Age-related change in human haematopoiesis causes reduced regenerative capacity1, cytopenias2, immune dysfunction3 and increased risk of blood cancer4–6, but the reason for such abrupt functional decline after 70 years of age remains unclear. Here we sequenced 3,579 genomes from single cell-derived colonies of haematopoietic cells across 10 human subjects from 0 to 81 years of age. Haematopoietic stem cells or multipotent progenitors (HSC/MPPs) accumulated a mean of 17 mutations per year after birth and lost 30 base pairs per year of telomere length. Haematopoiesis in adults less than 65 years of age was massively polyclonal, with high clonal diversity and a stable population of 20,000–200,000 HSC/MPPs contributing evenly to blood production. By contrast, haematopoiesis in individuals aged over 75 showed profoundly decreased clonal diversity. In each of the older subjects, 30–60% of haematopoiesis was accounted for by 12–18 independent clones, each contributing 1–34% of blood production. Most clones had begun their expansion before the subject was 40 years old, but only 22% had known driver mutations. Genome-wide selection analysis estimated that between 1 in 34 and 1 in 12 non-synonymous mutations were drivers, accruing at constant rates throughout life, affecting more genes than identified in blood cancers. Loss of the Y chromosome conferred selective benefits in males. Simulations of haematopoiesis, with constant stem cell population size and constant acquisition of driver mutations conferring moderate fitness benefits, entirely explained the abrupt change in clonal structure in the elderly. Rapidly decreasing clonal diversity is a universal feature of haematopoiesis in aged humans, underpinned by pervasive positive selection acting on many more genes than currently identified.

Rare hematopoietic stem and progenitor cell (HSPC) pools outside the bone marrow (BM) contribute to blood production in stress and disease but remain ill-defined. Although non-mobilized peripheral blood (PB) is routinely sampled for clinical management, the diagnosis and monitoring potential of PB HSPCs remains untapped, as no healthy PB HSPC baseline has been reported. Here we comprehensively delineate human extramedullary HSPC compartments comparing spleen, PB and mobilized PB (mPB) to BM using single-cell RNA-seq and/or functional assays. We uncover HSPC features shared by extramedullary tissues and others unique to PB. First, in contrast to actively dividing BM HSPCs, we find no evidence of substantial ongoing hematopoiesis in extramedullary tissues at steady state, but report increased splenic HSPC proliferative output during stress erythropoiesis. Second, extramedullary stem cells/multipotent progenitors (HSC/MPPs) from spleen, PB and mPB share a common transcriptional signature and increased abundance of lineage-primed subsets compared to BM. Third, healthy PB HSPCs display a unique bias towards erythroid-megakaryocytic differentiation. At HSC/MPP level, this is functionally imparted by a subset of phenotypic CD71+ HSC/MPPs, exclusively producing erythrocytes and megakaryocytes, highly abundant in PB but rare in other adult tissues. Finally, the unique erythroid-megakaryocytic-skewing of PB is perturbed with age, in essential thrombocythemia and in beta-thalassemia. Collectively, we identify extramedullary lineage-primed HSPC reservoirs that are non-proliferative in situ and report involvement of splenic HSPCs during demand-adapted hematopoiesis. Our data also establish aberrant composition and function of circulating HSPCs as potential clinical indicators of BM dysfunction.

Age-related change in human haematopoiesis causes reduced regenerative capacity, cytopenias, immune dysfunction and increased risk of blood cancer. The cellular alterations that underpin the abruptness of this functional decline after the age of 70 years remain elusive. We sequenced 3579 genomes from single-cell-derived colonies of haematopoietic stem cell/multipotent progenitors (HSC/MPPs) across 10 haematologically normal subjects aged 0-81 years. HSC/MPPs accumulated 17 mutations/year after birth and lost 30bp/year of telomere length. Haematopoiesis in adults aged <65 was massively polyclonal, with high indices of clonal diversity and a stable population of 20,000-200,000 HSC/MPPs contributing evenly to blood production. In contrast, haematopoiesis in individuals aged >75 showed profoundly decreased clonal diversity. In each elderly subject, 30-60% of haematopoiesis was accounted for by 12-18 independent clones, each contributing 1-34% of blood production. Most clones had begun their expansion before age 40, but only 22% had known driver mutations. Genome-wide selection analysis estimated that 1/34 to 1/12 non-synonymous mutations were drivers, occurring at a constant rate throughout life, affecting a wider pool of genes than identified in blood cancers. Loss of Y chromosome conferred selective benefits on HSC/MPPs in males. Simulations from a simple model of haematopoiesis, with constant HSC population size and constant acquisition of driver mutations conferring moderate fitness benefits, entirely explained the abrupt change in clonal structure in the elderly. Rapidly decreasing clonal diversity is a universal feature of haematopoiesis in aged humans, underpinned by pervasive positive selection acting on many more genes than currently identified.

Spinal muscular atrophy (SMA) is a neuromuscular disease caused by loss of the survival motor neuron (SMN) gene. While there are currently two approved gene-based therapies for SMA, availability, high cost, and differences in patient response indicate that alternative treatment options are needed. Optimal therapeutic strategies will likely be a combination of SMN-dependent and-independent treatments aimed at alleviating symptoms in the central nervous system and peripheral muscles. Krüppel-like factor 15 (KLF15) is a transcription factor that regulates key metabolic and ergogenic pathways in muscle. We have recently reported significant downregulation of Klf15 in muscle of presymptomatic SMA mice. Importantly, perinatal upregulation of Klf15 via transgenic and pharmacological methods resulted in improved disease phenotypes in SMA mice, including weight and survival. In the current study, we designed an adeno-associated virus serotype 8 (AAV8) vector to overexpress a codon-optimized Klf15 cDNA under the muscle-specific Spc5-12 promoter (AAV8-Klf15). Administration of AAV8-Klf15 to severe Taiwanese Smn −/− ; SMN2 or intermediate Smn 2B/− SMA mice significantly increased Klf15 expression in muscle. We also observed significant activity of the AAV8-Klf15 vector in liver and heart. AAV8-mediated Klf15 overexpression moderately improved survival in the Smn 2B/− model but not in the Taiwanese mice. An inability to specifically induce Klf15 expression at physiological levels in a time-and tissue-dependent manner may have contributed to this limited efficacy. Thus, our work demonstrates that an AAV8-Spc5-12 vector induces high gene expression as early as P2 in several tissues including muscle, heart, and liver, but highlights the challenges of achieving meaningful vector-mediated transgene expression of Klf15.

Age related clonal haematopoiesis (ARCH) is defined as the clonal expansion of hematopoietic stem cells (HSCs), driven by recurrent mutations. Many of these are also commonly seen in haematological malignancies, hence termed pre-leukemic mutations (pLM). ARCH carries an increased risk of haematological malignancies and cardiometabolic disease. Further understanding of the role of pLMs in HSC function is necessary to predict and possibly prevent leukemia. DNMT3A R882 is the most common pLM observed in ARCH and is associated with poor outcomes in acute myeloid leukemia (AML). It is acquired early in life and is positively selected in HSCs. HSCs of Dnmt3a knock-out or knock-in mouse models have increased self-renewal capacity and can differentiate towards all lineages. DNMT3A R882 mutation is observed in all mature blood lineages in ARCH individuals, indicating their multipotential differentiation capacity, but the dynamics of differentiation are not known. We hypothesise that DNMT3A R882 mutation affects the differentiation dynamics of HSCs, potentially contributing to disease risk. We characterised the functional changes in HSC differentiation driven by DNMT3A R882 at single cell resolution. Single phenotypic HSCs (CD33-/CD34+/CD45dim/CD38-/CD45RA-) from 9 individuals (Table 1) were cultured in media supporting differentiation into all major blood lineages. To assess changes in differentiation capacity between DNMT3A R882 and wild-type (WT) HSCs within each individual, each single-cell colony was genotyped by targeted DNA sequencing and scored by high-throughput flow cytometry. Flow cytometry data was analysed using a novel unbiased analytical pipeline, which we have named 'FlowPAC', allowing generation of a two-dimensional representation of the global output of HSC differentiation by identifying clusters based on fluorochrome intensity. Four samples were underpowered for either DNMT3A R882 or WT colonies and were excluded from this analysis. We did not observe any difference in erythroid versus myeloid or lymphoid (NK) differentiation capacity between DNMT3A R882 and WT HSC. DNMT3A R882 and WT HSCs also produced similar proportions of monocytic and neutrophil colonies. However, FlowPAC analysis identified differences in their level of maturity. CD15 (neutrophil marker) expression was significantly increased in myeloid clusters of DNMT3A R882 colonies compared to WT (p=0.0043), whereas CD14 (monocyte marker) expression was decreased compared to WT (p=0.0645). We further analysed mature neutrophil differentiation using CD66b expression. Consistent with promotion of neutrophil differentiation, CD66b median fluorescence intensity was significantly increased in the CD15+ population of DNMT3A R882 colonies compared to WT. To further investigate monocyte differentiation, we performed RNAseq on colonies containing only monocytes from 1 ARCH sample. Analysis of transcriptional profiles confirmed less mature monocytes in DNMT3A R882 colonies compared to WT. Overall, our data indicate that DNMT3A R882 mutation in HSCs alters neutrophil and monocyte production. Additionally, we observed that in contrast to samples with high LSC content leading to leukemic engraftment in mice, in samples where DNMT3A R882 HSCs were able to reconstitute normal blood production, the expression of the cell surface marker CD49f, a marker of the most potent HSCs, was significantly increased in DNMT3A R882 HSCs compared to WT at the time of sorting. This may suggest unequal distribution of this pLM within the preserved normal HSC pool prior to leukemic transformation. In conclusion, DNMT3A R882 alters the dynamics of human HSC myeloid differentiation. The propensity of DNMT3A R882 derived monocytes to retain an immature phenotype relative to WT cells could represent an early change later facilitating the complete differentiation block seen in AML, driven by the acquisition of additional mutations such as NPM1. DNMT3A R882 also promoted neutrophil maturation. Altered neutrophil differentiation has been observed in patients with germline DNMT3A mutation. As altered neutrophil function plays a key role in cardiovascular disease, future studies are required to investigate whether the effect of DNMT3A R882 on neutrophil differentiation may contribute to the increased cardiovascular disease risk associated with this mutation. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.