Molecular classification of breast carcinoma in situ

A Data Mining Approach to Predict In Situ Detoxification Potential of Chlorinated Ethenes

Despite advances in physicochemical remediation technologies, in situ bioremediation treatment based on Dehalococcoides mccartyi (Dhc) reductive dechlorination activity remains a cornerstone approach to remedy sites impacted with chlorinated ethenes. Selecting the best remedial strategy is challenging due to uncertainties and complexity associated with biological and geochemical factors influencing Dhc activity. Guidelines based on measurable biogeochemical parameters have been proposed, but contemporary efforts fall short of meaningfully integrating the available information. Extensive groundwater monitoring data sets have been collected for decades, but have not been systematically analyzed and used for developing tools to guide decision-making. In the present study, geochemical and microbial data sets collected from 35 wells at five contaminated sites were used to demonstrate that a data mining prediction model using the classification and regression tree (CART) algorithm can provide improved predictive understanding of a site's reductive dechlorination potential. The CART model successfully predicted the 3-month-ahead reductive dechlorination potential with 75.8% and 69.5% true positive rate (i.e., sensitivity) for the training set and the test set, respectively. The machine learning algorithm ranked parameters by relative importance for assessing in situ reductive dechlorination potential. The abundance of Dhc 16S rRNA genes, CH4, Fe(2+), NO3(-), NO2(-), and SO4(2-) concentrations, total organic carbon (TOC) amounts, and oxidation-reduction potential (ORP) displayed significant correlations (p < 0.01) with dechlorination potential, with NO3(-), NO2(-), and Fe(2+) concentrations exhibiting precedence over other parameters. Contrary to prior efforts, the power of data mining approaches lies in the ability to discern synergetic effects between multiple parameters that affect reductive dechlorination activity. Overall, these findings demonstrate that data mining techniques (e.g., machine learning algorithms) effectively utilize groundwater monitoring data to derive predictive understanding of contaminant degradation, and thus have great potential for improving decision-making tools. A major need for realizing the predictive capabilities of data mining approaches is a curated, open-access, up-to-date and comprehensive collection of biogeochemical groundwater monitoring data.

UK national survey of management of breast lobular carcinoma in situ

INTRODUCTION

There is no national standard treatment for patients with breast lobular carcinoma in situ (LCIS). Association of Breast Surgery guidelines for the management of breast cancer suggest that lesions containing LCIS should be excised for definitive diagnosis and recommend close surveillance after excision biopsy. The aim of this study was to form a picture of the current management of LCIS by UK breast surgeons.

METHODS

A questionnaire about the management of LCIS was sent to 490 UK breast surgeons.

RESULTS

Of 490 questionnaires sent out, 173 (35%) were returned. When LCIS is present in a core biopsy, 61% of breast surgeons perform surgical excision, 22% would not excise but would continue follow-up and the remainder perform neither or set no clear management plan. Over half (54%) follow patients up with five years of annual mammography. If classic LCIS were found at the margins of wide local excision, 92% would not re-excise. Conversely, if pleomorphic LCIS were found, 71% would achieve clear margins. Respondents were split evenly regarding management of classic LCIS with a family history as 54% would not alter management whereas 43% would treat the disease more aggressively.

CONCLUSIONS

Our survey has shown that in cases where LCIS is found at core biopsy, most surgeons follow Association of Breast Surgery guidance, obtaining further histological samples to exclude pleomorphic LCIS, ductal carcinoma in situ or invasive cancer, whereas others opt for annual surveillance and some discharge the patient. This study highlighted the huge variability in LCIS management, and the need for randomised controlled trials and input into national audits such as the Sloane Project to establish evidence-based national standard guidelines.

Delineating an epigenetic continuum for initiation, transformation and progression to breast cancer

Aberrant methylation of promoter CpG islands is a hallmark of human cancers and is an early event in carcinogenesis. We examined whether promoter hypermethylation contributes to the pathogenesis of benign breast lesions along a progression continuum to invasive breast cancer. The exploratory study cohort comprised 17 breast cancer patients with multiple benign and/or in situ lesions concurrently present with invasive carcinoma within a tumor biopsy. DNA from tumor tissue, normal breast epithelium when present, benign lesions (fibroadenoma, hyperplasia, papilloma, sclerosing adenosis, apocrine metaplasia, atypical lobular hyperplasia or atypical ductal hyperplasia), and in situ lesions of lobular carcinoma and ductal carcinoma were interrogated for promoter methylation status in 22 tumor suppressor genes using the multiplex ligation-dependent probe amplification assay (MS-MLPA). Methylation specific PCR was performed to confirm hypermethylation detected by MS-MLPA. Promoter methylation was detected in 11/22 tumor suppressor genes in 16/17 cases. Hypermethylation of RASSF1 was most frequent, present in 14/17 cases, followed by APC in 12/17, and GSTP1 in 9/17 cases with establishment of an epigenetic monocloncal progression continuum to invasive breast cancer. Hypermethylated promoter regions in normal breast epithelium, benign, and premalignant lesions within the same tumor biopsy implicate RASSF1, APC, GSTP1, TIMP3, CDKN2B, CDKN2A, ESR1, CDH13, RARB, CASP8, and TP73 as early events. DNA hypermethylation underlies the pathogenesis of step-wise transformation along a monoclonal continuum from normal to preneoplasia to invasive breast cancer.

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.

Malignant and nonmalignant gene signatures in squamous head and neck cancer

Genetic events specific to the pathogenesis of malignancy can offer clues to the tumorigenesis process. The objective of this study was to identify gene alterations that differentiate tumor and nontumor lesions in squamous head and neck cancer (HNSCC). DNA from 220 primary HNSCC with concurrently present tumor and nontumor lesions from the same patient was interrogated for genomic alterations of loss or gain of copy. Conditional logistic regression dealt with tumor and non-tumor records within a patient. Of 113 genes, 53 had univariate effects (P < 0.01), of which 16 genes remained in the multivariable model with P < 0.01. The model had a C-index (ROC) of 0.93. Loss of CDKN2B and gain of BCL6, FGF3, and PTP4A3 predicted tumor. Loss of BAK1 and CCND1 and gain of STCH predicted nontumor. This highly powered model assigned alterations in 16 genes specific for malignant versus nonmalignant lesions, supporting their contribution to the pathogenesis of HNSCC as well as their potential utility as relevant targets for further evaluation as markers of early detection and progression.

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.

Lobular neoplasia: morphology, biological potential and management in core biopsies

Lobular neoplasia has been traditionally recognized as a marker of increased risk for subsequent breast carcinoma development; however, molecular studies suggest that it also behaves in a non-obligate precursor manner. We do not know, as yet, how to identify the subgroup of cases that is most likely to progress, but the epidemiological data would indicate that this progression occurs after a long period of time. Thus, the current approach of conservative management of these lesions when identified in excision specimens is justified. Recently, several variants of lobular carcinoma in situ (LCIS), most notably pleomorphic LCIS, have been recognized and these can be difficult to differentiate from ductal carcinoma in situ. Application of strict diagnostic criteria and the judicial use of immunohistochemistry, particularly E-cadherin, can be helpful in this differential diagnosis. Another challenging issue is the management of lobular neoplasia when diagnosed on core biopsy. This controversial issue will be discussed in detail. The goals of this review are (1) to describe the morphological criteria used to diagnose the spectrum of lobular neoplastic lesions, including atypical lobular hyperplasia, LCIS and variants of LCIS; (2) to discuss the data exploring the biological potential of lobular neoplasia from an epidemiological and molecular viewpoint; and (3) to outline the recommendations for management of lobular neoplasia when encountered in core biopsies.

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.

Aurora A, centrosome structure, and the centrosome cycle

The centrosome, also known as the microtubule organizing center of the cell, is a membrane-less organelle composed of a pair of barrel-shaped centrioles surrounded by electron-dense pericentriolar material. The centrosome progresses through the centrosome cycle in step with the cell cycle such that centrosomes are duplicated in time to serve as the spindle poles during mitosis and that each resultant daughter cell contains a single centrosome. Regulation of the centrosome cycle with relation to the cell cycle is an essential process to maintain the ratio of one centrosome per new daughter cell. Numerous mitosis-specific kinases have been implicated in this regulation, and phosphorlyation plays an important role in coordinating the centrosome and cell cycles. Centrosome amplification can occur when the cycles are uncoupled, and this amplification is associated with cancer and with an increase in the levels of chromosomal instability. The aurora kinases A, B, and C are serine/threonine kinases that are active during mitosis. Aurora A is associated with centrosomes, being localized at the centrosome just prior to the onset of mitosis and for the duration of mitosis. Overexpression of aurora A leads to centrosome amplification and cellular transformation. The activity of aurora A is regulated by phosphorlyation and proteasomal degradation.

Noninvasive molecular detection of head and neck squamous cell carcinoma: an exploratory analysis

BACKGROUND

Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease evolving through multistep carcinogenesis, one of the steps being genetic alterations. Noninvasive identification of HNSCC-specific genetic alterations using saliva would have immense potential in early diagnosis and screening, particularly among high-risk patients.

DESIGN

In this exploratory study, a prospective cohort of 27 HNSCC and 10 healthy controls was examined to determine whether genetic alterations (losses and gains) in saliva DNA differentiated HNSCC patients from normal controls. Saliva DNA was interrogated by a candidate gene panel comprising 82 genes using the multiplex ligation-dependent probe amplification assay.

RESULTS

Eleven genes showed some predictive ability in identifying HNSCC cases from normal controls: PMAIP1, PTPN1, ERBB2, ABCC4, UTY, DNMT1, CDKN2B, CDKN2D, NFKB1, TP53, and DCC. Statistical analysis using the Classification and Regression Tree (CART) identified 2 genes, PMAIP1 and PTPN1, which correctly discriminated all 27 HNSCC patients (100%) from normal controls. Results were validated using the leave-one-out validation approach.

CONCLUSIONS

Noninvasive high-throughput multiplex ligation-dependent probe amplification identified discrete gene signatures that differentiated HNSCC patients from normal controls providing proof-of-concept for noninvasive HNSCC detection.

Molecular differentiation of early and late stage laryngeal squamous cell carcinoma: an exploratory analysis

BACKGROUND

A current shortcoming in cancer prognostication and treatment is a lack of methods that adequately address the complexity and diversity of the disease. Prognostic marker systems based on single parameters have generally proven inadequate. Thus, multiparametric methods, which rely on many pieces of information, are ideally suited to the grouping of tumor subtypes and the identification of specific patterns of disease progression.

DESIGN

This study investigated, on an exploratory basis, whether genome wide alterations of loss and gain, using a panel of 122 gene probes (112 unique genes), discriminated between early stage (stage 1 and 2) and late stage (stage 3 and 4) laryngeal squamous cell carcinomas (LSCC). The LSCC cohort comprised 29 patients, 12 early and 17 late staged. Formalin-fixed LSCC DNA was interrogated by a genome wide candidate gene panel (122 genes) using the multiplex ligation-dependent probe amplification assay.

RESULTS

Statistical analysis employed the nonparametric Wilcoxon 2-sample test. Significant differences between tumor stages of early versus late were seen for the following genes: ERBB4, CASP2, RECQL4, and BCL7A. Loss of ERBB4 (P=0.045) and BCL7A (P=0.019) significantly discriminated between early and late stage LSCC. Gain of RECQL4 copy number (P=0.043) was associated with late LSCC. Gain of CASP2 (P=0.043) marked early LSCC, whereas loss was associated with late LSCC.

CONCLUSIONS

High-throughput genome wide approaches have the potential to yield discrete gene repertoires of early and late stage LSCC differentiation.

Epigenetic events underlie the pathogenesis of sinonasal papillomas

Benign inverted papillomas have been reported as monoclonal but lacking common genetic alterations identified in squamous cell carcinoma of the head and neck. Epigenetic changes alter the heritable state of gene expression and chromatin organization without change in DNA sequence. We investigated whether epigenetic events of aberrant promoter hypermethylation in genes known to be involved in squamous head and neck cancer underlie the pathogenesis of sinonasal papillomas. Ten formalin-fixed paraffin DNA samples from three inverted papilloma cases, two exophytic (everted) papilloma cases, and two cases with inverted and exophytic components were studied. DNA was obtained from microdissected areas of normal and papilloma areas and examined using a panel of 41 gene probes, designed to interrogate 35 unique genes for aberrant methylation status (22 genes) using the methylation-specific multiplex-ligation-specific polymerase assay. Methylation-specific PCR was employed to confirm aberrant methylation detected by the methylation-specific multiplex-ligation-specific polymerase assay. All seven cases indicated at least one epigenetic event of aberrant promoter hypermethylation. The CDKN2B gene was a consistent target of aberrant methylation in six of seven cases. Methylation-specific PCR confirmed hypermethylation of CDKN2B. Recurrent biopsies from two inverted papilloma cases had common epigenetic events. Promoter hypermethylation of CDKN2B was a consistent epigenetic event. Common epigenetic alterations in recurrent biopsies underscore a monoclonal origin for these lesions. Epigenetic events contribute to the underlying pathogenesis of benign inverted and exophytic papillomas. As a consistent target of aberrant promoter hypermethylation, CDKN2B may serve as an important epigenetic biomarker for gene reactivation studies.