Galka-Marciniak Paulina, Urbanek-Trzeciak Martyna Olga, Kuznicki Daniel, Szostak Natalia, Tire Adrian, Nawrocka-Muszynska Paulina Maria, Chojnacka Katarzyna, Suszynska Malwina, Klonowska Katarzyna, Czubak Karol, Machowska Magdalena, Philips Anna, Maksin Konstantin, Susok Laura, Sand Michael, Rys Janusz, Jura Jolanta, Ratajska Magdalena, Dams-Kozlowska Hanna, Kowalewski Janusz, Lewandowska Marzena Anna, Kozlowski Piotr
Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.
Laboratory of Experimental Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland.
Nucleic Acids Res. 2025 Aug 27;53(16). doi: 10.1093/nar/gkaf812.
Interest in the genetic variation of noncoding genomic elements, including microRNAs (miRNAs), is growing, and several mutations in miRNA genes implicated in human diseases, including cancer, have already been detected. However, the lack of dedicated analytical tools severely hampers progress in this area. In this study, we developed the first whole-miRNome sequencing (WMS) platform, which enables the targeted sequencing of all human miRNA genes (n ∼2000) and 28 miRNA biogenesis genes. By sequencing various types of DNA samples, including ∼300 tumor/normal pairs, from lung, colorectal, ovarian, renal, and basal cell carcinomas, we identified ∼2000 mutations, including 879 in miRNA genes. These mutations were located in all parts of the genes, including seed or cleavage sites essential for the functioning of miRNA genes. The high reliability of the mutations was confirmed through various approaches, including different sequencing methods. The analysis identified several miRNA genes with functional enrichment of cancer mutations, including MIR3928, which was specifically mutated in basal cell carcinoma, suggesting its potential role in this cancer. WMS also allowed the identification of multiple copy number alterations, which often encompassed miRNA genes. WMS provides highly effective, low-cost sequencing of all miRNA genes in different types of samples, including highly degraded ones.
对包括微小RNA（miRNA）在内的非编码基因组元件的遗传变异的研究兴趣日益浓厚，并且已经在包括癌症在内的人类疾病相关的miRNA基因中检测到了几种突变。然而，缺乏专门的分析工具严重阻碍了该领域的进展。在本研究中，我们开发了首个全miRNA组测序（WMS）平台，该平台能够对所有人类miRNA基因（约2000个）和28个miRNA生物合成基因进行靶向测序。通过对来自肺癌、结直肠癌、卵巢癌、肾癌和基底细胞癌的各种类型的DNA样本（包括约300对肿瘤/正常样本）进行测序，我们鉴定出约2000个突变，其中包括miRNA基因中的879个突变。这些突变位于基因的各个部位，包括对miRNA基因功能至关重要的种子或切割位点。通过包括不同测序方法在内的各种方法证实了这些突变的高可靠性。分析鉴定出几个具有癌症突变功能富集的miRNA基因，包括在基底细胞癌中特异性突变的MIR3928，这表明其在这种癌症中的潜在作用。WMS还能够鉴定出多个拷贝数改变，这些改变通常包含miRNA基因。WMS为不同类型的样本（包括高度降解的样本）中的所有miRNA基因提供了高效、低成本的测序。
