Primary Human Hematopoietic Stem And Progenitor Cells Research Articles

Whole-Genome CRISPR-Cas9 Screening Identifies Genes Required for Human and Mouse Erythroid Development

Red blood cell (RBC) development is regulated by a few external signaling molecules which act to influence the ongoing intracellular processes responsible for producing erythrocytes. While much is known about the signaling molecules important for blood production, comparatively little is known about the genes required for successfully generating erythrocytes. Several genes have already been identified as essential for RBC development through loss-of-function studies in the mouse or in human erythroid cells in vitro. However, these studies have been limited in scope to genes that are already suspected or known to influence RBC production. Since there are ~10,000 genes expressed in erythroid cells, it is unclear how many of these genes are functionally required for erythroid development. To define the repertoire of genes required for human erythroid development, we performed a genome-scale CRISPR knock-out screen in the human erythroid progenitor cell line HUDEP-2, using the GeCKOv2 lentiviral library, which delivers Cas9 and one of 6 sgRNAs targeting virtually every gene in the genome. Following viral transduction and cell recovery for 9 days, we collected HUDEP-2 cells prior to the onset of differentiation as well as differentiated orthochromatic erythroblasts (right prior to enucleation) using flow sorting, on the basis of CD49d expression (CD49d is downregulated in the final stages of erythroid differentiation). As expected, sgRNAs targeting known erythroid essential genes (such as GATA1 and EPOR) were depleted in HUDEP-2 cells compared to the sgRNA library. Notably, we also identified genes for which sgRNAs were depleted in differentiated versus undifferentiated erythroid cells, representing genes that are likely required for terminal erythroid differentiation (such as ZFPM1, ALAS2, etc..). This supports the utility of the screen to identify novel regulators of erythropoiesis. Among highly ranked genes, NHLRC2, which was previously implicated in hemolytic anemia, was identified to be required in HUDEP-2 cells, suggesting that NHLRC2 is intrinsically required for human erythroid development. To validate the role of NHLRC2 in human erythropoiesis, we down-regulated NHLRC2 in primary human CD34+ hematopoietic stem and progenitor cells (HSPCs) undergoing erythroid differentiation, using one of 4 independent shRNAs. NHLRC2 down-regulation resulted in impaired proliferation and differentiation of human erythroid cells in vitro. To validate the results of the genome-scale screen, we generated a secondary library dedicated to examining genes that positively or negatively regulate the final stages of erythroid differentiation, while excluding common essential genes required for the survival of more than 90% of immortalized cell lines screened by the BROAD institute. The secondary screen yielded a list of over 500 genes found to influence erythroid differentiation (FDR<0.01). One of the novel genes, VAC14, was identified as a highly ranked gene in the secondary screen for erythroid differentiation. Validation experiments demonstrated that VAC14 down-regulation using one of 3 independent shRNAs result in erythroid cell proliferation defects, both in HUDEP2 cells and in erythroid cells derived from primary human HSPCs. Since germline loss of VAC14 is embryonic lethal in the mouse, to validate the role of VAC14 in erythropoiesis in vivo, we transplanted fetal livers from Vac14 null mice (or wild-type [WT] control mice) into WT recipients and examined the VAC14 deficient hematopoietic compartment. Mice transplanted with Vac14 null HSCs exhibited a profound reduction in absolute numbers of bone marrow erythroid cells with evidence of a block in erythroid maturation. Impaired bone marrow erythropoiesis was largely (but incompletely) compensated for by splenic extramedullary erythropoiesis. Vac14 null hematopoietic cells exhibited pronounced cytoplasmic vacuolation, also affecting numerous stages of erythroid cells. Altogether, we have performed an unbiased genome-scale CRISPR knock-out screen that identified (and validated) novel genes required in erythropoiesis.

Clonal Trajectories and Therapeutic Targeting of High-Risk SF3B1-Mutant Myelodysplastic Syndromes

Myeloid neoplasms are driven by acquisition of clonal genetic lesions, yet it remains unclear how these lesions cooperate to transform hematopoietic stem and progenitor cells (HSPCs) programs and modify drug responses. The integration of genomic profiling with clinical and cytogenetic data in the recent IPSS-M has significantly improved risk stratification of patients with myelodysplastic syndromes (MDS). Spliceosome mutations in SF3B1 are common initiating events in MDS and confer favorable prognosis, while secondary mutations in RUNX1 and STAG2 transform this low-risk condition into high-risk MDS or secondary acute myeloid leukemia. To understand how these events cooperate with SF3B1 mutations, we modeled these clonal trajectories in primary human HSPCs. SF3B1 K700E mutation was introduced in CD34+ cells isolated from cord blood or peripheral blood of healthy donors, using CRISPR/Cas9 editing and AAV6-mediated homology directed repair. By introducing an intronic fluorescent reporter, this system allows for the tracking and isolation of SF3B1-mutant cells for molecular and functional analysis. Edited cells were heterozygous for the K700E mutation and recapitulated alternative 3' splice site selection of genes previously identified in SF3B1-mutant patients. To model disease progression, we introduced secondary RUNX1 (S-R), STAG2 (S-S), or control AAVS1 (S-A) mutations into SF3B1 K700E knock-in CD34+ HSPCs, leading to a reduction of RUNX1 or STAG2 expression in SF3B1-mutant cells (50% and 90%, respectively). The S-R and S-S trajectories induced divergent alterations in lineage specification of SF3B1-mutant HSPCs. S-R promoted myeloid skewing at the expense of the erythroid lineage, while S-S induced a block in differentiation, impairing both myeloid and erythroid differentiation. Consistently, introduction of secondary RUNX1 or STAG2 mutations in an induced pluripotent stem cell (iPSC-HPCs) model of SF3B1-mutant MDS recapitulated S-R myeloid expansion and S-S maturation arrest identified in primary HSPCs. S-R and S-S genotypes resulted in divergent transcriptional programs including inflammation, immune response, and myeloid differentiation. However, both high-risk clonal trajectories expanded the immature CD34+CD38- HSCs/multipotent progenitors (MPPs). S-R selectively expanded CD34+CD38-CD133+ HSCs, whereas S-S expanded the more mature CD34+CD38-CD133- population. These data suggest that, despite divergent molecular pathways, high-risk mutations converge on expansion of stem cell potential of SF3B1-mutant HSPCs. To understand how genetic (co-mutation patterns) and epigenetic (HSC state) heterogeneity can influence drug responses, we profiled a panel of spliceosome inhibitors and 166 FDA approved and investigational compounds. Both S-R and S-S genotypes conferred decreased response to single and combinatorial agents conventionally used for the treatment of myeloid neoplasms. High-risk genotypes maintained elevated sensitivity to SF3B inhibition, but conferred differential response to novel classes of spliceosome modulators, with STAG2 but not RUNX1 loss selectively promoting response to type I PRMTs inhibitor MS023. By contrast, CHK1 inhibitor Prexasertib was highly selective for SF3B1-mutant cells irrespective of co-mutations, inhibiting growth and cell cycle progression. Taken together these data indicate that the presence of SF3B1 mutation offers therapeutic vulnerabilities that can be leveraged to target high-risk genotypes, and different SF3B1 co-mutated genes can further modulate drug response of SF3B1-mutant cells. In conclusion, progression from low-risk SF3B1-mutant MDS to high-risk disease is mediated by molecularly distinct trajectories driven by RUNX1 and STAG2 mutations that converge on expansion of the HSC compartment. Moreover, clonal progression is associated with genotype-specific drug responses and increased resistance to standard agents, and ongoing studies are elucidating how genetic and epigenetic states affect therapeutic responses.

3029 – COMBINATORIAL GENE TARGETING IN PRIMARY HUMAN HEMATOPOIETIC STEM AND PROGENITOR CELLS

The CRISPR/Cas9 system offers enormous versatility for functional genomics. However, many applications, such as combinatorial perturbations for disease modelling and studies of gene interactions, have proven to be challenging in primary human cells compared to cell lines or mouse cells. Here, we addressed the challenge of multiplexed gene perturbations in primary human cord blood-derived hematopoietic stem and progenitor cells (HSPCs) by co-delivering lentiviral sgRNA vectors expressing either Enhanced Green Fluorescent Protein (EGFP) or Kusabira Orange (KuO), together with Cas9 mRNA, to simultaneously edit two genetic loci. The use of fluorescent markers allows for tracing of single- or double-edited cells and we achieved robust double knockout of the cell surface markers CD45 and CD44 with an efficiency of around 70%. As a functional proof of concept, we demonstrated the use of this system to study gene dependencies for cell survival by simultaneously targeting the cohesin genes STAG1 and STAG2, as a model of synthetic lethality. Furthermore, we showed that this system can be used to study cooperative genetic events, and found a combinatorial effect with potential synergy for HSPC expansion when targeting the Aryl Hydrocarbon Receptor (AHR) in combination with members of the epigenetic modifier CoREST. Taken together, we established a paradigm for multiplexed CRISPR/Cas9 editing in primary human HSPCs, which enables studies of genetic dependencies and cooperation. This traceable multiplexed system has important implications for modelling polygenic diseases and for investigating gene interactions. The CRISPR/Cas9 system offers enormous versatility for functional genomics. However, many applications, such as combinatorial perturbations for disease modelling and studies of gene interactions, have proven to be challenging in primary human cells compared to cell lines or mouse cells. Here, we addressed the challenge of multiplexed gene perturbations in primary human cord blood-derived hematopoietic stem and progenitor cells (HSPCs) by co-delivering lentiviral sgRNA vectors expressing either Enhanced Green Fluorescent Protein (EGFP) or Kusabira Orange (KuO), together with Cas9 mRNA, to simultaneously edit two genetic loci. The use of fluorescent markers allows for tracing of single- or double-edited cells and we achieved robust double knockout of the cell surface markers CD45 and CD44 with an efficiency of around 70%. As a functional proof of concept, we demonstrated the use of this system to study gene dependencies for cell survival by simultaneously targeting the cohesin genes STAG1 and STAG2, as a model of synthetic lethality. Furthermore, we showed that this system can be used to study cooperative genetic events, and found a combinatorial effect with potential synergy for HSPC expansion when targeting the Aryl Hydrocarbon Receptor (AHR) in combination with members of the epigenetic modifier CoREST. Taken together, we established a paradigm for multiplexed CRISPR/Cas9 editing in primary human HSPCs, which enables studies of genetic dependencies and cooperation. This traceable multiplexed system has important implications for modelling polygenic diseases and for investigating gene interactions.

Introduction and Genetic Correction of Calreticulin Mutations in Human Hematopoietic Stem and Progenitor Cells Sheds Light on MPN Pathogenesis

Introduction:Recurrent mutations in calreticulin (CALR) are present in 70% to 80% of essential thrombocythemia (ET) and primary myelofibrosis (PMF) patients without a JAK2 or MPL mutation. Despite recent advances in understanding mutant CALR, the detailed mechanisms are not fully elucidated, and current knowledge is mainly based on transgenic mouse models or human cancer cell lines. Thus, to more faithfully model MPN pathogenesis, we first aimed to introduce heterozygous type-1 and type-2 CALR mutations into healthy human hematopoietic stem and progenitor cells (HSPCs) via targeted CRISPR/Cas9-mediated gene knock-in (KI) and investigate its impact on HSPC function in vitro and in vivo. Second, we aimed to correct CALR mutations in patient-derived HSPCs to study their dependence on the initial driver event to exert an MPN phenotype.Methods:We used CRISPR/Cas9 to introduce heterozygous CALR mutations into the endogenous gene locus of healthy cord blood-derived HSPCs. Our approach is based on homologous recombination using DNA repair templates delivered by adeno-associated virus serotype 6 (AAV6). Briefly, Cas9-sgRNA ribonucleoprotein (RNP) was used to cut the DNA. Simultaneously AAV6, carrying either a mutation-bearing or a wildtype control cDNA, was co-delivered to allow for targeted in-frame integration. This way, mutant CALR remains under the control of the endogenous promoter. Concurrent integration of a fluorescent reporter downstream of the mutated exon, enabled purification and tracking of modified cells via flow cytometry. Purified CRISPR-modified HSPCs were used for in vitro collagen-based colony-forming assays, proliferation and differentiation assays in liquid culture, and intrafemoral transplantation into immunodeficient NSG mice to assess their pathogenic potential.Results:Our CRISPR/Cas9 KI strategy enabled us to efficiently generate and enrich for heterozygous CALR mutant human HSPCs. Modified cells harbor the mutation at the endogenous CALR locus with intact gene regulatory regions. Correct integration and transcript expression were confirmed on DNA and RNA level by sanger sequencing. Additionally, CALR mutant protein expression was confirmed via immunohistochemistry using a diagnostically approved mutant-specific antibody.Type-1 and type-2 CALR mutations led to TPO-independent growth of CD34 + HSPC-derived cells and a two-fold (p<0.01) increase of megakaryocyte colonies in collagen-based media compared to wildtype control KI. These findings were corroborated by significantly enhanced CD41 + CD42b + megakaryocyte formation of CALR mutant HSPCs upon liquid culture differentiation.When transplanted into sublethally irradiated immunodeficient NSG mice, CALR mutant HSPCs showed robust engraftment in the bone marrow with a myeloid lineage skewing, outcompetition of wildtype cells and increased formation of CALR mutant CD41 + megakaryocyte progenitors.To investigate, if removal of type-1 and type-2 CALR mutations can ameliorate MPNs, we utilized our KI strategy to correct both CALR mutations in MPN patient-derived HSPCs by replacing them with wildtype sequences. A successful correction was confirmed on DNA and RNA level and by the absence of mutant CALR protein. Opposite to the results from introducing CALR mutations, correcting the mutations led to a two-fold decrease in megakaryocyte colony formation. Interestingly this was only seen in ET and post-ET MF samples, whereas primary MF samples were unaffected, underscoring the importance of other secondary genetic driver events in the pathogenesis of primary MF.Conclusion:Our system allows us to investigate human MPN pathogenesis prospectively and shed light on the transforming mechanisms of mutant CALR in primary HSPCs. We could show that CALR mutations prime HSPCs toward the formation of platelet-producing megakaryocytes. Genetic correction of CALR mutations in MPN patient-derived HSPCs revealed a dependence on the oncogenic mutant CALR driver event in ET and post-ET MF patients, opening the possibility of an ex vivo gene correction approach to remove mutant CALR in patient-derived HSPCs . Lastly, since MPN patient-derived cells have notoriously low engraftment potential in mice, our CRISPR/Cas9-engineered CALR mutant model also provides a powerful new strategy to generate MPN xenotransplants with defined genotypes for the evaluation of novel therapies. DisclosuresGreinix: Celgene: Consultancy; Therakos: Consultancy; Takeda: Consultancy; Sanofi: Consultancy; Novartis: Consultancy. Sill: Astellas: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; AbbVie: Consultancy, Membership on an entity's Board of Directors or advisory committees. Zebisch: Novartis: Consultancy; AbbVie: Consultancy; Celgene: Consultancy, Honoraria. Reinisch: Celgene: Research Funding; Pfizer: Consultancy.

Dissecting ELANE neutropenia pathogenicity by human HSC gene editing.

Severe congenital neutropenia (SCN) is a life-threatening disorder most often caused by dominant mutations of ELANE that interfere with neutrophil maturation. We conducted a pooled CRISPR screen in human hematopoietic stem and progenitor cells (HSPCs) that correlated ELANE mutations with neutrophil maturation potential. Highly efficient gene editing of early exons elicited nonsense-mediated decay (NMD), overcame neutrophil maturation arrest in HSPCs from ELANE-mutant SCN patients, and produced normal hematopoietic engraftment function. Conversely, terminal exon frameshift alleles that mimic SCN-associated mutations escaped NMD, recapitulated neutrophil maturation arrest, and established an animal model of ELANE-mutant SCN. Surprisingly, only -1 frame insertions or deletions (indels) impeded neutrophil maturation, whereas -2 frame late exon indels repressed translation and supported neutrophil maturation. Gene editing of primary HSPCs allowed faithful identification of variant pathogenicity to clarify molecular mechanisms of disease and encourage a universal therapeutic approach to ELANE-mutant neutropenia, returning normal neutrophil production and preserving HSPC function.

Efficient and nontoxic biomolecule delivery to primary human hematopoietic stem cells using nanostraws

Introduction of exogenous genetic material into primary stem cells is essential for studying biological function and for clinical applications. Traditional delivery methods for nucleic acids, such as electroporation, have advanced the field, but have negative effects on stem cell function and viability. We introduce nanostraw-assisted transfection as an alternative method for RNA delivery to human hematopoietic stem and progenitor cells (HSPCs). Nanostraws are hollow alumina nanotubes that can be used to deliver biomolecules to living cells. We use nanostraws to target human primary HSPCs and show efficient delivery of mRNA, short interfering RNAs (siRNAs), DNA oligonucleotides, and dextrans of sizes ranging from 6 kDa to 2,000 kDa. Nanostraw-treated cells were fully functional and viable, with no impairment in their proliferative or colony-forming capacity, and showed similar long-term engraftment potential in vivo as untreated cells. Additionally, we found that gene expression of the cells was not perturbed by nanostraw treatment, while conventional electroporation changed the expression of more than 2,000 genes. Our results show that nanostraw-mediated transfection is a gentle alternative to established gene delivery methods, and uniquely suited for nonperturbative treatment of sensitive primary stem cells.

Single-Cell RNA-Seq to Assess Differential Responses to Tnfα in Human Hematopoietic Stem and Progenitor Cells in Myeloproliferative Neoplasm

Somatic mutations in hematopoietic stem and progenitor cells (HSPCs) leading to constitutive activation of thrombopoietin receptor signaling result in myeloproliferative neoplasms (MPN). The most common mutation found in MPN patients occurs in the Janus kinase 2 gene (JAK2V617F). We have previously found that JAK2V617F hematopoietic progenitors are resistant to tumor necrosis factor alpha (TNFα), however this mechanism is not well defined. We hypothesize that resistance to TNFα in JAK2V617F hematopoietic stem and progenitors is a driver of the competitive advantage over non-malignant clones. Here, we used droplet-based single-cell RNA-sequencing to investigate transcriptional profiling in primary human HSPCs. First, we harvested white blood cells from fresh bone marrow aspirates from one MPN patient (Polycythemia Vera with 71% JAK2V617F allele burden) as well as one unaffected individual then sorted Lin-/CD34+/CD38- hematopoietic progenitors. Immediately following sorting, half of the cells were stimulated with TNFα for 4 hours while the other half of cells were used as unstimulated controls. We then utilized the 10X Chromium platform to generate single-cell droplets for the 8,129 total cells from the unaffected individual and 33,299 total cells from the MPN patient. We ran alignment using the CellRanger pipeline then performed analysis using the Seurat package in R. Expression profiles of untreated HSPCs in both normal and MPN cells revealed high expression of genes involved in important pathways for hematopoiesis (Polycomb repressive complexes, chromatin regulation, the ubiquitin proteasome system etc.). Expression of CD34 was confirmed in both MPN and non-MPN cells, though CD34 expression was reduced following TNFα stimulation. Expression of stem (i.e. THY1, ITGA6) and progenitor (i.e. PTPRC) genes were detected within both individuals, which highlights the heterogeneity within Lineage-/CD34+/CD38- cells. Following stimulation with TNFα, we observed expression of genes in canonical pathways downstream of TNF including NF-κB, Mitogen-Activated Protein Kinase (MAPK), and Transforming Growth Factor Beta (TGFβ). Indeed, we observed a baseline level of expression of TGFβ-related genes in both normal and MPN cells. Upon inflammatory stimulation, normal HSPCs upregulated SMAD expression which are involved in the TGFβ pathway. Strikingly, we did not observe an increase in SMAD expression in MPN cells following TNF. This suggests a dampened response via the TGFβ pathway to TNF in MPN cells. Additionally, we found that TNF-stimulated HPSCs from the unaffected individual expressed canonical genes of the TNF pathway that encode for chemokines, cytokines, transcription factors and negative feedback regulators. In normal TNF-stimulated cells, we identified highly expressed genes involved in the caspase cascade, suggesting a robust apoptotic response in normal HPSCs. However, there was a lower expression of caspases in stimulated MPN cells, suggesting a dampened apoptotic response to TNF. One observation that was unique to TNF-stimulated cells from the MPN individual was the expression of glycoproteins involved in angiogenesis and platelet aggregation. Taken together, these data serve as a proof of principle for transcriptional profiling of primary human hematopoietic stem and progenitor cells and that this cell population rapidly and robustly alter their gene expression program upon TNFα stimulation. In conclusion, we show that HSPCs from an MPN patient exhibit a dampened response to TNF compared to normal HSPCs. Specifically, we observed a lower expression of genes involved with apoptosis and TGFβ signaling in MPN cells compared to normal cells following TNF stimulation. The finding of a dampened apoptotic response to TNF is consistent with the hypothesis that JAK2V617F cells gain a selective advantage over normal cells under inflammatory stress. To our knowledge, this is the first report of single-cell RNA-seq analysis on primary human HSPCs following FACS and inflammatory stimulation. Disclosures Fleischman: incyte: Speakers Bureau.

Adenylate Kinase 2 Links Energy Metabolism and Cell Fate in Hematopoietic Stem and Progenitor Cells

While hematopoietic stem and progenitor cells (HSPCs) were thought to rely mainly on glycolysis for energy supply, emerging evidence suggests that defects in mitochondrial functions can impact HSPC development with respect to self-renewal, differentiation and aging. The exact mechanisms underlying metabolic reprogramming and cell fate decisions during human hematopoiesis, however, remain elusive. Biallelic mutations in the mitochondrial enzyme adenylate kinase 2 (AK2), cause reticular dysgenesis (RD), one of the most profound forms of severe combined immunodeficiency (SCID). AK2 catalyzes the interconversion between adenine nucleotides and thereby controls the availability of ADP for oxidative phosphorylation. Clinically, RD patients not only present with profound lymphopenia, typical for classic SCID, but also suffer from severe congenital neutropenia. The developmental arrest across the T, NK and granulocytic lineages suggests that AK2 deficiency causes a metabolic defect with global impact on hematopoiesis. Our prior work in induced pluripotent stem cells (iPSCs) from RD patients has shown that maturation-arrested iPSC-derived HSPCs exhibit increased oxidative stress and an energy-depleted adenine nucleotide profile, suggesting that AK2-regulated mitochondrial bioenergetics play an integral role in HSPC differentiation. Therefore, RD serves as an excellent model to study the impact of mitochondrial metabolism during human HSPC development. Methods: Since iPSCs do not recapitulate definitive hematopoiesis, we developed an AK2 biallelic knock-out model in primary human HSPCs using CRISPR/Cas9 gene editing. Employing a homologous recombination-mediated dual color reporter strategy, we were able to select for HSPCs with biallelic AK2 knock-out. HSPCs edited at the safe harbor AAVS1 site were used as a control. FACS purified AK2-/- and AAVS1-/- HSPCs were in vitro differentiated along the granulocytic lineage, and cells at various differentiation stages were sorted for RNA-seq and metabolomics analysis. Results: We analyzed the myeloid differentiation potential of AK2-/- HSPCs in vitro. Compared to AAVS1-/- controls, AK2-/- HSPCs displayed a severely decreased colony forming potential of both myeloid and erythroid lineages. In addition, AK2-/- HSPCs showed a granulocytic maturation arrest at the HLA-DR-, CD117+ promyelocyte stage, consistent with the characteristic phenotype observed in RD patients. We then performed RNA-seq studies on in vitro differentiated promyelocyte and neutrophil subpopulations derived from AK2-/- and control HSPCs. The RNA-seq analysis showed differential gene expression in glutathione metabolism and IL-10 signaling pathways, suggesting an increase in oxidative stress and inflammation, respectively, caused by AK2 deficiency. In addition, genes implicated in antimicrobial function and granule synthesis were downregulated in AK2-/- neutrophils, suggesting a functional defect. Liquid chromatography-mass spectrometry (LC-MS/MS) studies to delineate differences in metabolite profile conferred by AK2 deficiency at different stages of HSPC development are currently in progress. Conclusions: We have established the first cell-traceable biallelic AK2 CRISPR knock-out model in primary human HSPCs that recapitulates the myeloid phenotype of RD patients. This model allows us to profile AK2 knock-out cells at different developmental stages. AK2-/- granulocyte precursors showed a transcriptional signature suggestive of worsening oxidative stress, inflammation and defective effector cell functions during maturation. To understand the mechanistic underpinnings for these observations we are now using a global metabolomics approach to profile the changes in energy metabolites that occur during development in AK2-deficient and control HSPC subpopulations. Understanding how metabolism governs differentiation and self-renewal of human HSPCs has important translational implications to improve hematopoietic stem cell products and transplantation outcomes. Disclosures Morrison: Frequency Therapeutics: Consultancy, Membership on an entity's Board of Directors or advisory committees; OncoMed Pharmaceuticals: Equity Ownership; GI Therapeutics: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Kolon Gene Therapeutics: Consultancy; Protein Fluidics: Other: Stock Options.

Gene Editing ELANE in Human Hematopoietic Stem and Progenitor Cells Reveals Disease Mechanisms and Therapeutic Strategies for Severe Congenital Neutropenia

Newburger: TransCytos LLC: Consultancy; X4 Pharmaceuticals: Consultancy, Honoraria.

ATG4A is a Novel Regulator of Mitophagy during Human Erythropoiesis

Autophagy is a highly conserved pathway that degrades and recycles intracellular components. While autophagy is activated in response to cellular stress, it also contributes to hematopoietic cell differentiation. Previous studies in mice lacking core autophagy proteins have identified mitochondrial clearance as a critical function of autophagy in erythroid differentiation and maturation. Impaired autophagy results in anemia, retained mitochondria and elevated levels of reactive oxygen species in mice. However, the kinetics and regulation of mitophagy in human erythropoiesis have not been investigated. To better understand the kinetics of mitophagy in human erythropoiesis we have developed a lentiviral mitophagy reporter (MT-Keima) and used it to monitor mitochondrial clearance during erythroid differentiation of primary human CD34+ hematopoietic stem and progenitor cells (HSPCs). Measurement of mitophagy during erythroid differentiation revealed active mitochondrial clearance during early and late stages of erythropoiesis culminating with total clearance of mitochondria at the terminal stages of differentiation. Gene expression analysis during human erythroid differentiation identified the upregulation of the core autophagy program including ATG4A encoding a cysteine protease, which was restricted to the erythroid lineage. Knockdown of ATG4A in primary human HSPCs significantly reduced mitophagy in early and late erythroid cells and resulted in increased mitochondrial mass in terminally differentiated reticulocytes. Furthermore decreased expression of ATG4A, but not its paralog ATG4B, reduced the (i) expansion of erythroid progenitors, (ii) total number of erythroblasts (iii) and significantly reduced enucleation relative to luciferase controls. Finally significantly fewer erythroid colonies were found in methylcellulose culture only in HSPCs with ATG4A KD when compared to luciferase controls, while numbers of myeloid colonies were preserved, supporting a role for ATG4A selectively in the human erythroid lineage. Together these results identify ATG4A as a novel erythroid-specific regulator of mitophagy and a new potential target for the therapeutic modulation of autophagy in human erythropoiesis. Disclosures No relevant conflicts of interest to declare.

Cohesin Complex Mutations Impair Differentiation of Human Hematopoietic Stem and Progenitor Cells

The cohesin complex is a multiprotein complex involved in a number of cellular processes including sister chromatid cohesion in mitosis, replication fork organization, and regulation of chromatin accessibility for gene expression. Mutations in genes encoding the members of the cohesin complex (SMC1A, SMC3, STAG2, and RAD21) occur in about 10-15% of de novo acute myeloid leukemia (AML) patients. Apart from AML, cohesin mutations have been found in many human cancers indicating a central role for this complex in oncogenesis. In AML, our prior studies have demonstrated that cohesin mutations occur in pre-leukemic hematopoietic stem and progenitor cells (HSPC) that retain normal differentiation potential. Thus, these mutations are likely key initiating events in leukemia pathogenesis. Due to their importance in AML evolution, we sought to determine the effect of these mutations on human hematopoiesis.Cohesin mutations typically occur as heterozygous mutations throughout the genes suggesting either a haploinsufficiency or dominant negative effect. Co-immunoprecipitation experiments in primary human AML samples showed marked decrease in binding between RAD21 and SMC1A in RAD21/SMC1A-mutant AML. These results suggest a dominant negative effect of cohesin mutants on complex formation.In an effort to characterize the phenotype of cohesin complex mutations in AML, we generated human AML cell lines engineered to express wildtype (WT) or mutant cohesin components under the control of a doxycycline-inducible promoter. We chose the TF-1 erythroleukemia cell line due to its ability to differentiate down the erythroid lineage in response to erythropoietin (EPO). We found that cohesin mutant cell lines showed a significant decrease in erythroid differentiation upon exposure to EPO as determined by surface expression of glycophorin A (GPA) and RNA expression of fetal hemoglobin and KLF-1, a key erythroid transcription factor, suggesting that cohesin mutations act in a dominant negative manner to impair differentiation.We next investigated the impact of cohesin complex mutations on normal HSPCs from primary human cord blood. We transduced CD34+ cord blood cells with lentivirus encoding constitutive expression of either WT or mutant cohesin components. Transduced cells were isolated and cultured under several conditions. First, cells were cultured with cytokines designed to promote retention of HSPCs, and cord blood cells expressing mutant cohesin showed significant retention of CD34+ expression as compared to WT or control cells. Second, cells were cultured under conditions designed to promote granulocytic/monocytic differentiation, and cohesin mutant-expressing cells showed a significant decrease in CD14+ expression compared to controls. Third, cells were cultured under conditions designed to promote erythroid differentiation, and cohesin mutant cells showed a significant decrease in CD71 and GPA-double positive erythroid cells. Together, this data suggests that cohesin complex mutations impart a differentiation block on primary human HSPCs. Finally, we investigated whether cohesin mutations affected the serial colony replating ability of human HSPCs in vitro. Primary human cord blood HSPCs were transduced with cohesin mutant-encoding lentivirus, sorted, and cultured in methylcellulose for 14 days. No differences were observed in the colony number or type in the primary plating. However, cohesin-mutant cells exhibited increased serial replating potential beyond the 3rd replating, with essentially no control or WT colonies after the 2ndreplating.In summary, our results indicate that cohesin complex mutations impair HSPC differentiation and increase in vitro replating of primary human cells. The mechanisms by which this occurs are currently being investigated, but preliminary data suggests that mutations in cohesin affect global chromatin accessibility. These results are consistent with a model of mutational acquisition in AML that we have proposed, in which pre-leukemic mutations occur in genes involved in global regulation of gene expression through epigenetic mechanisms that impair differentiation and/or affect self-renewal (such as IDH1/2, TET2, DNMT3A, and cohesin), whereas late mutations occur in genes that generally lead to an increase in activated signaling and proliferation (such as FLT3 and RAS). DisclosuresNo relevant conflicts of interest to declare.