Matthew Bott

The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma.

Malignant pleural mesotheliomas (MPMs) often show CDKN2A and NF2 inactivation, but other highly recurrent mutations have not been described. To identify additional driver genes, we used an integrated genomic analysis of 53 MPM tumor samples to guide a focused sequencing effort that uncovered somatic inactivating mutations in BAP1 in 23% of MPMs. The BAP1 nuclear deubiquitinase is known to target histones (together with ASXL1 as a Polycomb repressor subunit) and the HCF1 transcriptional co-factor, and we show that BAP1 knockdown in MPM cell lines affects E2F and Polycomb target genes. These findings implicate transcriptional deregulation in the pathogenesis of MPM.

New Strategies in Pleural Mesothelioma: BAP1 and NF2 as Novel Targets for Therapeutic Development and Risk Assessment

Malignant pleural mesothelioma (MPM) is a highly lethal cancer with limited therapeutic options. Recent work has focused on the frequent somatic inactivation of two tumor suppressor genes in MPM—NF2 (Neurofibromatosis type 2) and the recently identified BAP1 (BRCA associated protein 1). In addition, germline mutations in BAP1 have been identified that define a new familial cancer syndrome, which includes MPM, ocular melanoma, and other cancers. These recent advances may allow screening of high-risk individuals and the development of new therapies that target key pathways in MPM. Clin Cancer Res; 18(17); 4485–90. ©2012 AACR.

Clinical Characteristics of Patients with Malignant Pleural Mesothelioma Harboring Somatic BAP1 Mutations

Introduction: Genomic studies of malignant pleural mesothelioma (MPM) have recently identified frequent mutations in the BRCA-associated protein 1(BAP1) gene. In uveal melanoma and clear cell renal cell carcinoma, BAP1 mutations are associated with poor outcomes but their clinical significance in MPM is unknown. We therefore undertook this study to define the characteristics of patients whose MPM tumors harbor somatic BAP1 mutation and to examine the relationship between BAP1 mutation and survival. Methods: We reviewed the charts of 121 patients with MPM tumors diagnosed between 1991 and 2009 tested for BAP1 mutation, and extracted the following information: age at diagnosis, sex, histology, stage, smoking status, asbestos exposure, family or personal history of malignancy, and treatment including surgery, chemotherapy, and radiation as well as survival status. Results: Twenty-four of the 121 tumors (20%) harbored somatic BAP1 mutations. The percentage of current or former smokers among cases with BAP1 mutations was significantly higher than in BAP1 wild-type cases, (75% versus 42%; p = 0.006). However, the types of nucleotide substitutions in BAP1 did not suggest that this association was because of a causative role of smoking in BAP1 mutations. No other clinical feature was significantly different among those with and without BAP1 mutations in their MPM. There was also no difference in survival according to somatic BAP1 mutation status. Conclusion: There is no apparent distinct clinical phenotype for MPM with somatic BAP1 mutation. The significance of the more frequent history of smoking among patients with BAP1-mutated MPM warrants further study.

Coactivation of receptor tyrosine kinases in malignant mesothelioma as a rationale for combination targeted therapy.

Introduction:To identify new therapeutic approaches in malignant mesothelioma (MM), we examined the expression and activation of receptor tyrosine kinases (RTKs) and the effects of specific RTK inhibitors and the mammalian target of rapamycin (mTOR) inhibitor rapamycin; the latter being of special interest in MM given the recent linkage between NF2 loss and mTOR activation. Methods:We performed a screen for mutated or activated RTKs in 14 MM cell lines and 70 primary tumors. Expression of phosphorylated RTKs was analyzed by Western blotting and a membrane-based antibody array in normal growth conditions and after treatment by specific inhibitors. MET and epidermal growth factor receptor (EGFR) mutations were screened by sequencing. MET, hepatocyte growth factor, insulin-like growth factor 1 receptor, and EGFR expression were studied by Western blotting, immunohistochemistry, enzyme-linked immunosorbent assay, and by Affymetrix expression microarrays. Results:Profiling of the phosphorylation status of 42 RTKs showed prominent coactivation of MET and EGFR in 8 of 14 (57%) MM cell lines. MET, EGFR, and insulin-like growth factor 1 receptor were the main RTKs activated after mTOR inhibition and contributed to AKT feedback activation. Knockdown of MET by RNA interference inhibited not only the phosphorylation of MET but also that of EGFR. Conversely, stimulation with hepatocyte growth factor increased both phospho-MET and phospho-EGFR. The combination of PHA-665752 and the EGFR inhibitor, erlotinib, suppressed cell growth more than either agent alone in three of six cell lines tested. Finally, combinations of rapamycin and different RTK inhibitors were more active than either drug alone in 12 of 13 cell lines. Conclusion:Combination targeting of kinase signaling pathways is more effective than single agents in most MM.

Pericardial effusions in the cancer population: Prognostic factors after pericardial window and the impact of paradoxical hemodynamic instability

OBJECTIVE In the cancer population, pericardial effusions are a common and potentially life-threatening occurrence. Although decompression benefits most patients, paradoxical hemodynamic instability (PHI) develops in some, with hypotension and shock in the immediate postoperative period. This study examines paradoxical hemodynamic instability after pericardial window and identifies prognostic factors in patients with cancer who are treated for pericardial effusion. METHODS Retrospective review of 179 consecutive pericardial windows performed for pericardial effusion in a tertiary cancer center over a 5-year period (January 2004 through March 2009). Demographic, surgical, pathologic, and echocardiographic data were analyzed for the end points of paradoxical hemodynamic instability (pressor-dependent hypotension requiring intensive care unit admission) and overall survival. RESULTS The most common malignancies were lung (44%), breast (20%), hematologic (10%), and gastrointestinal (7%). Overall survival for the group was poor (median, 5 months); patients with hematologic malignant disease fared significantly better than the others (median survival 36 months; P = .008). Paradoxical hemodynamic instability occurred in 19 (11%) patients. These patients were more likely to have evidence of tamponade on echocardiogram (89% vs 56%; P = .005), positive cytology/pathology (68% vs 41%; P = .03), and higher volume drained (674 mL vs 495 mL; P = .003). Overall survival was significantly shorter in those in whom paradoxical hemodynamic instability developed (median survival 35 vs 189 days; hazard ratio = 3; P < .001), and the majority of them (11/19, 58%) did not survive their hospitalization. CONCLUSIONS Postoperative hemodynamic instability after pericardial window portends a grave prognosis. Evidence of tamponade, larger effusion volumes, and positive cytologic findings may predict a higher risk of paradoxical hemodynamic instability and anticipate a need for invasive monitoring and intensive care postoperatively.

Management and Outcomes of Relapse After Treatment for Thymoma and Thymic Carcinoma

BACKGROUND Although surgery is the mainstay of treatment for thymic tumors, recurrence is common despite resection. The optimal approach to the management of disease relapse after treatment for thymic tumors remains unclear. METHODS This study is a retrospective analysis of a single-institution experience assessing treatment patterns and outcomes in patients with recurrence or disease progression after surgical treatment for thymic tumors. Data included demographics, stage, treatment, pathologic findings, and postoperative outcomes. RESULTS From 1995 to 2006, 120 patients had initial resection of a thymic tumor at our institution, of which 112 had recurrence data available. Twenty-five patients developed recurrence or progression of disease after their initial resection (10 thymic carcinoma, 15 thymoma). Median follow-up was 51.4 months. Higher Masaoka stages predominated (I: 0; II: 4; III: 8; IV: 13). Eleven patients (44%) underwent surgery for their relapse with curative intent, while 14 (56%) were managed nonsurgically. Surgery was considered when disease was intrathoracic, unilateral, and technically resectable. The 11 patients receiving surgery had a total of 16 reoperations (range 1 to 4). An R0 re-resection was obtained in half of cases (8 of 16, 50%) but the majority of operative patients (9 of 11, 82%) recurred again. The 5-year overall survival of the 25 patients with recurrent or persistent disease was 58% (median survival = 82 months). Kaplan-Meier curves demonstrate a trend (p = 0.08) toward improved overall survival in patients treated with surgery versus those treated nonoperatively (median survival = 156 months versus 50 months). Patients with thymoma demonstrated a trend (p = 0.12) toward improved survival for over thymic carcinoma (median survival = 90 months versus 35 months). CONCLUSIONS Treatment of patients with recurrent or progressive thymic tumors is associated with long-term survival. Despite the historical enthusiasm for re-resection, the majority of patients will recur again, therefore reoperation should be considered only in selected patients.

Soluble mesothelin related peptides (SMRP) and osteopontin as protein biomarkers for malignant mesothelioma: analytical validation of ELISA based assays and characterization at mRNA and protein levels

Abstract Background: There is a need to identify reliable markers for malignant mesothelioma. Soluble mesothelin related peptides (SMRP) and osteopontin (OPN) have gained interest in recent years for this purpose. Methods: SMRP (Fujirebio Diagnostics Inc.) and OPN (R&D Inc.) ELISA methods were evaluated for multiple parameters. Concentrations were measured in blood from patients with mesothelioma, normal healthy volunteers, and patients with other (non-mesothelioma) cancers. In silico analysis was performed using the GeoProfiles database. At the protein level, SMRP and OPN were measured in cell culture supernatants, and values were compared in patients pre- and post-extrapleural pneumonectomy. Results: The SMRP assay demonstrates intra-assay CVs of 2.3% and 3% (at 4.6 nM and 13.7 nM, respectively), and inter-assay CVs of 3.5% and 3.7% at the same concentrations. The limit of detection (LOD) is 0.182 nM. The OPN assay demonstrates intra-assay CVs of 5.8%, 4.1%, and 5.2% (at 1.9, 5.1, and 11.1 ng/mL, respectively), and inter-assay CVs of 8.5%, 8.4%, and 12.1% at the same concentrations. The LOD is 0.032 ng/mL. Both SMRP and OPN in mesothelioma patients were significantly higher than in patients with other (non-mesothelioma) cancer and in healthy volunteers. The two markers do not appear to correlate with each other and exhibit different tissue expression patterns. Protein concentrations of these markers are highest in different sets of cell lines. Finally, SMRP but not OPN concentrations were decreased in five of seven consecutive patients after extrapleural pneumonectomy, compared to their respective pre-operative values. Conclusions: These assays provide reliable and reproducible quantitation of SMRP and OPN proteins. Both are increased in mesothelioma patients compared to non-mesothelioma controls. However, the two analytes do not correlate with each other and show distinct expression profiles and protein expression. Concentrations of SMRP but not OPN are decreased in post-surgical samples. Our results further characterize these markers, establish assay performance characteristics, and lay the groundwork for further studies to measure these markers in blood. Clin Chem Lab Med 2010;48:271–8.

Pulmonary metastasectomy with therapeutic intent for soft-tissue sarcoma

Objective: Soft‐tissue sarcoma is a heterogeneous disease that frequently includes the development of pulmonary metastases. The purpose of this study is to determine factors associated with improved survival among patients with soft‐tissue sarcoma to help guide selection for pulmonary metastasectomy. Methods: We reviewed a prospectively maintained database and identified 803 patients who underwent pulmonary metastasectomy for metastatic soft‐tissue sarcoma between September 1991 and June 2014; of these, 539 patients undergoing 760 therapeutic‐intent pulmonary metastasectomies were included. Clinicopathologic variables and characteristics of treatment were examined. The outcomes of interest were overall survival and disease‐free survival. Survival was estimated with the Kaplan‐Meier method and compared between variables with the log‐rank test. Factors associated with hazard of death and recurrence were identified via the use of univariable and multivariable Cox proportional hazards models. Results: Median overall survival was 33.2 months (95% confidence interval, 29.9–37.1), and median disease‐free survival was 6.8 months (95% confidence interval, 6.0–8.0). In multivariable analyses, leiomyosarcoma histologic subtype (P = .007), primary tumor size ≤10 cm (P = .006), increasing time from primary tumor resection to development of metastases (P < .001), solitary lung metastasis (P = .001), and minimally invasive resection (P = .023) were associated with lower hazard of death. Disease‐free interval ≥1 year (P = .002), and 1 pulmonary metastasis (P < .001) were associated with lower hazard of disease recurrence. Conclusions: In a large single‐institution study, primary tumor histologic subtype and size, numbers of pulmonary metastases, disease‐free interval, and selection for minimally invasive resection are associated with increased survival in patients undergoing pulmonary metastasectomy for soft‐tissue sarcoma.

Important recent insights into the genetics and biology of malignant pleural mesothelioma

Knowledge of the disease-specific genetic mutations in malignant pleural mesothelioma (MPM) has the potential to lead to rational targeted therapies. Recent studies have reported previously unknown recurrent genetic alterations in the BAP1 and LATS2 genes. Additional work has increased our understanding of the mechanism by which inactivating mutations in NF2 cause tumorigenesis. This review will highlight these recent discoveries and their relevance to MPM therapeutics.

Definitive chemoradiotherapy versus neoadjuvant chemoradiotherapy followed by surgery for stage II to III esophageal squamous cell carcinoma

Objective: Definitive chemoradiotherapy (CRT) remains the most commonly used treatment for locally advanced esophageal squamous cell carcinoma (SCC), because of perceptions that esophagectomy offers an unclear survival advantage. We compare recurrence, overall survival (OS), and disease‐free survival (DFS) in patients treated with definitive CRT or neoadjuvant CRT followed by surgery (trimodality). Methods: This was a retrospective cohort study of patients with stage II and III SCC of the middle and distal esophagus in patients who completed CRT. Treatment groups were matched (1:1) on covariates using a propensity score‐matching approach. The effect of trimodality treatment, compared with definitive CRT, on OS, DFS, and site‐specific recurrence was evaluated as a time‐dependent variable and analyzed using Cox regression with a gamma frailty term for matched units. Results: We included 232 patients treated between 2000 and 2016: 124 (53%) with definitive CRT and 108 (47%) with trimodality. Trimodality was used less frequently over time (61% before 2009 and 29% after 2009; P < .0001). After matching, each group contained 56 patients. Median OS and DFS were 3.1 and 1.8 years for trimodality versus 2.3 and 1.0 years for CRT. Surgery was independently associated with improved OS (hazard ratio, 0.57; 95% confidence interval, 0.34–0.97; P = .039) and DFS (hazard ratio, 0.51; 95% confidence interval, 0.32–0.83; P = .007). Conclusions: CRT followed by surgery might decrease local recurrence and increase DFS and OS in patients with esophageal SCC. Until better tools to select patients with pathological complete response are available, surgery should remain an integral component of the treatment of locally advanced esophageal SCC.