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Protocol for identification and computational analysis of human natural killer cells using flow cytometry and R.

ABSTRACT: Identifying differential protein expression is routinely used to delineate natural killer (NK) cells from various sample cohorts. This protocol describes key steps for NK cell analysis: identifying human NK cells using flow gating, data export from FlowJo, data loading in R, dimensionality reduction and visualization with Uniform Manifold Approximation and Projection, and generalized linear modeling with CyotGLMM. These analyses can help generate potential biomarkers of interest to identify NK cells across aging, treatment groups, and others. For complete details on the use and execution of this protocol, please refer to Kroll et al. (2022).¹.

SUBMITTER: Kroll K

PROVIDER: S-EPMC9871333 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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Protocol for identification and computational analysis of human natural killer cells using flow cytometry and R.

Kroll Kyle K Reeves R Keith RK

STAR protocols 20230119 1

Identifying differential protein expression is routinely used to delineate natural killer (NK) cells from various sample cohorts. This protocol describes key steps for NK cell analysis: identifying human NK cells using flow gating, data export from FlowJo, data loading in R, dimensionality reduction and visualization with Uniform Manifold Approximation and Projection, and generalized linear modeling with CyotGLMM. These analyses can help generate potential biomarkers of interest to identify NK c ...[more]

PMID: 36853664

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Project description:BackgroundNatural Killer (NK) cells are effector lymphocytes of the innate immune system and are subclassed into CD56BrightCD16Dim/- and CD56DimCD16+ NK cells. Intracellular calcium (Ca2+) is fundamental to regulate a number of intracellular signalling pathways and functions in NK cells, which are essential in mediating their natural cytotoxic function. Transient receptor potential melastatin 2 (TRPM2) is a Ca2+-permeable non-selective cation channel that possesses a critical role in calcium-dependent cell signalling to maintain cellular homeostasis. TRPM2 and CD38 protein surface expression has yet to be determined on NK cells using flow cytometry. Characterisation of TRPM2 has been previously identified by in vivo models, primarily using methods such as genetic remodification, immunohistochemistry and whole cell electrophysiology. The aim of this study was to develop an in vitro methodology to characterise TRPM2 and CD38 surface expression on NK cell subsets using an antibody that has not been previously applied using flow cytometry.ResultsAt 2 h/1 h, TRPM2 (Fig. 2 A, B, p < 0.05) and TRPM2/CD38 (Fig. 3A, B, p < 0.05) surface expression significantly increased between 1:300 and 1:50 at 2 h/1 h. TRPM2/CD38 surface expression furthermore increased between 1:100 and 1:50 at 2 h/1 h (Fig. 3A, p < 0.05). Interestingly, TRPM2/CD38 surface expression significantly decreased from 1:50 to 1:5 on CD56BrightCD16Dim/- NK cells. These consistent findings highlight that 1:50 is the optimal antibody dilution and threshold to measure TRPM2 and TRPM2/CD38 surface expression on NK subsets. 2 h/1 h was determined as the optimal incubation period to ensure a sufficient timeframe for maximal antibody binding and surface expression.ConclusionFor the first time, we describe an in vitro methodology to characterise TRPM2 and CD38 surface expression on NK cells in healthy participants. Finally, using an antibody that has not been previously applied in flow cytometry, we determined an antibody concentration and incubation time that is robust, rapid and sensitive for the application of flow cytometry.

Dataset Information

Protocol for identification and computational analysis of human natural killer cells using flow cytometry and R.

Publications

Protocol for identification and computational analysis of human natural killer cells using flow cytometry and R.

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