Abstract
The process of immune system regeneration after allogeneic stem cell transplantation is slow, complex, and insufficiently understood. An entire immune system with all of its cell populations must regenerate from infused donor hematopoietic stem cells over the course of weeks and months post-transplantation. Both innate and adaptive arms of the immune system differ in their capacity and speed to reconstitiute in the recipient, which contributes to inadequacy in global immunity during the delayed reconstitution period. Systems-level analyses of immune systems in human patients have been made possible by high-throughput and high-dimensional, state-of-the-art, single-cell methodologies such as mass cytometry. Mass cytometry has revolutionized our ability to comprehensively profile all immune cell populations simultaneously in blood or tissue samples, providing signatures of differentially regulated cells in a range of clinical conditions. Such kind of systems immunology analyses promise not only for more accurate descriptions of variation between patients but also within individual patients over time, inter-dependencies between cell populations and the inference of developmental trajectories for specific cell populations. Here, we took advantage of a recently performed longitudinal mass cytometry analysis in 26 patients with hematological malignancies followed during the first 12 months following allogeneic stem cell transplantation. We present a proof-of-principle analysis to understand the evolution of individual immune cell populations. By applying non-linear dimensionality reduction and feauture extraction algorithms, we infer trajectories for individual immune cell populations, and map continuous marker expression changes occuring during immune cell regeneration that add novel information about this developmental process.
Highlights
MATERIALS AND METHODSPatients and Blood SamplesHuman immune systems are highly variable between individuals and complex within individuals, consisting of multiple specialized cell populations that circulate and establish unique tissue niches
The protein concentration was determined by measurement of absorbance at 280 nm, and cellaccense.com) (Shekhar et al, 2014) to visualize single-cell level data in 2D and classify cell populations not based on individual markers, but on the basis of all 37 parameters analyzed (Supplementary Figure 1A)
In the tstochastic neighborhood embedding (tSNE) 2-d distribution plots, individual cells are aggregated into local neighborhoods together with other cells of similar phenotypes based not just on a few markers, but on the entire marker set analyzed (Supplementary Figure 1 and Figure 1). These mass cytometry analyses reveal phenotypic changes occurring throughout regeneration albeit at different time intervals for different cell types, adding yet another layer of complexity to the process of immune cell reconstitution in patients undergoing stem cell transplantation
Summary
MATERIALS AND METHODSPatients and Blood SamplesHuman immune systems are highly variable between individuals and complex within individuals, consisting of multiple specialized cell populations that circulate and establish unique tissue niches. The protein concentration was determined by measurement of absorbance at 280 nm, and cellaccense.com) (Shekhar et al, 2014) to visualize single-cell level data in 2D (tSNE) and classify cell populations not based on individual markers, but on the basis of all 37 parameters analyzed (Supplementary Figure 1A). Using this method we selected T-, B-, and NK-cells, monocytes and basophils in each of the 26 patients at 1, 2, 3, 6, and 12 Months post-transplantation (Supplementary Figure 1A).
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