How Epigenetics Influences the Risk of Disease
“Probably the most important aspect of germline epigenetic vulnerability is that it is at its
highest during pregnancy. This vulnerability occurs within the cells that will form the
gametes (sperm or eggs) of the developing child.”
Susan K. Murphy, PhD, is Associate Professor, Department of Obstetrics and Gynecology at Duke University in North Carolina. She has a PhD in Microbiology and Immunology from Wake Forest University and did postdoctoral training at Duke. Her research is focused on how epigenetics influences the risk of disease throughout the lifespan, from studies of how the in utero environment modifies the epigenome (the Newborn Epigenetics STudy, or NEST) to studies of cancer, including cervical and ovarian cancers.
Interviewed by Jill Escher, April 2014
Interviewed by Jill Escher, April 2014
Could you explain for a lay audience what is meant by "epigenetics"?
Epigenetics refers to the mechanisms that are used in a cell to control when, where and how genes are used. The DNA in our cells contains tens of thousands of different genes, but the different cell types in our bodies each use a particular subset of these genes. The ability to control which genes are used and in what amount to help the cell function, and to control which are turned off because they are not needed in that cell type, is largely determined by epigenetics. Epigenetic gene regulation does not alter the DNA sequence; rather it adds an “instruction manual” to each of the genes within the DNA.
How do environmental factors affect epigenetic mechanisms?
The environment encompasses many factors, including (but not limited to) what we are exposed to in our daily living, the things that we eat and social influences. The in utero environment includes the things we are exposed to before we are born. Within each cell there are specific enzymes and cofactors that are responsible for establishing the epigenetic profiles (instruction manuals) at the right location on the DNA and at the right time. These enzymes and cofactors make sure that as cells divide, the epigenetic profiles associated with the DNA in the parent cell are copied exactly to the daughter cell's DNA. Environmental influences can disrupt how well these processes occur. This in turn changes the way the “instruction manual” is interpreted by the cell – and can disrupt how the cell functions.
Everyone has basically two types of cells: somatic cells, which make up our bodies, and germ cells, which are our reproductive cells, better known in their final form as sperm and egg. Are the epigenetic mechanisms and vulnerabilities in germ cells different than somatic cells?
The sperm and egg each carry different epigenetic information that reflects the sex of the individual in which these cells reside. These epigenetic differences give the gametes a “sex” and are required for a viable pregnancy. During early pregnancy, the developing embryo begins to form the germ cells that will eventually produce the sperm or eggs that may be used to create the next generation. When these germ cells begin to form, they undergo a “reprogramming” process during which all epigenetic information is first erased and then is re-established in a way that reflects the sex of the embryo.
This process is carried out by slightly different mechanisms in each germ cell depending on if the embryo is a boy or a girl, but in a way that marks the same parts of the genome with different epigenetic information in developing male versus female germ cells. The most vulnerable time for germ cells is thought to be during this reprogramming in early pregnancy. However, for males, sperm are continually produced from adolescence onward. The final touches on the epigenetic profiles in sperm are made as the sperm go through the last stages of maturation, meaning that sperm may be vulnerable to environmental insults over the entire course of an adult male’s lifetime.
Just after fertilization occurs, there is a second epigenetic reprogramming event where most but not all of the epigenetic information is erased and re-established again. Around the time of implantation in the uterus, the reprogramming process is largely completed and this epigenetic information helps to guide certain cells to form the placenta, other cells to form the developing embryo, and within the embryo, helps direct cells to form tissues and organs, and provides the instructions for when and where to do this. For these somatic cells, vulnerability is likely highest during the period of post-fertilization reprogramming, before a woman realizes she is pregnant.
Somatic cells are also vulnerable once tissues and organs have formed, but this is expected to be more tissue specific. In the somatic cells, it is important that the epigenetic information is copied precisely as cells divide. This "maintenance" function is performed by a different cellular enzyme than the enzymes that establish new epigenetic information during the two reprogramming events. Things that perturb how well these enzymes work can also affect epigenetic shifts, including genetic differences in the DNA sequence that encode these enzymes, epigenetic deregulation of these genes themselves and dietary intake of nutrients involved in one-carbon metabolism (e.g., folate, methionine, betaine, choline), the biochemical pathway that generates methyl groups for DNA methylation.
How did you become involved in this field of research?
My doctoral research was actually in the field of molecular virology. During my second year of graduate school, my then 3-year-old son, who had been born early at 26 weeks and spent nearly 11 months in the neonatal intensive care unit, died of hepatoblastoma (a rare form of liver cancer). Several months prior to his death, my younger son was diagnosed with autism. I made the decision at that time to complete my dissertation research but with the intent to change research direction during my postdoctoral training to an area that would honor my sons.
I then joined Dr. Randy Jirtle’s laboratory at Duke University. Dr. Jirtle’s research in liver cancer, epigenetics and genomic imprinting (an amazing form of epigenetic gene regulation that results in activity of only one of the two inherited copies of a gene in a manner that depends on the sex of the parent from whom that copy was inherited) along with his interest in how epigenetics is involved in neurodevelopment and autism drew me to his lab. As a faculty member for the last eleven years, I have continued with epigenetics research with a focus on early development, but also have an active research program studying epigenetics and therapeutic targeting of gynecologic malignancies.
Do you think that ovarian cancer and breast cancer risk might be linked to prenatal exposures? If so, what type of exposures, and is epigenetics involved?
I think it’s certainly a possibility. We know that there are exposure-related epigenetic shifts in newborn human cord blood at genes that are implicated in cancer, but no one has yet followed children with these epigenetic changes long enough to know if they are linked to increased risk of developing cancer.
Please tell us about the Newborn Epigenetics STudy (NEST) and how it evaluates prenatal influence on somatic cell epigenetics in children.
NEST is a longitudinal cohort study of mother-infant pairs that was started in 2005 at Duke University to specifically address how the in utero environment influences the establishment and maintenance of epigenetic profiles in the child, and how this is related to risk of later disorders and disease. NEST has thus far primarily focused on imprinted genes since we know more about their epigenetic regulation than most other genes, and because imprinted genes are so important to appropriate early development and growth. In addition, many imprinted genes are also involved in cancer.
NEST is now studying epigenetic changes on a genome-wide scale. Over 2,500 mothers were enrolled in the study during pregnancy and were asked to complete detailed questionnaires about their demographics, health and nutrition and to provide blood specimens. When their child was born, umbilical cord blood was collected to allow for research on the relationships between information collected from the mother and her exposures to the epigenetic profiles of their child. NEST continues to follow these children to monitor their growth and development, including neurodevelopment.
A subset of the NEST participants are being followed through the Duke NICHES Children’s Environmental Health and Disease Prevention Research Center, which is examining epigenetic alterations as a potential mechanistic explanation for the link between tobacco smoke exposure during early life and increased risk of attention deficit / hyperactivity disorder.
You also have a study called TIEGER, or The Influence of the Environment on Gametic Epigenetic Reprogramming. This subject goes to the very heart of this website's mission to educate the public about environmental vulnerability of our gametes. What, in general, do you think the public should know about germline epigenetic vulnerability?
Probably the most important aspect of germline epigenetic vulnerability is that it is at its highest during pregnancy. This vulnerability occurs within the cells that will form the gametes (sperm or eggs) of the developing child. These gametes contain the DNA and accompanying epigenetic information that may eventually create grandchildren for the pregnant mother. These gametes begin to develop in the embryo, and part of this process involves an erasure of all of the epigenetic information from the prior generation in the DNA of the cells that will form the gametes.
During pregnancy for a woman, the environment has an effect on three generations at once: the woman who is pregnant, her developing child, and that child’s children. While we still do not understand much about how the environment might affect gametes in the developing child during gestation, we know even less about the factors that might perturb epigenetic reprogramming in sperm of adults and how this might be transmitted to subsequent generations. TIEGER is specifically looking at how body mass index and exposure to endocrine disrupting agents influences the establishment of methylation profiles at imprinted genes.
Do you think approaches to toxicology and drug safety testing should change in light of what we're learning about germline epigenetics?
Yes! Toxicology and drug safety testing rarely take into account the effects of chemicals and drugs on the epigenome of the germ cells of the developing embryo during pregnancy, and such effects could have consequences for future generations much more widespread than DNA mutations. We need to develop more cost-effective technologies to enable assessment of the epigenome in its entirety, or identify a group of sentinel genes that are representative of those affected so that these can be implemented in safety testing.
You have stated publicly that you have a son, now a young adult, with autism. Do you ever speculate about any potential epigenetic origins of his condition or about autism and abnormal neurodevelopment generally?
It's difficult not to speculate, but there are so many past life circumstances that could have contributed it's not possible to pinpoint a particular cause. In my case, during my entire pregnancy with my son who has autism, my older son was born at 26 weeks due to eclampsia and spent nearly 11 months in the NICU with severe lung disease due to his prematurity (a constant source of stress and worry); I took antidepressant medicine before I knew I was pregnant with my younger son due to that stress and worry ("safe" to take while pumping breast milk or during pregnancy; potentially linked to autism); we lived directly adjacent to a freeway (linked to increased risk of prematurity and autism) prior to and throughout our son's early lives in an older four-plex that we remodeled ourselves before we had children (possible lead exposure); both my mother and father smoked, including while I was in utero; and my husband spent part of his adolescence in Salinas, California, a block away from the lettuce fields where pesticide use was ubiquitous (potential effects on gametic reprogramming). These types of exposure histories, for which we all have a version, is a huge problem with trying to decipher cause-effect relationships in humans - each of us has a multifaceted exposure history.
What do you think the autism research community should learn about epigenetics, which in that field remains a new and somewhat mysterious concept?
Over the last several years there has been a rapidly growing interest in the role of epigenetics in autism. This interest needs to be expanded and research in this area should be further prioritized. We need to develop models that can be used to study the relationships between environmental factors, epigenetic changes and autism.
Studies of epigenetics in autism in humans are exceedingly challenging in the affected tissue since autism is a brain disorder. It is also vital that we work toward identifying epigenetic marks in more accessible tissues (blood, saliva, etc.) that can be used as a proxy for altered epigenetic profiles in the brain for human studies. If such concordant relationships exist, then it may be possible to use these profiles to identify children with autism much earlier, allowing for earlier intervention strategies to have an effect during critical periods of neural development.
Epigenetics refers to the mechanisms that are used in a cell to control when, where and how genes are used. The DNA in our cells contains tens of thousands of different genes, but the different cell types in our bodies each use a particular subset of these genes. The ability to control which genes are used and in what amount to help the cell function, and to control which are turned off because they are not needed in that cell type, is largely determined by epigenetics. Epigenetic gene regulation does not alter the DNA sequence; rather it adds an “instruction manual” to each of the genes within the DNA.
How do environmental factors affect epigenetic mechanisms?
The environment encompasses many factors, including (but not limited to) what we are exposed to in our daily living, the things that we eat and social influences. The in utero environment includes the things we are exposed to before we are born. Within each cell there are specific enzymes and cofactors that are responsible for establishing the epigenetic profiles (instruction manuals) at the right location on the DNA and at the right time. These enzymes and cofactors make sure that as cells divide, the epigenetic profiles associated with the DNA in the parent cell are copied exactly to the daughter cell's DNA. Environmental influences can disrupt how well these processes occur. This in turn changes the way the “instruction manual” is interpreted by the cell – and can disrupt how the cell functions.
Everyone has basically two types of cells: somatic cells, which make up our bodies, and germ cells, which are our reproductive cells, better known in their final form as sperm and egg. Are the epigenetic mechanisms and vulnerabilities in germ cells different than somatic cells?
The sperm and egg each carry different epigenetic information that reflects the sex of the individual in which these cells reside. These epigenetic differences give the gametes a “sex” and are required for a viable pregnancy. During early pregnancy, the developing embryo begins to form the germ cells that will eventually produce the sperm or eggs that may be used to create the next generation. When these germ cells begin to form, they undergo a “reprogramming” process during which all epigenetic information is first erased and then is re-established in a way that reflects the sex of the embryo.
This process is carried out by slightly different mechanisms in each germ cell depending on if the embryo is a boy or a girl, but in a way that marks the same parts of the genome with different epigenetic information in developing male versus female germ cells. The most vulnerable time for germ cells is thought to be during this reprogramming in early pregnancy. However, for males, sperm are continually produced from adolescence onward. The final touches on the epigenetic profiles in sperm are made as the sperm go through the last stages of maturation, meaning that sperm may be vulnerable to environmental insults over the entire course of an adult male’s lifetime.
Just after fertilization occurs, there is a second epigenetic reprogramming event where most but not all of the epigenetic information is erased and re-established again. Around the time of implantation in the uterus, the reprogramming process is largely completed and this epigenetic information helps to guide certain cells to form the placenta, other cells to form the developing embryo, and within the embryo, helps direct cells to form tissues and organs, and provides the instructions for when and where to do this. For these somatic cells, vulnerability is likely highest during the period of post-fertilization reprogramming, before a woman realizes she is pregnant.
Somatic cells are also vulnerable once tissues and organs have formed, but this is expected to be more tissue specific. In the somatic cells, it is important that the epigenetic information is copied precisely as cells divide. This "maintenance" function is performed by a different cellular enzyme than the enzymes that establish new epigenetic information during the two reprogramming events. Things that perturb how well these enzymes work can also affect epigenetic shifts, including genetic differences in the DNA sequence that encode these enzymes, epigenetic deregulation of these genes themselves and dietary intake of nutrients involved in one-carbon metabolism (e.g., folate, methionine, betaine, choline), the biochemical pathway that generates methyl groups for DNA methylation.
How did you become involved in this field of research?
My doctoral research was actually in the field of molecular virology. During my second year of graduate school, my then 3-year-old son, who had been born early at 26 weeks and spent nearly 11 months in the neonatal intensive care unit, died of hepatoblastoma (a rare form of liver cancer). Several months prior to his death, my younger son was diagnosed with autism. I made the decision at that time to complete my dissertation research but with the intent to change research direction during my postdoctoral training to an area that would honor my sons.
I then joined Dr. Randy Jirtle’s laboratory at Duke University. Dr. Jirtle’s research in liver cancer, epigenetics and genomic imprinting (an amazing form of epigenetic gene regulation that results in activity of only one of the two inherited copies of a gene in a manner that depends on the sex of the parent from whom that copy was inherited) along with his interest in how epigenetics is involved in neurodevelopment and autism drew me to his lab. As a faculty member for the last eleven years, I have continued with epigenetics research with a focus on early development, but also have an active research program studying epigenetics and therapeutic targeting of gynecologic malignancies.
Do you think that ovarian cancer and breast cancer risk might be linked to prenatal exposures? If so, what type of exposures, and is epigenetics involved?
I think it’s certainly a possibility. We know that there are exposure-related epigenetic shifts in newborn human cord blood at genes that are implicated in cancer, but no one has yet followed children with these epigenetic changes long enough to know if they are linked to increased risk of developing cancer.
Please tell us about the Newborn Epigenetics STudy (NEST) and how it evaluates prenatal influence on somatic cell epigenetics in children.
NEST is a longitudinal cohort study of mother-infant pairs that was started in 2005 at Duke University to specifically address how the in utero environment influences the establishment and maintenance of epigenetic profiles in the child, and how this is related to risk of later disorders and disease. NEST has thus far primarily focused on imprinted genes since we know more about their epigenetic regulation than most other genes, and because imprinted genes are so important to appropriate early development and growth. In addition, many imprinted genes are also involved in cancer.
NEST is now studying epigenetic changes on a genome-wide scale. Over 2,500 mothers were enrolled in the study during pregnancy and were asked to complete detailed questionnaires about their demographics, health and nutrition and to provide blood specimens. When their child was born, umbilical cord blood was collected to allow for research on the relationships between information collected from the mother and her exposures to the epigenetic profiles of their child. NEST continues to follow these children to monitor their growth and development, including neurodevelopment.
A subset of the NEST participants are being followed through the Duke NICHES Children’s Environmental Health and Disease Prevention Research Center, which is examining epigenetic alterations as a potential mechanistic explanation for the link between tobacco smoke exposure during early life and increased risk of attention deficit / hyperactivity disorder.
You also have a study called TIEGER, or The Influence of the Environment on Gametic Epigenetic Reprogramming. This subject goes to the very heart of this website's mission to educate the public about environmental vulnerability of our gametes. What, in general, do you think the public should know about germline epigenetic vulnerability?
Probably the most important aspect of germline epigenetic vulnerability is that it is at its highest during pregnancy. This vulnerability occurs within the cells that will form the gametes (sperm or eggs) of the developing child. These gametes contain the DNA and accompanying epigenetic information that may eventually create grandchildren for the pregnant mother. These gametes begin to develop in the embryo, and part of this process involves an erasure of all of the epigenetic information from the prior generation in the DNA of the cells that will form the gametes.
During pregnancy for a woman, the environment has an effect on three generations at once: the woman who is pregnant, her developing child, and that child’s children. While we still do not understand much about how the environment might affect gametes in the developing child during gestation, we know even less about the factors that might perturb epigenetic reprogramming in sperm of adults and how this might be transmitted to subsequent generations. TIEGER is specifically looking at how body mass index and exposure to endocrine disrupting agents influences the establishment of methylation profiles at imprinted genes.
Do you think approaches to toxicology and drug safety testing should change in light of what we're learning about germline epigenetics?
Yes! Toxicology and drug safety testing rarely take into account the effects of chemicals and drugs on the epigenome of the germ cells of the developing embryo during pregnancy, and such effects could have consequences for future generations much more widespread than DNA mutations. We need to develop more cost-effective technologies to enable assessment of the epigenome in its entirety, or identify a group of sentinel genes that are representative of those affected so that these can be implemented in safety testing.
You have stated publicly that you have a son, now a young adult, with autism. Do you ever speculate about any potential epigenetic origins of his condition or about autism and abnormal neurodevelopment generally?
It's difficult not to speculate, but there are so many past life circumstances that could have contributed it's not possible to pinpoint a particular cause. In my case, during my entire pregnancy with my son who has autism, my older son was born at 26 weeks due to eclampsia and spent nearly 11 months in the NICU with severe lung disease due to his prematurity (a constant source of stress and worry); I took antidepressant medicine before I knew I was pregnant with my younger son due to that stress and worry ("safe" to take while pumping breast milk or during pregnancy; potentially linked to autism); we lived directly adjacent to a freeway (linked to increased risk of prematurity and autism) prior to and throughout our son's early lives in an older four-plex that we remodeled ourselves before we had children (possible lead exposure); both my mother and father smoked, including while I was in utero; and my husband spent part of his adolescence in Salinas, California, a block away from the lettuce fields where pesticide use was ubiquitous (potential effects on gametic reprogramming). These types of exposure histories, for which we all have a version, is a huge problem with trying to decipher cause-effect relationships in humans - each of us has a multifaceted exposure history.
What do you think the autism research community should learn about epigenetics, which in that field remains a new and somewhat mysterious concept?
Over the last several years there has been a rapidly growing interest in the role of epigenetics in autism. This interest needs to be expanded and research in this area should be further prioritized. We need to develop models that can be used to study the relationships between environmental factors, epigenetic changes and autism.
Studies of epigenetics in autism in humans are exceedingly challenging in the affected tissue since autism is a brain disorder. It is also vital that we work toward identifying epigenetic marks in more accessible tissues (blood, saliva, etc.) that can be used as a proxy for altered epigenetic profiles in the brain for human studies. If such concordant relationships exist, then it may be possible to use these profiles to identify children with autism much earlier, allowing for earlier intervention strategies to have an effect during critical periods of neural development.