用于黑色素瘤精准诊断和预后分层的微RNA表达特征的RNA-seq验证。

IF 2.1 4区 医学 Q3 GENETICS & HEREDITY BMC Medical Genomics Pub Date : 2024-10-25 DOI:10.1186/s12920-024-02028-w
Christopher G Love, Lauren Coombs, Ryan Van Laar
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引用次数: 0

摘要

背景:需要新的诊断工具来改进皮肤黑色素瘤的诊断和风险分层。此前,通过对实体活检组织和血浆进行 NanoString 分析,已经描述了疾病特异性 microRNA 特征。本研究通过新一代测序技术验证了这些特征,并将其性能与临床指标和其他已发表的黑色素瘤特征进行了比较:方法:从侵袭性黑色素瘤或相关良性/对照表型患者的 64 份血浆和 60 份 FFPE 活检样本中提取 RNA,并对其进行 microRNA 富集。进行RNA测序以计算MEL38/MEL12特征得分。结果与已发表的NanoString和RNA测序数据集(包括548份实体组织样本和217份血浆样本)进行了评估,以预测疾病状态和患者预后:结果:MEL38诊断特征通过实体组织或血浆中的RNA测序将患者分为不同的诊断组(P结论):MEL38和MEL12特征可通过RNA-seq在实体组织或血浆中进行评估,是疾病状态和患者预后的有力预测指标。与其他基因组学方法相比,MEL12 被证明是预后不良的最强预测因子。微RNA表达谱分析提供了客观、准确的基因组学信息,可预测患者患侵袭性黑色素瘤的可能性和预后。
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RNA-seq validation of microRNA expression signatures for precision melanoma diagnosis and prognostic stratification.

Background: New diagnostic tools are needed to improve the diagnosis and risk stratification of cutaneous melanoma. Disease-specific microRNA signatures have been previously described via NanoString profiling of solid biopsy tissue and plasma. This study validated these signatures via next-generation sequencing technology and compared their performance against clinical metrics and other published melanoma signatures.

Methods: RNA from 64 plasma and 60 FFPE biopsy samples from individuals with invasive melanoma or related benign/control phenotypes was extracted and enriched for microRNA. RNA sequencing was performed to compute MEL38/MEL12 signature scores. The results were evaluated with published NanoString and RNA sequencing datasets, comprising 548 solid tissue samples and 217 plasma samples, to predict disease status and patient outcome.

Results: The MEL38 diagnostic signature classifies patients into discrete diagnostic groups via RNA sequencing in either solid tissue or plasma (P < 0.001). In solid tissue, the prognostic MEL12 signature stratifies patients into low-, intermediate- and high-risk groups, independent of clinical covariates. The hazard ratios for 10-year overall survival, based on observed survival intervals, were 2.2 (MEL12 high-risk vs low-risk, P < 0.001) and 1.8 (intermediate-risk vs low-risk, P < 0.001), outperforming other published prognostic models. MEL12 also exhibited prognostic significance in the plasma of 42 patients with invasive disease.

Conclusions: The MEL38 and MEL12 signatures can be assessed in either solid tissue or plasma using RNA-seq and are strong predictors of disease state and patient outcome. Compared with other genomic methods, MEL12 was shown to be the strongest predictor of poor prognosis. MicroRNA expression profiling offers objective, accurate genomic information about a patient's likelihood of invasive melanoma and prognosis.

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来源期刊
BMC Medical Genomics
BMC Medical Genomics 医学-遗传学
CiteScore
3.90
自引率
0.00%
发文量
243
审稿时长
3.5 months
期刊介绍: BMC Medical Genomics is an open access journal publishing original peer-reviewed research articles in all aspects of functional genomics, genome structure, genome-scale population genetics, epigenomics, proteomics, systems analysis, and pharmacogenomics in relation to human health and disease.
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