scholarly journals Sexual dimorphism of the pulmonary transcriptome in neonatal hyperoxic lung injury: identification of angiogenesis as a key pathway

2017 ◽  
Vol 313 (6) ◽  
pp. L991-L1005 ◽  
Author(s):  
Cristian Coarfa ◽  
Yuhao Zhang ◽  
Suman Maity ◽  
Dimuthu N. Perera ◽  
Weiwu Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Injury ◽  
Mrna Level ◽  
Sexually Dimorphic ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Data Set ◽  
Vascular Growth ◽  
Hyperoxic Lung Injury ◽  
High Concentrations

Bronchopulmonary dysplasia (BPD) is characterized by impaired alveolar secondary septation and vascular growth. Exposure to high concentrations of oxygen (hyperoxia) contributes to the development of BPD. The male sex is considered an independent risk factor for the development of BPD. The reasons underlying sexually dimorphic outcomes in premature neonates are not known. We hypothesized that sex-specific modulation of biological processes in the lung under hyperoxic conditions contributes to sex-based differences. Neonatal male and female mice (C57BL/6) were exposed to hyperoxia [95% [Formula: see text], postnatal day (PND) 1–5: saccular stage of lung development] and euthanized on PND 7 or 21. Pulmonary gene expression was studied using RNA-Seq on the Illumina HiSeq 2500 platform. Analysis of the pulmonary transcriptome revealed differential sex-specific modulation of crucial pathways such as angiogenesis, response to hypoxia, inflammatory response, and p53 pathway. Candidate genes from these pathways were validated at the mRNA level by qPCR. Analysis also revealed sex-specific differences in the modulation of crucial transcription factors. Focusing on the differential modulation of the angiogenesis pathway, we also showed sex-specific differential activation of Hif-1α-regulated genes using ChIP-qPCR and differences in expression of crucial genes ( Vegf, VegfR2, and Phd2) modulating angiogenesis. We demonstrate the translational relevance of our findings by showing that our murine sex-specific differences in gene expression correlate with those from a preexisting human BPD data set. In conclusion, we provide novel molecular insights into differential sex-specific modulation of the pulmonary transcriptome in neonatal hyperoxic lung injury and highlight angiogenesis as one of the crucial differentially modulated pathways.

Changes in gene expression in hyperoxia-induced neonatal lung injury

1990 ◽  
Vol 258 (2) ◽  
pp. L107-L111 ◽  
Author(s):  
S. Horowitz ◽  
D. L. Shapiro ◽  
J. N. Finkelstein ◽  
R. H. Notter ◽  
C. J. Johnston ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Injury ◽  
Regulatory Protein ◽  
Adult Rabbit ◽  
Biochemical Basis ◽  
Neonatal Lung ◽  
Hyperoxic Lung Injury ◽  
High Concentrations ◽  
Surfactant Apoprotein ◽  
Surfactant Apoprotein A

Exposure to high concentrations of oxygen (hyperoxia) can result in lung injury. The biochemical basis of this injury is poorly understood, but it is likely to include alterations in gene expression. Hyperoxia-induced (H-I) cDNAs have been molecularly cloned (Horowitz et al. J. Biol. Chem. 264: 7092-7095, 1989) from the lungs of an adult rabbit exposed to toxic levels of oxygen. One of them (H-I 1) was identified as encoding the tissue inhibitor of metalloproteinases (TIMP), a key regulatory protein of extracellular matrix turnover. Here we identify another clone (H-I 3) as encoding pulmonary surfactant apoprotein A (SP-A). We also show that in neonatal rabbits exposed to 100% oxygen for 96 h, the mRNAs corresponding to TIMP, SP-A, and another H-I gene are increased. These studies have begun to explore specific changes in gene expression associated with neonatal hyperoxic lung injury.

scholarly journals Analysis of the Transcriptome in Hyperoxic Lung Injury and Sex-Specific Alterations in Gene Expression

PLoS ONE ◽  
2014 ◽  
Vol 9 (7) ◽  
pp. e101581 ◽  
Author(s):  
Krithika Lingappan ◽  
Chandra Srinivasan ◽  
Weiwu Jiang ◽  
Lihua Wang ◽  
Xanthi I. Couroucli ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Injury ◽  
Hyperoxic Lung Injury

130 A CATALOG OF REFERENCE GENES WITH HIGH, MEDIUM, AND LOW LEVELS OF EXPRESSION DURING BOVINE IN VIVO PRE-IMPLANTATION DEVELOPMENT

2017 ◽  
Vol 29 (1) ◽  
pp. 173
Author(s):  
Z. Jiang ◽  
J. Sun ◽  
S. Marjani ◽  
H. Dong ◽  
X. Zheng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Target Genes ◽  
Stable Expression ◽  
Bovine Embryo ◽  
Rna Seq ◽  
Rt Pcr ◽  
Data Set ◽  
Low Expression

Appropriate reference genes for accurate normalization in RT-PCR are essential for the study of gene expression. Ideal reference genes should not only have stable expression across stages of embryo development, but also be expressed at comparable levels to the target genes. Using RNA-seq data from in vivo-produced bovine oocytes and embryos from the 2-cell to blastocyst stage (Jiang et al., 2014 BMC Genomics 15, 756), we tried to establish a catalogue of all reference genes for RT-PCR analysis. One-way ANOVA generated 4055 genes that did not differ across stages. To reduce this list, we used the entire RNA-seq data set and first removed genes with a FPKM (fragments per kilobase of transcript per million mapped reads) of <1, and then rescaled each gene’s expression values within a range of 0 to 1. We subsequently calculated the expression variance for each gene across all stages. By assuming that the calculated variances follow a Gaussian distribution and that the majority of the genes do not have a stable expression level, a gene was classified as a reference if its variance significantly deviated (P < 0.05) from these assumptions. We identified 346 potential reference genes, all of which were among the candidates from the ANOVA analysis. We arbitrarily assigned genes in this list to high (FPKM ≥ 100), medium (10 < FPKM < 100), and low expression levels (FPKM ≤ 10), and 37, 154, and 155 genes, respectively, fell into these groups. Surprisingly, none of the commonly used reference genes, such as GAPDH, PPIA, ACTB, PRL15, GUSB, and H3F2A, were identified as being stably expressed across in vivo development. This is consistent with findings of prior RT-PCR studies (Robert et al. 2002 Biol. Reprod. 67, 1465–1472; Ross et al. 2010 Cell Reprogram. 12, 709–717). The following gene ontology terms were significantly enriched for the 346 genes: cell cycle, translation, transport, chromatin, cell division, and metabolic process, indicating that the early embryos maintained constant levels of genes involved in fundamental biological functions. Finally, we performed RT-PCR to validate the RNA-seq results using different bovine in vivo-derived oocytes and embryos (n = 3/stage). We successfully validated 10 selected genes, including those in the high (CS, PGD, and ACTR3), medium (CCT5, MRPL47, COG2, CRT9, and HELLS), and low expression groups (CDC23 and TTF1). In conclusion, we recommend the use of reference genes that are expressed at comparable levels to target genes. This study offers a useful resource to aid in the appropriate selection of reference genes, which will improve the accuracy of quantitative gene expression analyses across bovine embryo pre-implantation development.

A-To-I RNA Editing By ADAR1 Is Essential For Hematopoiesis

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1199-1199 ◽  
Author(s):  
Brian Liddicoat ◽  
Robert Piskol ◽  
Alistair Chalk ◽  
Miyoko Higuchi ◽  
Peter Seeburg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Editing ◽  
Fetal Liver ◽  
Expression Profiles ◽  
In Utero ◽  
Tamoxifen Treatment ◽  
Rna Seq ◽  
Data Set ◽  
Hematopoietic Stem

Abstract The role of RNA and its regulation is becoming increasingly appreciated as a vital component of hematopoietic development. RNA editing by members of the Adenosine Deaminase Acting on RNA (ADAR) gene family is a form of post-transcriptional modification which converts genomically encoded adenosine to inosine (A-to-I) in double-stranded RNA. A-to-I editing by ADAR directly converts the sequence of the RNA substrate and can alter the structure, function, processing, and localization of the targeted RNA. ADAR1 is ubiquitously expressed and we have previously described essential roles in the development of hematopoietic and hepatic organs. Germline ablation of murine ADAR1 results in a significant upregulation of interferon (IFN) stimulated genes and embryonic death between E11.5 and E12.5 associated with fetal liver disintegration and failed hemopoiesis. To determine the biological importance of A-to-I editing by ADAR1, we generated an editing dead knock-in allele of ADAR1 (ADAR1E861A). Mice homozygous for the ADAR1E861A allele died in utero at ∼E13.5. The fetal liver (FL) was small and had significantly lower cellularity than in controls. Analysis of hemopoiesis demonstrated increased apoptosis and a loss of hematopoietic stem cells (HSC) and all mature lineages. Most notably erythropoiesis was severely impaired with ∼7-fold reduction across all erythrocyte progenitor populations compared to controls. These data are consistent with our previous findings that ADAR1 is essential for erythropoiesis (unpublished data) and suggest that the ADAR1E861A allele phenocopies the null allele in utero. To assess the requirement of A-to-I editing in adult hematopoiesis, we generated mice where we could somatically delete the wild-type ADAR1 allele and leave only ADAR1E861A expressed in HSCs (hScl-CreERAdar1fl/E861A). In comparison to hScl-CreERAdar1fl/+ controls, hScl-CreERAdar1fl/E861A mice were anemic and had severe leukopenia 20 days post tamoxifen treatment. Investigation of marrow hemopoiesis revealed a significant loss of all cells committed to the erythroid lineage in hScl-CreERAdar1fl/E861A mice, despite having elevated phenotypic HSCs. Upon withdrawal of tamoxifen diet, all blood parameters were restored to control levels within 12 weeks owing to strong selection against cells expressing only the ADAR1E861A allele. To understand the mechanism through which ADAR1 mediated A-to-I editing regulates hematopoiesis, RNA-seq was performed. Gene expression profiles showed that a loss of ADAR1 mediated A-to-I editing resulted in a significant upregulation of IFN signatures, consistent with the gene expression changes in ADAR1 null mice. To define substrates of ADAR1 we assessed A-to-I mismatches in the RNA-seq data sets. 3,560 previously known and 353 novel A-to-I editing sites were identified in our data set. However, no single editing substrate discovered could account for the IFN signature observed or the lethality of ADAR1E861A/E861A mice. These results demonstrate that ADAR1 mediated A-to-I editing is essential for the maintenance of both fetal and adult hemopoiesis in a cell-autonomous manner and a key suppressor of the IFN response in hematopoiesis. Furthermore the ADAR1E861A allele demonstrates the essential role of ADAR1 in vivo is A-to-I editing. Disclosures: Hartner: TaconicArtemis: Employment.

scholarly journals Sex-specific differences in neonatal hyperoxic lung injury

2016 ◽  
Vol 311 (2) ◽  
pp. L481-L493 ◽  
Author(s):  
Krithika Lingappan ◽  
Weiwu Jiang ◽  
Lihua Wang ◽  
Bhagavatula Moorthy
Keyword(s):  
Lung Injury ◽  
Lung Development ◽  
Molecular Mechanisms ◽  
Neutrophil Infiltration ◽  
Sexually Dimorphic ◽  
Female Mice ◽  
Hyperoxia Exposure ◽  
Hyperoxic Lung Injury ◽  
Mean Linear Intercept ◽  
Radial Alveolar Count

Male sex is considered an independent predictor for the development of bronchopulmonary dysplasia (BPD) after adjusting for other confounders. BPD is characterized by an arrest in lung development with marked impairment of alveolar septation and vascular development. The reasons underlying sexually dimorphic outcomes in premature neonates are not known. In this investigation, we tested the hypothesis that male neonatal mice will be more susceptible to hyperoxic lung injury and will display larger arrest in lung alveolarization. Neonatal male and female mice (C57BL/6) were exposed to hyperoxia [95% FiO2, postnatal day (PND) 1–5] and euthanized on PND 7 and 21. Extent of alveolarization, pulmonary vascularization, inflammation, and modulation of the NF-κB pathway were determined and compared with room air controls. Macrophage and neutrophil infiltration was significantly increased in hyperoxia-exposed animals but was increased to a larger extent in males compared with females. Lung morphometry showed a higher mean linear intercept (MLI) and a lower radial alveolar count (RAC) and therefore greater arrest in lung development in male mice. This was accompanied by a significant decrease in the expression of markers of angiogenesis (PECAM1 and VEGFR2) in males after hyperoxia exposure compared with females. Interestingly, female mice showed increased activation of the NF-κB pathway in the lungs compared with males. These results support the hypothesis that sex plays a crucial role in hyperoxia-mediated lung injury in this model. Elucidation of the sex-specific molecular mechanisms may aid in the development of novel individualized therapies to prevent/treat BPD.

scholarly journals Basal Contamination of Sequencing: Lessons from the GTEx dataset

2019 ◽  
Author(s):  
Tim O. Nieuwenhuis ◽  
Stephanie Yang ◽  
Rohan X. Verma ◽  
Vamsee Pillalamarri ◽  
Dan E. Arking ◽  
...  
Keyword(s):  
Gene Expression ◽  
Tissue Expression ◽  
Rna Seq ◽  
Data Set ◽  
Low Level ◽  
Allelic Differences ◽  
Highly Expressed Genes ◽  
Next Generation Sequencing Ngs ◽  
Cell Data ◽  
Generation Sequencing

AbstractOne of the challenges of next generation sequencing (NGS) is read contamination. We used the Genotype-Tissue Expression (GTEx) project, a large, diverse, and robustly generated dataset, to understand the factors that contribute to contamination. We obtained GTEx datasets and technical metadata and validating RNA-Seq from other studies. Of 48 analyzed tissues in GTEx, 26 had variant co-expression clusters of four known highly expressed and pancreas-enriched genes (PRSS1, PNLIP, CLPS, and/or CELA3A). Fourteen additional highly expressed genes from other tissues also indicated contamination. Sample contamination by non-native genes was associated with a sample being sequenced on the same day as a tissue that natively expressed those genes. This was highly significant for pancreas and esophagus genes (linear model, p=9.5e-237 and p=5e-260 respectively). Nine SNPs in four genes shown to contaminate non-native tissues demonstrated allelic differences between DNA-based genotypes and contaminated sample RNA-based genotypes, validating the contamination. Low-level contamination affected 4,497 (39.6%) samples (defined as 10 PRSS1 TPM). It also led ≥ to eQTL assignments in inappropriate tissues among these 18 genes. We note this type of contamination occurs widely, impacting bulk and single cell data set analysis. In conclusion, highly expressed, tissue-enriched genes basally contaminate GTEx and other datasets impacting analyses. Awareness of this process is necessary to avoid assigning inaccurate importance to low-level gene expression in inappropriate tissues and cells.

scholarly journals SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis

2015 ◽  
Author(s):  
Benjamin K Johnson ◽  
Matthew B Scholz ◽  
Tracy K Teal ◽  
Robert B Abramovitch
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Quality Analysis ◽  
Rna Seq ◽  
Sequencing Data ◽  
Data Set ◽  
Bacterial Rna ◽  
Analysis Workflow ◽  
Differential Gene ◽  
Reference Counting

Summary: SPARTA is a reference-based bacterial RNA-seq analysis workflow application for single-end Illumina reads. SPARTA is turnkey software that simplifies the process of analyzing RNA-seq data sets, making bacterial RNA-seq analysis a routine process that can be undertaken on a personal computer or in the classroom. The easy-to-install, complete workflow processes whole transcriptome shotgun sequencing data files by trimming reads and removing adapters, mapping reads to a reference, counting gene features, calculating differential gene expression, and, importantly, checking for potential batch effects within the data set. SPARTA outputs quality analysis reports, gene feature counts and differential gene expression tables and scatterplots. The workflow is implemented in Python for file management and sequential execution of each analysis step and is available for Mac OS X, Microsoft Windows, and Linux. To promote the use of SPARTA as a teaching platform, a web-based tutorial is available explaining how RNA-seq data are processed and analyzed by the software. Availability and Implementation: Tutorial and workflow can be found at sparta.readthedocs.org. Teaching materials are located at sparta-teaching.readthedocs.org. Source code can be downloaded at www.github.com/abramovitchMSU/, implemented in Python and supported on Mac OS X, Linux, and MS Windows. Contact: Robert B. Abramovitch ([email protected]) Supplemental Information: Supplementary data are available online

scholarly journals RNA-Seq-Based Analysis of Cortisol-Induced Differential Gene Expression Associated with Piscirickettsia salmonis Infection in Rainbow Trout (Oncorhynchus mykiss) Myotubes

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2399
Author(s):  
Rodrigo Zuloaga ◽  
Phillip Dettleff ◽  
Macarena Bastias-Molina ◽  
Claudio Meneses ◽  
Claudia Altamirano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Rainbow Trout ◽  
Enrichment Analysis ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Transcriptomic Response ◽  
Bacterial Gene ◽  
Intensive Farming ◽  
Piscirickettsia Salmonis

Salmonid rickettsial septicemia (SRS) is the major infectious disease of the Chilean salmonid aquaculture industry caused by Piscirickettsia salmonis. Intensive farming conditions generate stress and increased susceptibility to diseases, being skeletal muscle mainly affected. However, the interplay between pathogen infection and stress in muscle is poorly understood. In this study, we perform an RNA-seq analysis on rainbow trout myotubes that are pretreated for 3 h with cortisol (100 ng/mL) and then infected with P. salmonis strain LF-89 for 8 h (MOI 50). Twelve libraries are constructed from RNA samples (n = 3 per group) and sequenced on Illumina HiSeq 4000. A total of 704,979,454 high-quality reads are obtained, with 70.25% mapped against the reference genome. In silico DETs include 175 total genes—124 are upregulated and 51 are downregulated. GO enrichment analysis reveals highly impacted biological processes related to apoptosis, negative regulation of cell proliferation, and innate immune response. These results are validated by RT-qPCR of nine candidate transcripts. Furthermore, cortisol pretreatment significantly stimulated bacterial gene expression of ahpC and 23s compared to infection. In conclusion, for the first time, we describe a transcriptomic response of trout myotubes infected with P. salmonis by inducing apoptosis, downregulating cell proliferation, and intrinsic immune-like response that is differentially regulated by cortisol.

scholarly journals Analysis of thein plantatranscriptome expressed by the corn pathogenPantoea stewartiisubsp.stewartiivia RNA-Seq

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3237 ◽  
Author(s):  
Holly Packard ◽  
Alison Kernell Burke ◽  
Roderick V. Jensen ◽  
Ann M. Stevens
Keyword(s):  
Gene Expression ◽  
Quorum Sensing ◽  
Critical Role ◽  
Wilt Disease ◽  
Sample Type ◽  
Dependent Manner ◽  
Rna Seq ◽  
In Planta ◽  
Data Set

Pantoea stewartiisubsp.stewartiiis a bacterial phytopathogen that causes Stewart’s wilt disease in corn. It uses quorum sensing to regulate expression of some genes involved in virulence in a cell density-dependent manner as the bacterial population grows from small numbers at the initial infection site in the leaf apoplast to high cell numbers in the xylem where it forms a biofilm. There are also other genes important for pathogenesis not under quorum-sensing control such as a Type III secretion system. The purpose of this study was to compare gene expression during anin plantainfection versus either a pre-inoculumin vitroliquid culture or anin vitroagar plate culture to identify genes specifically expressedin plantathat may also be important for colonization and/or virulence. RNA was purified from each sample type to determine the transcriptome via RNA-Seq using Illumina sequencing of cDNA. Fold gene expression changes in thein plantadata set in comparison to the twoin vitrogrown samples were determined and a list of the most differentially expressed genes was generated to elucidate genes important for plant association. Quantitative reverse transcription PCR (qRT-PCR) was used to validate expression patterns for a select subset of genes. Analysis of the transcriptome data via gene ontology revealed that bacterial transporters and systems important for oxidation reduction processes appear to play a critical role forP. stewartiias it colonizes and causes wilt disease in corn plants.

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