Potential Immunotherapy Targets Discovered by CRISPR That Reveals The Immune Escape of Cancer Cells

Cancer immunotherapy is a revolutionary breakthrough that changes the landscape of cancer treatment. However, even though there are already many FDA-approved immunotherapies on the market, only a small number of cancer patients can benefit from it. This is because cancer cells are also very “cunning”, they can use a variety of means to prevent being targeted and eliminated by immune cells. At present, the targets of a variety of immune checkpoint inhibitors are one of the methods used by cancer cells to evade the immune system. Researchers are also working towards a more comprehensive and systematic understanding of the mechanism of cancer cell immune escape.

A few days ago, researchers from the University of Toronto and Agios Pharmaceuticals have collaborated to use CRISPR screening technology to systematically search for the driving genes that trigger cancer cells to escape the immune system. They found that multiple genes related to autophagy are the key to immune escape! The result was published in the scientific journal of Nature.

In order to systematically study the impact of different genes on cancer cells evading the immune system, the researchers used CRISPR-Cas9 technology to construct a guide RNA (gRNA) library that can knock out 19,069 genes encoding proteins. With this tool, they knocked out genes encoding proteins in six different cancer cell lines one by one. These six cancer cell lines come from breast cancer, colon cancer, kidney cancer and skin cancer tumors, and represent cancer models with a very broad genetic background.

Researchers put these cell lines together with activated cytotoxic T cells (CTL) to observe which genes are knocked out to make cancer cells more sensitive to CTL, which genes are knocked out to make cancer cells resistant to CTL attack. The results of the screening found 182 genes, which showed the same ability in more than 3 cell lines, which can make cancer cells more sensitive or resistant to the killing effect of CTL. Researchers call these genes "core cancer intrinsic immune evasion genes".

By analyzing the characteristics of these 182 genes, the researchers found that many of them are related to signaling pathways that regulate interferonγ (IFNγ). Interferonγ is a cytokine that plays an important role in various immune responses. Further analysis revealed that multiple genes related to autophagy play a key role in regulating the interferonγ signaling pathway, some of which have not been found to be related to interferonγbefore. For example, researchers discovered a gene called FITM2, which plays a key role in fat storage in mouse fat tissue. However, if the FITM2 gene is knocked out in the cell, it makes the three cancer cell lines more sensitive to CTL.

The research clarifying the role of autophagy won the Nobel Prize in Physiology or Medicine in 2016. Autophagy is like a "waste recycling station" in the cell. By recycling the amino acids produced during autophagy, cells can provide raw materials for the synthesis of new proteins and the construction of organelles. In previous studies, researchers have found that the combination of drugs that inhibit autophagy and other anti-cancer drugs may produce better anti-cancer effects. For example, multiple research teams have found that the combination of autophagy inhibitors and MAPK signaling pathway inhibitors can inhibit the growth of different types of tumors.

In this study, the researchers found that an autophagy inhibitor called autophinib can make multiple tumor cell lines more sensitive to another cytokine, TNFα, which plays an important role in cellular immune responses. It shows the potential of inhibiting autophagy in improving the efficacy of immunotherapy.

The researchers also pointed out in the paper that the interaction between different genes can have a great impact on the immune escape of tumor cells. When they studied the interaction between genes related to autophagy, they found that knocking out the gene called ATG12 would cause tumor cells to be more sensitive to cytotoxic lymphocytes. However, knocking out ATG5 or ATG16L1 while knocking out ATG12 will instead make tumor cells resistant to cytotoxic lymphocytes. This result shows that certain gene mutations already carried by the tumor may determine whether a specifically targeted drug will inhibit the progress of cancer or whether it will have a counterproductive effect.

Finally, the researchers stated in the discussion section of the paper that the core genes and signaling pathways that mediate tumor evasion of cytotoxic T cells discovered in this study may provide insights for guiding the development of new cancer immunotherapies.