Hematopoietic Stem And Progenitor Cells Clones Research Articles

Clonal Hematopoiesis Is Common in Long-Term Survivors of Pediatric Hematopoietic Cell Transplantation, Including Umbilical Cord Blood Transplantation

Background 1. Approximately 20.000 to 200.000 hematopoietic stem and progenitor cells (HSPCs) contribute to steady-state adult hematopoiesis. During ageing, the overall diversity of the HSPC pool decreases, which is in part driven by the selective expansion of HSPC clones with driver mutations, a process called clonal hematopoiesis (CH). CH is an age-related condition that predisposes to hematologic malignancy, cardiovascular disease, and all-cause mortality. Hematopoietic stem cell transplantation (HCT) recipients are at increased risk of CH, but the mechanisms driving the emergence and expansion of CH clones are largely unknown. Furthermore, the prevalence of CH in pediatric HCT recipients, in whom the long-term consequences of CH are particularly relevant, remains to be defined. Aim To determine the prevalence and risk factors of CH in long-term survivors of HCT at pediatric age. Methods We included survivors of HCT at pediatric age, with a minimum survival of 5 years after HCT. CH was assessed by targeted, error-corrected sequencing of mutations in 27 cancer driver genes in whole blood, at a variant allele frequency detection threshold of 1%. HSC age was calculated by the sum of the age of the donor and the interval after HCT. In case the age of a donor was unknown (n=53), the median age for donors of the same donor relation were used (i.e., 12.6 years for sibling donors and 28.7 for matched unrelated donors). Clinical characteristics were compared using the Wilcoxon signed ranked test for continuous variables and Chi-squared or Fisher's exact test for categorical variables. Results Here, we report the interim results of the first 120 HCT survivors in this study. The median age of the survivors was 20.4 years (range 6.7-51.8), and the median interval after HCT was 11.8 years (range 5.2-38.2). Indications for HCT were hemato-oncology (n=95), bone marrow failure (n=22), or immune deficiency (n=3). The median calculated age of the HSCs was 31 years (range 5.2-61.8). CH was present in 13.3% of survivors (n=16). Mutated genes were DNMT3A (n=15), TET2 (n=4) and MPL (n=1), with three individuals having more than one driver mutation. The median variant allele frequency of the CH clones was 2.2%, but allele frequencies up to 30% were found. No differences were observed in recipient age or interval after HCT between individuals with or without CH (Figure 1A). However, the age of the HSCs was significantly higher in individuals with CH compared to those without (38.6 versus 26.3 years, p = 0.01, Figure 1B). Surprisingly, we detected CH in two recipients of umbilical cord blood grafts, at an interval of 11 and 15 years after HCT. Conclusion Clonal hematopoiesis is common in long-term survivors of pediatric HCT. After HCT, the prevalence of CH is related to the age of the transplanted HSCs, rather than the age of the survivor. The presence of CH in cord blood HSCs within two decades after HCT suggests that HCT-related factors may drive the de novo emergence and/or outgrowth of donor-derived CH. Ongoing research is aimed at investigating how factors such as stem cell source and post-transplant complications affect clonal expansion after HCT. Furthermore, we are investigating the prevalence of CH in an age-matched control cohort using the same detection pipeline, enabling direct comparison of the prevalence of CH in HCT survivors compared to the general population.

Germline SAMD9/9L MDS Predisposition Syndromes Are Characterized By Complex Clonal Architecture and Lineage-Specific Escape Mechanisms Including Somatic Genetic Rescue in T and B Lymphocytes

Inherited bone marrow failure (BMF) and MDS predisposition syndromes have an intrinsic defect resulting in loss and/or dysfunction of hematopoietic stem and progenitor cells (HSPC). HSPC clones can escape this process by acquiring gene- or genome-level genetic changes (compensatory mutations or uniparental disomies (UPD)) thereby increasing cellular fitness. This process, referred to as somatic genetic rescue (SGR) has been shown to occur in >70% of patients with gain-of-function mutations in SAMD9 and SAMD9L (SAMD9/9L) genes, which are a common cause of early onset BMF and pediatric MDS with monosomy 7. It is unknown how SGR arises and in which cells it originates. Furthermore, little is known about the epistatic interactions of various rescue events. We aimed to address these questions by utilizing a newly established single cell (sc)-proteogenomic platform that can simultaneously detect single nucleotide variants (SNVs) and copy number variation (CNVs) in addition to protein expression. We applied this technology to study clonal architecture and cellular origins of SGR lesions in a cohort of clinically annotated SAMD9/9L-mutated (SAMD9/9Lmut) patients. We also asked if monosomy 7, traditionally assessed by karyotyping, can be also detected in peripheral blood (PB) of affected patients. We first performed whole exome and panel sequencing to characterize 67 germline SAMD9/9Lmut patients. Guided by this data, we designed a sc-proteogenomic panel with 69 amplicons specific to variants in SAMD9/9L and leukemia driver genes, and 250 amplicons covering high-frequency SNVs on chromosome 7q. For validation of initial findings, we developed a second panel targeting full coding regions of SAMD9/9L genes, and additional 7p SNVs allowing for a precise delineation of uniparental isodisomy 7q (UPD7q). We included oligonucleotide-conjugated antibodies specific to major hematopoietic antigens, including CD19, CD3, CD11b, CD38 and CD34. Using this panel, we analyzed 22 samples (15 bone marrow (BM) and 7 PB) of 10 patients enrolled in local biobanking protocols. On average, 3,845 high-quality cells were genotyped per sample, and we robustly identified SNVs, monosomy 7 and UPD7q changes in single cells. Somatic rescue SAMD9/9Lmut were found only in clones with normal (diploid) chromosome 7, UPD7q (containing two wild type SAMD9/9L alleles after mitotic recombination event) was a stand-alone clone, while monosomy 7 (SAMD9/9Lmut lost) occurred alone or together with leukemia driver mutations. We also detected lesions that were previously missed using routine clinical sequencing in 3 patients (somatic SAMD9/9Lmut or UPD7q). Most patients had branching clonal architecture (i.e., independent monosomy 7, UPD7q, and somatic SAMD9/9Lmut), while linear trajectories were rare (i.e., monosomy 7 à + leukemia driver mutation). Serial assessment of 4 patients with stable hematology (3 with monosomy 7 and 1 with an additional somatic SAMD9/9Lmut) for a period of up to 4.8 years, revealed stable clonal populations without acquisition of additional driver mutations. Quantification of clones in paired BM and PB in 4 patients demonstrated equal frequencies of monosomy 7 and somatic SAMD9/9Lmut in both compartments, demonstrating the utility of this assay in surveillance. Our findings were confirmed by sorting BM cells into different lineages followed by sequencing, error-corrected sequencing, and ddPCR. Finally, analysis of protein expression data revealed that while monosomy 7 is present exclusively in cells with myeloid phenotype, the SGR events can arise in lymphocyte lineage only; 4 patients carried clones with somatic SAMD9/9Lmut in CD3+ lymphocytes, and 2 patients had UPD7q clones in either CD3+ or CD19+ lymphocytes. These findings provide clues why most of the SGR events in patients do not result in long-lasting clinical remission since the genetic rescue can be restricted only to certain hematopoietic lineages. In conclusion, single cell proteogenomic analysis is useful for the understanding the mechanisms of clonal evolution in SAMD9/9L syndromes. This method also offers the opportunity for less invasive surveillance of karyotype abnormalities from peripheral blood in patients who are at high risk for MDS progression.

Dual Targeting of HDM2 and PPM1D As a Novel Therapeutic Approach for Myelofibrosis

Dysregulation of TP53 in myeloproliferative neoplasms (MPNs) has been hypothesized to be a key driver of disease progression (Kubesova et al, Leukemia. 2018;32 (2):450-61). Targeting of double minute protein 2 (HDM2), a negative regulator of TP53, results in activation of the TP53 pathway which induces cell death in hematopoietic stem and progenitor cells (HSPCs). Nutlins, antagonists of HDM2, are currently being evaluated in multiple MPN clinical trials with promising results to date. Protein Phosphatase Mg2+/Mn2+ dependent 1D protein (PPM1D) is another key negative regulator of the TP53 pathway that dephosphorylates TP53 and stabilizes HDM2 (Hsu et al. Cell Stem Cell. 2018 Nov 1;23(5):700-13). We and others have previously reported the presence of PPM1D mutations in MPNs that result in overexpression of the protein (Grinfeld et al, N Engl J Med. 2018 Oct 11;379 (15):1416-30). We have also reported overexpression of PPM1D in the mononuclear cells (MNC) of a subset of MPN patients not harboring PPM1D mutations. We hypothesize that inhibition of PPM1D in myelofibrosis (MF) would target the MF HSPC and sensitize MF HSPCs to HDM2 inhibitors resulting in further depletion of MF HSPCs. To further characterize PPM1D expression in the MF HSPC compartment, we utilized quantitative real time-PCR, to assess PPM1D transcript levels in CD34+ cells from 28 MF patients and compared these transcript levels to levels in CD34+ normal control cells (n=6). Forty-three percent (12/28) of the MF samples had overexpression of PPM1D (>1.5 fold increase) and the fold increase ranged from 1.8-59. To identify whether PPM1D is a viable therapeutic target for MF HSPCs, we utilized hematopoietic colony assays to test the activity of GSK2830371, an allosteric inhibitor of PPM1D (PPM1Di) alone and in combination with a low dose HDM2 inhibitor (HDM2i). Eight samples from distinct MF patients were tested under these conditions. There was not a significant reduction in the number of JAK2V617F+ colonies upon treatment with single agent HDM2i (50 nM) (p>0.05) or PPM1Di (1uM) (p>0.05). Combination of PPM1Di (1 uM) + HDM2i (50 nM) resulted in decreased JAK2V617F+ colony formation in all 8 samples (p<0.005) (Fig. 1). The reduction in JAK2V617F+ colony number was significant compared to either single agent treatment with HDM2i (p<0.001) or PPM1Di (p<0.05) (Fig. 1). Four samples had persistence of or an increase in JAK2 wild-type (WT) colony number with combination treatment. The MF samples utilized were from a heterogenous population of patients that all had WT TP53 and PPM1D but included patients with high risk myeloid mutations (in ASXL1, NRAS), complex cytogenetics and prior exposure to standard MF directed therapies. Additionally, to validate the on-target effect of PPM1Di, we showed that treatment of leukemia cell lines with PPM1Di led to increased protein levels of phosphorylated-p53 and p21 and resulted in decreased viability and increased apoptosis. To determine the effect of PPM1Di +/- HDM2i on distinct subclones we employed a multi-omics approach that allows for single cell mutation and epitope analysis of a clonally complex patient sample. We analyzed MNCs from a JAK2V617F, NRASG12D, TET2T1884A, ASXL1W960* MF patient treated in suspension culture with PPM1Di (1uM) alone, low dose HDM2i (50 nM) alone and PPM1Di (1uM) + low dose HDM2i (50 nM) in combination. Compared to vehicle alone or either drug alone, a marked effect was seen with the combination approach whereby the percent of WT cells increased by nearly 5 fold (4% to 19%) and 4/6 mutated clones were decreased in size, demonstrated by the fishplot (Fig. 2). These results show that the combination of the HDM2i + PPM1Di depletes multiple MF clones, while allowing for the emergence of more WT cells. Furthermore these studies demonstrate the utility of single cell genotyping to evaluate the effects of novel therapeutic strategies on MF clonal architecture. These studies indicate that PPM1Di sensitizes MF HSPCs to an HDM2i and is a promising strategy to treat MF patients. To this purpose, we are currently developing a novel clinical grade PPM1D targeting agent. Dual targeting of PPM1D and HDM2 has the potential to further deplete multiple MF HSPC clones while allowing the persistence of WT cells. Additional combinatorial mutation + epitope studies are underway to determine degree of MF HSPC subpopulation depletion utilizing this treatment strategy. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

A macaque clonal hematopoiesis model demonstrates expansion of TET2-disrupted clones and utility for testing interventions

AbstractIndividuals with age-related clonal hematopoiesis (CH) are at greater risk for hematologic malignancies and cardiovascular diseases. However, predictive preclinical animal models to recapitulate the spectrum of human CH are lacking. Through error-corrected sequencing of 56 human CH/myeloid malignancy genes, we identified natural CH driver mutations in aged rhesus macaques matching genes somatically mutated in human CH, with DNMT3A mutations being the most frequent. A CH model in young adult macaques was generated via autologous transplantation of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9–mediated gene-edited hematopoietic stem and progenitor cells (HSPCs), targeting the top human CH genes with loss-of-function (LOF) mutations. Long-term follow-up revealed reproducible and significant expansion of multiple HSPC clones with heterozygous TET2 LOF mutations, compared with minimal expansion of clones bearing other mutations. Although the blood counts of these CH macaques were normal, their bone marrows were hypercellular and myeloid-predominant. TET2-disrupted myeloid colony-forming units isolated from these animals showed a distinct hyperinflammatory gene expression profile compared with wild type. In addition, mature macrophages purified from the CH macaques showed elevated NLRP3 inflammasome activity and increased interleukin-1β (IL-1β) and IL-6 production. The model was used to test the impact of IL-6 blockage by tocilizumab, documenting a slowing of TET2-mutated expansion, suggesting that interruption of the IL-6 axis may remove the selective advantage of mutant HSPCs. These findings provide a model for examining the pathophysiology of CH and give insights into potential therapeutic interventions.

Clonal Tracking By Whole Genome Sequencing Permits Comprehensive Mapping of the Genomic Landscape in Pre- and Post-Gene Therapy Sickle Cell Patients

▪Recent advances in clonal stem cell tracking strategies have enabled interrogation of unperturbed human hematopoiesis. Whole genome sequencing (WGS) can be used to map the clonal dynamics of hematopoietic stem and progenitor cells (HSPCs) by employing spontaneous somatic mutations as unique clonal tags (Lee-Six et al., Nature, 2018). These tags allow for retrospective analysis of individual stem cell clones and the construction of phylogenetic trees mapping out stem cell relatedness, with mutations being acquired in a near-linear fashion over the course of an individual's life. The unprecedented level of information obtained in these studies is particularly well-suited to understanding genomic changes in gene therapy trials aimed at curing diseases such as sickle cell disease (SCD). In addition to mapping relatedness between stem cells, sequencing data can be used to better define mutational signatures for HSPC clones that have been successfully gene-modified as well as those that lack an integrated copy of the therapeutic vector. Given this method's ability to identify low frequency mutations in individual HSPC clones, mutations with extremely low variant allele frequencies can be detected much more readily than through traditional bulk sequencing approaches, something that is particularly relevant given recent safety concerns in some SCD gene therapy trials. In this study, we have mapped the clonal dynamics of HSPCs obtained from pre- and post-gene therapy samples from 4 SCD patients who have undergone autologous gene therapy performed using a BCL11A shmiR lentivirus vector (NCT 03282656, 12-36 months follow-up). HSPCs from mobilized peripheral blood (pre-gene therapy), bone marrow aspirates (both pre- and post-gene therapy) or unmobilized peripheral blood (post-gene therapy) were expanded as single clones and 1508 individual colonies were then sequenced using WGS to an average sequencing depth of 12.3x. Initial results indicate that the mean mutation burden per cell in a pre-gene therapy sample is elevated for some patients compared to what would be expected based on patient age in similar studies. In pre-gene therapy samples, the structure of the phylogenetic trees appeared to be highly polyclonal, indicating that there were no significant clonal expansion events prior to gene therapy. In one patient where we undertook extensive profiling, approximately 15-20 excess mutations per HSPC were observed across the entire genome 24 months after transplantation, presumably acquired as a consequence of gene therapy and/or reconstitution post-transplantation, which is equivalent to approximately one year of normal ageing without a transplantation intervention. However, no clonal expansions or driver mutations were identified at this 24 month follow-up timepoint, suggesting that no strong selective advantage or pre-leukemic events were present prior to or following the gene therapy protocol. Extending this approach to a wider range and larger number of patients will allow for comprehensive mapping of the genomic landscape and clonal evolution of stem cells in sickle cell patients and will also set the stage for improved assessment of safety and potential leukemia-initiating events in the context of gene therapy. DisclosuresEsrick: bluebird bio: Consultancy. Williams: bluebird bio: Membership on an entity's Board of Directors or advisory committees, Other: Insertion Site Analysis Advisory Board, Patents & Royalties: BCH licensed certain IP relevant to hemoglobinopathies to bluebird bio. The current license includes the potential for future royalty/milestone income. Bluebird has indicated they will not pursue this as a clinical program and BCH is negotiating return of, Research Funding; BioMarin: Membership on an entity's Board of Directors or advisory committees, Other: Insertion Site Advisory Board; Beam Therapeutics: Membership on an entity's Board of Directors or advisory committees, Other: Scientific Advisory Board; Emerging Therapy Solutions: Membership on an entity's Board of Directors or advisory committees, Other: Chief Scientific Chair; Geneception: Membership on an entity's Board of Directors or advisory committees, Other: Scientific Advisory Board; Alerion Biosciences: Other: Co-founder (now licensed to Avro Bio, potential for future milestones/royalties); Novartis: Membership on an entity's Board of Directors or advisory committees, Other: Steering Committee, Novartis ETB115E2201 (eltrombopag in aplastic anemia). Advisory fees donated to NAPAAC.; Orchard Therapeutics: Membership on an entity's Board of Directors or advisory committees, Other: Membership on a safety advisory board (SAB): SAB position ended 05/20/2021. Co-founder , Patents & Royalties: Potential for future royalty/milestone income, X-SCID. Provided GMP vector for clinical trial, Research Funding. Campbell: Mu Genomics: Current holder of individual stocks in a privately-held company, Membership on an entity's Board of Directors or advisory committees. Kent: STRM.bio: Research Funding.

Loss of nr4a1 abrogates Fitness of asxl1-mutant Hematopoietic Clones

Clonal fitness of mutant hematopoietic stem and progenitor cells (HSPCs) underlies clonal hematopoiesis (CH), a state of clonal expansion associated with increased risk of blood malignancies and cardiovascular disease. Mechanisms by which acquired mutations lead to clonal fitness are not known. We used a zebrafish model to study the effect of acquired asxl1 mutations on HSPC clonality with TWISTR (Tissue editing With Inducible Stem cell Tagging via Recombination) that combined mosaic CRISPR-Cas9 mutagenesis with color labeling of HSPC clones. TWISTR asxl1 mutants showed clonal dominant states with the expansion of single-colored clones contributing to over 30% of myelopoiesis. These zebrafish had normal hematopoietic output and no major lineage skewing. Single-cell RNA sequencing analysis of TWISTR mutant marrow cells harboring asxl1 mutations showed >10-fold upregulation of inflammatory cytokines in mutant mature myeloid cells and >30-fold upregulation of anti-inflammatory modulators in immature progenitors. Increased inflammation has been widely documented in persons with CH with acquired mutations in DNMT3A, TET2, ASXL1 and other genes. Moreover, chronic inflammation due to infection was shown to promote relative clonal fitness in Dnmt3a mutant mice. Based on our results, we proposed the hypothesis that upregulation of the anti-inflammatory genes, including nr4a1, served as a mechanism of resistance to chronic inflammation created by the mutant HSPC progeny, resulting in a self-perpetuating cycle of clonal fitness in that environment. To test this, we used TWISTR to generate mosaic mutants of asxl1 and nr4a1 by injecting zebrafish with guide RNAs targeting exon 12 of asxl1 and exon 3 of nr4a1 together. Our model would predict that abrogation of nr4a1 expression in asxl1-mutant clones would weaken their fitness relative to clones that maintained nr4a1 expression. We sorted over 300 clones of various sizes from this cohort of zebrafish and sequenced the two targeted genes. We found that clones with frameshift mutations in asxl1 with either no nr4a1 mutations or heterozygous nr4a1 mutations had a clone size of 20%±14% or 19.7%±15% in myeloid cells, respectively. Asxl1-mutant clones with biallelic frameshift mutations in nr4a1 were significantly smaller with a clone size of 13.8±11.5% (p < 0.015). Clones with intact asxl1 did not differ in their clone size independent of nr4a1 genetic status (11.9% wildtype nr4a1 vs 11.5% homozygous nr4a1 mutant). Chemical inhibition of nr4a1 over 3 months resulted in reduced change of edited clones in asxl1-mutant zebrafish compared to vehicle-treated zebrafish, with median change in allelic fraction of 3%±4.8% vs 5.3%±7.5%, respectively. This suggested that upregulation of nr4a1 in asxl1-mutant clones maintains their fitness in inflammatory conditions, potentially by limiting HSPC exhaustion. We successfully used TWISTR to study asxl1 induced CH in zebrafish and identified nr4a1 upregulation as a critical pathway engaged for establishing clonal fitness. DisclosuresZon: Fate Therapeutics: Current equity holder in publicly-traded company, Other: Founder; CAMP4 Therapeutics: Current holder of individual stocks in a privately-held company, Other: Founder; Amagma Therapeutics: Current holder of individual stocks in a privately-held company, Other: Founder; Scholar Rock: Current equity holder in publicly-traded company, Other: Founder; Branch Biosciences: Current holder of individual stocks in a privately-held company, Other: Founder; Celularity: Consultancy; Cellarity: Consultancy.

Abstract 3051: On the origin of pediatric leukemia: studying somatic mutations in human blood

Abstract The acquisition of oncogenic mutations with age is believed to be rate limiting for carcinogenesis and aging is the biggest risk factor for cancer. However, children can also develop cancers even though their cells are less damaged by age. Here, we studied the cellular origin and time of onset during development of pediatric acute myeloid leukemia (pAML) to increase our understanding of why children can get cancer. We compared by whole genome sequencing individual hematopoietic stem and progenitor cells (HSPCs) and pAML blasts of the same leukemic bone marrow as well as nonmatching healthy HSPCs. We found that the number of clonal mutations in the majority of pAML cases was increased and mutational process contribution altered as compared to normal HSPCs, showing activity of specific processes that are either unique to fetal development or normally not observed in healthy HSPCs. These observations could be explained by altered selection dynamics early in life. Surprisingly, pAML cases with an overall mutation burden comparable to age matched healthy HSPCs showed worse overall and event-free survival. Identifying shared somatic mutations between individual HSPC clones and pAML using single-cell genotyping allowed us to pinpoint the developmental lineage that gave rise to the pAML. Our study provides new insights into the etiology of pAML and underscores the clinical potential of whole genome sequencing in pediatric leukemia. Citation Format: Arianne Brandsma. On the origin of pediatric leukemia: studying somatic mutations in human blood [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3051.

Visualizing Clonal Hematopoiesis Associated with gata2 Deficiency in Zebrafish Using Color-Barcoding

Myeloid neoplasms, such as myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), arise from abnormal hematopoietic stem and progenitor cells (HSPCs) with acquired somatic mutations. Germline GATA2 haploinsufficiency is associated with an autosomal dominant familial MDS/AML syndrome. Leukemic transformation in GATA2 haploinsufficiency occurs with acquisition of secondary mutations or cytogenetic abnormalities. We generated gata2 heterozygous zebrafish to model this germline predisoposition syndrome, and evaluate clonal architecture and dynamics over time at steady-state and in the presence of additional mutations. We hypothesized that clinically benign clonal hematopoiesis precedes the establishment of myeloid neoplasms in GATA2 haploinsufficiency. We used a lineage tracing system of zebrafish Brainbow, Zebrabow, to track the hematopoietic output of individually colored HSPC clones, with the goal to detect abnormal expansion of single color clones in the early stages of leukemogenesis, indicating clonal hematopoiesis. A heterozygous line of GATA2 zebrafish ortholog gata2b was generated in the Zebrabow background. We introduced combinations of genetic mutations described in GATA2 associated MDS and AML into Zebrabow embryos with CRISPR/Cas9 technology. Zebrafish embryos, either wild-type or heterozygous for gata2b, were injected with Cas9 protein and guide RNAs targeting zebrafish orthologs of ASXL1 and STAG2. Zebrabow color recombination was induced to color-label stem cells prior to their emergence from the dorsal aorta. At this time roughly 20 stem cell clones exist in the zebrafish embryo. The animals were then raised to adulthood. Kidney marrow cells of juvenile zebrafish were analyzed at various time points in between 2-4 months post-fertilization (mpf) by flow cytometry and morphology on cytospins. At steady-state, juvenile gata2b+/- zebrafish had a decreased myeloid compartment in the kidney marrow. A third of gata2b+/- zebrafish also had an expansion of single color clones in the kidney marrow by 3 mpf, contributing to ≥30% of granulocytes, while no wild-type clutchmate demonstrated single color expansion to this degree at steady-state. Mosaic combinations of mutations in the presence of gata2b deficiency resulted in an increase of precursor and a more pronounced decrease of myeloid populations in the kidney marrow at 3 mpf, compared to wild-type zebrafish injected with same mutations. No changes were observed in the lymphoid compartment. Single color expansion was observed in gata2b+/- zebrafish three times more frequently than in wild-type zebrafish. In summary, gata2b deficiency sensitizes juvenile zebrafish to developing myelocytopenia at steady-state, reminiscent of well-characterized monocytopenia in GATA2 deficiency. We found that myelocytopenia is more profound and associated with an increase in early precursors upon additional somatic mutations associated with MDS/AML, possibly due to a differentiation block in myelopoiesis. Single color dominance observed in the hematopoeitic compartment of juvenile gata2b+/- zebrafish using the Zebrabow color-barcoding system presents a potential mechanism underlying the predisposition to myeloid neoplasms associated with GATA2 deficiency, and provides a tool for visualizing asymptomatic premalignant state in disease pathogenesis. DisclosuresZon:Scholar Rock, Inc: Consultancy, Equity Ownership; Marauder, Inc.: Consultancy, Equity Ownership; Stemgent: Consultancy; Fate, Inc.: Consultancy, Equity Ownership.

Bone Marrow Transplantation Procedures in Mice to Study Clonal Hematopoiesis.

Clonal hematopoiesis is a prevalent age-associated condition that results from the accumulation of somatic mutations in hematopoietic stem and progenitor cells (HSPCs). Mutations in driver genes, that confer cellular fitness, can lead to the development of expanding HSPC clones that increasingly give rise to progeny leukocytes harboring the somatic mutation. Because clonal hematopoiesis has been associated with heart disease, stroke, and mortality, the development of experimental systems that model these processes is key to understanding the mechanisms that underly this new risk factor. Bone marrow transplantation procedures involving myeloablative conditioning in mice, such as total-body irradiation (TBI), are commonly employed to study the role of immune cells in cardiovascular diseases. However, simultaneous damage to the bone marrow niche and other sites of interest, such as the heart and brain, is unavoidable with these procedures. Thus, our lab has developed two alternative methods to minimize or avoid possible side effects caused by TBI: 1) bone marrow transplantation with irradiation shielding and 2) adoptive BMT to non-conditioned mice. In shielded organs, the local environment is preserved allowing for the analysis of clonal hematopoiesis while the function of resident immune cells is unperturbed. In contrast, the adoptive BMT to non-conditioned mice has the additional advantage that both the local environments of the organs and the hematopoietic niche are preserved. Here, we compare three different hematopoietic cell reconstitution approaches and discuss their strengths and limitations for studies of clonal hematopoiesis in cardiovascular disease.

The TRACE-Seq method tracks recombination alleles and identifies clonal reconstitution dynamics of gene targeted human hematopoietic stem cells

Targeted DNA correction of disease-causing mutations in hematopoietic stem and progenitor cells (HSPCs) may enable the treatment of genetic diseases of the blood and immune system. It is now possible to correct mutations at high frequencies in HSPCs by combining CRISPR/Cas9 with homologous DNA donors. Because of the precision of gene correction, these approaches preclude clonal tracking of gene-targeted HSPCs. Here, we describe Tracking Recombination Alleles in Clonal Engraftment using sequencing (TRACE-Seq), a methodology that utilizes barcoded AAV6 donor template libraries, carrying in-frame silent mutations or semi-randomized nucleotides outside the coding region, to track the in vivo lineage contribution of gene-targeted HSPC clones. By targeting the HBB gene with an AAV6 donor template library consisting of ~20,000 possible unique exon 1 in-frame silent mutations, we track the hematopoietic reconstitution of HBB targeted myeloid-skewed, lymphoid-skewed, and balanced multi-lineage repopulating human HSPC clones in mice. We anticipate this methodology could potentially be used for HSPC clonal tracking of Cas9 RNP and AAV6-mediated gene targeting outcomes in translational and basic research settings.

Cellular Barcoding of HSCs during Development Reveals Long-Term Persistence of T Cell Progenitor Clones in the Thymus

Developmental hematopoietic stem and progenitor cells (HSPCs) have been thought to be largely replaced by adult hematopoietic stem cells (HSCs) after birth. Here, we performed simultaneous genetic lineage tracing by cellular barcoding and transcriptional profiling of zebrafish hematopoiesis to investigate HSPC clonal dynamics and gain insight into the developmental origin of adult blood cells. We took advantage of a recently developed dynamic lineage tracing system, scGESTALT, a CRISPR-based approach that allows for inducible cellular barcoding at two different time points during zebrafish embryonic development. We induced the first stage of lineage recording in the early embryo via microinjection at the one-cell stage and selected 28 hours post-fertilization, just before the birth of definitive blood stem cells, for additional recording activity. In this way, we were able to barcode HSCs, which will pass their unique barcodes on to their progeny, thereby enabling lineage tracing. To study the clonal dynamics and developmental origins of adult blood cells, we dissected paired adult kidney marrow and thymi tissues from barcoded fish between 3 and 7 months of age. We then performed single-cell RNA sequencing (scRNA-seq) in combination with lineage tracing by specifically amplifying the GESTALT barcode and sequencing both transcriptional and GESTALT barcode libraries. In total, we recovered transcriptional profiles from 71,109 cells across 9 fish. By optimizing promoter choice, we improved barcode recovery by almost 3-fold (17.7% vs. 6.5%) for detection in cells from the zebrafish kidney marrow. In two of these more efficient lineage recording fish, we detected 61 and 72 unique HSPC clones that contributed to adult hematopoiesis. The majority of these HSPC clones did not exhibit significant lineage biases; however, we demonstrated that 6/61 and 4/72 clones from the two fish, respectively, were significantly enriched in the myeloid lineage and 8/61 and 8/72 clones were significantly enriched in the lymphoid lineage (p&amp;lt; 0.05). These findings demonstrate that myeloid and lymphoid biased clones arise during normal development. From our paired thymus and kidney marrow sample, we identified 51 unique kidney marrow clones, 10 shared, and 2 unique thymus clones. This latter finding of unique thymus clones was surprising and suggests that long-lived embryonic T cell progenitors persist and contribute to adult T cell production in the zebrafish. Taken together, we have demonstrated how scGESTALT can uncover complex lineage relationships in blood, mapping the origins and contributions of HSCs and embryonic progenitors to the adult hematopoietic system. Disclosures Zon: Amagma Therapeutics: Current equity holder in private company, Other: Founder; Celularity: Consultancy; Cellarity: Consultancy; CAMP4 Therapeutics: Current equity holder in private company, Other: Founder; Fate Therapeutics: Current equity holder in publicly-traded company, Other: Founder; Scholar Rock: Current equity holder in publicly-traded company, Other: Founder.

Macaque Age-Related Clonal Hematopoiesis Model Demonstrates Expansion of TET2-Disrupted Clones and Utility for Testing Therapeutic Approaches

Individuals with age-related clonal hematopoiesis (CH) are at greater risk for hematologic malignancies and cardiovascular diseases, however, there are no predictive preclinical animal models. We generated a rhesus macaque model via CRISPR/Cas9-mediated gene editing of hematopoietic stem and progenitor cells (HSPCs), followed by autologous transplantation. Long-term follow-up revealed reproducible and significant expansion of multiple HSPC clones with heterozygous TET2 loss-of-function mutations, compared to minimal expansion of clones bearing other mutations, suggesting a decrease in intrinsic TET2 activity is sufficient for CH. Blood counts were normal, but bone marrow of these animals were hypercellular and myeloid-predominant. Myeloid cells were hyperinflammatory with elevated interleukin (IL)-1β and IL-6. Blockade of IL-6 by tocilizumab reduced TET2 mutated allele frequency, suggesting that interruption of the IL-6 axis removes the selective advantage of mutant HSPCs. These findings provide a model for examining the pathophysiology of CH and testing of potential therapeutic interventions.

Cxcl8 Expands Hematopoietic Stem and Progenitor Cells and Alters Their Interaction with the Endothelial Niche

We currently have little understanding of the mechanisms by which hematopoietic stem and progenitor cells (HSPCs) gain a selective advantage in patients with clonal hematopoiesis and other myeloid neoplasms. The chemokine CXCL8 is elevated in a subset of patients with myeloid neoplasms. Our previous work in zebrafish has discovered a novel role for cxcl8 and its receptor, cxcr1, in supporting colonization of HSPCs within the sinusoidal endothelial cell niche of the embryonic zebrafish known as the caudal hematopoietic tissue (CHT). We hypothesized that mosaic overexpression of cxcl8 in a population of HSPCs during development would alter HSPC-niche interactions, selectively favor HSPCs expressing cxcl8 and lead to their expansion in adults. To test this hypothesis, we microinjected DNA constructs encoding cxcl8-2A-GFP or GFP alone under the control of the HSPC-specific Runx1+23 enhancer into zebrafish embryos at the single-cell stage. Time lapse fluorescence video microscopy and single-cell tracking was performed on HSPCs within the CHT. Overexpression of cxcl8 nearly doubled the amount of time HSPCs resided within the CHT when compared to expression of GFP alone as a control (cxcl8: 4.94 ± 0.86 h vs GFP: 2.54 ± 0.18 h, p=0.01, N=142 tracked cells). Substitution of WT cxcl8 with a mutant cxcl8 construct lacking the ELRCXC motif required for receptor binding reduced these effects (WT cxcl8: 6.6 ± 0.48 h vs ELRCXC-cxcl8: 5.3 ± 0.33 h, p=0.02, N=355 tracked cells). To observe HSPC-niche interactions, kdrl:mCherry endothelial cell reporter zebrafish were microinjected with Runx1+23:cxcl8-2A-GFP or Runx1+23:GFP DNA constructs. The percent of time individual HSPCs spent closely interacting with a single group of CHT endothelial cells (endothelial cell cuddling) was quantified over the period from 52 to 72 hours post-fertilization. Overexpression of cxcl8 by HSPCs increased HSPC-endothelial cell cuddling time by 30% (cxcl8: 87% vs GFP: 57%, p=0.001). To directly test competition between wild type and cxcl8 overexpressing HSPCs, zebrafish embryos were microinjected with a 1:1 molar ratio of Runx1+23:cxcl8-2A-mCherry and Runx1+23:clover DNA. Single cxcl8-2A-mCherry+ and clover+ competitor cells were tracked by time-lapse fluorescence confocal microscopy. HSPCs expressing cxcl8 resided longer within the CHT than competitor HSPCs when quantified over the period from 72 to 96 hours post-fertilization (cxcl8: 4.0 ± 0.20 h vs competitor: 2.5 ± 0.25 h, p=2.0 x 10-6, n=426 tracked cells). Single cell RNA-sequencing (scRNA-seq) of zebrafish embryos with mosaic expression of cxcl8 in HSPCs showed upregulation of cxcl12a in endothelial cells compared to endothelial cells from control embryos (p=5.19 x 10-3), suggesting a possible mechanism to explain the increased CHT residency time. Zebrafish with mosaic expression of Runx1+23:cxcl8 were raised to adulthood and the kidney marrow cells were analyzed by flow cytometry. Compared to clutchmate controls, Runx1+23:cxcl8 mosaic transgenics had a higher hematopoietic progenitor/precursor to lymphocyte ratio, suggesting a mild differentiation block and possible lineage skewing (cxcl8: 2.0 ± 0.15 vs control: 1.6 ± 0.10, p=0.048, N=25 animals). Taken together, these data support a model in which pre-malignant HSPC clones aberrantly express cxcl8 and acquire a selective advantage over normal clones through enhanced interactions with the endothelial cell niche. Disclosures Zon: Fate Therapeutics: Equity Ownership; Scholar Rock: Equity Ownership; CAMP4: Equity Ownership.

PS1229 CHARACTERIZING THE ETIOLOGY OF PEDIATRIC ACUTE MYELOID LEUKEMIA BY STUDYING MUTATION ACCUMULATION IN NORMAL HEMATOPOIESIS

Background:The incidence of leukemia peaks early in life and decreases before rising again later in life. Considering that recurrent somatic DNA mutations are thought to be the driving force behind the genesis of leukemia, this phenomenon represents an apparent paradox as young cells have less somatic (oncogenic) mutations than adult cells. Although therapy and outcome have significantly improved over the last decades, pediatric acute myeloid leukemia (pAML) remains a cancer with a high relapse rate and poor prognosis. Approximately 60% of pAML has somatic chromosomal abnormalities like translocations and inversions, while the rest is cytogenetically normal (CN). The most common chromosomal translocation 8;21 (∼11% of pAML) fuses the AML1 gene on chromosome 21 to the ETO gene on chromosome 8, leading to the driver event of this pAML. In CN pAML, often single‐gene mutations can be found in driver genes like FLT3, WT1 and NPM1. The various chromosomal abnormalities and mutations in combination with the different ages of onset underscore the large genetic heterogeneity of pAML. However, all these pAML subtypes receive the same treatment regimen.Aims:To develop more targeted therapies aimed at improving survival, increased understanding of the etiology and genetic landscape of pAML is needed. We hypothesize that the underlying etiology of these different pAML subtypes differ in cellular origin and time of onset during development.Methods:To test this hypothesis, we characterized the somatic mutations in the genomes of pAML and matched normal hematopoietic stem and progenitor cells (HSPCs) of pediatric patients with either a CN‐ or an AML1‐ETO‐driven subtype. With this knowledge, we can identify and study the mutational processes underlying the genesis of pAML as well as track down the cellular origin of the disease using a phylogenetic approach. To identify somatic mutations in the normal HSPCs, we clonally expanded primary single cells from the bone marrow biopsies to obtain sufficient DNA for whole genome sequencing (WGS) analysis.Results:Previously, we have performed similar analyses in bone marrow‐ and umbilical cord blood‐derived HSPCs of healthy donors and created a healthy reference line for lifelong mutation accumulation. We found that the mutation rate is higher in the pAMLs compared to the healthy HSPCs of the same patient as well as our reference line. In addition, we performed WGS on 10 HSPC clones of one pAML patient to track down its clonal origin. For this, we genotyped the observed leukemic blast somatic mutations in healthy HSPCs of the same patient and determined the genetic relatedness between these cells and the blasts. Using this approach, we constructed a developmental lineage tree and tracked down the branch that gave rise to the pAML.Summary/Conclusion:This research provides novel insights into the etiology of pAML and differences therein between subtypes, which may contribute to the development of more targeted treatment.

Therapeutic Modulation of Autophagy in Leukaemia and Lymphoma.

Haematopoiesis is a tightly orchestrated process where a pool of hematopoietic stem and progenitor cells (HSPCs) with high self-renewal potential can give rise to both lymphoid and myeloid lineages. The HSPCs pool is reduced with ageing resulting in few HSPC clones maintaining haematopoiesis thereby reducing blood cell diversity, a phenomenon called clonal haematopoiesis. Clonal expansion of HSPCs carrying specific genetic mutations leads to increased risk for haematological malignancies. Therefore, it comes as no surprise that hematopoietic tumours develop in higher frequency in elderly people. Unfortunately, elderly patients with leukaemia or lymphoma still have an unsatisfactory prognosis compared to younger ones highlighting the need to develop more efficient therapies for this group of patients. Growing evidence indicates that macroautophagy (hereafter referred to as autophagy) is essential for health and longevity. This review is focusing on the role of autophagy in normal haematopoiesis as well as in leukaemia and lymphoma development. Attenuated autophagy may support early hematopoietic neoplasia whereas activation of autophagy in later stages of tumour development and in response to a variety of therapies rather triggers a pro-tumoral response. Novel insights into the role of autophagy in haematopoiesis will be discussed in light of designing new autophagy modulating therapies in hematopoietic cancers.

Abstract PR01: Modeling clonal hematopoietic disorders in zebrafish using combinatorial mutagenesis and color barcoding

Abstract Myeloid neoplasms, including myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), are clonal hematopoietic malignancies arising from mutant hematopoietic stem and progenitor cells (HSPCs). To follow the hematopoietic output of HSPC clones endogenously, we characterized a novel marking strategy with color barcoding, in which each HSPC clone is labeled with a unique fluorescent hue. The transgenic zebrafish line Zebrabow uses a Cre/lox system where stochastic recombination of multiple transgenic insertions, harboring three fluorescent proteins, produces stable and heritable color barcodes in blood stem cells and their mature cell progeny. The tamoxifen-dependent Cre recombinase under blood-specific promoter draculin allows temporal and spatial control of labeling. The result of Zebrabow labeling is a collection of colored blood cells which can be clustered into distinct groups based on their hue. Equipped with this endogenous color barcoding system, we perturbed the hematopoietic system to induce clonal blood disorders by introducing combinations of known genetic mutations found in MDS and AML. Zebrabow embryos at the 1-cell stage were injected with combinations of mutations and HSPC color labeling was performed at 36 to 48 hours post-fertilization, during peak emergence of definitive blood stem cells from the dorsal aorta. The transgenic overexpression of Jak2V617F, FLT3ITD, IDH2R140Q, NPM1c, or KRASG12D under the zebrafish draculin promoter was combined with somatic mutagenesis of endogenous tet2, asxl1, dnmt3a, ezh2, gata2, or tp53 via the CRISPR/Cas9 system. Mosaic mutations in epigenetic factors resulted in the expansion of single color clones contributing &amp;gt;30% of granulocytes in approximately 30% of zebrafish at 8 months post-fertilization. The majority of zebrafish exhibiting clonal expansion harbored frame-shift mutations in asxl1 with &amp;gt;25% variant allele frequency. Combinations of asxl1 or tet2 mutations with overexpression of Jak2V617F or FLT3ITD also led to single color dominance by 3 months post-fertilization. These combinations led to significant expansion of blast-like cells in the zebrafish marrow and spleen with concomitant decrease in myeloid cells but no effect on lymphocyte count. We have successfully utilized a color barcoding system to model clonal hematopoietic disorders ranging from benign clonal expansion to myleoid leukemia via mosaic mutagenesis in an endogenous setting in zebrafish. This abstract is also being presented as Poster 38. Citation Format: Serine Avagyan, Jonathan E. Henninger, William Mannherz, Jessica Moore, Leonard I. Zon. Modeling clonal hematopoietic disorders in zebrafish using combinatorial mutagenesis and color barcoding [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr PR01.

Modeling Clonal Hematopoietic Disorders in Zebrafish Using Color Barcoding

Myeloid neoplasms, including myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), are clonal hematopoietic disorders that arise from abnormal hematopoietic stem and progenitor cells (HSPCs)with acquired somatic mutations. To follow the hematopoietic output of HSPC clones endogenously, we have developed a novel marking strategy in which each HSPC clone is labeled in a unique fluorescent hue. The transgenic zebrafish line Zebrabow uses a Cre/lox system where stochastic recombination of multiple transgenic insertions harboring three fluorescent proteins (dTomato, YFP and CFP) provide stable and heritable color barcodes. Tissue-specificity is ensured by tamoxifen-induced Cre activation under the draculin promoter which is highly expressed in zebrafish HSPCs throughout development. The result of Zebrabow labeling is a collection of colored blood cells, which are grouped by their hue, and largely cluster in various groups, each representing a clonal population of cells that arise from a specific HSPC. To induce clonal hematopoietic states in zebrafish assessed by color dominance in hematopoietic cells, we introduced combinations of known genetic mutations founds in MDS and AML into Zebrabow embryos. Embryos at the 1-cell stage were injected with combinations of mutations and HSPC color labeling was performed at 36 to 48 hours post fertilization, during peak emergence of definitive blood stem cells from the dorsal aorta. The injected mutations were grouped by known co-occurence in patients with MDS and AML. The transgenic overexpression of Jak2V617F, FLT3ITD, IDH2R140Q, HOXA9 or HOXB4 under the zebrafish blood-specific promoter draculin, was combined with somatic mutagenesis of endogenous tet2, asxl1, dnmt3a, ezh2, ptena/b and tp53 via the CRISPR/Cas9 system. Mosaic combinations of these mutations resulted in the expansion of single color clones, contributing to ≥30% of granulocytes, with concomittant myeloid expansion in a third of these zebrafish. The majority of zebrafish exhibiting clonal expansion harbored frame-shift mutations in asxl1 with >25% variant allelic frequency identified by next-generation sequencing. Similarly, combinations including Jak2V617F, tet2, or asxl1 mutations lead to single color expansion in kidney marrow cells in 30% of injected zebrafish, with the occasional presence of a blast-like population of cells in the marrow and spleen. We have successfully modeled early stages of clonal hematopoietic expansion with myeloproliferation in the presence of Jak2V617F and asxl1 deletion using the unique color barcoding system in zebrafish. DisclosuresZon:Marauder Therapeutics: Equity Ownership, Other: Founder; Scholar Rock: Equity Ownership, Membership on an entity's Board of Directors or advisory committees, Other: Founder; Fate, Inc.: Equity Ownership, Membership on an entity's Board of Directors or advisory committees, Other: Founder.

Clonal Expansion and Long-Term Persistence of Rhesus Macaque NK Cells with an Adaptive Phenotype

Natural killer (NK) cells are defined as lymphocytes capable of target cell killing and cytokine production independent of somatic antigen receptor recombination. Challenging the paradigm of continuous production of non-specific cytotoxic NK cells from undifferentiated precursors, a subset of murine NK cells sharing many properties with cytotoxic effector T cells was shown to specifically respond to a viral infection, resulting in expansion and protective immunity upon adoptive transfer, uncovering unexpected "adaptive" capabilities for NK cells. In humans, CD56dimCD16+ NK cells expressing NKG2C and variegated patterns of KIR are associated with Cytomegalovirus (CMV) infection, and may represent human analogs of murine adaptive NK cells. In contrast to CD56bright and canonical CD56dim NK cells, we recently showed that human adaptive NK cells lack expression of specific signaling proteins and transcription factors, and epigenetically resemble CD8+ effector T cells, suggesting shared pathogen-driven developmental pathways (Schulms et al, 2015). NK cell heterogeneity, ontogeny, and mechanisms sustaining NK cell memory are poorly understood, particularly in humans, because in contrast to adaptive T and B cells, clonal tracking of NK cells based on receptor gene structure is not possible. We applied autologous transplantation of genetically barcoded CD34+ rhesus macaque hematopoietic stem and progenitor cells (HSPC) to interrogate the landscape of NK cell production and expansion at a clonal level. We followed 3 monkeys for up to 4 years post-transplantation, and observed a distinct clonal ontogeny for CD56-CD16+ (corresponding to human CD56dimCD16+ NK) versus CD56+CD16- rhesus NK cells. CD56-CD16+ NK were oligoclonal, and dominated by small numbers of highly biased clones, a pattern showing little overlap with highly polyclonal multipotent contributions to T, B, myeloid and CD56+CD16- NK cell lineages. There were clear expansions and contractions of groups of these highly biased CD56-CD16+ NK cell clones over time, with individual clones contributing up to 20% to this lineage, similar to patterns of waxing and waning T cell clones, suggesting responses of both cell types to extrinsic cues such as viruses. In contrast, all other lineages, including CD56+CD16- NK cells, were characterized by very stable contributions from long-term engrafting multipotent HSPC clones over time. The highly biased, greatly expanded, and waxing and waning CD56-CD16+ NK cell clones were specifically enriched in a subpopulation of CD56+CD16- NK with high KIR and low SYK expression,and decreased methylation at IFNG the CNS1 locus, analogous to human CMV-associated adaptive NK cells. This population of cells was increased in CMV+ compared to CMV- macaques; our transplanted macaques were CMV+. Canonical CD56+CD16- NK cells, lacking an adaptive phenotype, had clonal patterns similar to CD56+CD16- NK cells. We profoundly depleted CD56-CD16+ NK cells with an anti-CD16 antibody, and observed rapid regeneration of the same CD56-CD16+ NK clonal pattern, without recruitment of contributions from multipotent HSPC via CD56+CD16- putative precursor NK cells. There was a marked increase in cycling of CD56-CD16dim NK cells just prior to reappearance of CD56-CD16bright NK cells, and no change in cycling of CD56+CD16- cells. Thus, adaptive NK cell clones, both at steady state and under regenerative stress do not appear to require ongoing production from HSPC via CD56+CD16- precursors. These results suggest that adaptive NK cells or their immediate precursors have acquired self-renewal properties and high proliferative potential, with clonal restriction potentially based selection and expansion of cells with specific, epigenetically-controlled receptor expression able to interact with external stimuli such as viruses. In conclusion, via tracking of individual NK cell clonal histories in rhesus macaques, we provide the first direct evidence for persistence of adaptive NK cell clones in any species, offering potential insights into the acquisition of NK cell memory. DisclosuresDunbar:GSK/Novartis: Research Funding.

A Zebrafish Model of Fetal Bone Marrow Provides a Dynamic View of Hematopoietic Stem Cell Niche Colonization

The entire blood system is supported throughout life by a small number of hematopoietic stem and progenitor cells (HSPCs) that are produced exclusively during embryonic development. These stem cells are generated from the hemogenic endothelium of the dorsal aorta, then migrate to the fetal liver where they expand, before making a final migration to the fetal bone marrow. After seeding the bone marrow, the stem cell pool stabilizes and the total number of HSPCs remains relatively constant. Very little is known about this early stage of bone marrow niche colonization. A better understanding of native stem cell pool establishment will likely lead to improved clinical HSPC transplantation that depends on repopulation of the bone marrow niche. Currently, imaging technology does not allow direct visualization of the bone marrow niche during colonization because it occurs in utero in the long bones of the fetus. The zebrafish is an advantageous model because the embryos develop externally and are transparent. To quantify the early stem cell pool, we employed long term fate mapping with clonal analysis using the multicolor Zebrabow system, which imparts a unique fluorescent hue to stem cells and their progeny. Our findings reveal that 21 HSPC clones exist prior to HSPC emergence (24 hours post fertilization) and 30 clones are present during peak production from the aorta (48 hours post fertilization). Seeding of the presumptive adult marrow niche in zebrafish begins 4-5 days post fertilization, versus 16.5 days in the mouse. We previously described a transgenic zebrafish line (Runx:mCherry) that marks long term repopulating HSPCs throughout development and into adulthood. HSPC-specific expression is driven by the well-characterized Runx1 +23 kb mouse enhancer element. We used this line to directly observe the earliest immigration events of HSPCs as they arrive in the marrow. To achieve this, we immobilized the zebrafish by injection of the snake venom protein alpha-bungarotoxin directly into circulation. This allowed long term live imaging of the niche (~16 hours) so we could quantify the dynamics of HSPC colonization and expansion. To rapidly acquire high resolution imaging data for this deep tissue we applied lightsheet microscopy. By simultaneously illuminating the sample in the X plane, while taking images in the Z plane, hundreds of optical sections can be captured in seconds. The high pixel and temporal resolution of lightsheet microscopy in a large volume of tissue provides a highly dynamic view of the entire marrow niche. We could assess the localization of HSPCs in relation to other cell types within the niche. For example, HSPCs were closely associated with endothelial cells in a perivascular niche, similar to what has been described in mammalian bone marrow. Furthermore, we could quantify single Runx+ nuclei over time on one side of the bilateral kidney marrow. During this early stage of niche colonization, we found the number of HSPCs per side was ~50 (so ~100 total) and that remained relatively constant. This was in fact a dynamic equilibrium achieved by ingress and egress of cells, as well as occasional cell divisions. This cell number was independently validated using another transgenic zebrafish line, cd41:GFP, that also marks HSPCs. This quantification, combined with our data from earlier development, suggests that HSPCs undergo around two population doublings between emergence from the aorta and engraftment in the marrow. This unique platform for the quantification of a total stem cell pool will allow further functional and mechanistic studies using both genetics and chemical biology. Our goal is to gain insights into the establishment of the stem cell pool within the niche microenvironment and how this could improve clinical transplantation outcomes. DisclosuresZon:Marauder Therapeutics: Equity Ownership, Other: Founder; Scholar Rock: Equity Ownership, Membership on an entity's Board of Directors or advisory committees, Other: Founder; Fate, Inc.: Equity Ownership, Membership on an entity's Board of Directors or advisory committees, Other: Founder.

Clonal Tracking of the Geographic Distribution of Hematopoiesis in Nonhuman Primates Provides New Insights into HSPC Migration and Differentiation

Hematopoietic stem and progenitor cells (HSPC) primarily reside in bone marrow (BM) niches, but are also found in peripheral blood (PB) in small numbers. Large numbers of HSPC can be pharmacologically mobilized from the BM into the PB and home back to BM niches following transplantation. We used the rhesus macaque to study the process of hematopoiesis in both space and time following autologous transplantation, as a model with great relevance to humans. We labeled individual CD34+ HSPC and their progeny with genetic "barcodes" via lentiviral transduction with a very high diversity barcode library, allowing tracking of the output from individual HSPC clones in vivo following autologous transplantation, in a quantitative and sensitive manner (Wu et al., 2014). In this study we investigated the pattern of HSPC clonal output in various anatomic niches, sampling left (L) vs right (R) iliac crest BM, PB and lymph node (LN) over time post ablative autologous transplantation, for all major hematopoietic lineages and CD34+ HSPC.We tracked thousands of HSPC clones in 6 rhesus macaques from 3.5 months (m) to up to 18.5m post transplantation. L and R iliac crest BM and PB were serially collected and CD34+ HSPC along with CD3+CD4+ T, CD3+CD8+ T, CD20+ B, CD14+ monocytes (Mo), CD33+ granulocytes (Gr), and two NK cell subsets (CD3-CD20-CD14-CD16+/ or CD56+) were purified. In all animals, there was marked geographic segregation of CD34+ HSPC for at least 6m post-transplant, with individual clones localized only to the L or R side but not both (Pearson correlation at 3.5-6m: r=0.019±0.08 for CD34+ L vs R, n=6), despite rapid expansion of CD34+ HSPC during early engraftment. This result suggests that during this phase of recovery, HSPC spread contiguously in the BM, and there is little geographic "mixing" via egress into and re-entry from the PB. With time between 7m and 18.5m post-transplant, the distribution of CD34+ HSPC became more homogeneous, with clones detected on both L and R (r=0.52±0.22 at 12-18.5m, n=3). The geographic restriction of clones at earlier time points suggests that release and homing may be dependent on local contiguous niche occupancy status, with migration only occurring following hematopoietic recovery. We next examined the clonal distribution of the more mature lineage-committed cells in the L vs R BM and in PB. Gr, Mo and B cells were produced locally in BM, with the clonal pattern of each lineage matching the CD34+ cells collected from the same side BM time point through 6m (r>0.80 for each lineage vs same side CD34+ cells), and distinct from same lineages (r<0.16 for each lineage in L vs in R BM) and CD34+ cells on the other side (r<-0.01 for each lineage vs other side CD34+ cells). CD16+CD56-/dim NK clones were completely shared between PB and both L and R BM, suggesting they were not produced locally in BM, but instead in other sites with homogenous lodging or homing back to BM. Most surprisingly, we found population of CD3+CD8+ T cells that appeared to be produced locally, with barcodes matching the CD34+ HSPC at the same location, suggesting a novel T cell development pathway within the BM for this subset during early hematopoietic reconstitution. In contrast, CD3+CD4+ BM T cells had similar clonal constitution on the L vs R, and matched the PB, suggesting they had re-circulated back to the BM following maturation elsewhere, such as the thymus. T, B and NK cells from two LNs obtained simultaneously were also analyzed. Clonal contributions to T, B, and NK cells from L vs R LNs were highly correlated (r=0.95, r=0.88, and r=0.89 respectively). The clonal composition of T or B cells in LN were shared with circulating T or B cells (r=0.88, r=0.85 respectively), while LN NK cells (which are primarily CD56+/CD16-) shared barcodes with circulating CD16-CD56+ NK (r=0.81), not with PB CD16+CD56- cells(r=0.26), suggesting a non-precursor/progeny relationship.Our model for the first time documents the dynamics of HSPC geographic distribution and migration in primates following transplantation, findings with direct clinical relevance, and provides new insights into hematopoietic lineage development, including a potential novel T cell development pathway in the BM. Our findings may also help explain the extremely patchy distribution of hematopoiesis in humans following transplantation or in the setting of marrow failure or aging, and suggest that analysis of individual BM samples may not fully reflect ongoing global hematopoiesis. DisclosuresNo relevant conflicts of interest to declare.