Laidlaw Sean, Alonso-Crisostomo Luz, Bailey Shivani, Saini Harpreet K, Molnár Attila, Nicholson James C, Enright Anton J, Scarpini Cinzia G, Rahbari Raheleh, Coleman Nicholas, Murray Matthew J
Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
Department of Pathology, University of Cambridge, Cambridge, UK.
Andrology. 2023 May;11(4):738-755. doi: 10.1111/andr.13312. Epub 2022 Oct 26.
Analyses of small non-coding RNA (ncRNA) expression in malignant germ cell tumours (GCTs) have focused on microRNAs (miRNAs). As GCTs all arise from primordial germ cells, and piwi-interacting RNAs (piRNAs) have important roles in maintaining germline integrity via transposon silencing, we hypothesised that malignant GCTs are characterised by fundamental piRNA dysregulation.
We undertook global small ncRNA sequencing in malignant GCTs, in order to describe small ncRNA expression changes for both miRNAs and piRNAs.
We performed small ncRNA next generation sequencing on a representative panel of 47 samples, comprising malignant GCT (n = 31) and control (n = 16) tissues/cell lines. Following quality control and normalisation, filtered count reads were used for differential miRNA and piRNA expression analyses via DESeq2. Predicted mRNA targets for piRNAs were identified and utilised for pathway enrichment analyses.
Overall, miRNAs and piRNAs comprised 21.9% and 43.0% of small ncRNA species, respectively. There were 749 differentially expressed miRNAs in malignant GCTs, of which 536 (72%) were over-expressed and 213 (28%) under-expressed. The top-ranking over-expressed miRNAs were exclusively from the miR-371∼373 and miR-302/367 clusters. The most significantly under-expressed miRNAs were miR-100-5p, miR-214-3p, miR-125b-5p and let-7 family members, including miR-202-3p. There were 1,121 differentially expressed piRNAs in malignant GCTs, of which 167 (15%) were over-expressed and 954 (85%) under-expressed. Of note, of the top-20 differentially expressed piRNAs, 16 were over-expressed, of which piR-hsa-2506793 was both top-ranking and most abundant. Mobile element (ME; i.e., transposon)-associated piRNAs comprised 166 (15%) of the 1,121 differentially expressed piRNAs, of which 165 (>99%) were down-regulated. The remaining 955 (85%) non-ME-associated piRNAs may have wider cellular roles. To explore this, predicted mRNA targets of differentially expressed piRNAs identified putative involvement in cancer-associated pathways.
This study confirms previous miRNA observations, giving credence to our novel demonstration of global piRNA dysregulation in gonadal malignant GCTs, through both ME and non-ME-associated pathways, which likely contributes to GCT pathogenesis.
恶性生殖细胞肿瘤（GCT）中小非编码RNA（ncRNA）表达的分析主要集中在微小RNA（miRNA）上。由于GCT均起源于原始生殖细胞，且PIWI相互作用RNA（piRNA）在通过转座子沉默维持种系完整性方面具有重要作用，我们推测恶性GCT的特征是piRNA基本失调。
我们对恶性GCT进行了全基因组小ncRNA测序，以描述miRNA和piRNA的小ncRNA表达变化。
我们对47个样本的代表性面板进行了小ncRNA下一代测序，包括恶性GCT（n = 31）和对照（n = 16）组织/细胞系。在质量控制和标准化之后，通过DESeq2将过滤后的计数读数用于差异miRNA和piRNA表达分析。鉴定了piRNA的预测mRNA靶标并将其用于通路富集分析。
总体而言，miRNA和piRNA分别占小ncRNA种类的21.9%和43.0%。恶性GCT中有749个差异表达的miRNA，其中536个（72%）过表达，213个（28%）低表达。排名靠前的过表达miRNA仅来自miR-371∼373和miR-302/367簇。表达最显著下调的miRNA是miR-100-5p、miR-214-3p、miR-125b-5p和let-7家族成员，包括miR-202-3p。恶性GCT中有1121个差异表达的piRNA，其中167个（15%）过表达，954个（85%）低表达。值得注意的是，在差异表达最显著的前20个piRNA中，有16个过表达，其中piR-hsa-2506793排名第一且最为丰富。移动元件（ME；即转座子）相关的piRNA占1121个差异表达piRNA中的166个（15%），其中165个（>99%）下调。其余955个（85%）非ME相关的piRNA可能具有更广泛的细胞作用。为了探究这一点，差异表达piRNA的预测mRNA靶标确定了其在癌症相关通路中的假定参与。
本研究证实了先前关于miRNA的观察结果，证实了我们通过ME和非ME相关通路在性腺恶性GCT中对全基因组piRNA失调的新证明，这可能导致GCT发病机制。
