Bursch Karina L, Goetz Christopher J, Jiao Guanming, Nuñez Raymundo, Olp Michael D, Dhiman Alisha, Khurana Mallika, Zimmermann Michael T, Urrutia Raul A, Dykhuizen Emily C, Smith Brian C
Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
J Biol Chem. 2024 Apr;300(4):107146. doi: 10.1016/j.jbc.2024.107146. Epub 2024 Mar 7.
The polybromo, brahma-related gene 1-associated factors (PBAF) chromatin remodeling complex subunit polybromo-1 (PBRM1) contains six bromodomains that recognize and bind acetylated lysine residues on histone tails and other nuclear proteins. PBRM1 bromodomains thus provide a link between epigenetic posttranslational modifications and PBAF modulation of chromatin accessibility and transcription. As a putative tumor suppressor in several cancers, PBRM1 protein expression is often abrogated by truncations and deletions. However, ∼33% of PBRM1 mutations in cancer are missense and cluster within its bromodomains. Such mutations may generate full-length PBRM1 variant proteins with undetermined structural and functional characteristics. Here, we employed computational, biophysical, and cellular assays to interrogate the effects of PBRM1 bromodomain missense variants on bromodomain stability and function. Since mutations in the fourth bromodomain of PBRM1 (PBRM1-BD4) comprise nearly 20% of all cancer-associated PBRM1 missense mutations, we focused our analysis on PBRM1-BD4 missense protein variants. Selecting 16 potentially deleterious PBRM1-BD4 missense protein variants for further study based on high residue mutational frequency and/or conservation, we show that cancer-associated PBRM1-BD4 missense variants exhibit varied bromodomain stability and ability to bind acetylated histones. Our results demonstrate the effectiveness of identifying the unique impacts of individual PBRM1-BD4 missense variants on protein structure and function, based on affected residue location within the bromodomain. This knowledge provides a foundation for drawing correlations between specific cancer-associated PBRM1 missense variants and distinct alterations in PBRM1 function, informing future cancer personalized medicine approaches.
多溴、与布拉马相关基因1相关因子（PBAF）染色质重塑复合体亚基多溴-1（PBRM1）包含六个溴结构域，这些结构域可识别并结合组蛋白尾巴和其他核蛋白上的乙酰化赖氨酸残基。因此，PBRM1溴结构域在表观遗传翻译后修饰与PBAF对染色质可及性和转录的调节之间提供了一种联系。作为几种癌症中的假定肿瘤抑制因子，PBRM1蛋白表达常常因截断和缺失而被消除。然而，癌症中约33%的PBRM1突变是错义突变，且集中在其溴结构域内。此类突变可能产生具有未确定结构和功能特征的全长PBRM1变体蛋白。在此，我们采用计算、生物物理和细胞分析方法来探究PBRM1溴结构域错义变体对溴结构域稳定性和功能的影响。由于PBRM1的第四个溴结构域（PBRM1-BD4）中的突变占所有与癌症相关的PBRM1错义突变的近20%，我们将分析重点放在PBRM1-BD4错义蛋白变体上。基于高残基突变频率和/或保守性选择16个潜在有害的PBRM1-BD4错义蛋白变体进行进一步研究，我们发现与癌症相关的PBRM1-BD4错义变体表现出不同的溴结构域稳定性和结合乙酰化组蛋白的能力。我们研究结果证明了基于溴结构域内受影响残基的位置来识别单个PBRM1-BD4错义变体对蛋白质结构和功能的独特影响的有效性。这一知识为建立特定癌症相关PBRM1错义变体与PBRM1功能的不同改变之间的关联提供了基础，为未来癌症个性化医疗方法提供了依据。
