Overview
This lecture covers epigenetics: how environmental and lifestyle factors modify gene expression on top of the fixed DNA sequence, why this matters for the majority of common (complex) diseases, and how it underlies the emerging field of precision (personalised) medicine.
Single-gene versus complex disease
- Single gene disorders involve only ONE gene, e.g. cystic fibrosis, Duchenne muscular dystrophy, Fragile X, rheumatoid arthritis (placed toward the “totally genetic” end of the genetic-environmental spectrum).
- Complex diseases are caused by many contributing factors: multiple genes/gene networks combined with environmental and lifestyle factors, and are the majority of genetic diseases today, e.g. cancer, PKU, multiple sclerosis, diabetes, asthma, heart disease, schizophrenia, Alzheimer’s, obesity, autism, meningococcus.
- Features of complex disease genetics:
- Any single mutation has a weak effect on gene expression.
- Strong environmental/lifestyle influence on manifestation or severity.
- Do not follow typical (Mendelian) inheritance patterns.
- Model: genes (Gene A-E on different chromosomes) are acted on by +/- signals from environmental stimuli and lifestyle choices, are transcribed/translated into proteins, which interact in a network and converge on the phenotype.
Gene expression as integration of signals
Gene expression profile of a cell at a given time is the integrated sum of:
- Primary DNA sequence
- Regulatory sequences
- Gene networks
- Chromatin architecture
- Epigenetics/epigenomics
Fluctuations in functional gene product level (from natural variation or epigenetic/epigenomic marks) matter differently by gene: for some genes this has little importance, for others it has severe clinical consequences, reflecting how important that gene product is in its pathway.
Mechanisms of epigenetic regulation
Three main mechanisms link environmental/lifestyle factors to gene expression outcomes:
- DNA methylation — hypermethylation of a promoter silences the gene; hypomethylation permits expression.
- Covalent modification of histones — produces a relaxed or compact chromatin structure, which differentially affects transcriptional activity.
- Regulation of miRNA expression — DNA methylation of miRNA loci leads to translational repression or transcript degradation.
Factors reported to influence these marks include diet (folate, EGCG from green tea, selenium, polyphenols), physical activity, tobacco smoke, intrauterine life/maternal diet, alcohol, pollutants (arsenic, chromate, particulate matter, benzene, PAHs, POPs), aging, stress, and shiftwork.
Epigenetics in disease
- Cancer: hypermethylation of promoters of tumour suppressor genes and/or hypomethylation of promoters of oncogenes. Confirmed in genes causing breast and colorectal cancer. Early cancer detection is possible by assessing promoter methylation of tumour suppressor/oncogenes (e.g. APC, RASSF1A, TP53). [slide does not elaborate further mechanism beyond invasion/metastasis as the downstream disease consequence]
- Autoimmune disease:
- Rheumatoid arthritis: DNA promoter hypomethylation of histone deacetylase genes; hypermethylation of histone H3 at lysine 9 in synovial tissue.
- Multiple sclerosis: hypomethylation of DNA in CNS white matter.
- Other examples: asthma, coeliac disease.
- Neurodegenerative/psychological disorders: epigenetic marks undergo major changes during normal brain development; abnormal marks are linked to disease.
- Alzheimer’s and schizophrenia: DNA promoter hypomethylation of many genes.
- Other examples with known abnormal epigenetic marks (particularly DNA methylation changes): autism, Fragile-X, Rett syndrome (abnormal brain development in infancy), Parkinson’s.
- Addiction: genetic background affects susceptibility to drug addiction, but altered epigenetic marks from substance exposure (e.g. opiates, chronic morphine) can drive drug-seeking behaviour, relapse and increased risk of other disease.
- Morphine alters DNA methylation of brain-derived neurotrophic factor (BDNF).
- Cocaine increases histone acetylation of certain oncogenes/proto-oncogenes.
- Diabetes: genetic background matters for all types, but poor lifestyle produces altered epigenetic marks that increase disease risk. Pathway: obesity/inheritance/other factors → insulin resistance → muscle cannot use glucose → raised blood glucose → pancreas secretes more insulin → type 2 diabetes. Differential DNA methylation → altered gene expression → impaired insulin secretion and insulin resistance → type 2 diabetes, with implicated genes differing by tissue (liver, blood, pancreatic islets, adipose tissue, skeletal muscle).
Lifestyle and environmental modifiers of epigenetic marks
- Exercise: changes DNA methylation of gene promoters in ways that enhance health, e.g. increased methylation of lipogenesis genes; methylation changes that increase tumour suppressor gene expression or decrease oncogene expression (often via modulating miRNA expression); improved miRNA expression patterns in leukocytes. A sedentary lifestyle has the opposite effect.
- Diet: also changes promoter methylation beneficially.
- Folate and B vitamins provide methyl groups that hypermethylate (silence) certain gene promoters, including genes that inhibit “beneficial” genes via gene-network interactions.
- Folate keeps DNA repair genes transcriptionally active via methylation patterns, and hypermethylates genomic DNA to protect against colorectal cancer.
- Soy and anthocyanins keep DNA repair genes transcriptionally active via methylation patterns.
- Environmental chemicals and toxins: effects tend to be more permanent and can be passed to offspring.
- Decreased/no expression of tumour suppressor (“P”) genes → cancer.
- Toxins from bacteria such as Listeria monocytogenes and Streptococcus pneumoniae dramatically change histone acetylation patterns.
- Cigarette smoke alters DNA methylation and miRNA expression: increases asthma risk, and induces demethylation of metastatic genes in lung cancer cells.
- [slide does not elaborate mechanistic detail for the individual chemicals in the summary table (arsenic, cadmium, nickel, chromium, methylmercury, TCE/DCA/TCA, air pollution, benzene, vinclozolin, DES, BPA, POPs) beyond the gene(s)/tissue affected]
- Maternal influences: the in-utero environment modulates fetal development via epigenetic modification.
- Maternal stress (work stress, poverty, domestic violence, abuse) → hypermethylation of the glucocorticoid receptor gene promoter → abnormal fetal brain development → neurological disease, psychiatric disorder, lower cognitive ability, suicidal tendencies.
- Lack of maternal care/affection → hypomethylation alters glucocorticoid receptor gene expression → increased cortisol production → unhealthy adult outcomes (suppressed immunity, hypertension, hyperglycaemia, type 2 diabetes, obesity, reduced libido). This is reversible: the glucocorticoid receptor gene promoter can be remethylated through behavioural therapy and stress-alleviating activities.
- Transgenerational inheritance: altered epigenetic marks can affect generations not directly exposed.
- Non-gestational exposure: exposure in the F0 generation produces health effects reported in the F2 generation (not directly exposed).
- Gestational exposure: exposure of the mother (F0) affects the fetus (F1) and its reproductive cells (F2), with health effects reported in the F3 generation (not directly exposed).
Key takeaway (slides 91-105)
Unique sets of genes are induced or silenced epigenetically at different life stages to direct normal development and adaptation to environmental signals. Throughout life, exposures (medicinal/recreational drugs, chemicals, diet, stress, exercise, and other environmental factors) trigger chemical changes that activate or silence genes, producing positive or negative epigenetic modifications with lasting effects on development, metabolism and health — effects that can permanently alter an individual’s epigenetic profile and/or that of future generations. Many complex genetic diseases arise, or become more severe, because of dysregulated gene expression caused by altered epigenetic marks. [slide states the examples and mechanistic detail above are not required, only this summary]
Precision (personalised) medicine
- Definition: using information about a person’s genome sequence and biochemical individuality as the basis for person-specific treatment.
- Rationale — the scale of adverse drug reactions (ADRs):
- 28% of hospitalised patients have drug-related ADRs (Miller et al., 1973).
- 17% of hospitalised children have drug-related ADRs (Mitchell et al., 1979).
- Overall incidence of drug-related ADRs is 7% (Lazarou et al., 1998).
- Cost of drug-related morbidity and mortality is $177 billion (Ernst et al., 2001).
- “One dose (and one drug) does NOT fit all” — the same diagnosis and prescription can be toxic-and-beneficial, toxic-and-not-beneficial, not-toxic-and-not-beneficial, or not-toxic-and-beneficial across different patients.
- Precision medicine aims to deliver the right drug/intervention, in the right dose, to the right person, at the right time, based on individual genetics, requiring molecular testing of genetic background and metabolic responses. In principle, all patients benefit from tailored treatment with no ADR.
- Benefits: a more precise dose can be calculated, or a drug selected/avoided for treatment, decreasing ADRs and other toxic effects and maximising therapeutic effect.
- Limitations: identifying genes that influence drug response is very difficult, especially since most genes act within gene networks; the interaction with environmental/lifestyle factors (and other drugs) must be determined before conclusions can be drawn about genetic influence on drug action.
- Epigenetic therapy: alteration of epigenetic marks in genetic disease is a reason many treatment approaches fail. Epigenetics-based drug development (“epigenetic therapy”) could be developed once the underlying mechanisms and influencing factors are understood, and would be an important part of precision medicine since chemical modifications of DNA and histones are as important as the DNA sequence itself. DNA methylation inhibitors are currently used against various cancers and psychiatric diseases (schizophrenia and bipolar disorder).
Key takeaway (slides 107-111)
Precision medicine is conceptually a “medical magic bullet,” but because of the complexity of epigenetic marks, gene networks, lifestyle choices and environment, it is currently challenging to achieve or perfect in practice.
Self-test
- Distinguish single-gene disorders from complex diseases in terms of number of genes involved, effect size of individual mutations, environmental influence, and inheritance pattern.
- List the five components that together determine a cell’s gene expression profile at a given time.
- Describe the three main epigenetic mechanisms that link environmental/lifestyle exposures to changes in gene expression.
- Explain how promoter methylation changes contribute to cancer development, and name three genes used for early cancer detection via promoter methylation.
- Describe the epigenetic changes reported in rheumatoid arthritis and in multiple sclerosis.
- Explain the mechanism by which maternal stress during pregnancy can lead to neurological or psychiatric disease in the offspring.
- Explain how lack of maternal care can affect adult health via the glucocorticoid receptor gene, and describe how this effect can be reversed.
- Distinguish non-gestational from gestational transgenerational epigenetic inheritance in terms of which generation shows the reported health effect.
- Give one example each of how exercise and how diet can beneficially alter DNA methylation patterns.
- Define precision (personalised) medicine and explain why the scale of adverse drug reactions motivates it.
- Describe the main limitation to identifying which genes influence an individual’s drug response.
- Integrative: using the diabetes and maternal-stress examples, explain how a single overarching principle (gene-environment interaction via epigenetic marks) can lead both to a metabolic disease and to a psychiatric outcome.
Answers
Reveal answers
- Single-gene disorders involve only one gene, sit toward the “totally genetic” end of the spectrum (e.g. cystic fibrosis, Duchenne muscular dystrophy, Fragile X, rheumatoid arthritis), and are less environmentally modified. Complex diseases involve multiple genes/gene networks plus environmental and lifestyle factors, each contributing mutation has only a weak effect on expression, environmental/lifestyle influence on manifestation or severity is strong, and they do not follow typical inheritance patterns.
- Primary DNA sequence, regulatory sequences, gene networks, chromatin architecture, and epigenetics/epigenomics.
- DNA methylation (hypermethylation of a promoter silences the gene, hypomethylation permits expression); covalent modification of histones (produces relaxed or compact chromatin, altering transcriptional activity); regulation of miRNA expression (DNA methylation of miRNA loci causes translational repression or transcript degradation).
- Hypermethylation of promoters of tumour suppressor genes and/or hypomethylation of promoters of oncogenes silences protective genes and activates growth-promoting genes, contributing to cancer. Promoter methylation of APC, RASSF1A and TP53 is used for early cancer detection.
- Rheumatoid arthritis: DNA promoter hypomethylation of histone deacetylase genes, and hypermethylation of histone H3 at lysine 9 in synovial tissue. Multiple sclerosis: hypomethylation of DNA in central nervous system white matter.
- Maternal stress (e.g. work stress, poverty, domestic violence, abuse) causes hypermethylation of the glucocorticoid receptor gene promoter, which leads to abnormal fetal brain development and results in neurological disease, psychiatric disorder, lower cognitive ability and suicidal tendencies.
- Lack of maternal care/affection causes hypomethylation that alters glucocorticoid receptor gene expression, increasing cortisol production and producing an unhealthy adult phenotype (suppressed immunity, hypertension, hyperglycaemia, type 2 diabetes, obesity, reduced libido). This can be reversed by remethylating the glucocorticoid receptor gene promoter through behavioural therapy and stress-alleviating activities.
- Non-gestational exposure: the exposed individual is F0, and the reported health effect appears in the F2 generation (not directly exposed). Gestational exposure: the mother is F0, the fetus is F1, and because the fetus’s reproductive cells (which become F2) are also exposed in utero, the reported health effect appears in the F3 generation (not directly exposed).
- Exercise: increases DNA methylation of lipogenesis genes (among other beneficial methylation changes). Diet: folate and B vitamins provide methyl groups that hypermethylate (silence) certain gene promoters, and folate hypermethylates genomic DNA to help protect against colorectal cancer.
- Precision medicine uses information about a person’s genome sequence and biochemical individuality to give person-specific treatment (right drug, right dose, right person, right time). It is motivated by the high scale of adverse drug reactions: 28% of hospitalised patients and 17% of hospitalised children have drug-related ADRs, overall ADR incidence is 7%, and the associated cost is $177 billion, showing that “one dose does not fit all.”
- Identifying genes that influence drug response is very difficult because most such genes act as part of gene networks rather than in isolation, and their interaction with environmental/lifestyle factors and other drugs must also be worked out before genetic influence on drug response can be concluded.
- In both cases genetic background sets a baseline that is modified by an environmental exposure acting through epigenetic marks: in diabetes, obesity/lifestyle factors alter DNA methylation across tissues (liver, pancreatic islets, adipose, muscle), changing gene expression and impairing insulin secretion/action; in the maternal-stress example, a psychosocial exposure alters methylation of the glucocorticoid receptor gene, changing cortisol signalling and brain development. In each case genetics alone does not determine outcome — an environmental trigger acting via epigenetic modification of gene expression is required to produce the disease phenotype.