OS01.7.A Detection of methylation-based prognostic signatures in liquid biopsy specimens from patients with meningiomas

Background

Detection of distinct epigenetic biomarkers in circulating cell-free DNA (cfDNA) of liquid biopsy (LB) specimens (e.g. blood) fosters opportunity for prognostication of central nervous system (CNS) tumors and has not been thoroughly explored in patients with meningiomas.

Material and Methods

We profiled the cfDNA methylome (EPIC array) in serum specimens from patients with meningiomas (MNG; n= 63) and harnessed internal and external meningioma tissue methylome data with reported follow up (n=48). To predict recurrence risk (RR), we consolidated a tissue cohort with at least 5 years of follow up and divided them into confirmed recurrence (CR; either reported progressive disease in post-surgical imaging, or additional resections following initial surgery) and confirmed no-recurrence (CNR: no confirmed disease progression w/in at least 5-years of follow-up). Then through application of an iterative process consisting of multiple tissue- and serum-based supervised analyses, we identified risk-specific methylation markers with serum specific features which, when inputted into a random forest algorithm allowed for segregation of both tumor tissue and liquid biopsy specimens according to recurrence risk. We estimated immune cell composition using MethylCIBERSORT, where a reference methylome atlas of chosen immune cell types was utilized to deconvolute the MNG samples.

Results

The resulting recurrence risk classifier demonstrated an appreciable predictive power in classifying samples as high or low recurrence risk across the tumor tissue cohort (ACC: 87.5%, CUI+: 85.2%). When compared to another classifier, our model demonstrated statistically significant agreement across primary meningioma samples (κ=0.269, p=0.002), and more accurately predicted samples to recur across an expanded time window (time to recurrence >5yrs). Across resulting liquid biopsy classifications, recurrence risk subgroups were analogous with reported risk factors, including WHO grade, extent of resection, and tumor location. Recurrence risk subgroups (high and low) also demonstrated differential estimated immune cell contributions, with low-risk samples exhibiting a “hot” profile, or enrichment of B-Cells, CD56- and CD4 T-Cells, and natural killer cells. Notably, the estimated neutrophil to lymphocyte ratio, previously purported to be relevant to tumor prognosis, was appreciably higher for those meningioma samples with the highest recurrence risk.

Conclusion

DNA methylation markers identified in the serum are suitable for the development of machine learning-based models which present high predictive power to prognosticate patients with meningioma and estimate a differential immune profile across recurrence risk groups. After validation in an external cohort, this noninvasive approach may improve the presurgical therapeutic management of patients with meningiomas.

P01.02 Serum-derived DNA methylation markers distinguish functional and invasiveness subtypes in patients harboring pituitary tumors

BACKGROUND

Molecular profiling of circulating biomarkers released by tumors has a relevant clinical value in central nervous system (CNS) tumors, but its feasibility has not been investigated in pituitary tumors (PT) despite being the second common intraaxial tumors of the CNS (~15%). Although usually benign and slow-growing, they can be nonfunctioning and invade surrounding structures resulting in significant comorbidities. DNA methylation aberrations distinguish PT according to their functional status but their role in invasiveness is still unclear. Pre-surgical detection of clinically relevant molecular markers associated with tumor behavior can address current diagnostic and therapeutic challenges. We hypothesized that PT release cell-free DNA (cfDNA) into the bloodstream allowing for the profiling of epigenetic markers associated with relevant clinicopathological features.

MATERIAL AND METHODS

Genome-wide methylome profile of paired serum cfDNA (EPIC array) and tissue from 13 patients with pituitary macroadenomas (9 males; median age: 62; 9 NFPT, 6 invasive) and 3 controls serum (patients with epilepsy).

RESULTS

Unsupervised analysis of the serum methylome from patients harboring PT was distinct from controls and other diseases (hypopituitarism, glioma and colorectal cancer) and supervised analysis (Wilcoxon Rank-sum Test) identified significant differentially methylated probes (DMP) that segregated PT from control serum specimens. Nonfunctioning and invasive-specific DMPs identified in the serum also defined functional, and less prominently invasive status, in the tissue of an independent cohort of PT.

CONCLUSION

This is the first study to show the feasibility to profile the methylome in the serum of patients with PT using cfDNA. In addition, we identified unique methylation signatures that distinguished PT according to functional and invasiveness subtypes. These results underpin the potential role of methylation profile and liquid biopsy as a noninvasive approach to assess clinically relevant molecular features in the serum of patients harboring PT.

OS1.5 Detection of glioma and prognostic subtypes by non-invasive circulating cell-free DNA methylation markers

BACKGROUND: Genome-wide DNA methylation profiling has shown that epigenetic abnormalities are biologically important in glioma and can be used to classify these tumors into distinct prognostic groups. Thus far, DNA profiling has required surgically resected glioma tissue; however, gliomas release tumoral material into biofluids providing an opportunity for a minimally invasive testing. While prior studies have shown that molecular markers can be detected in liquid biopsy (LB), there has been low sensitivity for tumor-specific markers. We hypothesize that the low sensitivity is due to the targeted assay methods. METHODS: Genome-wide CpG methylation levels in DNA of tumor tissue and cell-free DNA serum of glioma patients. RESULTS: We defined glioma-specific and IDH-specific epigenetic LB (eLB) signatures (Glioma-eLB and IDH-eLB, respectively) from serum cell-free DNA from patients diagnosed with glioma (N=15 IDH mutant and N=7 IDH wildtype) and with epilepsy (N=3). The epigenetic profiles of the matched tissue demonstrate that these eLB signatures reflected the signature of the tumor. Through cross-validation we show that Glioma-eLB can accurately predict a patient’s glioma from those with other neoplasias (N=6 Colon; N=14 Pituitary; N=3 Breast; N=4 Lung), non-neoplastic immunological conditions (N=22 sepsis; N=9 pancreatic islet transplantation), and from healthy individuals (sensitivity: 98%; specificity: 99%). Finally, IDH-eLB includes promoter methylated markers associated with genes known to be involved in glioma tumorigenesis (PVT1 and CXCR6). CONCLUSIONS: The application of the non-invasive eLB signature discovered in this study has the potential to complement the standard of care for patients harboring glioma.

This project is supported by the Henry Ford Health System, Department of Neurosurgery and the Hermelin Brain Tumor Center Foundation (A30935), United States National Institutes of Health (R01CA222146), and United States Department of Defense (CA170278)

Methylation markers differentiate thyroid cancer from benign nodules

PURPOSE

The incidence of thyroid cancer (TC) is increasing. Cytology by itself cannot distinguish TC from some benign nodules especially in certain subtypes of TC. Our immediate goal is to identify DNA methylation markers for early detection of TC and to molecularly differentiate TC subtypes from benign nodules.

METHODS

Promoter methylation status of 21 candidate genes was examined on formalin-fixed paraffin-embedded tissue (FFPE) utilizing quantitative methylation-specific polymerase chain reaction (QMSP) in a retrospective cohort of 329 patients (56% white, 29% African American, 61% female) comprising 71 normal thyroid, 83 benign nodules [follicular adenomas (FA)], 90 follicular TC (FTC) and 85 papillary TC (PTC). All genes were analyzed individually (Kruskal-Wallis and Wilcoxon rank sum tests) and in combination (logistic regression models) to identify genes whose methylation levels might best separate groups.

RESULTS

Combination gene panels TPO and UCHL1 (ROC = 0.607, sensitivity 78%) discriminated FTC from FA, and RASSF1 and TPO (ROC = 0.881, sensitivity 78%) discriminated FTC from normal. Methylation of TSHR distinguished PTC from FTC (ROC = 0.701, sensitivity 84%) and PTC from FA (ROC = 0.685, sensitivity 70%). The six gene panel of TIMP3, RARB2, SERPINB5, RASSF1, TPO and TSHR, which differentiates PTC from normal thyroid, had the best combination sensitivity (91%) and specificity (81%) of the panels addressing discrimination of cancer tissue.

CONCLUSIONS

Aberrant gene methylation used in combination panels may be useful clinically in differentiating FTC and PTC from benign nodules. If confirmed in additional studies, these findings could help reduce the over diagnosis of thyroid cancer and surgeries related to over diagnosis.

Abstract P1-04-06: Network integration of epigenomic data: Leveraging the concept of master regulators in ER negative breast cancer

Background: There has been relatively little advancement in changing the management of women with estrogen receptor (ER) negative breast cancer (BC), mainly due to a dearth of actionable therapeutic targets. Therefore, understanding the underlying biology of such a complex disease is necessary for bringing new therapeutic treatments to light. A key question in cancer genomics is how to distinguish 'driver' or essential alterations, which contribute to tumorigenesis, from functionally neutral or 'passenger' alterations that go along for the ride. The majority of published studies investigating driver genes have focused primarily on genomic mutations which have led to novel study designs (basket trials) where patients with a rare mutation, regardless of tumor histology, are matched to a drug expected to work through the mutated pathway. This dominant focus on mutations has overshadowed consideration of inclusion of epigenetic information. This study illustrates network integration of epigenomic data to prioritize ER negative specific methylated genes as potential epigenetic drivers of aggressive disease.

Methods: Causal Networks are small hierarchical networks of regulators whose activity can be modulated by the expression of downstream target genes to enhance understanding of the effect of upstream master regulators on disease or function. A master regulator is a gene or drug positioned as the central or master hub that has the ability to command or influence downstream events. Causal Network Analysis (CNA) was used to find networks that connect upstream master regulators with a 16 candidate methylation gene signature differentiating ER negative from ER positive BC. The 16 ER-negative specific gene methylation signature (AHNAK, ALPL, ANXA2R, CCND1, CIRBP, CPQ, DST, EGFR, ESR1, GPRC5B, HERC5, IL22RA2, MITF, OBSL1, POU3F3, RB1CC1) was identified via our drill-down approach starting from a discovery approach (Illumina 450k BeadChip) followed by expression verification, significant rankings in biological pathways (Ingenuity Pathway Analysis), confirmation by targeted sequencing using Illumina MiSeq, and additional filtering in 450K TCGA data sets.

Results: CNA software identified 4 hierarchical networks and their corresponding master regulatory molecules, diethylstilbestrol, transcription regulator SP1, MSH2, and 15-ketoprotaglandin E2. Diethylstilbestrol and SP1 had direct regulatory influence (depth level 1) to the candidate molecules ALPL, CCND1, EGFR, ESR1 and CCND1, CIRBP, EGFR, ESR1, respectively.

Conclusion: In this study, direct regulatory influence, noted for 5/16 candidate genes indicates additional rationale for further consideration and validation of ALPL, CCND1, CIRBP, EGFR, ESR1 as potential epigenetic driver targets in ER negative BC. As cancer therapies become increasingly more specific and begin to move past cytotoxic agents, determining the molecular features of a tumor that predict response to a given drug has become increasingly essential to match patients with optimal therapy. Currently epigenetic therapy in the form of hypomethylating agents (e.g: decitabine) exhibit clinical efficacy in patients with AML and MDS including those patients not responding to cytotoxic therapy.

Support: Komen Foundation: KG110218.

Citation Format: Worsham MJ, Chen KM, Datta I, Stephen JK, Chitale D, Divine G. Network integration of epigenomic data: Leveraging the concept of master regulators in ER negative breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-04-06.

Abstract P6-12-14: Comparative analysis of breast cancer phenotypes in African American, White American, and African patients- Correlation between African ancestry and triple negative breast cancer

Introduction: Population-based incidence rates of triple negative breast cancer (TNBC) are higher for African American (AA) compared to White American (WA) women, but it is unclear whether TNBC risk is genetically associated with African ancestry because AA women represent an ancestrally admixed population. Higher frequencies of TNBC have also been observed in sub-Saharan African breast cancer (BC) patients, but comparative analyses of biomarker expression among datasets that include AA, WA, and African women are sparse. We report findings from an international registry that features specimens from a diverse patient population in Detroit, Michigan as well as a hospital in Kumasi, Ghana.

Methods: The study dataset included formalin-fixed, paraffin-embedded invasive BC tumors diagnosed between 1998 and 2014 at the Komfo Anokye Teaching Hospital in Ghana and the prospectively-maintained/annotated Henry Ford Health System cohort in Michigan. All Ghanaian tumors underwent pathology confirmation and immunohistochemistry for estrogen receptor (ER), progesterone receptor (PR) and HER2/neu expression at the University of Michigan. Women were classified into five BC phenotypes and dichotomized into two age groups, <50 and ≥50 years. Polychotomous multivariate GLM models were developed to estimate the risk for each BC phenotype. Statistical analyses were performed in SAS v. 9.0 (Carey, NC). This research was approved by the Institutional Review Boards of the participating institutions.

Results: A total of 234 Ghanaian cases with mean age 49 years (range 24-92); 271 AA with mean age 60 (range 27-87); and 321 WA with mean age 62 (range 31-91) (P=0.001) contributed to this study. Prevalence of histologic grade 3 was lowest in WA (n=107, 33.7%) which was statistically significant from the observed prevalence in AA (n=135, 50.4%) and Ghanaians (n=84, 53.8%) (P<0.0001). ER-negative and TNBC were more common among Ghanaian and AA compared to WA cases (frequency ER-negativity 67.5%, 37.1%, and 19.8%, respectively, p<0.0001; frequency TNBC 53.2%, 29.8%, and 15.5%, respectively, p<0.0001). In the age group <50 years, 82 women (42.5%) were diagnosed with ER+/PR+/HER2-, 65 (33.7%) with TNBC, 27 (14.0%) with ER+/PR+/HER2+, 14 (7.2%) with ER-/PR-/HER2+ and 5(2.6%) with ER-/PR+/HER2- phenotypes. In this young age group, prevalence of TNBC remained highest among Ghanaian women (50.8%), followed by AA (34.3%) and WA (15.9%); (P=.0006). In contrast, highest prevalence of ER+/PR+/HER2+ and ER+/PR+/HER2- phenotypes was observed in WA, followed by AA and Ghanaians. On multivariate analysis histologic grade 3 and racial heritage remained statistically significantly associated with the TNBC phenotype (OR for AA vs. WA with TNBC 1.87, 95% CI 1.15-3.04; OR for Ghanaian vs. WA with TNBC 10.63, 95% CI 5.32-21.25; OR for Grade 3 vs Grade 1 histology with TNBC 33.3, 95% CI 13.45-82.4).

Conclusions: This study confirms an association between the TNBC phenotype and African ancestry; furthermore, extent of African ancestry appears to be associated with an increased likelihood of having a TNBC tumor, since frequency of TNBC among AA patients was intermediate between WA and Ghanaian patients.

Citation Format: Newman LA, Jiagge E, Bensenhaver JM, Chitale D, Kleer C, Merajver S, Kyei I, Aitpillah F, Oppong J, Amankwaa-Frempong E, Adjei E, Wicha M, Awuah B, Stark A. Comparative analysis of breast cancer phenotypes in African American, White American, and African patients- Correlation between African ancestry and triple negative breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-12-14.

Abstract P2-03-01: Differentially methylated miRNA methylomes of normal breast tissue from ER negative and ER positive breast cancer mimic their respective tumor phenotypes

Background: The unique structure and function of normal tissues is known to be regulated by epigenetic mechanisms. Understanding how normal cells in their respective tumor milieus might affect their susceptibility to become not only malignant but acquire breast cancer (BC) subtype-specific phenotypes, may determine tumor clinical behavior outcomes. The goal was to compare genome wide methylation profiles of non-coding miRNAs of breast cancer tissue and normal breast epithelium, respectively, from ER negative and ER positive tumors, and assess their miRNA methylomes in the context of tumor ER phenotypes as ER negative vs ER positive.

Methods: Breast cancer tissue from 79 patients (40 ER-positive and 39 ER-negative) and normal tissue from 39 of these patients (19 ER-negative and 20-ER-positive) were assayed using the Illumina 450K bead array. A sub analysis focused on 2249 miRNA CpGs assigned to 615 unique miRNAs. M-values were computed as a logit function [(log (beta/ (1-beta))] of the methylation beta values. T-tests were used to compare the means of the M-values for the ER-positive and ER-negative groups. The t-test p-values were used to generate adaptive FDR (aFDR) levels and aFDRs of 0.05 or lower were considered to be statistically significant (Tier 1). Tier 1 CpGs were subsequently filtered to select only those with a mean beta ratio between ER-positive and ER-negative of under 0.5 or over 2.0 (Tier 2). The Tier 2 CpGs were further filtered to select only those with a mean beta difference of 0.2 or more (Tier 3).

Results: In the tumor cohort, 1224/2249 (54%) CpGs were differentially methylated between ER negative and ER positive BC at Tier 1 (aFDR 0.05 or lower). Of the 1224, 963 (78.7%) were hypermethylated, and 1035 (84.6%) were associated with the promoter region. The 1224, 24 and 2 CpGs were associated with 379, 22 and 2 genes for Tiers 1, 2 and 3, respectively. When the same analysis was performed on normal tissue only (19 ER-negative and 20-ER-positive) 76 of the 2249 CpGs had significant aFDR values and none of those met the Tier 2 or Tier 3 criteria. Seventy-one of the 76 (93.4%) where hypermethylated, and 65 (85.5%) were associated with the promoter region. The 76 significant Tier 1 (aFDR) differentially methylated CpGs were associated with 48 genes of which 43 were common to tumor Tier 1 differentially methylated miRNA genes, 10 were common to tumor Tier 2 genes, and 5 were restricted to normal tissue only.

Conclusions Normal epithelial tissues demonstrated similar differential methylation directionality as their respective tumor counterparts (although to a lesser extent), favoring promoter region localization. Accordingly, the recognition of normal breast tissue-specific epigenetic propensities that align with their tumor phenotypes, suggest the possibility of progression markers specific for estrogen receptor status as well as markers not associated with progression. This provides insights into our view of possible links between epigenetic programming, progression continuums, and how hormonal receptor subtypes may be determined. Support: Komen Foundation: KG110218.

Citation Format: Worsham MJ, Chen KM, Chitale D, Stephen JK, Divine G. Differentially methylated miRNA methylomes of normal breast tissue from ER negative and ER positive breast cancer mimic their respective tumor phenotypes. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-03-01.

Abstract P4-09-10: Epigenetically altered microRNA mediated pathway dysregulation in ER negative breast cancer

Background: Micro RNAs (miRNA) are endogenous, small non-coding RNAs that control gene expression by directing their target mRNAs for degradation and/or posttranscriptional repression. Compared to mRNA signatures, miRNAs have better and stronger biomarker properties with 20 times more power in biomarker studies as compared to mRNAs (when comparing 20,000 mRNAs to ∼1,000 miRNAs). Emerging evidence now supports the idea that DNA methylation is crucially involved in the dysregulation of miRNAs in cancer, representing a novel class of potential biomarkers for diagnosis, prediction of treatment, or prognosis. ER-negative breast cancer (BC) is an aggressive histological subtype with limited treatment options and very poor prognosis. Our long term objective is to derive a diagnostic, prognostic, and predictive ER-negative specific miRNA panel for detection of early cancer, recurrence/metastasis, and as potential therapeutic targets for better management of ER-negative BC.

Methods: The initial discovery step profiled 39 primary ER negative and 40 ER positive BC cases using the Illumina Infinium HumanMethylation450 BeadChip followed by a subanalysis focusing on 2249 miRNA CpGs assigned to 615 unique miRNAs. T-tests were used to compare the means of the M-values for the ER-positive and ER-negative groups. The t-test p-values were used to generate adaptive FDR (aFDR) levels and aFDRs of 0.05 or lower were considered to be statistically significant (Tier 1). Tier 1 CpGs were subsequently filtered to select only those with a mean beta ratio between ER positive and ER negative of under 0.5 or over 2.0 (Tier 2). The Tier 2 CpGs were further filtered to select only those with a mean beta difference of 0.2 or more (Tier 3). Because miRNAs perform their important functions via their targets, the targets of miRNAs were assessed for functional enrichment analysis in IPA for biologic involvement.

Results: Over half of the miRNA CpGs (1224/2249, 54%) were differentially methylated between ER negative and ER positive BC with significant aFDR levels. The 1224 CpGs at Tier 1 were associated with 379 miRNAs; the 24 and 2 CpGs for Tiers 2 and 3 with 22 and 2 miRNAs, respectively. The 22 miRNA genes were assigned to 4621 targets using online databases that predict miRNA targets. The degree of confidence that a target gene is associated with a miRNA is characterized in these databases as either "experimentally observed", or just as "high" (predicted). Of these 4621 targets, 87 were designated as experimentally observed and were examined in IPA. Top pathways and networks designated by miRNA targets included the cell cycle G1/S checkpoint regulation canonical pathway, and the cell-to-cell interaction/cancer networks among others. MiRNA targets in top pathways and networks were circled back to their respective miRNAs revealing cooperatively mediated pathway dysregulation of ER negative BC.

Conclusion: Aberrantly methylated miRNAs showed perturbation of biologically significant pathways and networks, suggesting that miRNAs mediate pathway dysregulation in a coordinated manner, strengthening the case for utility of miRNAs as viable biomarkers in ER negative BC. Support: Komen Foundation: KG110218.

Citation Format: Worsham MJ, Chen KM, Datta I, Stephen JK, Chitale D, Divine G. Epigenetically altered microRNA mediated pathway dysregulation in ER negative breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-09-10.

Erratum: Epigenetic silencing of miR-34a in human prostate cancer cells and tumor tissue specimens can be reversed by BR-DIM treatment

Androgen Receptor (AR) signaling is critically important during the development and progression of prostate cancer (PCa). The AR signaling is also important in the development of castrate resistant prostate cancer (CRPC) where AR is functional even after androgen deprivation therapy (ADT); however, little is known regarding the transcriptional and functional regulation of AR in PCa. Moreover, treatment options for primary PCa for preventing the occurrence of CRPC is limited; therefore, novel strategy for direct inactivation of AR is urgently needed. In this study, we found loss of miR-34a, which targets AR, in PCa tissue specimens, especially in patients with higher Gleason grade tumors, consistent with increased expression of AR. Forced over-expression of miR-34a in PCa cell lines led to decreased expression of AR and prostate specific antigen (PSA) as well as the expression of Notch-1, another important target of miR-34a. Most importantly, BR-DIM intervention in PCa patients prior to radical prostatectomy showed reexpression of miR-34a, which was consistent with decreased expression of AR, PSA and Notch-1 in PCa tissue specimens. Moreover, BR-DIM intervention led to nuclear exclusion both in PCa cell lines and in tumor tissues. PCa cells treated with BR-DIM and 5-aza-dC resulted in the demethylation of miR-34a promoter concomitant with inhibition of AR and PSA expression in LNCaP and C4-2B cells. These results suggest, for the first time, epigenetic silencing of miR-34a in PCa, which could be reversed by BR-DIM treatment and, thus BR-DIM could be useful for the inactivation of AR in the treatment of PCa.[This corrects the article on p. 14 in vol. 4.].

Abstract P2-09-04: DNA methylation landscapes in ER-negative breast cancer

The biological significance of DNA methylation in the regulation of gene expression and its role in cancer is increasingly recognized. The underlying hypothesis of this study is that strategic global approaches will identify aberrantly methylated genes that underlie the pathogenesis of ER-negative (ER−) breast cancer (BC). We used the Infinium HumanMethylation450 BeadChip to profile the methylome of ER− breast cancers. The 450K array includes 485,577 cytosine positions of the human genome. From these cytosine sites, 99.3% are CpG dinucleotides.

Whole genomic DNA from 20 primary ER− and 8 normal breast tissue samples were assayed for genome-wide methylation using the Illumina 450K array. We had 8634 hypermethylated CpGs or 1.8% of the 485,577 sites on the 450K array. The proportion with hypermethylation was higher for promoter regions (2.1% vs 1.5%), and highest for the “FirstExon” promoter subregion. Of the 8634 CpGs, 2980 (adjusted p = 0.05) were differentially methylated between tumor and normal samples. This resulted in 206 genes with significant hypermethylation (all mean breast cancer betas >= −0.2, and ratio of tumor to normal mean beta >= 2.0).

Estrogen receptor-negative BC is a more aggressive form than ER positive BC with approximately double the incidence in African Americans than in Caucasian Americans. The emerging differential methylation pattern within hormone receptor negative breast cancers would further help stratify them into distinct subgroups. Promotor methylation being potentially reversible, methylated genes may serve as future molecular targets for demethylating therapies.

Support: Komen Foundation: KG110218

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-09-04.

Ductal carcinoma in situ (DCIS) of the breast: Race- and treatment-adjusted specific disease-free probability

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Background: Findings of DCIS outcome between African-American (AA) and White-American (WA) women are inconclusive.

Methods: We conducted a retrospective longitudinal study with the objective of comparing the risk of any second breast cancer after the first primary DCIS, adjusting for pathologic prognostic indicators, treatment, age, and the established epidemiologic risk factors. Women were diagnosed and treated in one institution between 1990-1999. Diagnostic slides were reviewed and prognostic indicators documented; demographic, clinical and method of detection, screening mammography vs. palpation, were collected from medical records. We applied Accelerated Failure Time Modeling (AFTM) to determine the variables that were best associated with the risk of a second cancer.

Results: 335 women, 29.6% (n=100) AA with mean age of 60 (±13) and 70.4% (n=235) WA with mean age of 57 (±12.4), contributed to this study. Distributions of some of the prognostic indicators and final treatment are presented. (Table) During the 10 years of follow-up 12.0% (n=12) of AA and 3.0% (n=7) WA experienced second cancer in ipsilateral breasts; 5.0% (n=5) of AA and 3.8% (n=9) WA in their contralateral breasts and 2 women, 1 AA and 1 WA, in both breasts. Results from the AFTM yielded race as the only variable associated with the risk of a second cancer but only in ipsilateral breasts (HR= 4.11, 95% CI=1.6-10.5 p=0.003).

Conclusions: No difference in the risk of a second cancer in contralateral breast between AA and WA women support the notion of equal access and equal treatment in comparable treatment outcome. Reasons for increased risk of a second cancer in ipsilateral breast in AA women are being evaluated.

[Table: see text]

An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors

To address the biological heterogeneity of lung cancer, we studied 199 lung adenocarcinomas by integrating genome-wide data on copy number alterations and gene expression with full annotation for major known somatic mutations in this cancer. This revealed non-random patterns of copy number alterations significantly linked to EGFR and KRAS mutation status and to distinct clinical outcomes, and led to the discovery of a striking association of EGFR mutations with under-expression of DUSP4, a gene within a broad region of frequent single-copy loss on 8p. DUSP4 is involved in negative feedback control of EGFR signaling and we provide functional validation for its role as a growth suppressor in EGFR-mutant lung adenocarcinoma. DUSP4 loss also associates with p16/CDKN2A deletion and defines a distinct clinical subset of lung cancer patients. Another novel observation is that of reciprocal relationship between EGFR and LKB1 mutations. These results highlight the power of integrated genomics to identify candidate driver genes within recurrent broad regions of copy number alteration and to delineate distinct oncogenetic pathways in genetically complex common epithelial cancers.

Smoking history and frequency of somatic KRAS mutations in adenocarcinoma of the lung

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Background: Somatic mutations in the epidermal growth factor receptor (EGFR) gene are more common in patients with adenocarcinoma, especially those who smoked < 15 pack years (py). KRAS mutations are found in ∼25% of lung adenocarcinomas, most commonly in codons 12 and 13 of exon 2 (∼85%) and have been associated with poor prognosis in resected disease [Winton NEJM 2005] and resistance to EGFR tyrosine kinase inhibitors [Pao PLoS Med 2005]. KRAS mutations are uncommon in non-small cell lung cancer histologies other than adenocarcinoma. We sought to determine the association between quantitative measures of cigarette smoking and presence of KRAS mutations in lung adenocarcinomas. Methods: Standard direct sequencing techniques were used to identify KRAS codon 12 and 13 mutations in lung adenocarcinoma specimens from surgical resections between 2001 and 2006 and tumor specimens sent for KRAS molecular analysis in 2006. Surgical specimens were obtained from an institutional tumor bank. Detailed smoking history (age at first cigarette, packs per day, years smoked, years since quitting smoking) was obtained from the medical record and a patient-completed smoking questionnaire. Results: KRAS mutational analysis was performed on 408 lung adenocarcinomas from 242 women and 166 men. Median age was 68 (range 33–89). KRAS mutations were present in 19% (78/408, 95% CI 15 to 23%). The frequency of KRAS mutation was not associated with age or gender. The presence of KRAS mutations was not related to smoking history with 15% (9/61) of never smokers having KRAS mutations compared with 19% (51/275) of former smokers. When compared with never smokers, there was no significant difference in frequency of KRAS mutations for tumors from patients with 1–5 py (5%, p=0.44), 6- 10 py (12%, p=0.99), 11–15 py (25%, p=0.45), 16–25 py (16%, p=0.99), 26–50 py (25%, p=0.129), 51–75 py (20%, p=0.48), >75 py (20%, p=0.47) history of cigarette smoking. Conclusions: While the incidence of EGFR mutations has a strong inverse relationship with the amount of cigarettes smoked, allowing the selective molecular testing for EGFR mutations, the frequency of KRAS mutations cannot be predicted by age, gender, or smoking history. KRAS mutational analysis of all adenocarcinomas is required to reliably identify patients with KRAS mutations.

No significant financial relationships to disclose.

Integrated genomic analysis of lung adenocarcinomas identifies loss of the MAPK phosphatase gene DUSP4 in most EGFR mutant tumors

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Background: Genomic analyses of lung adenocarcinoma have yielded striking advances that are already impacting on clinical management. Further advances in understanding the biological heterogeneity of this disease will require integration of multiple types of genomic data. To this end, we have assembled a large integrated genomics dataset of lung adenocarcinomas. Here, we highlight one of the novel findings emerging from its initial analysis. Methods: 173 primary lung adenocarcinomas were included in this analysis. Profiling of genomic gains and losses was done by array comparative genomic hybridization (aCGH) on Agilent 44K arrays. Expression profiling was based on Affymetrix U133A arrays. The dataset was annotated for EGFR mutations (exon 19 deletion and L858R) by sensitive PCR-based assays and for KRAS mutations by sequencing. Results: By unsupervised analysis of the aCGH data, the 173 tumors clustered robustly into two or three patterns of co-occurring gains and losses. One aCGH cluster was strongly associated with EGFR mutation (p<10−4) and was characterized by 7p gains (in the EGFR region) and 8p losses. Remarkably, by expression profiling the most consistently underexpressed gene (p<10−9) in EGFR mutant cases compared to EGFR wild type cases was a MAPK phosphatase gene at 8p12, DUSP4 (MKP-2). The DUSP4 region showed genomic loss in 27/35 EGFR mutant cases vs 47/138 non-mutated cases (p<10−4). A limited screen (n=11) has so far revealed no DUSP4 mutations. Western blotting shows low DUSP4 in most EGFR mutant lines, compared to KRAS mutant lines. Conclusions: EGFR mutations in lung adenocarcinomas are strongly associated with genomic loss and low expression of DUSP4. DUSPs are known to be transcriptionally upregulated by MAPK signaling as a negative feedback mechanism and DUSP family members are emerging as putative tumor suppressors in other cancers. We hypothesize that DUSP4 loss cooperates with EGFR mutation to allow full oncogenic activation of the MAPK pathway. Functional studies of DUSP4 in lung adenocarcinoma cell lines are in progress. Our data highlight the value of large, integrated, highly annotated genomic datasets in generating novel insights and hypotheses.

No significant financial relationships to disclose.