scholarly journals Candidate gene expression patterns in rabbit preimplantation embryos developed in vivo and in vitro

2014 ◽  
Vol 31 (7) ◽  
pp. 899-911 ◽  
Author(s):  
Gibence Rose Winnie Henderson ◽  
Sambasiva Rao Brahmasani ◽  
Uma Mahesh Yelisetti ◽  
Suman Konijeti ◽  
Venu Charan Katari ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candidate Gene ◽  
Expression Patterns ◽  
Preimplantation Embryos ◽  
Gene Expression Patterns

68 GENE EXPRESSION COMPARISONS BETWEEN BOVINE IN VIVO AND CLONED EMBRYOS PRODUCED BY THREE DIFFERENT METHODS

2006 ◽  
Vol 18 (2) ◽  
pp. 142
Author(s):  
N. Ruddock ◽  
K. Wilson ◽  
M. Cooney ◽  
R. Tecirlioglu ◽  
V. Hall ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Remodeling ◽  
Nuclear Transfer ◽  
Expression Patterns ◽  
Experimental Models ◽  
Gene Expression Patterns ◽  
Imprinted Genes ◽  
Mammalian Embryo

Developmental pathways in the mammalian embryo are profoundly influenced by the epigenetic interaction of the environment and the genome. Loss of epigenetic control has been implicated in aberrant gene expression and altered imprinting patterns with consequence to the physiology and viability of the conceptus. Bovine somatic cell nuclear transfer (SCNT) is contingent on in vitro culture, and both SCNT and culture conditions are known to induce changes in embryonic gene expression patterns. Using these experimental models, this study compared gene expression of Day 7 cloned blastocysts created from three different SCNT protocols using the same cell line, with Day 7 in vivo blastocysts to elucidate mechanisms responsible for variations in phenotypic outcomes. SCNT methods included: (1) traditional SCNT by subzonal injection (SI); (2) handmade cloning (HMC); and (3) modified serial nuclear transfer (SNT), developed within the group. Four imprinted genes (Grb10, Ndn, Nnat, and Ube3a), four chromatin remodeling genes (Cbx1, Cbx3, Smarca4, and Smarcb1) and two genes implicated in polycystic liver disease (Prkcsh and Sec63) were analyzed in single blastocysts from each treatment (n = 5). All blastocysts expressed Actin, Oct-4 and Ifn-tau. All genes were sequence verified. Several genes were expressed ubiquitously across all groups, including Ndn, Ube3a, Cbx1, Cbx3, and Smarcb1. Interestingly, Grb10 was not expressed in two HMCs and one SNT blastocyst. Nnat was weakly expressed in one in vivo blastocyst and in the majority of cloned blastocysts in all groups. Prkcsh and Sec63 were expressed in all but one HMC blastocyst. While gene expression patterns were mostly maintained following SCNT, the imprinted genes Nnat and Grb10 showed instances of differential or abnormal expression in SCNT embryos. The chromatin remodeling genes were maintained in all SCNT treatments. Prkcsh and Sec63 were both absent in one HMC blastocyst, with implications for liver dysfunction, a condition previously reported in abnormal cloned offspring. The variable mRNA expression following SCNT provides an insight into genetic and environmental factors controlling implantation, placentation, organ formation, and fetal growth.

scholarly journals From In Vivo to In Vitro: Dynamic Analysis of Plasmodium falciparum var Gene Expression Patterns of Patient Isolates during Adaptation to Culture

PLoS ONE ◽  
2011 ◽  
Vol 6 (6) ◽  
pp. e20591 ◽  
Author(s):  
Qingfeng Zhang ◽  
Yilong Zhang ◽  
Yufu Huang ◽  
Xiangyang Xue ◽  
He Yan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plasmodium Falciparum ◽  
Dynamic Analysis ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Var Gene

scholarly journals Developmental and molecular correlates of bovine preimplantation embryos

Reproduction ◽  
2006 ◽  
Vol 131 (5) ◽  
pp. 895-904 ◽  
Author(s):  
Hakan Sagirkaya ◽  
Muge Misirlioglu ◽  
Abdullah Kaya ◽  
Neal L First ◽  
John J Parrish ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methyltransferase ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Blastocyst Stage ◽  
Culture Conditions ◽  
Preimplantation Embryos ◽  
Developmental Potential

Expression of embryonic genes is altered in different culture conditions, which influence developmental potential both during preimplantation and fetal development. The objective of this study was to define the effects of culture conditions on: bovine embryonic development to blastocyst stage, blastocyst cell number, apoptosis and expression patterns of a panel of developmentally important genes. Bovine embryos were culturedin vitroin three culture media containing amino acids, namely potassium simplex optimization medium (KSOMaa), Charles Rosenkrans 1 (CR1aa) and synthetic oviductal fluid (SOFaa). Apoptosis in blastocysts was determined by TUNEL assay and expression profiles of developmentally important genes were assayed by real-time PCR.In vivo-produced bovine blastocysts were used as controls for experiments determining gene expression patterns. While the cleavage rates did not differ, embryos cultured in SOFaa had higher rates of development to blastocyst stage (P< 0.05). Mean cell numbers and percentages of apoptotic cells per blastocyst did not differ among the groups. Expression of the heat shock protein 70 (Hsp70) gene was significantly up-regulated in both CR1aa and KSOMaa when compared with SOFaa (P< 0.001). DNA methyltransferase 3a (Dnmt3a) expression was higher in embryos cultured in CR1aa than in those cultured in SOFaa (P< 0.001). Expression of interferon tau (IF-τ) and insulin-like growth factor II receptor (Igf-2r) genes was significantly up-regulated in KSOMaa when compared with CR1aa (P< 0.001). Gene expression did not differ betweenin vivo-derived blastocysts and theirin vitro-derived counterparts. In conclusion, SOFaa supports higher development to blastocyst stage than KSOMaa and CR1aa, and the culture conditions influence gene expression.

scholarly journals Recapitulation of Transcriptomic Characteristics of Primary Breast Tumours in Patient-Derived 3D Cultures in Vitro

2021 ◽  
Vol 75 (1) ◽  
pp. 20-24
Author(s):  
Dina Nitiša ◽  
Nityanand Jain ◽  
Arvīds Irmejs ◽  
Valdis Pirsko ◽  
Inese Čakstiņa
Keyword(s):  
Gene Expression ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
3D Cell Culture ◽  
Model System ◽  
Gene Expression Patterns ◽  
3D Cultures ◽  
Culture Development

AbstractBreast cancer (BC) is the most common cause of cancer-related deaths among women in Europe and worldwide. Adherent (2D) cell cultures have been the routine in vitro model system employed in preclinical BC research for the last half-century. Over the past decade, new protocols have been developed allowing patient-derived three-dimensional organoid (3D) cell culture development from a range of solid tumours, including BC. These 3D models offer a promise of closer resemblance to the native tumour than the 2D cultures. To test the assumption that an in vitro 3D BC model system provides increased faithfulness to the molecular processes happening in vivo, as compared to 2D BC cultures, post-operational material from three BC patients was used to simultaneously develop 2D and 3D cultures in vitro. When analysed by quantitative polymerase chain reaction (PCR), the gene expression patterns of the cells from 3D cultures resembled the original tissues, while the gene expression patterns of the conventional 2D cultures were more distant.

scholarly journals Gene expression patterns in synchronized islet populations

2018 ◽  
Author(s):  
Nikita Mukhitov ◽  
Michael G. Roper
Keyword(s):  
Gene Expression ◽  
Environmental Changes ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Protein Translation ◽  
Gene Set Enrichment Analysis ◽  
Gene Expression Patterns ◽  
Insulin Synthesis

AbstractIn vivo levels of insulin are oscillatory with a period of ~5-10 minutes, implying that the numerous islets of Langerhans within the pancreas are synchronized. While the synchronizing factors are still under investigation, one result of this behavior is expected to be coordinated intracellular [Ca2+] ([Ca2+]i) oscillations throughout the islet population. The role that coordinated [Ca2+]i oscillations have on controlling gene expression within pancreatic islets was examined by comparing gene expression levels in islets that were synchronized using a low amplitude glucose wave and an unsynchronized population. The [Ca2+]i oscillations in the synchronized population were homogeneous and had a significantly lower drift in their oscillation period as compared to unsynchronized islets. This reduced drift in the synchronized population was verified by comparing the drift of in vivo and in vitro profiles from published reports. Microarray profiling indicated a number of Ca2+-dependent genes were differentially regulated between the two islet populations. Gene set enrichment analysis revealed that the synchronized population had reduced expression of gene sets related to protein translation, protein turnover, energy expenditure, and insulin synthesis, while those that were related to maintenance of cell morphology were increased. It is speculated that these gene expression patterns in the synchronized islets results in a more efficient utilization of intra-cellular resources and response to environmental changes.

scholarly journals Human 21T breast epithelial cell lines mimic breast cancer progression in vivo and in vitro and show stage-specific gene expression patterns

2010 ◽  
Vol 90 (8) ◽  
pp. 1247-1258 ◽  
Author(s):  
Lesley H Souter ◽  
Joseph D Andrews ◽  
Guihua Zhang ◽  
Amy C Cook ◽  
Carl O Postenka ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cancer Progression ◽  
Expression Patterns ◽  
Breast Epithelial Cell ◽  
Gene Expression Patterns ◽  
Specific Gene ◽  
Epithelial Cell Lines

Molecular Basis of Proliferation/Survival and Migration of CLL in Peripheral Blood, Bone Marrow and Lymph Nodes

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 546-546
Author(s):  
Amit K Mittal ◽  
Javeed Iqbal ◽  
Tara Marie Nordgren ◽  
Margaret Moragues ◽  
R. Gregory Bociek ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
B Cell ◽  
Chemokine Receptors ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Bcr Signaling ◽  
And Migration

Abstract B-cell chronic lymphocytic leukemia (CLL) is a heterogenous and incurable B-cell malignancy. CLL cells migrate and accumulate in different sites including the peripheral blood (PB), bone marrow (BM) and lymph nodes (LN) in vivo, but undergo apoptosis in vitro. Therefore, we hypothesized that CLL cells at these sites are different and receive different microenvironmental signals that regulate their proliferation/survival and migration. Most reports on the microenvironmental influence on CLL cells have used in vitro models consisting of stromal and CLL cells. However, in this study, to better understand the influence of site-specific microenvironments in vivo, gene expression patterns of CLL cells obtained from PB, BM and LN were investigated. CLL cells were isolated from patients’ PB (PB-CLL, n= 20), BM (BM-CLL, n=14) and LN (LN-CLL, n=15) and used to determine the gene expression patterns by microarray analysis. In addition, we also included PB-CLL cases from our previous study (n=40) to further validate the findings of this study. Significant Analyses of Microarray (SAM) revealed differential expression of more than 500 genes among these three sites. To understand the potential roles of these differentially-expressed genes and their association with relevant functional pathways in CLL, Gene Set Enrichment Analysis (GSEA) was performed. The validation of pathway specific genes was further confirmed by quantitative real time PCR. Among the pathways identified, the most active pathways associated with the migration and proliferation/survival of CLL cells, namely chemokine-signaling, BCR signaling, BAFF/APRIL-signaling, and NFκB-signaling pathways, were selected for further analyses. We hypothesized that chemokines and their receptors mediate the migration of CLL cells between PB and LN or BM, and that molecules of the BCR, BAFF/APRIL and NFκB pathways regulate proliferation/survival. To determine the role of chemokines and their receptors in CLL cell migration, we studied the expression of 52 chemokine/chemokine receptors and found that PB-CLL cells significantly (p&lt;0.005) overexpressed CXCR4 and CCR7 compared to BM-CLL and LN-CLL cells. The ligands CCL21 and CXCL13 were significantly overexpressed (p&lt;0.005 and p&lt;0.01 respectively) in LN-CLL. These results indicate that PB-CLL cells express distinct chemokine receptors which may lead them to home to BM or LN and receive stimuli to form proliferation centers. Based on GSEA analysis, the stimuli for proliferation/survival for CLL cells in the LN and BM are provided by Syk and Btk (BCR signaling), BAFF and TRAF2 (BAFF/APRIL signaling), and several targets of the NFκB pathways. Syk and Btk were significantly overexpressed in LN-CLL (p&lt;0.05) and PB-CLL (p&lt;0.005) compared to BM-CLL, with the highest expression in LN-CLL, suggesting chronic activation of CLL cells in lymph node. Similarly, BAFF and TRAF2 were significantly overexpressed (p&lt;0.03) in LN-CLL compared to PB-CLL and BM-CLL. Furthermore, the NFκB pathway, which is important for the proliferation and survival, also showed distinct association in different CLL-cell compartments. The RELA, NFκB1, NFκB2, TNFAIP3 and NFκB regulators such as NFκBIA, NFκBIE were also significantly (p&lt;0.01) overexpressed in PB-CLL and BM-CLL compared to LN-CLL with highest expression in BM-CLL. Whereas few NFκB associated genes such as NFκB1L1 and RelB were significantly (p&lt;0.02) expressed in LN-CLL cells. Thus, differentially-expressed NFkB genes among PB-CLL, BM-CLL and LN-CLL cells indicate that these different CLL cells utilize different NFκB molecules for proliferation/survival. Together, our results show that CLL cells from different in vivo microenvironments such as PB, BM and LN exhibit differential gene expression patterns, and many of the genes are involved in regulation of migration and proliferation/survival. Furthermore, LN-CLL cells expressing chemokine ligands, BCR, BAFF and NFκB signaling molecules attract other cells including more CLL cells to form an optimal microenvironment which provide prosurvival and proliferative signals to CLL cells.

Gene expression patterns of the liver in response to alcohol: In vivo and in vitro models compared

2006 ◽  
Vol 80 (3) ◽  
pp. 241-251 ◽  
Author(s):  
Fawzia Bardag-Gorce ◽  
Barbara A. French ◽  
Jennifer Dedes ◽  
Jun Li ◽  
Samuel W. French
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
In Vitro Models ◽  
Gene Expression Patterns

scholarly journals IFN-g-induced Jmjd3-Zeb1 axis contributes to an aggressive phenotype in lung adenocarcinoma

2020 ◽  
Author(s):  
Jianjian Yang ◽  
Xue Wang ◽  
Bing Huang ◽  
Rong Liu ◽  
Hui Xiong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Cell Migration ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Ifn Γ ◽  
Zeb1 Expression

Abstract Background Active IFN-γ signaling is a common feature of tumors responding to PD-1 checkpoint blockade. IFN-γ exhibits both anti- and pro-tumor activities. Therefore, identifying the pro-tumor effects of IFN-γ and their underlying molecular mechanisms could be a critical step for developing therapeutic strategies to maximize the anti-tumor efficacy of immunotherapies. Methods Western blot, immunofluorescence, and quantitative real-time PCR assays were used to evaluate the expression of ZEB1 and EMT associated biomarkers. Trans-well assay was used to examine the role of IFN-γ on cancer cell migration in vitro. Murine tumor xenograft models were performed to examine the effect of IFN-γ on cancer cell metastasis in vivo. Colony formation assay was performed to detect the role of ZEB1 in cell proliferation. RNA-seq was performed to analyze the EMT-associated gene expression patterns in response to IFN-g treatment. Loss-of-function analysis and chromatin immunoprecipitation were used to reveal the mechanism underlying ZEB1 induction by IFN-γ. Results we demonstrate that the treatment of lung adenocarcinoma cells with IFN-γ leads to a rapid increase of ZEB1 expression and a significant change in epithelial-mesenchymal-transition (EMT)-associated gene expression patterns. Moreover, functional analysis shows that IFN-γ promotes cell migration in vitro and metastasis in vivo. Mechanistically, IFN-γ-induced JMJD3 significantly reduces H3K27 trimethylation in the promoter of the ZEB1 gene, thereby activating ZEB1 transcription. Inhibition of JMJD3 abrogates IFN-γ-induced ZEB1 expression. We previously demonstrated that IFN-γ-mediated anti-tumor response, including suppression of cell proliferation and induction of CXCL9 and CXCL10 expression, is STAT1-IRF1 dependent. The knockdown of ZEB1 diminishes IFN-γ-mediated cell migration and metastasis, but it does not affect STAT1 and IRF1 expression and has no effect on cell proliferation as well as the induction of CXCL9 and CXCL10 expression. Conclusion Inhibition or downregulation of ZEB1 may prevent the pro-tumor activity of IFN-γ while retaining its anti-tumor function. The study expands our understanding of IFN-γ-mediated signaling and helps to identify therapeutic targets to improve current immunotherapies.

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