Digital Commons Network^™

Survival Associated Pathway Identification With Group Lp Penalized Global Auc Maximization., Zhenqiu Liu, Laurence S Magder, Terry Hyslop, Li Mao

Department of Pharmacology and Experimental Therapeutics Faculty Papers

It has been demonstrated that genes in a cell do not act independently. They interact with one another to complete certain biological processes or to implement certain molecular functions. How to incorporate biological pathways or functional groups into the model and identify survival associated gene pathways is still a challenging problem. In this paper, we propose a novel iterative gradient based method for survival analysis with group Lp penalized global AUC summary maximization. Unlike LASSO, Lp (p < 1) (with its special implementation entitled adaptive LASSO) is asymptotic unbiased and has oracle properties 1. We first extend Lp for individual gene identification to group Lp penalty for pathway selection, and then develop a novel iterative gradient algorithm for penalized global AUC summary maximization (IGGAUCS). This method incorporates the genetic pathways into global AUC summary maximization and identifies survival associated pathways instead of individual genes. The tuning parameters are determined using 10-fold cross validation with training data only. The prediction performance is evaluated using test data. We apply the proposed method to survival outcome analysis with gene expression profile and identify multiple pathways simultaneously. Experimental results with simulation and gene expression data demonstrate that the proposed procedures can be used for identifying important biological pathways that are related to survival phenotype and for building a parsimonious model for predicting the survival times.

The Marine Sponge Metabolite Mycothiazole: A Novel Prototype Mitochondrial Complex I Inhibitor., J Brian Morgan, Fakhri Mahdi, Yang Liu, Veena Coothankandaswamy, Mika B. Jekabsons, Tyler A. Johnson, Koneni V. Sashidhara, Phillip Crews, Dale G. Nagle, Yu-Dong Zhou

Natural Sciences and Mathematics | Faculty Scholarship

A natural product chemistry-based approach was applied to discover small-molecule inhibitors of hypoxia-inducible factor-1 (HIF-1). A Petrosaspongia mycofijiensis marine sponge extract yielded mycothiazole (1), a solid tumor selective compound with no known mechanism for its cell line-dependent cytotoxic activity. Compound 1 inhibited hypoxic HIF-1 signaling in tumor cells (IC(50) 1nM) that correlated with the suppression of hypoxia-stimulated tumor angiogenesis in vitro. However, 1 exhibited pronounced neurotoxicity in vitro. Mechanistic studies revealed that 1 selectively suppresses mitochondrial respiration at complex I (NADH-ubiquinone oxidoreductase). Unlike rotenone, MPP(+), annonaceous acetogenins, piericidin A, and other complex I inhibitors, mycothiazole is a mixed polyketide/peptide-derived compound …

Thinking Outside The Curve, Part Ii: Modeling Fetal-Infant Mortality, Richard Charnigo, Lorie W. Chesnut, Tony Lobianco, Russell S. Kirby

Statistics Faculty Publications

BACKGROUND: Greater epidemiologic understanding of the relationships among fetal-infant mortality and its prognostic factors, including birthweight, could have vast public health implications. A key step toward that understanding is a realistic and tractable framework for analyzing birthweight distributions and fetal-infant mortality. The present paper is the second of a two-part series that introduces such a framework.

METHODS: We propose estimating birthweight-specific mortality within each component of a normal mixture model representing a birthweight distribution, the number of components having been determined from the data rather than fixed a priori.

RESULTS: We address a number of methodological issues related to our …

S-Glutathionylation Activates Stim1 And Alters Mitochondrial Homeostasis., Brian J Hawkins, Krishna M Irrinki, Karthik Mallilankaraman, Yu-Chin Lien, Youjun Wang, Cunnigaiper D Bhanumathy, Ramasamy Subbiah, Michael F Ritchie, Jonathan Soboloff, Yoshihiro Baba, Tomohiro Kurosaki, Suresh K Joseph, Donald L Gill, Muniswamy Madesh

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Oxidant stress influences many cellular processes, including cell growth, differentiation, and cell death. A well-recognized link between these processes and oxidant stress is via alterations in Ca(2+) signaling. However, precisely how oxidants influence Ca(2+) signaling remains unclear. Oxidant stress led to a phenotypic shift in Ca(2+) mobilization from an oscillatory to a sustained elevated pattern via calcium release-activated calcium (CRAC)-mediated capacitive Ca(2+) entry, and stromal interaction molecule 1 (STIM1)- and Orai1-deficient cells are resistant to oxidant stress. Functionally, oxidant-induced Ca(2+) entry alters mitochondrial Ca(2+) handling and bioenergetics and triggers cell death. STIM1 is S-glutathionylated at cysteine 56 in response to …

Growth, Immune And Viral Responses In Hiv Infected African Children Receiving Highly Active Antiretroviral Therapy: A Prospective Cohort Study., Philippa M. Musoke, Peter Mudiope, Linda N. Barlow-Mosha, Patrick Ajuna, Danstan Bagenda, Michael M. Mubiru, Thorkild Tylleskar, Mary G. Fowler

Journal Articles: Epidemiology

BACKGROUND: Scale up of paediatric antiretroviral therapy in resource limited settings continues despite limited access to routine laboratory monitoring. We documented the weight and height responses in HIV infected Ugandan children on highly active antiretroviral therapy and determined clinical factors associated with successful treatment outcomes.

METHODS: A prospective cohort of HIV infected children were initiated on HAART and followed for 48 weeks. Body mass index for age z scores(BAZ), weight and height-for-age z scores (WAZ & HAZ) were calculated: CD4 cell % and HIV-1 RNA were measured at baseline and every 12 weeks. Treatment outcomes were classified according to; both …

Harnessing The Effect Of Adoptively Transferred Tumor-Reactive T Cells On Endogenous (Host-Derived) Antitumor Immunity, Yolanda Nesbeth, Jose R. Conejo-Garcia

Dartmouth Scholarship

Adoptive T cell transfer therapy, the ex vivo activation, expansion, and subsequent administration of tumor-reactive T cells, is already the most effective therapy against certain types of cancer. However, recent evidence in animal models and clinical trials suggests that host conditioning interventions tailored for some of the most aggressive and frequent epithelial cancers will be needed to maximize the benefit of this approach. Similarly, the subsets, stage of differentiation, and ex vivo expansion procedure of tumor-reactive T cells to be adoptively transferred influence their in vivo effectiveness and may need to be adapted for different types of cancer and host …

Diaphragm Weakness And Mechanical Ventilation – What's The Critical Issue?, Leigh Ann Callahan, Gerald S. Supinski

Internal Medicine Faculty Publications

While animal studies indicate that controlled mechanical ventilation (MV) induces diaphragm weakness and myofiber atrophy, there are no data in humans that confirm MV per se produces diaphragm weakness. Whether or not diaphragm weakness results from MV, sepsis, corticosteroids, hyperglycemia, or a combination of these factors, however, is not the most important issue raised by the recent study from Hermans and colleagues. This study makes an important contribution by providing additional evidence that many critically ill patients have profound diaphragm weakness. If diaphragm weakness of this magnitude is present in most mechanically ventilated patients, a strong argument can be made …

Cross-Reactivity Of Antibodies Against Leptospiral Recurrent Uveitis-Associated Proteins A And B (Lrua And Lrub) With Eye Proteins, Ashutosh Verma, Pawan Kumar, Kelly Babb, John F. Timoney, Brian Stevenson

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Infection by Leptospira interrogans has been causally associated with human and equine uveitis. Studies in our laboratories have demonstrated that leptospiral lipoprotein LruA and LruB are expressed in the eyes of uveitic horses, and that antibodies directed against LruA and LruB react with equine lenticular and retinal extracts, respectively. These reactivities were investigated further by performing immunofluorescent assays on lenticular and retinal tissue sections. Incubation of lens tissue sections with LruA-antiserum and retinal sections with LruB-antiserum resulted in positive fluorescence. By employing two-dimensional gel analyses followed by immunoblotting and mass spectrometry, lens proteins cross-reacting with LruA antiserum were identified to …

Hyperpolarized (3)He Magnetic Resonance Imaging-Derived Pulmonary Pressure-Volume Curves, Stephen Choy, Andrew Wheatley, David G Mccormack, Grace Parraga

Medical Biophysics Publications

We aimed to evaluate the potential for the use of hyperpolarized helium-3 magnetic resonance imaging (MRI) apparent diffusion coefficient (ADC) surrogates of alveolar size, together with literature-based morphological parameters in a theoretical model of lung mechanics to simulate noninvasive transpulmonary pressure-volume curves. Fourteen ex-smokers with chronic obstructive pulmonary disease (COPD) (n = 8 stage II, n = 6 stage III/IV COPD) and five age-matched never-smokers, provided written, informed consent and were evaluated at baseline and 26 + or - 2 mo later (n = 15 subjects) using plethysmography, spirometry, and (3)He MRI at 3.0 T. Total lung capacity, residual volume, …

Asian Race/Ethnicity As A Risk Factor For Bile Duct Injury During Cholecystectomy., Stephanie R. Downing, Ghazala Datoo, Tolulope A. Oyetunji, Terrence Fullum, David C. Chang, Nita Ahuja

Manuscripts, Articles, Book Chapters and Other Papers

Iatrogenic bile duct injury (BDI) is an uncommon but serious complication of cholecystectomy, with identified risk factors of acute cholecystitis, male sex, older age, and aberrant biliary anatomy. The Nationwide Inpatient Sample (1998-2006) was queried for cholecystectomy performed on hospital day 0 or 1. Bile duct injury repair procedure codes were used as a surrogate for BDI. We identified 377,424 patients who underwent cholecystectomy, with 1124 BDIs (0.3%). On multivariate logistic regression analysis, Asian race/ethnicity was a significant risk factor for BDI (odds ratio [OR], 2.26; 95% confidence interval [CI], 1.59-3.23; P < .001). This persisted for laparoscopic (OR, 2.62; 95% CI, 1.28-5.39; P = .009) and open (2.21; 1.59-3.07; P < .001) cholecystectomies. No other race/ethnicity was identified as a risk factor for BDI. We report a new finding that Asian race/ethnicity is a significant risk factor for BDI in laparoscopic and open cholecystectomies.

A Smac Mimetic Reduces Tnf Related Apoptosis Inducing Ligand (Trail)-Induced Invasion And Metastasis Of Cholangiocarcinoma Cells., Christian D. Fingas, Boris R.A. Blechacz, Rory L. Smoot, Maria E. Guicciardi, Justin L. Mott, Steve F. Bronk, Nathan W. Werneburg, Alphonse E. Sirica, Gregory J. Gores

Journal Articles: Biochemistry & Molecular Biology

UNLABELLED: Cholangiocarcinoma (CCA) cells paradoxically express tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), a death ligand that, failing to kill CCA cells, instead promotes their tumorigenicity and especially the metastatic behaviors of cell migration and invasion. Second mitochondria-derived activator of caspase (smac) mimetics are promising cancer therapeutic agents that enhance proapoptotic death receptor signaling by causing cellular degradation of inhibitor of apoptosis (IAP) proteins. Our aim was to examine the in vitro and in vivo effects of the smac mimetic JP1584 in CCA. Despite JP1584-mediated loss of cellular inhibitor of apoptosis-1 (cIAP-1) and cIAP-2, TRAIL failed to induce apoptosis in KMCH-1, …

Distribution Of Left Ventricular Ejection Fraction In Angina Patients With Severe Coronary Artery Disease Not Amenable To Revascularization., Shuchita Gupta, Gregg S. Pressman, D Lynn Morris, Vincent M. Figueredo, M.D.

Division of Cardiology Faculty Papers

BACKGROUND: As the number of angina patients with severe coronary artery disease not amenable to revascularization increases, new therapies will be developed. How patients with depressed compared to normal left ventricular ejection fraction (LVEF) will respond to new therapies may differ.

HYPOTHESIS: We conducted a retrospective chart review to determine the distribution of LVEF in angina patients with severe coronary artery disease (three-vessel disease with >50% stenosis major epicardial vessels or >50% stenosis left main) not amenable to revascularization.

METHODS: Patients underwent cardiac catheterization between 2004 and 2009. LVEF, measured by echocardiography, nuclear-gated imaging or radioventriculography within 6 months of …

The Perils Of The Imperfect Expectation Of The Perfect Baby., Frank A Chervenak, Laurence B Mccullough, Robert L Brent

Department of Pediatrics Faculty Papers

Advances in modern medicine invite the assumption that medicine can control human biology. There is a perilous logic that leads from expectations of medicine's control over reproductive biology to the expectation of having a perfect baby. This article proposes that obstetricians should take a preventive ethics approach to the care of pregnant women with expectations for a perfect baby. We use Nathaniel Hawthorne's classic short story, "The Birthmark," to illustrate the perils of the logic of control and perfection through science and then identify possible contemporary sources of the expectation of the perfect baby. We propose that the informed consent …

Meditation Acutely Improves Psychomotor Vigilance, And May Decrease Sleep Need, Prashant Kaul, Jason Passafiume, Craig R. Sargent, Bruce F. O'Hara

Biology Faculty Publications

BACKGROUND: A number of benefits from meditation have been claimed by those who practice various traditions, but few have been well tested in scientifically controlled studies. Among these claims are improved performance and decreased sleep need. Therefore, in these studies we assess whether meditation leads to an immediate performance improvement on a well validated psychomotor vigilance task (PVT), and second, whether longer bouts of meditation may alter sleep need.

METHODS: The primary study assessed PVT reaction times before and after 40 minute periods of mediation, nap, or a control activity using a within subject cross-over design. This study utilized novice …

Multiple Mechanisms Of Consciousness: The Neural Correlates Of Emotional Awareness., Jayna M Amting, Steven G Greening, Derek G V Mitchell

Brain and Mind Institute Researchers' Publications

Emotional stimuli, including facial expressions, are thought to gain rapid and privileged access to processing resources in the brain. Despite this access, we are conscious of only a fraction of the myriad of emotion-related cues we face everyday. It remains unclear, therefore, what the relationship is between activity in neural regions associated with emotional representation and the phenomenological experience of emotional awareness. We used functional magnetic resonance imaging and binocular rivalry to delineate the neural correlates of awareness of conflicting emotional expressions in humans. Behaviorally, fearful faces were significantly more likely to be perceived than disgusted or neutral faces. Functionally, …

Thinking Outside The Curve, Part I: Modeling Birthweight Distribution, Richard Charnigo, Lorie W. Chesnut, Tony Lobianco, Russell S. Kirby

Statistics Faculty Publications

BACKGROUND: Greater epidemiologic understanding of the relationships among fetal-infant mortality and its prognostic factors, including birthweight, could have vast public health implications. A key step toward that understanding is a realistic and tractable framework for analyzing birthweight distributions and fetal-infant mortality. The present paper is the first of a two-part series that introduces such a framework.

METHODS: We propose describing a birthweight distribution via a normal mixture model in which the number of components is determined from the data using a model selection criterion rather than fixed a priori.

RESULTS: We address a number of methodological issues, including how the …

Enalapril In Infants With Single Ventricle: Results Of A Multicenter Randomized Trial., Daphne T. Hsu, Victor Zak, Lynn Mahony, Lynn A. Sleeper, Andrew M. Atz, Jami C. Levine, Piers C. Barker, Chitra Ravishankar, Brian W. Mccrindle, Richard V. Williams, Karen Altmann, Nancy S. Ghanayem, Renee Margossian, Wendy K. Chung, William L. Border, Gail D. Pearson, Mario P. Stylianou, Seema Mital, Pediatric Heart Network Investigators, Girish S. Shirali

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Angiotensin-converting enzyme inhibitor therapy improves clinical outcome and ventricular function in adults with heart failure. Infants with single-ventricle physiology have poor growth and are at risk for abnormalities in ventricular systolic and diastolic function. The ability of angiotensin-converting enzyme inhibitor therapy to preserve ventricular function and improve somatic growth and outcomes in these infants is unknown.

METHODS AND RESULTS: The Pediatric Heart Network conducted a double-blind trial involving 230 infants with single-ventricle physiology randomized to receive enalapril (target dose 0.4 mg . kg(-1) . d(-1)) or placebo who were followed up until 14 months of age. The primary end …

Distorting The Sarcomere, Kenneth S. Campbell

Physiology Faculty Publications

No abstract provided.

Density Estimation And Adaptive Bandwidths: A Primer For Public Health Practitioners, Heather A. Carlos, Xun Shi, James Sargent, Susanne Tanski, Ethan M. Berke

Dartmouth Scholarship

Background: Geographic information systems have advanced the ability to both visualize and analyze point data. While point-based maps can be aggregated to differing areal units and examined at varying resolutions, two problems arise 1) the modifiable areal unit problem and 2) any corresponding data must be available both at the scale of analysis and in the same geographic units. Kernel density estimation (KDE) produces a smooth, continuous surface where each location in the study area is assigned a density value irrespective of arbitrary administrative boundaries. We review KDE, and introduce the technique of utilizing an adaptive bandwidth to address the …

Deltanp63 Transcriptionally Regulates Atm To Control P53 Serine-15 Phosphorylation., Ashley L. Craig, Jitka Holcakova, Lee E. Finlan, Marta Nekulova, Roman Hrstka, Nuri Gueven, James Direnzo, Graeme Smith, Ted R. Hupp, Borivoj Vojtesek

Dartmouth Scholarship

Background: ΔNp63α is an epithelial progenitor cell marker that maintains epidermal stem cell self-renewal capacity. Previous studies revealed that UV-dam age induced p53 phosphorylation is confined to ΔNp63α-positive cells in the basal layer of human epithelium. Results: We now report that phosphorylatio n of the p53 tumour suppressor is po sitively regulated by ΔNp63α in immortalised human keratinocytes. ΔNp63α depletion by RNAi reduces steady-state ATM mRNA and protein levels, and attenuates p53 Serine-15 phosphorylation. Conversely, ectopic expression of ΔNp63α in p63-null tumour cells stimulates ATM transcription and p53 Seri ne-15 phosphorylation. We show that AT M is a …

Passive Transfer Of Igg Anti-Gm1 Antibodies Impairs Peripheral Nerve Repair, Pablo H Lopez, Gang Zhang, Jiangyang Zhang, Helmar C Lehmann, John W Griffin, Ronald L Schnaar, Kazim A Sheikh

Faculty, Staff and Student Publications

Anti-GM1 antibodies are present in some patients with autoimmune neurological disorders. These antibodies are most frequently associated with acute immune neuropathy called Guillain-Barré syndrome (GBS). Some clinical studies associate the presence of these antibodies with poor recovery in GBS. The patients with incomplete recovery have failure of nerve repair, particularly axon regeneration. Our previous work indicates that monoclonal antibodies can inhibit axon regeneration by engaging cell surface gangliosides (Lehmann et al., 2007). We asked whether passive transfer of human anti-GM1 antibodies from patients with GBS modulate axon regeneration in an animal model. Human anti-GM1 antibodies were compared with other GM1 …

Vestibular Heading Discrimination And Sensitivity To Linear Acceleration In Head And World Coordinates, Paul R. Macneilage, Martin S. Banks, Gregory C. Deangelis, Dora E. Angelaki

Open Access Publications

Effective navigation and locomotion depend critically on an observer's ability to judge direction of linear self-motion, i.e., heading. The vestibular cue to heading is the direction of inertial acceleration that accompanies transient linear movements. This cue is transduced by the otolith organs. The otoliths also respond to gravitational acceleration, so vestibular heading discrimination could depend on (1) the direction of movement in head coordinates (i.e., relative to the otoliths), (2) the direction of movement in world coordinates (i.e., relative to gravity), or (3) body orientation (i.e., the direction of gravity relative to the otoliths). To quantify these effects, we measured …

The Role Of Gender In Single Vs Married Individuals With Bipolar Disorder., Daniel Z Lieberman, Suena H Massey, Frederick K Goodwin

Psychiatry and Behavioral Sciences Faculty Publications

BACKGROUND: Despite the importance of marriage as a source of social support, it has been largely neglected in studies of bipolar disorder; and differential effects on men and women have not been explored.

METHODS: Data on episodes of depression, mania, and mixed states were collected for the previous 2 years from a sample of 282 bipolar individuals using the National Institute of Mental Health Life Chart Methodology.

RESULTS: Effects unique to women included the following: Bipolar women were significantly more likely to be married. Married women had fewer episodes of depression during the past 2 years than never-married women, and …

Cross-Trimester Repeated Measures Testing For Down's Syndrome Screening: An Assessment., D. Wright, I. Bradbury, F. Malone, M. D'Alton, A. Summers, T. Huang, S. Ball, A. Baker, B. Nix, D. Aitken, J. Crossley, H. Cuckle, K. Spencer

Peninsula Medical School

OBJECTIVES: To provide estimates and confidence intervals for the performance (detection and false-positive rates) of screening for Down's syndrome using repeated measures of biochemical markers from first and second trimester maternal serum samples taken from the same woman. DESIGN: Stored serum on Down's syndrome cases and controls was used to provide independent test data for the assessment of screening performance of published risk algorithms and for the development and testing of new risk assessment algorithms. SETTING: 15 screening centres across the USA, and at the North York General Hospital, Toronto, Canada. PARTICIPANTS: 78 women with pregnancy affected by Down's syndrome …

Chronic Obstructive Pulmonary Disease: Longitudinal Hyperpolarized (3)He Mr Imaging, Miranda Kirby, Lindsay Mathew, Andrew Wheatley, Giles E Santyr, David G Mccormack, Grace Parraga

Medical Biophysics Publications

PURPOSE: To quantitatively evaluate a small pilot group of ex-smokers with chronic obstructive pulmonary disease (COPD) and healthy volunteers during approximately 2 years by using hyperpolarized helium 3 ((3)He) magnetic resonance (MR) imaging.

MATERIALS AND METHODS: All subjects provided written informed consent to the study protocol, which was approved by the local research ethics board and Health Canada and was compliant with the Personal Information Protection and Electronic Documents Act and HIPAA. Hyperpolarized (3)He MR imaging, hydrogen 1 MR imaging, spirometry, and plethysmography were performed in 15 ex-smokers with COPD and five healthy volunteers (with the same mean age and …

Deficits In Attention To Emotional Stimuli Distinguish Youth With Severe Mood Dysregulation From Youth With Bipolar Disorder., Brendan A Rich, Melissa A Brotman, Daniel P Dickstein, Derek G V Mitchell, R James R Blair, Ellen Leibenluft

Brain and Mind Institute Researchers' Publications

Studying attention in the context of emotional stimuli may aid in differentiating pediatric bipolar disorder (BD) from severe mood dysregulation (SMD). SMD is characterized by chronic irritability, arousal, and hyper-reactivity; SMD youth frequently receive a BD diagnosis although they do not meet DSM-IV criteria for BD because they lack manic episodes. We compared 57 BD (14.4 +/- 2.9 years old, 56% male), 41 SMD (12.6 +/- 2.6 years old, 66% male), and 33 control subjects (13.7 +/- 2.5 years old, 52% male) using the Emotional Interrupt task, which examines how attention is impacted by positive, negative, or neutral distracters. We …

A Randomized Comparison Of Online And Paper Mood Charts For People With Bipolar Disorder., Daniel Z Lieberman, Tammas F Kelly, Lanny Douglas, Frederick K Goodwin

Psychiatry and Behavioral Sciences Faculty Publications

BACKGROUND: Longitudinal mood instability is the essential feature of bipolar disorder, however most rating scales are cross sectional in nature, and focus on acute symptoms. By contrast, the NIMH Life Chart Methodology (LCM) characterizes in detail the severity, duration, and frequency of mood episodes. Adherence to daily rating, however, tends to be low. In this study an online version of the LCM, designed to enhance adherence, was compared to the standard paper version.

METHODS: Patients from a mood disorders specialty clinic were randomized to the standard LCM or an online, open-source adaptation. The online version used hypertext links embedded in …

Dopaminergic Neurons Derived From Human Induced Pluripotent Stem Cells Survive And Integrate Into 6-Ohda-Lesioned Rats., Jingli Cai, Ming Yang, Elizabeth Poremsky, Sarah Kidd, Jay S Schneider, Lorraine Iacovitti

Farber Institute for Neuroscience Faculty Papers

Cell replacement therapy could be an important treatment strategy for Parkinson's disease (PD), which is caused by the degeneration of dopamine neurons in the midbrain (mDA). The success of this approach greatly relies on the discovery of an abundant source of cells capable of mDAergic function in the brain. With the paucity of available human fetal tissue, efforts have increasingly focused on renewable stem cells. Human induced pluripotent stem (hiPS) cells offer great promise in this regard. If hiPS cells can be differentiated into authentic mDA neuron, hiPS could provide a potential autologous source of transplant tissue when generated from …

Human Papillomavirus And Survival Of Patients With Oropharyngeal Cancer., K Kian Ang, Jonathan Harris, Richard Wheeler, Randal Weber, David I Rosenthal, Phuc Felix Nguyen-Tân, William H Westra, Christine H Chung, Richard C Jordan, Charles Lu, Harold Kim, Rita S. Axelrod, Md, C Craig Silverman, Kevin P Redmond, Maura L Gillison

Jefferson Hospital Staff Papers and Presentations

BACKGROUND: Oropharyngeal squamous-cell carcinomas caused by human papillomavirus (HPV) are associated with favorable survival, but the independent prognostic significance of tumor HPV status remains unknown.

METHODS: We performed a retrospective analysis of the association between tumor HPV status and survival among patients with stage III or IV oropharyngeal squamous-cell carcinoma who were enrolled in a randomized trial comparing accelerated-fractionation radiotherapy (with acceleration by means of concomitant boost radiotherapy) with standard-fractionation radiotherapy, each combined with cisplatin therapy, in patients with squamous-cell carcinoma of the head and neck. Proportional-hazards models were used to compare the risk of death among patients with HPV-positive …

Breast Cancer Dna Methylation Profiles Are Associated With Tumor Size And Alcohol And Folate Intake, Brock C. Christensen, Karl T. Kelsey, Shichun Zheng, E. Andres Houseman, Carmen J. Marsit, Margaret R. Wrensch, Joseph L. Wiemels, Heather H. Nelson, Margaret R. Karagas

Dartmouth Scholarship

Although tumor size and lymph node involvement are the current cornerstones of breast cancer prognosis, they have not been extensively explored in relation to tumor methylation attributes in conjunction with other tumor and patient dietary and hormonal characteristics. Using primary breast tumors from 162 (AJCC stage I-IV) women from the Kaiser Division of Research Pathways Study and the Illumina GoldenGate methylation bead-array platform, we measured 1,413 autosomal CpG loci associated with 773 cancer-related genes and validated select CpG loci with Sequenom EpiTYPER. Tumor grade, size, estrogen and progesterone receptor status, and triple negative status were significantly (Q-values <0.05) associated with altered methylation of 209, 74, 183, 69, and 130 loci, respectively. Unsupervised clustering, using a recursively partitioned mixture model (RPMM), of all autosomal CpG loci revealed eight distinct methylation classes. Methylation class membership was significantly associated with patient race (P<0.02) and tumor size (P<0.001) in univariate tests. Using multinomial logistic regression to adjust for potential confounders, patient age and tumor size, as well as known disease risk factors of alcohol intake and total dietary folate, were all significantly (P<0.0001) associated with methylation class membership. Breast cancer prognostic characteristics and risk-related exposures appear to be associated with gene-specific tumor methylation, as well as overall methylation patterns.