Aaron O. Bungum

Added value of a serum proteomic signature in the diagnostic evaluation of lung nodules.

Background: Current management of lung nodules is complicated by nontherapeutic resections and missed chances for cure. We hypothesized that a serum proteomic signature may add diagnostic information beyond that provided by combined clinical and radiographic data. Methods: Cohort A included 265 and cohort B 114 patients. Using multivariable logistic regression analysis we calculated the area under the receiver operating characteristic curve (AUC) and quantified the added value of a previously described serum proteomic signature beyond clinical and radiographic risk factors for predicting lung cancer using the integration discrimination improvement (IDI) index. Results: The average computed tomography (CT) measured nodule size in cohorts A and B was 37.83 versus 23.15 mm among patients with lung cancer and 15.82 versus 17.18 mm among those without, respectively. In cohort A, the AUC increased from 0.68 to 0.86 after adding chest CT imaging variables to the clinical results, but the proteomic signature did not provide meaningful added value. In contrast, in cohort B, the AUC improved from 0.46 with clinical data alone to 0.61 when combined with chest CT imaging data and to 0.69 after adding the proteomic signature (IDI of 20% P = 0.0003). In addition, in a subgroup of 100 nodules between 5 and 20 mm in diameter, the proteomic signature added value with an IDI of 15% (P ≤ 0.0001). Conclusions: The results show that this serum proteomic biomarker signature may add value to the clinical and chest CT evaluation of indeterminate lung nodules. Impact: This study suggests a possible role of a blood biomarker in the evaluation of indeterminate lung nodules. Cancer Epidemiol Biomarkers Prev; 21(5); 786–92. ©2012 AACR.

Development and validation of a plasma biomarker panel for discerning clinical significance of indeterminate pulmonary nodules.

Introduction: The recent findings of the National Lung Screening Trial showed 24.2% of individuals at high risk for lung cancer having one or more indeterminate nodules detected by low-dose computed tomography–based screening, 96.4% of which were eventually confirmed as false positives. These positive scans necessitate additional diagnostic procedures to establish a definitive diagnosis that adds cost and risk to the paradigm. A plasma test able to assign benign versus malignant pathology in high-risk patients would be an invaluable tool to complement low-dose computed tomography–based screening and promote its rapid implementation. Methods: We evaluated 17 biomarkers, previously shown to have value in detecting lung cancer, against a discovery cohort, comprising benign (n = 67) cases and lung cancer (n = 69) cases. A Random Forest method based analysis was used to identify the optimal biomarker panel for assigning disease status, which was then validated against a cohort from the Mayo Clinic, comprising patients with benign (n = 61) or malignant (n = 20) indeterminate lung nodules. Results: Our discovery efforts produced a seven-analyte plasma biomarker panel consisting of interleukin 6 (IL-6), IL-10, IL-1ra, sIL-2R&agr;, stromal cell-derived factor-1&agr;+&bgr;, tumor necrosis factor &agr;, and macrophage inflammatory protein 1 &agr;. The sensitivity and specificity of our panel in our validation cohort is 95.0% and 23.3%, respectively. The validated negative predictive value of our panel was 93.8%. Conclusion: We developed a seven-analyte plasma biomarker panel able to identify benign nodules, otherwise deemed indeterminate, with a high degree of accuracy. This panel may have clinical utility in risk-stratifying screen-detected lung nodules, decrease unnecessary follow-up imaging or invasive procedures, and potentially avoid unnecessary morbidity, mortality, and health care costs.

Common Oncogene Mutations and Novel SND1-BRAF Transcript Fusion in Lung Adenocarcinoma from Never Smokers

Lung adenocarcinomas from never smokers account for approximately 15 to 20% of all lung cancers and these tumors often carry genetic alterations that are responsive to targeted therapy. Here we examined mutation status in 10 oncogenes among 89 lung adenocarcinomas from never smokers. We also screened for oncogene fusion transcripts in 20 of the 89 tumors by RNA-Seq. In total, 62 tumors had mutations in at least one of the 10 oncogenes, including EGFR (49 cases, 55%), K-ras (5 cases, 6%), BRAF (4 cases, 5%), PIK3CA (3 cases, 3%), and ERBB2 (4 cases, 5%). In addition to ALK fusions identified by IHC/FISH in four cases, two previously known fusions involving EZR- ROS1 and KIF5B-RET were identified by RNA-Seq as well as a third novel fusion transcript that was formed between exons 1–9 of SND1 and exons 2 to 3′ end of BRAF. This in-frame fusion was observed in 3/89 tested tumors and 2/64 additional never smoker lung adenocarcinoma samples. Ectopic expression of SND1-BRAF in H1299 cells increased phosphorylation levels of MEK/ERK, cell proliferation, and spheroid formation compared to parental mock-transfected control. Jointly, our results suggest a potential role of the novel BRAF fusion in lung cancer development and therapy.

Network-based approach identified cell cycle genes as predictor of overall survival in lung adenocarcinoma patients

Lung adenocarcinoma is the most common type of primary lung cancer. The purpose of this study was to delineate gene expression patterns for survival prediction in lung adenocarcinoma. Gene expression profiles of 82 (discovery set) and 442 (validation set 1) lung adenocarcinoma tumor tissues were analyzed using a systems biology-based network approach. We also examined the expression profiles of 78 adjacent normal lung tissues from 82 patients. We found a significant correlation of an expression module with overall survival (adjusted hazard ratio or HR=1.71; 95% CI=1.06-2.74 in discovery set; adjusted HR=1.26; 95% CI=1.08-1.49 in validation set 1). This expression module contained genes enriched in the biological process of the cell cycle. Interestingly, the cell cycle gene module and overall survival association were also significant in normal lung tissues (adjusted HR=1.91; 95% CI, 1.32-2.75). From these survival-related modules, we further defined three hub genes (UBE2C, TPX2, and MELK) whose expression-based risk indices were more strongly associated with poor 5-year survival (HR=3.85, 95% CI=1.34-11.05 in discovery set; HR=1.72, 95% CI=1.21-2.46 in validation set 1; and HR=3.35, 95% CI=1.08-10.04 in normal lung set). The 3-gene prognostic result was further validated using 92 adenocarcinoma tumor samples (validation set 2); patients with a high-risk gene signature have a 1.52-fold increased risk (95% CI, 1.02-2.24) of death than patients with a low-risk gene signature. These results suggest that a network-based approach may facilitate discovery of key genes that are closely linked to survival in patients with lung adenocarcinoma.

EGFR Somatic Mutations in Lung Tumors: Radon Exposure and Passive-smoking in Former- and Never-smoking U.S. Women

Background: Patients with lung cancer with mutations in EGF receptor (EGFR) tyrosine kinase have improved prognosis when treated with EGFR inhibitors. We hypothesized that EGFR mutations may be related to residential radon or passive tobacco smoke. Methods: This hypothesis was investigated by analyzing EGFR mutations in 70 lung tumors from a population of never and long-term former female smokers from Missouri with detailed exposure assessments. The relationship with passive smoking was also examined in never-smoking female lung cancer cases from the Mayo clinic. Results: Overall, the frequency of EGFR mutation was 41% [95% confidence interval (CI), 32%–49%]. Neither radon nor passive-smoking exposure was consistently associated with EGFR mutations in lung tumors. Conclusions: The results suggest that EGFR mutations are common in female, never-smoking lung cancer cases from the United States, and EGFR mutations are unlikely due to exposure to radon or passive smoking. Cancer Epidemiol Biomarkers Prev; 21(6); 988–92. ©2012 AACR.

Granulomatous inflammation detected by endobronchial ultrasound-guided transbronchial needle aspiration in patients with a concurrent diagnosis of cancer: a clinical conundrum.

Background:Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is increasingly used for evaluating mediastinal and/or hilar lymphadenopathy in patients with malignancy. Granulomatous inflammation is occasionally identified in this setting and has unclear clinical implications. Therefore, we set out to describe a cohort of patients found to have evidence of granulomatous inflammation during EBUS-TBNA done for diagnosis and/or staging of concurrent cancer. Methods:A retrospective analysis of all EBUS-TBNA cases performed over 32 months at our institution was completed. Patients with evidence of granulomatous inflammation during EBUS-TBNA that was not attributable to an infectious etiology or prior sarcoidosis and a concurrent diagnosis of cancer were included. Results:Granulomatous inflammation was identified in 154/1275 patients (12.1%), of whom 12/154 (7.8%) had a concurrent diagnosis of cancer. Primary cancer diagnoses varied, but the primary site of malignancy was in or near the thorax in 10/12 cases (83.3%). When available, 7/8 cases (87.5%) of granulomatous lymphadenopathy were detectable by positron emission tomography. The most common histologic pattern consisted of well-formed non-necrotizing granulomas without fibrosis in 6/12 patients (50%). Conclusions:Granulomatous inflammation is occasionally identified in mediastinal and/or hilar lymphadenopathy in patients with concurrent malignancy. Although the clinical implications of this phenomenon remain to be clarified, these findings emphasize the importance of histologic confirmation of suspected lymph node involvement and suggest that the presence of granulomatous inflammation on EBUS-TBNA may occasionally be consistent with active malignancy and prompt further investigations.

Endobronchial ultrasound-guided transbronchial needle aspiration: determinants of sampling adequacy.

Background:Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is increasingly used to sample mediastinal and hilar lymph nodes and has excellent diagnostic test characteristics. The determinants of sampling adequacy, however, have not been extensively examined. We set out to determine which procedural variables were associated with acquisition of tissue sufficient for pathologic analysis during EBUS-TBNA. Methods:A retrospective analysis of all EBUS-TBNA cases performed over 32 months by 10 proceduralists at our institution was completed. Variables potentially associated with sampling adequacy were analyzed. Results:A total of 1304 procedures performed by 10 proceduralists while the patient received conscious sedation were included for analysis. Sampling adequacy was 94.2% overall and varied with the primary proceduralist (87% to 99.2%; P<0.001). Diagnostic yield per procedure for malignancy or a specific benign diagnosis was 43.2% overall. Proceduralists with a higher average number of lymph node stations sampled per procedure had improved sampling adequacy (parameter estimate=1.32; P=0.007). Sampling adequacy was lower with lymph nodes smaller than 10 mm (parameter estimate=−0.7; P=0.002) but was not associated with procedural environment (hospital procedural suite vs. clinic-based procedural suite) (P=0.08), lymph node station (P=0.69), propofol use (P=0.90), or average annual proceduralist cases performed (P=0.21). Only 6/216 (2.8%) patients had subsequent procedures (EBUS-TBNA or surgery) that indicated the initial EBUS-TBNA had inadequate sampling potentially leading to a missed cancer diagnosis. Conclusions:Excellent EBUS-TBNA sampling adequacy can be achieved by pulmonologists in a large group setting, who are not exclusively dedicated to interventional pulmonary medicine, using only moderate conscious sedation.

Neoantigenic potential of complex chromosomal rearrangements in mesothelioma

Introduction: Malignant pleural mesothelioma is a disease primarily associated with exposure to the carcinogen asbestos. Whereas other carcinogen‐related tumors are associated with a high tumor mutation burden, mesothelioma is not. We sought to resolve this discrepancy. Methods: We used mate‐pair (n = 22), RNA (n = 28), and T cell receptor sequencing along with in silico predictions and immunologic assays to understand how structural variants of chromosomes affect the transcriptome. Results: We observed that inter‐ or intrachromosomal rearrangements were present in every specimen and were frequently in a pattern of chromoanagenesis such as chromoplexy or chromothripsis. Transcription of rearrangement‐related junctions was predicted to result in many potential neoantigens, some of which were proven to bind patient‐specific major histocompatibility complex molecules and to expand intratumoral T cell clones. T cells responsive to these predicted neoantigens were also present in a patients circulating T cell repertoire. Analysis of genomic array data from the mesothelioma cohort in The Cancer Genome Atlas suggested that multiple chromothriptic‐like events negatively impact survival. Conclusions: Our findings represent the discovery of potential neoantigen expression driven by structural chromosomal rearrangements. These results may have implications for the development of novel immunotherapeutic strategies and the selection of patients to receive immunotherapies.

Abstract 5726: Rearrangement-related peptides with neoantigenic potential in malignant pleural mesothelioma

Malignant pleural mesothelioma is a disease primarily associated with exposure to the carcinogen asbestos. Consistent with this carcinogenic exposure, cytogenetic analyses have identified multiple recurrent structural chromosomal abnormalities in this malignancy, but more recent high-throughput sequencing evaluations of point mutations suggest that there is a low mutational burden in mesothelioma. Since tumor mutational burden has been correlated with responses to treatment with immune checkpoint inhibitors such as nivolumab, it was not consistent that patients with mesothelioma and low mutation burdens would have similar response rates in clinical trials with immune checkpoint inhibitors as patients with non-small cell lung cancer which is associated with a high mutation burden. In order to reconcile these differences, and given the potential for an improved understanding of the molecular pathogenesis of mesothelioma to improve therapeutic options, we used mate-pair sequencing (MPseq) and RNA sequencing (RNAseq) to understand how structural variants affect the transcriptome. MPseq differs from standard next generation sequencing approaches by tiling the whole genome with larger fragments (2-5kb) to reliably detect structural variants such as insertions, deletions and rearrangements. Amongst 22 mesothelioma specimens there were 1535 chromosomal rearrangements (median 41, range 3-298 per specimen), that resulted in junctions or novel fusions of non-coding DNA or genes. Six-hundred thirty-seven of these rearrangements (median 22, range 5-103 range per specimen) resulted in novel fusions of genes. Many of these inter- or intra-chromosomal rearrangements were consistent with a pattern of chromoanagesis such as chromoplexy or chromothripsis. Chromosomal rearrangements detected by MPseq were used to guide analysis of RNAseq data and revealed that these chromosomal junctions resulted in the expression of 179 novel amino acid sequences (median 5, 0-51 range per specimen). To determine whether transcription of chromosomal rearrangement-related junctions have neoantigenic potential, we used in silico tools to determine whether any of the expressed junctions contained peptides that could be presented by patient-specific HLA molecules. The top candidate rearrangement-related peptides with neoantigenic potential bound patient-specific HLA molecules nearly as well or as well as a positive control in competitive binding assays. Our findings represent the discovery of potential neoantigen expression driven by structural chromosomal rearrangements. These results may have implications for the development of novel therapeutic strategies, the selection of patients to receive immunotherapy, and blood-based treatment monitoring strategies. Citation Format: Aaron S. Mansfield, Tobias Peikert, James B. Smadbeck, Julia B. Udell, Farhad Kosari, Stephen J. Murphy, Hongzheng Ren, Vishnu V. Serla, Janet L. Schaefer Klein, Giannoula Karagouga, Faye R. Harris, Carlos Sosa, Sarah H. Johnson, Wendy Nevala, Svetomir N. Markovic, Aaron O. Bungum, Eric S. Edell, Haidong Dong, John C. Cheville, Marie Christine Aubry, Jin Jen, George Vasmatzis. Rearrangement-related peptides with neoantigenic potential in malignant pleural mesothelioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5726.

Abstract 5060: Gene network predicts overall survival in patients with primary lung adenocarcinoma

Lung adenocarcinoma is the most common type of primary lung cancer. Previous studies have shown that gene expression signatures may predict clinical outcome. In this study, we used a systems biology approach, weighted gene co-expression network analysis (WGCNA), to identify survival related networks and gene signatures. We first analyzed whole genome gene expression profiles in 82 lung adenocarcinoma tumor tissues from never smokers (smoked −4 ) and overall survival (OS, p =0.027, HR, 1.71; 95% CI, 1.06-2.74) after adjusting for potential confounders (age and tumor grade). When this module signature was incorporated and compared to the conventional model consisting of clinical variables only, the survival prediction accuracy was increased from 0.70 to 0.75. Gene Ontology (GO) enrichment analysis indicated this module was significantly enriched in biological process GO term “cell cycle” (p = 2.1×10 −53 ). To explore the effect of this network module at germline level, we performed the WGCNA on normal lung tissues derived from 78 of the 82 patients and observed significant association of an expression module with OS (adjusted p=3×10 −4 , HR=1.98; 95% CI, 1.36-2.87). Interestingly, this module was also significantly enriched in cell cycle-related genes (p=4.1×10 −41 ). To further validate this result, we analyzed an independent microarray gene expression dataset including 442 lung adenocarcinoma patients from NCI Director9s Challenge Consortium. We found the same association: the cell cycle-enriched module was correlated with tumor grade of cell differentiation (r=0.55, p-value=5×10 −37 ) and OS (adjusted p=7.4×10 −3 ; HR, 1.20; 95% CI, 1.05-1.37). We further identified 30 genes in the OS-related module that overlapped between the discovery and validation data sets. Furthermore, all these 30 genes were found to be up-regulated in adenocarcinoma compared to adjacent normal lung tissues in the discovery data set. Of the 30 genes, three key genes, UBE2C, TPX2 and MELK, were identified with highest connectivity in cell cycle-enriched module; their expression levels were significantly associated with OS in both discovery and validation sets. UBE2C and TPX2 have been reported as gene signatures for human lung cancer prognosis in vitro lung carcinogenesis system; MELK was identified as a key regulator of the proliferation of malignant brain tumors and malignant grade in human astrocytomas, and was also associated with breast cancer prognosis. Our results suggest that genes involved in cell-cycle are likely related with tumor aggressiveness and therefore can predict survival in lung adenocarcinoma. Further studies are needed to validate the key genes that could improve survival prediction and provide potential new targets to intervene progression of lung adenocarcinoma. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5060. doi:10.1158/1538-7445.AM2011-5060