Duodenal intraepithelial lymphocytosis in Helicobacter pylori gastritis: comparison before and after treatment

Our aims were to assess performance of duodenal intraepithelial lymphocyte counting for diagnosis of Helicobacter pylori (H. pylori) gastritis, and effects of eradication therapy on intraepithelial lymphocytosis. Paired duodenal and gastric biopsies from subjects with a pathologic diagnosis of H. pylori gastritis were reviewed. Higher duodenal intraepithelial lymphocyte counts were observed in 40 subjects with H. pylori gastritis (26 ± 5 per villus) than 52 subjects negative for H. pylori (12 ± 2 per villus). After successful eradication therapy, duodenal lymphocytes were indistinguishable from H. pylori-negative subjects, whereas they remained elevated after failed eradication therapy. This study confirms previous reports of increased duodenal intraepithelial lymphocytes in patients with concurrent Helicobacter pylori gastritis. Intraepithelial lymphocyte counts of > 15 per villus or > 10 per 100 enterocytes were predictive of infection. Duodenal lymphocytosis decreases significantly after successful eradication therapy but remains elevated when treatment fails.

Associations between molecular characteristics of colorectal serrated polyps and subsequent advanced colorectal neoplasia

PURPOSE

BRAF mutation and DNA hypermethylation have linked sessile serrated adenomas/polyps (SSA/Ps) to serrated colorectal cancer (CRC) in cross-sectional studies, but they have not been evaluated in a longitudinal study. We aimed to evaluate the associations between molecular markers of serrated polyps and subsequent advanced colorectal neoplasia.

METHODS

Study subjects included Kaiser Permanente Washington members aged 20-75 years who received an index colonoscopy between 1/1/1998 and 12/31/2007 and had hyperplastic polyps (HPs) or SSA/Ps according to study pathology review. Polyps from index colonoscopies were removed and assayed for BRAF mutation, CpG island methylator phenotype (CIMP), and MLH1 methylation. Pathology reports and biopsies from the subsequent lower gastrointestinal endoscopy through 1/1/2013 were reviewed for advanced colorectal neoplasia. We identified additional incident CRC cases through linkage to the Seattle-Puget Sound Surveillance Epidemiology and End Results registry. We used generalized estimating equations to calculate adjusted odds ratios (OR) and 95% confidence intervals (CI) for subsequent advanced colorectal neoplasia, comparing index serrated polyps with different molecular markers.

RESULTS

We included 553 individuals with index serrated polyps (420 HPs and 133 SSA/Ps) and 795 subsequent endoscopies. The prevalence of BRAF-mutant, CIMP-high, and MLH1-methylated serrated polyps were 51%, 4%, and 2%, respectively. BRAF and CIMP were not associated with subsequent advanced colorectal neoplasia. MLH1-methylated SSP/As were significantly more likely to have subsequent advanced neoplasia (OR = 4.66, 95% CI 1.06-20.51).

CONCLUSION

Our results suggest that BRAF-mutant and CIMP-high serrated polyps are not associated with subsequent advanced colorectal neoplasia. Among SSA/Ps, MLH1 methylation may be an important marker to identify high-risk CRC precursors.

Prediction of survival of HPV16-negative, p16-negative oral cavity cancer patients using a 13-gene signature: A multicenter study using FFPE samples

OBJECTIVES

To test the performance of an oral cancer prognostic 13-gene signature for the prediction of survival of patients diagnosed with HPV-negative and p16-negative oral cavity cancer.

MATERIALS AND METHODS

Diagnostic formalin-fixed paraffin-embedded oral cavity cancer tumor samples were obtained from the Fred Hutchinson Cancer Research Center/University of Washington, University of Calgary, University of Michigan, University of Utah, and seven ARCAGE study centers coordinated by the International Agency of Research on Cancer. RNA from 638 Human Papillomavirus (HPV)-negative and p16-negative samples was analyzed for the 13 genes using a NanoString assay. Ridge-penalized Cox regressions were applied to samples randomly split into discovery and validation sets to build models and evaluate the performance of the 13-gene signature in predicting 2-year oral cavity cancer-specific survival overall and separately for patients with early and late stage disease.

RESULTS

Among AJCC stage I/II patients, including the 13-gene signature in the model resulted in substantial improvement in the prediction of 2-year oral cavity cancer-specific survival. For models containing age and sex with and without the 13-gene signature score, the areas under the Receiver Operating Characteristic Curve (AUC) and partial AUC were 0.700 vs. 0.537 (p < 0.001), and 0.046 vs. 0.018 (p < 0.001), respectively. Improvement in predicting prognosis for AJCC stage III/IV disease also was observed, but to a lesser extent.

CONCLUSIONS

If confirmed using tumor samples from a larger number of early stage oral cavity cancer patients, the 13-gene signature may inform personalized treatment of early stage HPV-negative and p16-negative oral cavity cancer patients.

Telomere length differences between colorectal polyp subtypes: a colonoscopy-based case-control study

Background

Short telomeres have been associated with increased risk of many cancers, particularly cancers of the gastrointestinal tract including esophagus and stomach. However, the association between telomere length (TL) and colorectal cancer and its precursors, colorectal polyps, is not clear.

Methods

We investigated the relationship between TL and risk of colorectal polyp subtypes in a colonoscopy-based study in western Washington. Participants were 35–79 year-old enrollees at an integrated health care system, who underwent a colonoscopy between 1998 and 2007 (n = 190), completed a self-administered questionnaire, provided blood samples, and were distinguished as having adenomas, serrated polyps, or as polyp-free controls through a standardized pathology review. Telomere length (T) relative to a single copy gene (S) was measured in circulating leukocytes from stored buffy coat samples using quantitative polymerase chain reaction. Multivariable polytomous logistic regression was used to compare case groups with polyp-free controls and other case groups; adjusted odds ratios (OR) and 95% confidence intervals (CI) were estimated.

Results

TL in the shortest tertile (T/S ratio < 0.58) was associated with increased risk of adenomas and serrated polyps [OR (95%CI) were 1.77(0.81–3.88) and 2.98(1.15–7.77), respectively). When evaluated by lesion severity within each pathway, short TL was more strongly associated with advanced adenomas and sessile serrated polyps [OR (95% CI) = 1.90(0.76–4.73) and 3.82(0.86–16.86), respectively], although the associations were not statistically significant.

Conclusions

Our results suggest that short TL may be associated with an increased risk of colorectal polyps in both the adenoma-carcinoma and serrated pathways. The risk was particularly notable for sessile serrated polyps, although the association was not statistically significant and sample size was limited.

High prevalence of Helicobacter pylori clarithromycin resistance mutations among Seattle patients measured by droplet digital PCR

BACKGROUND

Treatment of Helicobacter pylori infection is often empiric; however, current guidelines for management of Helicobacter pylori infection advise against the use of standard triple therapy (clarithromycin, amoxicillin, and proton-pump inhibitor) when clarithromycin resistance exceeds 20%. We developed and tested a new culture-free assay to detect clarithromycin resistance-conferring mutations to determine the prevalence of H. pylori clarithromycin resistance in patients from the United States Pacific Northwest.

MATERIALS AND METHODS

Droplet digital PCR (ddPCR) was used to detect the H. pylori 23S rRNA gene, and resistance-conferring mutations, in archived, formalin-fixed, paraffin-embedded (FFPE) gastric tissue and to retrospectively determine the prevalence of clarithromycin-resistant H. pylori among 110 patients at an academic medical center in the Northwest United States between 2012 and 2014.

RESULTS

Of 102 patients with the H. pylori 23S rRNA gene detected by the ddPCR assay, 45 (44%) had clarithromycin resistance mutations. Thirty-three of the 45 patients with clarithromycin resistance mutations had a mix of wild-type and resistance alleles. Prevalence of clarithromycin resistance mutations differed among racial groups and was highest among Asians, with mutations detected in 14 (67%) of the 21 patient samples.

CONCLUSIONS

The prevalence of clarithromycin resistance detected in this region exceeds 20%, indicating that standard triple therapy should not be the first-line antibiotic treatment for H. pylori infection. Culture-free assays for detecting clarithromycin resistance mutations can be performed on archived tissue samples and will aid in informing tailored treatment for effective H. pylori eradication.

Impact of tumoral carbonic anhydrase IX and Ki-67 expression on survival in oral squamous cell carcinoma patients

Oral squamous cell carcinoma (OSCC) is the most commonly diagnosed type of head and neck cancer, accounting for ~300,000 new cases worldwide annually. Carbonic anhydrase IX (CAIX) and Ki-67 have been associated with reduced disease-specific survival (DSS) in patients with OSCC. We previously proposed a combined CAIX and Ki-67 signature of 'functional hypoxia' and sought to replicate this association in a larger independent cohort of patients with OSCC at the Fred Hutchinson Cancer Research Center (FHCRC) in Seattle. The study population included patients with incident primary OSCC treated at the University of Washington Medical Center and the Harborview Medical Center in Seattle between December 2003 and February 2012. Archived tumor blocks were obtained with tissue samples from 189 patients, and triplicate 0.6 mm cores were assembled into tissue microarrays (TMAs). Fluorescence immunohistochemistry and AQUAnalysis® were used to quantify the expression of tumoral CAIX (tCAIX) and stromal CAIX (sCAIX) and tumoral Ki-67 for each TMA core. Hazard ratios for DSS were calculated using Cox proportional hazards analysis. High tCAIX and sCAIX expression levels were associated with reduced DSS (aHR=1.003, 95% CI:1.00-1.01 and aHR=1.010, 95% CI:1.001-1.019, per AQUA score unit, respectively). Ki-67 expression was not associated with survival (aHR=1.01, 95% CI:0.99-1.02) in the FHCRC cohort. DSS for patients with high sCAIX and low Ki-67 did not differ from that of other patient groups. Elevated tCAIX was associated with reduced DSS as a continuous and as a dichotomized (75%) variable. sCAIX was associated with DSS as a continuous variable but not when dichotomized (75%). However, the previously proposed 'functional hypoxia' signature was not replicated in the current FHCRC study. The failure to replicate our prior observation of poorer survival in patients with combined high sCAIX and low tumoral Ki-67 was likely due to the absence of an association between tumoral Ki-67 and DSS in this cohort. However, the association between DSS and tCAIX and sCAIX supports a role for CAIX in OSCC clinical outcomes.

An International Collaborative Standardizing a Comprehensive Patient-Centered Outcomes Measurement Set for Colorectal Cancer

IMPORTANCE

Global health systems are shifting toward value-based care in an effort to drive better outcomes in the setting of rising health care costs. This shift requires a common definition of value, starting with the outcomes that matter most to patients.

OBJECTIVE

The International Consortium for Health Outcomes Measurement (ICHOM), a nonprofit initiative, was formed to define standard sets of outcomes by medical condition. In this article, we report the efforts of ICHOM's working group in colorectal cancer.

EVIDENCE REVIEW

The working group was composed of multidisciplinary oncology specialists in medicine, surgery, radiation therapy, palliative care, nursing, and pathology, along with patient representatives. Through a modified Delphi process during 8 months (July 8, 2015 to February 29, 2016), ICHOM led the working group to a consensus on a final recommended standard set. The process was supported by a systematic PubMed literature review (1042 randomized clinical trials and guidelines from June 3, 2005, to June 3, 2015), a patient focus group (11 patients with early and metastatic colorectal cancer convened during a teleconference in August 2015), and a patient validation survey (among 276 patients with and survivors of colorectal cancer between October 15, 2015, and November 4, 2015).

FINDINGS

After consolidating findings of the literature review and focus group meeting, a list of 40 outcomes was presented to the WG and underwent voting. The final recommendation includes outcomes in the following categories: survival and disease control, disutility of care, degree of health, and quality of death. Selected case-mix factors were recommended to be collected at baseline to facilitate comparison of results across treatments and health care professionals.

CONCLUSIONS

A standardized set of patient-centered outcome measures to inform value-based health care in colorectal cancer was developed. Pilot efforts are under way to measure the standard set among members of the working group.

Massive Gastric Juvenile Polyposis: A Clinicopathologic Study Using SMAD4 Immunohistochemistry

OBJECTIVES

Juvenile polyps involving the stomach are uncommon. Massive gastric juvenile polyposis is even rarer.

METHODS

We describe the clinicopathologic features of nine cases of massive gastric juvenile polyposis.

RESULTS

All patients had anemia; four had hypoalbuminemia. The polyps were composed predominantly of dilated crypts lined by columnar epithelium and abundant edematous stroma with mixed inflammatory infiltrates. One patient had a poorly differentiated adenocarcinoma, arising in juvenile polyp-associated intraepithelial neoplasia. A second patient had a well-differentiated intramucosal adenocarcinoma arising in a juvenile polyp with high-grade dysplasia. Three of our cases had polyposis restricted to the stomach. Six (66.6%) had loss of SMAD4 immunoreactivity, making them subject to severe bleeding and hypoproteinemia, as well as developing severe dysplasia or adenocarcinoma.

CONCLUSIONS

SMAD4 immunohistochemstry is a helpful ancillary diagnostic test in cases of suspected juvenile polyposis syndrome involving the stomach.

Reproductive factors and risk of colorectal polyps in a colonoscopy-based study in western Washington State

BACKGROUND

Oral contraceptives (OC) are associated with a decreased risk of colorectal cancers; however, a recent study reported an increased risk of small colorectal adenomas associated with OC use. To determine if these results were replicable in a different study population, we investigated the relationship between OC use and other reproductive factors and risk of colorectal polyps in a case-control study in western Washington.

METHODS

Study participants were 24-79-year-old female enrollees at an integrated health care system in western Washington who were diagnosed as having adenomas (n = 299), serrated polyps (n = 337), both types of polyps (n = 105) or as polyp-free controls (n = 615) through an index colonoscopy and completed a structured interview to collect reproductive history information. Multivariable polytomous logistic regression was used to compare case groups to controls and to each other; odds ratios (OR) and 95% confidence intervals were estimated.

RESULTS

There was no association between OC use, duration of use, or recency of use and the risk of either adenomas or serrated polyps [adjusted OR for OC ever use (95% CI) 0.85 (0.58-1.23) and 0.96 (0.66-1.40), respectively], and associations did not differ by lesion severity within the adenoma or serrated pathways. Further, no associations were observed between other reproductive factors and risk of colorectal polyp subtypes.

CONCLUSIONS

Our results suggest that reproductive factors, including OC use, are not associated with early colorectal cancer precursor lesions.

Cytomegalovirus (CMV) in gastrointestinal mucosal biopsies: should a pathologist perform CMV immunohistochemistry if the clinician requests it?

Cytomegalovirus (CMV) causes clinically significant gastrointestinal (GI) injury. CMV inclusions can be identified on routine hematoxylin and eosin (H&E) stain, but immunohistochemistry (IHC) is also available for identifying CMV in tissue. The advent of accountable care organization models of care bring into question whether it is cost-effective for immunohistochemistry to be performed upfront at the request of clinicians and whether the quality of viral detection is compromised when the diagnosis of CMV is predicated on histologic review. In this study, a retrospective review of GI biopsies with CMV evaluations was performed. There were 449 cases with clinical requests to rule out CMV and 238 CMV analyses initiated by the pathologist without a clinical request. Among the cases that included a clinician's request, 37 had CMV detected. Immunostaining was performed on 26 cases, while a diagnosis based on readily identifiable viral inclusions on H&E-stained slides was made in 11. Among pathologist-initiated work-ups, 15 were CMV+, 3 of which had inclusions identified by H&E only. Among 38 CMV cases for which IHC had been performed, 27 had overt viral inclusions obvious on H&E. Seventy-two cases revealed uninflamed GI mucosa, and although a clinical concern about CMV infection was present, a CMV IHC work-up was not initially performed; all were negative for CMV by IHC and H&E. Clinical suspicion for CMV has a high yield for CMV detection, but "upfront" testing is likely unnecessary. Careful histopathologic review by a pathologist remains critical in the efficient and cost-effective detection of CMV.

Glutamine Synthetase Immunoreactivity in Peritumoral Hyperplasia in Liver: Case Report of a Metastatic Paraganglioma With Focal Nodular Hyperplasia-Like Changes and Review of an Additional 54 Liver Masses

OBJECTIVES

Focal nodular hyperplasia (FNH) and peritumoral hyperplasia in the liver exhibit increased immunoreactivity for glutamine synthetase (GS). We observed FNH-like changes with map-like GS staining surrounding a metastatic paraganglioma and sought to determine how often such changes occur around primary and metastatic liver lesions.

METHODS

We performed GS immunohistochemistry in liver cases of 20 metastatic neuroendocrine carcinomas (NECs), 21 metastatic colon carcinomas (CCs), seven hepatocellular carcinomas (HCCs), and six FNHs and assessed lesions for size, degree of fibrosis (scored 1-3), and peritumoral hyperplasia.

RESULTS

Most NEC or CC cases had few peritumoral hyperplastic features. Three NECs, two CCs, and one HCC (13%) had patchy GS staining at the periphery of the lesions. One CC case had both histologic and immunohistochemical peritumoral hyperplasia.

CONCLUSIONS

Peritumoral hyperplasia or FNH-like changes are uncommon findings around primary or metastatic lesions in the liver. GS immunohistochemistry assists in distinguishing true peritumoral hyperplasia from mass effect.

Initiation of universal tumor screening for Lynch syndrome in colorectal cancer patients as a model for the implementation of genetic information into clinical oncology practice

BACKGROUND

Lynch syndrome confers a hereditary predisposition to colorectal and other cancers. Universal tumor screening (UTS) for Lynch syndrome is recommended by several professional societies, but the implementation can be complex. This article describes the evaluation, process development, and initiation of Lynch syndrome UTS at a tertiary referral cancer center.

METHODS

A multidisciplinary team developed the new process design. Issues in 5 themes were noted: timing, funding, second-opinion patients, result processing, and the role of genetics providers. A committee approach was used to examine each issue for process-improvement development.

RESULTS

The issues related to testing were addressed individually for the successful implementation of UTS at the institutional level. In the conventional-care period, 9 of 30 cases (30%) received Lynch syndrome screening, and 4 cases were referred to medical genetics. During the 6 months following the implementation of UTS, 32 of 44 patients (73%) received Lynch syndrome screening. The 13 unscreened patients all had identified reasons for nonscreening (eg, financial limitations). Ten patients were referred to medical genetics, which identified no new cases of Lynch syndrome, but a low-risk adenomatous polyposis coli (APC) variant was detected in 1 individual.

CONCLUSIONS

The implementation of effective Lynch syndrome UTS can feasibly alter practice at the institutional level. This experience with the assessment and management of issues relevant to the successful implementation of a new clinical care paradigm based on emerging technology has implications for the uptake of advances across molecular oncology into clinical practice, and this is highly relevant in the current era of rapidly evolving genomic technology.

Lymphangiomatous Lesions of the Gastrointestinal Tract: A Clinicopathologic Study and Comparison Between Adults and Children

OBJECTIVES

Lymphangiomatous lesions involving the gastrointestinal (GI) tract remain incompletely characterized, and their clinical and histopathologic features have not been systematically evaluated. The distinction between a primary lymphatic malformation (lymphangioma) and a dilation of existing lymphatics (lymphangiectasia) is of clinical significance, since lymphangiectasia may occur in the setting of lymphatic obstruction due to an unsampled malignancy. We describe clinical and morphologic features of lymphangiomas of the GI tract in adult and pediatric populations and contrast them with lymphangiectasia.

METHODS

We performed a retrospective review of adult and pediatric lymphangiomas and lymphangiectasia involving the GI tract.

RESULTS

Thirty-six cases of lymphangioma and lymphangiectasia were retrieved, and clinical presentation and histologic features were compared. Lymphangiomas had distinct clinical presentations in adults and children, with adult lesions being more frequently asymptomatic and more frequently involving the superficial mucosal layers of the GI tract. Microscopically, lymphangiomas mostly consisted of confluent dilated spaces with a smooth muscle component. This appearance differed from lymphangiectasia, which lacked a complete distinct endothelial or smooth muscle lining and diffusely involved the mucosa and submucosa.

CONCLUSIONS

Morphologic features of GI tract lymphangiomas can be reliably distinguished from lymphangiectasia by clinical and pathologic characteristics.

Genome-Wide Loss of Heterozygosity and DNA Copy Number Aberration in HPV-Negative Oral Squamous Cell Carcinoma and Their Associations with Disease-Specific Survival

Oral squamous cell cancer of the oral cavity and oropharynx (OSCC) is associated with high case-fatality. For reasons that are largely unknown, patients with the same clinical and pathologic staging have heterogeneous response to treatment and different probability of recurrence and survival, with patients with Human Papillomavirus (HPV)-positive oropharyngeal tumors having the most favorable survival. To gain insight into the complexity of OSCC and to identify potential chromosomal changes that may be associated with OSCC mortality, we used Affymtrix 6.0 SNP arrays to examine paired DNA from peripheral blood and tumor cell populations isolated by laser capture microdissection to assess genome-wide loss of heterozygosity (LOH) and DNA copy number aberration (CNA) and their associations with risk factors, tumor characteristics, and oral cancer-specific mortality among 75 patients with HPV-negative OSCC. We found a highly heterogeneous and complex genomic landscape of HPV-negative tumors, and identified regions in 4q, 8p, 9p and 11q that seem to play an important role in oral cancer biology and survival from this disease. If confirmed, these findings could assist in designing personalized treatment or in the creation of models to predict survival in patients with HPV-negative OSCC.

Abstract 294: Blood lipids, colorectal adenomas, and non-adenomatous polyps: A comparison of associations from clinical measurements and Mendelian randomization

Background: Numerous studies have assessed associations between lipid levels and risk of colorectal neoplasia, but findings have been inconsistent. Recent genetic studies have identified &gt;100 loci associated with lipid levels. Knowledge of the magnitude and direction of genetic effects permits evaluation of allele scores that can serve as proxies for phenotypes.

Methods: We collected information on blood lipids as part of a colonoscopy study among enrollees, ages 25-79, of Group Health, a large healthcare system in Washington State. Low-density lipoprotein (LDL), high-density lipoprotein (HDL), triglycerides (TG), and total cholesterol (TC) measurements were extracted from electronic medical records for 98% of participants. For each participant, we identified the highest LDL, TG, and TC measurement (zenith) and lowest HDL measurement (nadir) prior to colonoscopy. All participants were genotyped for 96 single-nucleotide polymorphisms (SNPs) identified by the Global Lipids Genetics Consortium. For each lipid trait, we estimated 3 associations: 1) phenotype-polyp odds ratios (OR) with 95% confidence intervals (CI) comparing non-advanced adenoma cases to controls, advanced adenoma cases (≥10 mm in diameter, with villous components, or high-grade dysplasia) to controls, and non-adenomatous polyp cases to controls from polytomous logistic regression; 2) genotype-phenotype associations from linear regression; and 3) genotype-polyp ORs from two-stage linear-logistic regression.

Results: In total, 1,791 participants had information on phenotype and genotype (518 non-advanced adenoma cases, 139 advanced adenoma cases, 380 non-adenomatous polyp cases, and 754 polyp-free controls). Individuals with advanced adenomas were more likely than controls to have higher LDL and TG (adjusted OR per 20 mg/dL increase in zenith LDL: 1.16, CI 1.03-1.30 and OR per 40 mg/dL increase in zenith TG: 1.09, 1.03-1.16). Associations from allele scores were in the same direction (OR per increase in allele score scaled to be comparable to a 20 mg/dL LDL increase: 1.17, CI 0.78-1.75, and OR per increase in allele score scaled to be comparable to a 40 mg/dL TG increase: 1.12, 0.91-1.38). SNPs most strongly related to phenotype, however, were not associated with polyps, and SNPs that were, including variants of NAT2, MC4R, and APOE, may function through alternative pathways. Analyses among statin-naïve participants were not meaningfully different.

Conclusions: Mendelian randomization estimates did not achieve statistical significance, but the direction of associations suggests that polyps are more prevalent among those with inherited susceptibility to increased LDL and TG. Results also highlight difficulties interpreting results from Mendelian randomization analyses of traits with complex biology, given that variants may be pleiotropic and not suitable for use as instrumental variables.

Citation Format: Michael N. Passarelli, Polly A. Newcomb, Karen W. Makar, Andrea N. Burnett-Hartman, John D. Potter, Melissa P. Upton, Lee-Ching Zhu, Michael E. Rosenfeld, Stephen M. Schwartz, Carolyn M. Rutter. Blood lipids, colorectal adenomas, and non-adenomatous polyps: A comparison of associations from clinical measurements and Mendelian randomization. [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 294. doi:10.1158/1538-7445.AM2014-294

Abstract 299: Circulating microRNAs in association with colorectal neoplasia

Purpose: MicroRNAs (miRNAs) are non-coding regulatory RNAs that are stable in circulation and implicated in the etiology of many cancers including colorectal cancer (CRC). In this study we investigated whether candidate miRNAs could serve as blood-based biomarkers of colorectal adenoma.

Methods: We conducted a colonoscopy-based case-control study of men and women ages 50-79; this report includes data from 48 polyp-free controls, 43 advanced adenoma, 73 non-advanced adenomas, and 8 CRC cases. We selected 12 miRNA candidates that are highly expressed in adenoma tissue and have low expression in blood cells, in addition to miRNAs previously reported as biomarkers of adenoma. miRNAs were extracted from stored plasma samples, and copy number assessed with qRT-PCR. Odds ratios (ORs) and area-under-the-curve (AUC) from receiver-operator characteristic curves were estimated to quantify the association between plasma copy-number of these candidate miRNAs and each case group.

Results: No miRNA transcripts were associated with risk of adenoma or advanced adenomas, or with an AUC significantly above 0.5 that would indicate usefulness in discriminating either category of adenoma cases from controls. In contrast, statistically significant and strong associations (ORs&gt;5) with CRC were observed for 6 miRNA candidates, with corresponding AUCs significantly greater than 0.5.

Conclusions: Our results suggest that these candidate miRNAs, assayed with qRT-PCR, are unlikely to have clinical utility as blood-based screening biomarkers of adenomas. However, strong associations were observed with CRC. Circulating miRNAs may therefore have promise as potential early detection biomarkers to augment current CRC screening methods, but an optimal screening biomarker would detect pre-malignant colorectal adenomas as well as frank CRC.

Citation Format: Scott V. Adams, Polly A. Newcomb, Andrea N. Burnett-Hartman, Melissa P. Upton, Lee-Ching Zhu, Margaret Mandelson, John D. Potter, Karen W. Makar. Circulating microRNAs in association with colorectal neoplasia. [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 299. doi:10.1158/1538-7445.AM2014-299

Variation in the association between colorectal cancer susceptibility loci and colorectal polyps by polyp type

We conducted a case-control study of the association between subsets of colorectal polyps, including adenomas and serrated polyps, and single-nucleotide polymorphisms (SNPs) related to colorectal cancer through prior genome-wide association studies (GWAS). Participants were enrollees in the Group Health Cooperative (Seattle, Washington) aged 24-79 years who received a colonoscopy from 1998 to 2007, donated a buccal or blood sample, and completed a structured questionnaire. We performed genotyping of 13 colorectal cancer susceptibility SNPs. Polytomous logistic regression models were used to estimate odds ratios and 95% confidence intervals for associations between polyps and the colorectal cancer risk allele for each SNP under a log-additive model. Analyses included 781 controls, 489 cases with adenoma, 401 cases with serrated polyps, and 188 cases with both polyp types. The following SNPs were associated with advanced adenomas: rs10936599, rs10795668, rs16892766, and rs9929218 (P < 0.05). For nonadvanced adenomas and for serrated polyps overall, only rs961253 was statistically significant (P < 0.05). These associations were in the same directions as those in prior colorectal cancer GWAS. No SNP was significantly associated with hyperplastic polyps, and only rs6983267 was significantly associated with sessile serrated polyps, but this association was opposite of that found in colorectal cancer GWAS. Our results suggest that the association between colorectal cancer susceptibility SNPs and colorectal polyps varies by polyp type.

Phenotypic and transcriptional fidelity of patient-derived colon cancer xenografts in immune-deficient mice

Xenografts of human colorectal cancer (CRC) in immune-deficient mice have great potential for accelerating the study of tumor biology and therapy. We evaluated xenografts established in NOD/scid/IL2Rγ-null mice from the primary or metastatic tumors of 27 patients with CRC to estimate their capacity for expanding tumor cells for in vitro studies and to assess how faithfully they recapitulated the transcriptional profile of their parental tumors. RNA-seq analysis of parental human CRC tumors and their derivative xenografts demonstrated that reproducible transcriptional changes characterize the human tumor to murine xenograft transition. In most but not all cases, the human stroma, vasculature, and hematopoietic elements were systematically replaced by murine analogues while the carcinoma component persisted. Once established as xenografts, human CRC cells that could be propagated by serial transplantation remained transcriptionally stable. Three histologically atypical xenografts, established from patients with peritoneal metastases, contained abundant human stromal elements and blood vessels in addition to human tumor cells. The transcriptomes of these mixed tumor/stromal xenografts did not closely resemble those of their parental tumors, and attempts to propagate such xenografts by serial transplantation were unsuccessful. Stable expression of numerous genes previously identified as high priority targets for immunotherapy was observed in most xenograft lineages. Aberrant expression in CRC cells of human genes that are normally only expressed in hematopoietic cells was also observed. Our results suggest that human CRC cells expanded in murine xenografts have great utility for studies of tumor immunobiology and targeted therapies such as immunotherapy but also identify potential limitations.

Differences in epidemiologic risk factors for colorectal adenomas and serrated polyps by lesion severity and anatomical site

Using a case-control design, we evaluated differences in risk factors for colorectal polyps according to histological type, anatomical site, and severity. Participants were enrollees in the Group Health Cooperative aged 20-79 years who underwent colonoscopy in Seattle, Washington, between 1998 and 2007 and comprised 628 adenoma cases, 594 serrated polyp cases, 247 cases with both types of polyps, and 1,037 polyp-free controls. Participants completed a structured interview, and polyps were evaluated via standardized pathology review. We used multivariable polytomous logistic regression to compare case groups with controls and with the other case groups. Factors for which the strength of the association varied significantly between adenomas and serrated polyps were sex (P < 0.001), use of estrogen-only postmenopausal hormone therapy (P = 0.01), and smoking status (P < 0.001). For lesion severity, prior endoscopy (P < 0.001) and age (P = 0.05) had significantly stronger associations with advanced adenomas than with nonadvanced adenomas; and higher education was positively correlated with sessile serrated polyps but not with other serrated polyps (P = 0.02). Statistically significant, site-specific associations were observed for current cigarette smoking (P = 0.05 among adenomas and P < 0.001 among serrated polyps), postmenopausal estrogen-only therapy (P = 0.01 among adenomas), and obesity (P = 0.01 among serrated polyps). These findings further illustrate the epidemiologic heterogeneity of colorectal neoplasia and may help elucidate carcinogenic mechanisms for distinct pathways.

Genomic aberrations occurring in subsets of serrated colorectal lesions but not conventional adenomas

A subset of aggressive colorectal cancers exhibit BRAF mutation, MLH1 methylation, and a CpG island methylator phenotype (CIMP), but precursors are poorly established. In this study, we determined the status of these markers in colorectal polyps and evaluated associated risk factors. The study included 771 polyp cases and 1,027 controls who were ages 24 to 80 years, part of a group health program, received a colonoscopy from 1998 to 2007, and completed a structured questionnaire assessing risk factors. Following standard pathology review, polyps were assayed for BRAF mutation (V600E) and tested for MLH1 and CIMP methylation, the latter including the genes, CACNA1G, IGF2, NEUROG1, RUNX3, and SOCS1. Polytomous logistic regression was used to estimate ORs and 95% confidence intervals for the association between molecularly defined subsets of polyps and potential risk factors. There were 580 conventional adenomas and 419 serrated lesions successfully assayed. For adenomas, the prevalence of each marker was ≤1%. In contrast, 55% of serrated lesions harbored mutant BRAF, 26% were CIMP-high, and 5% had methylated MLH1. In these lesions, the highest prevalence of markers was in sessile-serrated polyps (SSP) of ≥10 mm that were in the right-side/cecal regions of the colon. Risk factors for CIMP-high-serrated lesions included Caucasian race, current smoking status, and a history of polyps, whereas for serrated lesions with mutant BRAF, the significant risk factors were male sex, current smoking status, obesity, and a history of polyps. Our results suggest that SSPs and other large, right-sided serrated lesions have a unique molecular profile that is similar to CIMP-high, BRAF-mutated colorectal cancers.

Increased IgG4+ cells in duodenal biopsies are not specific for autoimmune pancreatitis

Endoscopic ampullary biopsies showing increased immunoglobulin (Ig) G4+ plasma cells have been reported as an alternative to pancreatic biopsy in diagnosing autoimmune pancreatitis (AIP). This study assessed whether increased IgG4+ cells can be seen outside the context of AIP. Fifty-four cases (45 duodenal or ampullary biopsies, 9 ampullae from pancreatic resections) were selected, and all specimens were immunostained for IgG4 and IgG. Duodenal or ampullary biopsies containing normal duodenal mucosa (n = 6) and increased intraepithelial lymphocytes without villous blunting (n = 7) were negative for IgG4. Increased IgG4+ cells (>10 per high-power field) were found in 7 cases of 18 serologically confirmed celiac disease patients and in 3 of 14 patients with duodenitis or gastric heterotopias. Two of 6 ampullae from patients with pancreatic cancer showed increased IgG4+ cells. In summary, 12 of 51 patients without AIP had duodenal biopsies or ampullae showing increased IgG4+ plasma cells. The finding of increased IgG4+ cells in duodenal biopsies is not specific for AIP without the correct clinical context.

Integrative genomics in combination with RNA interference identifies prognostic and functionally relevant gene targets for oral squamous cell carcinoma

In oral squamous cell carcinoma (OSCC), metastasis to lymph nodes is associated with a 50% reduction in 5-year survival. To identify a metastatic gene set based on DNA copy number abnormalities (CNAs) of differentially expressed genes, we compared DNA and RNA of OSCC cells laser-microdissected from non-metastatic primary tumors (n = 17) with those from lymph node metastases (n = 20), using Affymetrix 250K Nsp single-nucleotide polymorphism (SNP) arrays and U133 Plus 2.0 arrays, respectively. With a false discovery rate (FDR)<5%, 1988 transcripts were found to be differentially expressed between primary and metastatic OSCC. Of these, 114 were found to have a significant correlation between DNA copy number and gene expression (FDR<0.01). Among these 114 correlated transcripts, the corresponding genomic regions of each of 95 transcripts had CNAs differences between primary and metastatic OSCC (FDR<0.01). Using an independent dataset of 133 patients, multivariable analysis showed that the OSCC–specific and overall mortality hazards ratio (HR) for patients carrying the 95-transcript signature were 4.75 (95% CI: 2.03–11.11) and 3.45 (95% CI: 1.84–6.50), respectively. To determine the degree by which these genes impact cell survival, we compared the growth of five OSCC cell lines before and after knockdown of over-amplified transcripts via a high-throughput siRNA–mediated screen. The expression-knockdown of 18 of the 26 genes tested showed a growth suppression ≥30% in at least one cell line (P<0.01). In particular, cell lines derived from late-stage OSCC were more sensitive to the knockdown of G3BP1 than cell lines derived from early-stage OSCC, and the growth suppression was likely caused by increase in apoptosis. Further investigation is warranted to examine the biological role of these genes in OSCC progression and their therapeutic potentials.

Neck lymph node metastasis is the most important prognostic factor in oral squamous cell carcinoma (OSCC). To identify genes associated with this critical step of OSCC progression, we compared DNA copy number aberrations and gene expression differences between tumor cells found in metastatic lymph nodes versus those in non-metastatic primary tumors. We identified 95 transcripts (87 genes) with metastasis-specific genome abnormalities and gene expression. Tested in an independent cohort of 133 OSCC patients, the 95 gene signature was an independent risk factor of disease-specific and overall death, suggesting a disease progression phenotype. We knocked down the expression of over-amplified genes in five OSCC cell lines. Knockdown of 18 of the 26 tested genes suppressed the cell growth in at least one cell line. Interestingly, cell lines derived from late-stage OSCC were more sensitive to the knockdown of G3BP1 than cell lines derived from early-stage OSCC. The knockdown of G3BP1 increased programmed cell death in the p53-mutant but not wild-type OSCC cell lines. Taken together, we demonstrate that CNA–associated transcripts differentially expressed in carcinoma cells with an aggressive phenotype (i.e., metastatic to lymph nodes) can be biomarkers with both prognostic information and functional relevance. Moreover, results suggest that G3BP1 is a potential therapeutic target against late-stage p53-negative OSCC.

A 13-gene signature prognostic of HPV-negative OSCC: discovery and external validation

PURPOSE

To identify a prognostic gene signature for patients with human papilloma virus (HPV)-negative oral squamous cell carcinomas (OSCC).

EXPERIMENTAL DESIGN

Two gene expression datasets were used: a training dataset from the Fred Hutchinson Cancer Research Center (FHCRC, Seattle, WA; n = 97) and a validation dataset from the MD Anderson Cancer Center (MDACC, Houston, TX; n = 71). We applied L1/L2-penalized Cox regression models to the FHCRC data on the 131-gene signature previously identified to be prognostic in patients with OSCCs to identify a prognostic model specific for patients with high-risk HPV-negative OSCCs. The models were tested with the MDACC dataset using a receiver operating characteristic (ROC) analysis.

RESULTS

A 13-gene model was identified as the best predictor of HPV-negative OSCC-specific survival in the training dataset. The risk score for each patient in the validation dataset was calculated from this model and dichotomized at the median. The estimated 2-year mortality (± SE) of patients with high-risk scores was 47.1% (± 9.24%) compared with 6.35% (± 4.42) for patients with low-risk scores. ROC analyses showed that the areas under the curve for the age, gender, and treatment modality-adjusted models with risk score [0.78; 95% confidence interval (CI), 0.74-0.86] and risk score plus tumor stage (0.79; 95% CI, 0.75-0.87) were substantially higher than for the model with tumor stage (0.54; 95% CI, 0.48-0.62).

CONCLUSIONS

We identified and validated a 13-gene signature that is considerably better than tumor stage in predicting survival of patients with HPV-negative OSCCs. Further evaluation of this gene signature as a prognostic marker in other populations of patients with HPV-negative OSCC is warranted.

Synthesis and characterization of anti-EGFR fluorescent nanoparticles for optical molecular imaging

Molecular imaging, the visualization of molecular and cellular markers, is a promising method for detection of dysplasia and early cancer in the esophagus and can potentially be used to identify regions of interest for biopsy or tumor margins for resection. EGFR is a previously reported cell surface receptor with stepwise increases in expression during the progression from Barrett's metaplasia to adenocarcinoma. In this work, a 200 nm fluorescent nanoparticle contrast agent was synthesized for targeted imaging of EGFR through a series of surface modifications to dye-encapsulated polystyrene particles. Amino-functionalized polystyrene particles were PEGylated using a heterobifunctional PEG linker. Subsequently, thiolated M225 antibodies were conjugated to maleimide functional groups on attached PEGs for EGFR targeting. In vitro binding studies using flow cytometry demonstrated specific binding of M225-PEG-NP to EGFR-expressing cells with minimal nonspecific binding in EGFR(-) cells. Binding was shown to increase proportionally with the number of conjugated M225 antibodies. Adsorbed formulations with unmodified M225 antibodies, M225 + PEG-NP, were synthesized using the same antibody feeds used in M225-PEG-NP synthesis to determine the contribution of adsorbed antibodies to EGFR targeting. Adsorbed antibodies were less efficient at mediated nanoparticle targeting to EGFR than conjugated antibodies. Finally, M225-PEG-NP demonstrated binding to EGFR-expressing regions in human esophageal tissue sections.

Gene expression in uninvolved oral mucosa of OSCC patients facilitates identification of markers predictive of OSCC outcomes

Oral and oropharyngeal squamous cell carcinomas (OSCC) are among the most common cancers worldwide, with approximately 60% 5-yr survival rate. To identify potential markers for disease progression, we used Affymetrix U133 plus 2.0 arrays to examine the gene expression profiles of 167 primary tumor samples from OSCC patients, 58 uninvolved oral mucosae from OSCC patients and 45 normal oral mucosae from patients without oral cancer, all enrolled at one of the three University of Washington-affiliated medical centers between 2003 to 2008. We found 2,596 probe sets differentially expressed between 167 tumor samples and 45 normal samples. Among 2,596 probe sets, 71 were significantly and consistently up- or down-regulated in the comparison between normal samples and uninvolved oral samples and between uninvolved oral samples and tumor samples. Cox regression analyses showed that 20 of the 71 probe sets were significantly associated with progression-free survival. The risk score for each patient was calculated from coefficients of a Cox model incorporating these 20 probe sets. The hazard ratio (HR) associated with each unit change in the risk score adjusting for age, gender, tumor stage, and high-risk HPV status was 2.7 (95% CI: 2.0–3.8, p = 8.8E-10). The risk scores in an independent dataset of 74 OSCC patients from the MD Anderson Cancer Center was also significantly associated with progression-free survival independent of age, gender, and tumor stage (HR 1.6, 95% CI: 1.1–2.2, p = 0.008). Gene Set Enrichment Analysis showed that the most prominent biological pathway represented by the 71 probe sets was the Integrin cell surface interactions pathway. In conclusion, we identified 71 probe sets in which dysregulation occurred in both uninvolved oral mucosal and cancer samples. Dysregulation of 20 of the 71 probe sets was associated with progression-free survival and was validated in an independent dataset.

Integrative analysis in oral squamous cell carcinoma reveals DNA copy number-associated miRNAs dysregulating target genes

OBJECTIVE

To better understand possible mechanisms involved in the dysregulation of gene expression unique to oral squamous cell carcinoma (OSCC) metastasis, the investigators examined the differential expression of microRNAs (miRNAs) in OSCC metastasis and their functional impact on target gene expression.

STUDY DESIGN

Observational assessment of DNA copy number, miRNA, and RNA expression in primary and metastatic OSCC.

SETTING

University of Washington Medical Center and affiliated hospitals.

SUBJECTS

Tumor samples were taken from patients with primary incident OSCC; cells were laser-capture microdissected from 17 nonmetastatic primary tumors and 20 metastatic lymph nodes.

METHODS

DNA copy number aberrations and gene expression profiles were previously determined using Affymetrix 250K Nsp I SNP arrays and HU133 plus 2.0 expression arrays. miRNAs were interrogated with Exiqon's Ready-to-Use PCR Panels assessing the expression of 368 human miRNAs.

RESULTS

Investigators found 31 miRNAs differentially expressed between metastatic and nonmetastatic samples (false discovery rate <0.4; 26 overexpressed and 5 underexpressed in metastatic samples). Expression of 7 of these miRNAs was significantly associated with their DNA copy numbers, and expressions of 8 of these miRNAs were significantly associated with their target genes. Among these unique miRNAs, miR-140-3p, miR-29c, and miR-29a were differentially expressed in metastasis versus nonmetastatic samples and had a strong positive correlation with their DNA copy numbers and a negative correlation with the expression of their target genes.

CONCLUSION

Results suggest that DNA copy number aberration may play a role in the dysregulation of some differentially expressed miRNAs in OSCC metastasis, warranting further investigation.

Abstract 1673: BRAF mutation is associated with large, proximal sessile serrated polyps, but not with adenomas

Background: Different colorectal cancer (CRC) pathways result in tumors with distinct phenotypic and molecular signatures. The adenoma-carcinoma pathway involves conventional adenoma precursors, resulting in tumors that tend to exhibit chromosomal instability but lack microsatellite instability. Less is established about the origin of microsatellite unstable CRC. This sub-set of tumors includes some tumors with aberrant methylation, which often exhibit activating mutations in the BRAF oncogene, and are commonly found in the proximal colon. Objective: We aimed to compare the prevalence of BRAF-mutation between distinct colorectal polyp types. Methods: We conducted a case-case comparison of BRAF-mutation status in polyp tissue DNA from participants aged 24-79 in a colonoscopy-based study, who were diagnosed with colorectal adenomas or hyperplastic polyps (HPs). During colonoscopy, polyps were biopsied, fixed in paraffin, and H&E slides prepared. All participants underwent a standard pathology review to confirm the diagnosis and determine the percent of lesional tissue in the block. Polyps classified as tubular adenomas or tubulovillous adenomas were considered conventional adenomas; those classified as HPs, sessile serrated polyps, or traditional serrated adenomas were considered serrated polyps. Medical records were abstracted to ascertain polyp location and size; tissue blocks from polyps at least 3 mm in diameter and containing at least 80% lesional tissue were selected for BRAF analyses. BRAF-mutation status was determined using 2 assays specific for the V600E mutation. A validated TaqMan assay was run on all samples, and a fluorescent allele-specific PCR assay was run on a subset for quality control. Of the 1044 polyp DNA samples tested, 880 (84%) were successfully assayed. Results: Of 529 conventional adenomas, including 129 tubulovillous adenomas, only 2 (0.4%) had V600E BRAF-mutations. Among serrated polyps, 176 of 351 (50%) were BRAF-mutation positive. Of these, sessile serrated polyps had the highest prevalence of a BRAF-mutation: 74 of 120 (62%), followed by traditional serrated adenomas: 5 of 11 (45%), and HPs: 97 of 220 (44%). Polyp location and size were also associated with a BRAF-mutation. For serrated polyps, 45 of 98 (46%) rectal, 39 of 95 (41%) distal colon, and 92 of 156 (59%) proximal colon polyps were BRAF-mutated. Serrated polyps ≤ 10 mm had a higher prevalence of BRAF-mutation than those &lt; 10 mm (69% vs. 48% with BRAF-mutation, respectively). Discussion: Our results suggest that BRAF-mutation is commonly found in serrated polyps, but rarely occurs in conventional adenomas. Among serrated polyps, the prevalence of BRAF-mutation was highest in polyps that were proximally located, β10 mm, and with sessile serrated histology. These findings support the thesis that serrated polyps may be important precursors for the subset of CRC exhibiting BRAF-mutation.

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 1673. doi:1538-7445.AM2012-1673

Abstract 645: Differences in epidemiologic risk factors for colorectal adenomas and serrated polyps by anatomic site and lesion severity

Colorectal cancer (CRC) is a heterogeneous disease, and different subsets of CRC probably have different precursor lesions. Some colorectal polyps are considered precursors to CRC and are broadly classified into: 1) adenomas, including tubular, tubulovillous, and villous adenomas, and 2) serrated polyps, including hyperplasic polyps (HPs), sessile serrated polyps (SSPs), and traditional serrated adenomas (TSAs). Adenomas are established CRC precursors, particularly for advanced lesions ≤ 10 mm, with villous components, or high-grade dysplasia. HPs were previously considered innocuous lesions, but new data suggests that a subset of these may progress to CRC via advanced serrated lesions, such as SSPs and TSAs. To gain insight into the factors associated with initiation and progression for divergent CRC pathways, we tested differences in risk factors for polyps according to histologic type, anatomic site, and severity. Participants, aged 20-79, were sampled from enrollees of Group Health, a large healthcare provider in Washington State, who underwent colonoscopy for any indication between 1998 and 2007. Participants completed a structured interview, and all lesions received a standardized pathology review. We evaluated 1,469 cases, including 628 with adenomas only, 594 with serrated polyps only, and 247 with both types of polyps, as well as 1,037 controls who were free of colorectal pathologies during colonoscopy. We focused on the following risk factors: age, sex, race, education, body mass index (BMI), NSAID use, family history of CRC, hormone use among women, endoscopy screening, smoking status, alcohol use, and physical activity. Multivariable polytomous logistic regression models were used to compare case groups to controls adjusted for all factors. Our study confirmed previously described risk factors for adenomas: age, male sex, obesity, never use of NSAIDs, no previous endoscopy, and physical inactivity. Risk factors for serrated polyps were smoking and never use of estrogen-only therapy. There were statistically significant differences in the association between several risk factors and polyp type. Male sex (P&lt;0.001) and smoking (P&lt;0.001) were stronger risk factors for adenomas than for serrated polyps. With respect to anatomic site, smoking (P=0.05) and never use of estrogen-only therapy (P=0.01) were stronger risk factors for distal/rectal than for proximal adenomas. Smoking (P&lt;0.001) and BMI (P=0.01) were stronger risk factors for distal/rectal than for proximal serrated polyps. With respect to lesion severity, lack of prior endoscopy was a stronger risk factor for advanced adenomas (P&lt;0.001) than for non-advanced adenomas, and higher education level was a stronger risk factor for SSP/TSAs than for HPs (P=0.02). These findings may suggest carcinogenic mechanisms that distinguish the adenoma-carcinoma pathway and the serrated pathway to CRC.

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 645. doi:1538-7445.AM2012-645

Abstract 724: Gene expression in clinically normal oral mucosa of oral cancer patients facilitates identification of markers predictive of OSCC outcomes

Oral and oropharyngeal squamous cell carcinomas (OSCC) are among the most common cancers worldwide. The overall 5-yr survival rate of OSCC patients is approximately 50% but is higher than 80% in early-stage patients. The high mortality of OSCC is due in part to late diagnosis and high recurrence rates. Thus, early detection of OSCC and identification of a good predictor of disease progression are important in improving OSCC outcomes. To identify potential markers for early diagnosis and disease progression, we used Affymetrix U133 plus 2.0 arrays to examine the gene expression profiles of 167 primary OSCC from newly diagnosed patients, 58 “normal” oral mucosa from oral cancer patients (NCA) and 45 normal oral mucosa from patients without cancer (controls), all of whom were enrolled at three University of Washington-affiliated medical centers from 2003 to 2008. We first compared gene expression in the 45 controls to the 167 tumors using ANOVA implemented in Partek® Genomics Suite™ software, adjusting for age, sex, cigarette-smoking, alcohol use and HPV status. We found 2,596 probe sets differentially expressed between tumors and controls, using the criteria of a FDR of 0.05 and at least a two-fold difference in the expression level. We then used linear regression to compare the gene expression level of these 2,596 probe sets between controls and NCA, and between NCA and tumors. Among 2,596 probe sets, 60 were significantly up-regulated and 11 were significantly down-regulated in both comparisons using the Bonferroni correction with a p-value of 1.93x10-5 and a difference in gene expression greater than 1 standard deviation of the expression in NCA. A cluster analysis on gene expression of the 71 probe sets identified a subgroup of 45 OSCC patients with highest/lowest expression of these probe sets. These 45 OSCC patients had a higher risk of disease progression after treatment (defined by persistence or recurrence of OSCC) and higher OSCC-specific mortality when compared with the remaining 122 OSCC patients; the respective Cox regression hazard ratio (HR) and 95% CI, adjusted for age, sex, and stage for disease progression and OSCC-specific mortality were 2.7 (1.5-4.6) and 3.8 (2.1-7.0). The top gene associated with both outcomes was dermatan sulfate epimerase (DSE). A high level of DSE expression in tumor (higher than mean expression among tumors) was associated with a higher risk of disease progression (HR 2.8, 95% CI: 1.5-5.1) and of OSCC-specific mortality (HR 6.0, 95% CI: 2.9-12.2) after adjusting for age, sex and stage. DSE encodes a tumor-rejection antigen that could potentially serve as a target for cancer immunotherapy. In conclusion, we identified 71 probe sets in which dysregulation occurred in both NCA and cancer samples. Some of these genes could potentially serve as early diagnostic markers, markers to predict disease progression, or as potential targets for new therapy.

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 724. doi:1538-7445.AM2012-724

Human papillomavirus-positive oral cavity and oropharyngeal cancer patients do not have better quality-of-life trajectories

OBJECTIVE

To determine the role of human papillomavirus (HPV) status on quality of life (QOL) in patients with oral cavity and oropharyngeal squamous cell carcinoma (OSCC). Since OSCC that are associated with high-risk HPV have an improved response to treatment and survival, we hypothesized that patients with these tumors would have better QOL trajectories.

STUDY DESIGN

Prospective cohort study.

SETTING

Tertiary care academic medical center and 2 affiliated hospitals.

SUBJECTS AND METHODS

Head and neck-specific QOL was determined using the University of Washington Quality of Life scale version 4 in patients with newly diagnosed invasive OSSC (N = 228).

RESULTS

Pretreatment QOL was higher in patients with high-risk HPV-associated tumors compared with patients with HPV-negative or low-risk HPV-associated tumors (P = .015). Patients with high-risk HPV-associated tumors had larger decreases in QOL from pretreatment to immediate posttreatment compared with patients with HPV-negative or low-risk HPV-associated tumors (P = .041). There was no association between HPV status and 1-year posttreatment QOL.

CONCLUSION

Among OSCC patients, high-risk HPV-associated tumors were associated with higher pretreatment QOL and a larger decrease in QOL from pretreatment to immediate posttreatment, suggesting that treatment intensity in this unique population may adversely affect QOL.

Aberrantly methylated PKP1 in the progression of Barrett's esophagus to esophageal adenocarcinoma

The aberrant DNA methylation of tumor suppressor genes occurs frequently in Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) and likely affects the initiation and progression of BE to EAC. In the present study, we discovered PKP1 as a novel methylated gene in EAC and then investigated the role of loss of PKP1, a constituent of the desmosome complex found in stratified epithelial layers, on the behavior of Barrett's esophagus and esophageal adenocarcinoma cells. By using primary esophageal tissue samples we determined that PKP1 was rarely methylated in normal squamous esophagus (5/55; 9.1%) and BE (5/39; 12.8%) and more frequently methylated in Barrett's esophagus with high-grade dysplasia (HGD) or EAC (20/60; 33.3%; P < 0.05). Furthermore, PKP1 levels were decreased in BE and HGD/EAC cases compared to normal squamous esophagus cases. Knockdown of PKP1 in the BE cell lines CP-A and CP-D (both normally express PKP1) resulted in increased cell motility. Thus, PKP1 loss secondary to promoter methylation, as well as other mechanisms, may promote the progression of BE to EAC in a subset of patients via decreased desmosome assembly and increased cell motility.

Barrett's esophagus: surveillance and reversal

The following on surveillance and reversal of Barrett's esophagus (BE) includes commentaries on criteria for surveillance even when squamous epithelium stains normally with a variety of biomarkers; the long-term follow-up of surgery versus endoscopic ablation of BE; the recommended surveillance intervals in patients without dysplasia; the sampling problems related to anatomic changes following fundoplication; the value of tissue spectroscopy and optical coherence tomography; the cost-effectiveness of biopsy protocols for surveillance; the quality of life of Barrett's patients; and risk stratification and surveillance strategies.

Esophageal disease and pathology

The following on esophageal disease and pathology contains commentaries on the varied definitions of Barrett's esophagus (BE); the optimal biopsy strategy in BE; reliable biomarkers for progression to neoplasia in BE; and the role of bone marrow stem cells in the morphogenesis of Barrett's esophagus.

Tumor and salivary matrix metalloproteinase levels are strong diagnostic markers of oral squamous cell carcinoma

BACKGROUND

The matrix metalloproteinases (MMP) cause degradation of the extracellular matrix and basement membranes, and thus may play a key role in cancer development.

METHODS

In our search for biomarkers for oral squamous cell carcinomas (OSCC), we compared primary OSCC, oral dysplasia and control subjects with respect to: (i) expression of MMP1, MMP3, MMP10, and MMP12 in oral epithelial tissue using Affymetrix U133 2.0 Plus GeneChip arrays, followed by quantitative reverse transcription-PCR (qRT-PCR) for MMP1, and (ii) determination of MMP1 and MMP3 concentrations in saliva.

RESULTS

MMP1 expression in primary OSCC (n = 119) was >200-fold higher (P = 7.16 × 10(-40)) compared with expression levels in nonneoplastic oral epithelium from controls (n = 35). qRT-PCR results on 30 cases and 22 controls confirmed this substantial differential expression. The exceptional discriminatory power to separate OSCC from controls was validated in two independent testing sets (AUC% = 100; 95% CI: 100-100 and AUC% = 98.4; 95% CI: 95.6-100). Salivary concentrations of MMP1 and MMP3 in OSCC patients (33 stage I/II, 26 stage III/IV) were 6.2 times (95% CI: 3.32-11.73) and 14.8 times (95% CI: 6.75-32.56) higher, respectively, than in controls, and displayed an increasing trend with higher stage disease.

CONCLUSION

Tumor and salivary MMPs are robust diagnostic biomarkers of OSCC.

IMPACT

The capacity of MMP gene expression to identify OSCC provides support for further investigation into MMPs as potential markers for OSCC development. Detection of MMP proteins in saliva in particular may provide a promising means to detect and monitor OSCC noninvasively.

Barrett's esophagus: endoscopic treatments II

The following on endoscopic treatments of Barrett's esophagus includes commentaries on animal experiments on cryotherapy; indications for cryotherapy, choice of dosimetry, number of sessions, and role in Barrett's esophagus and adenocarcinoma; recent technical developments of RFA technology and long-term effects; the comparative effects of diverse ablation procedures and the rate of recurrence following treatment; and the indications for treatment of dysplasia and the role of radiofrequency ablation.

Abstract 3819: Matrix metalloproteinase-1 (MMP1) is an important marker of oral squamous cell carcinoma

The matrix metalloproteinase genes have frequently been identified as important in cancer development and progression, including in oral squamous cell carcinoma (OSCC). These proteases are believed to cause degradation of the extracellular matrix and basement membranes and therefore to play a key role in tumor metastasis, cell migration, cancer cell growth, and angiogenesis. We compared MMP1 expression levels in primary OSCC (n=119) with expression levels in normal oral epithelium from control subjects (n=35), as measured by Affymetrix U133 2.0 Plus GeneChip arrays, adjusting for age and sex. MMP1 was expressed more than 200-fold higher in OSCC compared with normal control epithelium. qRT-PCR results on 30 of the cases and 22 of the controls confirmed the substantial differential expression of MMP1, with a difference in mean threshold cycle (Ct) value for cases versus controls of 9.85 (95% CI, 8.74-10.97, p&lt;0.001). In an independent testing set of 48 OSCC tissue samples and 10 control samples, MMP1 had exceptional discriminatory power to separate cases from controls (AUC=100%). This result was further validated in an external data set from Gene Expression Omnibus (GEO; GSE6791) of 42 OSCC cases and 14 controls (AUC=98.4%; 95% CI, 95.6%-100%). The mean of the log2 MMP1 expression levels on the Affymetrix arrays for 45 normal oral epithelium was 3.49 (95% CI, 3.21-3.78), 17 dysplasia tissue samples had mean expression of 6.69 (95% CI, 5.21-8.17), 108 stage T1/T2 cases had a mean of 10.93 (95% CI,10.49-11.37), and the mean of 57 stage T3/T4 cases was 11.38 (95% CI,10.81-11.95). These results suggest that MMP1 is increasingly dysregulated during the process of oral carcinogenesis. The capacity of MMP1 to identify OSCC provides support for further investigation into this enzyme as a potential marker for OSCC development and/or progression.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3819. doi:10.1158/1538-7445.AM2011-3819

Abstract 3762: CIMP is common for right-sided colon sessile serrated polyps but not for colorectal adenomas

Background: Several pathways for colorectal cancer (CRC) have been described. The well-known adenoma-to-carcinoma pathway usually results in microsatellite stable tumors and accounts for about 75% of CRC. Less is established about the origins of microsatellite unstable (MSI) CRC. These tumors are more often in the right colon and commonly characterized as having a CpG Island Methylator Phenotype (CIMP).

Objective: We aimed to better understand precursors for MSI colorectal tumors by determining the correlation between CIMP-status and polyp type.

Methods: We conducted a case-case comparison of CIMP status among participants aged 24-79 of a colonoscopy-based study, who were diagnosed with colorectal adenomas or hyperplastic polyps (HPs). During colonoscopy, polyps were biopsied, fixed in paraffin, and H&E slides prepared. All participants underwent a standard pathology review to confirm the diagnosis, determine the percent of lesional tissue in the block, and classify each polyp as tubular adenoma, tubulovillous adenoma, HP (both goblet cell and microvesicular), sessile serrated polyp, or serrated adenoma. Medical records were abstracted to ascertain polyp location and size; tissue blocks from polyps at least 3 mm in diameter and containing at least 80% lesional tissue were selected for CIMP analyses. DNA methylation was quantified in 905 polyps by real-time PCR (MethyLight) using a validated CIMP marker panel (CACNA1G, IGF2, NEUROG1, RUNX3, SOCS1). ALU was used to monitor DNA quality. Of the 905 polyps tested, 752 (83%) had an ALU cycle threshold &lt;23, and thus appropriate for CIMP analyses.

Results: Of 434 adenomatous polyps, including 113 tubulovillous adenomas, only 2 (&lt;0.5%) were CIMP-positive, both tubulovillous adenomas. For HPs and other serrated polyps, 87 out of 318 (27%) were CIMP-positive. Among these, sessile serrated polyps had the highest proportion of CIMP positivity: 59 of 108 (55%), followed by serrated adenomas: 4 of 11 (37%), and hyperplastic polyps: 24 of 199 (12%). Polyp location was also associated with CIMP status. For HPs/other serrated polyps, 2 of 87 (2%) rectal polyps were CIMP positive, 10 of 75 (13%) left colon polyps were positive, and 75 of 155 (48%) right were positive.

Discussion: Until recently, sessile serrated polyps were classified as hyperplastic polyps and therefore, were thought to have little clinical significance. However, our investigation suggests that these polyps, like MSI CRC tumors, are commonly CIMP-positive. Adenomatous polyps, in contrast, were largely CIMP-negative. This finding supports other investigations suggesting MSI CRC is not likely to have an adenomatous precursor, and probably arises from serrated polyps. If confirmed by longitudinal studies, this will have important implications for CRC surveillance.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3762. doi:10.1158/1538-7445.AM2011-3762

Abstract 4983: Integrative analysis of DNA copy number and gene expression identifies G3BP1 and HIRA as potential therapeutic targets against metastatic oral squamous cell carcinoma

The presence of lymph node metastasis is associated with a 50% reduction of 5-year survival in patients with oral squamous cell carcinoma (OSCC). We set out to combine DNA copy number aberrations (CNAs) with gene expression profiles, to identify CNAs-associated genes dysregulated in metastatic OSCC, and determine whether these genes can be targeted to selectively kill metastatic OSCC tumor cells. Toward this end, we interrogated DNA and RNA of the same OSCC cell populations laser micro-dissected from non-metastatic primary tumors (n=17) and metastatic lymph nodes (n=20) using Affymetrix 250K Nsp single-nucleotide polymorphism (SNP) arrays and U133 Plus 2.0 arrays, respectively. With a false discovery rate (FDR) &lt; 5%, 1988 transcripts were found to be differentially expressed between primary and metastatic OSCC. Out of these, 114 transcripts showed significant correlation between their DNA copy number alternations (estimated using SNPs within 250 kb upstream and downstream of the transcript) and gene expression (FDR &lt; 0.01). Among these CNA-correlated transcripts, 95 had significantly different DNA copy numbers between metastatic and non-metastatic OSCC (FDR &lt;0.01 by Wilcoxon rank test). These 95 transcripts (representing 87 genes) mainly clustered around three genomic locations: 3p25.3-22.1, 9p24.1- 22.3 and 18q21.1-22.3. Among these 87 genes, we selected 28 of the 58 genes that were over-amplified and over-expressed in metastatic OSCC and conducted a high-throughput siRNA-mediated gene knockdown screen in five cell lines derived from primary and lymph node metastatic OSCC. The expression-knockdown of 18 genes showed 30% or more growth suppression in at least one cell line as compared to mock controls in which the cells were treated with transfection reagent only without the siRNA (P &lt; 0.01). In particular, knocking-down G3BP1 and HIRA selectively suppressed the growth of all OSCC cell lines derived from lymph node metastases when compared to non-metastatic lines. Further investigation is warranted to confirm these findings and to examine the biological role of G3BP1 and HIRA in OSCC metastasis and their potential as therapeutic targets.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4983. doi:10.1158/1538-7445.AM2011-4983

Can a metastatic gene expression profile outperform tumor size as a predictor of occult lymph node metastasis in oral cancer patients?

PURPOSE

To determine the differential gene expression between oral squamous cell carcinoma (OSCC) with and without metastasis to cervical lymph nodes and to assess prediction of nodal metastasis by using molecular features.

EXPERIMENTAL DESIGN

We used Affymetrix U133 2.0 plus arrays to compare the tumor genome-wide gene expression of 73 node-positive OSCCs with 40 node-negative OSCCs (≥ 18 months). Multivariate linear regression was used to estimate the association between gene expression and nodal metastasis. Stepwise logistic regression and receiver operating characteristics (ROC) analysis were used to generate predictive models and to compare these with models by using tumor size alone.

RESULTS

We identified five genes differentially expressed between node-positive and node-negative OSCCs after adjusting for tumor size and human papillomavirus status: REEP1, RNF145, CTONG2002744, MYO5A, and FBXO32. Stepwise regression identified a four-gene model (MYO5A, RFN145, FBXO32, and CTONG2002744) as the most predictive of nodal metastasis. A leave-one-out ROC analysis revealed that our model had a higher area under the curve (AUC) for identifying occult nodal metastasis compared with that of a model by tumor size alone (respective AUC: 0.85 and 0.61; P = 0.011). A model combining tumor size and gene expression did not further improve the prediction of occult metastasis. Independent validation using 31 metastatic and 13 nonmetastatic cases revealed a significant underexpression of CTONG2002744 (P = 0.0004).

CONCLUSIONS

These results suggest that our gene expression markers of OSCC metastasis hold promise for improving current clinical practice. Confirmation by others and functional studies of CTONG2002744 is warranted.

The biopsied donor liver: incorporating macrosteatosis into high-risk donor assessment

To expand the donor liver pool, ways are sought to better define the limits of marginally transplantable organs. The Donor Risk Index (DRI) lists 7 donor characteristics, together with cold ischemia time and location of the donor, as risk factors for graft failure. We hypothesized that donor hepatic steatosis is an additional independent risk factor. We analyzed the Scientific Registry of Transplant Recipients for all adult liver transplants performed from October 1, 2003, through February 6, 2008, with grafts from deceased donors to identify donor characteristics and procurement logistics parameters predictive of decreased graft survival. A proportional hazard model of donor variables, including percent steatosis from higher-risk donors, was created with graft survival as the primary outcome. Of 21,777 transplants, 5051 donors had percent macrovesicular steatosis recorded on donor liver biopsy. Compared to the 16,726 donors with no recorded liver biopsy, the donors with biopsied livers had a higher DRI, were older and more obese, and a higher percentage died from anoxia or stroke than from head trauma. The donors whose livers were biopsied became our study group. Factors most strongly associated with graft failure at 1 year after transplantation with livers from this high-risk donor group were donor age, donor liver macrovesicular steatosis, cold ischemia time, and donation after cardiac death status. In conclusion, in a high-risk donor group, macrovesicular steatosis is an independent risk factor for graft survival, along with other factors of the DRI including donor age, donor race, donation after cardiac death status, and cold ischemia time.

Integrative analysis of DNA copy number and gene expression in metastatic oral squamous cell carcinoma identifies genes associated with poor survival

Background

Lymphotropism in oral squamous cell carcinoma (OSCC) is one of the most important prognostic factors of 5-year survival. In an effort to identify genes that may be responsible for the initiation of OSCC lymphotropism, we examined DNA copy number gains and losses and corresponding gene expression changes from tumor cells in metastatic lymph nodes of patients with OSCC.

Results

We performed integrative analysis of DNA copy number alterations (CNA) and corresponding mRNA expression from OSCC cells isolated from metastatic lymph nodes of 20 patients using Affymetrix 250 K Nsp I SNP and U133 Plus 2.0 arrays, respectively. Overall, genome CNA accounted for expression changes in 31% of the transcripts studied. Genome region 11q13.2-11q13.3 shows the highest correlation between DNA CNA and expression. With a false discovery rate < 1%, 530 transcripts (461 genes) demonstrated a correlation between CNA and expression. Among these, we found two subsets that were significantly associated with OSCC (n = 122) when compared to controls, and with survival (n = 27), as tested using an independent dataset with genome-wide expression profiles for 148 primary OSCC and 45 normal oral mucosa. We fit Cox models to calculate a principal component analysis-derived risk-score for these two gene sets ('122-' or '27-transcript PC'). The models combining the 122- or 27-transcript PC with stage outperformed the model using stage alone in terms of the Area Under the Curve (AUC = 0.82 or 0.86 vs. 0.72, with p = 0.044 or 0.011, respectively).

Conclusions

Genes exhibiting CNA-correlated expression may have biological impact on carcinogenesis and cancer progression in OSCC. Determination of copy number-associated transcripts associated with clinical outcomes in tumor cells with an aggressive phenotype (i.e., cells metastasized to the lymph nodes) can help prioritize candidate transcripts from high-throughput data for further studies.