Cardiorespiratory Fitness and Metabolic Syndrome in Postmenopausal African-American Women

We examined the association of cardiorespiratory fitness with metabolic syndrome in overweight/obese postmenopausal African-American women. Pooled baseline data on 170 African-American women from 2 exercise trials were examined. Metabolic syndrome was defined as at least 3 of the following: abdominal obesity, glucose intolerance, hypertension, low high-density lipoprotein cholesterol (HDL-C), and high triglycerides. Cardiorespiratory fitness (VO2peak) was determined using the Bruce treadmill protocol and categorized as: Very Low (VLCRF<18 mL·kg(-1) min(-1)), Low (LCRF=18.0-220-22-22.0 mL·kg(-1) min(-1)), and Moderate (MCRF>22.0 mL·kg(-1) min(-1)). Associations of metabolic syndrome with cardiorespiratory fitness were analyzed using one-way ANOVA and linear regression. VO2peak was significantly lower in the VLCRF compared to the MCRF group. Lower cardiorespiratory fitness was associated with higher prevalence of metabolic syndrome, abdominal obesity, hypertriglyceridemia, and low HDL among overweight/obese postmenopausal African-American women. In fully adjusted models, higher waist circumference and triglycerides were associated with lower VO2peak levels (P<0.01) and higher HDL-C was associated with higher VO2peak levels (P=0.03). Overweight/obese postmenopausal African-American women with very low cardiorespiratory fitness are more likely to have metabolic syndrome, higher body mass index, and unhealthier levels of certain metabolic syndrome components than women with moderate cardiorespiratory fitness.

Canine brain tumours: a model for the human disease?

Canine brain tumours are becoming established as naturally occurring models of disease to advance diagnostic and therapeutic understanding successfully. The size and structure of the dog's brain, histopathology and molecular characteristics of canine brain tumours, as well as the presence of an intact immune system, all support the potential success of this model. The limited success of current therapeutic regimens such as surgery and radiation for dogs with intracranial tumours means that there can be tremendous mutual benefit from collaboration with our human counterparts resulting in the development of new treatments. The similarities and differences between the canine and human diseases are described in this article, emphasizing both the importance and limitations of canines in brain tumour research. Recent clinical veterinary therapeutic trials are also described to demonstrate the areas of research in which canines have already been utilized and to highlight the important potential benefits of translational research to companion dogs.

Abstract P3-14-01: Molecular definition of the transition of ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC)

Background: Ductal carcinoma in situ (DCIS) is thought to be a precursor lesion to invasive ductal carcinoma and sometimes occurs in combination with invasive disease. However, the majority of DCIS lesions do not progress to invasive disease. To date no molecular markers have been identified that associate with the potential for development to invasive disease. Our work has sought to identify molecular markers that can be used to determine the likelihood of DCIS being associated with invasive disease. Identification of such markers could be of direct therapeutic benefit, since patients with a high likelihood of associated or subsequent invasive disease could be managed more aggressively.

Methods: We have compiled matched pairs, consisting of patients that have recurred with DCIS, compared to those who have DCIS plus invasive disease. Laser-capture microdissection was used to isolate in situ and invasive components of the latter, and in situ components of the former. We analyzed these samples by parallel cDNA-mediated Annealing, Selection, Extension, and Ligation (DASL) analysis of transcription, and DNA copy number analysis by resequencing. In addition, exome capture deep re-sequencing has been conducted on multiple cored in situ versus invasive components of DCIS from the same tumor sample.

Results: Gene expression analysis revealed candidate genes that were specific to DCIS and others that were expressed only in the adjacent invasive component of the tissue. These genes are currently being evaluated to identify interesting candidates. Additionally, we characterized the gene expression signatures from tumors that recurred as DCIS only, to the DCIS component of those tumors that recurred with adjacent invasive disease. We identified genes that were differentially expressed between these data sets.

The DNA copy number analysis of laser-captured samples indicated a single dominant clone in each DCIS. In contrast to previously reported observations, the profiles of invasive versus non-invasive lesions differ significantly from one another. Observations of non-invasive versus invasive components of adjacent disease in two of the pairs indicate that the profile of the invasive lesions differ from that of the non-invasive component, however the profiles share many individual features.

Discussion: Our data identify differences between in situ and neighboring invasive tumor that may mark features associated with progression. Integration of the copy number and transcription profiling datasets will reveal the extent to which genomic alterations drive changes in gene expression. Identification of markers that distinguish indolent and aggressive subsets of DCIS that can be used to predict an association with invasive disease has the potential for near term clinical utility and may identify therapeutic targets for aggressive DCIS.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-14-01.

Association of PTEN loss with outcome of patients (pts) with early high-risk prostate cancer (CaP) treated with adjuvant docetaxel following radical prostatectomy (RP)

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Background: Loss of the PTEN tumor suppressor and subsequent activation of the PI3K pathway is common and has potential clinical and therapeutic value in CaP. We examined the PTEN status of primary tumors in pts who underwent adjuvant docetaxel tx in a prospective clinical trial.

Methods: Of the 77 pts enrolled in a prospective multi-institutional adjuvant docetaxel trial (TAX 2501, J Urol 2007), we prospectively collected 56 primary tumor pathology specimens suitable for analysis of PTEN status by immunoreactivity (IHC) and/or fluorescence in situ hybridisation (FISH) assay. Protocol defined progression included a PSA of ≥ 0.4 ng/mL, radiological/pathological evidence of recurrent disease or death from any cause. Univariate and multivariable analyses based on the Cox proportional hazards regression model were used to analyze the independent association of PTEN and other known prognostic factors with progression free survival (PFS).

Results: PTEN loss was observed in 37/56 pts (66%). Pts with PTEN loss vs detectable PTEN were balanced regarding clinical stage, combined Gleason score, seminal vesicles and surgical margins involvement, and lymph nodes status. Pts with a detectable PTEN had a significantly higher pre-RP PSA (median 14 vs 8.6 ng/mL, p=0.015). 41/56 (73.2%, median followup of 37.5 months, range 10.4 to 44.5) progressed with an overall median PFS of 13 months (mos) (95% CI 9.8–15.8). Independent prognostic factors of progression by multivariate analysis were: seminal vesicles involvement (HR 2.19, p=0.024), combined Gleason score 9–10 (HR 2.46, p=0.027) and PTEN loss (HR 2.36, p=0.037). PFS on pts without PTEN loss (median not reached at a followup time of 37.5 mos, range 10.4–44.5 mos) was significantly longer (log rank test, p = 0.026) compared to those with undetectable PTEN (median PFS 12.9 mos, 95% CI 9.7–15.3).

Conclusions: PTEN loss may be an independent prognostic factor associated with poorer outcome of pts with early high-risk CaP treated with adjuvant docetaxel following RP. These findings may have important prognostic and therapeutic implications in CaP.

No significant financial relationships to disclose.

High Resolution Comparative Genomic Hybridization (CGH) Indicates That Genomic Profiles Are Very Heterogeneous for HER2 and TOP2A in FISH-Amplified Human Breast Cancer Specimens

Background: Clinical studies relating TOP2A and HER2 status by FISH and response to specific drug therapies, including anthracyclines, have yielded inconsistent results. The discordance across studies appears to reflect, in part, the well-documented limitations of FISH testing, including the use of large FISH probes to evaluate the relatively small genes of interest. However, it is also likely that the dichotomization of gene status into “amplified” or “non-amplified” categories inadequately describes complex changes across the gene areas of interest. Identification and delineation of specific amplification-deletion patterns in this region may be of significant clinical interest and could provide deeper insight into mechanisms of drug resistance. Consequently, we selected a subset of HER2 and TOP2A amplified specimens (by FISH) from an ongoing study of CGH, and examined individual amplification-deletion patterns by CGH.Methods: 471 consecutive, archived, formalin-fixed paraffin-embedded, &gt;1cm, HER2 2+ and 3+ by immunohistochemistry primary breast cancer specimens diagnosed between January 2000 and 2006 were selected. HER2 status was evaluated by FISH at MSKCC and CGH at Cold Spring Harbor Laboratory (CSHL) for all 471 specimens in a double-blinded experiment and clinical correlates evaluated. TOP2A status was also evaluated by FISH at MSKCC and CGH at CSHL in the subset of 64 HER2 2+ by IHC, HER2 FISH-positive specimens. Individual genome profiles by CGH were examined for 20 HER2 and TOP2A FISH co-amplified specimens.Results: 45 specimens had results available for analysis, 20 of which were amplified for both HER2 and TOP2A by FISH. By CGH: 6/20 (30%) were not amplified for HER2 or TOP2A; 4/20 (20%) had homogeneous amplification of HER2 and TOP2A; 8/20 (40%) had HER2 &gt; TOP2A amplification; and 2/20 (10%) had TOP2A &gt; HER2 amplification. Individual genome profiles around HER and TOP2A were examined by CGH. Marked heterogeneity was observed across specimens.Conclusions: CGH at the genome level suggests that current dichotomization strategies for classifying HER2 and TOP2A status appear to incompletely describe and represent the heterogeneity of genomic lability in these regions. The dichotomization of gene amplification results by FISH may contribute to the discordance demonstrated in reported some clinical studies. Studies exploring clinical correlates are underway.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3165.

Genome-Wide DNA Methylation Profiles of Breast Tumors Reveal Loci Associated with Relapse Risk

Background:Breast cancer prognosis is used in determining the course of adjuvant therapy for patients. Clinical prognostic indices like the Nottingham Prognostic Index have poor specificity, overestimate the risk of disease recurrence and necessitate more specific and robust prognostic markers. Prognostic gene expression markers are already in clinical use and show improved decision support. Methylation of CpG islands, an important regulator of gene expression, is reported to be disregulated in tumors, thus making methylation markers an important alternative to gene expression markers. We present the results of a genome-wide study that explored loci whose methylation status was significantly associated with recurrence risk.Methods:We used 108 frozen primary breast cancer specimens with ten year follow-up and extensive clinical data including histopathological measurements to identify potential epigenetic markers associated with recurrence risk. Using a previously validated array based method (Kamalakaran et. al., Nucleic Acids Research, 2009) we performed genome-wide measurements of differential CpG island methylation covering over 150,000 loci. We evaluated each locus for its ability to stratify patients into good or poor prognosis groups depending on its methylation status. Statistical significance was established using permutation analysis with appropriate multiple testing corrections. Prognostic markers independent of histopathological factors (ER, PR, HER2, tumor size, grade, node status, age) were identified using multivariate Cox regression analysis.Results:The methylation status of several loci proximal to genes significantly stratified samples independent of other clinical variables. Demethylation of several loci were associated with poor prognosis including ADAMTS4 (Hazard Ratio = 17.5, p-value&lt;&lt;0.001), a metalloproteinase previously implicated in the progression of glioma; DNA Topoisomerase I (HR = 3.81; 95% CI = 1.953-7.462; p&lt;&lt;0.001), implicated in chemotherapy resistance; and JMJD2C (HR = 3.7; 95% CI = 1.828-7.519; p&lt;&lt;0.001), which was found to be frequently amplified in esophageal cancers. The methylation of several loci also had significant association with poor prognosis, such as several members in the forkhead box family (FOXF1, FOXG1B, FOXJ1, FOXL2) and FHL1 (HR = 4.78; 95% CI = 2.38-9.62; p&lt;&lt;0.001). We selected several loci to form an ensemble classifier with statistically significant performance on our dataset. We show that this classifier achieved much higher specificity when compared to the Nottingham Prognostic Index, while maintaining high sensitivity.Discussion:Our retrospective study of genome-wide DNA methylation in breast cancer has identified several novel markers for prognosis. We found methylation deregulation of CpG islands proximal to genes implicated in metastasis and chemotherapy resistance is associated with poor prognosis. Furthermore, the potential for clinical benefit of these markers is their ability to jointly identify significantly larger number of low-risk patients compared to the Nottingham Prognostic Index.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4046.

Genome-Wide Profiling of Archived Material from CALGB 9840 and 9342 for Paclitaxel (P) and Trastuzumab (T) Response Biomarkers Using Gene Expression and Copy Number Analysis

Background:Emerging data suggest that RNA obtained from formalin-fixed, paraffin-embedded (FFPE) tissue can produce reliable gene expression profiles. Archived material from two taxane monotherapy studies, CALGB 9342 (comparison of 3 doses of P) and 9840 (weekly vs. q3 week P)were profiled for gene expression and DNA copy number.Methods: A total of 238 patients had primary tumor blocks available from a combined sample size of 680. DNA and RNA was extracted from 1.5mm punch cores and the Ambion Recover-All kit™. quality was measured by spectrophotometric analysis, Bioanalyzer RNA Integrity Number (RIN), and housekeeping genes (RPL13A and Actin). A custom DASL™ array containing 779 genes in two-fold redundancy was designed with genes selected to represent the PAM50 intrinsic subtypes, the Oncotype Dx Score, the Netherlands prognostic signature and the genes most frequently found on recurrent breast cancer amplicons. Several methods for identifying outliers were evaluated, including principal components analysis, pairwise correlations as well as the reproducibility of the platform based on replicate samples.Results: Adequate RNA was obtained from 237/238 of these cases which ranged in age from 12-18 years. Of these, 215/237DASL arrays passed further quality control measures. Adequate DNA for CGH was obtained from 227/238 samples. Analysis of PAM50 intrinsic subtypes showed an excess of basal-like tumors (30%) in the primary tumors of this metastatic cohort compared with expected frequency in an early stage population. Luminal A tumors were less frequent than expected (20%). Patients with basal-like tumors did far worse than other tumor types for both PFS on P (p=0.015) and OS (p=2.7X10-6), which persisted in multivariable analysis (p=0.0047), however the interaction term was not significant (Wald p=0.26). While basal-like tumors had similar PFS and OS on both weekly and q3 week P, luminal A tumors appear to achieve more benefit from weekly P (p= 0.0041).The HER2-enriched expression subtype had a similar prognosis to Luminal A and B tumors. This appeared to be due to the presence of T, as the addition of this agent improved PFS (p=0.026) and OS (p=2.0X10-4). Of note, some centrally confirmed HER2 FISH amplified tumors were classified into luminal A, B, and basal-like subtypes. These tumors have similar prognoses to the overall group, for example the basal-like and HER2 tumors had a poor prognosis despite T (p=0.00086). This suggests that HER2 FISH positive tumors may behave based on the underlying tumor subtype. Sawtooth genomes (45% vs 15%) were more frequent than predicted by an early stage tumor dataset as were simplex genomes (3% vs 24%). HER2 by FISH and CGH were highly concordant suggesting data on gene amplification from this platform is robust.Conclusions: Gene expression and copy number profiling of FFPE material from archived tumor blocks (&gt;10 years) produces quality data for biomarker discovery in CALGB clinical trial datasets. These tools allow discovery of novel patterns of gene expression and genomic aberrations that are associated with differential response to P and T. Further studies using these platforms should be performed.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4032.

Subtype Dependent Alterations of the DNA Methylation Landscape in Breast Cancer

Background: The diversity of breast cancers at the clinical, histopathological and molecular level reflects variation in underlying biology and affects the clinical implications for patients. Gene expression studies have identified five breast cancer subtypes with distinct expression profiles – Luminal A, Luminal B, basal, ErbB2 enriched and Normal-Like. DNA methylation is an important regulator of gene expression that is also known to be deregulated in tumors. We set out to determine the relationship between DNA methylation and breast cancer subtypes in 108 breast cancer samples with previously determined expression subtypes.Methods: We performed high-throughput genome-wide scans of CpG methylation in 108 tumors and 11 normal tissues using our previously validated Methylation Oligonucleotide Microarray Analysis (MOMA) method [Kamalakaran, S et al. Nucleic Acids Research, 2009)]. We identified loci that were most varied across all tumors or had the most significant alterations and performed unsupervised hierarchical clustering on those loci. We then used a genetic algorithm based feature selection method to identify a subset of those loci that could cluster the sample set by expression subtype. We then characterized the loci contributing to subsetting and where possible, the relationship between methylation and gene expression.Results: Unsupervised hierarchical clustering using the 500 most differentially methylated loci across all tumors and 100 most significant altered loci between tumors and Normal tissues clustered the tumors into 3 major clusters – 82% of Cluster I belonged to Luminal Subtypes (22 Luminal A and 4 Luminal B), and 86% of Cluster II samples were of Basal or ErbB2+ subtypes. Cluster III did not show any expression subtype specific enrichment, but contained samples whose expression subtype was inconclusive with weak correlations to multiple expression subtypes. Interestingly, methylation loci that contributed to this clustering were not localized to CpG islands immediately upstream of genes, with 354 loci far from gene transcription start sites. These non-geneic loci did not show any significant regulatory potential based on cross-species conservation measures and no clear function could be assigned to these regions. The remaining 146 loci could be mapped to known genes. Gene expression microarray measurements were available for 79 of these geneic loci and 36 showed significant correlation of methylation to expression levels (p&lt;0.05), implying possible functional effects of the methylation on gene expression. Additionally, distinct subtype specific patterns of methylation could also be detected in known cancer associated genes. CpG islands in the HOXA gene cluster and many other homeobox genes were significantly more methylated in Luminal A tumors.Conclusions: Our results suggest that there are subtype dependant genome-wide alterations in the methylation landscape in breast cancers, especially near homeobox genes. Many more CpG islands with no apparent functional significance get methylated according to subtype in addition to those CpG islands associated with genes with known cancer related functions.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 1144.

First direct observation of a nearly ideal graphene band structure

Angle-resolved photoemission and x-ray diffraction experiments show that multilayer epitaxial graphene grown on the SiC(0001) surface is a new form of carbon that is composed of effectively isolated graphene sheets. The unique rotational stacking of these films causes adjacent graphene layers to electronically decouple leading to a set of nearly independent linearly dispersing bands (Dirac cones) at the graphene K point. Each cone corresponds to an individual macroscale graphene sheet in a multilayer stack where AB-stacked sheets can be considered as low density faults.

Multiple ganglion cysts (‘cystic ganglionosis’): an unusual presentation in a child

A case of multifocal and recurrent ganglion cysts is described. An 11-year-old boy was referred because of symptomatic cystic masses in the extremities since the age of 2 years. Over the years, he had experienced intermittent appearance of these lesions, which were associated with pain, but without any systemic manifestations. Magnetic resonance imaging (MRI) showed cystic lesions with synovio-capsular thickening along the temporomandibular joints (TMJ), atlanto-axial synovial articulation, and tendons and joints of the right wrist and hand. Histopathological examination of one lesion showed anastomosing fibro-connective tissue surrounded by a wall of smooth muscle and fibrous connective tissue, findings that were consistent with ganglion cyst. The early onset of the disease, as well as the involvement of multiple and unusual sites, including the TMJ, implies a genetic susceptibility to these lesions that we refer to as 'cystic ganglionosis'.