Gene regulatory mechanisms play important roles in cancer progression

Cambridge, Massachusetts-As cancer cells evolve, many of their genes become overactive and others are rejected. These genetic changes help the tumor grow uncontrollably, become more aggressive, adapt to changing conditions, and eventually the tumor metastasizes and spreads elsewhere in the body.

Researchers at MIT and Harvard University have planned a series of structural changes that lead to this evolution: an additional regulatory layer, the “chromatin,” a mixture of proteins, DNA, and RNA that make up the cell’s chromosomes. In a study of mouse lung tumors, researchers identified 11 chromatin states, also called epigenome states. These cancer cells can pass through when they become more aggressive.

“This study provides one of the first examples of comprehensively characterizing the genes that regulate tumor evolution in cancer using single-cell epigenome data,” said the lead author of the study at a postdoc at MIT. Says Lindsay LaFave.

In addition, researchers found that the key molecules found in more aggressive tumor cell states were also associated with more advanced forms of human lung cancer and could be used as biomarkers to predict patient outcomes. Was shown.

Tyler Jacks, director of the Koch Institute for Integrative Cancer Research at MIT, and Jason Buenrostro, assistant professor of stem cell and regenerative biology at Harvard University, are senior authors of the study published today in Cancer Cell.

Epigenome control

Although the cell’s genome contains all of the genetic material, the epigenome plays an important role in determining which of these genes are expressed. All cell genomes have epigenomic modifications-proteins and chemical compounds that attach to DNA but do not change its sequence. These changes, which depend on the cell type, affect the accessibility of the gene and help, for example, make lung cells different from neurons.

Changes in the epigenome are also thought to affect cancer progression. In this study, the MIT/Harvard team set out to analyze epigenetic changes that occur when lung tumors develop in mice. They studied a mouse model of lung adenocarcinoma. This is the result of two specific gene mutations, which closely replicates the development of human lung tumors.

Using a new technique for single-cell epigenome analysis previously developed by Buen Rostro, researchers analyzed epigenome changes that occur as tumor cells evolve from an early stage to a more aggressive stage. They also examined tumor cells that had spread beyond the lungs.

This analysis revealed 11 different chromatin states based on the location of epigenome changes and chromatin density. Within a single tumor, cells in all 11 states may be present, suggesting that cancer cells may follow different evolutionary pathways.

For each state, the researchers also identified corresponding changes in the location of gene regulators called transcription factors that bind to the chromosome. When transcription factors bind to the promoter region of a gene, they initiate the copy of that gene into messenger RNA, essentially controlling which gene is active. Chromatin modifications allow transcription factors to gain some access to gene promoters.

“When chromatin is open, transcription factors can bind to and activate certain gene programs,” LaFave said. “We were trying to understand those transcription factor networks and then what were their downstream targets.”

As the structure of chromatin in tumor cells changed, transcription factors tended to target genes that help cells lose their original lung cell identity and reduce differentiation. Eventually, they also gained the ability of many cells to leave their original location and seed new tumors.

Much of this process was controlled by a transcription factor called RUNX2. In more aggressive cancer cells, RUNX2 promotes transcription of genes for proteins secreted by the cell. These proteins rebuild the environment that surrounds the tumor, making it easier for cancer cells to escape.

The researchers also found that these aggressive pre-metastatic tumor cells were very similar to those that had already metastasized.

“This suggests that when these cells were in the primary tumor, they actually change the state of chromatin and look like metastatic cells before they enter the environment,” LaFave said. I am. “We believe that they undergo epigenetic alterations in the primary tumor, allowing them to become mobile and subsequently disseminated to distant locations such as lymph nodes or the liver.”

New biomarker

The researchers also compared the chromatin status found in mouse tumor cells with the chromatin status found in human lung tumors. They found that RUNX2 was also elevated in more aggressive human tumors. This suggests that it may serve as a biomarker to predict patient outcome.

“The positive status of RUNX was a very high predictor of poor survival in human lung cancer patients,” says LaFave. “We also had the signs of early conditions and showed the reverse, which predicts a better prognosis for patients. This suggests that these single-cell gene regulatory networks could be used as a predictive module for patients.”

RUNX may also be a potential drug target, but the lack of a well-defined structure that normally functions as a drug docking site has made it difficult to design drugs that target transcription factors. Researchers are also looking for other potential targets within the epigenetic changes identified in more aggressive tumor cell states. These targets may include proteins known as chromatin regulators that are involved in controlling the chemical modification of chromatin.

“Chromatin regulators tend to be enzymes, so they are more easily targeted,” LaFave says. “We are using this framework to try to understand what are the key targets driving these state transitions, and which targets can be therapeutically targeted.”