MicroRNA stability in FFPE tissue samples: dependence on GC content

MicroRNAs (miRNAs) are small non-coding RNAs responsible for fine-tuning of gene expression at post-transcriptional level. The alterations in miRNA expression levels profoundly affect human health and often lead to the development of severe diseases. Currently, high throughput analyses, such as microarray and deep sequencing, are performed in order to identify miRNA biomarkers, using archival patient tissue samples. MiRNAs are more robust than longer RNAs, and resistant to extreme temperatures, pH, and formalin-fixed paraffin-embedding (FFPE) process. Here, we have compared the stability of miRNAs in FFPE cardiac tissues using next-generation sequencing. The mode read length in FFPE samples was 11 nucleotides (nt), while that in the matched frozen samples was 22 nt. Although the read counts were increased 1.7-fold in FFPE samples, compared with those in the frozen samples, the average miRNA mapping rate decreased from 32.0% to 9.4%. These results indicate that, in addition to the fragmentation of longer RNAs, miRNAs are to some extent degraded in FFPE tissues as well. The expression profiles of total miRNAs in two groups were highly correlated (0.88

微小RNA（miRNAs）是一类小型非编码RNA，负责在转录后水平精准调控基因表达。miRNA表达水平的异常改变会显著影响人体健康，常诱发严重疾病的发生。当前研究多借助存档患者组织样本，通过微阵列（microarray）与深度测序（deep sequencing）等高通量分析手段筛选miRNA生物标志物。相较于长链RNA，miRNA稳定性更强，可耐受极端温度、酸碱度变化以及福尔马林固定石蜡包埋（FFPE）处理过程。本研究借助下一代测序（next-generation sequencing）技术，对比分析了FFPE处理的心脏组织中miRNA的稳定性。FFPE样本的测序读长众数为11核苷酸（nt），而匹配的冷冻样本的读长众数则为22 nt。尽管与冷冻样本相比，FFPE样本的测序读段数提升了1.7倍，但miRNA的平均比对率却从32.0%降至9.4%。上述结果表明，除长链RNA发生片段化外，FFPE组织中的miRNA也会在一定程度上发生降解。两组样本中总miRNA的表达谱呈现高度相关性（0.88