Comparison of human cardiac gene expression profiles in paired samples of right atrium and left ventricle collected in vivo

2012 ◽  
Vol 44 (1) ◽  
pp. 89-98 ◽  
Author(s):  
Julia Asp ◽  
Jane Synnergren ◽  
Marianne Jonsson ◽  
Göran Dellgren ◽  
Anders Jeppsson
Keyword(s):  
Gene Expression ◽  
Left Ventricle ◽  
Right Atrium ◽  
Expression Profiles ◽  
Artery Bypass ◽  
Global Gene Expression ◽  
Differentially Expressed ◽  
Tissue Samples ◽  
The Right

Studies of expressed genes in human heart provide insight into both physiological and pathophysiological mechanisms. This is of importance for extended understanding of cardiac function as well as development of new therapeutic drugs. Heart tissue for gene expression studies is generally hard to obtain, particularly from the ventricles. Since different parts of the heart have different functions, expression profiles should likely differ between these parts. The aim of the study was therefore to compare the global gene expression in cardiac tissue from the more accessible auricula of the right atrium to expression in tissue from the left ventricle. Tissue samples were collected from five men undergoing aortic valve replacement or coronary artery bypass grafting. Global gene expression analysis identified 542 genes as differentially expressed between the samples extracted from these two locations, corresponding to ∼2% of the genes covered by the microarray; 416 genes were identified as abundantly expressed in right atrium, and 126 genes were abundantly expressed in left ventricle. Further analysis of the differentially expressed genes according to available annotations, information from curated pathways and known protein interactions, showed that genes with higher expression in the ventricle were mainly associated with contractile work of the heart. Transcription in biopsies from the auricula of the right atrium on the other hand indicated a wider area of functions, including immunity and defense. In conclusion, our results suggest that biopsies from the auricula of the right atrium may be suitable for various genetic studies, but not studies directly related to muscle work.

196 EMBRYO BIOPSY TRANSCRIPTOMICS: A POTENTIAL TOOL TO IDENTIFY TRANSCRIPTS DIRECTLY RELATED TO THE ABILITY OF THE EMBRYO TO INDUCE PREGNANCY AFTER TRANSFER

2009 ◽  
Vol 21 (1) ◽  
pp. 196
Author(s):  
D. Tesfaye ◽  
N. Ghanem ◽  
F. Rings ◽  
E. Tholen ◽  
C. Phatsara ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pregnancy Outcome ◽  
Expression Profile ◽  
Expression Profiles ◽  
Transcript Abundance ◽  
Differentially Expressed ◽  
Embryo Biopsy ◽  
Bovine Embryo

The incidence of pregnancy loss due to embryonic mortality in cattle is one of the major causes of reproductive failure. The early embryonic loss can be due to problems with the embryo itself, the uterine environment, or interactions between the embryo and the uterus. So, this study was conducted to investigate the gene expression profile of bovine embryo biopsies produced in vivo and in vitro that resulted in different pregnancy outcomes. For this, biopsies representing 30 to 40% of the intact in vitro and in vivo blastocysts were taken, and 60 to 70% part was allowed to re-expand prior to transfer to recipients. Based on the pregnancy outcome after transfer, biopsies (n = 10 per pool) were grouped into 3 distinct phenotypes: those that resulted in no pregnancy, those that resulted in resorption, and those that resulted in successful pregnancy and subsequent calf delivery. A bovine cDNA microarray with 2000 clones was used to analyze the gene expression profiles of 3 replicates from each embryo biopsy group. Array data analysis revealed a total of 50 and 52 genes to be differentially expressed between biopsies derived from in vivo blastocysts that resulted in no pregnancy v. calf delivery and resorption v. calf delivery, respectively. Similarly, a total of 52 and 58 transcripts were differentially expressed between biopsies derived from in vitro-produced blastocysts that resulted in no pregnancy v. calf delivery and resorption v. calf delivery, respectively. Quantitative real-time PCR has confirmed the expression profile of 6 selected candidate genes. A distinct set of genes were found to be commonly expressed between in vitro- and in vivo-derived blastocyst biopsies, which ended up with the same pregnancy outcome. Biopsies, which ended up with calf delivery, were found to be enriched with transcripts involved in nucleosome assembly (KRT8), translation (RPLPO), electron transport (COX-2), and placenta specific (PLAC8). On the other hand, transcripts regulating immune response (TNFa), response to stress (HSPD1), and cell adhesion (CD9) were up-regulated in embryos that resulted in no pregnancy or resorption. Differences in transcript abundance of some genes have been seen between biopsies derived from in vitro and in vivo blastocysts. Biopsies from in vivo-derived blastocysts and that ended up with resorption were found to be enriched with transcripts regulating calcium-binding protein (S100A10, S100A14). Transcription factor-related transcripts (CDX2, HOXB7) were up-regulated in vitro-derived blastocyst biopsies that resulted in no pregnancy. In conclusion, the results evidenced that embryos derived from either in vitro or in vivo have more similarities than differences in their transcript abundance with respect to the ability in initiating pregnancy.

137 SPLITTING OF IVP BOVINE BLASTOCYST AFFECTS MORPHOLOGY AND GLOBAL GENE EXPRESSION OF RESULTING DEMI-EMBRYOS DURING ELONGATION

2015 ◽  
Vol 27 (1) ◽  
pp. 161
Author(s):  
A. E. Velásquez ◽  
D. Veraguas ◽  
J. F. Cox ◽  
F. O. Castro ◽  
L. l. Rodriguez
Keyword(s):  
Gene Expression ◽  
Embryo Development ◽  
Average Length ◽  
Global Gene Expression ◽  
Differentially Expressed ◽  
Control Group ◽  
Molecular Characteristics ◽  
Bovine Embryo ◽  
Developmental Potential

Embryo splitting has been used since the early 1980s to produce identical twins and increase the pregnancy rate per available embryo. However, very little is known about the effect of splitting on embryo development and competence. Indeed splitting could provoke a negative effect on embryo survival and it can be presumed that each demi-embryo might respond differently to the injury. In this sense, even when embryos are genetically and morphologically identical at the moment of splitting, their developmental potential and molecular characteristics might change as a consequence of the intense manipulation or epigenetic differences due to the interaction with the environment. We have proposed an approach to evaluate the effect of blastocyst splitting on the morphological and gene expression in in vivo development up to the filamentous stage. For that, the effect of splitting on bovine embryo development was evaluated during the elongation period by transferring split and nonsplit IVF-derived blastocysts to cattle recipients and collecting them at Day 17 of development. The number of collected embryos, embryo size, and global gene expression was compared between both groups. Collected elongated embryos derived from split blastocyst were compared with time matched collected control embryos. From 14 transferred hemi-embryos, 5 (35.7%) were collected while 9 elongated from 17 controls were recovered (52.9%). Neither the recovery rate nor the average length of the elongated embryos was significantly different between the two treatments. However, when embryos were rated depending on their size, more than 50% of embryos from the control group had a length surpassing 100 mm, while only 33% of the split embryos reached that size. Global gene expression was performed using 2-colour microarray-based gene expression analysis. This was a whole-genome microarray study comparing 10 individual elongated embryos derived from split and nonsplit IVF blastocysts. Genes were considered differentially expressed if the fold change is greater than 2 (up or down-regulation) with P ≤ 0.05. A total of 29 585 transcripts were detected in all embryos. From those, 449 (1.5%) were differentially expressed between elongated embryos derived from split and nonsplit IVF blastocysts, among them, 248 (0.83%) genes were down-regulated and 201 (0.67%) genes were up-regulated in split embryos. Gene ontology analysis identified deregulated genes related with intrinsic component of membrane (ELOVL7, GJA1, LAPTM4B, LDLR, SLC18A2, SLC1A3, SLC38A5, TSPAN13), lipid transporter activity (RBP4, APOA1, MTTP), and organophosphate ester transport (GJA1, GJB1, ATP9B). In conclusion, we showed that splitting affect the in vivo developmental capability and gene expression profile during the elongation period of bovine embryos. However, further studies are needed to determine the long-term effect of this technique to produce viable offspring. This work was partially supported by Fondecyt No. 11100082 and Fondequip No. EQM12113 from the Ministry of Education of Chile.

Gene expression profiles of RAW264.7 macrophages stimulated with preparations of LPS differing in isolation and purity

2011 ◽  
Vol 18 (1) ◽  
pp. 80-88 ◽  
Author(s):  
Holly R Rutledge ◽  
Weiwen Jiang ◽  
Jun Yang ◽  
Laura A Warg ◽  
David A Schwartz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Transcriptional Networks ◽  
Molecular Pathways ◽  
Raw264.7 Macrophages ◽  
Lps Treatment

Lipopolysaccharide is a major component of the cell wall of Gram-negative bacteria and a potent stimulator of innate immune response via TLR4. Studies on the LPS action both in vivo and in vitro have used different preparations of LPS, including ultra-pure LPS (LIST) and a less pure but less expensive form (Sigma) isolated from Escherichia coli serotype O111:B4. The difference between the effects of these compounds has not been well studied although this information is important in understanding TLR stimulation. In this study, we compared response of RAW264.7 macrophage cells treated LIST or Sigma LPS for 6 h and 24 h. Gene expression data were analyzed to identify specific genes and pathways that are in common and unique to the two LPS preparations. Seven hundred fifty-five genes were differentially expressed at 6 h in response to Sigma LPS and 973 were differentially expressed following LIST LPS treatment, with 503 in common. At 24 h, Sigma LPS induced or repressed 901 genes while 1646 genes were differentially regulated by LIST LPS treatment; 701 genes were shared by two forms of LPS. Although considerably more genes were differentially expressed in response to LIST LPS, similar molecular pathways and transcriptional networks were activated by the two LPS preparations. We also treated bone marrow-derived macrophages (BMMs) from three strains of mice with different concentrations of LIST and Sigma LPS and showed that BMMs produced more IL-6 and TNF-α in response to LIST LPS at low LPS concentrations but, at higher LPS concentrations, more cytokines were produced in response to stimulation by Sigma LPS. Together, these findings suggest that, despite activation of similar molecular pathways by LIST and Sigma LPS preparations, residual protein impurities in the Sigma LPS preparation may nevertheless influence the transcriptional profile attributed to TLR4 stimulation.

scholarly journals Blood gene expression studies in migraine: Potential and caveats

Cephalalgia ◽  
2016 ◽  
Vol 36 (7) ◽  
pp. 669-678 ◽  
Author(s):  
Zachary Gerring ◽  
Astrid J Rodriguez-Acevedo ◽  
Joseph E Powell ◽  
Lyn R Griffiths ◽  
Grant W Montgomery ◽  
...  
Keyword(s):  
Gene Expression ◽  
Peripheral Blood ◽  
Expression Profiles ◽  
Global Gene Expression ◽  
Current Evidence ◽  
Expression Data ◽  
Tissue Samples ◽  
Blood Gene Expression ◽  
Post Mortem Brain ◽  
Gene Expression Studies

Background Global gene expression analysis may be used to obtain insights into the functional processes underlying migraine. However, there is a shortage of high-quality post-mortem brain tissue samples for genetic analysis. One approach is to use a more accessible tissue as a surrogate, such as peripheral blood. Purpose Discuss the benefits and caveats of blood genomic profiling in migraine and its potential application in the development of biomarkers of migraine susceptibility and outcome. Demonstrate the utility of blood-based expression profiles in migraine by analysing pilot Illumina HT-12 expression data from 76 (38 case, 38 control) whole-blood samples. Conclusion Current evidence suggests peripheral blood is a biologically valid substrate for genetic studies of migraine, and may be used to identify biomarkers and therapeutic pathways. Pilot blood gene expression data confirm that expression profiles significantly differ between migraine case and non-migraine control individuals.

Elucidating the molecular mechanism of cardiac remodeling using a comparative genomic approach

2003 ◽  
Vol 15 (2) ◽  
pp. 115-126 ◽  
Author(s):  
Maria Mirotsou ◽  
Coran M.H. Watanabe ◽  
Peter G. Schultz ◽  
Richard E. Pratt ◽  
Victor J. Dzau
Keyword(s):  
Gene Expression ◽  
Left Ventricle ◽  
Cardiac Remodeling ◽  
Molecular Mechanisms ◽  
Global Gene Expression ◽  
Comparative Genomic ◽  
Sham Operation ◽  
Free Wall ◽  
In Vivo Models

It is proposed that analysis of global gene expression would provide an understanding of the molecular mechanisms of cardiac remodeling. However, previous studies have only provided “snapshots” of differential gene expression. Furthermore, the differences in gene expression between regions of the heart that can result in sampling variability have not been characterized. In this study, we employed the Affymetrix GeneChip technology to evaluate the patterns of expression in two different in vivo models of cardiac remodeling and in two different regions (left ventricle free wall and intraventricular septum) of the heart. Mice underwent transverse aortic constriction (TAC), myocardial infarction (MI), or sham operation, and RNA from the left ventricle free wall and the septum was isolated 1 wk later. Histological analysis showed profound myocyte hypertrophy and fibrosis in both the septum and the left ventricle free wall of the TAC model, whereas, in the MI model, only the left ventricle exhibited hypertrophy. These differences were also reflected in the expression analysis. In conclusion, our analysis shows that regional differences in gene expression exist in the heart. Moreover, common pathways that are coregulated in both models exist, and these might be central to the hypertrophic phenotype regardless of the initial hypertrophic stimuli.

Identification of key biomarkers for thyroid cancer by integrative gene expression profiles

2021 ◽  
pp. 153537022110088
Author(s):  
Jinyi Tian ◽  
Yizhou Bai ◽  
Anyang Liu ◽  
Bin Luo
Keyword(s):  
Gene Expression ◽  
Thyroid Cancer ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Thyroid Tissue ◽  
Gene Signature ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Tissue Samples

Thyroid cancer is a frequently diagnosed malignancy and the incidence has been increased rapidly in recent years. Despite the favorable prognosis of most thyroid cancer patients, advanced patients with metastasis and recurrence still have poor prognosis. Therefore, the molecular mechanisms of progression and targeted biomarkers were investigated for developing effective targets for treating thyroid cancer. Eight chip datasets from the gene expression omnibus database were selected and the inSilicoDb and inSilicoMerging R/Bioconductor packages were used to integrate and normalize them across platforms. After merging the eight gene expression omnibus datasets, we obtained one dataset that contained the expression profiles of 319 samples (188 tumor samples plus 131 normal thyroid tissue samples). After screening, we identified 594 significantly differentially expressed genes (277 up-regulated genes plus 317 down-regulated genes) between the tumor and normal tissue samples. The differentially expressed genes exhibited enrichment in multiple signaling pathways, such as p53 signaling. By building a protein–protein interaction network and module analysis, we confirmed seven hub genes, and they were all differentially expressed at all the clinical stages of thyroid cancer. A diagnostic seven-gene signature was established using a logistic regression model with the area under the receiver operating characteristic curve (AUC) of 0.967. Seven robust candidate biomarkers predictive of thyroid cancer were identified, and the obtained seven-gene signature may serve as a useful marker for thyroid cancer diagnosis and prognosis.

Global Gene Expression Profiles of Activated CD4+CD25high (Regulatory) and CD4+CD25− (Non-Regulatory) T Cells.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3308-3308
Author(s):  
ChaoYan Liu ◽  
Qi-Hong Sun ◽  
Gian Paolo Visentin
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Cd4 T Cells ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
Differentially Expressed ◽  
Platelet Factor ◽  
Homogeneous Population

Abstract Autoreactive T and B cells can be detected in healthy individuals but are normally kept in check by regulatory mechanisms. Among those is an active suppression of naïve T cells by endogenous T regulatory (Tr) cells. Several types of Tr cells exist, including CD4+ T cells which constitutively express the IL-2 receptor α chain (CD25), do not secrete IL-10, and suppress immune responses via direct cell-to-cell interactions. CD4+CD25+ T regulatory cells represent 5%–10% of the endogenous CD4+ T cells subset and are able to suppress CD4+ and CD8+ T cell responses in vitro and in vivo upon TCR ligation. Our recent observation that human platelet factor 4 (PF4; CXCL4) inhibits the proliferative response of human CD4+CD25− T cells, while inducing expansion of CD4+CD25+ Tr cells, and that PF4-induced CD4+CD25+ Tr cells lose their potent suppressor function in vitro, suggests a previously unrecognized role of PF4 in the regulation of immune responsiveness (Liu, et al. J Immunol174:2680–86, 2005). A large body of evidence suggests that human CD4+CD25+ Tr cells share many of the characteristics of murine CD4+CD25+ Tr cells. McHugh et al. (Immunity16:311–23, 2002), have successfully used the microarray approach to identify genes differentially expressed in resting CD4+CD25+ and CD4+CD25− mouse T cells, but with the only exception of a small preliminary report (Pati et al. Ann N Y Acad Sci. 1005:279–83, 2003), little information is available on the gene expression profile of human CD4+CD25+ and CD4+CD25− T cells. We performed global gene expression analysis using oligo-DNA microarrays (CodeLink, Amersham Biosciences) that monitor the expression of whole human genome, to define the gene expression profiles in CD4+CD25+ Tr cells stimulated by anti-CD3 mAb and exposed to PF4. CD4+ T cells were isolated from normal donor’s peripheral blood mononuclear cells by positive selection on magnetic beads (Miltenyi Biotec, Auburn, CA), then labeled with PE-conjugated anti-CD4 and FITC-conjugated anti-CD25 and sorted on a FACStar (BD Biosciences, San Jose, CA) to obtain a homogeneous population of T cells consisting of CD4+CD25+ Tr cells expressing CD25 at high levels (CD4+CD25high) and CD4+CD25− T cells (non-regulatory). Total RNA was extracted from the freshly isolated CD4+CD25high and CD4+CD25− T cells subsets, stimulated with anti-CD3 mAb in the presence or the absence of PF4 for 24 hours. Using this approach, we have identified a little over 100 genes that are differentially expressed, in the presence of PF4, in CD4+CD25+ Tr cells following activation with anti-CD3 mAb. We have focused our attention on about 40 target genes whose increased expression has been validated using real time PCR and, were appropriate, at the protein levels, by flow cytometry or Luminex 100 multiplex cytokine quantification (Table 1). Our data suggest that PF4 modulates proliferation and function of CD4+CD25+ Tr cells by the coordinate increasing expression of a relatively large number of genes, coupled with a further enhanced expression of a limited number of growth promoting genes and the specific silencing of a small subset of negative growth regulatory genes.

Global Gene Expression Revealed a Set of Genes Involved in the Modification of Cells during Erythropoiesis.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 4074-4074
Author(s):  
Anderson F. Cunha ◽  
Ana F. Brugnerotto ◽  
Adriana S.S. Duarte ◽  
Gustavo G.L. Costa ◽  
Sara T.O. Saad ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Differentiation ◽  
Blood Cell ◽  
Red Blood Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Erythroid Differentiation ◽  
Global Gene Expression ◽  
Differentially Expressed ◽  
Globin Genes

Abstract Erythroid differentiation is a dynamic and complex process in which a pluripotent stem cell undergoes a series of developmental changes that commit it to a specific lineage. These alterations involve changes in gene expression profiles. Extensive studies have led to a considerable understanding of the cellular and molecular control of hemoglobin production during red blood cell differentiation, however, a complete understanding of human erythropoiesis will require a robust description of the entire transcriptome of these cells during differentiation. From a global point of view of cell metabolic regulation, where genomic information could be complemented with gene expression, the use of methods that enable quantification of the entire transcriptome of the red blood cell during differentiation is of great importance. In this study, the gene expression profiles during differentiation of Human erythroid cells of a normal blood donor in a two-phase liquid culture (Fibach & Rachmilewitz, 1993) were evaluated using Serial analysis of gene expression (SAGE). Global gene expression was evaluated in cells collected immediately before the addition of erythropoeitin (0 hour) and 192 and 336 hours after the addition of this hormone. We generated a total of 30512 tags at 0h, 30117 tags at 192h and 30189 tags at 336h, representing 12026, 11709 and 11337 unique tags, respectively. In the 0h library, a high expression of ferritin genes and CD74 antigen gene was observed. As expected, the expression of globin genes started during intermediate stages of differentiation (predominantly basophilic erythroblasts) and were the most expressed genes at the end of the culture (predominantly orthocromatic erythroblasts). Ribosomal genes were the most expressed genes at 192 hours, indicating an increase in protein synthesis. To identify the genes that were differentially expressed between the libraries, a P value < 0.01 and fold ≥ 5 were considered as statistically significant. In the comparison of the 0h and 192h libraries, 179 differentially expressed transcripts were identified. From these genes, in addition to the globin genes, we found an up-regulation of several genes related to protein binding (LXN, GSTM3, and TRIP6), transcription factor (GATA-1), hydrolase activity (TPSAB1), ion transport (SLC12A9) and regulation of apoptosis (PRDX2). Comparing the 192h and 336h libraries, 103 differentially expressed transcripts were identified. The up-regulated genes were generally related to hemoglobin synthesis, such as ALAS2, involved in the biosynthesis of the heme group or related to intracellular transport such as MSCP and NUDT4 and cell differentiation such as GDF15. The transcription of some of these genes, such as SLC12A9, TRB3, EYA3 and TWIST2 are described for the first time during erythroid differentiation. The results indicated that the global aspects of the transcriptome were similar during differentiation for the majority of the genes and that probably a relative small set of genes is involved in the modification of erythroid cells during differentiation. The results of this study amplify the previous published data (Komor et al, 2005) and may contribute to the comprehension of erythroid differentiation and identification of new target genes involved in some erythroid diseases.

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