Large-scale analysis of BAP1 expression reveals novel associations with clinical and molecular features of malignant pleural mesothelioma

Abstract

BRCA1-associated protein-1 (BAP1) expression is commonly lost in several tumors including malignant pleural mesothelioma (MPM). Presence or absence of immunohistochemical BAP1 nuclear staining in tumor cells is currently used for differential diagnosis of MPM. In this study, a large cohort of 596 MPM tumors with available clinical data was analyzed to examine associations of BAP1 staining pattern with clinical and molecular features that may reflect the impact of BAP1 mutation on MPM biology. Cases were classified according to the BAP1 staining pattern of tumor cells. Exome and RNA-sequencing data were available for subsets of cases. Levels of mRNA encoding claudin 15 (CLDN15) and vimentin (VIM) were determined using RT-qPCR on 483 cases to estimate the relative proportions of epithelial-like and mesenchymal-like components in each tumor. Four BAP1 staining patterns were observed: single-pattern nuclear staining (36%), single-pattern cytoplasmic staining (25%), single-pattern absent staining (12%), and combinations of these staining patterns (27%). This study confirmed prior reports that nuclear BAP1 is more frequently associated with wild-type BAP1 and sarcomatoid histology. However, no associations between BAP1 staining pattern(s) and mutations in specific protein domains and/or mutation type were observed. BAP1 staining patterns were significantly associated (p < 0.001) with BAP1 gene expression, MPM histologic subtypes, molecular clusters, and markers of epithelial-to-mesenchymal transition. Frequent observation of combinations of BAP1 staining patterns in MPM tumors indicated intra-tumoral heterogeneity of BAP1 status. Cytoplasmic BAP1 staining was identified as a putative indicator of favorable prognosis in non-epithelioid MPM. In conclusion, novel significant associations among different BAP1 staining patterns and subgroups of MPM tumors were observed, suggesting that the role of BAP1 in tumor progression may be more complex than its presumed tumor suppressor function. Cytoplasmic staining was identified as a putative indicator of favorable prognosis in non-epithelioid MPM, potentially addressing a critical need in clinical decision-making in this disease. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

Keywords: BAP1; epithelial-to-mesenchymal transition; gene expression; immunohistochemistry; intra-tumor heterogeneity; mesothelioma; prognostic biomarker; tumor suppressor gene.

Figure 1

Representative images of BAP1 immunohistochemistry in MPM samples. (A) Epithelioid case displaying single‐pattern nuclear BAP1 staining; (B) epithelioid case displaying single‐pattern cytoplasmic BAP1 staining; (C) epithelioid case displaying absence of BAP1 staining; (D) biphasic case displaying absent/nuclear/cytoplasmic staining with (E) magnification (600×) of the epithelioid component with loss of nuclear BAP1 staining, and (F) magnification (600×) of the sarcomatoid component with nuclear BAP1 staining.

Figure 2

Distribution of BAP1 staining patterns in MPM subtypes. (A) Venn diagrams depicting the relation between BAP1 staining patterns and the major histological subgroups of MPM. (B) Bar charts illustrating proportions of cases demonstrating each staining pattern within histological MPM subgroups.

Figure 3

Distribution of BAP1 staining patterns among MPM molecular clusters. (A) Venn diagrams depicting the frequency of observed BAP1 staining patterns in cluster E relative to the combined remaining clusters (BE, BS, S). (B) Bar charts illustrating proportions of cases demonstrating each staining pattern within cluster E relative to the combined remaining clusters (BE, BS, S).

Figure 4

Association of BAP1 staining patterns with C/V scores and gene set expression analysis for EMT pathway. Boxplots displaying the distributions of C/V scores in relation to single‐pattern nuclear BAP1 staining, single‐pattern cytoplasmic BAP1 staining, single‐pattern absence of BAP1 staining, and combination absent/cytoplasmic staining determined using (A) RNAseq data from 155 specimens and (B) RT‐PCR data from 483 specimens. GSEA enrichment plots from RNAseq data for genes associated with the EMT process in (C) the single‐pattern nuclear BAP1 staining versus single‐pattern cytoplasmic BAP1 staining and (D) the single‐pattern absent staining versus single‐pattern cytoplasmic BAP1 staining.

Figure 5

Analysis of survival in patients with MPM according to BAP1 staining pattern. Kaplan–Meier curves of patients with (A) epithelioid MPM tumors showing single‐pattern nuclear (median overall survival 19.5 months), single‐pattern cytoplasmic (median overall survival 24.8 months), and single‐pattern absent BAP1 staining (median overall survival 12.7 months); (B) non‐epithelioid MPM tumors showing single‐pattern cytoplasmic (median overall survival 17.4 months) versus other BAP1 staining patterns (median overall survival 9.3 months), p = 0.005; (C) biphasic MPM tumor showing single‐pattern nuclear (median overall survival 12.7 months), single‐pattern cytoplasmic (median overall survival 21.6 months), and single‐pattern absent BAP1 staining (median overall survival 16.5 months); and (D) biphasic MPM tumor showing single‐pattern cytoplasmic (median overall survival 21.6 months) versus other BAP1 staining patterns (median overall survival 11.6 months), p = 0.009. Overall survival was calculated from the date of surgery. Survival curves were truncated at 60 months.