Derek Brown

An Integrated Prognostic Classifier for Stage I Lung Adenocarcinoma Based on mRNA, microRNA, and DNA Methylation Biomarkers.

Introduction: Up to 30% stage I lung cancer patients suffer recurrence within 5 years of curative surgery. We sought to improve existing protein-coding gene and microRNA expression prognostic classifiers by incorporating epigenetic biomarkers. Methods: Genome-wide screening of DNA methylation and pyrosequencing analysis of HOXA9 promoter methylation were performed in two independently collected cohorts of stage I lung adenocarcinoma. The prognostic value of HOXA9 promoter methylation alone and in combination with mRNA and miRNA biomarkers was assessed by Cox regression and Kaplan–Meier survival analysis in both cohorts. Results: Promoters of genes marked by polycomb in embryonic stem cells were methylated de novo in tumors and identified patients with poor prognosis. The HOXA9 locus was methylated de novo in stage I tumors (p < 0.0005). High HOXA9 promoter methylation was associated with worse cancer-specific survival (hazard ratio [HR], 2.6; p = 0.02) and recurrence-free survival (HR, 3.0; p = 0.01), and identified high-risk patients in stratified analysis of stages IA and IB. Four protein-coding gene (XPO1, BRCA1, HIF1&agr;, and DLC1), miR-21 expression, and HOXA9 promoter methylation were each independently associated with outcome (HR, 2.8; p = 0.002; HR, 2.3; p = 0.01; and HR, 2.4; p = 0.005, respectively), and when combined, identified high-risk, therapy naive, stage I patients (HR, 10.2; p = 3 × 10−5). All associations were confirmed in two independently collected cohorts. Conclusion: A prognostic classifier comprising three types of genomic and epigenomic data may help guide the postoperative management of stage I lung cancer patients at high risk of recurrence.

An analysis of genetic factors related to risk of inflammatory bowel disease and colon cancer

BACKGROUND AND AIMS Patients with inflammatory bowel disease (IBD) have a higher risk of developing colorectal cancer than the general population. Genome-wide association studies have identified and replicated several loci associated with risk of IBD; however, it is currently unknown whether these loci are also associated with colon cancer risk. METHODS We selected 15 validated SNPs associated with risk of either Crohns disease, ulcerative colitis, or both in previous GWAS and tested whether these loci were also associated with colon cancer risk in a two-stage study design. RESULTS We found that rs744166 in STAT3 was associated with colon cancer risk in two studies; however, the direction of the observation was reversed in TP53 mutant tumors possibly due to a nullification of the effect by mutant p53. The SNP, which lies within intron 1 of the STAT3 gene, was associated with lower expression of STAT3 mRNA in TP53 wild-type, but not mutant, tumors. CONCLUSIONS These data suggest that the STAT3 locus is associated with both IBD and cancer. Further understanding the function of this variant in relation to TP53 could possibly explain the role of this gene in autoimmunity and cancer. Furthermore, an analysis of this locus, specifically in a population with IBD, could help to resolve the relationship between this SNP and cancer.

Identification of serum inflammatory markers as classifiers of lung cancer mortality for stage I adenocarcinoma

Background Lung cancer is the leading cause of cancer-related mortality worldwide. Low-dose CT (LDCT) imaging is now recommended to screen high-risk lung cancer individuals in the USA. LDCT has resulted in increased detection of stage I lung cancer for which the current standard of care is surgery alone. However, approximately 30% of these patients develop recurrence and therefore are in need of further treatment upon diagnosis. This study aims to explore blood-based inflammatory biomarkers to identify patients at high-risk of mortality for which additional treatment modalities can be offered at time of diagnosis. Patients and Methods Recent work on a small panel of circulating cytokines identified elevated levels of IL-6, a pro-inflammatory cytokine, as an indicator of poor survival for lung cancer patients. To reflect the broader role of inflammation in lung cancer, we examined a large panel of 33 inflammatory proteins in the sera of 129 lung cancer patients selected from the National Cancer Institute-Maryland case-control study. To reduce heterogeneity, we specifically focused our study on stage I lung adenocarcinoma patients. Results We replicated the previous observations that IL-6 is associated with prognosis of lung cancer and extended its utility to prognosis in this highly-selected population of stage I lung adenocarcinoma patients. In addition, we developed a multi-marker, combined prognostic classifier that includes the pro-inflammatory Th-17 cell effector cytokine, IL-17. Patients with high levels of IL-6 and IL-17A had a significantly adverse survival compared with patients with low levels (P for trend <0.0001). Patients in the high risk group, with high levels of both proteins had a 5-year survival rate of 46% in comparison to 93% for those with low levels of both markers. Furthermore, we validated the same trends for the IL-6 and IL-17A prognostic signature in an independent data set. Conclusions The results identified here justify further investigation of this novel, combined cytokine prognostic classifier for the identification of high-risk stage I lung adenocarcinoma patients. This classifier has the much-needed potential to identify patients at high risk of recurrence and thus prospectively identify the subset of patients requiring more aggressive treatment regimens at the time of diagnosis.

Relationship between anti-depressant use and lung cancer survival

OBJECTIVES In recent years, the anti-cancer properties of several commonly used drugs have been explored, with drugs such as aspirin and beta-blockers associated with improved cancer outcomes. Previous preclinical work demonstrated that tricyclic anti-depressants have antitumor efficacy in lung cancer. Our goal was to examine the association between anti-depressant use and survival in lung cancer. MATERIALS AND METHODS We examined the association between use of common anti-depressants and survival in 1,097 lung cancer patients from the NCI-Maryland lung cancer study. The types of anti-depressants included in the study were norepinephrine and dopamine reuptake inhibitors, serotonin reuptake inhibitors, selective serotonin reuptake inhibitors, non-selective serotonin reuptake inhibitors, and tricyclic anti-depressants. Anti-depressant use was extracted from the medical history section of a detailed interviewer-administered questionnaire. Specific use in the three months before a lung cancer diagnosis was determined. Cox portioned hazards modeling was used to estimate the association between anti-depressant use with lung cancer-specific death with adjustment for potential confounding co-factors. RESULTS Anti-depressant use was associated with extended lung cancer-specific survival. In an analysis of specific classes of anti-depressant use, NDRIs and TCAs were associated with improved survival. Importantly, the extended survival associated with anti-depressants was maintained after adjustment for the clinical indications for these drugs, suggestive of a direct effect on lung cancer biology. CONCLUSIONS Considering the manageable and largely tolerable side effects of anti-depressants, and the low cost of these drugs, these results indicate that evaluation of anti-depressants as adjunct therapeutics with chemotherapy may have a translational effect for lung cancer patients.

Abstract LB-182: Improved survival among lung cancer patients taking antidepressants

In recent years, the anti-cancer properties of several commonly used drugs have been explored, with drugs such as aspirin and beta-blockers associated with improved cancer outcomes. Emerging evidence suggests that the antidepressant family of drugs may target key pathways in cancer cells, raising the possibility that such drugs could be re-purposed for cancer treatment. Here, using the NCI-MD lung cancer study, we assessed antidepressant use in 1,098 lung cancer patients. Strikingly, antidepressant use was associated with a significant extension of lung cancer-specific survival (HR = 0.78, 95% C.I. = 0.63 - 0.97, P = 0.027) (model adjusted for age, gender, race, smoking status, pack-years of smoking, tumor stage and histology). When assessing distinct classes of antidepressants, we observed that NDRIs (norepinephrine and dopamine reuptake inhibitors) and TCAs (tricyclic antidepressants) were specifically associated with extended survival: TCA HR = 0.40, 95% C.I. = 0.18 - 0.91, P = 0.028 and NDRI HR = 0.61, 95% C.I. = 0.39 - 0.95, P = 0.027). In contrast, SRIs (serotonin reuptake inhibitors) were linked with worse survival (HR 1.94 95% C.I. 1.10 - 2.42, P = 0.023). Importantly, the extended survival time associated with antidepressants was not associated with the typical indications for these drugs, suggestive of a direct effect on lung cancer cells. In addition, as we assessed lung cancer-specific survival we conducted a competing risks analysis, the results of which showed that both NDRIs and TCAs were associated with lung cancer survival (fully adjusted model NDRI, HR: 0.63, 95% C.I. 0.40 - 1.00, P = 0.05) (fully adjusted model TCA, HR: 0.36, 95% C.I. 0.17 - 0.76, P = 0.007). We provide strong evidence that lung cancer patients taking antidepressants, particularly NDRIs and TCAs, have a significantly prolonged survival. Considering the manageable and largely tolerable side effects of antidepressants, and the low cost of these drugs, these results indicate that repositioning antidepressants as adjunct therapeutics with chemotherapy may have a rapid and significant translational impact for lung cancer patients. Citation Format: Adriana Zingone, Derek Brown, Elise Bowman, Oscar Vidal, Joel Neal, Julien Sage, Brid M. Ryan. Improved survival among lung cancer patients taking antidepressants. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-182. doi:10.1158/1538-7445.AM2015-LB-182

CDC Screening Recommendation for Baby Boomers and Hepatitis C Virus Testing in the US Military Health System

Objectives: Chronic hepatitis C virus (HCV) is the most common blood-borne infection in the United States, with an estimated 2.7 to 3.9 million cases as of 2014. In August 2012, the Centers for Disease Control and Prevention (CDC) recommended 1-time HCV testing of all baby boomers. The objectives of this study were to (1) determine the proportion of people screened for HCV in the US Department of Defense Military Health System before and after the CDC screening recommendation for baby boomers and (2) assess whether certain patient or system factors were associated with screening for HCV before and after August 2012. Methods: We used a dataset containing 5% of beneficiaries randomly selected from the Military Health System Data Repository medical claims database for the period July 2011 through September 2013. Results: Of 108 223 people eligible for HCV screening during the first period (July 2011 through July 2012), 1812 (1.7%) were screened. Of 109 768 people eligible during the second period (September 2012 through September 2013), 2599 (2.4%) were screened. HCV screening receipt was related to benefit type (Prime before August 2012: adjusted odds ratio [aOR] = 2.16; 95% confidence interval [CI], 1.89-2.46; Prime after August 2012: aOR = 1.93; 95% CI, 1.73-2.16) and care source (direct care before August 2012: aOR = 1.80; 95% CI, 1.57-2.07; direct care after August 2012: aOR = 2.45; 95% CI, 2.18-2.75); male sex (aOR = 1.17; 95% CI, 1.06-1.29) and black race (aOR = 1.20; 95% CI, 1.05-1.37) were associated with HCV testing only before August 2012. Conclusions: Interventions should be implemented to increase awareness and knowledge of the current national HCV testing recommendation among baby boomers to seek out testing and health care providers to perform screening.

Abstract B60: Inflammatory-based diagnostic markers of lung cancer in African Americans

Background: African Americans have a higher risk of developing lung cancer compared with all other ethnic groups in the USA. Previous studies based on a small panel of markers suggested that certain circulating cytokines were associated with lung cancer. Given the complexity of the immune response in lung cancer and the multitude of cell types involved, we reasoned that examining a broad panel of inflammatory markers — including cytokines, chemokines, angiogenic and other pro-inflammatory factors — might identify a diagnostic signature of lung cancer for African American patients. Methods: Differences in 30 inflammatory marker serum levels, were measured in 308 African-American cases and 501 African American controls from the National Cancer Institute-Maryland (NCI-MD) case-control study using a Mesoscale multiplex platform (MSD). The panel of 30 serum inflammatory markers, included chemokines, cytokines and other inflammatory related proteins (Mesoscale VPLEX assay). Associations of the serum cytokine levels with lung cancer were analyzed using Stata statistical software (StataCorp, TX) Results: Fifteen inflammatory markers (CRP, IFN-gamma, IL-10, IL-15, IL-17A, IL-1beta, IL-6, IL-7, IL-8, IP-10, MCP-4, MIP-1alpha, TARC, TNF-alpha and VEGF) were significantly different among African American cases compared with African American controls. In agreement with our previous observations, levels of IL-10, IL-1beta, IL-6, IL-8, and TNF-alpha were associated with lung cancer risk. In addition, we found that CRP, IFN-gamma, IL-15, IL-7, IP-10, MCP-4, MIP-1alpha, TARC, and VEGF were associated with lung cancer in African Americans. The associations between CRP, IFN-gamma, IL-10, IL-15, IL-1beta, IL-6, IL-7, IL-8, IP-10 and MCP-4 levels and lung cancer among African Americans were significant after adjustment for additional potential confounding factors. Conclusions: Serum cytokine levels vary by race and might contribute to lung cancer differently between African Americans and European Americans. The findings presented here build upon recent work that identified associations between elevated levels of IL-10, IL-1beta, IL-6, IL-8, TNF-alpha and lung cancer among African Americans. Furthermore, by analyzing a broader spectrum of inflammation, we have identified additional markers of lung cancer for African American patients. Citation Format: Claire L. Meaney, Khadijah A. Mitchell, Adriana Zingone, Derek Brown, Wei Tang, Yunkai Yu, Liang Cao, Brid M. Ryan. Inflammatory-based diagnostic markers of lung cancer in African Americans. [abstract]. In: Proceedings of the Ninth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2016 Sep 25-28; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2017;26(2 Suppl):Abstract nr B60.

Abstract 3406: The identification of serum cytokine inflammatory markers as classifiers of lung cancer mortality for stage I lung adenocarcinoma: a retrospective cohort study

Lung cancer is the leading cause of cancer-related mortality worldwide. Low-dose CT (LDCT) imaging is now recommended to screen high-risk lung cancer individuals in the USA. The sensitivity of LDCT has resulted in increased detection of stage I lung cancer and a 20% reduction in lung cancer mortality. The current standard of care for stage 1 lung cancer patients is surgery alone. However, between 20% and 30% of these patients will develop recurrence and therefore are in need of further treatment upon diagnosis. This study aims to explore and validate biomarkers to identify patients at high-risk of mortality so that additional treatment modalities can be offered at time of diagnosis. Our recent work on a small panel of circulating cytokines identified elevated levels of IL-6, a pro-inflammatory cytokine, as an indicator of poor survival. To further examine the potential of inflammatory biomarkers as prognostic indicators, 125 stage I lung adenocarcinoma cases were selected from the National Cancer Institute-Maryland lung cancer case-control study. This is an on-going prospective study of non-small cell lung cancer based in the greater Baltimore region of the USA. A panel of 33 inflammatory markers was measured for each case using the Mesoscale V-Plex assay. The magnitude of association between serum inflammatory marker expression levels and lung cancer-specific survival was tested using multivariable Cox proportional hazards regression modeling (Stata 12.0 statistical software). All calculations were adjusted for age, gender, stage and smoking status. Maximum follow up time was 15 years. Five analytes were significantly associated with shorter survival. In concordance with the previous study, IL-6 was again associated with shorter survival (HR, 2.63; 95% CI, 1.25-5.56). Other cytokines associated with shorter survival included CRP (HR, 2.25; 95% CI, 1.09-4.65), Eotaxin-3 (HR, 2.20; 95% CI, 0.97-4.86), IL-12p40 (HR 1.98; 95% C.I. 1.00 - 3.91), and IL-17 (HR, 2.22; 95% CI, 1.08-4.58). Although IL6 and CRP were positively correlated (Rho = 0.451, P These results support the potential of cytokine markers as a prognostic tool to further classify stage I lung cancer and thus identify patients in need of additional treatment. The associations identified here justify further investigation of a novel, combined cytokine prognostic classifier to serve as a robust predictor of stage I lung adenocarcinoma survival. Citation Format: Claire L. Meaney, Adriana Zingone, Derek Brown, Yunkai Yu, Liang Cao, Brid M. Ryan. The identification of serum cytokine inflammatory markers as classifiers of lung cancer mortality for stage I lung adenocarcinoma: a retrospective cohort study. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3406.

Abstract LB-295: Analysis of miR-21 isomiRs in lung cancer

microRNAs (miRNA) are small non-coding RNAs that target mRNA transcripts. Primarily, they bind to the 3′UTR of mRNA sequences and repress protein translation. They are involved in the regulation of over 60% of human genes. miRNAs are deregulated in cancer and expression signatures have been correlated with cancer diagnosis, progression and prognosis. Thus, they are being pursued for clinical application. isomiRs, or miRNA variants that are generated post-transcriptionally, were originally classified as experimental error in cloning and next generation sequencing studies. However, over the past five years it has become increasingly clear that isomiRs are evolutionarily conserved, prevalent and functional. miR-21 is overexpressed and associated with poor prognosis in multiple malignancies and as such it is currently under development as a therapeutic target. Thus, we examined the isomiR landscape of miR-21 in lung cancer using data from The Cancer Genome Atlas (lung adenocarcinoma n = 420 and squamous cell carcinoma n = 296). Raw sequence files were extracted from TCGA, cleaned and analyzed using STATA 13. We observed that there are significantly more isomiRs of miR-21 in both lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) compared to non-involved adjacent lung tissue. Specifically, LUAD had total of 244 5p variants and LUSC had 232 5p variants, compared with 74 and 105 in non-involved tissue, respectively. The most prevalent isomiR of miR-21 was not the canonical ‘miRBase’ isomiR and the most common edit was a 5′ deletion with 3′ addition. There were 15 miR-21-5p isomiRs in LUAD and 12 in LUSC that were prevalent (defined as detected in more than 50% of patients) and were expressed at a significantly higher level defined as detected with a FPKM value greater than 50) in tumor versus non-involved tissue samples. The average fold change was 5.7 in LUAD (range 2.8-21.1) and 2.7 in LUSC (range 1.7-5.6). Of the prevalent miR-21-5p isomiRs, 6 in LUAD and 4 in LUSC had a change in the canonical miR-21 seed sequence. An analysis of the targets of these isomiRs using the target prediction algorithms Targetscan and Diana revealed limited overlap in gene targets (0% to 54%) compared with canonical miR-21-5p targets. Our work highlights a high complexity of miRNA sequence heterogeneity in lung cancer. Combining the characterization of miR-21 isomiRs and pursuing translational laboratory studies will allow us to determine the functionality of these isomiRs and their relevance for human cancer diagnosis and treatment. Citation Format: Jennie D. Leikin, Adriana Zingone, Derek Brown, Khadijah Mitchell, Mohammed Khan, Oscar Vidal, Brid Ryan. Analysis of miR-21 isomiRs in lung cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-295. doi:10.1158/1538-7445.AM2015-LB-295