Transcriptomics

Dataset Information

33

Integrative Analysis of microRNA, mRNA and DNA Copy Number Data Reveals Asbestos-Related Changes in Non-Small Cell Lung Cancer


ABSTRACT: Background: Lung cancer has the highest mortality rate of all the cancers in the world and asbestos-related lung cancer is one of the leading occupational cancers. The identification of the asbestos-related molecular changes has been a topic of major research interest over the years. The aim of the current study was to identify novel asbestos-related molecular correlates by integrating miRNA expression profiling with previously obtained microarray data (aCGH and mRNA expression) from the same patient material. Results: Twelve novel asbestos-related miRNAs (over-expressed: miR-148b, miR-374a, miR-24-1*, Let-7d, Let-7e, miR-199b-5p, miR-331-3p and under-expressed: miR-939, miR-671-5p, miR-605, miR-1224-5p, miR-202) which inversely correlated with target genes (e.g. GADD45A, LTBP1, FOSB, NCALD, CACNA2D2, MTSS1, EPB41L3) were identified. In addition, several known and new lung cancer-associated miRNAs were identified. DNA copy number alterations were also correlated with the deregulation of four miRNAs in lung cancer. The importance of integrated analysis was highlighted by the interesting finding of linking of the over-expression of well known squamous cell carcinoma-associated miR-205 with the down-regulation of the gene DOK4. Conclusions: Novel deregulated miRNAs and inversely correlating expression of target genes associated with lung cancer etiology and histology were identified. In addition, DNA copy number alterations correlated with the deregulation of some of the miRNAs. The results of the current study could have potential diagnostic implications, but require further investigation. Methods: The patient material used in the study consisted of 26 tumour and normal lung tissue from highly asbestos-exposed (13 samples) and non-exposed (13 samples) patients. Control lung tissue samples were obtained from 7 patients without cancer as well as from a commercial lung tissue RNA. Data analysis on miRNA expression and integration of miRNA and mRNA data were performed using Chipster (http://chipster.csc.fi/). In addition, miRNA and aCGH data were integrated in a separate analysis. *** This submission represents the microRNA component of the study

ORGANISM(S): Homo sapiens  

SUBMITTER: Ali Faisal   Mohamed Guled  Ioana Borze  Penny Nymark  Sisko Anttila  Sakari Knuutila  Leo Lahti  Eeva Kettunen  Kaisa Salmenkivi 

PROVIDER: E-GEOD-25508 | ArrayExpress | 2011-04-30

SECONDARY ACCESSION(S): GSE25508PRJNA134653

REPOSITORIES: GEO, ArrayExpress

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Publications

Integrative analysis of microRNA, mRNA and aCGH data reveals asbestos- and histology-related changes in lung cancer.

Nymark Penny P   Guled Mohamed M   Borze Ioana I   Faisal Ali A   Lahti Leo L   Salmenkivi Kaisa K   Kettunen Eeva E   Anttila Sisko S   Knuutila Sakari S  

Genes, chromosomes & cancer 20110511 8


Lung cancer has the highest mortality rate of all of the cancers in the world and asbestos-related lung cancer is one of the leading occupational cancers. The identification of asbestos-related molecular changes has long been a topic of increasing research interest. The aim of this study was to identify novel asbestos-related molecular correlates by integrating miRNA expression profiling with previously obtained profiling data (aCGH and mRNA expression) from the same patient material. miRNA prof  ...[more]

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