Structural Genomics Defines PBRM1 Bromodomain Variant Function in ccRCC

Area of Science:

• Genomics and Proteomics
• Cancer Biology
• Computational Biology

Background:

• Poly-bromo-1 (PBRM1) is crucial for chromatin regulation and is altered in ~40% of clear cell renal cell carcinoma (ccRCC) cases.
• PBRM1 loss is linked to better responses to antiangiogenic and immune checkpoint blockade therapies in ccRCC.
• Missense variants in PBRM1, particularly in bromodomains, are found in 16% of ccRCC cases, but their functional impact and effect on therapy response remain unclear.

Purpose of the Study:

• To computationally assess the impact of ccRCC-associated missense variants in PBRM1 bromodomains on molecular fitness.
• To correlate computational predictions with experimental biophysical data for variant assessment.
• To understand how PBRM1 variants affect protein function and potentially influence ccRCC patient response to therapy.

Main Methods:

• Integrated structural genomics analysis (2D, 3D, 4D) of 33 ccRCC-associated missense variants in PBRM1 bromodomains.
• Evaluation of molecular fitness, including stability, structural integrity, and ligand binding.
• Comparison of computational predictions with biophysical assays (differential scanning fluorimetry, circular dichroism, NMR, AlphaScreen, EMSA).

Main Results:

• Computational molecular fitness scores correlated with acetylated histone binding.
• 3D and integrated molecular fitness scores showed correlation with thermal stability.
• The study provides a framework for assessing the functional impact of PBRM1 missense variants.

Conclusions:

• Integrated structural genomics analysis effectively predicts the impact of PBRM1 missense variants on bromodomain function.
• This approach accelerates understanding of variant effects on PBRM1 stability and ligand binding.
• Findings support correlating specific PBRM1 variants with tumor suppressor functions and therapeutic responses in ccRCC for personalized medicine.