Epigenetic effects of smoking

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Epigenetic effects of smoking concerns how epigenetics (hertiable characteristics that do not involve changes in DNA sequence) contributes to the deleterious effects of smoking. Cigarette smoking has been found to affect global epigenetic regulation of transcription across tissue types. Studies have shown differences in epigenetic markers like DNA methylation, histone modifications and miRNA expression between smokers and non-smokers. Similar differences exist in children whose mothers smoked during pregnancy. These epigenetic effects are thought to be linked to many of negative health effects associated with smoking.

Contents

Health impact

It has been well established that smoking cigarettes has a number of negative health effects, including increased risk for cancer, cardiovascular disease, and chronic obstructive pulmonary disease (COPD). [1] Children exposed prenatally to cigarette smoke demonstrate increased risk for fetal growth restriction, sudden infant death syndrome, and addictive behaviors later in life, as well as a host of other secondary health effects. It is thought that epigenetic changes that arise from smoking cigarettes or exposure to cigarette smoke play a role in the development of these conditions.

Epigenetic modifications to the genome, including histone modifications, DNA methylation, and the modulation of RNAi, are major epigenetic events used to modulate gene expression. When the epigenome of an organism is altered by an environmental cue like smoking, gene expression changes accordingly. Changes in the regulation of critical genes can have disastrous consequences on health and quality of life. Irregular gene expression is one of the hallmarks of cancer, but is also found in a number of diseases and disorders.

Mechanisms for changes in DNA methylation

One of the most prominent and well studied epigenetic consequences of cigarette smoke is altered DNA methylation. Cigarette smoke acts through a number of mechanisms to effect this, chief among these being smoke-induced damage to the DNA and altered expression levels of proteins involved in DNA methylation and transcriptional regulation.

Damage to DNA

Chemicals in smoke can damage DNA, which subsequently leads to changes in DNA methylation during the repair process. Damage typically comes in the form of double-strand breaks that are linked to carcinogens like arsenic, chromium, formaldehyde, polycyclic aromatic hydrocarbons, and nitrosamines which are found in cigarette smoke. DNMT1 is the enzyme involved in the maintenance of DNA methylation marks. DNMT1 is recruited to DNA during its replication, or during DNA repair. As a new DNA strand is synthesized, unmethylated cytosines are incorporated into the sequence. This leads to hemimethylated DNA, where an older methylated strand is bound to a younger unmethylated one.

DNMT1 is an enzyme which recognizes and corrects hemimethylation by transferring the appropriate methyl groups to the newly synthesized strand. Like all biological processes, DNMT1 based hemimethylation correction is not perfect. Mistakes in hemimethylation correction can occur, and are more likely to appear the more a DNA sequence is replicated or repaired. This is compounded by the fact that cigarette smoke compromises the expression and activity of DNMT1. The end result is a decrease in the body's ability to maintain proper methylation patterns, leading to misimpression of gene.

Effects on DNA methylating proteins

Exposure to cigarette smoke impacts proteins involved in DNA methylation. These effects come from either hypoxia induced by the cigarette smoke, or the chemical consequences of nicotine. Inhaling cigarette smoke increases blood levels of carbon monoxide which negatively affects oxygenation throughout the body leading to hypoxia. [1] One response to hypoxia is the upregulation in synthesis of the major methyl donor S-adenosylmethionine. Upregulation of this methyl donor through heightened expression of methionine adenosyltransferase 2A leads to increased DNA methylation, which can lead to the down-regulation of target genes.

Nicotine found in cigarette smoke binds to nicotinic acetylcholine receptors. [1] This binding leads to an increase in calcium levels which in turn can activate the cAMP response element-binding protein (CREB) transcription factor. The most striking downstream effect of the upregulation of this transcription factor is the downregulation of the DNMT1 gene, which has a cAMP response element in its promoter. This down-regulation of DNMT1 can have serious consequences on DNA methylation, namely a failure to maintain normal methylation patterns during DNA replication and repair. The upregulation of DNMT3b has also been shown to occur as a result of cigarette exposure. [2]

DNMT3b is thought to be critical to de novo methylation, or the production of new methylation marks on DNA. This increased expression of DNMT3b and methionine adenosyltransferase 2A, taken together with the down-regulation of DNMT1, results in myriad unintended epigenetic consequences.

Effects on transcription factors

Sp1, a transcription factor that plays a crucial role in early development, was shown to be expressed at higher rates in lung epithelial cells in the presence of cigarette-smoke condensate. [1] This is relevant because Sp1 binds to GC-rich promoter regions which prevent the methylation of these regions during embryonic development. Increased Sp1 expression can lead to a global reduction in DNA methylation, leading to a number of downstream health effects in developing embryos exposed to maternal cigarette smoke.

Consequences of altered DNA methylation

Regardless of mechanism, several known differences in DNA methylation have been observed between smokers and non-smokers. An overall average decrease in DNA methylation is observed, leading to an increase in the expression of a number of genes. Several genes known to be affected by differential methylation are the CYP1A1 xenobiotic response element, AHRR, and F2RL3. CYP1A1 is critical to the detoxification of carcinogens, and is found to be hypomethylated in frequent smokers. AHRR and F2RL3 are similarly hypomethylated in smokers. [1]

AHRR is known to inhibit the aryl hydrocarbon receptor, which is important to metabolizing harmful chemicals. The resultant increase in AHRR expression could lead to a decrease in the body's ability to break down carcinogens, increasing the risk of cancer. F2RL3 is known to be involved in blood clotting and the inflammation response. [1] Effects on the regulation of F2RL3 in particular could be a link between epigenetic changes from smoking and increased risk of heart disease. Time specific changes in methylation of D4Z4 and NBL2 repeats, which are known factors in carcinogenesis, have also been observed. [2]

Though smoking leads to an overall decrease in DNA methylation, several critical genes become hypermethylated. Two of the most noteworthy of these genes are p16 and p53. These genes are critical to cell cycle regulation and were shown to have higher levels of methylation in smokers than in non smokers. [3] The subsequent loss of function of these genes could potentially lead to dysregulation of the cell cycle, wherein cells are able to bypass normal growth impeding signals. Ultimately, uncontrolled cellular divisions and failure to properly regulate the cell cycle leads to cancer.

Fetuses exposed in utero to cigarette smoke are also known to have some distinct epigenetic differences from smoke-free cohorts. CYP1A1 was found to be hypomethylated in the placentas of fetuses prenatally exposed to cigarette smoke, along with the transposable element AluYB8. [4] Methylation of transposable elements is one of the primary ways they are prevented from replicating or moving within the genome. Similarly observed hypomethylation in a number of Alu elements results in a general decrease in genomic stability and an increase in the risk of cancer from mutation resulting from the random insertion of transposable elements. [2]

Strikingly, BDNF appears to be hypermethylated in children who were exposed to smoke prenatally. BDNF is critical to long term memory formation and the upkeep of neurons. Downregulation of BDNF has also been linked to clinical depression. [4] Taken as a whole, the epigentic consequences of prenatal exposure to cigarette smoke result in increased metabolic stress, decreased genomic stability, heightened risk of mutation and altered brain development.

Effects on histone modifications

Histone modifications are another epigenetic phenomenon known to be affected by smoking. Cigarette smoke has been observed to globally alter histone modifications near the promoter regions of pro-inflammatory genes, mainly through an overall increase in acetylation. [3] [5] Cigarette smoke can alter histone acetylation through a number of pathways. Chief among these is the degradation of HDAC2, thereby preventing the removal of acetylation marks in affected cells. The degradation of this enzyme results from phosphorylation and subsequent ubiquitination induced by cigarette smoke. [3]

In rat and mouse models, cigarette smoke was observed to increase acetylation of lysine 9 on histone H3 (H3K9), lysine 12 on histone H4 (H4K12) and phosphorylation of serine 10 on histone H3 (H3S10). These marks are associated with an increase in gene expression and prevent the accumulation of repressive histone modifications. Mechanistically, the increased frequency of these marks, especially the modifications on histone H3, are linked to the activation of IKK-α which directly phosphorylates histone H3 as a consequence of exposure to cigarette smoke. It is thought that this increase in acetylation of histones H3 and H4 in macrophages in the alveolus could potentially lead to the development of COPD.

Effects on miRNA

MicroRNAs, or miRNAs, are known to be major epigenetic regulators of gene expression in humans. These RNAs are short molecules which bind to mRNA through complementary base pairing. This binding impacts the expression of proteins encoded by those mRNAs by either inducing the cleavage of the mRNA, destabilizing the molecule, or limiting the efficiency of its translation. Unlike differences in DNA methylation, changes in miRNA activity induced by cigarette smoke are largely unknown. [1] Primary research data suggests that cigarette smoke promotes the dysregulation of a number of miRNA's. One such study showed that cigarette smoke downregulates miR-16, miR-21, and miR-146a in the placenta. [6]

A downregulation of miR-16 is predicted to inhibit apoptosis via the subsequent upregulation of BCL2L2 and EDA, both of which contribute to anti-apoptotic signaling. Downregulaton of miR-146a is predicted to influence the expression of TRAF6, which has a number of downstream effects, including regulation of inflammatory responses and anti-apoptotic signaling. Taken as a whole, dysregulation of these miRNA's could lead to dysregulation of normal cell death, cell cycling and immune responses, all of which have negative health impacts and could potentially lead to cancerous growths and improper placental formation.

See also

Related Research Articles

<span class="mw-page-title-main">Histone</span> Protein family around which DNA winds to form nucleosomes

In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei and in most Archaeal phyla. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn are wrapped into 30-nanometer fibers that form tightly packed chromatin. Histones prevent DNA from becoming tangled and protect it from DNA damage. In addition, histones play important roles in gene regulation and DNA replication. Without histones, unwound DNA in chromosomes would be very long. For example, each human cell has about 1.8 meters of DNA if completely stretched out; however, when wound about histones, this length is reduced to about 90 micrometers (0.09 mm) of 30 nm diameter chromatin fibers.

<span class="mw-page-title-main">Epigenetics</span> Study of DNA modifications that do not change its sequence

In biology, epigenetics is the study of heritable traits, or a stable change of cell function, that happen without changes to the DNA sequence. The Greek prefix epi- in epigenetics implies features that are "on top of" or "in addition to" the traditional genetic mechanism of inheritance. Epigenetics usually involves a change that is not erased by cell division, and affects the regulation of gene expression. Such effects on cellular and physiological phenotypic traits may result from environmental factors, or be part of normal development. They can lead to cancer.

<span class="mw-page-title-main">Regulation of gene expression</span> Modifying mechanisms used by cells to increase or decrease the production of specific gene products

Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products. Sophisticated programs of gene expression are widely observed in biology, for example to trigger developmental pathways, respond to environmental stimuli, or adapt to new food sources. Virtually any step of gene expression can be modulated, from transcriptional initiation, to RNA processing, and to the post-translational modification of a protein. Often, one gene regulator controls another, and so on, in a gene regulatory network.

<span class="mw-page-title-main">Histone acetylation and deacetylation</span> Biological processes used in gene regulation

Histone acetylation and deacetylation are the processes by which the lysine residues within the N-terminal tail protruding from the histone core of the nucleosome are acetylated and deacetylated as part of gene regulation.

<span class="mw-page-title-main">Histone-modifying enzymes</span> Type of enzymes

Histone-modifying enzymes are enzymes involved in the modification of histone substrates after protein translation and affect cellular processes including gene expression. To safely store the eukaryotic genome, DNA is wrapped around four core histone proteins, which then join to form nucleosomes. These nucleosomes further fold together into highly condensed chromatin, which renders the organism's genetic material far less accessible to the factors required for gene transcription, DNA replication, recombination and repair. Subsequently, eukaryotic organisms have developed intricate mechanisms to overcome this repressive barrier imposed by the chromatin through histone modification, a type of post-translational modification which typically involves covalently attaching certain groups to histone residues. Once added to the histone, these groups elicit either a loose and open histone conformation, euchromatin, or a tight and closed histone conformation, heterochromatin. Euchromatin marks active transcription and gene expression, as the light packing of histones in this way allows entry for proteins involved in the transcription process. As such, the tightly packed heterochromatin marks the absence of current gene expression.

<span class="mw-page-title-main">Cancer epigenetics</span> Field of study in cancer research

Cancer epigenetics is the study of epigenetic modifications to the DNA of cancer cells that do not involve a change in the nucleotide sequence, but instead involve a change in the way the genetic code is expressed. Epigenetic mechanisms are necessary to maintain normal sequences of tissue specific gene expression and are crucial for normal development. They may be just as important, if not even more important, than genetic mutations in a cell's transformation to cancer. The disturbance of epigenetic processes in cancers, can lead to a loss of expression of genes that occurs about 10 times more frequently by transcription silencing than by mutations. As Vogelstein et al. points out, in a colorectal cancer there are usually about 3 to 6 driver mutations and 33 to 66 hitchhiker or passenger mutations. However, in colon tumors compared to adjacent normal-appearing colonic mucosa, there are about 600 to 800 heavily methylated CpG islands in the promoters of genes in the tumors while these CpG islands are not methylated in the adjacent mucosa. Manipulation of epigenetic alterations holds great promise for cancer prevention, detection, and therapy. In different types of cancer, a variety of epigenetic mechanisms can be perturbed, such as the silencing of tumor suppressor genes and activation of oncogenes by altered CpG island methylation patterns, histone modifications, and dysregulation of DNA binding proteins. There are several medications which have epigenetic impact, that are now used in a number of these diseases.

While the cellular and molecular mechanisms of learning and memory have long been a central focus of neuroscience, it is only in recent years that attention has turned to the epigenetic mechanisms behind the dynamic changes in gene transcription responsible for memory formation and maintenance. Epigenetic gene regulation often involves the physical marking of DNA or associated proteins to cause or allow long-lasting changes in gene activity. Epigenetic mechanisms such as DNA methylation and histone modifications have been shown to play an important role in learning and memory.

In recent years it has become apparent that the environment and underlying mechanisms affect gene expression and the genome outside of the central dogma of biology. It has been found that many epigenetic mechanisms are involved in the regulation and expression of genes such as DNA methylation and chromatin remodeling. These epigenetic mechanisms are believed to be a contributing factor to pathological diseases such as type 2 diabetes. An understanding of the epigenome of diabetes patients may help to elucidate otherwise hidden causes of this disease.

Embryonic stem cells are capable of self-renewing and differentiating to the desired fate depending on their position in the body. Stem cell homeostasis is maintained through epigenetic mechanisms that are highly dynamic in regulating the chromatin structure as well as specific gene transcription programs. Epigenetics has been used to refer to changes in gene expression, which are heritable through modifications not affecting the DNA sequence.

The epigenetics of schizophrenia is the study of how inherited epigenetic changes are regulated and modified by the environment and external factors and how these changes influence the onset and development of, and vulnerability to, schizophrenia. Epigenetics concerns the heritability of those changes, too. Schizophrenia is a debilitating and often misunderstood disorder that affects up to 1% of the world's population. Although schizophrenia is a heavily studied disorder, it has remained largely impervious to scientific understanding; epigenetics offers a new avenue for research, understanding, and treatment.

Epigenetic regulation of neurogenesis is the role that epigenetics plays in the regulation of neurogenesis.

Epigenetic therapy refers to the use of drugs or other interventions to modify gene expression patterns, potentially treating diseases by targeting epigenetic mechanisms such as DNA methylation and histone modifications.

Epigenetics of physical exercise is the study of epigenetic modifications to the cell genome resulting from physical exercise. Environmental factors, including physical exercise, have been shown to have a beneficial influence on epigenetic modifications. Generally, it has been shown that acute and long-term exercise has a significant effect on DNA methylation, an important aspect of epigenetic modifications.

<span class="mw-page-title-main">Epigenetics of neurodegenerative diseases</span> Field of study

Neurodegenerative diseases are a heterogeneous group of complex disorders linked by the degeneration of neurons in either the peripheral nervous system or the central nervous system. Their underlying causes are extremely variable and complicated by various genetic and/or environmental factors. These diseases cause progressive deterioration of the neuron resulting in decreased signal transduction and in some cases even neuronal death. Peripheral nervous system diseases may be further categorized by the type of nerve cell affected by the disorder. Effective treatment of these diseases is often prevented by lack of understanding of the underlying molecular and genetic pathology. Epigenetic therapy is being investigated as a method of correcting the expression levels of misregulated genes in neurodegenerative diseases.

Epigenetics of depression is the study of how epigenetics contribute to depression.

Pharmacoepigenetics is an emerging field that studies the underlying epigenetic marking patterns that lead to variation in an individual's response to medical treatment.

Epigenetics of anxiety and stress–related disorders is the field studying the relationship between epigenetic modifications of genes and anxiety and stress-related disorders, including mental health disorders such as generalized anxiety disorder (GAD), post-traumatic stress disorder, obsessive-compulsive disorder (OCD), and more. These changes can lead to transgenerational stress inheritance.

H3K9me2 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the di-methylation at the 9th lysine residue of the histone H3 protein. H3K9me2 is strongly associated with transcriptional repression. H3K9me2 levels are higher at silent compared to active genes in a 10kb region surrounding the transcriptional start site. H3K9me2 represses gene expression both passively, by prohibiting acetylation as therefore binding of RNA polymerase or its regulatory factors, and actively, by recruiting transcriptional repressors. H3K9me2 has also been found in megabase blocks, termed Large Organised Chromatin K9 domains (LOCKS), which are primarily located within gene-sparse regions but also encompass genic and intergenic intervals. Its synthesis is catalyzed by G9a, G9a-like protein, and PRDM2. H3K9me2 can be removed by a wide range of histone lysine demethylases (KDMs) including KDM1, KDM3, KDM4 and KDM7 family members. H3K9me2 is important for various biological processes including cell lineage commitment, the reprogramming of somatic cells to induced pluripotent stem cells, regulation of the inflammatory response, and addiction to drug use.

Epigenetics of autoimmune disorders is the role that epigenetics play in autoimmune diseases. Autoimmune disorders are a diverse class of diseases that share a common origin. These diseases originate when the immune system becomes dysregulated and mistakenly attacks healthy tissue rather than foreign invaders. These diseases are classified as either local or systemic based upon whether they affect a single body system or if they cause systemic damage.

Epigenetics of chronic pain is the study of how epigenetic modifications of genes affect the development and maintenance of chronic pain. Chromatin modifications have been found to affect neural function, such as synaptic plasticity and memory formation, which are important mechanisms of chronic pain. In 2019, 20% of adults dealt with chronic pain. Epigenetics can provide a new perspective on the biological mechanisms and potential treatments of chronic pain.

References

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