Proteome analysis of human CD56^neg NK cells reveals a homogeneous phenotype surprisingly similar to CD56^dim NK cells

Abstract

NK cells lacking CD56 (CD56^neg ) were first identified in chronic HIV-1 infection. However, CD56^neg NK cells also exist in healthy individuals, albeit in significantly lower numbers. Here, we provide an extensive proteomic characterisation of human CD56^neg peripheral blood NK cells of healthy donors and compare them to their CD56^dim and CD56^bright counterparts. Unbiased large-scale surface receptor profiling clustered CD56^neg cells as part of the main NK cell compartment and indicated an overall CD56^dim -like phenotype. Total proteome analyses of CD56^neg NK cells further confirmed their similarity with CD56^dim NK cells, and revealed a complete cytolytic inventory with high levels of perforin and granzyme H and M. In the present study, twelve proteins discriminated CD56^neg NK cells from CD56^dim NK cells with nine up-regulated and three down-regulated proteins in the CD56^neg NK cell population. Those proteins were functionally related to lytic granule composition and transport, interaction with the extracellular matrix, DNA transcription or repair, and proliferation. Corroborating these results, CD56^neg NK cells showed modest cytotoxicity, degranulation, and IFN-ɣ secretion as compared to CD56^dim NK cells. In conclusion, CD56^neg NK cells constitute functionally competent cells sharing many features of bona fide CD56^dim NK cells in healthy individuals, but with some distinct characteristics.