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Comparison of gene expression profiling of human lung at four developmental stages and lung adenocarcioma

ABSTRACT: It is gradually becoming a new aspect in research to search and explore embryo development for malignant information hidden in tumor cells. In this study, the gene expression profiles for human lungs at four developmental stages and lung adenocarcinoma (ADC) were depicted, respectively. The molecular dynamics was compared for development and lung ADC, and it was proposed that primary lung ADC may hijack part of the molecular mechanisms of lung development to down-regulate homeostasis-associated genes and up-regulate stemness-associated genes; and it was revealed that the genes with monotonely decreasing expression trend during lung development process are enriched with lung ADC prognostic information. The study material for developing lung consisted of 29 cases of therapeutic or spontaneous abortion. The samples included whole embryos aged 3 to 5 weeks post ovulation (n = 10, named WholeE), lungs at 6 to 8 postovulatory weeks (PWs) (n = 10, named EarlyL) and lungs at 16 to 24 PWs (n = 9, named MiddleL). WholeE and EarlyL samples were carefully obtained from medical waste with the guidance of a Nikon stereo microscope SMZ1500 (Japan). MiddleL were collected when autopsies were performed. Embryo/Fetuses with known or suspected genetic disorders were excluded. Uninvolved peripheral lung tissue from adults (named MatureL) was obtained from fifteen patients operated on for benign lung diseases. 69 Lung ADC samples used for expression profiling analysis were obtained from patients. All these samples were examined with Agilent Whole Human Genome 4×44k microarray.

ORGANISM(S): Homo sapiens

SUBMITTER: Feng L

PROVIDER: S-ECPF-GEOD-43767 | biostudies-other | 2014

REPOSITORIES: biostudies-other

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Project description:BackgroundLung cancers are the most common type of human malignancy and are intractable. Lung cancers are generally classified into four histopathological subtypes: adenocarcinoma (AD), squamous cell carcinoma (SQ), large cell carcinoma (LC), and small cell carcinoma (SC). Molecular biological characterization of these subtypes has been performed mainly using DNA microarrays. In this study, we compared the gene expression profiles of these four subtypes using twelve human lung cancer cell lines and the more reliable quantitative real-time PCR (qPCR).ResultsWe selected 100 genes from public DNA microarray data and examined them by DNA microarray analysis in eight test cell lines (A549, ABC-1, EBC-1, LK-2, LU65, LU99, STC 1, RERF-LC-MA) and a normal control lung cell line (MRC-9). From this, we extracted 19 candidate genes. We quantified the expression of the 19 genes and a housekeeping gene, GAPDH, with qPCR, using the same eight cell lines plus four additional validation lung cancer cell lines (RERF-LC-MS, LC-1/sq, 86-2, and MS-1-L). Finally, we characterized the four subtypes of lung cancer cell lines using principal component analysis (PCA) of gene expression profiling for 12 of the 19 genes (AMY2A, CDH1, FOXG1, IGSF3, ISL1, MALL, PLAU, RAB25, S100P, SLCO4A1, STMN1, and TGM2). The combined PCA and gene pathway analyses suggested that these genes were related to cell adhesion, growth, and invasion. S100P in AD cells and CDH1 in AD and SQ cells were identified as candidate markers of these lung cancer subtypes based on their upregulation and the results of PCA analysis. Immunohistochemistry for S100P and RAB25 was closely correlated to gene expression.ConclusionsThese results show that the four subtypes, represented by 12 lung cancer cell lines, were well characterized using qPCR and PCA for the 12 genes examined. Certain genes, in particular S100P and CDH1, may be especially important for distinguishing the different subtypes. Our results confirm that qPCR and PCA analysis provide a useful tool for characterizing cancer cell subtypes, and we discuss the possible clinical applications of this approach.

Project description:BACKGROUND: Vitis vinifera berry development is characterised by an initial phase where the fruit is small, hard and acidic, followed by a lag phase known as veraison. In the final phase, berries become larger, softer and sweeter and accumulate an array of organoleptic compounds. Since the physiological and biochemical makeup of grape berries at harvest has a profound impact on the characteristics of wine, there is great interest in characterising the molecular and biophysical changes that occur from flowering through veraison and ripening, including the coordination and temporal regulation of metabolic gene pathways. Advances in deep-sequencing technologies, combined with the availability of increasingly accurate V. vinifera genomic and transcriptomic data, have enabled us to carry out RNA-transcript expression analysis on a global scale at key points during berry development. RESULTS: A total of 162 million 100-base pair reads were generated from pooled Vitis vinifera (cv. Shiraz) berries sampled at 3-weeks post-anthesis, 10- and 11-weeks post-anthesis (corresponding to early and late veraison) and at 17-weeks post-anthesis (harvest). Mapping reads from each developmental stage (36-45 million) onto the NCBI RefSeq transcriptome of 23,720 V. vinifera mRNAs revealed that at least 75% of these transcripts were detected in each sample. RNA-Seq analysis uncovered 4,185 transcripts that were significantly upregulated at a single developmental stage, including 161 transcription factors. Clustering transcripts according to distinct patterns of transcription revealed coordination in metabolic pathways such as organic acid, stilbene and terpenoid metabolism. From the phenylpropanoid/stilbene biosynthetic pathway at least 46 transcripts were upregulated in ripe berries when compared to veraison and immature berries, and 12 terpene synthases were predominantly detected only in a single sample. Quantitative real-time PCR was used to validate the expression pattern of 12 differentially expressed genes from primary and secondary metabolic pathways. CONCLUSIONS: In this study we report the global transcriptional profile of Shiraz grapes at key stages of development. We have undertaken a comprehensive analysis of gene families contributing to commercially important berry characteristics and present examples of co-regulation and differential gene expression. The data reported here will provide an invaluable resource for the on-going molecular investigation of wine grapes.

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Comparison of gene expression profiling of human lung at four developmental stages and lung adenocarcioma

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