Alden M. Parsons

Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically important, and correspond to normal cell types.

Purpose: Lung squamous cell carcinoma (SCC) is clinically and genetically heterogeneous, and current diagnostic practices do not adequately substratify this heterogeneity. A robust, biologically based SCC subclassification may describe this variability and lead to more precise patient prognosis and management. We sought to determine if SCC mRNA expression subtypes exist, are reproducible across multiple patient cohorts, and are clinically relevant. Experimental Design: Subtypes were detected by unsupervised consensus clustering in five published discovery cohorts of mRNA microarrays, totaling 382 SCC patients. An independent validation cohort of 56 SCC patients was collected and assayed by microarrays. A nearest-centroid subtype predictor was built using discovery cohorts. Validation cohort subtypes were predicted and evaluated for confirmation. Subtype survival outcome, clinical covariates, and biological processes were compared by statistical and bioinformatic methods. Results: Four lung SCC mRNA expression subtypes, named primitive, classical, secretory, and basal, were detected and independently validated (P < 0.001). The primitive subtype had the worst survival outcome (P < 0.05) and is an independent predictor of survival (P < 0.05). Tumor differentiation and patient sex were associated with subtype. The expression profiles of the subtypes contained distinct biological processes (primitive: proliferation; classical: xenobiotic metabolism; secretory: immune response; basal: cell adhesion) and suggested distinct pharmacologic interventions. Comparison with lung model systems revealed distinct subtype to cell type correspondence. Conclusions: Lung SCC consists of four mRNA expression subtypes that have different survival outcomes, patient populations, and biological processes. The subtypes stratify patients for more precise prognosis and targeted research. Clin Cancer Res; 16(19); 4864–75. ©2010 AACR.

Differential Pathogenesis of Lung Adenocarcinoma Subtypes Involving Sequence Mutations, Copy Number, Chromosomal Instability, and Methylation

Background Lung adenocarcinoma (LAD) has extreme genetic variation among patients, which is currently not well understood, limiting progress in therapy development and research. LAD intrinsic molecular subtypes are a validated stratification of naturally-occurring gene expression patterns and encompass different functional pathways and patient outcomes. Patients may have incurred different mutations and alterations that led to the different subtypes. We hypothesized that the LAD molecular subtypes co-occur with distinct mutations and alterations in patient tumors. Methodology/Principal Findings The LAD molecular subtypes (Bronchioid, Magnoid, and Squamoid) were tested for association with gene mutations and DNA copy number alterations using statistical methods and published cohorts (n = 504). A novel validation (n = 116) cohort was assayed and interrogated to confirm subtype-alteration associations. Gene mutation rates (EGFR, KRAS, STK11, TP53), chromosomal instability, regional copy number, and genomewide DNA methylation were significantly different among tumors of the molecular subtypes. Secondary analyses compared subtypes by integrated alterations and patient outcomes. Tumors having integrated alterations in the same gene associated with the subtypes, e.g. mutation, deletion and underexpression of STK11 with Magnoid, and mutation, amplification, and overexpression of EGFR with Bronchioid. The subtypes also associated with tumors having concurrent mutant genes, such as KRAS-STK11 with Magnoid. Patient overall survival, cisplatin plus vinorelbine therapy response and predicted gefitinib sensitivity were significantly different among the subtypes. Conclusions/ Significance The lung adenocarcinoma intrinsic molecular subtypes co-occur with grossly distinct genomic alterations and with patient therapy response. These results advance the understanding of lung adenocarcinoma etiology and nominate patient subgroups for future evaluation of treatment response.

Management of Stage I and II Thymoma

With a knowledgeable assessment of the clinical presentation and demographic and radiologic characteristics, most thymomas can be reliably identified preoperatively without the need for a biopsy. Surgery is the mainstay of treatment for stage I and II thymoma. The rate of complete resection is essentially 100% by open techniques, and recurrences are rare. A complete thymectomy via a sternotomy is the standard approach. Adjuvant radiotherapy after a complete resection does not appear to be of benefit. In the rare event of a recurrence, an aggressive approach should be taken with re-resection whenever possible.

Multifocal right atrial myxoma and pulmonary embolism

Multifocal cardiac myxoma with greater than two foci is rarely reported in the literature. We report a case of a 22-year-old woman who presented with profound right heart failure, and was found to have seven right atrial myxomas with bilateral pulmonary embolism, including near-complete occlusion of right pulmonary arterial flow. Multifocal atrial myxoma occurs most often in the familial setting, and often is associated with recurrence. Her disease was nonfamilial. She was successfully treated with surgical resection, and has had complete recovery with no evidence of recurrence over a 4-year period.

Alterations of LKB1 and KRAS and Risk of Brain Metastasis: Comprehensive Characterization by Mutation Analysis, Copy Number, and Gene Expression in Non-Small-Cell Lung Carcinoma.

BACKGROUND Brain metastases are one of the most malignant complications of lung cancer and constitute a significant cause of cancer related morbidity and mortality worldwide. Recent years of investigation suggested a role of LKB1 in NSCLC development and progression, in synergy with KRAS alteration. In this study, we systematically analyzed how LKB1 and KRAS alteration, measured by mutation, gene expression (GE) and copy number (CN), are associated with brain metastasis in NSCLC. MATERIALS AND METHODS Patients treated at University of North Carolina Hospital from 1990 to 2009 with NSCLC provided frozen, surgically extracted tumors for analysis. GE was measured using Agilent 44,000 custom-designed arrays, CN was assessed by Affymetrix GeneChip Human Mapping 250K Sty Array or the Genome-Wide Human SNP Array 6.0 and gene mutation was detected using ABI sequencing. Integrated analysis was conducted to assess the relationship between these genetic markers and brain metastasis. A model was proposed for brain metastasis prediction using these genetic measurements. RESULTS 17 of the 174 patients developed brain metastasis. LKB1 wild type tumors had significantly higher LKB1 CN (p<0.001) and GE (p=0.002) than the LKB1 mutant group. KRAS wild type tumors had significantly lower KRAS GE (p<0.001) and lower CN, although the latter failed to be significant (p=0.295). Lower LKB1 CN (p=0.039) and KRAS mutation (p=0.007) were significantly associated with more brain metastasis. The predictive model based on nodal (N) stage, patient age, LKB1 CN and KRAS mutation had a good prediction accuracy, with area under the ROC curve of 0.832 (p<0.001). CONCLUSION LKB1 CN in combination with KRAS mutation predicted brain metastasis in NSCLC.

Abstract 2164: Lung adenocarcinoma subtypes have unique gene mutations (EGFR, TP53), DNA copy number alterations (3q26, 16p13), and patient smoking histories

Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC Introduction: Lung adenocarcinoma is a clinically and genetically heterogenous disease. Recently, three validated and clinically relevant gene expression subtypes (Magnoid, Bronchioid, and Squamoid) have been described (Hayes, 2006); however, the subtypes’ origins are unknown. We hypothesized that the subtypes are the result of unique gene mutations and DNA copy number alterations in unique patient populations. Methods: 85 lung adenocarcinomas were collected and assayed for gene expression and DNA copy number (CN), using Agilent 44K and Affymetrix 250K_Sty microarrays. 376 lung adenocarcinomas with gene expression microarrays and CN arrays or gene mutations were obtained from three published cohorts (Ding, 2008; Tomida, 2009; Chitale, 2009). Tumor subtype classification was completed using published methods. CN was calculated and significantly altered CN segments were detected (Beroukhim, 2007; Bengtsson, 2008). Subtype segment CN was compared by z -scores (FDR < 1%). Mutations and clinical variables were compared by Cochran-Mantel-Haenszel tests adjusting for cohort and by Kruskal-Wallace tests. Subtype 3-year survival was compared by log rank tests and Cox proportional hazards models adjusted by cohort. Results: Three gene expression subtypes were detected in each of four cohorts and uniquely corresponded to the known Magnoid (M), Bronchioid (B) and Squamoid (S) subtypes. Gene mutations were significantly associated with subtype, including EGFR increased in B (M/B/S: 16%, 39%, 23%; P ≪ 0.01) and TP53 increased in M (M/B/S: 45%, 24%, 15%; P ≪ 0.01). Additionally, numerous genomic regions had significantly different mean DNA copy number across the subtypes including amplifications (M: 3q26, 7q31; B: 5q34, 16p13) and deletions (M: 4q35.1, 17p12). Interestingly, a more broad measure of overall genomic stability (chromosome arm variation) was also significantly different among subtypes, with M having the highest instability (P ≪ 0.01). In terms of clinical significance, 3-year subtype patient survival was significantly different (M/B/S − 66%, 87%, 83%; P ≪ 0.01), and remained so after adjustment for mutations, stage, and sex. Patient smoking history was significantly different among the subtypes (pack year median M/B/S: 40/10/34; P ≪ 0.01). Also, previously reported associations of subtype and morphology were confirmed, with lower grade (P ≪ 0.01) and increased micropapillary features in B (P = 0.04). Conclusions: Lung adenocarcinoma gene expression subtypes have different levels of EGFR and TP53 gene mutations, global genomic instability, specific DNA copy number alterations, and clinical and morphologic characteristics. This integrated analysis supports that different mutation events in concert with different patient populations contribute to produce these distinct and clinically relevant gene expression subtypes. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2164.