Maps of natural killer cells offer insight into COVID-19 immune response

By Samantha Black, PhD, The Science Advisory Board editor in chief

August 24, 2020 -- New research that sought to classify immune white blood cells, called natural killer (NK) cells, during COVID-19 infection revealed that certain cellular subtypes may contribute to the severity of disease progression, according to a recent Science Immunology article.

High levels of interleukin-6 and resulting cytokine storm in the absence of appropriate type I and III interferon responses are associated with severe COVID-19 disease. Research suggests that protective immunity is formed with neutralizing antibodies and SARS-CoV-2-specific T cells; however, less is known about innate lymphocyte responses toward SARS-CoV-2 infection and how they relate to host responses and disease progression.

NK cells are innate effector lymphocytes that respond to acute viral infections but that might also contribute to immunopathogenicity. NK cells have the ability to directly target and kill infected cells but can also influence adaptive T-cell responses. Low peripheral blood NK cell numbers in COVID-19 patients have been reported in patients with moderate and severe disease.

NK cells are divided into two main subpopulations based on the expression level of the CD56 marker. Most periphery NK cells (around 90%) have low-density expression of CD56 (CD56dim cells), whereas about 10% of NK cells express CD56 at high levels (CD56bright cells) and are more abundant in tissues.

Detecting NK cells in COVID-19 patients

To evaluate NK cell activation in the context of SARS-CoV-2 infection and resulting COVID-19 disease, researchers from the Karolinska Institutet in Sweden used 28-color flow cytometry on 27 in-hospital patients with COVID-19 at Karolinska University Hospital as part of a larger immune cell atlas effort. The researchers found generally strong NK cell activation across distinct subsets in peripheral blood of COVID-19 patients.

Next, the team performed phenotypic assessment of CD56bright and CD56dim NK cells in patients. Flow cytometry analysis showed increased expression of perforin, Ksp37, MIP-1β, CD98, Tim-3, and granzyme B in CD56bright NK cells from COVID-19 patients, as well as CD98, Tim-3, NKG2C, MIP-1β, and CD62L, among other markers, in CD56dim NK cells. These results did not reveal an obvious separation in NK activation between moderate and severe COVID-19 patients.

Adaptive NK cells are linked to COVID-19 disease

Adaptive NK cells are a subpopulation that are terminally differentiated and co-express NKG2C and CD57. The researchers found that patients with severe disease almost exclusively had increased frequencies of NKG2C+CD57+ CD56dim NK cells as compared to moderate COVID-19 patients and healthy controls.

The team also found that a significant portion of adaptive NK cells actively proliferate in COVID-19 patients, albeit at a lower rate compared to non-adaptive NK cells. This suggests that their accumulation might be related to their ability to persist in circulation.

NK cell immunotypes are linked to disease severity

By including clinical data that was associated with disease severity, the researchers were able to identify two immunotypes associated with severe COVID-19 cases. The immunotype linked to moderate disease was associated with upregulation of MIP-1β, CD98, and TIGIT (a checkpoint inhibitor).

The immunotype associated with severe disease displayed high expression of perforin, Ksp37, and NKG2C. Interestingly, high perforin, NKG2C, and Ksp37 are features of adaptive NK cell expansions which were also associated with severe disease.

Furthermore, CD56bright NK cells were severely reduced but strongly activated in COVID-19 patients. This "arming" of activated NK cells with cytotoxic molecules was correlated with the development of severe disease.

Severe hyperinflammation, as defined by clinical parameters, was associated with a high presence of adaptive NK cell expansions and arming of CD56bright NK cells. The researchers also found that the systemic immune changes caused by NK cells during severe COVID-19 disease were linked to a soluble factor protein interaction network that is also seen in other viral infections.

The authors concluded by suggesting that emergence of adaptive NK cell expansions and arming of CD56bright NK cells appear to be specific to severe COVID-19, but that future studies are needed to map responses with other immune cell responses to create a base for understanding the role of NK cells in patients with COVID-19.

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