Genetics, and Disease A Literature Review

By: Anthony M. Pasek

Faculty Advisor: Rodger Tepe, PhD

A senior research project submitted in partial requirement for the degree Doctor of Chiropractic

August 11, 2011

Abstract

Objective – This article provides an overview of the scientific literature available on the subject of genetic mechanisms of disease etiology as compared to epigenetic mechanisms of disease etiology. The effects of environmental influences on genetic expression and transgenerational inheritance will also be examined. Methods – Searches of the keywords listed below in the databases PubMed and EBSCO yielded referenced articles from indexed journals, literature reviews, pilot studies, longitudinal studies, and conference meeting reports. Conclusion – Although current research indicate a relationship between the static and the dynamic environment and offer epigenetics as a mechanism, further research is necessary. Epigenetic processes have been implicated in many diseases including diabetes mellitus, obesity, cardiovascular disease, metabolic disease, , autism, Alzheimer’s disease, depression, and addiction. Keywords – genetics, central dogma of , , , genomic imprinting, epigenetics, modification, DNA methylation, agouti mice, epigenetic drift, Överkalix, Avon Longitudinal Study of Parents and Children (ALSPAC).

2 Introduction

Genetics has long been the central field of biology and it’s central dogma states that DNA leads to RNA, which leads to and ultimately determines or sickness1. The Project marked a great triumph for humanity and researchers expected to solve the riddle of many complex diseases with the knowledge gleamed from this project. However, many more questions were raised than answered.

Several rare genetic disorders including hemophilia and cystic fibrosis were explained by alterations in the but true genetic diseases only affect about one percent of the human population2. Epidemic disorders such as obesity, cardiovascular disease, metabolic diseases, and cancer were determined to be multifactorial and not entirely genetic in origin1.

Epigenetics is the study of changes in phenotype or expression caused by mechanisms other than changes in the underlying genotype, i.e., DNA sequence of the organism3. Environmental influences play a crucial role in altering the epigenome. The influence of environmental forces on genetic material revolutionized the central dogma of biology. Epigenetics has been dubbed the new biology and it’s implications on health and disease are profound1. Researchers and physicians are now realizing that to facilitate lasting change in patients lifestyle and environmental factors must be taken into consideration.

3 Discussion

Genetics

Every human is either a somatic cell or a reproductive cell. Reproductive cells are known as and include cells and egg cells. Every other cell is considered a somatic cell. Cells contain a nucleus that houses the genetic material known as deoxyribonucleic acid (DNA) arranged in compact called chromosomes4.

Each somatic cell contains 46 made up of 23 pairs of homologous chromosomes, where one in each pair is paternal in origin, and the other is maternal in origin4. One chromosome consists of two sister connected by a . Somatic , or , is a process that results in two genetically identical cells by cleaving the centromere and dividing the two sister chromatids equally into two daughter cells4. Reproductive cell division, or , is a process that results in genetically diverse cells with half of the normal number of chromosomes. When reproductive cells combine, the result is a zygote that is genetically disctinct from both the paternal and maternal genome4. Meiosis and sexual fertilization account for the genetic variability between individuals of a species4.

The DNA is complexed with many diverse to condense and organize the genetic material. This complex is referred to as . are proteins that act as a spool for the DNA to coil around. Other proteins form structures similar to scaffolding to aid in looping and folding the DNA. Chromatin morphology changes throughout the cell cycle and is a key factor in genetic accessibilty1. Condensed chromatin is present during cell division to enable the chromosome to be easily divided

4 and prevents most of the from being transcribed1. Loosely packed chromatin is present throughout most of the cell cyle and allows the genes to be transcribed1, 4.

Every cell of an contains the same genetic code, but have approximately 200 different cell types. Cell differentiation is the process by which cells alter their form and to become specific cell types. Differential is the expression of different genes by cells with same genome. Epigenetic mechanisms initiate and maintain cellular differentiation3. Skin cells express their genes differently than nerve and muscle cells even though they all have the same genetic code4.

Chromatin morphology, histone modification, and DNA methylation play a role in differential gene expression5. When an acetyl group is bound to the tail of a histone it’s charge is neutralized and the histone is less attracted to neighboring chromatin structures.

This results in a looser chromatin and increased accessability of the genes for . Methyl groups bound to histone tails will have the opposite effect by condensing the chromatin further4. Methyl groups bound to DNA bases result in similar suppression of genetic transcription and these DNA methylation patterns are maintained through successive cell divisions. These patterns are also passed to the next generation4.

The inheritance of traits through mechanisms not involving the sequence is called epigentic inheritance4. DNA methylation accounts for genomic imprinting throughout the of an organism and epigenetic inheritance across generations6.

5 The collective DNA or genetic code of an individual is known as the genotype, while the expressed traits of the individual are known as the phenotype4. For certain characteristics the genotype produces a very specific and predictable phenotype, while in other instances the genotype may result in a variety of . This phenotypic range is called the norm of reaction4. Characteristics that exhibit a broad norm of reaction, such as skin color, are considered multifactorial because both the genotype and the environment collectively influence the resultant phenotype4. A character is a heritable biological feature, such as hair color, that varies among individuals. Each variant for a character, such as blonde or brown hair, is called a trait. The transmission of traits from one generation to the next is called inheritance, or heredity4. The scientific field of genetics examines and heriditary variation.

Gregor Mendel’s experiments and hypotheses formed the foundation for modern genetics and inheritance4. Mendel’s research first described what are now known as , or alternate versions of the same gene, which account for character variants.

Mendel noted that for each character, an individual inherits two distinct alleles, one from each parent. Mendel also descibed the occurrence of two different alleles present in the same individual. When this occurs, one is dominant and determines the phenotype while the other is recessive and has no noticeable effect on the phenotype. Mendel also origninated the concept that became known as the law of segregation. This law states that the two alleles for a heritable character segregate during formation4. An organism having a pair of identical alleles for a character is said to be homozygous for the gene

6 controlling that character4. An organism that has two different alleles for a gene is said to be heterozygous for that gene4.

Genetic Disorders

Thousands of genetic disorders are known to be inherited as simple recessive traits4. These disorders range in severity from albinism to cystic fibosis4. Heterozygotes are phenotypically normal due to the presence of the dominant allele but may transmit the recessive allele to their offspring and thus are called carriers. Homozygotes express the disorder phenotypically. The most common lethal genetic disease in the United States of

America is cystic fibrosis4. The incidence of cystic fibrosis among those of European descent is one in 2,5004. The incidence of carriers of cystic fibrosis among those of

European descent is one in 25, or 4%4. The most common inherited disorder among those of African descent is sickle-cell disease4. The incidence of sickle-cell disease is one in four hundred among those of African descent4.

Dominant alleles that cause a lethal disease are much less common than recessive alleles that cause a lethal disease. All lethal alleles occur as a result of DNA in a gamete. Achondroplasia and Huntington’s disease are examples of genetic disorders caused by a dominant allele4. The incidence of Huntington’s disease in the Unites States of America is one in 10,0004. Children born to a parent with Huntington’s disease have a

50% chance of inheriting the allele and the disorder4.

7 Human is determined by the presence of sex chromosomes. have two X chromosomes present while males have one and one present. A gene located on a , specifically on the X chromosome, is referred to as a sex-linked gene4, 7. Fathers pass sex-linked alleles to all of their daughters but to none of their sons. Mothers can pass sex-linked alleles to both daughters and sons. Recessive sex-linked traits in are only expressed in homozygotes, while any male that inherits the recessive allele will express the trait. As a result, sex-linked recessive disorders are much more common in males than females4.

Color blindness, Duchenne , and hemophilia are examples of sex- linked recessive disorders4.

Aneuploidy describes an abnormal number of one particular chromosome4.

Monosomy describes one chromosome and trisomy describes three chromosomes. Down is often the result of trisomy 21. The risk of Down syndome increases with the age of the mother4. Sex chromosome can produce diverse .

Klinefelter’s syndrome is the presence of at least two X chromosomes and at least one Y chromosome4. Turner syndrome is the presence of only one X chromosome and is known as monosomy X4. Chromosomal translocations are the result of the transfer of one chromosome fragment to another chromosome. Different structural alterations through translocation can result in disorders such as cri du chat syndrome or chronic myelogenous leukemia4.

8 Phenotypes can vary based on the source of the dominant allele. A paternally inherited dominant allele for a particular trait may be more likely to be expressed than a maternally inherited dominant allele for the same trait. This variation in phenotypic expression dependent on the gender of origin is known as genomic imprinting6. Genomic imprinting occurs during the formation of gametes and results in the silencing of one allele of certain genes4, 6. Within a , imprinted genes are always imprinted in the same way. Generation after generation a gene imprinted for paternal expression will always be imprinted for paternal expression. A common mechanism of genomic imprinting is methylation of on one of the alleles5. Methylation of alleles tends to inactivate or silence them but in some cases methylation of alleles will activate them4, 5. Genomic imprinting only affects a small fraction of genes in humans but most of the known imprinted genes are crucial for normal embryonic development4, 5.

Epigenetics and Epigenetic Disorders

Epigenetics is the study of changes in phenotype or gene expression caused by mechanisms other than changes in the underlying DNA sequence of the organism3. The term epigenetics was coined by Conrad Waddington in the early 1940s8. The molecular basis of epigenetic inheritance has since been studied in a variety of organisms5. Two epigenetic systems (the DNA methylation system and the Polycomb/Trithorax systems) are good molecular models of epigenetics because alterations in these systems are often inherited by subsequent generations of cells and sometimes by sebsequent genearations of organisms5. DNA methylation is associated with stable gene silencing5. The Polycomb

9 group of proteins maintain suppressed transcription states while the Trithorax group of proteins maintain active transciption states5.

The mouse agouti gene, which affects coat color and other traits, is the best- studied epigenetic phenomenon5, 9. DNA methylation differences at this gene cause genetically identical parents to have different epigenetic states and as a result produce offspring with different coat colors5. Viable yellow agouti mice are larger, obese, hyperinsulinemic, more susceptible to cancer, and shorter lived than their pseudoagouti siblings who are brown, lean, healthy, and longer lived10. Maternal supplementation of methyl groups produced more pseudoagouti offspring. The methyl supplementation increased methylation of the agouti gene which suppressed it’s expression and resulted in a more pseudoagouti phenotype offspring10.

Nutrition and environmental factors influence a developing individual but the specific disease risk is more complex than early exposure alone11. An induced epigenetic change in an individual will only result in disease later in life if disease-inducing environmental cues persist throughout their life11. If these environmental cues are absent, a healthy phenotype may be achieved11 (Figure 1). Interestingly, both abundant and constrained imposed on an will enduce epigenetic change that could develop into metabolic and cardiovascular disease or cancer, respectively11 (Figure 1).

Monozygotic do not always show the same disease susceptibility which suggests that epigenetic differences that arise with age may affect one differently

10 than the other12. It has been reported that young twins have similar DNA methylation patterns while older twins differ considerably in their DNA methylation patterns13 (Figure

2). As a result, the same genotype can result in radically different phenotypes due to distinct epigenotypes present in each individual13. This divergence of gene expression over time is known as epigenetic drift13. This dynamic model of methylation plasticity between individuals and over time illuminates the neccessity for longitudinal epigenetic studies to enable a more clear understanding of this phenomenon12.

Maternal nurturing and it’s effects on the health of offspring have long been acknowledged5. Studies on have suggested an epigenetic mechanism may be at work involving DNA methylation of the gene responsible for the glucocoticoid receptor14. In the absence of quality nurturing this gene is less methylated in the hippocampus which results overproduction of the glucocorticoid receptor later in life14. This would suggest that an offspring’s ability to appropriately regulate a stress response via the hypothalamic-pituitary-adrenal axis is dependant on maternal nurturing in youth4, 14.

Several recent studies have showed that prenatal environmental conditions are associated with persistent changes of the human epigenome15, 16, 17. The epigenome systematically controls gene expression during embryonic development and throughout life18. The epigenome is a very reactive system which allows it to detect and respond to environmental changes to ensure survival of the organism, especially during fetal growth18. This plastic also can lead to aberrant epigenetic modifications that may persist into later life and result in numerous disorders18. Compounds such as bisphenol A

11 (BPA) can alter epigenetic methylation via a process known as epigenotoxicity18.

Epigenotoxicity could result in developmental, metabolic, and behavioral disorders and the transgenerational inheritance of these epigentic modifications raises new concerns over the safety of BPA, pesticides, pharmaceuticals, and heavy metals16, 18.

Analysis of the detailed agricultural and genealogical records from the isolated parish of Överkalix in Northern Sweden revealed interesting transgenerational epigenetic effects19. A link was established between nutritional intake of one generation and the risk of cardiovascular and diabetes mellitus mortality in the paternal grandchildren of that generation19. If a grandfather was exposed to food surplus and overate during his prepubertal slow growth period his paternal grandson was more likely to suffer diabetic mortality19. Similar results were found relating a grandmother’s food supply to her maternal granddaughter’s mortality risk20. The correlation is a sex-specific transgenerational response where a grandfather affects his grandson and the grandmother affects her granddaughter (Figure 3) but the grandfather has minimal impact on his granddaughter and the grandmother has minimal impact on her grandson7 (Figure 4). The same researchers analyzed data from the Avon Longitudinal Study of Parents and

Children (ALSPC) and determined a sex-specific male line transgenerational response that correlated early paternal smoking with increased body mass index (BMI) of sons, but not daughters, at age nine7, 21. Studies of individuals who were prenatally exposed to famine during the Dutch Hunger Winter of 1944-45 showed persistent DNA hypomethylation six decades later22. This association was specific for periconceptional exposure that reinforces the presence of a sensitive window in very early development

12 where epigenetic marks are established and maintained22, 23. Epigenetic transgenerational inheritance is not fully understood and further research is needed to decode these complex patterns24.

Cancer cells tend to have more DNA hypomethylation than noncancerous cells25.

This suggests an epigenetic mechanism in tumorigenesis and the progression of neoplasia26. Interestingly, the emerging field of epigenetic therapeutics utilizes epigenetic drugs to modify the altered epigenome in an attempt to normalize cancer cells and halt their progression3, 27, 28. Epigenetic therapeutics is not limited to treatment of cancer.

Neurodegenerative conditions may respond to this of treatment as well29.

Many neural developmental disorders such as autism, Rett Syndrome, Fragile X

Syndrome, , and Prader-Willi Syndrome are multifactorial in origin but involve epigenetic changes during early development3, 30. Certain psychiatric disorders such as addiction, depression, and are similarly multifactorial and involve epigenetic events3, 29, 31, 32.

Epigenetic mechanisms also play a crucial role in neuroplasticity33, 34. These mechanisms have been utilized in models of learning and memory formation involving the dentate gyrus35. Chronic low back pain involves changes in expression of immediate early genes (IEGs) and late response genes (LRGs) in wide dynamic range (WDR) neurons36 (Figure 5). Spinal manipulative therapy (SMT) and other mechanoreceptive input to the WDR neuron normalize the expression of IEGs and LRGs36 (Figure 6).

13 Conclusion

Epigenetics is a complex field of that relates environmental influences to disease etiology and disease inheritance. It represents a revolutionary approach to genetic and biological processes that has many implications including new understanding of disease mechanisms, therapeutic mechanisms, public health, and political policy. While the existing research on this subject is very compelling, it is limited in breadth. The top researchers in the field insist that more research is needed to fully understand epigenetics and all that it entails, but the consensus is that this knowledge will change the way we discuss disease forever.

The Human catalogued the entire human genome and involved a massive multi-year collaboration among scientists around the world and cost billions of dollars. Researchers found approximately 30,000 genes2. It is estimated that over 8,000 human diseases are caused by defects in single genes2. These diseases are unifactorial and affect approximately one percent of the human population2. In contrast, major common diseases like cancer and diabetes are much more complex in origin and often involve susceptibility genes and their interaction with the environment2. In light of this knowledge and recent epigenetic breakthroughs, the aims to identify, catalogue, and interpret genome-wide DNA methylation phenomena37. A pilot study has already completed profiling DNA methylation of the human major histocompatibilty complex and illustrates how the Human Epigenome Project will be orders of magnitude more complex than the Human Genome Project37.

14 References

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2) Liu, Liang, Yuanyuan Li and Trygve O Tollefsbol. "Gene-environment interactions and epigenetic basis of human diseases." Current Issues of (2008): 25- 36.

3) Delcuve, Genevieve P, Mojgan Rastegar and James R Davie. "Epigenetic Control." Journal of Cellular (2009): 243-250.

4) Campbell, Neil A and Jane B Reece. Biology. 7th Edition. Pearson Benjamin Cummings, 2005.

5) Bird, Adrian. "Perceptions of epigenetics." Nature 447 (2007): 396-398.

6) Durcova-Hills, Gabriela, et al. "Influence of sex chromosome constitution on the genomic imprinting of germ cells." Proceedings of the National Academy of (2006): 11184-11188.

7) Pembrey, Marcus E, et al. "Sex-specific, male-line transgenerational responses in humans." European Journal of Human Genetics 14 (2006): 159-166.

8) Jabloka, Eva and Marion J Lamb. "The changing concept of epigenetics." Annals New York Academy of Sciences (2002): 82-96.

9) Haemer, Matthew A, Terry T Huang and Stephen R Daniels. "The effect of neurohormonal factors, epigenetic factors, and gut microbiota on risk of obesity." Preventing Chronic Disease (2009): 1-8.

10) Wolff, George L, et al. "Maternal epigenetics and methyl supplements affect agouti gene expression in Avy/a mice." The FASEB Journal 12 (1998): 949-957.

11) Burdge, Graham C, Karen A Lillycrop and Alan A Jackson. "Nutrition in early life, and risk of cancer and metabolic disease: alternative endings in an epigenetic tale?" British Journal of Nutrition (2009): 619-630.

12) Wong, Chloe Chung Yi, et al. "A longitudinal study of epigenetic variation in twins." Epigenetics (2010): 516-526.

13) Fraga, Mario F, et al. "Epigenetic differences arise during the lifetime of monozygotic twins." Proceedings of the National Academy of Sciences (2005): 10604- 10609.

15 14) Weaver, Ian CG. "Epigenetic programming by maternal behavior and pharmacological intervention." Epigentics (2007): 22-28.

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17) Wadhwa, Pathik D, et al. "Developmental origins of health and disease: brief history of the approach and current focus on epigenetic mechanisms." Seminars in Reproductive (2009): 358-368.

18) Bernal, Autumn J and Randy L Jirtle. "Epigenomic disruption: the effects of early developmental exposures." Birth Defects Research 88 (2010): 938-944.

19) Kaati, G, L O Bygren and S Edvinsson. "Cardiovascular and diabetes mortality determined by nutrition during parents’ and grandparents’ slow growth period." European Journal of Human Genetics 10 (2002): 682-688.

20) Kaati, Gunnar, et al. "Transgenerational response to nutrition, early life circumstances and ." European Journal of Human Genetics 15 (2007): 784-790.

21) Ness, Andy R. "The Avon Longitudinal Study of Parents and Children (ALSPAC) – a for the study of the environmental determinants of childhood obesity." European Journal of Endocrinology (2004): 141-149.

22) Heijmans, Bastiaan T, et al. "Persistent epigenetic differences associated with prenatal exposure to famine in humans." Proceedings of the National Academy of Sciences 105 (2008): 17046-17049.

23) Zeisel, Steven H. "Epigenetic mechanisms for nutrition determinants of later health outcomes." American Journal of Clinical Nutrition (2009): 1488-1493.

24) Slatkin, Montgomery. "Epigenetic inheritance and the missing problem." Genetics (2009): 845-850.

25) De Smet, Charles and Axelle Loriot. "DNA hypomethylation in cancer: epigenetic scars of a neoplastic journey." Epigenetics (2010): 206-213.

26) Rattner, Barbara P. "Cancer epigenetics and biology symposium Barcelona, May 28– 29, 2009." Epigenetics (2009): 421-424.

27) Selcuklu, S Duygu and Charles Spillane. "Translational epigenetics: clinical approaches to epigenome therapeutics for cancer." Epigenetics (2008): 107-112.

16 28) Sigalotti, Luca, et al. "Epigenetics of human cutaneous melanoma: setting the stage for new therapeutic strategies." Journal of Translational Medicine 8 (2010).

29) Mehler, Mark F. "Epigenetic principles and mechanisms underlying nervous system functions in health and disease." Progress in Neurobiology (2008): 305-341.

30) Zhao, Xinyu, et al. "Epigenetics and neural developmental disorders Washington DC, September 18 and 19, 2006." Epigenetics (2007): 126-138.

31) Murgatroyd, Chris, et al. "Genes learn from stress: how infantile trauma programs us for depression." Epigenetics (2010): 194-199.

32) McQuown, Susan C and Marcelo A Wood. "Epigenetic regulation in substance use disorders." Current Reports (2010): 145-153.

33) Borrelli, Emiliana, et al. "Decoding the epigenetic of neuronal plasticity." Neuron (2008): 961-974.

34) Fagiolini, Michela, Catherine L Jensen and Frances A Champagne. "Epigenetic influences on development and plasticity." Current Opinion in Neurobiology (2009): 207-212.

35) Reul, Johannes MHM, et al. "Epigenetic mechanisms in the dentate gyrus act as a molecular switch in hippocampus-associated memory formation." Epigenetics (2009): 434-439.

36) Boal, Robert W and Richard G Gillette. "Central neuronal plasticity, low back pain and spinal manipulative therapy." Journal of Manipulative and Physiological Therapeutics (2004): 314-326.

37) Rakyan, Vardhman K, et al. "DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project." PLoS Biology (2004): 2170-2182.

17 Figure 1

Source: Burdge, Graham C, Karen A Lillycrop and Alan A Jackson. "Nutrition in early life, and risk of cancer and metabolic disease: alternative endings in an epigenetic tale?" British Journal of Nutrition (2009): 619-630.

18 Figure 2

Source: Fraga, Mario F, et al. "Epigenetic differences arise during the lifetime of monozygotic twins." Proceedings of the National Academy of Sciences (2005): 10604-10609.

19 Figure 3

Source: Pembrey, Marcus E, et al. "Sex-specific, male-line transgenerational responses in humans." European Journal of Human Genetics 14 (2006): 159-166.

20 Figure 4

Source: Pembrey, Marcus E, et al. "Sex-specific, male-line transgenerational responses in humans." European Journal of Human Genetics 14 (2006): 159-166.

21 Figure 5

Source: Boal, Robert W and Richard G Gillette. "Central neuronal plasticity, low back pain and spinal manipulative therapy." Journal of Manipulative and Physiological Therapeutics (2004): 314-326.

22 Figure 6

Source: Boal, Robert W and Richard G Gillette. "Central neuronal plasticity, low back pain and spinal manipulative therapy." Journal of Manipulative and Physiological Therapeutics (2004): 314-326.

23