Epigenetic Modifications and the Cell's Fate

One of the most interesting questions is how a cell's fate is determined despite having the same DNA sequence.

For example, heart cells pump blood through the heart and out through the body, whereas immune cells protect us from pathogens and diseases. The fate of cells is determined by epigenetics, as it plays a role in allowing the heart cell to turn “on” genes to make proteins important for its job and turn “off” genes important for an immune cell’s job.

In our previous article, we learned about a detailed overview of epigenetics. This article will discuss the three main epigenetic signatures (DNA methylation, histone modification, and non-coding RNA), how they are regulated, and how their disruption causes diseases. For a more clinical approach, check out the Epigenetics Module of the Health Optimization and Practice (HOMe/HOPe) Essential Certification here. 

DNA Methylation

DNA methylation is one of the key epigenetic modifications that play a role in regulating genes. DNA methylation is present exclusively on the 5th carbon of cytosine residues in higher eukaryotes and methylated cytosine, known as 5-methylcytosine (5mC). DNA methylation is also an inheritable symmetrical epigenetic mark. The most common sites of DNA methylation are CpG dinucleotides. DNA methylation in promoter regions acts as a repressor of gene expression. We lose methylation capacity as we age, leading to more genes turned on errantly. 

DNA Methyltransferase (DNMT)

DNA cytosine methylation is facilitated by DNA methyltransferase (DNMT). The transfer of a methyl group from an S-adenosyl-L-methionine cofactor to a cytosine residue in DNA is catalyzed by DNMT. Three types of DNMT play a role in the methylation of DNA, and they are: 

1. DNMT1
2. DNMT3a
3. DNMTb

DNA Demethylation

DNA demethylation is facilitated by the ten-eleven translocation (TET) family enzyme. The 5mC in DNA is hydroxylated to 5-hydroxymethylcytosine (5hmC) by TET enzymes, which can also catalyze the oxidation of 5hmC to 5-formylcytosine (5fC) and ultimately to 5-carboxycytosine (5caC).

DNA Methylation in Diseases

Aberrant DNA methylation has been associated with many diseases. Here we will list some common diseases and how DNA methylation plays a role in them:

• Acute Myeloid Lymphoma (AML) [1]

40% of cytogenic AML patients have reported mutation in DNMT3a, associated with hypo and hypermethylation of DNA [1,2]. DNMT3a is now considered an early-stage biomarker for AML [1,2]. Mutation in TET enzymes is associated with a poor prognosis of AML [1,3,4]. DNMT inhibitors are one of the approved therapies for AML patients [5]. 

• Lung Cancer 

Studies have shown that the initiation and development of lung cancer results from abnormalities in DNA methylation, which silences tumor suppressor genes [6]. Overexpression of DNMTs is frequently associated with lung cancer [6,7]. Loss of function mutations of TET enzymes correlates with poor survival in lung cancer patients [8]. Studies have found that combining azacytidine, DNMT inhibitors, and anti-PD-1 therapy dramatically decreased lung cancer tumor growth compared to anti-PD-1 therapy alone [9].

• Systemic Lupus Erythematosus (SLE)

Global hypomethylation on CD4+ T cells, which involves the extracellular signal-regulated kinase (ERK) signaling pathway, is a hallmark of altered DNA methylation in SLE [10]. The increase in global hypomethylation of CD4+ T cells is associated with loss-of-function mutation or downregulation of DNMTs.

• Type 2 Diabetes (T2DM)

T2DM is associated with aberrant DNA methylation and overexpression of DNMTs [11,12]. Studies have found that the promoters of Cdkn1a and Pde7b are hypermethylated in T2DM, which causes the downregulation of these two genes, a decrease in β-cell transcription activity, and aberrant insulin production [11-13].

• Grave Disease (GD)

The grave disease (GD) is an autoimmune disease causing hyperthyroidism or an overactive thyroid [10]. Studies have found that GD is associated with lower DNMT expression and hypomethylation in T and B lymphocytes [14,15]. Guo et al. found that administering antithyroid drugs or radioiodine treatment could restore global DNA methylation and DNMT1 expression with concurrent relief of hyperthyroidism [15].

Histone Modifications 

Histones are the most highly conserved eukaryotic proteins, being a family of small, positively charged proteins. Chromatin packing in nucleosomes is carried out by the core histones. These histones are subjected to various post-translational modifications (PTMs), which play a vital role in gene expression. The most common PTMs that are well-studied and understood in the context of DNA repair, gene expression, and regulation are acetylation and methylation. 

Histone Acetylation/Deacetylation

The addition of an acetyl group on a lysine residue in a histone protein is carried out by a group of enzymes known as histone acetyltransferases (HATs). In contrast, histone deacetylase (HDAC) removes the acetyl group from lysine residues. Histone acetylation/deacetylation acts like a switch in gene expression by turning it on/off [16].

Histone Methylation/Demethylation

Histone methylation is performed by histone methyl transferase (HMT) enzymes. HMT adds a methyl group to lysine or arginine residues. HMTs act as “writers” in histone code, as they can add up to three methyl groups on lysine or arginine [17,18]. Histone demethyltransferases (HMDTs) are a group of enzymes playing the role of “erasers” in histone code by removing methyl groups from histone [17,18]. 

Depending on the context and extent of methylation, histone methylation can activate or repress gene expression. Mono-methylation of H3K9 (H3K9me1) and di- or tri-methylation of H3K4 (H3K4me2, H3K4me3) are associated with active transcription. Repressive transcription marks include di- and tri-methylation of H3K9 (H3K9me2, H3K9me3) and H3K27 (H3K27me2, H3K27me3) [17-19].

Histone Modification in Diseases

• Acute Myeloid Lymphoma

Enzymes responsible for histone methylation and demethylation are frequently mutated in AML [20-22]. One of the key histone demethylases, lysine-specific demethylase (LSD), is overexpressed in more than 60% of AML patients [22]. Studies have found that LSD inhibits differentiation, enhances proliferation, invasiveness, and cell motility, and is associated with poor prognosis in AML [23,24]. Hence, inhibiting the expression of LSD1 has become a promising target for AML. Many clinical trials using the inhibitors of LSD1 are in phase I and II [23–25]. Aberrant expression of HDACs is associated with the development of AML, multiple myeloma (MM), and lymphomas. Four HDAC inhibitors (HDACi) have been approved by the US FDA for MM and T-cell lymphomas [26-29].

• Lung Cancer

Aberrant histone modifications (acetylation and methylation) play a key role in the development of lung cancer. Studies have found that reduced global histone modification levels lead to a higher risk of relapse and shorter survival time in lung cancer patients [30]. Lung adenocarcinoma with shortened survival was associated with the loss of H4K20 trimethylation [31]. Numerous HDACi are in clinical trials for lung cancer, either as monotherapy or as combination therapy [30,32]. 

• Grave Disease

In GD patients, lower levels of histone H4 acetylation and higher levels of HDAC1 and HDAC2 have been observed [10].

• Major Depressive Disorder

Recently, it was observed that many histone modifications can occur in the human brain in response to stressful events, leading to transcriptional changes and aiding in the development of major depressive disorder [33].

• Asthma

Higher expression of H4 acetylation has been reported in asthma patients compared to controls [10,34]. The higher expression of H4 acetylation leads to reduced HDAC activity and overexpression of inflammation-associated genes [34]. 

Non-coding RNA

Non-coding RNAs (ncRNA) are a group of biologically active RNA molecules that play an important role in regulating gene expression in cells. Unlike coding RNAs, ncRNAs are not translated into proteins; instead, they participate in the upregulation and downregulation of gene expression, translation, splicing, and catalysis [35]. 

Micro RNA (miRNA), small interfering RNA (siRNA), Piwi-interacting RNA (piRNA), and long non-coding RNA (lncRNA) are the key players in the epigenetic regulation of gene expression [35].

miRNA

Single-stranded RNAs called miRNAs have a length of between 19 and 24 nucleotides, and 50% are found in areas of the chromosome susceptible to structural alterations [35]. Nearly 1,800 putative miRNAs have been found in the human genome, and as high-throughput sequencing technology advances, the number of miRNAs is still rising quickly [36]. miRNA plays its role in regulating gene expression by targeting HMT and DNMT. In mouse embryonic stem cells lacking Dicer, the miR-29 family was responsible for downregulating DNMT3a and 3b activity [35,36].

siRNA 

siRNA are homologous to a target gene and consist of two complementary RNA molecules with a length of 21-25 nucleotides. DNA methylation and histone modifications caused by siRNA can result in cell transcriptional gene silencing [36,37]. siRNAs are involved in chromatin organization and have been viewed as guardians of the genome's integrity [36].

piRNA 

piRNAs, which have a length of 26-32 nucleotides, have been associated with the transcriptional control of de novo DNA methylation in germ cells. Recently, piRNAs were discovered in somatic cells like neurons, which may play a crucial role in memory storage.

lncRNA 

lncRNAs are typically >200 nucleotides long, found in the cytoplasm or nucleus, and infrequently encode proteins. One of the most important lncRNAs in epigenetic regulation is Xist (X-inactive specific transcript) RNA. Xist RNA plays a key role in the X-chromosome inactivation process. The detailed role of X-chromosome inactivation by Xist RNA is explained in this review by Dossin and Heard [41].

Non-coding RNA in Diseases

• Gastric Cancer

Genome-wide studies have found that the upregulation of several miRNAs, including miR-99a, miR-202, and miR-133a, is associated with an increased risk of gastric cancer [10]. Studies have found that many miRNAs could be a favorable prognostic marker for gastric cancer [42]. Xist RNA has been shown to exert drug resistance in gastric cancer [40]. 

• Crohn’s Disease

Crohn’s disease (CD) is inflammatory bowel syndrome [10]. CD can affect the entire digestive tract but most commonly involves the small intestine and colon [10]. Numerous miRNAs, such as miR-21, miR-16, and miR-594, were shown to be overexpressed in inflamed mucosal samples from CD patients in comparison to samples from normal regions in CD patients and healthy controls, suggesting that these miRNAs are involved in the etiology of CD [10].

• Atherosclerosis

According to studies, miRNAs have a significant impact on the development of atherosclerosis [10]. Recent research has demonstrated that miRNAs can control lipoprotein levels, HDL and LDL accumulation, and function [10,43]. 

• Hypertension

Vascular function and integrity can be affected by dysregulated miR-126. Damage to blood vessel structure and function is linked to deleted miR-126, which aids in developing hypertension [10,43]. Other miRNAs are associated with increased blood pressure risk [10].

Conclusion

Environmental influences can affect epigenetic modification, which produces heritable but reversible alterations in gene expression in the absence of DNA sequence changes. A greater knowledge of the pathophysiology of human diseases has been made possible by extensive research on DNA methylation, histone modification, and ncRNAs. As a result, drugs that can alter gene expression have been developed to reverse epigenetic alterations.

For more information on a clinical approach to detecting and correcting epigenetics, go to homehope.org and check out the epigenetics module for practitioners. 

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