Clinical Value of MLPA for Prognostic Assessment of Chromosomal Rearrangements and DNA Methylation in Uveal Melanoma.

IF 5 2区医学 Q1 OPHTHALMOLOGY

Investigative ophthalmology & visual science Pub Date : 2025-03-03 DOI:10.1167/iovs.66.3.51

Andrea Soltysova, Dana Dvorska, Andrej Ficek, Martina Pecimonova, Marek Samec, Ivana Kasubova, Viera Horvathova Kajabova, Lucia Demkova, Pavel Babal, Jela Valaskova, Zuzana Dankova, Bozena Smolkova, Alena Furdova

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引用次数: 0

Abstract

Purpose: Uveal melanoma (UM) is the most prevalent primary intraocular malignancy in adults, with prognosis significantly influenced by genetic and epigenetic factors. Reliable and cost-effective methods to detect chromosomal aberrations and DNA methylation changes are essential for improving prognostication and informing treatment strategies in UM. This study evaluated the effectiveness of multiplex ligation-dependent probe amplification (MLPA) in detecting UM-specific copy number variations (CNVs) and promoter methylation changes across 25 tumor suppressor genes (TSGs).

Methods: DNA from 58 UM tissues was analyzed with the SALSA MLPA Probemix P027 Uveal melanoma kit, and a subset of 18 samples was further assessed using the SALSA MLPA Probemix ME002-C1 Tumour suppressor mix 2 kit to identify key CNVs and methylation alterations linked to poor prognosis. Validation was carried out with a high-resolution comparative genomic hybridization (CGH) array on 10 samples and the Illumina Infinium Methylation EPIC v1.0 BeadChip array on 25 samples.

Results: Our findings indicate that MLPA is a versatile and robust method for detecting CNVs, showing strong correlations with CGH data and highlighting specific CNV patterns linked to clinical outcomes in UM. However, the ME002-C1 kit showed limited utility for comprehensive methylation analysis, as differential methylation was not observed in the studied TSG loci.

Conclusions: Although MLPA effectively identifies CNVs relevant to UM prognosis, integrating additional methylation-specific approaches could broaden the scope of DNA methylation analysis, offering a more comprehensive molecular understanding of UM that may enhance prognostication and personalized treatment.

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目的：葡萄膜黑色素瘤（UM）是成人中最常见的原发性眼内恶性肿瘤，其预后受遗传和表观遗传因素的影响很大。检测染色体畸变和DNA甲基化变化的可靠且经济有效的方法对于改善UM的预后和治疗策略至关重要。本研究评估了多重连接依赖性探针扩增（MLPA）在检测25个肿瘤抑制基因（TSGs）的UM特异性拷贝数变异（CNVs）和启动子甲基化变化方面的有效性：用SALSA MLPA Probemix P027葡萄膜黑色素瘤试剂盒分析了58个UM组织的DNA，并用SALSA MLPA Probemix ME002-C1 Tumour suppressor mix 2试剂盒进一步评估了18个样本的子集，以确定与不良预后相关的关键CNV和甲基化改变。用高分辨率比较基因组杂交（CGH）阵列对10个样本进行了验证，用Illumina Infinium Methylation EPIC v1.0 BeadChip阵列对25个样本进行了验证：我们的研究结果表明，MLPA是一种检测CNV的多功能且稳健的方法，它与CGH数据显示出很强的相关性，并突出了与UM临床结果相关的特定CNV模式。然而，ME002-C1试剂盒在全面甲基化分析中的作用有限，因为在所研究的TSG位点中未观察到差异甲基化：结论：虽然 MLPA 能有效识别与 UM 预后相关的 CNV，但整合其他甲基化特异性方法可拓宽 DNA 甲基化分析的范围，提供对 UM 更全面的分子认识，从而加强预后判断和个性化治疗。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Investigative ophthalmology & visual science 医学-眼科学

CiteScore

6.90

自引率

4.50%

发文量

339

审稿时长

1 months

期刊介绍： Investigative Ophthalmology & Visual Science (IOVS), published as ready online, is a peer-reviewed academic journal of the Association for Research in Vision and Ophthalmology (ARVO). IOVS features original research, mostly pertaining to clinical and laboratory ophthalmology and vision research in general.