The added value of BAP1 immunohistochemistry and fluorescence in situ hybridisation for CDKN2A/p16 and NF2 in the diagnosis and prognostication of pleural mesothelioma
Date of Award
Thesis - ECU Access Only
Doctor of Philosophy
School of Medical and Health Sciences
Siaw Ming Chai
Chris van Vliet
Background: Mesothelioma is a rare but aggressive malignancy with therapeutic options that are generally palliative. The malignancy can be challenging to diagnose, commonly due to scant samples, often requiring patients to undergo multiple procedures before a definitive diagnosis can be reached. In more recent years ancillary tests based on the common molecular alterations in the disease have become more widely available to pathologists. However, the role of these investigations in the diagnostic process, identification of early disease and the implications for therapeutic options are not well described.
Purpose: The objectives of this research were to assess: 1) whether chest tube samples could improve diagnostic yield; 2) the usefulness of ancillary investigations in the context of an atypical mesothelial proliferation in cytological preparations in the diagnosis of mesothelioma; 3) whether cytomorphological or molecular alterations are present in cytological samples taken from patients years prior to a definitive cytomorphological mesothelioma diagnosis; 4) the importance of molecular alterations in establishing the diagnosis and differential diagnosis, identification of therapeutic options and germline abnormalities; and 5) whether ancillary investigations are prognostic or predictive of a response to chemotherapy agents.
Methods: Four studies were conducted: one prospective study in patients with malignant pleural effusions (MPE), and three studies involving the retrospective analysis of samples from patients with mesothelioma. In addition, two case reports were prepared, centring on similar objectives. In the prospective study, samples were collected from chest drains (n=20) and assessed for histological composition and the presence of diagnostic material. In the first retrospective study, pleural fluid samples with an atypical mesothelial proliferation received over a 39 month period were identified (n = 50) with the results of routine investigations recorded and BRCA1-associated protein 1 (BAP1) immunohistochemistry (IHC) performed; a final diagnosis was sought from subsequent specimens and hospital records. The second retrospective study involved identification of all mesothelioma cases diagnosed over a 12 year period, with those patients who had a pleural fluid sample collected 24 months or more prior to the definitive diagnosis identified (n = 8). The cytomorphology of each sample was reviewed and BAP1 IHC and Cyclin-dependent kinase inhibitor 2A gene (CDKN2A) fluorescence in situ hybridisation investigations (FISH) were performed. Two patients whose cases highlighted the importance of molecular based analysis were selected and further explored in the form of two case reports. The final retrospective study involved the identification of a cohort of mesothelioma patients in Aalborg, Denmark (n=114) with collection of demographic, clinical and survival data from hospital records and performance of BAP1 IHC on tissue microarrays. Cox regression and Kaplan-Meier methods were used to assess BAP1 status and overall survival (OS). A validation cohort of mesothelioma patients in Perth, Australia was similarly tested (n=234).
Results: The collections in chest tubes were found to consist of fibrin with entrapped inflammatory cells. In 15 of 20 cases, malignant cells were identified. In three of these patients, analysis of the collections provided the first cytological evidence of MPE. In the first retrospective study, which involved analysis of fluid samples with atypical mesothelial proliferations, seven (14%) of samples demonstrated loss of BAP1, all of which (100%) went on to a diagnosis of mesothelioma. Of those with retained staining, 21 (52.5%) were subsequently diagnosed with mesothelioma and 16 (40%) had a nonmesothelioma diagnosis. The second retrospective analysis, involving early pleural fluid samples found that BAP1 loss was present in six (75%) of the initial fluid samples and CDKN2A homozygous loss in one further sample. Therefore, detectable molecular alterations were identifiable in seven of eight initial samples prior to the development of cytomorphological features diagnostic of mesothelioma. The architectural and morphological features of the fluid samples were described, with notable similaries across all samples. The first case report highlights one of the growing spectrum of molecular alterations identified in mesothelioma cases, an ALK fusion, proving important in the differential diagnosis considered and implications for treatment. The second case report describes the clinical and pathological cutaneous findings in a patient with a germline BAP1 abnormality. The final retrospective study, which assessed whether BAP1 status was predictive of chemotherapy response, found that BAP1 loss was an independent predictor of OS on multivariate analysis after correction for histological subtype, performance status, age, sex and treatment (HR = 2.49, < 0.001 and 1.48, p = 0.01 in each population, respectively). Those patients with BAP1 loss who received first line platinum and pemetrexed treatment in both cohorts demonstrated significantly longer median survival (20.1 vs 7.3 months, p < 0.001 and 19.6 vs 11.1 months, p < 0.01 in each cohort, respectively).
Louw, A. (2023). The added value of BAP1 immunohistochemistry and fluorescence in situ hybridisation for CDKN2A/p16 and NF2 in the diagnosis and prognostication of pleural mesothelioma. https://ro.ecu.edu.au/theses/2661