New breakthrough in understanding how deleting certain genes can lead to cancer growth

New breakthrough in understanding how deleting certain genes can lead to cancer growth

Genetic mutations cause cancer. Some mutations shuffle the genetic code, others arise from the deletion of key genes.

At the La Jolla Institute for Immunology (LJI), researchers have made a major breakthrough in understanding how deletion of the genes that encode TET proteins can lead to cancer growth. Their new study, published in Nature Communications, is the first to show the immediate consequences of deleting all three TET family genes in mouse embryonic stem cells.

Using this mouse model, researchers discovered that TET proteins are crucial for ensuring that the process of cell and DNA replication occurs smoothly. Without TET proteins, important genes are lost, leading to mutations or aneuploidies (an-new-trick-dees).

Aneuploidies are cases in which genetic material is added or removed on a large scale. Cells with aneuploidies don't just lack one gene. Instead, genes on an entire chromosome are lost.

Aneuploidies are a common feature of cancer cells.”

Hugo Sepulveda, Ph.D., postdoctoral researcher at LJI

Uncovering this direct link between TET loss of function and aneuploidies is an important discovery in the field of cell biology and gives researchers a clue on how to find genes that support cancer development. “We can now understand the mechanisms behind the development of aneuploidy, although we cannot say that these changes always occur through the same genes in other cell types,” says LJI postdoctoral researcher Hugo Sepulveda, Ph.D.

Sepulveda led the research alongside former LJI postdoctoral fellow Romain Georges, Ph.D., who created the mouse model and derived the stem cells for the project. LJI Professor Anjana Rao, Ph.D., served as senior author of the study.

What are TET proteins?

As a researcher at Harvard, Rao, along with Mamta Tahiliani, Ph.D., and L. Aravind, Ph.D., discovered the TET protein family. Their work has since shown that TET proteins are key players in cell growth and development. TET proteins can protect against cancer-causing mutations and even against inflammation and cardiovascular disease. TET proteins play such an important role in cells because they influence DNA methylation, a process that changes how DNA is read and genes are expressed.

Rao's work was particularly important for understanding TET function in immune cells such as T cells, B cells and myeloid cells. "Dr. Rao showed that every time you have a deletion of a TET gene in these cells, you see the development of another aggressive type of cancer," Sepulveda says.

As this research continued, the LJI team noticed something strange: cells with missing or impaired TET proteins are also prone to aneuploidy. Here was another connection between TET proteins and cancer.

Cells with TET loss of function were prone to aneuploidy, and cancer cells were prone to aneuploidy. But what comes first? Does TET loss of function trigger aneuploidy and cancer or is it the other way around?

An exciting discovery

To better understand cancer, Georges and Sepulveda turned to mouse embryonic stem cells as a model. These cells were naturally willing to divide rapidly but were not prone to developing cancer. The researchers needed to see how deleting TET proteins might shake things up.

Georges, Sepulveda and their colleagues repeatedly found that cells with TET deletion developed aneuploidies three times more often than normal cells. These modified cells lost genes very quickly and randomly. The scientists were able to see the effects in very early embryos, which consisted of only eight cells.

“This proved that the TET deletion had a direct effect on aneuploidies,” says Sepulveda. “It was very exciting and has never been shown before.”

Next, the researchers turned to a sequencing technique called RNA-seq to see how the TET deletion affected other genes. They saw a “downregulation” or shutdown of certain genes associated with cell and DNA replication. This finding suggested that TET deletion was a major blow to a system that maintains normal cell division.

So which genes are to blame?

The TET deletion in mouse embryonic stem cells appears to have the greatest effect on a gene called Khdc3, which was part of a system or complex previously studied for its activity in supporting oocyte division. This complex is not well studied, but Khdc3 was known to be important in maintaining genome stability in oocytes before and after fertilization as well as in the early stages of embryonic development.

When the researchers restored KHDC3 protein function in these cells, they were surprised to see that genome stability also returned. The aneuploidy was reversed. The complex that includes Khdc3 has done its job again.

The new study revealed two important facts about TET loss of function. First, this TET loss of function is a direct cause of the aneuploidies associated with cancer, as it resulted in reduced Khdc3 expression. Second, this TET loss of function in embryonic stem cells affects genome stability via a KHDC3-containing complex.

Sepulveda points out that the Khdc3 complex is known to be active only in early embryonic development and in embryonic stem cells. This means that even if aneuploidies are observed in TET-deficient cancers, scientists still need to determine whether these cancers upregulate KHDC3 (most cancers tend to upregulate embryonic genes) and, if so, whether the aneuploidies they develop are caused by aberrant KHDC3 function.

In particular, aneuploidies are observed in numerous cancers in which TETs are not mutated, but these cancers may have lost TET function due to metabolic disorders.

“Genome instability in cancer cells could occur through genes other than Khdc3, but through a similar regulatory mechanism that also involves changes in DNA methylation patterns,” says Sepulveda. “Whether TET-associated cancers develop aneuploidies by dysregulating genes other than Khdc3 is still an open question.”

In the future, Sepulveda hopes to uncover exactly how the Khdc3 complex promotes genome stability downstream of TET proteins in embryonic stem cells.

Source:

La Jolla Institute of Immunology

Reference:

Georges, RO, et al. (2022) Acute deletion of TET enzymes leads to aneuploidy in mouse embryonic stem cells through decreased expression of Khdc3. Nature communication. doi.org/10.1038/s41467-022-33742-7.

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