Hybridisation chain reaction-based visualisation and screening for lncRNA profiles in clear-cell renal-cell carcinoma
Hybridisation chain reaction-based visualisation and screening for lncRNA profiles in clear-cell renal-cell carcinoma
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DOI：
10.1038/s41416-022-01895-3
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发表时间：
2022-06-28
影响因子：
8.8
通讯作者：
Oya, Mototsugu
中科院分区：
文献类型：
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作者：
Kufukihara, Ryohei;Tanaka, Nobuyuki;Oya, Mototsugu
长链非编码RNA （lncRNA）在组织和亚细胞水平上的定位分析可以为了解对其功能重要的细胞类型提供重要的见解。方法应用新型荧光原位杂交技术——杂交链反应（hybridisation chain reaction， HCR），实现临床样品的高通量lncRNA可视化和评价。结果对1728对16个lncrna和透明细胞肾细胞癌（ccRCC）标本进行评估，发现3个lncrna （TUG1、HOTAIR和CDKN2B-AS1）与ccRCC的预后相关。此外，我们结合这三种lncRNA的表达水平，推导出了一个新的ccRCC预后的lncRNA风险组。研究这种分类背后的基因组改变揭示了肿瘤的突出特征，这些特征可以作为靶向lncrna的潜在生物标志物。然后，我们将HCR与扩增显微镜相结合，并在细胞核中可视化纳米级分辨率的HCR信号，揭示了癌细胞中三种lncRNA （TUG1， HOTAIR和CDKN2B-AS1）信号的细胞内共定位，例如位于细胞核内或核仁外的信号。结论lncrna有望成为肿瘤诊断和治疗的理想非编码靶点。HCR涉及由小DNA寡核苷酸组成的多个探针，在临床上使我们能够以较低的成本简单快速地检测癌性lncRNA信号。
Background Analysis of long noncoding RNA (lncRNA) localisation at both the tissue and subcellular levels can provide important insights into the cell types that are important for their function. Methods By applying new fluorescent in situ hybridisation technique called hybridisation chain reaction (HCR), we achieved a high-throughput lncRNA visualisation and evaluation of clinical samples. Results Assessing 1728 pairs of 16 lncRNAs and clear-cell renal-cell carcinoma (ccRCC) specimens, three lncRNAs (TUG1, HOTAIR and CDKN2B-AS1) were associated with ccRCC prognosis. Furthermore, we derived a new lncRNA risk group of ccRCC prognosis by combining the expression levels of these three lncRNAs. Examining genomic alterations underlying this classification revealed prominent features of tumours that could serve as potential biomarkers for targeting lncRNAs. We then derived combination of HCR with expansion microscopy and visualised nanoscale-resolution HCR signals in cell nuclei, uncovering intracellular colocalization of three lncRNA (TUG1, HOTAIR and CDKN2B-AS1) signals such as those located intra- or out of the nucleus or nucleolus in cancer cells. Conclusion LncRNAs are expected to be desirable noncoding targets for cancer diagnosis or treatments. HCR involves plural probes consisting of small DNA oligonucleotides, clinically enabling us to detect cancerous lncRNA signals simply and rapidly at a lower cost.