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CD56+ immune cell infiltration and MICA are decreased in breast lobules with fibrocystic changes

Purpose While the role of natural killer (NK) cells in breast cancer therapy has been investigated, little information is known about NK cell function and presence in nonmalignant and premalignant breast tissue. Here, we investigate and quantify NK cell marker CD56 and activating ligand MICA in breast tissue with benign breast disease. Methods Serial tissue sections from 88...

Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm

Figures in scientific publications are critically important because they often show the data supporting key findings. Our systematic review of research articles published in top physiology journals (n = 703) suggests that, as scientists, we urgently need to change our practices for presenting continuous data in small sample size studies. Papers rarely included scatterplots, box...

Postlactational involution biomarkers plasminogen and phospho-STAT3 are linked with active age-related lobular involution

Purpose Breast terminal duct lobular units undergo two distinctive physiological processes of involution: age-related lobular involution (LI), which is gradual and associated with decreased breast cancer risk, and postlactational involution, which is relatively precipitous, occurs with weaning, and has been associated with potentiation of tumor aggressiveness in animal models...

Associations of prodynorphin sequence variation with alcohol dependence and related traits are phenotype-specific and sex-dependent

We previously demonstrated that prodynorphin (PDYN) haplotypes and single nucleotide polymorphism (SNP) rs2281285 are associated with alcohol dependence and the propensity to drink in negative emotional states, and recent studies suggest that PDYN gene effects on substance dependence risk may be sex-related. We examined sex-dependent associations of PDYN variation with alcohol...

NanoString-based breast cancer risk prediction for women with sclerosing adenosis

PurposeSclerosing adenosis (SA), found in ¼ of benign breast disease (BBD) biopsies, is a histological feature characterized by lobulocentric proliferation of acini and stromal fibrosis and confers a two-fold increase in breast cancer risk compared to women in the general population. We evaluated a NanoString-based gene expression assay to model breast cancer risk using RNA...

Gene signature model for breast cancer risk prediction for women with sclerosing adenosis

Benign breast disease (BBD) is diagnosed in 1–2 million women/year in the US, and while these patients are known to be at substantially increased risk for subsequent development of breast cancer, existing models for risk assessment perform poorly at the individual level. Here, we describe a DNA-microarray-based transcriptional model for breast cancer risk prediction for patients...

PDYN rs2281285 Variant Association with Drinking to Avoid Emotional or Somatic Discomfort

Introduction One of the proposed psychobiological pathways of craving attributes the desire for drinking in the context of tension, discomfort or unpleasant emotions, to “negative” (or “relief”) craving. The aim of this study was to replicate a previously reported association of the PDYN rs2281285 variant with negative craving using a different phenotyping approach. Methods The...

A comparison of internal validation techniques for multifactor dimensionality reduction

Background It is hypothesized that common, complex diseases may be due to complex interactions between genetic and environmental factors, which are difficult to detect in high-dimensional data using traditional statistical approaches. Multifactor Dimensionality Reduction (MDR) is the most commonly used data-mining method to detect epistatic interactions. In all data-mining...

SNP interaction detection with Random Forests in high-dimensional genetic data

Background Identifying variants associated with complex human traits in high-dimensional data is a central goal of genome-wide association studies. However, complicated etiologies such as gene-gene interactions are ignored by the univariate analysis usually applied in these studies. Random Forests (RF) are a popular data-mining technique that can accommodate a large number of...

Methylation of leukocyte DNA and ovarian cancer: relationships with disease status and outcome

Stacey J Winham Kimberly R Kalli Devin C Koestler 0 David N Rider Viji Shridhar Janet E Olson Julie M Cunningham Ellen L Goode 0 Department of Biostatistics, University of Kansas, Medical Center , 3901

Methylation of leukocyte DNA and ovarian cancer: relationships with disease status and outcome

Genome-wide interrogation of DNA methylation (DNAm) in blood-derived leukocytes has become feasible with the advent of CpG genotyping arrays. In epithelial ovarian cancer (EOC), one report found substantial DNAm differences between cases and controls; however, many of these disease-associated CpGs were attributed to differences in white blood cell type distributions. We examined...

Identification of nine new susceptibility loci for endometrial cancer

. Werner in:Nature Research journals • PubMed • Google Scholar Search for Stacey J. Winham in:Nature Research journals • PubMed • Google Scholar Search for Alicja Wolk in:Nature Research journals • PubMed

Epigenome-wide ovarian cancer analysis identifies a methylation profile differentiating clear-cell histology with epigenetic silencing of the HERG K+ channel

4 Devin C. Koestler 6 Brooke L. Fridley 5 Kimberly R. Kalli 2 Sebastian M. Armasu 4 Melissa C. Larson 4 Chen Wang 4 Stacey J. Winham 4 Robert A. Vierkant 4 David N. Rider 4 Matthew S. Block 0 Brandy

Variants in genes encoding small GTPases and association with epithelial ovarian cancer susceptibility

Epithelial ovarian cancer (EOC) is the fifth leading cause of cancer mortality in American women. Normal ovarian physiology is intricately connected to small GTP binding proteins of the Ras superfamily (Ras, Rho, Rab, Arf, and Ran) which govern processes such as signal transduction, cell proliferation, cell motility, and vesicle transport. We hypothesized that common germline...