Prokaryotic Real-Time Gene Expression Profiling for Toxicity Assessment

2009 ◽  
Vol 43 (12) ◽  
pp. 4574-4581 ◽  
Author(s):  
Annalisa Onnis-Hayden ◽  
Haifeng Weng ◽  
Miao He ◽  
Sonja Hansen ◽  
Valentin Ilyin ◽  
...  
Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2277-2277
Author(s):  
Daruka Mahadevan ◽  
Catherine Spier ◽  
Kimiko Della Croce ◽  
Susan Miller ◽  
Benjamin George ◽  
...  

Abstract Background: WHO classifies NHL into B (~85%) and T (~15%) cell subtypes. Of the T-cell NHL, peripheral T-cell NHL (PTCL, NOS) comprises ~6–10% with an inferior response and survival to chemotherapy compared to DLBCL. Gene Expression Profiling (GEP) of DLBCL has provided molecular signatures that define 3 subclasses with distinct survival rates. The current study analyzed transcript profiling in PTCL (NOS) and compared and contrasted it to GEP of DLBCL. Methods : Snap frozen samples of 5 patients with PTCL (NOS) and 4 patients with DLBCL were analyzed utilizing the HG-U133A 2.0 Affymetrix array (~18,400 transcripts, 22,000 probe sets) after isolating and purifying total RNA (Qiagen, RNAeasy). The control RNA samples were isolated from normal peripheral blood (PB) B-cell (AllCell, CA), normal PB T-cell (AllCell, CA) and normal lymph node (LN). Immunohisto-chemistry (IHC) confirmed tumor lineage and quantitative real time RT-PCR was performed on selected genes to validate the microarray study. The GEP data were processed and analyzed utilizing Affymetrix MAS 5.0 and GeneSpring 5.0 software. Our data were analyzed in the light of the published GEP of DLBCL (lymphochip and affymtrix) and the validated 10 prognostic genes (by IHC and real time RT-PCR). Results : Data are represented as “robust” increases or decreases of relative gene expression common to all 5 PTCL or 4 DLBCL patients respectively. The table shows the 5 most over-expressed genes in PTCL or DLBCL compared to normal T-cell (NT), B-cell (NB) and lymph node (LN). PTCL vs NT PTCL vs LN DLVCL vs NB DLBCL vs LN COL1A1 CHI3L1 CCL18 CCL18 CCL18 CCL18 VNN1 IGJ CXCL13 CCL5 UBD VNN1 IGFBP7 SH2D1A LYZ CD52 RARRES1 NKG7 CCL5 MAP4K1 Of the top 20 increases, 3 genes were common to PTCL and DLBCL when compared to normal T and B cells, while 11 were common when compared to normal LN. Comparison of genes common to normal B-cell and LN Vs DLBCL or PTCL and normal T-cell and LN Vs PTCL or DLBCL identified sets of genes that are commonly and differentially expressed in PTCL and/or DLBCL. The 4 DLBCL patients analyzed express 3 of 10 prognostic genes compared to normal B-cells and 7 of 10 prognostic genes compared to normal LN and fall into the non-germinal center subtype. Quantitative real time RT-PCR on 10 functionally distinct common over-expressed genes in the 5 PTCL (NOS) patients (Lumican, CCL18, CD14, CD54, CD106, CD163, α-PDGFR, HCK, ABCA1 and Tumor endothelial marker 6) validated the microarray data. Conclusions: GEP of PTCL (NOS) and DLBCL in combination with quantitative real time RT-PCR and IHC have identified a ‘molecular signature’ for PTCL and DLBCL based on a comparison to normal (B-cell, T-cell and LN) tissue. The categorization of the GEP based on the six hallmarks of cancer identifies a ‘tumor profile signature’ for PTCL and DLBCL and a number of novel targets for therapeutic intervention.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2769-2769
Author(s):  
Si Chen ◽  
Shao-Hua Chen ◽  
Lijian Yang ◽  
Haitao Zheng ◽  
Xin Huang ◽  
...  

Abstract Abstract 2769 In order to analyze the regulation of differentiation and proliferation of the BCL11B gene in human T cells, as well as the related molecular mechanism, BCL11B (B cell lymphoma/leukemia11B, BCL11B) recombinant plasmid and small interfering RNA (siRNA) were transferred into naïve T cells (CD3+CD45RA+ T cells) from healthy individual respectively by gene transfer and RNA interference techniques. The eukaryotic expression plasmid pIRES2-BCL11B-EGFP (pBCL11B) and BCL11B-siRNA-935(si-935), obtained by chemosynthesis, were transferred into different cell lines by using transfection techniques. The transfection efficiencies were examined by fluorescence microscopy and FCM. The expression of the mRNA and the corresponding protein levels of BCL11B were detected by real-time quantitative PCR with TaqMan technique and Western blotting. The pBCL11B plasmid and si-935 were transferred into naïve T cells from healthy individual using the Nucleofector™ technique. The microscopic morphologies were detected by atomic force microscopy (AFM), the expression pattern and clonality of TCR Vβ subfamily genes were analyzed by RT-PCR and genescan techniques, the effect of BCL11B in T cells proliferation in vitro were evaluated by the capability of CFU-T, the changes of T cells immune phenotypes (CD3, CD4, CD8, CD45RA, CD45RO, CD25 and CD86) were examined by FCM. The expression patterns of BCL11B were up-regulated or down-regulated respectively, then, the global gene expression profiling was analyzed by the Affymetrix HG U133 Plus 2.0 Gene Chips. Some of the differentially expressed genes were verified by various techniques. The up- or down-regulated BCL11B expression of mRNA and protein levels could be confirmed in naïve T cells. The AFM images revealed that the surface of naïve T cells treated with pBCL11B showed more signs of expansion than others, and were coated with a larger number of extracellular polymers on the outer layer. Seventeen Vβ subfamily T cells displayed polyclonality could be detected in naïve T cells in up-regulated BCL11B manner. The more effective of capability of CFU-T was also confirmed in the same naïve T cells group. The Th subset was obviously changed after up-regulated of BCL11B in naïve T cells, while the ratio of CD4/CD8 was doubled increased. By contrast, in si-935 group, all of the 24 Vβ subfamilies were unable to detect, the number of CFU-T decreased substantially, and the ratio of CD4/CD8 showed no significant difference in compared with control group. Global gene expression profiling analysis showed that up-regulated genes were found in 95 probe sets, while 124 genes were down-regulated in naïve T cells transfected with BCL11B gene, while up-regulated 302 genes and down-regulated 209 genes were detected in naïve T cells from si-935 group. The up- or down-regulation genes were mainly involved in T cells activation and proliferation, which were associated with the high levels of CD3 and IL-2. BCL11B could promote the Th cells differentiation selectively owing to the increased expression of CXCL10 and CXCL11. Suppression BCL11B expression might inhibit the proliferation and effectively induce the apoptosis, which related to the changes of CFLAR-CASP8-CASP10 in mitochondrial pathways. The changes of expression levels of these genes were confirmed by real-time PCR and ELISA. In conclusions, This is the first report providing a detailed analysis of the regulation of the BCL11B gene in T cell differentiation and proliferation, and the possible mechanism of this gene. It was shown that BCL11B was required for the survival of T cells. Up-regulated BCL11B expression could increase the abilities of T cells activation, proliferation, and Th cells differentiation effectively. However, suppression BCL11B expression might inhibit the proliferation and induce the apoptosis. Disclosures: Li: The study was supported by grants from the National Natural Science Foundation (30771980) and the Guangdong Science & Technology Project (2009B050700029): Research Funding.


Sign in / Sign up

Export Citation Format

Share Document