Sep 15, 2022 / Oncology

Can single cell tools discover new immunotherapies for blood cancers?

Jeanene Swanson

Blood Cancer Awareness Month

Blood Cancer Awareness Month in September raises awareness about blood cancers including leukemia and lymphoma. According to the Leukemia and Lymphoma Society, someone in the United States is diagnosed with a blood cancer every three minutes (1). Fortunately, recent advances in chimeric antigen receptor (CAR) T-cell immunotherapy have increased treatment options, at least for certain types of hematological malignancies. In this blog, we feature a publication that describes the first-in-human clinical trial of natural killer (NK) cells modified with a T-cell receptor (TCR)-like CAR directed at a specific mutation in acute myeloid leukemia (AML). This work holds potential for improving upon existing adoptive cell therapies.

Cancers of the blood and lymphoid tissues, which include bone marrow, lymph nodes, and the lymphatic system, are the third leading cause of cancer deaths in the US (1). However, people diagnosed with hematological malignancies have good reason to be hopeful—all six FDA-approved CAR T-cell therapies are for the treatment of blood cancers (2). And, every day, researchers study more types and targets of adoptive cell therapy.

There are three main kinds of blood cancer: leukemia, lymphoma, and myeloma. AML is an aggressive type of leukemia that, left untreated, is fatal within weeks or months. Current CAR T-cell therapies are not effective for AML, and most patients die from their disease (3). In fact, the average survival time for AML patients receiving the current standard-of-care treatment is 3.9 months (4).

Patients with AML can be treated with bone marrow transplantation, to some degree of success. However, therapeutic efficacy is hampered in the long term by graft-versus-host disease and toxicity. While CAR immunotherapy using T cells has successfully treated B-cell cancers, a lack of tumor-specific antigens on AML cells results in toxic, off-target effects. In an effort to search out more targeted, less toxic immunotherapies for AML, scientists have set their sights on NK cells.

Not only have recent studies discovered that, in addition to T cells, NK cells play a significant role in successful transplantation (5), other studies have uncovered cytokine-induced memory-like (CIML) NK cells that show evidence of NK cell memory and display strong anti-leukemia activity (6). In this blog, we feature work led by Dana-Farber Cancer Institute’s Han Dong, PhD, formerly a postdoc in the lab of Dana-Farber President Laurie Glimcher, MD, wherein they published first-in-human clinical trial results using antigen receptor–modified NK cells for treating AML. Data from their phase 1 trial was positive: CIML NK cells showed a response in more than half of patients with relapsed refractory AML with no apparent toxicity (7). Moreover, these modified NK cells “proliferated, expanded, and maintained enhanced anti-leukemia responses” in patients (8).

Creating a new type of antigen-targeting CAR cell

Clinicians have used CAR T cells to treat B-cell malignancies such as lymphoma and myeloma; however, for AML, there is a lack of tumor-specific antigens, leading to toxic, off-target effects when T-cell therapy is used to attempt to treat AML. One of the most commonly occurring mutations in about 30% of adult AML cases is within the nucleophosmin-1 (NPM1) gene. With the intention of creating a therapy that specifically targets this mutation, Dr. Dong and her team took blood cells from healthy donors and transduced CIML NK cells with a lentivirus expressing a CAR recognizing the NPM1c neoepitope.

Single cell analysis maps cell-type gene expression

Aiming to characterize the CAR CIML NK cells, they used Chromium Single Cell Gene Expression to perform single cell RNA sequencing (scRNA-seq) on sorted CAR-positive CIML NK cells and CAR-negative CIML NK cells from the same culture generated from two different peripheral blood donors. To reduce the effects of variation among donors, they compared CAR-positive and CAR-negative cells from the same donors.

Their transcriptomic analyses uncovered increased expression of genes in CAR-positive cells for key pathways of cell proliferation, protein folding, immune responses, and metabolism, including glycolysis and mitochondrial function. The fact that pathways for activity and proliferation were enriched suggests that CAR-positive NK cells are likely to be successful against AML targets.

Crosstalk is key to a positive outcome—but only if a CAR is involved

The team wondered how subsets of CAR-positive NK cells might vary in their anti-tumor activity against AML target cells. Turning to their single cell transcriptomic signatures for clues, they first cultured CAR-positive CIML NK cells with and without AML target cells followed by scRNA-seq. Intriguingly, only one cluster of CAR-positive cells showed its distinct anti-tumor transcriptomic profile in the presence of AML cells; CAR-negative controls cultured with AML target cells did not show this same up-regulation. Their findings suggest specific CAR-positive cellular responses are dependent on tumor cell engagement.

Novel adoptive cell therapies on the horizon

More types of therapies for treating hematological malignancies can’t come fast enough: many patients die while waiting for CAR T-cell therapy, and, for patients with a type of blood cancer for which T-cell immunotherapy isn’t yet an option, the prognosis is even grimmer. This first-in-human trial demonstrates that the hurdles to using T cells for immunotherapy—including lack of efficacy and toxicity—can be overcome. As single cell technologies advance, scientists are bound for more translational successes in adoptive cell therapy specifically, as well as in the broader realm of cell and gene therapies.


  1. September is Blood Cancer Awareness Month | Leukemia and Lymphoma Society.
  2. CAR T Cells: Engineering Immune Cells to Treat Cancer – NCI.
  3. Dong H, et al. Memory-like NK cells armed with a neoepitope-specific CAR exhibit potent activity against NPM1 mutated acute myeloid leukemia. Proc Natl Acad Sci USA 119: e2122379119 (2022). doi: 10.1073/pnas.2122379119
  4. Beat AML in the Time of COVID-19: A Powerful New Video | Leukemia and Lymphoma Society.
  5. Venstrom JM, et al. HLA-C-dependent prevention of leukemia relapse by donor activating KIR2DS1. N Engl J Med 367: 805–16 (2012). doi: 10.1056/NEJMoa1200503
  6. Sun JC, Lanier LL. Is there natural killer cell memory and can it be harnessed by vaccination? NK cell memory and immunization strategies against infectious diseases and cancer. Cold Spring Harb Perspect Biol 10: a029538 (2018). doi: 10.1101/cshperspect.a029538
  7. Romee R, et al. Cytokine-induced memory-like natural killer cells exhibit enhanced responses against myeloid leukemia. Sci Transl Med 8: 357ra123 (2016). doi: 10.1126/scitranslmed.aaf2341
  8. Berrien-Elliott MM, et al. Multidimensional analyses of donor memory-like NK cells reveal new associations with response after adoptive immunotherapy for leukemia. Cancer Discov 10: 1854–1871 (2020). doi: 10.1158/2159-8290.CD-20-0312