New tool sheds light on enzymatic activity linked to blood cancers, heart disease

Scientists from the La Jolla Institute for Immunology (LJI) have provided a better understanding of a process in immune cells that could help explain why certain people develop cardiovascular disease.

TET enzymes control gene expression by triggering a process called demethylation, where a molecule called a methyl group is removed from where it sits in the genetic code. Demethylation is important because it alters how a cell “reads” DNA. Image Credit: Courtesy of La Jolla Institute for Immunology.

TET enzymes play a critical role in maintaining the immune cells on a healthy track as they age, according to the new study recently published in the Genome Biology journal. While other enzymes certainly play a role in this process, it is the TET enzymes that perform most of the work, found the researchers.

If we can figure out what’s going on with these enzymes, that could be important for controlling cardiovascular disease.”

Atsushi Onodera, PhD, Study First Author and Postdoctoral Researcher, La Jolla Institute for Immunology

While working at Harvard University with Mamta Tahiliani, Ph.D., and L. Aravind, Ph.D., LJI Professor Anjana Rao, Ph.D., had jointly discovered the TET enzymes. The researchers’ study revealed that this group of three enzymes modifies the way human genes are expressed.

In the last 10 years, Professor Rao has demonstrated how TET activity plays a crucial role in the development of cancer. Her study has revealed that TET enzymes are essential for the proper expression of genes in immune cells and that they can truly defend against mutations.

In this new analysis, Rao and Onodera explored how TET enzymes (a process known as passive demethylation) or a DNA repair enzyme referred to as TDG (active demethylation) can modify the immune cell DNA.

The researchers wanted to find out which demethylation mechanism plays a larger role in establishing the gene expression—the exact fate—of immune cells.

The investigators began with immune cell models—monocytes and CD4 “helper T cells. To help combat diseases, these cell types should proliferate and mature into more specific types of cells. But monocytes stop proliferating once they are differentiated into macrophages and activated with a molecule, known as LPS.

The researchers could gain a better understanding of proliferating and non-proliferating models by closely studying these macrophages and CD4 helper T cells.

Since the proliferation process is so rapid, it provides a great opportunity to observe how demethylation takes place and how it influences the expression of genes. Using an advanced computational analysis program designed for this study, Onodera employed CD4 helper T cells to examine the demethylation process. This method allows scientists to see which DNA regions inside a cell are methylated in unprecedented detail.

We found that in immune cells, most demethylation happens through the passive pathway.”

Atsushi Onodera, PhD, Study First Author and Postdoctoral Researcher, La Jolla Institute for Immunology

The researchers used a new approach known as pyridine borane sequencing and demonstrated that “active” demethylation—via TDG—is operating in immune cells. According to Onodera, TDG plays a minor role: it removes a couple of molecules produced by the activity of TET enzymes.

TET mutations can be life-threatening and hence this discovery is crucial. Mutations in the TET2 enzyme have previously been demonstrated to neutralize (or interfere with) some of the usual constraints on healthy monocytes. Monocytes become aggressive and develop into inflammatory macrophages. Individuals with TET2 mutations in macrophages have a 40% higher chance of developing cardiovascular disease.

Researchers would be able to intervene and aid patients with this mutation if they have a better understanding of the function of TET enzymes.

In addition, Onodera’s latest analysis program for detecting changes in DNA modification could help understand how TET mutations in immune cells can cause blood cancers. Scientists could use this program to identify individuals who may have varying treatment outcomes depending on where their DNA has been demethylated, explained Onodera.

Hopefully we can apply this technique to disease diagnoses.”

Atsushi Onodera, PhD, Study First Author and Postdoctoral Researcher, La Jolla Institute for Immunology

Onodera claimed that the new sequencing and analysis software developed in this study can be used on many types of immune cells and several disease models.

“At this point, we can make significant progress in understanding the molecular mechanisms behind DNA demethylation,” concluded Onodera.