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 A26: Network integration of epigenomic data in HPV-associated head and neck cancer

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 genomic mutations has overshadowed consideration of inclusion of epigenetic information. Epigenetic silencing of driver genes leads to various genomic alterations, including mismatch repair deficiency, altered DNA repair and loss of chromosomal stability. In human papilloma virus (HPV) positive head and neck squamous cell carcinoma (HNSCC), recent studies are beginning to establish a mechanistic role for DNA methylation with potential to impact improved survival outcomes. The purpose of this study was to illustrate network integration of epigenomic data in head and neck cancer to prioritize elements that drive biological states. 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. To further establish the driver potential of 11 genes: C14orf162/ CCDC177, CDH8, CRMP1, ELMO1, HTR1E, MEI1, MSX2, PCDH10, PCDHB11, PITX2, SYN2 previously reported as significantly differentially methylated between HPV positive and HPV negative HNSCC tumor samples, and subsequently validated by our group in two independent sample sets, their master regulatory networks were identified utilizing Causal Network Analysis (CNA) software from Ingenuity Pathway Analysis. To reflect expected gene expression direction implied by methylation changes, the inverse of the methylation ratio from HPV positive vs. HPV negative HNSCC was used for CNA. CNA identified 23 top hierarchical networks (significant z score of absolute 2) associated with HNSCC and their corresponding master regulatory molecules characterized as transcription regulators and kinase inhibitors among others. Of the 11 target genes, 7 had representation in multiple networks; CRMP1 in 21/23, MSX2 and SYN2 in 20/23, CDH8 and PITX2 in 17/23, PCDH10 in 10/23, and ELMO1 in 5/23 networks. Of the 23 networks, 12 indicated activation and 11 inhibition by at least 4 or more of the 7 target genes. Master regulators were within 2 or 3 hops (intermediate regulators) to the target genes. CNA raised the profile of CDH8, CRMP1, ELMO1, MSX2, PCDH10, SYN2, and PITX2 (7/11 target genes) for further consideration as epigenetic drivers of HPV-associated HNSCC.

Support: Komen Foundation: KG110218

Citation Format: Maria J. Worsham, Kang Mei Chen, Indrani Datta, Josena K. Stephen, Dhananjay Chitale, Tamer Ghanem, Lamont Jones, Laura Garcia-Rodriquez, George Divine. Network integration of epigenomic data in HPV-associated head and neck cancer [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr A26.

Association Between Benign Breast Disease in African American and White American Women and Subsequent Triple-Negative Breast Cancer

Importance

Compared with white American (WA) women, African American (AA) women have a 2-fold higher incidence of breast cancers that are negative for estrogen receptor, progesterone receptor, and ERBB2 (triple-negative breast cancer [TNBC]). Triple-negative breast cancer, compared with non-TNBC, likely arises from different pathogenetic pathways, and benign breast disease (BBD) predicts future non-TNBC.

Objective

To determine whether AA identity remains associated with TNBC for women with a prior diagnosis of BBD.

Design, Setting, and Participants

This study is a retrospective analysis of data of a cohort of 2588 AA and 3566 WA women aged between 40 and 70 years with a biopsy-proven BBD diagnosis. The data-obtained from the Pathology Information System of Henry Ford Health System (HFHS), an integrated multihospital and multispecialty health care system headquartered in Detroit, Michigan-include specimens of biopsies performed between January 1, 1994, and December 31, 2005. Data analysis was performed from November 1, 2015, to June 15, 2016.

Main Outcomes and Measures

Subsequent breast cancer was stratified on the basis of combinations of hormone receptor and ERBB2 expression.

Results

Case management, follow-up, and outcomes received or obtained by our cohort of 2588 AA and 3566 WA patients were similar, demonstrating that HFHS delivered care equitably. Subsequent breast cancers developed in 103 (4.1%) of AA patients (mean follow-up interval of 6.8 years) and 143 (4.0%) of WA patients (mean follow-up interval of 6.1 years). More than three-quarters of subsequent breast cancers in each subset were ductal carcinoma in situ or stage I. The 10-year probability estimate for developing TNBC was 0.56% (95% CI, 0.32%-1.0%) for AA patients and 0.25% (95% CI, 0.12%-0.53%) for WA patients. Among the 66 AA patients who developed subsequent invasive breast cancer, 16 (24.2%) developed TNBC compared with 7 (7.4%) of the 94 WA patients who developed subsequent invasive breast cancers and had complete biomarker data (P = .01).

Conclusions and Relevance

This study is the largest analysis to date of TNBC in the context of racial/ethnic identity and BBD as risk factors. The study found that AA identity persisted as a significant risk factor for TNBC. This finding suggests that AA identity is associated with inherent susceptibility for TNBC pathogenetic pathways.

Abstract 4434: MicroRNA methylomes of normal breast tissue from ER negative and ER positive breast cancer identify progression markers specific for estrogen receptor status

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 from estrogen receptor (ER) negative (-) and ER positive (+) tumors, and assess their miRNA methylomes in the context of tumor ER phenotypes as either ER- or ER+. BC tissue from 79 patients (39 ER- and 40 ER+) and normal tissue from 39 of these patients (19 ER- and 20-ER+) 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+ and ER- 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+ and ER- 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). In the tumor cohort, 1224/2249 (54%) CpGs were differentially methylated between ER- and ER+ BC at Tier 1. Of the 1224, 963 (78.7%) were hypermethylated, and 1035 (84.6%) were in promoter regions. The 1224 CpGs at Tier 1, the 24 at Tier 2, and 2 CpGs at Tier 3 were associated with 379, 22 and 2 genes respectively. When the same analysis was performed on normal tissue only (19 ER- and 20-ER+), 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%) were hypermethylated, and 65 (85.5%) were in promoter regions. 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. Normal epithelial tissues demonstrated similar differential methylation directionality as their respective tumor counterparts, 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 ER 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: Kang Mei Chen, Josena K. Stephen, Indrani Datta, Dhananjay Chitale, George Divine, Maria J. Worsham. MicroRNA methylomes of normal breast tissue from ER negative and ER positive breast cancer identify progression markers specific for estrogen receptor status [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4434. doi:10.1158/1538-7445.AM2017-4434

Abstract 3361: Methylome differences in differentiated thyroid cancers and benign adenomas

Many recent studies examining aberrant DNA methylation in thyroid cancer are restricted to either candidate genes or genome-wide methylation in specific thyroid tumor subtypes. The goal of this study was to identify differentially methylated genes globally and their association with molecular pathways and signaling networks. Common mutations in papillary thyroid cancer (PTC), follicular thyroid cancer (FTC), follicular adenoma (FA) and normal thyroid were also examined. Genome-wide methylation profiling using the Infinium HumanMethylation450FFPE (formalin fixed paraffin embedded) BeadChip Array was performed on 24 thyroid cases (8 PTC, 8 FTC, 4 FA and 4 normal thyroid). Ingenuity Pathway Analysis (IPA) was utilized to assess the roles of significantly differentially methylated genes in biological functions, signaling/metabolic pathways, and networks. Common mutations in 4 genes (BRAF, NRAS, HRAS, and KRAS) were assessed using TaqMan Mutation Detection assay. Twelve genes were significantly differentially methylated among 4 comparison groups: cancer vs normal, cancer vs adenoma, PTC vs normal, and PTC follicular variant (PTC-FV) vs PTC-Classic. CTU1 and HLA-DPB1 were significantly hypermethylated and AARS2, TMSB10, RNF216L, KIF15, KIAA1143, and SLC2A13 were significantly hypomethylated between cancer and normal. Significant differential hypermethylation was noted for PNPLA7 and NPC1L1 in cancer vs adenoma and SNX6 in PTC-FV vs PTC-Classic. NT5C1B was hypermethylated and AARS2 was hypomethylated in PTC vs normal. IPA identified 2 gene networks, involving 11/12 genes, characterized by 1) Cellular development, Cellular growth and proliferation, Connective tissue development and function and 2) Drug metabolism, Cell-mediated immune response, Cellular development. NT5C1B was involved in all 4 highly ranked canonical nucleotide degradation pathways. Several significant bio-functions involved NPC1L1. Mutations of NRAS codon 61 were identified in 1 sample each of FTC-Classic, PTC-FV and FA and BRAF V600E in one PTC-Classic sample. Differential methylation of AARS2, CTU1, HLA-DPB1, SLC2A13, PNPLA7, NPC1L1, NT5C1B and SNX6 suggest potential markers for discriminating thyroid cancers from adenomas and normal. NT5C1B was noted in highly ranked canonical pathways, suggesting a role in nucleotide degradation. Pathway analysis of differentially methylated genes support important biological processes in thyroid cancer pathogenesis. Supported by JFCI/CRAG A20038

Citation Format: Josena K. Stephen, Kang Mei Chen, Jason Merritt, Indrani Datta, Dhananjay Chitale, George Divine, Maria J. Worsham. Methylome differences in differentiated thyroid cancers and benign adenomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3361. doi:10.1158/1538-7445.AM2017-3361

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.

The biological significance of methylome differences in human papilloma virus associated head and neck cancer

In recent years, studies have suggested that promoter methylation in human papilloma virus (HPV) positive head and neck squamous cell carcinoma (HNSCC) has a mechanistic role and has the potential to improve patient survival. The present study aimed to replicate key molecular findings from previous analyses of the methylomes of HPV positive and HPV negative HNSCC in an independent cohort, to assess the reliability of differentially methylated markers in HPV-associated tumors. HPV was measured using real-time quantitative PCR and the biological significance of methylation differences was assessed by Ingenuity Pathway Analysis (IPA). Using an identical experimental design of a 450K methylation platform, 7 of the 11 genes were detected to be significantly differentially methylated and all 11 genes were either hypo- or hypermethylated, which was in agreement with the results of a previous study. IPA's enriched networks analysis identified one network with msh homeobox 2 (MSX2) as a central node. Locally dense interactions between genes in networks tend to reflect significant biology; therefore MSX2 was selected as an important gene. Sequestration in the top four canonical pathways was noted for 5-hydroxytryptamine receptor 1E (serotonin signaling), collapsin response mediator protein 1 (semaphorin signaling) and paired like homeodomain 2 (bone morphogenic protein and transforming growth factor-β signaling). Placement of 9 of the 11 genes in highly ranked pathways and bionetworks identified key biological processes to further emphasize differences between HNSCC HPV positive and negative pathogenesis.

Targeted Theranostic Approach for Glioma Using Dendrimer-Based Curcumin Nanoparticle

The delivery of anti-cancer agents to brain tumors represent a challenge because the blood-brain tumor barrier (BBTB) effectively limits the delivery of many agents. A new generation 3 (G3) dendrimer-based curcumin (Curc) conjugate was synthesized. The synthesized G3-Curc conjugate demonstrated full solubility in aqueous media. The in vitro study revealed that G3-Curc nanoparticles were internalized into glioma U-251 cells. Systemic delivery of G3-Curc conjugate led to preferentially accumulation in an orthotopic preclinical glioma model minimizing systemic toxic effect. Multicolor microscopy images of the tumor tissue showed that G3-Curc particles were internalized inside tumor cells selectively and further localized within nuclei. Enhanced bioavailability of G3-Curc conjugate was also observed with improved therapeutic efficacy against different cancers cells.

Abstract 4484: Differentially methylation between ER negative and ER positive breast cancer identifies master regulators to expose potential epigenetic drivers of aggressive disease

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 genomic mutations has yet to configure in epigenetics. There has been relatively little advancement in changing the management of women with ER negative BC, mainly due to a dearth of actionable therapeutic targets. Our drill-down approach to identified an ER negative-specific 16 gene methylation signature (AHNAK, ALPL, ANXA2R, CCND1, CIRBP, CPQ, DST, EGFR, ESR1, GPRC5B, HERC5, IL22RA2, MITF, OBSL1, POU3F3, RB1CC1) starting from a discovery approach (Illumina Infinium HumanMethylation450 BeadChip, 40 ER negative vs. 40 ER positive BC) followed by expression verification, significant rankings in biological pathways (Ingenuity Pathway Analysis), and confirmation by targeted sequencing using Illumina MiSeq.

Causal Networks are small hierarchical networks of regulators that control the expression/methylation of dataset targets. They can enhance understanding of the effect of master regulators on disease or function.

The objective of this study was to identify regulatory networks utilizing IPA's Causal Network Analysis (CNA) in order to illuminate possible causes and mechanisms underlying the biological activities of the 16 candidate gene signature differentiating ER negative from ER positive BC. To reflect expected gene expression direction implied by methylation changes for the 16 candidate genes, the inverse of the methylation ratio from ER negative vs. ER positive tissue was used for CNA.

CNA software identified 4 hierarchical networks and their corresponding master regulatory molecules, diethylstilbestrol, MSH2, 15-ketoprotaglandin E2, and transcription regulator SP1. Diethylstilbestrol and SP1 had direct regulatory influence (depth level 1) to the candidate molecules ALPL, CCND1, EGFR, ESR1 and CCND1, CIRBP, EGFR, ESR1, respectively. CNA raised the profile of ALPL, CCND1, CIRBP, EGFR, ESR1 (5/16 candidate genes) for further consideration as potential epigenetic drivers of ER negative BC.

Support: Komen Foundation: KG110218

Citation Format: Maria J. Worsham, Kang Mei Chen, Indrani Datta, Josena K. Stephen, Dhananjay Chitale, George Divine. Differentially methylation between ER negative and ER positive breast cancer identifies master regulators to expose potential epigenetic drivers of aggressive disease. [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 4484.

Investigation into the presence of human papillomavirus in patients with obstructive sleep apnea

OBJECTIVES/HYPOTHESIS

The human papillomavirus (HPV) is known to infect the tissues of the oropharynx as demonstrated in HPV-positive oropharyngeal squamous cell carcinoma (OPSCC). HPV has also been shown to induce benign lymphoid hypertrophy. We sought to investigate an association between obstructive sleep apnea (OSA) and the presence of HPV in palatine and lingual tonsillar oropharyngeal tissue.

STUDY DESIGN

Case series with chart review.

METHODS

This retrospective laboratory-based study of oropharyngeal tissue from patients with OSA included patients >18 years old who underwent surgical treatment for OSA at a single institution between January 2012 and May 2014. Surgical specimens of adequate size were analyzed for HPV6, 11, and 16 using real-time quantitative polymerase chain reaction from DNA extracted from formalin-fixed paraffin-embedded tissue blocks. Student t test, Pearson χ² test, and linear logistic regression were used to assess comparisons of body mass index (BMI), apnea-hypopnea index (AHI), age, and gender between HPV-positive and HPV-negative groups.

RESULTS

Of 99 cases included in the study, six were positive for HPV: two with HPV16 and four with HPV6. BMI, AHI, age, and gender showed no significant differences between the HPV-positive and HPV-negative groups. Logistic regression to predict HPV positivity accounting for each variable and multivariate analysis were not statistically significant.

CONCLUSIONS

Our study did not show HPV to have a statistically significant association with OSA. None of the covariates analyzed (BMI, AHI, gender, age) predicted HPV positivity in surgically resected oropharyngeal tissue from OSA patients.

LEVEL OF EVIDENCE

4 Laryngoscope, 127:1231-1234, 2017.

Causal network analysis of head and neck keloid tissue identifies potential master regulators

OBJECTIVES/HYPOTHESIS

To generate novel insights and hypotheses in keloid development from potential master regulators.

STUDY DESIGN

Prospective cohort.

METHODS

Six fresh keloid and six normal skin samples from 12 anonymous donors were used in a prospective cohort study. Genome-wide profiling was done previously on the cohort using the Infinium HumanMethylation450 BeadChip (Illumina, San Diego, CA). The 190 statistically significant CpG islands between keloid and normal tissue mapped to 152 genes (P < .05). The top 10 statistically significant genes (VAMP5, ACTR3C, GALNT3, KCNAB2, LRRC61, SCML4, SYNGR1, TNS1, PLEKHG5, PPP1R13-α, false discovery rate <.015) were uploaded into the Ingenuity Pathway Analysis software's Causal Network Analysis (QIAGEN, Redwood City, CA). To reflect expected gene expression direction in the context of methylation changes, the inverse of the methylation ratio from keloid versus normal tissue was used for the analysis. Causal Network Analysis identified disease-specific master regulator molecules based on downstream differentially expressed keloid-specific genes and expected directionality of expression (hypermethylated vs. hypomethylated).

RESULTS

Causal Network Analysis software identified four hierarchical networks that included four master regulators (pyroxamide, tributyrin, PRKG2, and PENK) and 19 intermediate regulators.

CONCLUSIONS

Causal Network Analysis of differentiated methylated gene data of keloid versus normal skin demonstrated four causal networks with four master regulators. These hierarchical networks suggest potential driver roles for their downstream keloid gene targets in the pathogenesis of the keloid phenotype, likely triggered due to perturbation/injury to normal tissue.

LEVEL OF EVIDENCE

NA Laryngoscope, 126:E319-E324, 2016.

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.

Abstract 3834: Validation of potential methylation biomarkers in HPV-associated HNSCC

Epidemiological and laboratory evidence indicate the human papilloma virus (HPV) as a causative agent for some squamous head and neck cancer (HNSCC). The biologic significance of HPV as independent risk factor is also underscored by the improved prognosis for patients with HPV positive HNSCC relative to HPV negative HNSCC, due in part to a better therapeutic response to chemoradiotherapy. The mechanism for this improved prognosis remains underexplored.

To assess the potential of HPV specific methylation biomarkers, we evaluated the status of 10 genes (CDH8, CRMP1, HTRE1, ELMO1, MEI1, MSX2, PCDH10, PCDHB11, C14orf162, and PITX2) in a cohort of 18 HPV positive and 14 HPV negative HNSCC using targeted sequencing (Illumina MiSeq). The genes were previously reported as significantly differentially methylated between HPV positive and HPV negative HNSCC using the Infinium HumanMethylation450 BeadChip (Lechner et al., 2013).

In our sample, of the 10 genes, targeted sequencing confirmed significant differential methylation between HPV positive and negative for C14orf162 (p = 0.007), MEI1(p = 0.004), MSX2 (p = 0.002), and PCDHB11(p = 0.002). PCDHB11 and MSX2 were hypermethylated; MEI1 and C14orf162 were hypomethylated, concordant with the Lechner et al., study.

In this independent sample set, confirmation of 4 of the 10 genes as differentially methylated in HPV positive vs HPV negative HNSCC with concordance of methylation direction (hypo- vs hypermethylated), validates their potential for differentiating HPV positive and HPV negative HNSCC. Cadherins are implicated in tumor progression and metastasis and are targets of the Polycomb group (PcG) proteins, which form chromatin-modifying complexes that are essential for embryonic development and stem cell renewal and are commonly deregulated in cancer. Our study further supports cadherin PCDHB11, together with C14orf162, MEI1, and MSX2 as likely biomarkers in HPV-associated HNSCC.

Support: Komen KG110218

Citation Format: Kang Mei Chen, Josena K. Stephen, George Divine, Dhananjay Chitale, Tamer Ghanem, Steven Chang, Maria J. Worsham. Validation of potential methylation biomarkers in HPV-associated HNSCC. [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 3834. doi:10.1158/1538-7445.AM2015-3834

Abstract 4765: A drill-down approach to identifying an ER negative-specific gene signature

There has been relatively little advancement in changing the management of women with ER negative (ER-) breast cancer (BC). Our objective is to examine the contribution of aberrantly methylated genes to the pathogenesis of ER- BC, determine their utility in refining classification of ER- subtypes [basal-like (BL) and Her2-enriched], in differentiating ER- BC in African American (AA) and Caucasian American (CA) women, and as new prognostic and therapeutic targets for better management of ER- BC.

The methylation status of 40 ER- and 40 ER positive (ER+) breast cancer samples was assessed using the Illumina 450K. A 3-tiered approach was used to call out genes most differentially methylated between ER- and ER+. The top 70 genes were further downsized using the TaqMan low-density array expression assays, Ingenuity Pathway Analysis (IPA) to assess their biologic significance, followed by targeted sequencing (Illumina Miseq). Further assessment of the genes in the 450K TCGA data sets (UCSC Brower 2015) was used for final downsizing.

Of the 70 highly ranked differentially methylated genes, 56 were hypermethylated and 14 hypomethylated, with positive correlation with gene expression for the majority of genes. Expression verification and significant rankings in canonical pathways and bionetworks resulted in further downsizing to 41 genes upon confirmation by targeted sequencing. Further filtering of the 41 genes with 450K TCGA data sets provided additional refinement to a 10 gene candidate panel currently being vetted in a retrospective cohort of over 1000 ER negative BC (with 40% AA).

Our iterative approach to identify an ER negative-specific gene signature has the potential to offer predictive and prognostic markers of improved classification for ER- BC in AA and CA women. Confirmation and validation of these methylation profiles in independent cohorts of BL BC defined by cDNA microarrays should further stratify poor prognosis breast cancers subgroups and serve as targets for epigenetic-modifying agents individualized to AA and CA women with ER- BC. Human therapeutic intervention trials to reverse deleterious epigenetic changes have shown promise in halting tumor growth by reactivation of the tumor suppressor genes or by reversing DNA hypomethylation.

Support: Komen Foundation: KG110218

Citation Format: Maria J. Worsham, Dhananjay Chitale, Kang Mei Chen, Indrani Datta, Josena K. Stephen, George Divine. A drill-down approach to identifying an ER negative-specific gene signature. [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 4765. doi:10.1158/1538-7445.AM2015-4765

Human papilloma virus (HPV) modulation of the HNSCC epigenome

Currently, the human papilloma virus (HPV), in addition to tobacco and alcohol, is considered another independent risk factor for oropharyngeal squamous head and neck cancer (OPSCC), where the prevalence of HPV-16 increases to 50-90 % for the oropharynx. Also, incidence and mortality in head and neck SCC (HNSCC) continue to be higher in African Americans (AA) than in Caucasian Americans (CA). A recent study found that poorer survival outcomes for AA versus CA with oropharyngeal tumors were attributable to racial differences in the prevalence of HPV positive (+) tumors; HPV negative (-) AA and CA patients had similar outcomes (Settle et al., Cancer Prev Res (Phila) 2:776-781, 2009). Evidence indicates that a HPV+ diagnosis has significant prognostic implications; these patients have at least half the risk of death when compared with the HPV- patient, due in part to a better response to chemoradiotherapy (Fakhry et al., J Natl Cancer Inst 100:261-269, 2008).Epigenetic events of promoter hypermethylation are emerging as promising molecular strategies for cancer detection, representing tumor-specific markers occurring early in tumor progression. HPV infection is now recognized to play a role in the pathogenesis of OPSCC, where HPV+ and HPV- patients appear to be clinically and biologically distinct with reported genome-wide hypomethylation and promoter hypermethylation in HPV+ HNSCC tumors. A recent study from our group applying pathway analysis to investigate the biological role of the differentially methylated genes in HPV+ and HPV- HNSCC reported 8 signal transduction pathways germane to HNSCC (Worsham et al., Otolaryngol Head Neck Surg 149:409-416, 2013).

Methylation Markers for Early Detection and Differentiation of Follicular Thyroid Cancer Subtypes

Thyroid cancer has the fastest rising incidence rates and is the fifth most common cancer in women. There are four main types of which the papillary and follicular types together account for >90%, followed by medullary cancers (3%−5%) and anaplastic carcinomas (<3%). For individuals who present with early stage disease of papillary and follicular cancers, there are no accurate markers to predict whether they will develop metastatic or recurrent disease. Our immediate goal is to molecularly differentiate follicular cancer subtypes for enhanced classification. Promoter methylation status of genes with reported associations in thyroid cancer (CASP8, CDKN2A, DAPK1, ESR1, NIS, RASSF1 and TIMP3) were examined in a cohort of follicular thyroid cancers comprising of 26 Hurthle and 27 Classic subtypes utilizing quantitative methylation-specific PCR. RASSF1 was differentially methylated in Classic tumor tissue compared to Hurthle (p<0.001). Methylation of RASSF1 pointed to racial group differences between African Americans and Caucasian Americans (p=0.05). Extra thyroidal extension was found to be associated with DAPK1 (p=0.014) and ESR1 (p=0.036) methylation. Late stage disease was associated with older age (p<0.001) and methylation of DAPK1 (p=0.034) and ESR1 (p=0.035). The methylation status of RASSF1, DAPK1 and ESR1 suggests the utility of methylation markers to molecularly differentiate thyroid cancer subtypes for enhanced classification and early detection of thyroid cancer.

IGSF4 methylation as an independent marker of human papillomavirus-positive oropharyngeal squamous cell carcinoma

IMPORTANCE

Human papillomavirus (HPV) is a known causative agent for oropharyngeal squamous cell carcinoma (OPSCC). Whereas it is becoming more firmly established that HPV-positive head and neck squamous cell carcinoma is associated with better survival outcomes, believed to be because of better response to chemoradiation therapy, the specific mechanisms for these improved survival outcomes remain underexplored.

OBJECTIVE

To examine the relationship between HPV status and promoter methylation in an OPSCC cohort.

DESIGN, SETTING, AND PARTICIPANTS

Real-time quantitative polymerase chain reaction was used to examine oncogenic HPV type 16 in a retrospective cohort of 121 patients with primary OPSCC. Aberrant promoter methylation of IGSF4, DAPK1, and ESR1 genes, known to be methylated in head and neck squamous cell carcinoma, including OPSCC, was examined by means of quantitative methylation-specific polymerase chain reaction.

INTERVENTIONS

Patients received standard therapy.

MAIN OUTCOMES AND MEASURES

Univariate associations between HPV and methylation were analyzed using Fisher exact tests followed by multivariable logistic regression. Cox proportional-hazards regression was used to model the risk of death given age, race, sex, HPV status, methylation, stage, smoking, and treatment.

RESULTS

In univariate logistic regression analyses, HPV-positive status was significantly associated with Caucasian race (P = .02), treatment (radiotherapy only, P = .01; chemoradiotherapy, P = .007), and IGSF4 methylation (P = .005). The final multivariate logistic model, after controlling for patient characteristics (sex, age, smoking, race, and treatment) with backward variable selection among genes, retained IGSF4 methylation (OR, 4.5 [95% CI, 1.6-12.8]; P = .005), Caucasian race (OR, 2.9 [95% CI, 1.0-8.3]; P = .053), treatment (radiotherapy only vs neither: OR, 11.62 [95% CI, 2.02-66.82]; P = .02; chemoradiotherapy vs neither: OR, 11.15 [95% CI, 1.92-64.65]; P = .01), male sex (OR, 4.7 [95% CI, 1.3-17.0]; P = .02), and younger age (OR, 0.9 [95% CI, 0.90-1.0]; P = .008) as independent predictors of HPV-positive status. Cox regression modeling indicated HPV-negative status, age, male sex, smoking, and radiation treatment as independent predictors of mortality.

CONCLUSIONS AND RELEVANCE

Methylation of IGSF4 is an independent predictor of HPV-positive status. DNA methylation in conjunction with HPV infection appears to play a role in OPSCC.

Abstract 1372: The methylome of ER-negative tumors is predominantly hypermethylated

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 to determine differentially methylated genes. The 450K array includes 485,577 cytosine positions of the human genome. Whole genomic DNA from 40 primary ER-, 40 ER positive (ER+), and 40 normal breast tissue samples were assayed for genome-wide methylation. Data were analyzed by GenomeStudio software (Illumina). Degree of methylation was calculated as a β-value (ranging from 0 to 1) and M-values [log (β/ (1- β)] were used for significance tests. With 30 sets of paired tumor/normal tissue, GEE was performed to account for their correlation. To identify methylated genes associated with ER- subtypes and distinct from ER+, a 3-tiered approach to call out genes in which methylation changed dramatically between ER+ and ER- subtypes was used. Tier 1: computed adjusted FDR values for all CpGs/ (or their averages for each gene) to be 0.05 or lower. Tier 2: the CpGs/genes to include genes with a 2-fold change (ratio &gt;= 2.0 or ratio &lt;= 0.5). Tier 3: CpGs/genes to include genes with an absolute difference between the mean β of =&gt;0.2.

Differentially methylated genes (DMGs) at tier 3 for the different comparison groups were as follows: all BC (n=80) vs normal (n=40): 1070 DMGs: 1001: hypermethylated, 69: hypemethylated; ER+ vs normal: 1720: 1518 hyper, 202 hypo; ER- vs normal: 1170, 1085 hyper, 85 hypo; ER- vs ER+ vs: 289, 191 hyper, 97 hypomethylated.

Overall, ER- BC tumors were more hypermethylated than hypomethylated when compared to normal breast tissue and ER+ BC. 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 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 Format: Maria J. Worsham, Dhananjay Chitale, Kang Mei Chen, George Divine. The methylome of ER-negative tumors is predominantly hypermethylated. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1372. doi:10.1158/1538-7445.AM2014-1372

Epigenetic modulation of signal transduction pathways in HPV-associated HNSCC

OBJECTIVE

Human papilloma virus (HPV) positive and HPV negative head and neck squamous cell cancer (HNSCC) are biologically distinct with a prognostic advantage for HPV positive patients compared to HPV negative cases. DNA promoter methylation is central to human diseases such as cancer, including HNSCC, with reported genome-wide hypomethylaton and promoter hypermethylation in HPV positive HNSCC tumors. The goal of this study was to identify differentially methylated genes in HPV positive versus HPV negative primary HNSCC genomes with clues to signaling networks.

STUDY DESIGN

Laboratory-based study.

SETTING

Primary care academic health care system.

SUBJECTS AND METHODS

DNA from 4 HPV positive and 4 HPV negative freshly frozen primary HNSCC were subject to comprehensive genome-wide methylation profiling. Differentially methylated gene lists were examined using the Signal Transduction Pathways (canonical) filter in the Genomatix Pathway System (GePS).

RESULTS

Twofold methylation differences were observed between HPV positive and HPV negative cases for 1168 genes. Pathway analysis applied to investigate the biological role of the 1168 differentially methylated genes revealed 8 signal transduction pathways forming a network of 66 genes, of which 62% are hypermethylated.

CONCLUSION

Our study reveals a predominant hypermethylation profile for genes in signal transduction pathways of HPV positive HNSCC tumor genomes. Because signaling events in the cell play a critical role in the execution of key biological functions, insights into how complex cellular signaling cascades and networks may be programmed in HNSCC are likely to be critical in the development of new biological agents designed to hit multiple targets.

Abstract 650: IGSF4 methylation is an independent marker of HPV positive OPSCC

Human papilloma virus (HPV) is a known causative agent for oropharyngeal squamous cell cancer (OPSCC). The goal of our study was to determine the relationship of HPV type 16 (HPV16) infection and methylation status in an OPSCC cohort. HPV16 was detected using real-time quantitative PCR (qPCR) in a retrospective cohort of 111 primary OPSCC. A 24 tumor suppressor gene candidate panel was assessed for methylation using the methylation specific-multiplex ligation-dependent probe amplification (MS-MLPA) assay. Univariate associations with HPV and gene methylation, age, gender, race and smoking were analyzed using Fisher's exact tests and logistic regression. A final multiple logistic regression model, to include patient characteristics and genes significant on univariate analysis, was built using backwards selection of genes. Statistical significance was set at p&lt;0.05 and all analyses were done using SAS 9.2. In univariate analyses, Caucasian American (CA) OPSCC were more likely to be HPV positive as compared to African American (AA) OPSCC (OR=3.01, 95% CI 1.28, 7.07, p=0.011). Also, smoking (never vs current) [OR=3.60 (1.06, 12.24), p=0.04], and TIMP3, DAPK1, ESR1, and IGSF4 were associated with HPV positive status (OR=5.03, p=0.021; OR=3.71, p=0.04; OR=5.03, p=0.021; OR=7.68, p=0.012, respectively). The final model, after controlling for patient characteristics and after backward elimination of genes, indicated IGSF4 methylation is an independent predictor of HPV positive status [OR=7.07 (1.22, 40.79), p=0.029]. HPV infection status is independently associated with methylation of IGSF4, indicating interplay of DNA methylation and HPV in OPSCC pathogenesis.

Citation Format: Kang Mei Chen, Josena K. Stephen, Meredith Mahan, Shaleta Havard, George Divine, Glendon Gardner, Vanessa P. Schweitzer, Maria J. Worsham. IGSF4 methylation is an independent marker of HPV positive OPSCC. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 650. doi:10.1158/1538-7445.AM2013-650

Improved survival with HPV among African Americans with oropharyngeal cancer

PURPOSE

A major limitation of studies reporting a lower prevalence rate of human papilloma virus (HPV) in African American patients with oropharyngeal squamous cell cancer (OPSCC) than Caucasian Americans, with corresponding worse outcomes, was adequate representation of HPV-positive African American patients. This study examined survival outcomes in HPV-positive and HPV-negative African Americans with OPSCC.

EXPERIMENTAL DESIGN

The study cohort of 121 patients with primary OPSCC had 42% African Americans. Variables of interest included age, race, gender, HPV status, stage, marital status, smoking, treatment, and date of diagnosis.

RESULTS

Caucasian Americans are more likely to be HPV positive (OR = 3.28; P = 0.035), as are younger age (age < 50 OR = 7.14; P = 0.023 compared with age > 65) or being married (OR = 3.44; P = 0.016). HPV positivity and being unmarried were associated with being late stage (OR = 3.10; P = 0.047 and OR = 3.23; P = 0.038, respectively). HPV-negative patients had 2.7 times the risk of death as HPV-positive patients (P = 0.004). Overall, the HPV-race groups differed (log-rank P < 0.001), with significantly worse survival for HPV-negative African Americans versus (i) HPV-positive African Americans (HR = 3.44; P = 0.0012); (ii) HPV-positive Caucasian Americans (HR = 3.11; P = < 0.049); and (iii) HPV-negative Caucasian Americans (HR = 2.21; P = 0.049).

CONCLUSIONS

HPV has a substantial impact on overall survival in African American patients with OPSCC. Among African American patients with OPSCC, HPV-positive patients had better survival than HPV negative. HPV-negative African Americans also did worse than both HPV-positive Caucasian Americans and HPV-negative Caucasian Americans. This study adds to the mounting evidence of HPV as a racially linked sexual behavior life style risk factor impacting survival outcomes for both African American and Caucasian American patients with OPSCC.

Human papilloma virus prevalence in a multiethnic screening population

OBJECTIVE

The goal was to determine the prevalence of high-risk HPV16 using saliva in a screening population in Detroit, Michigan.

MATERIALS AND METHODS

Real-time quantitative polymerase chain reaction was applied to detect HPV16 in saliva DNA from 349 screening subjects without head and neck cancer (HNC), 156 with HNC, and 19 controls. Cut points for human papilloma virus (HPV) positivity were >0 and >0.001 copy/cell. Proportions were compared between groups using exact χ(2) or Fisher exact tests (P < .05).

RESULTS

At a cut point >0, each group had an overall HPV prevalence of more than 5%, with a higher prevalence of 30.8% in the HNC patient group. At a cut point >0.001, the prevalence was lower: 0% in the control, 1.2% in the screening, and 16.7% in the HNC group. In the latter, for both cut points, HPV prevalence was different across sites (<0.001) and significantly higher in the oropharynx than larynx or site as other after Hochberg's adjustment. At >0, women in the screening group had a higher prevalence of HPV than did men (P = .010), and at >0.001, the prevalence was higher for men in the HNC group than for women (P = .035). In the screening group, at >0, only African Americans had a higher prevalence than Caucasian Americans (P = .025).

CONCLUSIONS

In the screening group, a 6.9% and 1.2% screening rate was noted at cut points >0 and >0.001, respectively. The results provide data to inform public health considerations of the feasibility of saliva as a screening tool in at-risk populations with the long-term goal of prophylactic vaccination against oral HPV.

Significance of p16 in Site-specific HPV Positive and HPV Negative Head and Neck Squamous Cell Carcinoma

Expression of p16^INK4A (p16 positive) is highly correlated with human papilloma virus (HPV) infection in head and neck squamous cell carcinoma (HNSCC), however, p16-positivity is not limited to HPV positive tumors and therefore, not a perfect surrogate for HPV. p16 survival outcomes are best documented for the oropharyngeal site (OP); non-OP sites such as the oral cavity (OC), larynx, and hypopharynx (HP) are understudied. The goal of this study was to evaluate p16 in the context of HPV16 and examine p16 survival outcomes in HPV16 positive and HPV16 negative site-specific HNSCC. p16 and HPV16 status were determined by immunohistochemistry and qPCR respectively, on 80 primary HNSCC from four sites: OC, OP, larynx and HP. p16 expression was different across sites (p<0.001), was more frequent in OP than non-OP sites (p<0.0001), and was different between Caucasian Americans (CA) and African Americans (AA) (p=0.031), similar to HPV (p=0.013). p16 was associated with marital status (p=0.008) and smoking (p=0.014). p16 positive patients had improved survival (similar to HPV16 positive cases). Patients with p16 negative/HPV16 negative status had the worst survival for all sites combined as well as for OP. p16 status is an important prognostic indicator in both OPSCC and non-OPSCC and the p16 positive/HPV16 negative group is likely a distinct subgroup lacking any HPV genotype. Cohorts with larger representations of non-OP sites examining multiple molecular markers will be key to deciphering and dissecting out p16's role as a useful prognostic indicator when assessed in combination with HPV status.

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 &gt;= −0.2, and ratio of tumor to normal mean beta &gt;= 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.

Molecular characterization of head and neck cancer: how close to personalized targeted therapy?

Molecular targeted therapy in head and neck squamous cell carcinoma (HNSCC) continues to make strides, and holds much promise. Cetuximab remains the sole US FDA-approved molecular targeted therapy available for HNSCC, though several new biologic agents targeting the epidermal growth factor receptor (EGFR) and other pathways are currently in the regulatory approval pipeline. While targeted therapies have the potential to be personalized, their current use in HNSCC is not personalized. This is illustrated for EGFR-targeted drugs, where EGFR as a molecular target has yet to be individualized for HNSCC. Future research needs to identify factors that correlate with response (or lack of one) and the underlying genotype-phenotype relationship that dictates this response. Comprehensive exploration of genetic and epigenetic landscapes in HNSCC is opening new frontiers to further enlighten and mechanistically inform newer as well as existing molecular targets, and to set a course for eventually translating these discoveries into therapies for patients. This opinion offers a snapshot of the evolution of molecular subtyping in HNSCC and its current clinical applicability, as well as new emergent paradigms with implications for controlling this disease in the future.

HPV Prevalence in a Multi-ethnic Screening Population

Objective: For optimal feasibility using saliva rinse screening of HPV for head and neck cancer (HNC), the prevalence should be 5% or higher in the population screened. The aim of our study was to determine the prevalence of HPV16 infection in a screening population in Detroit, MI.

Method: Real time quantitative PCR was applied to detect HPV16 in saliva DNA from 349 screening subjects without HNC, 157 HNC, and 19 controls. Cut points for HPV positivity were: >0 and >0.001 copy/cell. Proportions were compared between groups using exact chi-square or Fisher’s exact tests as appropriate (set at P < .05).

Results: At cut point >0, each group had an overall HPV prevalence of over 5%, with a much higher prevalence of 31.2% in the HNC patient group. At cut point >0.001, the prevalence was lower in each group, 0% in the control, 1.2% in the screening, and 17.2% in the HNC group. At >0, females in the screening group had a higher prevalence of HPV than males ( P = .010), and at >0.001, prevalence was higher for males in the HNC group than females ( P = .043). In the screening group, at >0, only AA had higher prevalence than CA ( P = .025).

Conclusion: In the screening group, a 5% and 1.2% screening rate was noted at cut-points >0 and >0.001, respectively. The results provide data to inform public health considerations of the feasibility of saliva as a screening tool in at-risk populations with the long term goal of prophylactic vaccination against oral HPV.

Signaling Networks in Methylated HPV Genomes

Objective: HPV-positive (+) and HPV-negative (–) HNSCC are biologically distinct with a prognostic advantage for HPV+ patients compared to HPV– cases. The goal of this study was to identify differentially methylated genes in HPV+ vs HPV– primary HNSCC genomes with clues to signaling networks that impact key biological functions.

Method: DNA from 4 HPV(+) and 4 HPV(–) freshly frozen primary HNSCC were subject to comprehensive genome-wide methylation profiling using the HumanMethylation27 Bead Array, which measures methylation as a β value ranging from 0 to 1. Genomatix Pathway System software was applied to build a network from differentially methylated genes.

Results: Two-fold methylation differences were observed between HPV+ and HPV– cases for 1168 genes. Pathway analysis applied to investigate the biological role of the 1168 differentially methylated genes revealed 8 signals transduction pathways forming a network of 66 genes, of which 62% are hypermethylated (41 of the 66). Of the 8 signal transduction pathways, the Beta catenin degradation, E-cadherin, ErbB receptor, and Integrin signaling networks have immediate association with HNSCC. The other 4 pathways are c-kit, ion channels, ppara elements, and RXR and RAR heterodimerization signaling events.

Conclusion: Signaling events in the cell play a critical role in the execution of key biological functions. Our results demonstrate that in signal transduction pathways, HPV genomes harbor a larger proportion of hypermethylated genes than HPV-negative tumors with potential for these genes as differential targets in HPV related HNSCC.

Abstract 722: Significance of p16 in site-specific HPV-positive and HPV-negative HNSCC

Expression of p16INK4A (p16+ve) is highly correlated with human papilloma virus (HPV) infection in head and neck squamous cell carcinoma (HNSCC), however, p16-positivityis not limited to HPV-positive (HPV+ve) tumors and therefore, not a perfect surrogate for HPV. Also, p16+ve status has a strong relationship with survival and treatment outcomes in HNSCC, which is best documented for the oropharyngeal site (OP); non-OP sites such as the oral cavity (OC), larynx, and hypopharynx (HP) are understudied. The goal of this study was to evaluate p16 in the context of HPV and examine p16 survival outcomes in HPV+ve and HPV-negative (HPV-ve) site-specific HNSCC. The cohort of 80 primary HNSCC consisted of 10 HPV16+ve and 10 HPV16-ve cases each for four sites: OC, OP, larynx and HP. Expression of p16 was significantly different across sites (p&lt;0.001), being more frequent in OP (65%) than in non-OP sites (13%). The frequency of p16 expression was different (p=0.031) between Caucasian Americans (CA, 38%) and African Americans (AA, 16%) similar to HPV (CA 65% vs AA 37%, p=0.013). p16+ve patients had improved survival for all sites combined and for the OP subgroup (similar to HPV+ve cases). However, subgroups defined by both HPV and p16, indicate that patients with p16-negative (-ve)/HPV-ve status had the worst survival for all sites combined as well as for OP. Cohorts with larger representations of non-OP sites examining multiple molecular markers will be key to deciphering and dissecting out p16's role as a useful prognostic indicator when assessed in combination with HPV status

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 722. doi:1538-7445.AM2012-722

Disparate molecular, histopathology, and clinical factors in head and neck squamous cell carcinoma racial groups

OBJECTIVE

There is a lack of consensus regarding the causes of the differences in the higher incidence of and the mortality from head and neck squamous cell carcinoma (HNSCC) in African Americans (AA) versus Caucasian Americans (CA). We examined a comprehensive array of risk factors influencing health and disease in an access-to-care, racially diverse, primary HNSCC cohort.

STUDY DESIGN

Cross-sectional study.

SETTING

Primary care academic health care system.

SUBJECTS AND METHODS

The cohort of 673 patients comprised 391 CA and 282 AA (42%). Risk variables included demographic, histopathology, and clinical/epidemiologic factors. Tumor DNA was interrogated for loss and gain of 113 genes with known involvement in HNSCC/cancer. Logistic regression for univariate analysis was followed by multivariate modeling with determination of model predictability (c-index).

RESULTS

Of the 39 univariate differences between AA and CA, multivariate modeling (c-index = 0.81) retained 7 differences (P < .05). AA were less likely to be married and more likely to have tumor lymphocytic response, undergo radiation treatment, and smoke. Insurance type was a significant predictor of race. AA were more likely to have Medicaid, Medicare, and other HMO types. AA tumors were more likely to have loss of CDKN2A and gain of SCYA3 versus CA.

CONCLUSIONS

Multivariate modeling indicated significant differences between AA and CA HNSCC for histopathology, treatment, smoking, marital status, type of insurance, and tumor gene copy number alterations. Our data reiterate that for HNSCC, as in the case of other complex diseases, tumor genetics or biology is only one of many potential contributors to differences among racial groups.

Delineating an epigenetic continuum in head and neck cancer

A tissue field of somatic genetic alterations precedes the histopathological phenotypic changes of carcinoma. Genomic changes could be of potential use in the diagnosis and prognosis of pre-invasive squamous head and neck carcinoma (HNSCC) lesions and as markers for cancer risk assessment. Studies of sequential molecular alterations and genetic progression of pre-invasive HNSCC have not been clearly defined. Studies have shown recurring alterations at chromosome 9p21 (location of the CDKN2A) and TP53 mutations in the early stages of HNSCC. However, gene silencing via hypermethylation is still a relatively new idea in the development of HNSCC and little is known about the contribution of epigenetics to the development of neoplasia, its transformation, progression, and recurrence in HNSCC. This review examines the role of promoter hypermethylation of tumor suppressor genes in the progression continuum from benign papillomas to malignancy in HNSCC.

Human papillomavirus outcomes in an access-to-care laryngeal cancer cohort

OBJECTIVE

Human papillomavirus (HPV), particularly HPV16, is a causative agent for 25% of head and neck squamous cell cancer, including laryngeal squamous cell cancer (LSCC). HPV-positive (HPV+ve) patients, particularly those with oropharyngeal SCC, have improved prognosis. For LSCC patients, this remains to be established. The goal was to determine stage and survival outcomes in LSCC in the context of HPV infection.

STUDY DESIGN

Historical cohort study.

SETTING

Primary care academic health system.

SUBJECTS AND METHODS

In 79 patients with primary LSCC, HPV was determined using real-time quantitative polymerase chain reaction. χ(2) or Fisher exact test was used to test the association of HPV+ve with 21 risk factors including race, stage, gender, age, smoking, alcohol, treatment, and health insurance. Kaplan-Meier and log-rank tests were used to study the association of HPV and LSCC survival outcome.

RESULTS

HPV16 was detected in 27% of LSCC patients. Caucasian American (CA) patients had higher HPV prevalence (33%) than did African American (AA) LSCC patients (16%; P = .058). HPV was significantly associated with gender (P = .016) and insurance type (P = .001). There were no differences in survival between HPV+ve and HPV-negative (HPV-ve) patients. There was no association with HPV and other risk factors including stage (early vs late).

CONCLUSION

We found a high prevalence of HPV in men and a lower prevalence of HPV infection in AA compared with CA. Despite the strikingly better survival of patients with HPV+ve oropharyngeal tumors, even when adjusted for smoking, this correlation does not seem to hold true in the larynx. Larger multiethnic LSCC cohorts are needed to more clearly delineate HPV-related survival across ethnicities.

Promoter methylation in head and neck tumorigenesis

In addition to genetic alterations of gains and losses, epigenetic events of promoter methylation appear to further undermine a destabilized genomic repertoire in squamous head and neck carcinoma (HNSCC). This chapter provides an overview of frequently methylated tumor suppressor genes in benign head and neck papillomas, primary HNSCC tumors, and HNSCC cell lines and their relevance as epigenetic markers in head and neck tumorigenesis.

Novel Dysregulated MicroRNAs in Primary Laryngeal Squamous Cell Cancer

Introduction

MicroRNAs (miRNAs) are endogenous, small, noncoding RNAs of 17 to 25 nucleotides that regulate approximately 30% of human genes. They are differentially expressed in various types of cancers compared with noncancerous tissues, suggesting that they may have crucial roles in tumorigenesis. The objective of this study was to identify laryngeal squamous cell cancer (LSCC)-specific miRNAs.

Materials and methods

A retrospective cohort of 10 LSCC and five normal laryngeal squamous epithelium samples were examined using a global miRNA profiling approach (HTG, Tucson, AZ, USA, 800 human miRNAs plus 10 endogenous control miRNAs). The expression status of selected dysregulated miRNAs that were significantly different from normal were verified by real-time quantitative PCR (qPCR).

Results

Twenty-three of the 800 human miRNAs had significantly different expression levels (p < 0.05) between LSCC and normal tissues. Fifteen of the 23 have not been previously reported in HNSCC and include: miR-663b, miR-663, miR-193b, miR-1291, miR-720, miR-191, miR-1224-3p, miR-214, miR- 1285, miR-1207-5p, miR-483-5p, miR-1225-3p, miR-1228, miR-1280 and miR-638. Consistently upregulated miR-31 and miR- 193b and differentially expressed miR-663b in LSCC were verified by qPCR.

Conclusion

The 15 novel miRNAs identified in this exploratory study, pending further confirmation and validation, may have clinical utility as LSCC-specific markers.

How to cite this article

Chen KM, Stephen JK, Havard S Shah V, Gardner G, Schweitzer VG, Worsham MJ. Novel Dysregulated MicroRNAs in Primary Laryngeal Squamous Cell Cancer. Int J Head Neck Surg 2012;3(2):76-81.

Distinct Gene Profiles for Tumor and Non-Tumor Tissue in the Head and Neck: An Analytical Approach

In a study of genetic alterations, the Multiplex Ligation-dependent Probe Amplification (MLPA) assay was used to measure gain or loss of 113 gene-probes in tumor and non-tumor tissue samples collected from each of the 220 patients with squamous head and neck cancer (HNSCC). Conditional and marginal models were available; both models account for correlated data but have different aspects. The conditional logistic regression model was proposed to estimate the subject-specific risk of tumor based on the paired tumor and non-tumor data collection, which was in contrast with the marginal model to estimate population-average risk.The modeling process included rigorous variable selection, an initial multivariable model, a final model selection, and model validation. Genes with individual effect (p<0.01) were considered as candidates for the initial multivariable model for tumor. The final model included gene-probes with p<0.01 and estimations of odds ratios (OR) 95% Confidence Intervals (CIs) and the model's predictive ability, measured by the receiver operating characteristic curve (ROC). A 10-fold cross-validation was performed to validate the model. Of 113 gene-probes, using the conditional approach, 16 genes in 7 chromosomes, remained in the final multivariable model with p<0.01 and an ROC score of 0.94. The cross-validation showed ROC mean (SD) score of 0.96(0.04). The marginal model, in contrast, ended with 8 gene-probes and had an observed ROC of 0.81. CONCLUSION: The conditional approach appears to be the model of choice when assessing gene-probe risks of subjects with paired data collection and fewer missing covariates, compared to the marginal approach. This multiple gene model demonstrated excellent ability to discriminate tumor from non-tumor, and supports its contribution to the pathogenesis of HNSCC as well as their potential utility for further markers of early tumor detection.

Disparate Molecular, Histopathology, and Clinical Factors in HNSCC Racial Groups

Objective: Causes of differences in the higher incidence of and mortality from squamous head and neck cancer (HNSCC) in African American (AA) vs Caucasian Americans (CA) lack a consensus. We examined a comprehensive array of risk factors influencing health and disease in an access to care, racially diverse, primary HNSCC cohort.

Method: The study cohort of 673 primary HNSCC comprised 391 CA and 282 AA. Risk variables included demographic, histopathology, and clinical/epidemiologic risk factors. Tumor DNA was interrogated for loss and gain of 113 genes with known involvement in HNSCC/cancer. Univariate analysis was followed by multivariate modeling with determination of c-index.

Results: Of the 39 univariate differences in race as AA and CA, multivariate modeling (c-index = 0.81) retained 6 variables (pCDKN2A) and aneupoidy of SCYA3 than CA tumors. AA were more likely to be unmarried, to have radiation treatment, and be more likely to be current and past smokers. Insurance type as HAP (Health Alliance Plan), Blue Cross, Medicaid, Medicare, and other was a significant determinant of race. AA were more likely to have Medicaid and Medicare. Insurance status by stage and radiation by stage were not significant.

Conclusion: Molecular modeling indicated significant differences between AA and CA for histopathology, patient factors, and tumor gene copy number alterations. Our data reiterate that for HNSCC, as in the case of other complex diseases, tumor genetics or biology is only one of many potential contributors to differences among racial groups.

Novel MicroRNA miR-923 Is Dysregulated in Primary LSCC

Objective: MicroRNAs (miRNAs) are endogenous, small, noncoding RNAs of 17 to 25 nucleotides that regulate approximately 30% of human genes. They are differentially expressed in various types of cancers compared with noncancerous tissues, suggesting that they may have crucial roles in tumorigenesis. The objective of this study was to discover LSCC-specific miRNAs.

Method: Global miRNA profiling (800 human miRNAs plus 10 endogenous control miRNAs) was performed on 8 formalin-fixed archival LSCC samples and 5 normal laryngeal squamous epithelium (HTG, Tucson, AZ, USA). Quantitative real-time PCR (qRT-PCR) approach was employed to verify expression status of selected miRNAs that were significantly different from normal controls.

Results: Thirty-one of the 800 human miRNAs were significantly differentially expressed ( P < .05) between LSCC vs normal tissues. Selected miRNAs (miR-31, miR-193b, miR-663b, miR-923, and miR-1826), by qRT-PCR, verified expression of consistently upregulated miR-31 and miR-193b as well as differentially expressed miR-663b, miR-923, and miR-1826. Dysregulation of miR-923 was newly observed and showed upregulation in 3 out of 8 and downregulation in 5 out of 8 LSCC.

Conclusion: We have identified a group of 31 aberrantly expressed miRNAs in LSCC. miR-923 has not been previously reported in HNSCC, including LSCC. Further detailed examinations of this miRNA will provide opportunities to dissect the complex molecular abnormalities driving LSCC.

HPV-Positive Outcomes in an Access to Care Laryngeal Squamous Cell Cancer Cohort

Objective: Oncogenic human papillomavirus (HPV) has been established as a causative agent for 25% of head and neck squamous cell cancer (HNSCC), including laryngeal squamous cell cancer (LSCC). HPV-positive oropharyngeal patients have improved prognosis. We determined outcomes in LSCC in the context of HPV infection.

Method: Seventy-nine primary LSCC were examined for 21 risk factors. HPV status was determined using real-time quantitative PCR. Chi-square/Fisher exact test were used to test association of HPV-positive with the other risk factors. Kaplan-Meier and log rank test were used to study the risk of HPV-positive status for overall survival.

Results: HPV-16 was detected in 21 out of 77 (27%) primary LSCC, 16% (5/32) African American (AA) and 33% (15/45) Caucasian American (CA). Significance between race and HPV status was marginal ( P = .058). HPV-positive status was significantly associated with male gender ( P = .017) and insurance type ( P = .001). HPV-positive LSCC had longer median survival (6.64 years) when compared with HPV-negative (6.25 years), but was not significant.

Conclusion: We found high prevalence of HPV in males vs females and lower prevalence of HPV infection in AA vs CA. Larger multi-ethnic LSCC cohorts are needed to more clearly delineate HPV-related survival outcomes across ethnicities.

Molecular classification of breast carcinoma in situ

Pleomorphic variant of invasive lobular carcinoma (PILC) is an aggressive variant of invasive lobular carcinoma (ILC). Its in situ counterpart, pleomorphic lobular carcinoma in situ (PLCIS) is a recently described entity. Morphologically it has the typical architectural pattern of LCIS, but the neoplastic cells resemble intermediate grade DCIS. Molecular signatures that distinguish PLCIS from DCIS and LCIS would provide additional tools to aid in the histopathologic classification of PLCIS as a lesion distinct from LCIS and DCIS. CIS lesions, obtained from a study cohort of 38 breast cancer patients, were divided into 18 DCIS, 14 PLCIS and 6 LCIS. DNA from microdissected archival tissue was interrogated for loss or gain of 112 breast-cancer-specific genes using the Multiplex Ligation-dependent Probe Amplification Assay (MLPA). Classification Regression Tree (CART) analysis was employed to develop a gene-based molecular classification to distinguish or separate out PLCIS from DCIS and LCIS. Molecular classification via CART, based on gene copy number, agreed with histopathology in 34/38 CIS cases. Loss of CASP1 was predictive of LCIS (n=4) with one misclassified PLCIS. Gain of RELA predicted only the LCIS classification (n=2 cases). STK15 and TNFRSF1B were predictive only for DCIS with no misclassifications. Gain of EHF and TNFRSF1B and loss of NCOA3 were predictive of PLCIS, but not without misclassification. Molecular reclassification by CART was accomplished in 4 CIS cases: 1 PLCIS was reclassified as LCIS, 1 LCIS reclassified as PLCIS, and 2 DCIS cases as PLCIS. This study provides additional rationale for molecular modeling strategies in the evaluation of CIS lesions. This diagnostic aid may serve to minimize misclassification between PLCIS and DCIS, and PLCIS and LCIS, aiding to increase accuracy in the differential diagnosis of CIS lesions.

Race as a social construct in head and neck cancer outcomes

OBJECTIVE

The authors examined ancestry informative markers (AIMs) to estimate the amount of population admixture and control for this heterogeneity for stage and survival in a primary head and neck squamous cell carcinoma (HNSCC) cohort.

STUDY DESIGN

Historical cohort study.

SETTING

Integrated health care system.

SUBJECTS

The cohort comprised 358 patients with HNSCC who self-reported race as Caucasian American (CA), African American (AA), or other.

METHODS

DNA was interrogated for West African (WA) and European genetic background by genotyping AIMs. Associations of race (self-report or WA ancestry) with stage and survival were analyzed using logistic regression and Cox regression modeling. A subgroup analysis for diagnosis (late vs early stage) and survival (time to death) and WA ancestry was performed for self-reported AAs.

RESULTS

There were significant associations between stage and self-reported race (P = .04 [univariate]) and with cancer site (oropharynx: P = .014; hypopharynx: P = .026 [multivariate]). For prognosis, there were significant multivariate associations between stage (P = .002), age (>65 years, P < .001), and cancer site (hypopharynx: P < .001; oral cavity: P = .049), but self-reported race was not associated with overall survival. Interestingly, there was no association with degree of WA ancestry and stage or survival. In the subgroup analysis of genetic ancestry among self-reported AAs, cancer site remained an independent risk factor for stage (other site: P = .026) and survival (oropharynx: P = .036). Late stage persisted as an independent variable for poor survival (P = .032).

CONCLUSIONS

Stratification within AAs by WA ancestry revealed no correlation with stage or survival, suggesting that HNSCC outcomes with race may be owing to social/behavior factors rather than biological differences.

Molecular characterization of late stomal recurrence following total laryngectomy

The goal was to determine recurrent or second primary status for late stomal malignancies, 16 and 17 years post-total laryngectomy in two laryngeal squamous cell carcinoma (LSCC) patients, based on DNA methylation signatures and HPV typing. Adopting a literature review based definition of late stomal recurrences as new primaries at the site of the stoma or neopharynx occurring >5 years after total laryngectomy, we employed a multi-gene candidate approach to examine promoter methylation in 24 tumor suppressor genes and PCR-based assays for HPV status offered additional insights into whether the late stomal tumors post-total laryngectomy were related or not. The primary tumor for Patient 1 was negative for HPV but had aberrant hypermethylation of APC, MLH1 and BRCA1. The stomal biopsy 17-years later showed presence of HPV-16 without any methylated genes. In Patient 2, HPV-11 and promoter methylation of APC identified in the primary tumor was also observed in the stomal malignancy 16 years post-total laryngectomy. Additional information provided by molecular typing for HPV and methylation markers underscored Patient 1's and 2's late stomal presentation as most likely a second primary and recurrence, respectively. DNA methylation markers are particularly advantageous because DNA methylation is an early event in tumorigenesis, and the epigenetic modification, 5-methylcytosine, is a stable marker. Molecular marks to discern genetic heterogeneity or relatedness of stomal malignancies several years post-total laryngectomy can provide clues to their status as either second primaries or likely recurrences. Our results support the hypothesis that a subset of stomal recurrences after total laryngectomy represents second primary tumors.

Novel approaches to global mining of aberrantly methylated promoter sites in squamous head and neck cancer

OBJECTIVE

Promoter hypermethylation is emerging as a promising molecular strategy for early detection of cancer. We examined promoter methylation status of 1143 cancer-associated genes to perform a global but unbiased inspection of methylated regions in head and neck squamous cell carcinoma (HNSCC).

STUDY DESIGN

Laboratory-based study.

SETTING

Integrated health care system.

SUBJECTS AND METHODS

Five samples, two frozen primary HNSCC biopsies and three HNSCC cell lines, were examined. Whole genomic DNA was interrogated using a combination of DNA immunoprecipitation (IP) and Affymetrix whole-genome tiling arrays.

RESULTS

Of the 1143 unique cancer genes on the array, 265 were recorded across five samples. Of the 265 genes, 55 were present in all five samples, and 36 were common to four of five samples, 46 to three of five, 56 to two of five, and 72 to one of five samples. Hypermethylated genes in the five samples were cross-examined against those in PubMeth, a cancer methylation database combining text mining and expert annotation (http://www.pubmeth.org). Of the 441 genes in PubMeth, only 33 are referenced to HNSCC. We matched 34 genes in our samples to the 441 genes in the PubMeth database. Of the 34 genes, eight are reported in PubMeth as HNSCC associated.

CONCLUSION

This pilot study examined the contribution of global DNA hypermethylation to the pathogenesis of HNSCC. The whole-genome methylation approach indicated 231 new genes with methylated promoter regions not yet reported in HNSCC. Examination of this comprehensive gene panel in a larger HNSCC cohort should advance selection of HNSCC-specific candidate genes for further validation as biomarkers in HNSCC.

DNA hypermethylation markers of poor outcome in laryngeal cancer

This study examined molecular (DNA hypermethylation), clinical, histopathological, demographical, smoking, and alcohol variables to assess diagnosis (early versus late stage) and prognosis (survival) outcomes in a retrospective primary laryngeal squamous cell carcinoma (LSCC) cohort. The study cohort of 79 primary LSCC was drawn from a multi-ethnic (37% African American), primary care patient population, diagnosed by surgical biopsies in the Henry Ford Health System from 1991 to 2004 and followed from 5 to 18 years (through 2009). Of the 41 variables, univariate risk factors of p < 0.10 were tested in multivariate models (logistic regression (diagnosis) and Cox (survival) models (p < 0.05)). Aberrant methylation of estrogen receptor 1 (ESR1; p = 0.01), race as African American (p = 0.04), and tumor necrosis (extensive; p = 0.02) were independent predictors of late stage LSCC. Independent predictors of poor survival included presence of vascular invasion (p = 0.0009), late stage disease (p = 0.03), and methylation of the hypermethylated in cancer 1 (HIC1) gene (p = 0.0002). Aberrant methylation of ESR1 and HIC1 signified independent markers of poorer outcome. In this multi-ethnic, primary LSCC cohort, race remained a predictor of late stage disease supporting disparate diagnosis outcomes for African American patients with LSCC.

Abstract 150: HPV and aberrant DNA methylation status in paired saliva and tumor samples in HNSCC

To examine the utility of non-invasive detection of high risk HPV and aberrant DNA methylation in matched saliva and tumor DNA in squamous head and neck cancer (HNSCC). In a cohort of 35 primary HNSCC with matched tumor (cases) and saliva specimens, HPV status was initially determined using the Linear Array HPV Genotyping kit and confirmed by PCR for HPV subtypes 16, 31, 33 and 45. Aberrant methylation of 24 tumor suppressor genes was interrogated using the methylation specific multiplex ligation probe amplification (MS-MLPA) assay. Of the 35 cases, 20 were negative for HPV in the saliva and tumor, 9 were positive for HPV in both and in 6 cases HPV was positive in the tumor specimen but not detected in the corresponding saliva. In the 9 cases that were positive for HPV in the tumor and matched saliva, 6 were HPV 16 positive and 1 case each was positive for HPV 31, 33 and 45. The sensitivity and specificity for HPV in this cohort were 100% and 60%, respectively. Promoter hypermethylation frequency in tumor samples was 60% (21/35) as compared to 14% (5/35) in saliva. The most frequently methylated genes in tumors included RARB-10/21, APC- 9/21, TIMP3 and CDKN2B- 7/21, CDKN2A and IGSF4- 5/21 tumor samples. The most frequently methylated genes in saliva samples included TIMP3, ESR1 and IGSF4 (3/5 saliva samples), followed by APC, CDKN2B and DAPK1 (2/3). Two of the 35 tumor and saliva pairs had commonly methylated genes, APC in one pair, and TIMP3, CDKN2B, ESR1 and IGSF4 in the other. There was no association between HPV and methylation. PCR analysis of HPV DNA in salivary rinses allows for detection of HPV and promoter methylation status in HNSCC and is a feasible noninvasive alternative to more invasive procedures.

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 150.

Consistent DNA hypermethylation patterns in laryngeal papillomas

INTRODUCTION: This study examined the contribution of promoter hypermethylation to the pathogenesis of respiratory papillomatosis (RP), including recurrences (RRP) and progression to squamous cell carcinoma (SSC). MATERIALS AND METHODS: A retrospective cohort of 25 laryngeal papilloma cases included 21 RRP, two of which progressed to SCC. Aberrant methylation status was determined using the multi-gene (22 tumor suppressor genes) methylation-specific multiplex ligation-dependent probe amplification assay and confirmed using methylation specific PCR. RESULTS: Twenty genes had altered DNA methylation in 22 of 25 cases. Aberrant methylation of CDKN2B and TIMP3 was most frequent. Promoter hypermethylation of BRCA2, APC, CDKN2A and CDKN2B was detected in 2 RRP cases with subsequent progression to SCC. Of the 25 cases, 22 were positive for HPV-6, 2 for HPV-11 and 1 for HPV-16 and 33. CONCLUSIONS: Consistent aberrant methylation of multiple tumor suppressor genes contributes to the pathogenesis of laryngeal papillomas. Persistent aberrant DNA methylation events in 2 RRP cases that progressed to cancer indicate an epigenetic monoclonal progression continuum to SCC.