Clonal expansion and compartmentalized maintenance of rhesus macaque NK cell subsets

Abstract

Natural killer (NK) cells recognize and eliminate infected and malignant cells. Their life histories are poorly understood, particularly in humans, due to lack of informative models and endogenous clonal markers. Here, we apply transplantation of barcoded rhesus macaque hematopoietic cells to interrogate the landscape of NK cell production, expansion, and life histories at a clonal level long term and after proliferative challenge. We identify oligoclonal populations of rhesus CD56−CD16+NK cells that are characterized by marked expansions and contractions over time yet remained long-term clonally uncoupled from other hematopoietic lineages, including CD56+CD16−NK cells. Individual or groups of CD56−CD16+expanded clones segregated with surface expression of specific killer immunoglobulin-like receptors. These clonally distinct NK cell subpopulation patterns persisted for more than 4 years, including after transient in vivo anti-CD16–mediated depletion and subsequent regeneration. Profound and sustained interleukin-15–mediated depletion was required to generate new oligoclonal CD56−CD16+NK cells. Together, our results indicate that linear NK cell production from multipotent hematopoietic progenitors or less mature CD56+CD16−cells is negligible during homeostasis and moderate proliferative stress. In such settings, peripheral compartmentalized self-renewal can maintain the composition of distinct, differentiated NK cell subpopulations.

barcodetrackR: an R package for the interrogation of clonal tracking data

“…This implies a more oligoclonal population of contributing progenitors. The finding that the mature NK cell compartment is largely composed of a few high-contributing clones post-transplantation is in agreement with rhesus macaque barcoded autologous HSPC transplant studies (10).…”

“…Measurement of each label's abundance in the pool of all recovered labels is directly associated with the abundance of that clone within the labelled population being assayed, for instance T cells, B cells or myeloid cells. These lineage abundance measurements can provide insights not only into the bias, stability, and ontogenetic relationships of HSPCs (8), but also into the dynamics of clones within cell populations whose abundances are largely independent of HSPC behavior, such as certain T cell (9) and natural killer (NK) cell subsets (10). Furthermore, such clonal tracking methods have also been leveraged to provide valuable insight into the clonal dynamics of cancer progression (11), in vitro differentiation (12), and clonal dynamics of CAR-T cells (13).…”

“…barcodetrackR encompasses a variety of flexible tools that can provide insights into clonal dynamics and the relationships between cellular compartments starting with clonal abundance data. We illustrate the utility of barcodetrackR by analyzing publicly available clonal tracking datasets from studies in lentivirally transduced non-human primates (8,10,21), xenograft mice transplanted with human cord blood cells (22) and blast cells (23), and lentiviral gene therapy patients (6,24). More details on each dataset and access paths are summarized in Table 1.…”

Characterizing the Dysfunctional NK Cell: Assessing the Clinical Relevance of Exhaustion, Anergy, and Senescence

“…Understanding the lifespan of the cell is critical to gaining an understanding of NK senescence, though this is challenging as the lifespan of an NK cell is not clearly defined. Estimates of the in vivo half-life of murine NK cells are ∼7-10 days (Yokoyama et al, 2004), and possibly <10 days in humans (Nayar et al, 2015), though this view has been expanded by advances in cell identification and barcoding techniques in non-human primates showing unique developmental pathways of NK subsets (Wu et al, 2014) and prolonged persistence (months) of specific NK clones (Wu et al, 2018). In vitro, this can be markedly manipulated, but the limit of healthy, normal human NK cells to grow in culture appears to be ∼15 weeks (Fujisaki et al, 2009a).…”

Dynamic changes in natural killer cell subset frequencies in the absence of cytomegalovirus infection

“…A key unanswered question concerns the nature of the stimuli provoking longitudinal changes in frequency of NK cell subsets. A recent study of barcoded hematopoietic cells in rhesus macaques noted significant fluctuations in the clonal composition of NK cells over time (Wu et al, 2018). Our study stringently controlled for CMV exposure via urine and blood analyses (Bernstein et al, 2016).…”