scholarly journals Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent

2011 ◽  
Vol 22 (3) ◽  
pp. 456-466 ◽  
Author(s):  
J. E. Powell ◽  
A. K. Henders ◽  
A. F. McRae ◽  
M. J. Wright ◽  
N. G. Martin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Control ◽  
Cell Lines ◽  
Whole Blood ◽  
Lymphoblastoid Cell Lines ◽  
Control Of Gene Expression

Cell-specific posttranscriptional regulation of CFTR gene expression via influence of MAPK cascades on 3′UTR part of transcripts

2005 ◽  
Vol 289 (5) ◽  
pp. C1240-C1250 ◽  
Author(s):  
Maryvonne Baudouin-Legros ◽  
Alexandre Hinzpeter ◽  
Amandine Jaulmes ◽  
Franck Brouillard ◽  
Bruno Costes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Posttranscriptional Regulation ◽  
P38 Map Kinase ◽  
Cftr Gene ◽  
Control Of Gene Expression ◽  
Cytosolic Proteins ◽  
Tnf Α ◽  
Ht 29

Expression of the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene, which contains the mutations responsible for CF, is regulated by cytokines (TNF-α and IL-1β) in a cell-specific manner. TNF-α decreases CFTR mRNA in human colon cell lines (HT-29), but not in pulmonary cell lines (Calu-3), and IL-1β increases it only in Calu-3 cells. We looked for the cytokine-induced posttranscriptional regulation of CFTR gene expression and studied the modulation of CFTR mRNA stability linked to its 3′ untranslated sequence (3′UTR) in HT-29 and Calu-3 cells. The stability of CFTR mRNA was analyzed by Northern blot after in vitro incubation of total RNAs from CFTR-expressing cells with cytosolic proteins extracted from control or cytokine-treated HT-29 and Calu-3 cells. CFTR mRNA was degraded only by extracts of TNF-α-treated HT-29 cells and not by cytosolic proteins from untreated or IL-1β-treated HT-29 cells. In contrast, extracts of untreated Calu-3 cells enhanced CFTR mRNA degradation, and IL-1β treatment inhibited this; TNF-α had no significant effect. The 3′UTR part of CFTR mRNA was found to be required for this posttranscriptional regulation. The 5′ part of the 3′UTR (the 217 first bases), which contains two AUUUA sequences, was implicated in CFTR mRNA destabilization and the following 136 bases, containing several C-repeats in U-rich environment, in its protection. The proteins, which reacted with the U- and C-repeats of CFTR mRNA 3′UTR, were mainly controlled by stimulation of the p42/p44 and p38 MAP kinase cascades with interaction between these pathways. This posttranscriptional control of gene expression is a common feature of CFTR and many proteins of inflammation.

scholarly journals The Effect of Freeze-Thaw Cycles on Gene Expression Levels in Lymphoblastoid Cell Lines

PLoS ONE ◽  
2014 ◽  
Vol 9 (9) ◽  
pp. e107166 ◽  
Author(s):  
Minal Çalışkan ◽  
Jonathan K. Pritchard ◽  
Carole Ober ◽  
Yoav Gilad
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Lymphoblastoid Cell Lines ◽  
Expression Levels ◽  
Freeze Thaw ◽  
Gene Expression Levels

scholarly journals Gene expression analysis of whole blood, peripheral blood mononuclear cells, and lymphoblastoid cell lines from the Framingham Heart Study

2012 ◽  
Vol 44 (1) ◽  
pp. 59-75 ◽  
Author(s):  
Roby Joehanes ◽  
Andrew D. Johnson ◽  
Jennifer J. Barb ◽  
Nalini Raghavachari ◽  
Poching Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Peripheral Blood Mononuclear Cells ◽  
Whole Blood ◽  
Peripheral Blood ◽  
Gene Expression Analysis ◽  
Mononuclear Cells ◽  
Smoking Status ◽  
Lymphoblastoid Cell Lines ◽  
Peripheral Blood Mononuclear ◽  
Blood Mononuclear Cells

Despite a growing number of reports of gene expression analysis from blood-derived RNA sources, there have been few systematic comparisons of various RNA sources in transcriptomic analysis or for biomarker discovery in the context of cardiovascular disease (CVD). As a pilot study of the Systems Approach to Biomarker Research (SABRe) in CVD Initiative, this investigation used Affymetrix Exon arrays to characterize gene expression of three blood-derived RNA sources: lymphoblastoid cell lines (LCL), whole blood using PAXgene tubes (PAX), and peripheral blood mononuclear cells (PBMC). Their performance was compared in relation to identifying transcript associations with sex and CVD risk factors, such as age, high-density lipoprotein, and smoking status, and the differential blood cell count. We also identified a set of exons that vary substantially between participants, but consistently in each RNA source. Such exons are thus stable phenotypes of the participant and may potentially become useful fingerprinting biomarkers. In agreement with previous studies, we found that each of the RNA sources is distinct. Unlike PAX and PBMC, LCL gene expression showed little association with the differential blood count. LCL, however, was able to detect two genes related to smoking status. PAX and PBMC identified Y-chromosome probe sets similarly and slightly better than LCL.

scholarly journals SUMO Paralog Specific Functions Revealed through Systematic Analysis of Human Knockout Cell Lines and Gene Expression Data

2021 ◽  
pp. mbc.E21-01-0031
Author(s):  
Danielle Bouchard ◽  
Wei Wang ◽  
Wei-Chih Yang ◽  
Shuying He ◽  
Anthony Garcia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Genotoxic Stress ◽  
Nuclear Body ◽  
Human Tissues ◽  
Cellular Functions ◽  
Systematic Analysis ◽  
Control Of Gene Expression ◽  
Knock Out ◽  
Sequence Homologies

The small ubiquitin-related modifiers (SUMOs) regulate nearly every aspect of cellular function, from gene expression in the nucleus to ion transport at the plasma membrane. In humans, the SUMO pathway has five SUMO paralogs with sequence homologies that range from 45% to 97%. SUMO1 and SUMO2 are the most distantly related paralogs, and also the best studied. To what extent SUMO1, SUMO2 and the other paralogs impart unique and non-redundant effects on cellular functions, however, has not been systematically examined and is therefore not fully understood. For instance, knockout studies in mice have revealed conflicting requirements for the paralogs during development and studies in cell culture have relied largely on transient paralog overexpression or knockdown. To address the existing gap in understanding, we first analyzed SUMO paralog gene expression levels in normal human tissues and found unique patterns of SUMO1-3 expression across 30 tissue types, suggesting paralog-specific functions in adult human tissues. To systematically identify and characterize unique and non-redundant functions of the SUMO paralogs in human cells, we next used CRISPR-Cas9 to knock out SUMO1 and SUMO2 expression in osteosarcoma (U2OS) cells. Analysis of these knockout cell lines revealed essential functions for SUMO1 and SUMO2 in regulating cellular morphology, PML nuclear body structure, responses to proteotoxic and genotoxic stress, and control of gene expression. Collectively, our findings reveal non-redundant regulatory roles for SUMO1 and SUMO2 in controlling essential cellular processes and provide a basis for more precise SUMO-targeting therapies.

scholarly journals DUX4 expressing immortalized FSHD lymphoblastoid cells express genes elevated in FSHD muscle biopsies, correlating with the early stages of inflammation

2020 ◽  
Vol 29 (14) ◽  
pp. 2285-2299 ◽  
Author(s):  
Christopher R S Banerji ◽  
Maryna Panamarova ◽  
Peter S Zammit
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Target Gene ◽  
Target Genes ◽  
Ectopic Expression ◽  
Lymphoblastoid Cell Lines ◽  
Immune Gene ◽  
Target Gene Expression ◽  
Early Stages ◽  
Muscle Biopsies

Abstract Facioscapulohumeral muscular dystrophy (FSHD) is an incurable disorder linked to ectopic expression of DUX4. However, DUX4 is notoriously difficult to detect in FSHD muscle cells, while DUX4 target gene expression is an inconsistent biomarker for FSHD skeletal muscle biopsies, displaying efficacy only on pathologically inflamed samples. Immune gene misregulation occurs in FSHD muscle, with DUX4 target genes enriched for those associated with inflammatory processes. However, there lacks an assessment of the FSHD immune cell transcriptome, and its contribution to gene expression in FSHD muscle biopsies. Here, we show that EBV-immortalized FSHD lymphoblastoid cell lines express DUX4 and both early and late DUX4 target genes. Moreover, a biomarker of 237 up-regulated genes derived from FSHD lymphoblastoid cell lines is elevated in FSHD muscle biopsies compared to controls. The FSHD Lymphoblast score is unaltered between FSHD myoblasts/myotubes and their controls however, implying a non-myogenic cell source in muscle biopsies. Indeed, the FSHD Lymphoblast score correlates with the early stages of muscle inflammation identified by histological analysis on muscle biopsies, while our two late DUX4 target gene expression biomarkers associate with macroscopic inflammation detectable via MRI. Thus, FSHD lymphoblastoid cell lines express DUX4 and early and late DUX4 target genes, therefore, muscle-infiltrated immune cells may contribute the molecular landscape of FSHD muscle biopsies.

scholarly journals Cellular Gene Expression That Correlates with EBER Expression in Epstein-Barr Virus-Infected Lymphoblastoid Cell Lines

2011 ◽  
Vol 85 (7) ◽  
pp. 3535-3545 ◽  
Author(s):  
G. Gregorovic ◽  
R. Bosshard ◽  
C. E. Karstegl ◽  
R. E. White ◽  
S. Pattle ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Epstein Barr Virus ◽  
Lymphoblastoid Cell Lines ◽  
Cellular Gene ◽  
Cellular Gene Expression ◽  
Barr Virus ◽  
Epstein Barr
Sign in / Sign up

Export Citation Format

Share Document