Research highlights how genome editing tool CRISPR knocks off genes in cancer cells

Mount Sinai researchers have created a novel method that allows them to correlate particular genes to complex tumor properties at a size and resolution that has never been achievable before. The findings might pave the way for new ways to target anti-cancer drugs.

Research highlights how genome editing tool CRISPR knocks off genes in cancer cells
Image Credit: The Mount Sinai Hospital / Mount Sinai School of Medicine

The Perturb-map technique employs a revolutionary genetic barcode system to label cancer cells with various gene alterations and picture the cancer cells, and also nearby non-cancer cells, inside the tissue. According to the study, which was published in the March edition of Cell, the scientists were able to discover particular genes affecting lung tumor development, immunological composition, and even immunotherapy response using this method.

Tumors are made up of a variety of cell types in addition to cancer cells, and drugs that target the tumor’s non-cancer cells have transformed cancer treatment during the last two decades. Immunotherapies like Keytruda and Tecentriq, which switch on immune cells in the tumor and allow them to attack cancer cells, and Avastin, which changes the tumor’s blood arteries and starves cancer, are among them.

Because the tumor’s environment has such a big impact on the patient, finding the genes that tumors utilize to manage their local ecology is critical. This knowledge is crucial for the development of new anti-cancer drugs.

However, because tumors produce hundreds of genes, identifying which ones to target necessitates a level of analysis that has been difficult to obtain in animal models of cancer and is required to accurately depict the whole-cell ecology of a patient’s tumor.

For several years, scientists have been utilizing CRISPR, a genome-editing tool, to knock off genes in cancer cells and analyze their function. Thanks to advancements in DNA sequencing technology, it is now possible to utilize thousands of CRISPRs at once to study every gene in the genome.

These CRISPR genetic screens, on the other hand, have only been able to discover genes and functions that act within cancer cells. Many important concerns, such as how cancer cells modify the activation and proliferation of immune cells in the tumor, a significant component in patient response to immunotherapy, remain unresolved by genetic screening.

The researchers discovered two major pathways that had a significant influence on tumor development, tumor morphology, and immune cell recruiting using Perturb-map. The cytokine interferon-gamma (IFNg) was in charge of one route, while the tumor growth factor-beta receptor was in charge of the other (TGFbR).

The researchers discovered that if the TGFbR2 gene or a gene coding for SOCS1, an IFNg regulator, was removed from cancer cells, the tumors grew bigger and more numerous. Although both genes had a comparable effect on tumor growth, imaging of the tumors using the Perturb-map platform indicated that the SOCS1 tumors were heavily penetrated by T cells, while the TGFbR tumors were devoid of T cells.

The former stayed infiltrated and the latter was excluded even when SOCS1 and TGFbR tumors were in close contact. This is significant because individuals with fewer immune cells in their cancers have a lower response to immunotherapy medicines.

Brain Brown explained, “These findings indicate that these genes’ effects over the tumor ecosystem are extremely localized.”

This is a notable insight because we are learning that many patient tumors are composed of genetically distinct subclones. If specific gene mutations are keeping T cells out of a subclonal region, this can serve as a pocket of resistance to immunotherapies like Keytruda. The local and distal effects of many other genes on tumor composition are still not known, but the Perturb-map platform will now give scientists a powerful means to tackle the problem.”

Brian Brown, Senior Author, PhD, Associate Director, Lipschultz Precision Immunology Institute, Mount Sinai

Brown is also the director of Icahn Genomics Institute.

Miriam Merad, MD, PhD, Study Co-author and the Director of PrIISM, “Perturb-map is allowing us to identify the specific genes that control a tumor’s environment at a scale that wasn’t possible before. This includes making it possible to find the genes that are responsible for recruiting or reprogramming cells that prevent the immune system from eliminating tumors. It’s remarkable.”

This is going to greatly enhance our ability to find new targets for better cancer therapies and that’s important for our patients,” Miriam Merad concluded.

Source:
Journal reference:

Dhainaut, M., et al. (2022) Spatial CRISPR genomics identifies regulators of the tumor microenvironment. Cell. doi.org/10.1016/j.cell.2022.02.015.

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