Index Catalog // ScholarsArchive@OSU

Reference-free deconvolution of DNA methylation data and mediation by cell composition effects

Creator:: Houseman, E. Andres, Kile, Molly L., Christiani, David C., Ince, Tan A., Kelsey, Karl T., and Marsit, Carmen J.
Abstract:: Background: Recent interest in reference-free deconvolution of DNA methylation data has led to several supervised methods, but these methods do not easily permit the interpretation of underlying cell types. Results: We propose a simple method for reference-free deconvolution that provides both proportions of putative cell types defined by their underlying...
Resource Type:: Article

In Utero Arsenic Exposure and Epigenome-Wide Associations in Placenta, Umbilical Artery and Human Umbilical Vein Endothelial Cells

Creator:: Cardenas, Andres, Houseman, E. Andres, Baccarelli, Andrea A., Quamruzzaman, Quazi, Rahman, Mahmuder, Mostofa, Golam, Wright, Robert O., Christiani, David C., and Kile, Molly L.
Abstract:: Exposure to arsenic early in life has been associated with increased risk of several chronic diseases and is believed to alter epigenetic programming in utero. In the present study, we evaluate the epigenome-wide association of arsenic exposure in utero and DNA methylation in placenta (n = 37), umbilical artery (n...
Resource Type:: Article

Understanding the Role of the Immune System in the Development of Cancer: New Opportunities for Population-Based Research

Creator:: Michaud, Dominique S., Houseman, E. Andres, Marsit, Carmen J., Nelson, Heather H., Wiencke, John K., and Kelsey, Karl T.
Abstract:: Understanding the precise role of the immune system in cancer has been hindered by the complexity of the immune response and challenges in measuring immune cell types in health and disease in the context of large epidemiologic studies. In this review, we present the rationale to study immunity in cancer...
Resource Type:: Article

Differential DNA methylation in umbilical cord blood of infants exposed to mercury and arsenic in utero

Creator:: Cardenas, Andres, Koestler, Devin C., Houseman, E. Andres, Jackson, Brian P., Kile, Molly L., Karagas, Margaret R., and Marsit, Carmen J.
Abstract:: Exposure to arsenic early in life has been associated with increased risk of several chronic diseases and is believed to alter epigenetic programming in utero. In the present study, we evaluate the epigenome-wide association of arsenic exposure in utero and DNA methylation in placenta (n=37), umbilical artery (n=45) and human...
Resource Type:: Article

Arsenic Exposure and Prevalence of the Varicella Zoster Virus in the United States: NHANES (2003-2004 and 2009-2010)

Creator:: Cardenas, Andres, Smit, Ellen, Houseman, E. Andres, Kerkvliet, Nancy I., Bethel, Jeffrey W., and Kile, Molly L.
Abstract:: Background: Arsenic is an immunotoxicant. Clinical reports observe the reactivation of varicella zoster virus (VZV) in people who have recovered from arsenic poisoning and in patients with acute promyelocytic leukemia that have been treated with arsenic trioxide. Objective: We evaluated the association between arsenic and the seroprevalence of VZV IgG...
Resource Type:: Article

Epigenetic remodeling in B-cell acute lymphoblastic leukemia occurs in two tracks and employs embryonic stem cell-like signatures

Creator:: Lee, Seung-Tae, Muench, Marcus O., Fomin, Marina E., Xiao, Jianqiao, Zhou, Mi, de Smith, Adam, Martín-Subero, José I., Heath, Simon, Houseman, E. Andres, Roy, Ritu, Wrensch, Margaret, Wiencke, John, Metayer, Catherine, and Wiemels, Joseph L.
Abstract:: We investigated DNA methylomes of pediatric B-cell acute lymphoblastic leukemias (B-ALLs) using whole-genome bisulfite sequencing and high-definition microarrays, along with RNA expression profiles. Epigenetic alteration of B-ALLs occurred in two tracks: de novo methylation of small functional compartments and demethylation of large intercompartmental backbones. The deviations were exaggerated in lamina-associated...
Resource Type:: Article

Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective

Creator:: Houseman, E. Andres, Kelsey, Karl T., Wiencke, John K., and Marsit, Carmen J.
Abstract:: BACKGROUND: The impact of cell-composition effects in analysis of DNA methylation data is now widely appreciated. With the availability of a reference data set consisting of DNA methylation measurements on isolated cell types, it is possible to impute cell proportions and adjust for them, but there is increasing interest in...
Resource Type:: Article

Quantitative reconstruction of leukocyte subsets using DNA methylation

Creator:: Accomando, William P., Wiencke, John K., Houseman, E. Andres, Nelson, Heather H., and Kelsey, Karl T.
Abstract:: BACKGROUND: Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune modulations in virtually any blood sample including...
Resource Type:: Article

Variants of Asthma and Chronic Obstructive Pulmonary Disease Genes and Lung Function Decline in Aging

Creator:: Poon, Audrey H., Houseman, E. Andres, Ryan, Louise, Sparrow, David, Vokonas, Pantel S., and Litonjua, Augusto A.
Abstract:: BACKGROUND: A substantial proportion of the general population has low lung function, and lung function is known to decrease as we age. Low lung function is a feature of several pulmonary disorders, such as uncontrolled asthma and chronic obstructive pulmonary disease (COPD). The objective of this study is to investigate...
Resource Type:: Article

Effects of Sulforaphane and 3,3'-Diindolylmethane on Genome-Wide Promoter Methylation in Normal Prostate Epithelial Cells and Prostate Cancer Cells

Creator:: Wong, Carmen P., Hsu, Anna, Buchanan, Alex, Palomera-Sanchez, Zoraya, Beaver, Laura M., Houseman, E. Andres, Williams, David E., Dashwood, Roderick H., and Ho, Emily
Abstract:: Epigenetic changes, including aberrant DNA methylation, result in altered gene expression and play an important role in carcinogenesis. Phytochemicals such as sulforaphane (SFN) and 3,3′-diindolylmethane (DIM) are promising chemopreventive agents for the treatment of prostate cancer. Both have been shown to induce re-expression of genes, including tumor suppressor genes silenced...
Resource Type:: Article

Blood-based profiles of DNA methylation predict the underlying distribution of cell types: a validation analysis

Creator:: Koestler, Devin C., Christensen, Brock C., Karagas, Margaret R., Marsit, Carmen J., Langevin, Scott M., Kelsey, Karl T., Wiencke, John K., and Houseman, E. Andres
Abstract:: The potential influence of underlying differences in relative leukocyte distributions in studies involving blood-based profiling of DNA methylation is well recognized and has prompted development of a set of statistical methods for inferring changes in the distribution of white blood cells using DNA methylation signatures. However, the extent to which...
Resource Type:: Article

Review of processing and analysis methods for DNA methylation array data

Creator:: Wilhelm-Benartzi, Charlotte S., Koestler, Devin C., Karagas, Margaret R., Flanagan, James M., Christensen, Brock C., Kelsey, Karl T., Marsit, Carmen J., Houseman, E. Andres, and Brown, Robert
Abstract:: The promise of epigenome-wide association studies (EWAS) and cancer specific somatic changes in improving our understanding of cancer coupled with the decreasing cost and increasing coverage of DNA methylation microarrays, has brought about a surge in the use of these technologies. Here, we aim to provide both a review of...
Resource Type:: Article

Differential DNA Methylation in Umbilical Cord Blood of Infants Exposed to Low Levels of Arsenic in Utero

Creator:: Koestler, Devin C., Avissar-Whiting, Michele, Houseman, E. Andres, Karagas, Margaret R., and Marsit, Carmen J.
Abstract:: Background: There is increasing epidemiologic evidence that arsenic exposure in utero, even at low levels found throughout much of the world, is associated with adverse reproductive outcomes and may contribute to long-term health effects. Animal models, in vitro studies, and human cancer data suggest that arsenic may induce epigenetic alterations,...
Resource Type:: Article

Recursively partitioned mixture model clustering of DNA methylation data using biologically informed correlation structures

Creator:: Koestler, Devin C., Christensen, Brock C., Marsit, Carmen J., Kelsey, Karl T., and Houseman, E. Andres
Abstract:: DNA methylation is a well-recognized epigenetic mechanism that has been the subject of a growing body of literature typically focused on the identification and study of profiles of DNA methylation and their association with human diseases and exposures. In recent years, a number of unsupervised clustering algorithms, both parametric and...
Resource Type:: Article

ScholarsArchive@OSU

Reference-free deconvolution of DNA methylation data and mediation by cell composition effects

In Utero Arsenic Exposure and Epigenome-Wide Associations in Placenta, Umbilical Artery and Human Umbilical Vein Endothelial Cells

Understanding the Role of the Immune System in the Development of Cancer: New Opportunities for Population-Based Research

Differential DNA methylation in umbilical cord blood of infants exposed to mercury and arsenic in utero

Arsenic Exposure and Prevalence of the Varicella Zoster Virus in the United States: NHANES (2003-2004 and 2009-2010)

Epigenetic remodeling in B-cell acute lymphoblastic leukemia occurs in two tracks and employs embryonic stem cell-like signatures

Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective

Quantitative reconstruction of leukocyte subsets using DNA methylation

Variants of Asthma and Chronic Obstructive Pulmonary Disease Genes and Lung Function Decline in Aging

Effects of Sulforaphane and 3,3'-Diindolylmethane on Genome-Wide Promoter Methylation in Normal Prostate Epithelial Cells and Prostate Cancer Cells

Blood-based profiles of DNA methylation predict the underlying distribution of cell types: a validation analysis

Review of processing and analysis methods for DNA methylation array data

Differential DNA Methylation in Umbilical Cord Blood of Infants Exposed to Low Levels of Arsenic in Utero

Recursively partitioned mixture model clustering of DNA methylation data using biologically informed correlation structures

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