Measuring gene expression by quantitative PCR (qPCR).

Author(s):  
I. Honeyborne
Author(s):  
Zahra Sokhanvar ◽  
Ameneh Elikaei ◽  
Zohreh Sharifi

Background: Liver disease is more severe in HDV+HBV co-infected patients than HBV infected patients which seems to be related to differences in the expression of genes and other factors such as MicroRNAs (miRNAs). The aim of this study was to investigate miR-222 expression in HBV infected patients in comparison with HDV+HBV co-infected patients. Methods: First, total RNA was extracted from the serum samples and then, complementary DNA (cDNA) was produced using cDNA synthesis kit. Finally, miR-222 gene expression was measured using U6 as the internal control by quantitative PCR (qPCR). Results: The level of miR-222 expression in HDV+HBV co-infected samples was significantly up regulated. The fold change of the miR-222 expression between two groups was 3.3 (95% CI; 0.011- 17.63) with p<0.001. Conclusion: The expression of miR-222 was higher in HBV+HDV co-infected patients than HBV infected patients. Further studies should be conducted to confirm whether miR-222 can be a biomarker for prognosis of severe liver diseases.


Author(s):  
Michael B. Sayers ◽  
Tara M. Dalton

Real-time quantitative Polymerase Chain Reaction (PCR) is an extremely sensitive and reliable method for quantifying gene expression, allowing subtle shifts in gene expression to be easily monitored. Currently, stationary real-time PCR is readily achieved using fluorescent labels which increase in fluorescence as the DNA is exponentially amplified. Quantitative PCR is used in a myriad of applications. However currently most commercial real-time PCR devices are batch process stationary well based systems, limiting their throughput. Continuous flow microfluidic PCR devices have allowed for advancement in terms of improved PCR throughput and reduced reagent usage. As part of an overall total analysis system a device integrating all the functional steps of continuous flow realtime quantitative PCR has been designed and fabricated. Initially the PCR reaction mixture is segmented into nano-litre PCR reactors which are then thermally cycled on a two temperature fifty cycle flow-through PCR device, which allows laser induced fluorescent imaging of the nanoreactors. Previous studies into continuous flow PCR have demonstrated endpoint fluorescent measurements, however this research allows PCR nanoreactors to be fluorescently monitored after every PCR thermal cycle. Fluorescent optical monitoring is achieved through laser excitation of the nanoreactors while a Charged Coupled Device (CCD) camera is used to record the fluorescent emissions from the nanoreactors. Intensity analysis of the recorded images is then preformed using MATLAB to accurately determine the fluorescence intensity level, thereby allowing real-time quantitative amplification curves to be generated. This has major advantages over existing continuous flow PCR devices which use endpoint fluorescence and capillary electrophoresis, as the amplification curves allow far more information to be gleaned and allow the initial DNA template concentration to be accurately determined.


2010 ◽  
Vol 27 (11) ◽  
pp. 599-604 ◽  
Author(s):  
Afrooz Habibi ◽  
Naser Farrokhi ◽  
Fernando Moreira da Silva ◽  
Bruno F. Bettencourt ◽  
Jácome Bruges-Armas ◽  
...  

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 1257-1257
Author(s):  
Emmanuel Zorn ◽  
Erik A. Nelson ◽  
Mehrdad Mohseni ◽  
Despina Litsa ◽  
Haesook Kim ◽  
...  

Abstract Recombinant IL-2 has been used extensively in clinical trials to enhance a wide range of immune responses. Overall this strategy has had limited efficacy. Recent evidence suggests that IL-2 plays a key role in the generation and maintenance of CD4+CD25+ regulatory T cells (Treg) in vivo. In our study, we investigated the effect of prolonged administration of recombinant IL-2 on Treg in vivo. In a retrospective analysis, we first examined CD4+CD25+ Treg in blood samples collected from 21 cancer patients before and after they started continuous treatment with IL-2 at a dose of 2 X 105 U/m2/day for 3 months. Nine patients received IL-2 beginning 3 months after CD6 T cell depleted allogeneic bone marrow transplantation (BMT) for CML. The remaining 12 patients received IL-2 as treatment for advanced solid tumors. Overall toxicity was minimal and none of the transplant patients developed GVHD following IL-2 administration. Previous reports demonstrated that this prolonged treatment with low-dose IL-2 resulted in the expansion of CD56+CD3− NK cells in peripheral blood. Further analysis showed that 15 patients exhibited an expansion of Treg in peripheral blood 26 to 77 days after beginning IL-2 as demonstrated by an increase in the CD4+CD25+/CD3+ ratio (median fold increase 2.68; range 1.3 to 59). Three patients had no significant change and 3 patients demonstrated a decreased Treg/CD3 ratio. Using RNA from the same samples we also measured the expression of the Treg specific transcription factor FOXP3 by quantitative PCR. Nineteen of 21 patients showed a marked increase in FOXP3 expression following IL-2 treatment (8.38 median fold increase; range 1.4 to 41.5). Only 2 of 21 patients had lower FOXP3 expression after IL-2 administration. Since IL-2 treatment resulted in the expansion of NK cells as well as Treg, we purified CD56+CD3− NK cells and CD4+ T cells from patient samples collected post-IL-2 treatment, and measured FOXP3 gene expression in both subsets. In 4 analyzed cases, FOXP3 was selectively expressed in CD4+ T cells. Further analysis of purified Treg and NK cells incubated with IL-2 in vitro confirmed that FOXP3 expression was selectively induced in Treg, and also suggested that the in vivo increase in FOXP3 expression resulted from both Treg expansion and up-regulation of gene expression at the single cell level. To study the duration of the IL-2 effect, we analyzed additional samples collected 2 to 8 months after IL-2 treatment was completed. Nine of 10 patient samples tested showed a decrease in the CD4+CD25+/CD3+ ratio (1.39 median fold decrease; range 1.13 to 15.02). Using quantitative PCR, expression of FOXP3 decreased for 6 of 8 patients tested (10.76 median fold decrease; range 1.22 to 88.31). These results indicate that prolonged administration of IL-2 promotes the expansion of CD4+CD25+ Treg in vivo and also has a direct effect on FOXP3 expression. Although administration of IL-2 has previously been used to enhance T and NK cell responses, this study demonstrates that IL-2 therapy predominantly reinforces the regulatory component of the immune response, and may provide a means for controlling immune reactions in vivo.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1283-1283 ◽  
Author(s):  
Maaike Luesink ◽  
Jeannet Nigten ◽  
Ruth H.J.N. Knops ◽  
Theo J.M. de Witte ◽  
Bert A. van der Reijden ◽  
...  

Abstract Abstract 1283 Poster Board I-305 Wilms' tumor 1 (WT1) and GATA binding protein 2 (GATA2) transcription factors are highly expressed in hematopoietic stem cells and progenitors. Differentiation of precursor blood cells towards mature blood cells is accompanied by rapid downregulation of both transcription factors. Overexpression of WT1 has been observed in the majority of acute myeloid leukemia (AML) cases. Furthermore, in 10-15% of the AML cases mutations in the WT1 gene occur, which have been correlated with poor prognosis. Aberrant expression of GATA2 in AML has been described as well, but no mutations in this gene have been reported in AML so far. How the (aberrant) expression of WT1 and GATA2 is controlled is not completely clear. A regulatory role for microRNAs (miRNAs) has been described for several transcription factors which regulate hematopoiesis. MiRNAs negatively regulate gene expression by translational repression or degradation of target messenger RNAs (mRNAs). In the present study we investigated the interplay between miRNAs and transcription factors that are involved in myeloid development and malignant transformation towards AML. We studied the expression of 158 miRNAs in the APL cell line NB4 during induction of granulocytic differentiation with all-trans retinoic acid (ATRA). Quantitative PCR specific for mature miRNAs was performed (Applied Biosystems). Twenty out of 158 miRNAs were more than 10-fold upregulated upon differentiation induction with ATRA. MiR-132 and miR212, which are derived from the same pri-miRNA transcript, were most strongly upregulated during ATRA-induced granulocytic differentiation (1200- and 350-fold respectively at 96 hours after ATRA-stimulation). In vitro ATRA-induction of primary APL cells also resulted in upregulation of miR-132 and miR-212. Computational target prediction algorithms were used to identify transcription factors which may be targeted by miR-132 and miR-212. Subsequently, the expression pattern of the predicted targets was determined experimentally in NB4 cells before and after differentiation induction with ATRA using microarray-based mRNA profiling (Affymetrix). In addition, further verification of target gene expression during ATRA-induced differentiation was performed using quantitative PCR. The transcription factors WT1 and GATA2 were predicted as targets of miR-132 and miR-212 by two out of four different prediction programs that were used. Both transcription factors contained putative binding sites for miR-132 and miR-212 in their 3'UTR. When tested on microarray and by quantitative PCR, the expression of WT1 and GATA2 was indeed strongly downregulated during ATRA-induced granulocytic differentiation of NB4 cells (65- and 165-fold respectively at 96 hours after ATRA stimulation) as well as in primary leukemia cells derived from APL patients (30- and 10-fold respectively at 48 hours after ATRA-stimulation). During ATRA-induced differentiation the expression levels of WT1 were positively correlated with the expression levels of GATA2. In addition, WT1 expression was also strongly correlated with GATA2 expression in a cohort of 27 pre-treatment AML cases as well as in 7 healthy controls, suggesting that these genes might be co-regulated to a large extent. To directly prove that WT1 and GATA2 are indeed targeted by miR-132 and miR-212, we are currently performing lentiviral-based overexpression studies of both miRNAs to determine the effect on endogenous WT1 and GATA2 mRNA expression. MicroRNAs which target WT1 and GATA2 may be valuable tools in controlling the aberrant expression of WT1 and GATA2 observed in AML. Disclosures No relevant conflicts of interest to declare.


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