We have utilized molecular techniques to gain new insights into the behavior of hematopoietic stem and progenitor cells (HSPCs) in vivo. We have continued active development and utilization of lentiviral barcoding with high-diversity 31-35 base pair genetic barcodes utilized to label individual hematopoietic stem and progenitor cells to study in vivo hematopoiesis in the non-human primate model. Our collaborator Rong Lu first devised this very powerful approach and applied it to study murine hematopoiesis. We have now transplanted 25 macaques with barcoded autologous CD34+ cells, and have been able to track hematopoietic output from thousands of individual HSPCs over time (up to 7 years) and in multiple lineages in a quantitative and highly reproducible manner. We are currently modifying our barcoding strategy to allow simultaneous retrieval of the barcode and single cell RNASeq in order to begin to be able to connect our cell fate findings (barcode-defined ontogeny) together with state characterization in terms of gene expression and we hope epigenetic marks at a single cell level. The new vector has the barcode placed in a position that allows high expression and retrieval via 10X and other standard single cell RNASeq platforms. We have already made a number of important and novel discoveries, including a surprising life history for mature NK cells, showing that the major fraction of circulating mature cytotoxic NK cells(CD16+CD56-) do not share barcodes with B, T or myeloid cells or their putative precursor CD56brightCD16neg NK cells, even 80 months post-transplant. In vitro and murine models have not previously been able to shed light on NK cell lineage relationships. These circulating NK cells consist of massively-expanded and oligoclonal populations, waxing and waning in a pattern suggesting responses to specific environmental cues such as viral infection or viral reactivation. Our data provides the first direct demonstration of clonal NK responses, providing insights into possible mechanisms for NK memory. We used differentially-expressed KIR surface molecules, previously linked to NK viral and tumor responses, to sort NK cells expressing different KIR, and documented clonal segregation within these specific KIR-expressing NK populations. This is the first direct demonstration of the generation and persistence of clonal populations of NK cells with specific receptor characteristics, presumably epigenetically-maintained. With in vivo NK depletion based on CD16 expression, the same expanded clones arise again, without recruitment from highly polyclonal HSPC but with recruitment from a residual highly proliferative CD16dim NK subset. This work was published this FY (Wu et al Science Immunology, 2018). We hypothesize that these clones might be generated in the context of a response to CMV, based on correlative data in human transplantation and blood donor studies, and are testing this via barcoded transplantation in CMV negative macaques, showing specific clonal changes occur in the mature NK cell populations (manuscript submitted). We continue to search for the precursor to these cells, tracking dominant clones in phenotypically purified samples from blood, bone marrow, lymph nodes, liver, and vaginal and intestinal lymphoid aggregates. We are also applying our methodology to understand the original of other classes of innate lymphoid cells (ILC), including ILC2 in the lung, and ILC3 in the gut and . We validated our model suggesting that adaptive CD56dimCD16+ NK cells are produced independently of multipotent HSPC by taking advantage of two human disease models. In the human disorder PNH, acquired somatic mutations result in loss of GPI-linked proteins on HSPC and their progeny with clonal expansion of GPI- cells over time. We demonstrated that human CD56dimCD16+ NK cells from PNH patients are almost 100% GPI+ despite CD56bright NK cells, B cells and myeloid cells all being GPI-, similar to the pattern in T memory cells, and suggesting that adaptive NK cells share properties with T memory cells and can homotypically self-renew without ongoing production from HSPC. We also demonstrated that human adaptive NK cells are retained patients with GATA2 deficiency syndrome, despite loss of HSPC, CD56bright NK cells, B cells and monocytes. We have extended our analysis of the geographic segregation of individual HSPCs long term in specific marrow sites, confirming our prior findings in mice using LEGO imaging techniques now in the macaque model utilizing barcoding. We can directly demonstrate in situ production of B cells, CD56+ NK cells and myeloid cells in localized marrow niches, and surprisingly, we now have strong evidence for in situ marrow production of T cells. We have followed the output of thousands of individual HSPC clones in several animals for up to 7.5 years, and demonstrate marked clonal stability of output from long-term repopulating clones producing myeloid, B cell and T cell lineages, along with CD56brightCD16- NK cells. We found no evidence for clonal succession in these young adult animals, directly refuting controversial murine data suggesting contributions from each clone lasting only several weeks. We have shown that myeloid vs lymphoid bias is common, and that this bias remains stable in individual clones over time. We have recently completed a project comparing the clonal behavior of young versus aged HSPC, demonstrating marked differences in clonal patterns, specifically very delayed contributions from multilineage clones with persistence of unilineage contributions, in both myeloid, B and T cell lineages, in contrast to murine models suggesting accumulation of only myeloid-biased clones. In the oldest animal, we observed clonal dropout and clonal expansions, potentially providing a model of human CHIP associated with aging (clonal hematopoiesis of indeterminate prognosis). We have continued to analyze clonal patterns following engraftment of ex vivo expanded HSPC. We have derived methodologies allowing investigation of red cell and platelet lineages. Red cell clonal patterns match those of other myeloid lineages very closely and this work is under revision at present at the journal Haematologica. We have very interesting preliminary data regarding emergence of unique highly biased clones contributing to platelets in the presence of inflammation, going along with in vitro and murine data suggesting unique behavior for platelet-biased but true self-renewing progenitor cells.
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