scholarly journals Molecular markers and mechanisms of stroke: RNA studies of blood in animals and humans

2011 ◽  
Vol 31 (7) ◽  
pp. 1513-1531 ◽  
Author(s):  
Frank R Sharp ◽  
Glen C Jickling ◽  
Boryana Stamova ◽  
Yingfang Tian ◽  
Xinhua Zhan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ischemic Stroke ◽  
Sensitivity And Specificity ◽  
Specific Gene ◽  
Gene Profiles ◽  
Study Gene Expression ◽  
Human Stroke ◽  
Alternatively Spliced ◽  
Expression Microarrays ◽  
Whole Genome Expression

Whole genome expression microarrays can be used to study gene expression in blood, which comes in part from leukocytes, immature platelets, and red blood cells. Since these cells are important in the pathogenesis of stroke, RNA provides an index of these cellular responses to stroke. Our studies in rats have shown specific gene expression changes 24 hours after ischemic stroke, hemorrhage, status epilepticus, hypoxia, hypoglycemia, global ischemia, and following brief focal ischemia that simulated transient ischemic attacks in humans. Human studies show gene expression changes following ischemic stroke. These gene profiles predict a second cohort with > 90% sensitivity and specificity. Gene profiles for ischemic stroke caused by large-vessel atherosclerosis and cardioembolism have been described that predict a second cohort with > 85% sensitivity and specificity. Atherosclerotic genes were associated with clotting, platelets, and monocytes, and cardioembolic genes were associated with inflammation, infection, and neutrophils. These gene profiles predicted the cause of stroke in 58% of cryptogenic patients. These studies will provide diagnostic, prognostic, and therapeutic markers, and will advance our understanding of stroke in humans. New techniques to measure all coding and noncoding RNAs along with alternatively spliced transcripts will markedly advance molecular studies of human stroke.

scholarly journals Modeling gene expression evolution with EvoGeneX uncovers differences in evolution of species, organs and sexes

2020 ◽  
Author(s):  
Soumitra Pal ◽  
Brian Oliver ◽  
Teresa M. Przytycka
Keyword(s):  
Gene Expression ◽  
Evolutionary Dynamics ◽  
Computational Method ◽  
Specific Gene ◽  
Species Variation ◽  
Evolutionary Divergence ◽  
Sequence Evolution ◽  
Study Gene Expression ◽  
Expression Evolution ◽  
Gene Expression Evolution

AbstractWhile DNA sequence evolution has been well studied, the expression of genes is also subject to evolution. Yet the evolution of gene expression is currently not well understood. In recent years, new tissue/organ specific gene expression datasets spanning several organisms across the tree of life, have become available providing the opportunity to study gene expression evolution in more detail. However, while a theoretical model to study evolution of continuous traits exist, in practice computational methods often cannot distinguish, with confidence, between alternative evolutionary scenarios. This lack of power has been attributed to the modest number of species with available expression data.To solve this challenge, we introduce EvoGeneX, a computationally efficient method to uncover the mode of gene expression evolution based on the Ornstein-Uhlenbeck process. Importantly, EvoGeneX in addition to modelling expression variations between species, models within species variation. To estimate the within species variation, EvoGeneX formally incorporates the data from biological replicates as a part of the mathematical model. We show that by modelling the within species diversity EvoGeneX significantly outperforms the currently available computational method. In addition, to facilitate comparative analysis of gene expression evolution, we introduce a new approach to measure the dynamics of evolutionary divergence of a group of genes.We used EvoGeneX to analyse the evolution of expression across different organs, species and sexes of the Drosophila genus. Our analysis revealed differences in the evolutionary dynamics of male and female gonads, and uncovered examples of adaptive evolution of genes expressed in the head and in the thorax.

scholarly journals Bfimpute: A Bayesian factorization method to recover single-cell RNA sequencing data

2021 ◽  
Author(s):  
Zi-Hang Wen ◽  
Jeremy L. Langsam ◽  
Lu Zhang ◽  
Wenjun Shen ◽  
Xin Zhou
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Single Cells ◽  
Cell Group ◽  
Specific Gene ◽  
Cell Type ◽  
Sequencing Data ◽  
Gene Expression Matrix ◽  
Study Gene Expression ◽  
Expression Matrix

AbstractSingle-cell RNA-seq (scRNA-seq) offers opportunities to study gene expression of tens of thousands of single cells simultaneously, to investigate cell-to-cell variation, and to reconstruct cell-type-specific gene regulatory networks. Recovering dropout events in a sparse gene expression matrix for scRNA-seq data is a long-standing matrix completion problem. We introduce Bfimpute, a Bayesian factorization imputation algorithm that reconstructs two latent gene and cell matrices to impute final gene expression matrix within each cell group, with or without the aid of cell type labels or bulk data. Bfimpute achieves better accuracy than other six publicly notable scRNA-seq imputation methods on simulated and real scRNA-seq data, as measured by several different evaluation metrics. Bfimpute can also flexibly integrate any gene or cell related information that users provide to increase the performance. Availability: Bfimpute is implemented in R and is freely available at https://github.com/maiziezhoulab/Bfimpute.

scholarly journals A neuron-optimized CRISPR/dCas9 activation system for robust and specific gene regulation

2018 ◽  
Author(s):  
Katherine E. Savell ◽  
Svitlana V. Bach ◽  
Morgan E. Zipperly ◽  
Jasmin S. Revanna ◽  
Nicholas A. Goska ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Transcriptional Activation ◽  
Target Genes ◽  
Adult Brain ◽  
Model Systems ◽  
Neuronal Cultures ◽  
Specific Gene ◽  
Highly Efficient ◽  
Study Gene Expression

Recent developments in CRISPR-based gene editing have provided new avenues to interrogate gene function. However, application of these tools in the central nervous system has been delayed due to difficulties in transgene expression in post-mitotic neurons. Here, we present a highly efficient, neuron-optimized dual lentiviral CRISPR-based transcriptional activation (CRISPRa) system to drive gene expression in primary neuronal cultures and the adult brain of rodent model systems. We demonstrate robust, modular, and tunable induction of endogenous target genes as well as multiplexed gene regulation necessary for investigation of complex transcriptional programs. CRISPRa targeting unique promoters in the complex multi-transcript gene Brain-derived neurotrophic factor (Bdnf) revealed both transcript- and genome-level selectivity of this approach, in addition to highlighting downstream transcriptional and physiological consequences of Bdnf regulation. Finally, we illustrate that CRISPRa is highly efficient in vivo, resulting in increased protein levels of a target gene in diverse brain structures. Taken together, these results demonstrate that CRISPRa is an efficient and selective method to study gene expression programs in brain health and disease.

Loss of the B-lineage–specific gene expression program in Hodgkin and Reed-Sternberg cells of Hodgkin lymphoma

Blood ◽  
2003 ◽  
Vol 101 (4) ◽  
pp. 1505-1512 ◽  
Author(s):  
Ines Schwering ◽  
Andreas Bräuninger ◽  
Ulf Klein ◽  
Berit Jungnickel ◽  
Marianne Tinguely ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cells ◽  
B Cell ◽  
Hodgkin Lymphoma ◽  
Cell Lines ◽  
Expression Profiles ◽  
Specific Gene ◽  
Mrna Levels ◽  
Study Gene Expression ◽  
B Lineage

Hodgkin and Reed-Sternberg (HRS) cells represent the malignant cells in classical Hodgkin lymphoma (HL). Because their immunophenotype cannot be attributed to any normal cell of the hematopoietic lineage, the origin of HRS cells has been controversially discussed, but molecular studies established their derivation from germinal center B cells. In this study, gene expression profiles generated by serial analysis of gene expression (SAGE) and DNA chip microarrays from HL cell lines were compared with those of normal B-cell subsets, focusing here on the expression of B-lineage markers. This analysis revealed decreased mRNA levels for nearly all established B-lineage–specific genes. For 9 of these genes, lack of protein expression was histochemically confirmed. Down-regulation of genes affected multiple components of signaling pathways active in B cells, including B-cell receptor (BCR) signaling. Because several genes down-regulated in HRS cells are positively regulated by the transcriptional activator Pax-5, which is expressed in most HRS cells, we studied HL cell lines for mutations in the Pax-5gene. However, no mutations were found. We propose that the lost B-lineage identity in HRS cells may explain their survival without BCR expression and reflect a fundamental defect in maintaining the B-cell differentiation state in HRS cells, which is likely caused by a novel, yet unknown, pathogenic mechanism.

scholarly journals Alternatively spliced isoforms of WT1 control podocyte-specific gene expression

2015 ◽  
Vol 88 (2) ◽  
pp. 321-331 ◽  
Author(s):  
Jonathan Lefebvre ◽  
Michael Clarkson ◽  
Filippo Massa ◽  
Stephen T. Bradford ◽  
Aurelie Charlet ◽  
...  
Keyword(s):  
Gene Expression ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Alternatively Spliced

scholarly journals Interaction of Ets-1 and the POU-homeodomain protein GHF-1/Pit-1 reconstitutes pituitary-specific gene expression.

1997 ◽  
Vol 17 (3) ◽  
pp. 1065-1074 ◽  
Author(s):  
A P Bradford ◽  
C Wasylyk ◽  
B Wasylyk ◽  
A Gutierrez-Hartmann
Keyword(s):  
Gene Expression ◽  
Specific Protein ◽  
Protein Domain ◽  
Specific Gene ◽  
Homeodomain Protein ◽  
Specific Expression ◽  
Specific Gene Expression ◽  
Cis Element ◽  
Alternatively Spliced ◽  
Combinatorial Interactions

The pituitary-specific, POU-homeodomain factor GHF-1/Pit-1 is necessary, but not sufficient, for cell-specific expression of prolactin (PRL), growth hormone (GH), and thyrotropin. Combinatorial interactions of GHF-1 with other factors are likely to be required; however, such factors and their mechanisms of action remain to be elucidated. Here we identify Ets-1 as a factor that functionally and physically interacts with GHF-1 to fully reconstitute proximal PRL promoter activity. In contrast, Ets-2 has no effect, and the alternatively spliced GHF-2/Pit-1beta variant fails to synergize with Ets-1. The Ets-1-GHF-1 synergy requires a composite Ets-1-GHF-1 cis element and is dependent on an Ets-1-specific protein domain. Furthermore, the ancestrally related and GHF-1-dependent GH promoter, which lacks this composite element, does not exhibit this response. Finally, Ets-1, but not Ets-2, binds directly to GHF-1 and GHF-2. These data show that a functional interaction of GHF-1 and Ets-1, acting via a composite DNA element, is required to establish lactotroph-specific PRL gene expression, thus providing a molecular mechanism by which GHF-1 can discriminate between the GH and PRL genes. These results underscore the importance of transcription factors that are distinct from, but interact with, homeobox proteins to establish lineage-specific gene expression.

scholarly journals IL-6R Protective Variant rs7529229 Reduces Interleukin-6 Signaling and Contributes To A Decreased Ischemic Stroke Risk

2020 ◽  
Author(s):  
Haihua Zhang ◽  
Wenbo Zhao ◽  
Bian Liu ◽  
Tao Wang ◽  
Zhifa Han ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ischemic Stroke ◽  
Expression Analysis ◽  
Interleukin 6 ◽  
Whole Blood ◽  
Gene Expression Analysis ◽  
Minor Allele ◽  
Specific Gene ◽  
Healthy Controls ◽  
Increased Risk

Abstract Background Interleukin-6 (IL-6) signaling is associated with an increased risk of coronary artery disease (CAD) and ischemic stroke (IS). Growing evidence shows that the minor alleles of IL-6 receptor gene (IL-6R) variants rs2228145, rs7529229, and rs4129267 significantly increase soluble IL-6R levels and reduce CAD risk. However, the role of IL-6R variants in IS is largely unknown, prompting us to perform a comprehensive analysis. Methods In stage 1 of this study, we performed a meta-analysis of three genome-wide association study datasets from MEGASTROKE, UK Biobank, and the Million Veteran Program to evaluate the association of rs7529229 with IS. In stage 2, we conducted an expression quantitative trait loci analysis to examine the effects of rs7529229 on IL-6R expression in neuropathologically healthy individuals from the UK Brain Expression Consortium, GTEx project, and the eQTLGen Consortium. In stage 3, we used a tissue-specific gene expression analysis to evaluate differences in IL-6R expression across human tissues using gene expression data from GTEx. In stage 4, we conducted a case–control gene expression analysis to explore the differential expression of IL-6R in the whole blood of IS patients and healthy controls. Results We found that: (1) the rs7529229 minor allele significantly reduced the risk of developing IS (odds ratio=0.97, 95% confidence interval 0.95–0.99, P=2.30E-03); (2) the rs7529229 minor allele significantly reduced IL-6R expression in relevant tissues especially in blood vessels and whole blood; (3) IL-6R was mainly expressed in skeletal muscle and whole blood; and (4) IL-6R expression was significantly reduced in the whole blood of healthy controls compared with IS patients. Importantly, the biological senses in stages 1–4 were all convergent. Conclusions Taken together, our findings indicate that the rs7529229 minor allele decreases IL-6R expression in relevant tissues, diminishes IL-6 signaling, and eventually reduces the IS risk. Hence, IL-6R may be a potential therapeutic target for IS. Tocilizumab, a monoclonal antibody that blocks both membrane-bound and circulating IL-6R, might be effective in treating IS or lowering its risk of development, so warrants further testing in suitably powered randomized controlled trials.

scholarly journals Development of an Efficient Transient Gene Expression Assay Based on Tobacco ((Nicotiana tabacum var. Xanthi) Male Gametophytes

1970 ◽  
Vol 19 (1) ◽  
pp. 9-23 ◽  
Author(s):  
M. A. Y. Akhond ◽  
G. C. Machray
Keyword(s):  
Gene Expression ◽  
Nicotiana Tabacum ◽  
Expression System ◽  
Transient Gene Expression ◽  
Specific Gene ◽  
Loss Of Function ◽  
Pollen Selection ◽  
Gene Expression Assay ◽  
Study Gene Expression

Optimization of direct DNA delivery into tobacco ((Nicotiana tabacum var. Xanthi) male gametophytes was devised together with development of an efficient transient expression system to study gene expression under controlled conditions. Use of a GFP gene driven by strong promoter and enhancer sequences allowed an efficient non-lethal transient gene expression assay with an overall transient gene expression frequency of > 4% for uninucleate microspores and between 10 and 20% for binucleate pollen. The technique demonstrated its suitability for analysis of developmental stage-specific gene expression. The assay allowed observation of real-time transgene expression during microspore maturation proving useful for in vitro pollen selection. We have also used this protocol to determine the recombination potential of tobacco male gametic cells by assessing the frequency of extra-chromosomal homologous recombination events after co-delivery of two loss-of-function GFP genes. No increase of extrachromosomal recombination was observed in assays for transient transformation. Key words: Biolistic, GFP, Microspore, Tobacco, Nicotiana tabacum, Transformation D.O.I. 10.3329/ptcb.v19i1.4078 Plant Tissue Cult. & Biotech. 19(1): 9-23, 2009 (June)

scholarly journals Sex-specific changes in gene expression and delayed sex differentiation in response to estrogen pollution in grayling (Salmonidae)

2017 ◽  
Author(s):  
Oliver M. Selmoni ◽  
Diane Maitre ◽  
Julien Roux ◽  
Laetitia G. E. Wilkins ◽  
Lucas Marques da Cunha ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sex Differentiation ◽  
Molecular Genetic ◽  
Gonadal Development ◽  
Yolk Sac ◽  
Specific Gene ◽  
Genetic Sexing ◽  
Early Stages ◽  
Study Gene Expression

AbstractThe synthetic 17α-ethinylestradiol (EE2) is an estrogenic compound of oral contraceptives and therefore a common pollutant that has been suspected to affect the demography of river-dwelling salmonids. We study a population of European grayling (Thymallus thymallus) that suffers from sex ratio distortions. Here we test how ecologically relevant concentrations of EE2 affect sex-specific gene expression around early stages of sex differentiation. We collected gametes from F1s of wild spawners, used them for in vitro fertilizations, and raised the resulting embryos singly under experimentally controlled conditions. Embryos were either exposed to 1ng/L EE2 or sham-exposed. RNA was collected from samples taken 10 days before hatching, at the day of hatching, and towards the end of the yolk-sac stage, to study gene expression and relate it to genetic sex (sdY genotype). We found that EE2 affects gene expression of a very large number of genes especially at the day of hatching. The effects of EE2 on gene expression is strongly sex-specific. At the day of hatching, EE2 affected about twice as many genes in females than in males, and towards the end of the yolk-sac larval stage, EE2 effects were nearly exclusively observed in females. Among the many effects was, for example, a surprising EE2-induced molecular masculinization in the females’ heads. Histological examination of gonadal development of EE2-treated or sham-exposed juveniles during the first 4.5 months after hatching revealed a delaying effect of EE2 on sex differentiation. Because grayling sex determination goes through an all-male stage (a rare case of undifferentiated gonochorism), the rate of EE2-induced sex reversal could not be unequivocally determined during the observational period. However, two EE2-treated genetic males had ovarian tissues at the end of the study. We conclude that common levels of EE2 pollution affect grayling from very early stages on by interfering with male and female gene expression around the onset of sex differentiation, by delaying sex differentiation, and by feminizing some males.Author contributionMRR and CW initiated the project. OS, DM, LW, LMC, and CW sampled the adult fish, did the experimental in vitro fertilizations, and prepared the embryos for experimental rearing in the laboratory. All further manipulations on the embryos and the larvae were done by OS, DM, LW, and LMC. The RNA-seq data were analyzed by OS, JR, and MRR, the histological analyses were done by DM, supervised by SK, the molecular genetic sexing was performed by OS and DM, and EV supervised the EE2 analytics. OS and CW performed the remaining statistical analyses and wrote the first version of the manuscript that was then critically revised by all other authors.

Identification of unique gene expression signatures in colon cancer stroma using microarray technology.

2011 ◽  
Vol 29 (4_suppl) ◽  
pp. 447-447
Author(s):  
S. X. Wang ◽  
J. Wang ◽  
E. Ozhegov ◽  
R. Srinivasan ◽  
O. O. Olowokure ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colon Cancer ◽  
Pathway Analysis ◽  
Tumor Invasion ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Tumor Stroma ◽  
Gene Signature ◽  
Specific Gene ◽  
Study Gene Expression

447 Background: Microarrays are widely used to study gene expression patterns in cancer. In colorectal cancer, it has proven useful to predict recurrence. The majority of expression profiles are generated from the cancer itself. Given the increasing evidence of importance of the microenvironment for tumor invasion, progression and metastasis, we explored tumor stroma gene signature using microarrays. Methods: Four formalin-fixed paraffin embedded (FFPE) colon cancer specimen carrying a pathological stage of T3-4/N0-2 were retrieved. Tumor stroma and normal stroma were separated using microdissection technology. Random sampling was used to minimize sampling bias. Total RNA was extracted, amplified, and labeled using Nugene FFPE kit, with array analysis using Affymetrix Human Gene 1.0. Eight samples, four normal stroma and four tumor stroma, were analyzed and compared. Array data were balanced and analyzed using standard software. To identify gene signature differences in tumor vs normal stroma, ComparativeMarker analysis and unsupervised cluster analysis were carried out. Results: We identified a 969 Affymetrix probe set as a signature that is highly expressed in tumor stroma. The top 117 genes were further analyzed to carry out a pathway analysis. We found a strong signature evident in tumor stroma, and much of this signature comprised the genes of the extracellular matrix. The pathway analysis revealed evidence of the generalized IGF1/TGFbeta/CTGF/activin mediated effect on the stroma, raising the possibility that some of this derives from, or is accompanied by, angiotensin receptor signaling. Through literature search, we found that several upregulated genes (e.g., FAP) were reported to be associated with stroma activation in vitro and in vivo. Conclusions: In this study, we successfully applied microarrays to study reactive colon tumor stroma in FFPE samples. We identified a specific gene signature reflecting stromal reaction to tumor invasion. We further identified the potential pathway that was activated in the reactive tumor stroma. We provide evidence that microarrays are useful in stroma analysis and may help identify new stromal pathways with potential diagnostic and therapeutic value. No significant financial relationships to disclose.

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