4 research outputs found
Identification of importin (IPO-8) as the most accurate reference gene for the clinicopathological analysis of lung specimens
Abstract
Background: The accurate normalization of differentially expressed genes in lung cancer is
essential for the identification of novel therapeutic targets and biomarkers by real time RT-PCR
and microarrays. Although classical "housekeeping" genes, such as GAPDH, HPRT1, and beta-actin
have been widely used in the past, their accuracy as reference genes for lung tissues has not been
proven.
Results: We have conducted a thorough analysis of a panel of 16 candidate reference genes for
lung specimens and lung cell lines. Gene expression was measured by quantitative real time RTPCR
and expression stability was analyzed with the softwares GeNorm and NormFinder, mean of
|ΔCt| (= |Ct Normal-Ct tumor|) ± SEM, and correlation coefficients among genes. Systematic
comparison between candidates led us to the identification of a subset of suitable reference genes
for clinical samples: IPO8, ACTB, POLR2A, 18S, and PPIA. Further analysis showed that IPO8 had
a very low mean of |ΔCt| (0.70 ± 0.09), with no statistically significant differences between normal
and malignant samples and with excellent expression stability.
Conclusion: Our data show that IPO8 is the most accurate reference gene for clinical lung
specimens. In addition, we demonstrate that the commonly used genes GAPDH and HPRT1 are
inappropriate to normalize data derived from lung biopsies, although they are suitable as reference
genes for lung cell lines. We thus propose IPO8 as a novel reference gene for lung cancer samples
Búsqueda de nuevas moléculas relacionadas con el metabolismo del RNA. Valoración de su papel en carcinogénesis pulmonar
Lung cancer is one of the most common diseases in Western countries, and is the malignancy with the highest mortality. A better understanding of the molecular mechanisms associated with lung carcinogenesis is needed to improve survival rates.
In this work we searched for genes related to RNA metabolism with an altered expression in non-small cell lung cancer (NSCLC). We used available data from previous microarray studies, which compared gene expression between normal and lung cancer tissues. We found mRNA expression differences between normal and tumor samples in several genes. Results were validated both in primary lung tumors and cell lines. We selected two of the genes for further studies, ADARB1 and PTB
Identification of novel deregulated RNA metabolism-related genes in non-small cell lung cancer
Lung cancer is a leading cause of cancer death worldwide. Several alterations in RNA metabolism have been found in lung cancer cells; this suggests that RNA metabolism-related molecules are involved in the development of this pathology. In this study, we searched for RNA metabolism-related genes that exhibit different expression levels between normal and tumor lung tissues. We identified eight genes differentially expressed in lung adenocarcinoma microarray datasets. Of these, seven were up-regulated whereas one was down-regulated. Interestingly, most of these genes had not previously been associated with lung cancer. These genes play diverse roles in mRNA metabolism: three are associated with the spliceosome (ASCL3L1, SNRPB and SNRPE), whereas others participate in RNA-related processes such as translation (MARS and MRPL3), mRNA stability (PCBPC1), mRNA transport (RAE), or mRNA editing (ADAR2, also known as ADARB1). Moreover, we found a high incidence of loss of heterozygosity at chromosome 21q22.3, where the ADAR2 locus is located, in NSCLC cell lines and primary tissues, suggesting that the downregulation of ADAR2 in lung cancer is associated with specific genetic losses. Finally, in a series of adenocarcinoma patients, the expression of five of the deregulated genes (ADAR2, MARS, RAE, SNRPB and SNRPE) correlated with prognosis. Taken together, these results support the hypothesis that changes in RNA metabolism are involved in the pathogenesis of lung cancer, and identify new potential targets for the treatment of this disease
Identification of importin (IPO-8) as the most accurate reference gene for the clinicopathological analysis of lung specimens
Abstract
Background: The accurate normalization of differentially expressed genes in lung cancer is
essential for the identification of novel therapeutic targets and biomarkers by real time RT-PCR
and microarrays. Although classical "housekeeping" genes, such as GAPDH, HPRT1, and beta-actin
have been widely used in the past, their accuracy as reference genes for lung tissues has not been
proven.
Results: We have conducted a thorough analysis of a panel of 16 candidate reference genes for
lung specimens and lung cell lines. Gene expression was measured by quantitative real time RTPCR
and expression stability was analyzed with the softwares GeNorm and NormFinder, mean of
|ΔCt| (= |Ct Normal-Ct tumor|) ± SEM, and correlation coefficients among genes. Systematic
comparison between candidates led us to the identification of a subset of suitable reference genes
for clinical samples: IPO8, ACTB, POLR2A, 18S, and PPIA. Further analysis showed that IPO8 had
a very low mean of |ΔCt| (0.70 ± 0.09), with no statistically significant differences between normal
and malignant samples and with excellent expression stability.
Conclusion: Our data show that IPO8 is the most accurate reference gene for clinical lung
specimens. In addition, we demonstrate that the commonly used genes GAPDH and HPRT1 are
inappropriate to normalize data derived from lung biopsies, although they are suitable as reference
genes for lung cell lines. We thus propose IPO8 as a novel reference gene for lung cancer samples