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

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

背景：肺癌是全球所有癌症中死亡率最高的癌种，而与石棉相关的肺癌是主要的职业性癌症之一。多年来，针对石棉相关分子改变的鉴定始终是学界的核心研究热点。本研究旨在通过整合微RNA（miRNA）表达谱与同一患者样本中既往获取的微阵列数据（阵列比较基因组杂交（aCGH）及mRNA表达谱数据），以鉴定新型石棉相关分子关联因子。
结果：本研究共鉴定出12种与石棉相关的新型miRNA，其中过表达的miRNA包括miR-148b、miR-374a、miR-24-1*、Let-7d、Let-7e、miR-199b-5p、miR-331-3p；低表达的miRNA包括miR-939、miR-671-5p、miR-605、miR-1224-5p、miR-202。上述miRNA均与靶基因（如GADD45A、LTBP1、FOSB、NCALD、CACNA2D2、MTSS1、EPB41L3）呈负相关。此外，本研究还鉴定出多种已知及新型肺癌相关miRNA。同时，DNA拷贝数变异与肺癌中4种miRNA的表达失调存在显著关联。值得注意的是，本研究发现经典鳞状细胞癌相关miR-205的过表达与基因DOK4的下调存在关联，这一结果凸显了整合分析的重要价值。
结论：本研究鉴定出了与肺癌病因及组织学特征相关的新型表达失调miRNA，以及与之呈负相关的靶基因表达模式。此外，DNA拷贝数变异与部分miRNA的表达失调存在关联。本研究结果或具有潜在的临床诊断应用价值，但仍需开展进一步的验证与拓展研究。
方法：本研究使用的患者样本共包含26份肺组织样本，其中13份取自高石棉暴露患者、13份取自非暴露患者，样本涵盖肿瘤组织与正常肺组织。对照肺组织样本取自7名无癌患者，同时还使用了商业化肺组织RNA样本。本研究的miRNA表达数据分析，以及miRNA与mRNA数据的整合分析均通过Chipster平台（http://chipster.csc.fi/）完成。此外，本研究还单独开展了miRNA与aCGH数据的整合分析。
*** 本次提交内容对应本研究的microRNA组分。