Expression profiles and initial confirmation of long non-coding RNAs in Chinese patients with pulmonary adenocarcinoma
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE56850 | GEO | 2014/04/17
SECONDARY ACCESSION(S): PRJNA244766
REPOSITORIES: GEO
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Project description:There are significant differences in the lncRNA expression profiles in Chinese patients with pulmonary adenocarcinoma. LncRNAs such as AK124939 may be anti-cancer factors related to the progress of pulmonary adenocarcinoma. RNA extracted from three paired pulmonary adenocarcinoma tissue and adjacent normal lung tissue specimens was used to synthesize double-stranded complementary DNA (cDNA) after labeling and hybridization. The cDNA was labeled and hybridized to the lncRNA expression microarray, and array data were analyzed for hierarchical clustering. Gene coexpression networks were constructed to identify interactions among genes. To validate the microarray findings, we measured the relative expression levels of four random differentially expressed lncRNAs in the same tissue used for microarray using real-time quantitative polymerase chain reaction (qRT-PCR). The expression level of one lncRNA AK124939, in the paired pulmonary adenocarcinoma/adjacent normal lung tissue of another 30 patients was measured using qRT-PCR. The experimental data were further analyzed and compared with clinical features.
2014-04-17 | E-GEOD-56850 | biostudies-arrayexpress
Project description:BACKGROUND:The purpose of this study was to investigate differentially expressed long noncoding RNAs (lncRNAs) in pulmonary adenocarcinoma tissue and adjacent noncancerous tissue from Chinese patients using lncRNA expression microarray and preliminary analysis. METHODS:RNA extracted from three paired pulmonary adenocarcinoma tissue and adjacent noncancerous tissue specimens was used to synthesize double-stranded complementary DNA after labeling and hybridization. The complementary DNA was labeled and hybridized to the lncRNA expression microarray, and array data were analyzed for hierarchical clustering. Gene coexpression networks were constructed to identify interactions among genes. To validate the microarray findings, we measured the relative expression levels of four random differentially expressed lncRNAs in the same tissue used for microarray using real-time quantitative polymerase chain reaction. The expression level of one lncRNA, AK124939, in the paired pulmonary adenocarcinoma/adjacent noncancerous tissue of another 30 patients was measured using real-time quantitative polymerase chain reaction. The experimental data were further analyzed and compared with clinical features. RESULTS:Of 39,000 lncRNAs investigated, 704 were differentially expressed in pulmonary adenocarcinoma tissue; 385 were upregulated and 319 were downregulated compared with those in the adjacent noncancerous tissue (fold change ?2 and ?-2, P<0.05). AK124939 expression levels in poorly differentiated adenocarcinoma tissue were lower than those found in well to moderately differentiated adenocarcinoma tissue (P=0.05). CONCLUSION:There are significant differences in the lncRNA expression profiles in Chinese patients with pulmonary adenocarcinoma. LncRNAs such as AK124939 may be anticancer factors related to the progression of pulmonary adenocarcinoma.
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Project description:Study designed to obtain microRNA profile of tumorigenic Sca-1+CD34+ cells during the formation of pulmonary adenocarcinoma. After intranasal infection with adenovirus CRE (Ad-Cre), lung adenocarcinoma was identified pathologically in Lox-stop-lox Kras (LSL-Kras) G12D mice. Sca-1+CD34+ cells were sorted by flow cytometry and tested for the tumor-initiating ability to undergo self-renewal and differentiation. MiRNA profile was obtained from the microarray and further confirmed by qRT-PCR.The function of miRNAs was predicted bioinformatically, and miR-294 was verified to explore its relationship with tumor migration and invasion. We taken lung tissues from the LSL-Kras G12D mouse on the 0, 15th, 30th days, and defined as Group A, B, C respectively. These 3 samples were analyzed. Each kind of probe has 4 repeat spots on the microarray. Total RNA are harvested using TRIzol (Invitrogen) and RNeasy mini kit (QIAGEN). All processing conducted at the Kang Cheng Biological chip Company Limited. Microarray was synthesized using μParafloTM microfluidic chip technology, and the information of miRNA probe sequence of each region was obtained from the database of Sanger miRBase version 11.0.
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