IsoPlexis’ Unique Single-Cell Proteomics Accelerates CRISPR-Engineered NK Cell Therapy to Predict Enhanced Anti-Tumor Activity & Persistence

Highly Polyfunctional Superhero Cells Lead to Increased Anti-Tumor Response Against Leukemia

A recent publication in Cell Stem Cell featured IsoPlexis’ single-cell proteomics in a study testing CRISPR-edited NK cells and their ability to exhibit anti-tumor function as well as their effect on leukemia. NK cells have the ability to kill tumor cells or cells infected with viruses without any stimulation from antigens, making them ideal to work with in immune therapies. However, they don’t tend to last very long in vivo, so their anti-tumor response is short lived. In order to overcome this challenge, researchers Zhu et al. first sought to create a sustainable supply of NK cells by deriving them from induced pluripotent stem cells (iPSCs). They then used CRISPR-editing to engineer the NK cells. IsoPlexis’ single-cell proteomics was used to identify the polyfunctional engineered NK cells with “superpowers” that function as “superhero” cells. These data were recently published in Cell Stem Cell.

Researchers Zhu et al. identified a gene that would likely improve the function of the engineered cells greatly. Using CRISPR, they deleted CISH, the human gene for cytokine-inducible SH2-containing protein (CIS), which is a critical negative regulator for IL-15 signaling within NK cells. Both deriving NK cells from iPSCs and editing them are incredible feats on their own, but Zhu et al. dove further and utilized IsoPlexis’ single-cell proteomics to analyze these novel cells and discover if the CRISPR edits really did improve cellular function. These CRISPR-engineered NK cells were found to have increased persistence compared to the wild type NK cells.1 IsoPlexis’ single-cell proteomics was able to predict that these newly engineered superhero cells would be persistent. When these cells were tested against acute myeloid leukemia, the CISH-KO iPSC-NK cells demonstrated enhanced anti-tumor function and persistence in vivo compared to the wild type iPSC-NK cells. Increased polyfunctionality contributed to this improved anti-tumor function.

The CRISPR-engineered NK cells showed high levels of polyfunctionality, identified by IsoPlexis’ single-cell proteomics, which was associated with persistence in vivo.

Increased Polyfunctionality Leads to Increased Anti-Tumor Activity

These functionally hyperactive engineered NK cells are considered “superhero” cells due to their increased polyfunctionality which has led to increased persistence and anti-tumor response. Reported in the Cell Stem Cell paper, researchers Zhu et al. wanted to identify if the enhanced function of the CISH-KO iPSC-NK cells correlated to improved cytotoxicity. After treating with rapamycin, the CISH-KO iPSC-NK cells “resulted in decreased cytotoxicity, degranulation, and cytokine production…and directly contributes to enhanced NK cell functions.”1 IsoPlexis’ single-cell proteomics was used to analyze each individual cell’s function. Not only was it found that the CISH-KO iPSC-NK cells were more polyfunctional, but their functional potency was increased >10-fold, compared to the wild type iPSC-NK cells and the PB-NK cells.1

The increased polyfunctionality correlated to increased anti-tumor activity and removing CISH increased in vivo persistence of the NK cells after transfer. Researchers also determined “improved single-cell polyfunctionality measured by production of multiple effector cytokines that might also contribute to their improved anti-tumor functions.”1 This cell subset has superpowers because of their increased polyfunctionality and the specific cytokines they are secreting, which lead to anti-tumor functions. These cells are considered “superman” cells, however, not all polyfunctional superpowered cells have beneficial functions, as shown in our previous blog post.

Researchers Zhu et al. engineered these superhero cells using CRISPR to fight cancers like acute myeloid leukemia and IsoPlexis’ single-cell proteomics identified a polyfunctional subset of cells that did improve cell function. This technology also verified that the increased function resulted from the gene edits and that the increased polyfunctionality correlated with anti-tumor activity.

To learn more about how IsoPlexis’ single-cell proteomics can be used to empower gene-edited and engineered therapies, download our CRISPR eBook.


  1. Zhu H et al. Metabolic Reprogramming via Depletion of CISH in Human iPSC-Derived NK Cells Promotes In Vivo Persistence and Enhances Anti-tumor Activity. Cell Stem Cell 27: 1-14, 2020.
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