Posted: September 22, 2015

DNA Methylation Inhibitor Triggers Anti-Viral Immune Response in Cancer

Amy E Blum, M.A.

The human immune system is an extremely powerful defense against disease. Repeatedly tweaked and improved over millions of years of evolution, the complex interplay between immune cells is capable of targeting a wide range of foreign agents, learning the signatures of specific attackers through "immune memory," and amplifying the number of cells on the prowl by a thousand-fold or more when an attacker strikes. Yet in the majority of cases, this army of immune cells is significantly less effective in the fight against cancer. In the case of cancer, the "foreign" attackers are actually our own cells, making them more difficult to target. This is because the immune system has evolved to recognize agents that come from outside of the body, based on genomic characteristics like genetic material and proteins, to prevent immune cells from attacking the body and causing autoimmune disease.

Harnessing the immune system against cancer therefore presents a great challenge for scientists, but one worth pursuing. In the last fifteen years, cancer immunotherapy has taken off as researchers have discovered ways to induce the immune system to recognize cancer cells as foreign, unleashing its power against cancer.

In a report published in Cell on August 27th, 2015, researchers led by Stephen Baylin, M.D., revealed that DNA methyltransferase inhibitors (DNMTis) can trigger an anti-viral immune response that may sensitize cancers to already developed immunotherapies like immune checkpoint therapy. Using TCGA data, the scientists also showed that patients with certain cancers can be grouped based on their cancer’s expression of genes that defend against viruses. These low or high expression groups may help to predict which patients respond the best to immune checkpoint therapy, and which patients may benefit from co-treatment with DNMTis to help alert the immune system to cancer.

DNMTis, like 5-azacytidine (Aza), inhibit DNA methyltransferase enzymes. These enzymes add chemical compounds called methyl groups to DNA that regulate gene expression in a process called epigenetics. Past research has shown that blocking the epigenetic changes made by DNA methyltransferases with DNMTis can induce an immune response in cancer cells. Using ovarian cancer cell lines, Dr. Baylin and his colleagues found that treatment with Aza triggers the production of type 1 interferons, proteins that alert the immune system to a virus lurking inside of the cell.

The researchers then set out to understand the mechanism behind Aza’s stimulation of the interferon response. When treating ovarian cancer cells with Aza, they observed that double stranded RNA (dsRNA), a type genetic material produced by viruses, stimulated the cells’ production of interferons. When dsRNA was digested by an enzyme, eliminating it from the cells, the interferon response subsided, indicating the dsRNA caused the interferon response. To further confirm the role of dsRNA, the researchers reduced the expression of proteins that detect dsRNA in the cell using a method called a gene knockdown. As predicted, when the cells could not detect dsRNA, they failed to produce interferons.

But how does Aza stimulate the production of double stranded RNA, a genetic macromolecule used by viruses, in human cells? Between 100,000 and 40 million years ago, viral infection of germline cells caused the insertion of genes called endogenous retrovirual sequences (ERVs) into mammals, and now these ERVs make up more than eight percent of the human genome. In healthy cells, these genes are typically silenced with an epigenetic signature called hypermethylation. However, Dr. Baylin and his colleagues observed that by inhibiting DNA methylation in ovarian cancer cells, Aza induces the expression of ERVs. The resulting ERV messenger RNA can then form dsRNA in the cell, setting off the interferon anti-viral response. To confirm this connection, the researchers overproduced ERVs without Aza treatment and found that the presence of ERVs induces interferon production, sometimes to a greater degree than through Aza treatment.

The finding that treatment with DNA methyltransferase inhibitors (DNMTis) promotes the expression of viral genes, stimulating an anti-viral immune response, has important implications for immunotherapy against cancer. Using TCGA data on ovarian, breast, colon, and lung cancers, the researchers found that these tumors can be grouped into low and high expression subtypes based on their level of expression of viral defense genes. Importantly, patients with high expression respond better to immune checkpoint therapy, a type of immunotherapy that blocks cancer cells from evading the immune system, than do patients with low expression. Expression of these Aza-associated viral defense genes may therefore be useful for patient stratification and prediction of individual responses to immunotherapies.

DNMTis may also be effective as co-treatments to sensitize cancer cells to immunotherapy. To investigate this hypothesis directly, the researchers utilized Aza treatment in combination with immune checkpoint therapy in a mouse model of melanoma and found that Aza treatment improved responses to immune checkpoint therapy. Future research will show whether the same principle can improve cancer immunotherapy in humans. By bringing out the viral genes in cancer cells, treatment with DMNTis may strengthen the immune system’s attack on cancer, making immunotherapy possible for low expression patients who may not otherwise respond.

Chiappinelli, K.B., Strissel, P.L., Desrichard, A., Li, H., Henke, C., Akman, B., Hein, A., Rote, N.S., Cope, L.M., Snyder, A., et al. (2015) Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses. Cell. 162(5):974-986. View PubMed Abstract