Palafox Maria F, Boatner Lisa, Wilde Blake R, Christofk Heather, Backus Keriann M, Arboleda Valerie A
Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Pathology and Lab Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA 90095, USA.
Am J Hum Genet. 2025 Jul 3;112(7):1649-1663. doi: 10.1016/j.ajhg.2025.04.017. Epub 2025 May 23.
Missense variants are the most common type of protein-altering genetic variation. Due to their wide-ranging potential functional consequences, missense variants are challenging to interpret and, as a result, are often classified as unknown pathogenicity or as variants of uncertain significance (VUSs). Genomic-based predictive tools have made significant inroads into the challenge of accurately pinpointing functional missense variants by providing genome-wide assessments of deleteriousness or potential pathogenicity. Complementary to these tools, here we provide an initial study into the utility of harnessing protein-based measures of amino acid reactivity to delineate functionally significant missense variants. These reactivity measurements, which are generated using mass spectrometry-based chemoproteomic methods, have already proved capable of pinpointing functional sites on proteins, which provide the added value of delineating potential sites suitable for drug-development efforts. Here, using published chemoproteomic datasets for three specific privileged amino acids, cysteine, lysine, and tyrosine, we assessed the utility of proteomic reactivity measurements to identify clinically important variants and regions within monogenic-disease-associated genes. We found that genes where amino acids are detected via chemoproteomics are enriched for monogenic-disease phenotypes, indicative of functional importance. Chemoproteomic-detected amino acids (CpDAAs) are enriched at and around sites with known pathogenic missense variants when assessed with either one- or three-dimensional protein structures. To further illustrate the utility of our findings, we found that regions at or around CpDAAs in fumarate hydratase (FH) were enriched for VUSs and pathogenic variants, which we validate through demonstration of an altered FH oligomerization state. Collectively, our study highlights the potential of chemoproteomic and genetic data integration for enhancing the identification of functional genetic variants and protein sites with potential value for drug-development efforts.
错义变体是最常见的一类可改变蛋白质的基因变异。由于其潜在的功能后果范围广泛，错义变体难以解释，因此常常被归类为致病性未知或意义未明的变体（VUS）。基于基因组的预测工具通过提供全基因组范围的有害性或潜在致病性评估，在准确确定功能性错义变体的挑战方面取得了重大进展。作为这些工具的补充，我们在此初步研究利用基于蛋白质的氨基酸反应性测量来描绘具有功能意义的错义变体的效用。这些使用基于质谱的化学蛋白质组学方法生成的反应性测量结果，已经证明能够确定蛋白质上的功能位点，这为描绘适合药物开发工作的潜在位点提供了附加价值。在此，我们使用已发表的针对三种特定优先氨基酸（半胱氨酸、赖氨酸和酪氨酸）的化学蛋白质组学数据集，评估了蛋白质组反应性测量在识别单基因疾病相关基因内临床重要变体和区域方面的效用。我们发现，通过化学蛋白质组学检测到氨基酸的基因富含单基因疾病表型，表明其具有功能重要性。当用一维或三维蛋白质结构评估时，化学蛋白质组学检测到的氨基酸（CpDAA）在已知致病性错义变体的位点及其周围富集。为了进一步说明我们研究结果的效用，我们发现富马酸水合酶（FH）中CpDAA处或其周围区域富含VUS和致病性变体，我们通过证明FH寡聚化状态改变对此进行了验证。总体而言，我们的研究突出了化学蛋白质组学和遗传数据整合在增强功能性遗传变体和具有药物开发潜在价值的蛋白质位点识别方面的潜力。
