BAP1 Immunohistochemistry and p16 FISH to Separate Benign From Malignant Mesothelial Proliferations

Abstract

A variety of immunohistochemical (IHC) stains have been proposed to mark either benign or malignant mesothelial proliferations. Loss of the p16 tumor suppressor (CDKN2A), through homozygous deletions of 9p21, is a good marker of mesotheliomas but lacks sensitivity. Recent reports indicate that some mesotheliomas are associated with loss of BRCA-associated protein 1 (BAP1) expression. Here we investigate BAP1 and p16 as potential markers of malignancy and compare test characteristics with previously proposed markers using a well-characterized tissue microarray. BAP1 protein expression was interrogated by IHC. The p16 locus was examined by fluorescence in situ hybridization (FISH) directed toward chromosome 9p21. Loss of BAP1 was identified in 7/26 mesotheliomas and 0/49 benign proliferations. Loss of p16 was identified in 14/27 mesotheliomas and 0/40 benign proliferations, yielding 100% specificity and positive predictive value for each marker. Together, BAP1 IHC and p16 FISH were 58% sensitive for detecting malignancy. Various combinations of p53, EMA, IMP3, and GLUT1 showed reasonably high specificity (96% to 98%) but poor to extremely poor sensitivity. Combined BAP1 IHC/p16 FISH testing is a highly specific method of diagnosing malignant mesotheliomas when the question is whether a mesothelial proliferation is benign or malignant and is particularly useful when tissue invasion by mesothelial cells cannot be demonstrated. However, combined BAP1/p16 FISH testing is not highly sensitive, and negative results do not rule out a mesothelioma. The test characteristics of previously proposed markers EMA, p53, GLUT1, IMP3 suggest that, even in combination, these markers are not useful tools in this clinical setting.

BAP1 (BRCA1-associated protein 1) is a highly specific marker for differentiating mesothelioma from reactive mesothelial proliferations

“…Remarkably, BAP1 protein loss was paralleled by homozygous deletion of the BAP1 locus in the vast majority of BAP1-negative tumors (31/41, 76%). Our results show the high specificity (100%) of BAP1 loss for mesothelioma diagnosis, in keeping with data recently obtained on a small series of tissue microarray mesothelial lesions; 39 in contrast with the latter study, however, sensitivity was much higher (66% versus 27%), probably because of the higher number of epithelioid/biphasic mesothelioma cases included in the present study.…”

“…54 Yoshikawa et al 55 observed frequent deletion of the 3p21.1 region in mesothelioma primary cultures and cell lines; the same authors subsequently detected somatic biallelic BAP1 alterations in 14 of 23 cases of mesothelioma (61%); 56 similar percentages of cases showing loss of BAP1 protein expression were found in other more recent studies. 57,58 In a recent study performed on tissue microarray containing 49 benign and 26 malignant mesothelial proliferations, Sheffield et al 39 showed that BAP1 immunostain separates benign from malignant processes, with a 100% specificity and 27% sensitivity; sensitivity increased to 58% when BAP1 stain was combined with 9p21 FISH analysis. In their study, a roughly equivalent number of epitheloid/biphasic and sarcomatoid mesothelioma cases were included, but whether BAP1 reactivity differed between subtypes was not specified.…”

The prognostic significance of BAP1, NF2, and CDKN2A in malignant peritoneal mesothelioma

“…Immunohistochemical scoring of BAP1 expression was performed similar to those published previously. 17,29 Assessment of BAP1 was done blinded to any other patient data including outcome. Intact or "positive" expression of BAP1 was defined as nuclear staining within tumor cells, using stromal cells as a positive internal control.…”

“…[26][27][28] Mutations in the nuclear deubiquitinase, BAP1, result in either complete absence of protein expression or cytoplasmic sequestration of BAP1, which can be detected by immunohistochemistry, in 27-67% of pleural mesotheliomas. 18,29,30 In contrast to CDKN2A and NF2 alterations, loss of BAP1 protein expression portends improved prognosis for patients with pleural mesothelioma. 30,31 Analogous to pleural mesotheliomas, homozygous CDKN2A deletions are also present in peritoneal mesotheliomas and confer an unfavorable outcome after CRS and HIPEC.…”

Application of Immunohistochemistry in the Diagnosis of Pulmonary and Pleural Neoplasms

“…BRCA1-associated protein 1 (BAP1) has most recently emerged as a promising biomarker for pleural MM, with loss of nuclear BAP1 staining seen in some mesotheliomas but none of the benign cases. 92,93 BAP1 IHC has been shown to have a relatively high specificity (100%) but low sensitivity (27%). 93 Homozygous p16 (CDKN2A) gene deletion identified using fluorescence in situ hybridization techniques has also been described as an indicator of malignancies, including MM.…”