Abstract 874: Expanded detection of BAP1 alterations in cancer and comparison of tumor type-specific gene expression scores
Authors: Sturgill Ian R. , Raab Jesse R. , Hoadley Katherine A. 
Published: March 2024

Abstract
BAP1 is a tumor suppressor gene that was originally studied in uveal melanoma (UVM), kidney renal cell clear cell carcinoma (KIRC), and malignant mesothelioma (MESO). Early analyses focused on single-nucleotide variants, but other alteration types such as larger indels and gene-level copy number (CN) loss can also lead to loss of BAP1 expression. By incorporating these, we can improve our assessment of cancer type-specific consequences of BAP1 loss and broaden our findings beyond the initial small subset of cancer types which were studied in the context of mutations alone. We performed integrated multi-omic analyses using data from The Cancer Genome Atlas (TCGA), for 33 cancer types and more than 10,000 individuals. By combining and manually reviewing existing variant calls and new calls derived from a de novo local realignment pipeline across multiple independent variant callers including indel callers, we increased detection of high-quality somatic variant calls by 30% from 85 to 111, including 14 indels ≥5bp. Including CN loss alterations, we found a total of 1561 samples from 32 cancer types to be BAP1-altered, with alterations being predominantly CN-driven. We confirmed that expression of BAP1 was lower in altered versus unaltered tumors (p&lt;0.001). Alteration frequencies across cancer types were highly variable, ranging from 0% in thyroid cancer to &gt;30% in KIRC, cholangiocarcinoma (CHOL), UVM, MESO, lung squamous carcinoma (LUSC), and head-neck squamous cell carcinoma (HNSC). Tumor types such as CHOL, UVM, MESO, and liver hepatocellular carcinoma (LIHC) were relatively more mutation-driven whereas other tumor types like KIRC, LUSC, and HNSC were almost entirely CN-driven. To better understand the tissue and context-specific consequences of BAP1 alteration, we performed differential expression analyses across BAP1-altered and -unaltered samples. For each cancer type, we separately computed per-sample BAP1 alteration signature z-scores summarizing expression of the set of differentially expressed genes. In UVM, we observed distinct patterns of RNA expression, consistent with established literature on BAP1 loss and serving as a baseline for comparison for the biological effects of BAP1 loss in other less-studied cancer types. The BAP1 altered scores for 66% of cancer types were positively correlated with the UVM BAP1 altered signature, suggesting shared biological responses and affected pathways including immune responses, epithelial-mesenchymal transition, oxidative phosphorylation, and proliferation – all known roles of BAP1. In LIHC, we noted enrichment of bile duct gene expression in BAP1-altered tumors, suggesting a possible role for BAP1 in maintaining cell identity distinguishing hepatocytes and cholangiocytes. Our findings broadly emphasize the improvements that are gained by using new computational approaches in large cancer-genome studies such as TCGA.
Citation Format: Ian R. Sturgill, Jesse R. Raab, Katherine A. Hoadley. Expanded detection of BAP1 alterations in cancer and comparison of tumor type-specific gene expression scores [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 874.