scholarly journals Two thyroid hormone-mediated gene expression patterns in vivo identified by cDNA expression arrays in rat

2001 ◽  
Vol 29 (24) ◽  
pp. 5148-5155 ◽  
Author(s):  
J. M. Weitzel
2003 ◽  
Vol 31 (2) ◽  
pp. 291-303 ◽  
Author(s):  
JM Weitzel ◽  
S Hamann ◽  
M Jauk ◽  
M Lacey ◽  
A Filbry ◽  
...  

Thyroid hormone (T3) is essential for normal development, differentiation and metabolic balance. We have performed DNA microarray experiments using hepatic RNA from hypothyroid and T3-treated hypothyroid rats in order to characterize T3-induced gene expression patterns after various time points (6, 24 and 48 h after the administration of the hormone). Sixty-two of 4608 different genes displayed a reproducible T3-response, and cluster analysis divided these differentially regulated genes into six expression patterns. Thirty-six genes were not significantly regulated within the first 24 h. Transient transfection experiments of eight late-induced gene promoters failed to detect a thyroid hormone response element within their regulatory elements, suggesting an indirect activation mechanism(s). In search for an intermediate factor of T3 action, we examined whether various rather ubiquitous transcription factors, peroxisome proliferator-activated receptors (PPARs) and coactivators of the PPARgamma coactivator 1 family (PGC-1) are regulated by T3. Only PPARgamma and PERC/PGC-1beta exhibit a significant T3-response within the first 6 h after treatment, identifying these factors as candidate components for mediating the late-induced expression pattern. Regulation of early-induced genes within the first 6 h after administration of T3 on transcript levels correlates with altered protein levels after 24 and 48 h in vivo.


2006 ◽  
Vol 18 (2) ◽  
pp. 142
Author(s):  
N. Ruddock ◽  
K. Wilson ◽  
M. Cooney ◽  
R. Tecirlioglu ◽  
V. Hall ◽  
...  

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.


Author(s):  
Dina Nitiša ◽  
Nityanand Jain ◽  
Arvīds Irmejs ◽  
Valdis Pirsko ◽  
Inese Čakstiņa

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.


2018 ◽  
Author(s):  
Nikita Mukhitov ◽  
Michael G. Roper

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.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 546-546
Author(s):  
Amit K Mittal ◽  
Javeed Iqbal ◽  
Tara Marie Nordgren ◽  
Margaret Moragues ◽  
R. Gregory Bociek ◽  
...  

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<0.005) overexpressed CXCR4 and CCR7 compared to BM-CLL and LN-CLL cells. The ligands CCL21 and CXCL13 were significantly overexpressed (p<0.005 and p<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<0.05) and PB-CLL (p<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<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<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<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.


2007 ◽  
Vol 18 (11) ◽  
pp. 4245-4260 ◽  
Author(s):  
Annika M. Sääf ◽  
Jennifer M. Halbleib ◽  
Xin Chen ◽  
Siu Tsan Yuen ◽  
Suet Yi Leung ◽  
...  

Posttranslational mechanisms are implicated in the development of epithelial cell polarity, but little is known about the patterns of gene expression and transcriptional regulation during this process. We characterized temporal patterns of gene expression during cell–cell adhesion-initiated polarization of cultured human Caco-2 cells, which develop structural and functional polarity resembling enterocytes in vivo. A distinctive switch in gene expression patterns occurred upon formation of cell–cell contacts. Comparison to gene expression patterns in normal human colon and colon tumors revealed that the pattern in proliferating, nonpolarized Caco-2 cells paralleled patterns seen in human colon cancer in vivo, including expression of genes involved in cell proliferation. The pattern switched in polarized Caco-2 cells to one more closely resembling that in normal colon tissue, indicating that regulation of transcription underlying Caco-2 cell polarization is similar to that during enterocyte differentiation in vivo. Surprisingly, the temporal program of gene expression in polarizing Caco-2 cells involved changes in signaling pathways (e.g., Wnt, Hh, BMP, FGF) in patterns similar to those during migration and differentiation of intestinal epithelial cells in vivo, despite the absence of morphogen gradients and interactions with stromal cells characteristic of enterocyte differentiation in situ. The full data set is available at http://microarray-pubs.stanford.edu/CACO2 .


2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Yijiang Huang ◽  
Daniel Seitz ◽  
Yan Chevalier ◽  
Peter E. Müller ◽  
Volkmar Jansson ◽  
...  

Abstract Background Human TGF-β3 has been used in many studies to induce genes coding for typical cartilage matrix components and accelerate chondrogenic differentiation, making it the standard constituent in most cultivation media used for the assessment of chondrogenesis associated with various stem cell types on carrier matrices. However, in vivo data suggests that TGF-β3 and its other isoforms also induce endochondral and intramembranous osteogenesis in non-primate species to other mammals. Based on previously demonstrated improved articular cartilage induction by a using hTGF-β3 and hBMP-6 together on hADSC cultures and the interaction of TGF- β with matrix in vivo, the present study investigates the interaction of a chitosan scaffold as polyanionic polysaccharide with both growth factors. The study analyzes the difference between chondrogenic differentiation that leads to stable hyaline cartilage and the endochondral ossification route that ends in hypertrophy by extending the usual panel of investigated gene expression and stringent employment of quantitative PCR. Results By assessing the viability, proliferation, matrix formation and gene expression patterns it is shown that hTGF-β3 + hBMP-6 promotes improved hyaline articular cartilage formation in a chitosan scaffold in which ACAN with Col2A1 and not Col1A1 nor Col10A1 where highly expressed both at a transcriptional and translational level. Inversely, hTGF-β3 alone tended towards endochondral bone formation showing according protein and gene expression patterns. Conclusion These findings demonstrate that clinical therapies should consider using hTGF-β3 + hBMP-6 in articular cartilage regeneration therapies as the synergistic interaction of these morphogens seems to ensure and maintain proper hyaline articular cartilage matrix formation counteracting degeneration to fibrous tissue or ossification. These effects are produced by interaction of the growth factors with the polysaccharide matrix.


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