英国弗朗西斯·克里克研究所Gregory M. Findlay团队在研究中取得进展。他们利用饱和基因组编辑绘制了致病性on Hippel-Lindautumor（VHL）等位基因的功能谱系图。这一研究成果于2024年7月5日发表在国际学术期刊《自然-遗传学》上。

研究人员优化并应用饱和基因组编辑技术，检测了VHL编码序列中几乎所有可能的单核苷酸变异（SNV）。为了明确其致病机制，研究人员量化了mRNA的剂量效应，并比较了异源细胞系的功能效应。2,268个VHL SNV的功能评分准确无误地揭示了诱导ccRCC的一组核心致病等位基因，以及不同肿瘤类型的风险差异，并确定了变异影响功能的新机制。

这些结果对临床上VHL的变异分类具有直接实用性，并表明精确的功能测量是如何确定，完整基因的多效性和剂量依赖性基因型-表型的关系。

研究人员表示，要最大限度发挥精准医疗的作用，关键是要确定疾病相关基因变异并准确量化其功能。解析VHL抑制因子的基因变异存在一定挑战。VHL编码一种E3泛素连接酶，可调节细胞对缺氧的反应。VHL致病变体使患者容易发生透明细胞肾细胞癌（ccRCC）和嗜铬细胞瘤在内的肿瘤，而且在散发性肾癌中经常观察到体细胞VHL突变。

附：英文原文

Title: Saturation genome editing maps the functional spectrum of pathogenic VHL alleles

Author: Buckley, Megan, Terwagne, Chlo, Ganner, Athina, Cubitt, Laura, Brewer, Reid, Kim, Dong-Kyu, Kajba, Christina M., Forrester, Nicole, Dace, Phoebe, De Jonghe, Joachim, Shepherd, Scott T. C., Sawyer, Chelsea, McEwen, Mairead, Diederichs, Sven, Neumann-Haefelin, Elke, Turajlic, Samra, Ivakine, Evgueni A., Findlay, Gregory M.

Issue&Volume: 2024-07-05

Abstract: To maximize the impact of precision medicine approaches, it is critical to identify genetic variants underlying disease and to accurately quantify their functional effects. A gene exemplifying the challenge of variant interpretation is the von Hippel–Lindautumor suppressor (VHL). VHL encodes an E3 ubiquitin ligase that regulates the cellular response to hypoxia. Germline pathogenic variants in VHL predispose patients to tumors including clear cell renal cell carcinoma (ccRCC) and pheochromocytoma, and somatic VHL mutations are frequently observed in sporadic renal cancer. Here we optimize and apply saturation genome editing to assay nearly all possible single-nucleotide variants (SNVs) across VHL’s coding sequence. To delineate mechanisms, we quantify mRNA dosage effects and compare functional effects in isogenic cell lines. Function scores for 2,268 VHL SNVs identify a core set of pathogenic alleles driving ccRCC with perfect accuracy, inform differential risk across tumor types and reveal new mechanisms by which variants impact function. These results have immediate utility for classifying VHL variants encountered clinically and illustrate how precise functional measurements can resolve pleiotropic and dosage-dependent genotype–phenotype relationships across complete genes.

DOI: 10.1038/s41588-024-01800-z

Source: https://www.nature.com/articles/s41588-024-01800-z