Researchers at the Mount Sinai Health System in New York have developed a new method that allows for marking and imaging of cancer tissue at a scale and resolution that wasn't possible before, an institutional press release said.
Cancer tumors do not contain cancerous cells alone and recent successes in cancer therapies can be attributed to treatments that target the non-cancerous cells in the tumor. Although this may sound counter-intuitive, it has been found to be highly effective to target immune cells in a tumor and enable them to attack cancer the way immunotherapies such as Keytruda and Tencentriq do.
From cells to genes
Since the environment of the tumor has an impact on patient outcomes, researchers are keen to determine the genes cancerous cells use to control their environment. As hundreds of genes are active at a tumor site, cancer researchers have moved away from animal models to cancerous cell lines to identify the genes involved and the functions they carry out.
Using CRISPR, scientists are able to knock out genes in cancer cells and then follow it up with large-scale DNA sequencing to study the entire genome. While this method has been useful in studying cancerous cells, it cannot be used to study the noncancerous cells that are part of the tumor.
The researchers at Mount Sinai used a system called Perturb-map, which uses a new genetic barcode system to label genetic modifications in cancerous, as well as non-cancerous cells, in a tumor. Using this method, the researchers were able to identify genes that controlled tumor growth, immune composition, as well as response to immunotherapies.
Two pathways identified
The application of the method led the researchers to two key pathways that affected tumor growth and immune cell recruitment to the tumor site. One of these pathways was controlled by cytokine interferon-gamma (IFNg) while the other was controlled by the tumor growth factor beta receptor (TGFbR).
When genes for TGFbR or SOCS1, a regulator of IFNg, were removed from cancerous cells, tumors grew in size and became abundant. While the impact on tumor size was the same in either of the approaches, using imaging techniques the researchers found a difference in immune cell recruitment at the sites. SOCS1 tumors were infiltrated with T cells while TGFbr tumors had none. The situation remained the same, even when the two tumors were in direct contact.
"This is a notable insight because we are learning that many patient tumors are composed of genetically distinct subclones, "said Brian Brown, Director of the Icahn Genomics Institute at Mount Sinai. "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."
Details of the study were published in the journal, Cell.
Study abstract: While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes, existing approaches are suboptimal for identifying extracellular gene functions, particularly in the tissue context. Here, we developed an approach for spatial functional genomics called Perturb-map. We applied Perturb-map to knock out dozens of genes in parallel in a mouse model of lung cancer and simultaneously assessed how each knockout influenced tumor growth, histopathology, and immune composition. Moreover, we paired Perturb-map and spatial transcriptomics for unbiased analysis of CRISPR-edited tumors. We found that in Tgfbr2 knockout tumors, the tumor microenvironment (TME) was converted to a fibro-mucinous state, and T cells excluded, concomitant with upregulated TGFβ and TGFβ-mediated fibroblast activation, indicating that TGFβ-receptor loss on cancer cells increased TGFβ bioavailability and its immunosuppressive effects on the TME. These studies establish Perturb-map for functional genomics within the tissue at single-cell resolution with spatial architecture preserved and provide insight into how TGFβ responsiveness of cancer cells can affect the TME.