Perturb-map, A New Technology Cracking Tumor Microenvironment Mystery
Summary
Researchers at the Icahn School of Medicine at Mount Sinai in New York have made a major
breakthrough in identifying the extracellular functions of genes. They have developed a new spatial functional
genomics technique called Perturb-map, which enables the discovery of genes that regulate extracellular functions
on an unprecedented scale and with single-cell resolution. This novel technology, combining CRISPR pools, multiplex imaging, and spatial
transcriptomics, effectively identifies genetic determinants of tumor tissue composition and immunity, which can
help develop new cancer immunotherapies.
Background
The type of immune cells recruited into the tumor microenvironment are important determinants of
the efficacy of immunotherapy. The identification of genes that control the composition of the tumor
microenvironment can help develop strategies enabling immune cells to better break through the tumor milieu and
achieve therapeutic effects. However, existing CRISPR screens are more suitable for studying intracellular
processes, such as genetic mechanisms of protein expression and drug resistance, but not to elucidate the
extracellular function of genes.
Experiment
To perform multiplex imaging, researchers stain tissues with antibodies that detect protein bar
codes (Pro-Codes), a technology marking cells with different CRISPR gRNAs and enabling high-dimensional
phenotyping for CRISPR screens. The researchers transduced cells with a Pro-Code library and intravenously
injected them into Cas9 mice. The lungs of the mice were collected and analyzed 4 weeks later to determine how
knocking out different genes affects cancer progression.
In a parallel mouse experiment, mouse lung samples were collected 7 days, 14 days, and 28 days
after intravenous injection of transduced cells to examine the effect of Tgfbr2 knockout on tumor growth.
Result
Suppressor of Cytokine Signaling 1(SOCS1) and Tgfbr2, the multifunctional Cytokine receptor of
transforming growth factor β, showed the greatest influences on tumor growth.
Novel Immunotherapy: PD1/PDL1 Blockade Combined with SOCS1 Inhibition
Researchers found that SOCS1 loss accelerated lung tumor growth in mice. However, the paradox was
that, rather than a decrease, T cell recruitment into the tumor increased significantly. Further exploration
revealed that SOCS1 knockout led to increased PD-L1 on cancer cells, which incapacitated T cells. Therefore, even
if the number of T cells entering the tumor increased, it did not stop cancer progression. When the researchers
treated SOCS1 knockout tumors with drugs blocking PD-L1, the tumors shrank more than those in the control group.
This finding suggests that combining PD1/PDL1 blockade with SOCS1 inhibition can lead to more effective
immunotherapies.
Tgfbr2: the Cause of the Tumor Microenvironment
Tgfbr2 knockout experiments showed that lung tumors were larger and more abundant than those of the
control group 7 days after injection, and the tumor area expanded, doubling that from the control group within 28
days. In addition, the lung tumors of Tgfbr2 knockout mice were filled with fibrous mucinous stroma, which was not
observed in the control group. These results suggest that the loss of Tgfbr2 on cancer cells turns the tumor
microenvironment into a mucus-filled pool dotted with fibrocytes, which prevents T cell tumor infiltration and
accelerates tumor growth.
Reference
Dhainaut, Maxime, et al. "Spatial CRISPR genomics identifies regulators of the tumor
microenvironment." Cell (2022).
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