Neurodevelopment and Improving Children’s Health following Environmental tobacco Smoke exposure (NICHES)

NICHES is a Children’s Environmental Health and Disease Prevention Research Center led by Dr. Murphy and funded by the National Institute of Environmental Health Sciences and the US Environmental Protection Agency. The goal of the NICHES Childrens Center is to understand how neurodevelopment is affected by exposure to toxic chemical during pregnancy and in early life. We are currently working to determine if tobacco smoke exposure increases the risk of a child developing attention deficit hyperactivity disorder through changes in DNA methylation. NICHES has three main projects, a community outreach core and an administrative core. You can read more about the NICHES Children’s Center at our web site,

The Newborn Epigenetics STudy (NEST)

        Through animal and emerging human studies, it is now recognized that environmentally-induced variability in the establishment of epigenetic profiles in early development can influence later risk of disease. Anecdotal and retrospective studies, including human disasters of the past century (e.g., the Dutch Famine of 1944-45 and the Chinese Famine of 1959-61), have supported this postulate. Prospective studies in humans are extremely difficult due to the vast number of variable exposures that are incurred over the course of life.  The Duke-based Newborn Epigenetics STudy (NEST) was initiated in 2004 in order to prospectively test the influence of in utero environmental exposures on DNA methylation profiles in newborns.  

        The Murphy laboratory uses pyrosequencing to quantify DNA methylation at individual genetic loci, and we have also generated genome-wide DNA methylation profiles using the Illumina HumanMethylation 450k beadchip.  We are currently following our infant cohort to monitor developmental milestones and morbidities with the intent to examine relationships with DNA methylation, as well as to define how the in utero environment shapes these relationships over time. 

Cannabis-Induced Potential Heritability of Epigenetic Revisions in Sperm (CIPHERS)


         Amid the growing legalization of cannabis, surprisingly little is known about its potential health effects. We were interested in the potential effects on reprogramming of DNA methylation in sperm, and have recently shown that cannabis use in humans and exposure to delta9-tetrahydrocannabinol (the main psychoactive component of cannabis) in rats is associated with substantial changes in sperm DNA methylation (submitted for publication). The CIPHERS project will confirm the changes observed in humans and rats in independent cohorts and will examine the potential for inter-generational and trans-generational heritability of the altered DNA methylation from the father.

The Influence of the Environment on Gametic Epigenetic Reprogramming (TIEGER)

        DNA methylation is erased in primorodial germ cells (cells destined to become sperm in males and eggs in females) during embryogenesis.  Within these cells, erasure is followed by precise resetting of the methylation marks.  For the subgroup of genes that are imprinted, this methylation reset must reflect the sex of the embryo containing the gametes. As males reach adolescence, the final methylation pattern is set in mature spermatozoa.  Results from the NEST project from analysis done by Duke Postdoctoral Fellow Dr. Adelheid Soubry showed that paternal obesity was associated with incomplete methylation at an imprinted gene under study.  This may reflect subtle deficiencies in methylation resetting in the sperm that result from the effects of elevated levels of obesity-related estrogens, or may be due to other environmental exposures to endocrine-disrupting compounds, including persistent organic pollutants like the chemicals present in flame retardants.  The TIEGER study is a joint effort funded by the Duke University Medical Center (led by Dr. Susan K. Murphy) and the Nicholas School of the Environment (led by Dr. Heather Stapleton) to address these questions. 

Ovarian Cancer Research

Ovarian cancer epigenetics:  Epigenetics refers to the study of a powerful form of gene regulation that instructs the cell to either turn down or ramp up gene expression.  This is a normal and essential function. Since we have identical DNA in each of our cells, epigenetic gene regulation helps shape the identity and function of the many different cell types that make up our bodies.  This is done through modification of the histone proteins around which our DNA is wrapped and through the addition of a methyl group (one carbon and three hydrogen atoms) to specific nucleotide bases that make up our DNA.  This does not change the DNA sequence, but it does change the way the cellular machinery interacts with the DNA.  These two forms of epigenetic regulation work in concert to define the level of gene activity in a given cell.  Cancer cells usurp these forms of normal gene regulation to their advantage.  In cancer, genes that normally are active and help keep growth in check become silenced, and normally inactive genes that function to drive rapid growth and cell division (as would be necessary during normal periods of growth) become activated.  Much of this re-orchestration of gene expression is mediated through epigenetic mechanisms.  

The Murphy lab studies DNA methylation, and we are interested in the identification of genes that undergo methylation changes in cancer, how this happens, and how this information can be used to improve diagnosis, treatment and outcome.   We have used a single gene approach (e.g., see our publications in Nucleic Acids Research, Molecular Cancer Research and The International Journal of Cancer), as well as genome-wide approaches, including computational predictions of genes targeted by methylation mediated silencing, a project on which we collaborated with computational biologist Dr. Terry Furey, resulting in a publication in the journal Bioinformatics.  We have also profiled genome-wide gene expression changes following pharmacologic inhibition of DNA methylation, a study recently published in the journal, Genome Research.  This work was the first to document epigenetic deregulation of multiple genes within a major cancer regulatory pathway in ovarian cancer and provides a foundation for future research directed at understanding how tumor biology can be integrated with therapeutic applications. 


Ovarian cancer stem-like cells: The Murphy lab is also interested in the identification and characterization of ovarian cancer stem-like cells, thought to be the progenitor cell population responsible for the initiation of disease.  Our analysis of a large panel of ovarian cancer cell lines for cell surface expression of CD133, an established cancer stem-like cell marker, led to identification of several cell lines that exhibited heterogeneous expression of this cell surface protein.  This enabled sorting of the CD133+ from the CD133- cell populations and characterization of the phenotypes of each of these cells.  We showed that CD133+ cells undergo asymmetric cell division, exhibit enhanced tumorigenicity and are more chemoresistant than their CD133- counterparts.  Consistent with the fundamental importance of epigenetics in stem cell phenotypes, we also found that the promoter of CD133 is methylated in cells that do not express this molecule, while cells expressing CD133 were unmethylated at the promoter region.  We confirmed that CD133 is also present on discrete cell populations in human ovarian cancer tissues as well as on a small number of cancer cells in the fluid that often accumulates in the peritoneal cavity of women with this disease.  These findings together implicate CD133 as a cancer stem-like cell marker in ovarian cancer (published in Oncogene).

Targeting dormant ovarian cancer cells: We are interested in targeting ovarian cancer cells that are capable of surviving primary chemotherapy and that enter into a state of cellular dormancy, presumed to be ovarian cancer stem-like cells.  In a review article, Dr. Murphy proposed that these slower-proliferating cells are responsible for the emergence of recurrent ovarian cancer, which can happen months to years following diagnosis.  Using a simple bioinformatics approach, we have identified novel drugs that show increased efficacy against slower-proliferating cells, work published in the International Journal of Cancer

© The Murphy Lab 2021