Epigenetics and Disease: Research for Improving Human Health

Epigenetics research has played a valuable role in understanding different components of various diseases and disorders, and utilizing the proper tools and methods is vital. “The method of choice to analyze epigenetic modifications and their role in diseases is dependent on the epigenetics platform to be investigated,” explained Said Goueli, Senior Research Fellow at Promega. As reviewed in our recent articles, there are many important methods for epigenetic profiling. Using many different methodologies, two epigenetics specialists will delve into how their technologies are facilitating remarkable discoveries for the connection between epigenetics and human health.

Epigenetics Research in Cancer
Cancer research is one area of epigenetics research that is frequently explored to gain insights into the gene expression and molecular mechanisms involved in dysregulated cancer cells. These epigenetic modifications can play a significant role in the development and progression of cancer, offering researchers a chance to identify potential targets and therapeutic interventions. “Active Motif products are used globally for studying cancers, cardiac disease, congenital neurodevelopmental disorders, immunology, and several other kinds of disease,” explained Rwik Sen, Ph.D., Field Application Scientist and Product Manager-PIXUL at Active Motif.

Pointing to a recent publication in Cell Reports¹, Sen described how researchers used ATAC-seq and Ras GTPase kits from their company to investigate unknown aspects of RAS genes. “The study reported that oncogenic KRAS signaling upregulates noncoding RNA transcripts, many of which are transposable elements.” The findings highlighted the potential of using transposable elements as biomarkers for diagnosing RAS-driven cancers based on their enrichment in extracellular vesicles released from mutant KRAS cells.

Epigenetics and Heart Conditions
Studying the epigenetics of vital organs, such as the heart, not only enhances our understanding of its functioning but also highlights the multifaceted characteristics of heart-related conditions. “Heart disease is the number one cause of death in the U.S. and worldwide,” emphasized Sen. In an effort to understand a specific type of heart condition, a team of scientists investigating antenatal hypoxia, a heart condition characterized by decreased oxygen supply to the fetus in the womb, conducted a study in the U.S. and China². Using Active Motif’s methylated DNA immunoprecipitation (MeDIP) kit, they measured glucocorticoid receptor gene methylation. “The study showed that antenatal hypoxia causes reprogramming and epigenetic remodeling of an important gene, resulting in increased cardiac vulnerability,” explained Sen.

In another important cardiac-related study³, Sen described how their ChIP-IT Express kit was used with induced pluripotent stem cells to reveal how epigenetic modifications and transcription of NKX2-5, HAND1, and NOTCH1 contribute to cardiac malformations in the congenital condition known as Hypoplastic Left Heart Syndrome. This potentially life-threatening condition is characterized by underdevelopment or hypoplasia of the left side of the heart, which is unable to effectively pump oxygenated blood to the body, resulting in significant health complications. Focusing on the epigenetic programs of these cells provided the researchers valuable insights into the genetic circuits and molecular mechanisms involved in this complex cardiac abnormality.

Targeting Viral and Disease-Related Enzymes
Among the many types of epigenetics research, studying the epigenetics of viral infection and treatment has become markedly important in recent years. “Current antiviral drugs used to treat SARS-CoV-2 include a protease inhibitor that blocks the ability of the coronavirus to multiply and a nucleoside analog that aims to introduce errors into the genetic code of the virus,” stated Goueli. “We believe the armament against the virus can be augmented by the addition of another class of enzyme inhibitors that are required for viral survival and its ability to replicate. Enzymes like nsp14 and nsp10/16 methyltransferases (MTases) represent another class of drug targets since they are required for viral RNA translation and evading the host immune system.”

Goueli’s team successfully verified that MTase-Glo, a universal and homogeneous high-throughput-formatted MTase assay, can screen for inhibitors of these two crucial enzymes, nsp14 and nsp 10/16 of SARS CoV-2. “These enzymes are required for the translation of viral RNA by capping viral RNA (nsp14) and methylating the penultimate nucleotide from the 5’ for the viral to evade the host immune response (nsp 10/16),” added Goueli. The group performed extensive research on these enzymes with various RNA substrates⁴, testing their activity with different inhibitors, and verifying the utility of the assay for drug screening programs. “We anticipate our work will be pursued further to screen large libraries to discover new and selective inhibitors for the viral enzymes particularly since these enzymes are structurally different from their mammalian counterparts.”

In addition to these important methyltransferases, Goueli described the importance of new methyltransferase-like enzymes that function by adding a methyl group to RNA on the amino group of adenosine in the form of N6-methyladenosine (m6A). “[The methyl group] installed onto mRNA by the methyltransferase-like enzymes (METTL3/METTL14 methyltransferase complex) appears to be the most prevalent mRNA modification. m6A methylation regulates gene expression by influencing numerous aspects of mRNA metabolism, including pre-mRNA processing (splicing), nuclear export, RNA stability, polyadenylation, and translation efficiency. Thus, m6A plays a crucial role in the regulation of gene expression resulting in phenotypic changes manifested in tumor formation, metastasis, or other abnormalities.”

Due to the MTase-Glo assay’s universal nature, Goueli explained that it can quantify the activity of any methyltransferase regardless of the nature of its substrate. They have further used this assay to monitor the activity of these METTL enzymes, which makes it possible to determine when these proteins are mutated or overexpressed in a disease state. “These enzymes have been validated as promising drug targets for multiple diseases including cancer and many other metabolic diseases⁵.”

Additional Breakthroughs and the Future
Many other important studies have utilized advanced techniques to explore different aspects of epigenetics and human health. Sen further discussed epigenetics research in neuro diseases⁶, hormone responsiveness⁷, energy metabolism⁸, and cell identity and genome integrity⁹. Additionally, Goueli explained some of their developing assays that monitor the concentration of S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) known as the SAM/SAH index to use as potential biomarkers for disease. These studies collectively demonstrate the vast array of work exploring the role of epigenetics in human health.

The future of epigenetics research holds great promise for advancing our understanding of various diseases and disorders. With significant discoveries in fields such as cancer research, viral disease, and cardiology, researchers have provided valuable insights into the underlying molecular mechanisms.

References

1. Reggiardo RE, Maroli SV, Halasz H, et al. Mutant KRAS regulates transposable element RNA and innate immunity via KRAB zinc-finger genes. Cell Reports. 2022;40(3):111104. doi:https://doi.org/10.1016/j.celrep.2022.111104
2. Lv J, Ma Q, Dasgupta C, Xu Z, Zhang L. Antenatal Hypoxia and Programming of Glucocorticoid Receptor Expression in the Adult Rat Heart. Frontiers in Physiology. 2019;10. doi:https://doi.org/10.3389/fphys.2019.00323
3. Kobayashi J, Yoshida M, Suguru Tarui, et al. Directed Differentiation of Patient-Specific Induced Pluripotent Stem Cells Identifies the Transcriptional Repression and Epigenetic Modification of NKX2-5, HAND1, and NOTCH1 in Hypoplastic Left Heart Syndrome. PLOS ONE. 2014;9(7):e102796-e102796. doi:https://doi.org/10.1371/journal.pone.0102796
4. Hsiao K, Zegzouti H, Goueli S. High throughput bioluminescent assay to characterize and monitor the activity of SARS-CoV-2 methyltransferases. Selvaraj C, ed. PLOS ONE. 2022;17(11):e0274343. doi:https://doi.org/10.1371/journal.pone.0274343
5. Hsiao K, Zegzouti H, Goueli SA. Methyltransferase-Glo: a universal, bioluminescent and homogenous assay for monitoring all classes of methyltransferases. Epigenomics. 2016;8(3):321-339. doi:https://doi.org/10.2217/epi.15.113
6. Sheroy Minocherhomji, Hansen CD, Hyung Sik Kim, et al. Epigenetic remodelling and dysregulation of DLGAP4 is linked with early-onset cerebellar ataxia. Human Molecular Genetics. 2014;23(23):6163-6176. doi:https://doi.org/10.1093/hmg/ddu337
7. Hewitt SC, Wu SP, Wang T, Young SL, Spencer TJ, DeMayo FJ. Progesterone Signaling in Endometrial Epithelial Organoids. Cell. 2022;11(11):1760-1760. doi:https://doi.org/10.3390/cells11111760
8. Zhang Y, Higgins CB, Tine BAV, Bomalaski JS, DeBosch BJ. Pegylated arginine deiminase drives arginine turnover and systemic autophagy to dictate energy metabolism. Cell Reports Medicine. 2022;3(1). doi:https://doi.org/10.1016/j.xcrm.2021.100498
9. Recalde M, Gárate-Rascón M, Elizalde M, et al. The splicing regulator SLU7 is required to preserve DNMT1 protein stability and DNA methylation. Nucleic Acids Research. 2021;49(15):8592-8609. doi:https://doi.org/10.1093/nar/gkab649