinensis is identical to that of Ditrysia lepidopterans. The nucleotide composition of the T. sinensis mitochondrial genome is highly biased toward A + T nucleotides (81.1%) and exhibits negative AT and GC skew. All the other 13 PCGs except cox1 are initiated by ATN codons. All tRNA genes are folded into the typical cloverleaf secondary structure, except for trnS1, which lacked the dihydrouridine (DHU) stem. There are 20 intergenic spacer regions ranging from 1 to 56 bp in length, and two gene overlap regions throughout the entire genome. The AT-rich region includes the ATAGA motif, followed by a 19-bp poly T stretch, a microsatellite-like (AT)10, and a poly-A element. Analysis of phylogenetic relationships indicated that T. sinensis belongs to the Limacodidae, and the monophyly of each lepidopteran family was well supported.

Limited application of IL-2/CD25 leads to persistent IL-2R signaling that promotes gene expression for Treg expansion

Abstract Low-dose IL-2 expands Tregs to suppress autoimmunity. However, IL-2 has a short half-life that necessitates frequent administration to maintain increased Treg levels. To improve low-dose IL-2 therapy, we developed an IL-2-based fusion protein, mouse IL-2/CD25, that substantially increases IL-2 half-life to more effectively boost Tregs that controls diabetes in NOD mice. To provide a molecular underpinning for the Treg response to IL-2/CD25, transcriptional profiling was performed by RNAseq for purified Tregs from C57BL/6 mice that received an equivalent amount of IL-2 or IL-2/CD25. Initially, at 4 hr post-injection, differential gene expression analysis revealed a large overlap in significant genes modulated by IL-2 or IL-2/CD25. In striking contrast, at 16 and 72 hr post-injection, only IL-2/CD25 persistently modulated gene expression, with the largest number of IL-2-dependent genes detected at 72 hrs. Canonical pathway analysis revealed many interrelated pathways that control cell growth and signaling. This gene expression pattern by IL-2/CD25, but not IL-2, was also associated with extended STAT5 activation and expansion of Tregs with molecular and phenotypic changes corresponding to activated Tregs. IL-2/CD25 also enhanced gene expression associated with glycolysis and the mitochondrial electron transport chain. Seahorse analysis confirmed that IL-2/CD25 shifted Tregs to a more energetic metabolic phenotype due to an increase in mitocondrial ATP. Collectively, these findings demonstrate that a single injection of IL-2/CD25 persistently stimulates Tregs to activate gene expression to enhance Treg metabolism to fulfill the bio-energetic and biosynthetic demands of activation and proliferation.

An Epigenetic Signature for Within-Generational Plasticity of a Reef Fish to Ocean Warming

Elevated temperature can have detrimental effects on the physiological performance of many marine organisms. However, phenotypic plasticity may enable some populations to maintain their performance under thermal stress. Two longitudinally separated populations of the coral reef fish, Acanthochromis polyacanthus from the Great Barrier Reef have shown differing capacities for thermal plasticity – the southernmost Heron Island population restored aerobic scope within one generation at a higher temperature, whereas the northernmost Palm Island population restored aerobic scope only when two generations were exposed to warmer conditions. We recently discovered an epigenetic signature associated with transgenerational plasticity in the Palm Island population. Here, we aimed to determine if epigenetic changes are also associated with the within-generational plasticity observed in the Heron Island population and, if so, how this epigenetic signature compares to the Palm Island transgenerational epigenome. By sequencing and analyzing the genome-wide DNA methylome of fish reared at control (+0°C) or elevated temperatures (+1.5 and +3°C) since early life, we identified 480 differentially methylated genomic regions and 372 adjacent protein-coding genes associated with within-generational plasticity in the Heron Island population. Functions related to insulin, cardiovascular capacity, development, and heat response were significantly enriched in differentially methylated genes, suggesting that these functions are the core mechanisms for within-generational restoration of aerobic scope. Comparison to the differentially methylated genes identified from F2 Palm Island population revealed little overlap of genes and enriched functions, indicating that distinct genetic toolkits may be used for within- and between-generational plasticity to ocean warming in the same species from different latitudes.

ImmuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking.

SummaryB- and T-cell receptor repertoires of the adaptive immune system have become a key target for diagnostics and therapeutics research. Consequently, there is a rapidly growing number of bioinformatics tools for immune repertoire analysis. Benchmarking of such tools is crucial for ensuring reproducible and generalizable computational analyses. Currently, however, it remains challenging to create standardized ground truth immune receptor repertoires for immunoinformatics tool benchmarking. Therefore, we developed immuneSIM, an R package that allows the simulation of native-like and aberrant synthetic full-length variable region immune receptor sequences by tuning the following immune receptor features: (i) species and chain type (BCR, TCR, single and paired), (ii) germline gene usage, (iii) occurrence of insertions and deletions, (iv) clonal abundance, (v) somatic hypermutation and (vi) sequence motifs. Each simulated sequence is annotated by the complete set of simulation events that contributed to its in silico generation. immuneSIM permits the benchmarking of key computational tools for immune receptor analysis, such as germline gene annotation, diversity and overlap estimation, sequence similarity, network architecture, clustering analysis and machine learning methods for motif detection.Availability and implementationThe package is available via https://github.com/GreiffLab/immuneSIM and on CRAN at https://cran.r-project.org/web/packages/immuneSIM. The documentation is hosted at https://immuneSIM.readthedocs.io.Contact sai.reddy@ethz.ch or victor.greiff@medisin.uio.noSupplementary information Supplementary data are available at Bioinformatics online.

Supportive care medications coinciding with chemotherapy among children with hematologic malignancy

Pharmacokinetic (PK) conflicts can arise between supportive care medications (SCM) and chemotherapy in children with hematologic malignancy (HM). In this retrospective study, medical records for children (28 days–18 years) diagnosed with HM and receiving an SCM antimicrobial were collected from a hospital network between 1 May 2000 and 31 December 2014. PK drug–gene associations were obtained from a curated pharmacogenomics database. Among 730 patients (median age of 7.5 (IQR 3.7–13.9) years), primarily diagnosed with lymphoid leukemia (52%), lymphoma (28%), or acute myeloid leukemia (16%), chemotherapy was administered in 2846 hospitalizations. SCM accounted for 90.5% (n = 448) of distinct drugs with 93% (n = 679) of children, receiving ≥5 different SCM/hospitalization. Same-day SCM/chemotherapeutic PK gene overlap occurred in 48.3% of hospitalizations and was associated with age (p = 0.026), number of SCM, HM subtype, surgery, and hematopoietic stem cell transplant (p < 0.0001). A high and variable SCM burden among children with HM receiving chemotherapy poses a risk for unanticipated PK conflicts.

Hippocampal subfield transcriptome analysis in schizophrenia psychosis.

We have previously demonstrated functional and molecular changes in hippocampal subfields in individuals with schizophrenia (SZ) psychosis associated with hippocampal excitability. In this study, we use RNA-seq and assess global transcriptome changes in the hippocampal subfields, DG, CA3, and CA1 from individuals with SZ psychosis and controls to elucidate subfield-relevant molecular changes. We also examine changes in gene expression due to antipsychotic medication in the hippocampal subfields from our SZ ON- and OFF-antipsychotic medication cohort. We identify unique subfield-specific molecular profiles in schizophrenia postmortem samples compared with controls, implicating astrocytes in DG, immune mechanisms in CA3, and synaptic scaling in CA1. We show a unique pattern of subfield-specific effects by antipsychotic medication on gene expression levels with scant overlap of genes differentially expressed by SZ disease effect versus medication effect. These hippocampal subfield changes serve to confirm and extend our previous model of SZ and can explain the lack of full efficacy of conventional antipsychotic medication on SZ symptomatology. With future characterization using single-cell studies, the identified distinct molecular profiles of the DG, CA3, and CA1 in SZ psychosis may serve to identify further potential hippocampal-based therapeutic targets.

Evaluation via Supervised Machine Learning of the Broiler Pectoralis Major and Liver Transcriptome in Association With the Muscle Myopathy Wooden Breast.

The muscle myopathy wooden breast (WB) has recently appeared in broiler production and has a negative impact on meat quality. WB is described as hard/firm consistency found within the pectoralis major (PM). In the present study, we use machine learning from our PM and liver transcriptome dataset to capture the complex relationships that are not typically revealed by traditional statistical methods. Gene expression data was evaluated between the PM and liver of birds with WB and those that were normal. Two separate machine learning algorithms were performed to analyze the data set including the sequential minimal optimization (SMO) of support vector machines (SVMs) and Multilayer Perceptron (MLP) Artificial Neural Network (ANN). Machine learning algorithms were compared to identify genes within a gene expression data set of approximately 16,000 genes for both liver and PM, which can be correctly classified from birds with or without WB. The performance of both machine learning algorithms SMO and MLP was determined using percent correct classification during the cross-validations. By evaluating the WB transcriptome datasets by 5× cross-validation using ANNs, the expression of nine genes ranked based on Shannon Entropy (Information Gain) from PM were able to correctly classify if the individual bird was normal or exhibited WB 100% of the time. These top nine genes were all protein coding and potential biomarkers. When PM gene expression data were evaluated between normal birds and those with WB using SVMs they were correctly classified 95% of the time using 450 of the top genes sorted ranked based on Shannon Entropy (Information Gain) as a preprocessing step. When evaluating the 450 attributes that were 95% correctly classified using SVMs through Ingenuity Pathway Analysis (IPA) there was an overlap in top genes identified through MLP. This analysis allowed the identification of critical transcriptional responses for the first time in both liver and muscle during the onset of WB. The information provided has revealed many molecules and pathways making up a complex molecular mechanism involved with the progression of wooden breast and suggests that the etiology of the myopathy is not limited to activity in the muscle alone, but is an altered systemic pathology.

Identification of environmental chemicals targeting miscarriage genes and pathways using the comparative toxicogenomics database

BackgroundMiscarriage is a prevalent public health issue and many events occur before women are aware of their pregnancy, complicating research design. Thus, risk factors for miscarriage are critically understudied. Our goal was to identify environmental chemicals with a high number of interactions with miscarriage genes, based on known toxicogenomic responses. MethodsWe used miscarriage (MeSH: D000022) and chemical gene lists from the Comparative Toxicogenomics Database in human, mouse, and rat. We assessed enrichment for gene ontology biological processes among the miscarriage genes. We prioritized chemicals (n = 25) found at Superfund sites or in the blood or urine pregnant women. For chemical-disease gene sets of sufficient size (n = 13 chemicals, n = 20 comparisons), chi-squared enrichment tests and proportional reporting ratios (PRR) were calculated. We cross-validated enrichment results. ResultsMiscarriage was annotated with 121 genes and overrepresented in inflammatory response (q = 0.001), collagen metabolic process (q = 1 × 10−13), cell death (q = 0.02), and vasculature development (q = 0.005) pathways. The number of unique genes annotated to a chemical ranged from 2 (bromacil) to 5607 (atrazine). In humans, all chemicals tested were highly enriched for miscarriage gene overlap (all p < 0.001; parathion PRR = 7, cadmium PRR = 6.5, lead PRR = 3.9, arsenic PRR = 3.5, atrazine PRR = 2.8). In mice, highest enrichment (p < 0.001) was observed for naphthalene (PRR = 16.1), cadmium (PRR = 12.8), arsenic (PRR = 11.6), and carbon tetrachloride (PRR = 7.7). In rats, we observed highest enrichment (p < 0.001) for cadmium (PRR = 8.7), carbon tetrachloride (PRR = 8.3), and dieldrin (PRR = 5.3). Our findings were robust to 1000 permutations each of variable gene set sizes. ConclusionWe observed chemical gene sets (parathion, cadmium, naphthalene, carbon tetrachloride, arsenic, lead, dieldrin, and atrazine) were highly enriched for miscarriage genes. Exposures to chemicals linked to miscarriage, and thus linked to decreased probability of live birth, may limit the inclusion of fetuses susceptible to adverse birth outcomes in epidemiology studies. Our findings have critical public health implications for successful pregnancies and the interpretation of adverse impacts of environmental chemical exposures on pregnancy.

Abstract P3-09-05: Predictive markers of response to durvalumab concurrent with nab-paclitaxel and dose dense doxorubicin cyclophosphamide (ddAC) neoadjuvant therapy for triple negative breast cancer (TNBC)

Abstract Background: The goal of this analysis was to identify immune cell types and mRNA expression signatures that are associated with pathologic complete response (pCR: ypT0/N0) to neoadjuvant durvalumab concurrent with weekly nab-paclitaxel (100 mg/m2) x 12 followed by ddAC x 4 chemotherapy in stage I-III triple negative breast cancer (TNBC). Methods: Pre-treatment core needle biopsies were obtained from 57 patients (n=25 pCR, n=32 residual disease (RD)) who participated in Phase I/II clinical trial (NCT02489448) for RNA sequencing and histology assessment. Formalin-fixed paraffin-embedded (FFPE) core biopsies were stained by immunofluorescence for CD8, CD68 and cytokeratin, images were acquired on the Vectra-Polaris system and analyzed using InForm software with the adaptive segmentation into three compartments: Tumor, Stroma, and All (Tumor + Stroma). Correlation between immune cell density in the tissue compartments and pCR was assessed. RNA was extracted from core biopsies collected into RNAlater and poly-A enriched mRNAs were sequenced on Illumina platform using NovaSeq paired-end, 100bp fragments, with a depth of 50 million reads. Six specimens failed QC due to insufficient tumor cells in the sample. Correlation between pCR and immune markers and previously published immune, proliferation and DNA damage response deficiency (DDRD) gene signatures were assessed using logistic regression. Due to high overlap of genes across signatures, no multiple testing correction was done. Differentially expressed genes were found using DESeq2 R package with Benjamini-Hochberg correction for multiple testing. Broadside, an interaction mining tool, was used to extract sets of combinations of genes associated with pathologic response. Results: In cases with pCR, we detected significantly higher overall CD8 cell density and a trend for higher CD8 in tumor and stroma compartments. There was no significant difference in CD68 cell density between response groups. At the RNA level, high expression of DDRD, IFNγ, T-cell, B-cell, dendritic cell, M1 macrophage signatures and the tumor inflammation gene signature were significantly associated with higher rate of pCR. High expression of epithelial mesenchymal transition and TGFβ and IL8/VEGF gene signatures were associated with higher rate of residual disease. Proliferation gene signatures were not associated with response in this TNBC population. At individual gene level, the highest pCR predictive value was observed for the STAT1 + PCF11 and LAMP3 + SDR39U1 doublets. Conclusion: High CD8 cell density, high expression of a broad range of immune gene expression signatures and DNA damage response deficiency are associated with greater sensitivity to neoadjuvant anti-PD-L1 and chemotherapy. Citation Format: Kim RM Blenman, Xiaotong Li, Michal Marczyk, Tess O'Meara, Vesal Yaghoobi, Vignesh Gunasekharan, Tristen Park, David Rimm, Lajos Pusztai. Predictive markers of response to durvalumab concurrent with nab-paclitaxel and dose dense doxorubicin cyclophosphamide (ddAC) neoadjuvant therapy for triple negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-09-05.

Transcriptomic Features of T Cell-Barren Tumors Are Conserved Across Diverse Tumor Types.

Background: Understanding how tumors subvert immune destruction is essential to the development of cancer immunotherapies. New evidence suggests that tumors limit anti-tumor immunity by exploiting transcriptional programs that regulate intratumoral trafficking and accumulation of effector cells. Here, we investigated the gene expression profiles that distinguish immunologically “cold” and “hot” tumors across diverse tumor types.Methods: RNAseq profiles of tumors (n = 8,920) representing 23 solid tumor types were analyzed using immune gene signatures that quantify CD8+ T cell abundance. Genes and pathways associated with a low CD8+ T cell infiltration profile (CD8-Low) were identified by correlation, differential expression, and statistical ranking methods. Gene subsets were evaluated in immunotherapy treatment cohorts and functionally characterized in cell lines and mouse tumor models.Results: Among different cancer types, we observed highly significant overlap of genes enriched in CD8-Low tumors, which included known immunomodulatory genes (e.g., BMP7, CMTM4, KDM5B, RCOR2) and exhibited significant associations with Wnt signaling, neurogenesis, cell-cell junctions, lipid biosynthesis, epidermal development, and cancer-testis antigens. Analysis of mutually exclusive gene clusters demonstrated that different transcriptional programs may converge on the T cell-cold phenotype as well as predict for response and survival of patients to Nivo treatment. Furthermore, we confirmed that a top-ranking candidate belonging to the TGF-β superfamily, BMP7, negatively regulates CD8+ T cell abundance in immunocompetent murine tumor models, with and without anti-PD-L1 treatment.Conclusions: This study presents the first evidence that solid tumors of diverse anatomical origin acquire conserved transcriptional alterations that may be operative in the T cell-cold state. Our findings demonstrate the potential clinical utility of CD8-Low tumor-associated genes for predicting patient immunotherapy outcomes and point to novel mechanisms with potential for broad therapeutic exploitation.

Sex differences in adult mood and in stress-induced transcriptional coherence across mesocorticolimbic circuitry

Women are approximately two times as likely to be diagnosed with major depressive disorder (MDD) compared to men. While sex differences in MDD might be driven by circulating gonadal hormones, we hypothesized that developmental hormone exposure and/or genetic sex might play a role. Mice were gonadectomized in adulthood to isolate the role of developmental hormones. We examined the effects of developmental gonadal and genetic sex on anhedonia-/depressive-like behaviors under non-stress and chronic stress conditions and performed RNA-sequencing in three mood-relevant brain regions. We used an integrative network approach to identify transcriptional modules and stress-specific hub genes regulating stress susceptibility, with a focus on whether these differed by sex. After identifying sex differences in anhedonia-/depressive-like behaviors (female > male), we show that both developmental hormone exposure (gonadal female > gonadal male) and genetic sex (XX > XY) contribute to the sex difference. The top biological pathways represented by differentially expressed genes were related to immune function; we identify which differentially expressed genes are driven by developmental gonadal or genetic sex. There was very little overlap in genes affected by chronic stress in males and females. We also identified highly co-expressed gene modules affected by stress, some of which were affected in opposite directions in males and females. Since all mice had equivalent hormone exposure in adulthood, these results suggest that sex differences in gonadal hormone exposure during sensitive developmental periods program adult sex differences in mood, and that these sex differences are independent of adult circulating gonadal hormones.

Neutrophil-Related Oxidants Drive Heart and Brain Remodeling After Ischemia/Reperfusion Injury.

The inflammatory response associated with myocardial and brain ischemia/reperfusion injury (IRI) is a critical determinant of tissue necrosis, functional organ recovery, and long-term clinical outcomes. In the post-ischemic period, reactive oxygen species (ROS) are involved in tissue repair through the clearance of dead cells and cellular debris. Neutrophils play a critical role in redox signaling due to their early recruitment and the large variety of released ROS. Noteworthy, ROS generated during IRI have a relevant role in both myocardial healing and activation of neuroprotective pathways. Anatomical and functional differences contribute to the responses in the myocardial and brain tissue despite a significant gene overlap. The exaggerated activation of this signaling system can result in adverse consequences, such as cell apoptosis and extracellular matrix degradation. In light of that, blocking the ROS cascade might have a therapeutic implication for cardiomyocyte and neuronal loss after acute ischemic events. The translation of these findings from preclinical models to clinical trials has so far failed because of differences between humans and animals, difficulty of agents to penetrate into specific cellular organs, and specifically unravel oxidant and antioxidant pathways. Here, we update knowledge on ROS cascade in IRI, focusing on the role of neutrophils. We discuss evidence of ROS blockade as a therapeutic approach for myocardial infarction and ischemic stroke.

Abstract TP281: Transcriptome Analysis of the Human Brain Microvascular Endothelial Cells During and After Oxygen-Glucose Deprivation Stress as a Tool to Identify Novel Targets

Background: The blood-brain barrier (BBB) constitutes an important component of the neurovascular unit (NVU) by providing a physical and a chemical barrier critical for the brain homeostasis. The disruption of the BBB during cerebral ischemia constitutes a key event of the disease, resulting in its opening and ultimately the formation of cerebral edema. Therefore, targeting such BBB disruption by restoring the barrier function could mitigate such insult. In this study, we investigated change in gene expression profile of the human BBB in vitro using an induced pluripotent stem cell (iPSC) based model. Methods: BMECs derived from two human iPSC lines (CTR90F and CTR65M) were exposed to acute OGD stress (1% O2, no glucose) for 6h, followed by reoxygenation (21% O2, 1g/L glucose) for 18h and compared to control (21% O2, 1g/L glucose, 24h) Total RNA was extracted for cDNA microarray analysis to the University of Texas Southwestern Genomic Core Facility using a ClariomD® chip. Fold-change &gt;2 was considered statistically significant (P&lt;0.05). Results: OGD/reoxygenation resulted in almost 3700 genes differentially expressed, including over 600 coding genes. Most of such differential expression occurred during the OGD phase. Reoxygenation yielded to quasi-similar expression profile than controls. Several original pathways have been identified and include nuclear receptors, PI3K/Akt signaling pathways, microRNAs, and adhesion signaling pathways. Conclusions: Our preliminary findings suggest that our iPSC-derived model of the BBB based on BMECs showed an overlap of several genes commonly identified as hypoxic/ischemic responsive genes, but also highlighted novel signaling pathways that have little or no literature on their function at the BBB. We are currently refining our list of genes and focusing our attention on genes that have shown the highest enrichment or depletion.

Genetic architecture study of rheumatoid arthritis and juvenile idiopathic arthritis.

BackgroundRheumatoid arthritis and juvenile idiopathic arthritis are two types of autoimmune diseases with inflammation at the joints, occurring to adults and children respectively. There are phenotypic overlaps between these two types of diseases, despite the age difference in patient groups.MethodsTo systematically compare the genetic architecture of them, we conducted analyses at gene and pathway levels and constructed protein-protein-interaction network based on summary statistics of genome-wide association studies of these two diseases. We examined their difference and similarity at each level.ResultsWe observed extensive overlap in significant SNPs and genes at the human leukocyte antigen region. In addition, several SNPs in other regions of the human genome were also significantly associated with both diseases. We found significantly associated genes enriched in 32 pathways shared by both diseases. Excluding genes in the human leukocyte antigen region, significant enrichment is present for pathways like interleukin-27 pathway and NO2-dependent interleukin-12 pathway in natural killer cells.DiscussionThe identification of commonly associated genes and pathways may help in finding population at risk for both diseases, as well as shed light on repositioning and designing drugs for both diseases.

Properties and abundance of overlapping genes in viruses.

Overlapping genes are commonplace in viruses and play an important role in their function and evolution. However, aside from studies on specific groups of viruses, relatively little is known about the extent and nature of gene overlap and its determinants in viruses as a whole. Here, we present an extensive characterisation of gene overlap in viruses through an analysis of reference genomes present in the NCBI virus genome database. We find that over half the instances of gene overlap are very small, covering <10 nt, and 84 per cent are <50 nt in length. Despite this, 53 per cent of all viruses still contained a gene overlap of 50 nt or larger. We also investigate several predictors of gene overlap such as genome structure (single- and double-stranded RNA and DNA), virus family, genome length, and genome segmentation. This revealed that gene overlap occurs more frequently in DNA viruses than in RNA viruses, and more frequently in single-stranded viruses than in double-stranded viruses. Genome segmentation is also associated with gene overlap, particularly in single-stranded DNA viruses. Notably, we observed a large range of overlap frequencies across families of all genome types, suggesting that it is a common evolutionary trait that provides flexible genome structures in all virus families.

Interweaving Between Genetic and Epigenetic Studies on Childhood Asthma.

The cause and underlying mechanisms that contribute to asthma pathogenesis are not well known. Both genome- and epigenome-wide association studies have identified genes associated with asthma risk. It is unknown to what extent genes identified in these two types of studies overlap. Based on existing literature and the DisGeNET database, we extracted overlapping genes identified in genetic and epigenetic studies of childhood asthma. Through analyses of variance, we assessed whether DNA methylation (DNAm) at 5′-C-phosphate-G-3′ (CpGs) on the overlapping genes was associated with neighboring single-nucleotide polymorphisms (SNPs) within 1M base pairs (bps) and with low linkage disequilibrium (r2 < 0.2) in the childhood asthma-related genes. In total, 285 genes from genetic studies and 226 genes from epigenetic studies were shown to be associated with asthma risk, of which six overlap. Of the six genes, 79 CpGs and 8229 unique neighboring SNPs (1M bps) were included in methylation quantitative loci (methQTL) assessment analyses. We tested the association of DNAm at each of the 79 CpG sites with its neighboring SNPs. After adjusting for multiple testing by controlling the false discovery rate to 0.05 when testing methQTL for each CpG site, we found statistically significant associations in three genes with their neighboring SNPs and identified 34 unique methQTLs. The rather limited overlap in genes between genetic and epigenetic studies on asthma and the absence of methQTL in some of the overlapping genes highlight a need to jointly, rather than independently, examine genetic and epigenetic effects on asthma risk to improve our understanding of the underlying mechanisms of asthma.

Copy number variation (CNV) identification, interpretation, and database from Brazilian patients.

Copy number variations (CNVs) constitute an important class of variation in the human genome and the interpretation of their pathogenicity considering different frequencies across populations is still a challenge for geneticists. Since the CNV databases are predominantly composed of European and non-admixed individuals, and Brazilian genetic constitution is admixed and ethnically diverse, diagnostic screenings on Brazilian variants are greatly difficulted by the lack of populational references. We analyzed a clinical sample of 268 Brazilian individuals, including patients with neurodevelopment disorders and/or congenital malformations. The pathogenicity of CNVs was classified according to their gene content and overlap with known benign and pathogenic variants. A total of 1,504 autosomal CNVs (1,207 gains and 297 losses) were classified as benign (92.9%), likely benign (1.6%), VUS (2.6%), likely pathogenic (0.2%) and pathogenic (2.7%). Some of the CNVs were recurrent and with frequency increased in our sample, when compared to populational open resources of structural variants: 14q32.33, 22q11.22, 1q21.1, and 1p36.32 gains. Thus, these highly recurrent CNVs classified as likely benign or VUS were considered non-pathogenic in our Brazilian sample. This study shows the relevance of introducing CNV data from diverse cohorts to improve on the interpretation of clinical impact of genomic variations.