Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Queensland, Australia.
PLoS One. 2010 Sep 3;5(9):e12560. doi: 10.1371/journal.pone.0012560.
MicroRNAs (miRNAs) are a family of small, non-coding RNA species functioning as negative regulators of multiple target genes including tumour suppressor genes and oncogenes. Many miRNA gene loci are located within cancer-associated genomic regions. To identify potential new amplified oncogenic and/or deleted tumour suppressing miRNAs in lung cancer, we inferred miRNA gene dosage from high dimensional arrayCGH data. From miRBase v9.0 (http://microrna.sanger.ac.uk), 474 human miRNA genes were physically mapped to regions of chromosomal loss or gain identified from a high-resolution genome-wide arrayCGH study of 132 primary non-small cell lung cancers (NSCLCs) (a training set of 60 squamous cell carcinomas and 72 adenocarcinomas). MiRNAs were selected as candidates if their immediately flanking probes or host gene were deleted or amplified in at least 25% of primary tumours using both Analysis of Copy Errors algorithm and fold change (≥ ± 1.2) analyses. Using these criteria, 97 miRNAs mapped to regions of aberrant copy number. Analysis of three independent published lung cancer arrayCGH datasets confirmed that 22 of these miRNA loci showed directionally concordant copy number variation. MiR-218, encoded on 4p15.31 and 5q35.1 within two host genes (SLIT2 and SLIT3), in a region of copy number loss, was selected as a priority candidate for follow-up as it is reported as underexpressed in lung cancer. We confirmed decreased expression of mature miR-218 and its host genes by qRT-PCR in 39 NSCLCs relative to normal lung tissue. This downregulation of miR-218 was found to be associated with a history of cigarette smoking, but not human papilloma virus. Thus, we show for the first time that putative lung cancer-associated miRNAs can be identified from genome-wide arrayCGH datasets using a bioinformatics mapping approach, and report that miR-218 is a strong candidate tumour suppressing miRNA potentially involved in lung cancer.
微小 RNA（miRNA）是一组小的非编码 RNA 分子，作为多个靶基因（包括肿瘤抑制基因和癌基因）的负调节剂发挥作用。许多 miRNA 基因座位于与癌症相关的基因组区域内。为了在肺癌中鉴定潜在的新扩增致癌和/或缺失的肿瘤抑制 miRNA，我们从高维 arrayCGH 数据中推断 miRNA 基因剂量。从 miRBase v9.0（http://microrna.sanger.ac.uk）中，将 474 个人类 miRNA 基因物理映射到从 132 例原发性非小细胞肺癌（NSCLC）（一个包含 60 例鳞状细胞癌和 72 例腺癌的训练集）高分辨率全基因组 arrayCGH 研究中鉴定的染色体缺失或获得区域。如果其紧邻的探针或宿主基因在至少 25%的原发性肿瘤中缺失或扩增，则选择 miRNA 作为候选物，使用分析拷贝错误算法和倍数变化（≥±1.2）分析。使用这些标准，97 个 miRNA 映射到异常拷贝数区域。对三个独立的已发表的肺癌 arrayCGH 数据集的分析证实，其中 22 个 miRNA 基因座显示出方向性一致的拷贝数变异。miR-218 位于两个宿主基因（SLIT2 和 SLIT3）上的 4p15.31 和 5q35.1 内，位于拷贝数缺失的区域，被选为后续研究的优先候选物，因为它在肺癌中被报道表达下调。我们通过 qRT-PCR 在 39 例 NSCLC 中相对于正常肺组织证实成熟 miR-218 及其宿主基因的表达降低。发现 miR-218 的下调与吸烟史有关，但与人类乳头瘤病毒无关。因此，我们首次表明，通过生物信息学映射方法可以从全基因组 arrayCGH 数据集中鉴定出潜在的肺癌相关 miRNA，并报告 miR-218 是一个强有力的候选肿瘤抑制 miRNA，可能参与肺癌。
