Megakaryocyte-erythroid Progenitors Research Articles

An intricate regulatory circuit between FLI1 and GATA1/GATA2/LDB1/ERG dictates erythroid vs. megakaryocytic differentiation.

During hematopoiesis, megakaryocytic erythroid progenitors (MEPs) differentiate into megakaryocytic or erythroid lineages in response to specific transcriptional factors, yet the regulatory mechanism remains to be elucidated. Using the MEP‑like cell line HEL western blotting, RT‑qPCR, lentivirus‑mediated downregulation, flow cytometry as well as chromatin immunoprecipitation (ChIp) assay demonstrated that the E26 transformation‑specific (ETS) transcription factor friend leukemia integration factor 1 (Fli‑1) inhibits erythroid differentiation. The present study using these methods showed that while FLI1‑mediated downregulation of GATA binding protein 1 (GATA1) suppresses erythropoiesis, its direct transcriptional induction of GATA2 promotes megakaryocytic differentiation. GATA1 is also involved in megakaryocytic differentiation through regulation of GATA2. By contrast to FLI1, the ETS member erythroblast transformation‑specific‑related gene (ERG) negatively controls GATA2 and its overexpression through exogenous transfection blocks megakaryocytic differentiation. In addition, FLI1 regulates expression of LIM Domain Binding 1 (LDB1) during erythroid and megakaryocytic commitment, whereas shRNA‑mediated depletion of LDB1 downregulates FLI1 and GATA2 but increases GATA1 expression. In agreement, LDB1 ablation using shRNA lentivirus expression blocks megakaryocytic differentiation and modestly suppresses erythroid maturation. These results suggested that a certain threshold level of LDB1 expression enables FLI1 to block erythroid differentiation. Overall, FLI1 controlled the commitment of MEP to either erythroid or megakaryocytic lineage through an intricate regulation of GATA1/GATA2, LDB1 and ERG, exposing multiple targets for cell fate commitment and therapeutic intervention.

Abstract LB227: Accelerated intra-clonal transcriptomic diversification of hematopoietic stem cells during aging fuels leukemia evolution

Abstract Cancers are diseases of aging. Many cellular processes characteristic of cancer, e.g., epigenetic dysregulation, are similarly observed during aging. Acute myeloid leukemia (AML) is emblematic of this interplay. As a blood cancer stemming from hematopoietic stem and progenitors (HSPC), its median age of diagnosis is 65. AML is linked to age-related clonal hematopoiesis (CH), a condition resulting from the expansion of HSPC, marked by mutations in leukemia-associated genes. We aim to clarify the intrinsic role of aging in HSPC as it causes CH and leukemic transformation. Hypothesis: aging amplifies the heritable phenotypic variations in hematopoietic stem cells (HSC), enhancing epigenetic heterogeneity. This acts as a substrate for natural selection, driving leukemic transformation. Results: We found a significant increase in epigenetic and transcriptomic heterogeneity in long-term HSC (LT-HSC) from old mice compared to their younger counterparts via single-cell RNA-seq (scRNA-seq)s. This process occurs in an aged bone marrow with higher inflammation and altered HSPC support. Of relevance, we previously show that the rise of epigenetic and transcriptomic heterogeneity in HSC with Tet2 loss and Flt3 ITD precedes leukemic transformation. We further employed CellTag Indexing and scRNA-seq to track the fate of specific HSC subclones. We tracked HSPC cell culture (in vitro) after two-weeks and two-months following transplantation into recipient mice of matching ages (in vivo). Cells of the same clone manifest higher transcriptomic similarities than those from different clones, validating CellTag in mapping clonal evolution. We computed the progeny output activity (Ai) by the ratio of clone i abundance in the committed progenitors to its frequency in the HSC compartment. We found that young mice exhibit significantly higher variability and a higher mean of progeny output activity Ai, indicating the efficiency in self-renewal and cell differentiation. While both young and old mice have low-output (higher stemness) clones, only young mice had significant differential expression of key genes in low-output clones compared to high-output clones, e.g., Dpp4, Eps8, and Col5a1. Depite lower progeny output Ai variation, LT-HSCs from older mice exhibited greater clonal transcriptome diversification both in vitro and in vivo , evidenced by intra-clonal transcriptomic correlation. This pattern also existed in ST-HSC and MPP from older mice. Genes with higher expression variability in older mice highlighted pathways pivotal for HSPC fitness, e.g., ribosome synthesis (RS), inflammation response mechanisms (JAK-STAT), hematopoietic cell lineage, AML and cancer pathways (GSEA). The RS pathway were remarkably enriched in the megakaryocytic-erythroid progenitors, directly before differentiation where substantial protein translation is required. Conclusion: our results suggest that the synergy of aging and somatic mutations in epigenetic regulators may enhance cell-to-cell variations, offering additional heritable phenotypic variations. These, in turn, may facilitate clonal hematopoiesis and leukemic transformation. Future work will delineate specific epigenetic and transcriptomic configurations for mutant HSPC clonal expansion. This study provides a cohesive framework, linking the principles governing aging to cancer. Citation Format: Lamis Naddaf, Marco De Dominici, Xiaowen Chen, Travis Roeder, Hideyuki Oguro, Shilpita Karmakar, Eric Pietras, James DeGregori, Sheng Li. Accelerated intra-clonal transcriptomic diversification of hematopoietic stem cells during aging fuels leukemia evolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB227.

Abstract 6234: Single-cell analysis of state-transition from health to leukemia and the leukemic cell heterogeneities in inv(16) acute myeloid leukemia (AML)

Abstract AML is an aggressive hematological malignancy with heterogeneous genetic abnormalities. Using a conditional knock-in mouse model (Cbfb56M/+/Mx1-Cre) to mimic the somatic acquisition of fusion gene CBFB-MYH11 (CM), created in the recurrent chromosome translocation inv(16)(p13q22) of AML, we previously reported that the blood transcriptome undergoes state-transition from health to leukemia. In this study, we analyze the transcriptomic alterations and leukemic cell heterogeneities in a leukemia state-space using single-cell RNA sequencing (scRNA-seq). CM expression was induced in Cbfb56M/+/Mx1-Cre mice by poly (I:C) injection, and scRNA-seq analysis was performed on peripheral blood mononuclear cells (PBMC) and bone marrow (BM) cells from leukemic mice and age-matched wild-type (WT) controls. More than 105,000 cells were subjected to the following dimensionality reduction and cell type annotation. By performing principal component analysis (PCA), we observed a Y-shape cell distribution with emergence of a divergent branch occupied by leukemic cells which can be mapped to a leukemic state. The principal components 1 and 2 (PC1 and PC2) clearly distinguish the leukemic cells from normal cell types such as myeloid cells and lymphocytes. By accessing the eigenvalue of genes for PC1 and PC2, we quantified the crucial genes and pathways related to leukemia progression at a single-cell level. We characterized cKit+ leukemic cell clusters by transcriptome-based correlation and gene expression pattern and found that they resembled stem cells and megakaryocytic-erythroid progenitors (MEP) with dysregulated pathways, including upregulated "inflammatory response" and downregulated pathways related to Myc targets, oxidative phosphorylation, mitochondrial protein translation, and ribosomal biogenesis/assembly. Examining the 31 clusters (C0-C30) seen in cKit+ BM cells, we identified 9 leukemic clusters exhibiting distinct features, including high heme-metabolism (C0, C1, and C2), high proliferation (C1, C8), S phase (C4, C10), low oxidative phosphorylation (C2, C5, C17), high Cd9 (C10), high Egfl7 (C7, C8). In conclusion, our study unveils state-transition from health to leukemia at single-cell resolution, and uncovers diverse biological heterogeneities associated with the inv(16) AML state. Further refinement of transcriptome state-transition and single-cell analysis will provide an analytical framework for modeling the dynamic changes during disease evolution at the single-cell level. Citation Format: Yu-Hsuan Fu, Lianjun Zhang, Ying-Chieh Chen, David E. Frankhouser, Lisa Uechi, Denis O'Meally, Sergio Branciamore, Guido Marcucci, Russell Rockne, Ya-Huei Kuo. Single-cell analysis of state-transition from health to leukemia and the leukemic cell heterogeneities in inv(16) acute myeloid leukemia (AML) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6234.

Myelodysplastic neoplasms dissected into indolent, leukaemic and unfavourable subtypes by computational clustering of haematopoietic stem and progenitor cells.

Myelodysplastic neoplasms (MDS) encompass haematological malignancies, which are characterised by dysplasia, ineffective haematopoiesis and the risk of progression towards acute myeloid leukaemia (AML). Myelodysplastic neoplasms are notorious for their heterogeneity: clinical outcomes range from a near-normal life expectancy to leukaemic transformation or premature death due to cytopenia. The Molecular International Prognostic Scoring System made progress in the dissection of MDS by clinical outcomes. To contribute to the risk stratification of MDS by immunophenotypic profiles, this study performed computational clustering of flow cytometry data of CD34+ cells in 67 MDS, 67 AML patients and 49 controls. Our data revealed heterogeneity also within the MDS-derived CD34+ compartment. In MDS, maintenance of lymphoid progenitors and megakaryocytic-erythroid progenitors predicted favourable outcomes, whereas expansion of granulocyte-monocyte progenitors increased the risk of leukaemic transformation. The proliferation of haematopoietic stem cells and common myeloid progenitors with downregulated CD44 expression, suggestive of impaired haematopoietic differentiation, characterised a distinct MDS subtype with a poor overall survival. This exploratory study demonstrates the prognostic value of known and previously unexplored CD34+ populations and suggests the feasibility of dissecting MDS into a more indolent, a leukaemic and another unfavourable subtype.

Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue

Esophageal carcinoma (ESCA) is a leading cause of cancer-related death worldwide, and certain oral and intestinal pathogens have been associated with cancer development and progression. We asked if esophageal microbiomes had shared alterations that could provide novel biomarkers for ESCA risk. We extracted DNA from tumor and non-tumor tissue of 212 patients in the NCI-MD case control study and sequenced the 16S rRNA gene (V3-4), with TCGA ESCA RNA-seq (n = 172) and WGS (n = 123) non-human reads used as validation. We identified four taxa, Campylobacter, Prevotella, Streptococcus, and Fusobacterium as highly enriched in esophageal cancer across all cohorts. Using SparCC, we discovered that Fusobacterium and Prevotella were also co-enriched across all cohorts. We then analyzed immune cell infiltration to determine if these dysbiotic taxa were associated with immune signatures. Using xCell to obtain predicted immune infiltrates, we identified a depletion of megakaryocyte-erythroid progenitor (MEP) cells in tumors with presence of any of the four taxa, along with enrichment of platelets in tumors with Campylobactor or Fusobacterium. Taken together, our results suggest that intratumoral presence of these co-occurring bacterial genera may confer tumor promoting immune alterations that allow disease progression in esophageal cancer.

Vhl deletion in Dmp1-expressing cells alters MEP metabolism and promotes stress erythropoiesis

IntroductionErythropoiesis occurs in a specialized niche in the bone marrow and is regulated in part by oxygen-sensing signaling pathways. VHL is an E3 ubiquitin ligase that regulates the degradation of hypoxia-inducible factor (HIF) proteins under normoxic conditions. In hypoxia, VHL is inactivated resulting in enhancement of HIF signaling. Methods and resultsTo investigate the effects of HIF-activation in bone cells on erythropoiesis, we performed longitudinal analyses of conditional Vhl knockout mice (Dmp1-Cre;Vhlfl/fl; VhlcKO) mice, in which Vhl is deleted primarily in osteocytes but is retained in hematopoietic cells. VhlcKO mice display elevated red blood cell counts and erythropoietin levels starting at 10 weeks of age, resembling polycythemia. Using flow cytometry, we observed increased frequency of CD71loTER119hiFSClo orthochromatophilic erythroblasts and reticulocytes in 10- and 24-week-old VhlcKO bone marrow. Features of extramedullary hematopoiesis were observed in the spleen, including red pulp hyperplasia, the presence of megakaryocytes, and increased frequency of basophilic and polychromatophilic erythroblasts and of mature stress erythroid progenitors. To investigate the mechanisms that drive the accelerated erythropoiesis in the bone marrow, we enumerated myeloid progenitors and observed higher frequencies of megakaryocyte-erythroid progenitors (MEPs) at 6 and 10 weeks of age, but MEP frequency was similar to controls at 24 weeks. Despite this normalization in MEP frequencies, bulk RNA-Seq of MEPs at this age showed upregulation of Epas1 (Hif2a), consistent with a response to hypoxia, as well as genes involved in erythrocyte development. Surprisingly, genes involved in the response to glucose were also upregulated in VhlcKO MEPs. DiscussionOur studies implicate that HIF-driven alterations in skeletal homeostasis drive changes to the bone marrow microenvironment that influence erythroid cell development and MEP metabolism.

Thrombopoietin treats erythropoietin resistance by correcting EPO-induced progenitorcell depletion

Recombinant human erythropoietin (rHuEPO) is a prevalent treatment for anemia in patients with chronic kidney disease. However, up to 10% of these patients exhibit EPO resistance or hyporesponsiveness, which may be caused by the depletion of erythroid progenitor cells. Thrombopoietin (TPO) has the potential to promote the growth of early progenitor cells and correct the depletion. In this study, we investigate the efficacy and the underlying mechanism of the combination therapy of TPO and EPO to EPO resistance. First, the in vivo studies suggested that intensive EPO treatment induced progenitor cell depletion in the bone marrow, where the depletion was corrected by TPO. Then, colony assays showed that EPO and TPO synergistically enhanced the burst-forming unit-erythroid (BFU-E) production but antagonistically boosted the colony-forming units of megakaryocytes (CFU-MK) production. Also, we found TPO promoted hematopoietic stem and progenitor cells (HSPCs) production, while EPO drove HSPCs toward the erythroid lineage. Additionally, EPO induced more megakaryocytic-erythroid progenitors (MEPs) toward the erythroid output. Model-based simulations indicate the efficacy of this combination therapy for treating EPO-resistant anemia in rats. In conclusion, our study demonstrated the efficacy of combination therapy in addressing EPO-resistant anemia by correcting EPO-induced erythroid progenitor depletion.

ROBO1 deficiency impairs HSPC homeostasis and erythropoiesis via CDC42 and predicts poor prognosis in MDS.

Myelodysplastic syndrome (MDS) is a group of clonal hematopoietic neoplasms originating from hematopoietic stem progenitor cells (HSPCs). We previously identified frequent roundabout guidance receptor 1 (ROBO1) mutations in patients with MDS, while the exact role of ROBO1 in hematopoiesis remains poorly delineated. Here, we report that ROBO1 deficiency confers MDS-like disease with anemia and multilineage dysplasia in mice and predicts poor prognosis in patients with MDS. More specifically, Robo1 deficiency impairs HSPC homeostasis and disrupts HSPC pool, especially the reduction of megakaryocyte erythroid progenitors, which causes a blockage in the early stages of erythropoiesis in mice. Mechanistically, transcriptional profiling indicates that Cdc42, a member of the Rho-guanosine triphosphatase family, acts as a downstream target gene for Robo1 in HSPCs. Overexpression of Cdc42 partially restores the self-renewal and erythropoiesis of HSPCs in Robo1-deficient mice. Collectively, our result implicates the essential role of ROBO1 in maintaining HSPC homeostasis and erythropoiesis via CDC42.

DNMT3A Regulates Megakaryocyte-Primed HSC Lineage Fate Decisions

The de novo DNA methyltransferase DNMT3A is important for normal hematopoiesis and hematopoietic stem cell (HSC) differentiation. Mutations in DNMT3A in humans lead to clonal expansion and a higher risk of malignancy development. In mice, ablation of DNMT3A enhances self-renewal and inhibits differentiation. Given that the pool of HSCs is heterogeneous, we considered whether DNMT3A loss preferentially affected particular HSC sub-types and hypothesized a role in megakaryocyte (Mk)-primed HSCs, given their position at the very top of the HSC hierarchy. To examine this, we utilized Dnmt3a+/- mice in which Mk-primed HSCs are labeled with GFP due to an insertion of GFP under the von Willebrand factor (VWF) promoter (Sanjuan-Pla et al. 2013, Nature). This strain also facilitates the tracing of GFP pos megakaryocytes (Mks) and platelets in Dnmt3a+/- mice. We performed competitive transplantation with HSCs that were either GFP pos (Mk-primed) or GFP neg from WT and Dnmt3a+/- mice. The Dnmt3a+/- GFP pos HSCs exhibited significantly lower engraftment than the GFP neg conditions at 6 weeks post-transplant (Fig. A). While Mk-primed HSCs exhibited delayed lymphoid contribution, which was exacerbated in the Dnmt3a+/- condition, lymphoid contribution normalized in all groups by 18 weeks post-transplant. Strikingly, the Dnmt3a+/- GFP pos HSCs displayed significantly higher platelet contribution than all other groups relative to their engraftment without altering total platelet counts. We also performed competitive transplantation with WT or Dnmt3a+/- GFP pos whole bone marrow. Upon secondary transplant, the Dnmt3a+/- cells exhibited significantly higher overall contribution to blood production. Additionally, the Dnmt3a+/- bone marrow displayed a marked myeloid/Mk/platelet bias relative to engraftment (Fig. B), and a significantly higher percentage of the HSC compartment was Mk-primed, although the total progenitor pool was smaller. It is likely that the enhanced number of Mk-primed HSCs in the Dnmt3a+/- secondary transplant condition contributes to increased myeloid/Mk/platelet skewing but that overall engraftment is rescued by the presence of GFP neg HSCs. We next examined whether the differences observed in the HSC vs whole bone marrow transplant models were due to transplant stress or were present in the germline Dnmt3a+/- animals. Although we observed a slight increase in the number of Mks in the bone marrow in the germline Dnmt3a+/- animals, their Mks were the same size as WT. Their Mk ploidy, megakaryocyte-erythroid progenitor (MEP) composition, and %GFP pos HSCs were similar to littermate controls. However, while WT GFP pos HSCs were exceptionally enriched in the portion of HSCs with the highest stemness potential (marked by high Hoechst efflux and high CD150 expression), this enrichment was abrogated in Dnmt3a+/- GFP pos HSCs. Overall, these data indicate that megakaryocyte and platelet production is augmented from Dnmt3a+/- HSCs, likely due to shifts in the composition of the HSC pool, which are exacerbated after transplantation. To determine whether DNMT3A loss affects Mk and platelet function, we cultured bone-marrow-derived Mks and isolated platelets from mouse blood. Dnmt3a+/- Mks formed proplatelets at similar rates to WT. Dnmt3a+/- platelets activated and aggregated in response to agonists, although at the gene and protein expression levels, several coagulation factors and key cytoskeletal components were downregulated. Finally, we subjected WT and Dnmt3a+/- MEPs and Mks to enzymatic DNA methyl-sequencing to examine how genome-wide methylation patterns are altered during the differentiation trajectory in the WT and Dnmt3a+/- contexts. Our findings demonstrate that DNMT3A plays an important role in the lineage fate decisions of Mk-primed HSCs and implicates DNA methylation in Mk differentiation. Our data suggest that platelets generated from DNMT3A-mutant Mks may be over-represented in the blood of individuals with clonal hematopoiesis (CH) relative to apparent clone size. Given the association between CH and increased risk of cardiovascular disease and stroke, the role of DNMT3A-loss in Mk and platelet biogenesis and function warrants further investigation.

Trp53-Loss in Hematopoietic Stem Cells Drives the Evolutionary Process of Leukemic Transformation in a Jak2V617F-Driven Myeloproliferative Neoplasms Mouse Model

Myeloproliferative neoplasms (MPNs) are clonal disorders resulting from genetic lesions in hematopoietic stem cells (HSCs). The development of post-MPN AML is treatment resistant and associated with very poor outcomes. This leukemic transformation is due to TP53 inactivation in approximately 50% of cases. Existing mouse models with double mutant Jak2 V617F and Trp53 have demonstrated that Trp53-lossalone is sufficient to induce leukemic transformation in Jak2 V617F-driven MPN. These models were generated either by crossing Jak2 V617F transgenic mice with Trp53 R172H knock-in or Trp53 knock-out mice, or by retroviral expression of Jak2 V617F in Trp53 knock-out bone morrow (BM) cells. These germline mutated models do not accurately model the sequential somatic Trp53 mutations that arise in Jak2 V617F MPN, or track their clonal expansion in vivo. Here, we used CRISPR-Cas9 to induce Trp53-loss in HSCs of Jak2 V617F mice to generate a novel mouse model of high molecular risk MPN that transforms to AML. We isolated lineage -/low Sca1 +c-Kit + (LSK) cells from BM of donor mice expressing a conditional allele of mutant Jak2 from its endogenous locus ( Jak2 fl-V617F) in combination with an inducible Cas9-IRES-GFP allele and CreER-fusion allele, both from the Rosa26 locus ( Rosa26 CreER/lsl-Cas9-IRES-GFP). LSKs were transduced with lentivirus expressing a sgRNA targeting exon 4 of Trp53 (sgTrp53), located in the DNA-binding domain of Trp53. These transfected sgTrp53 LSKs, along with control groups transduced with either empty vector (EV) or a sgRNA targeting Catsper1 (sgCatsper1, off target cutting control), were transplanted into lethally irradiated recipients. Successful engraftment and CreER activity, induced by a 2-week period of Tamoxifen chow, were confirmed by flow cytometry. Validation of Trp53-editing was performed using amplicon sequencing, revealing the most common mutations were frameshift mutations. A subset of these frameshift mutations exhibited an extremely high frequency, conferring a selective advantage within the cell populations in sgTrp53 mice. We further examined the levels of p53 induced by nutlin-3a (an MDM2 inhibitor) in edited BM cells from three groups of mice and found that Trp53 editing leads to a reduction in p53 levels and prevents the loss of viability in response to MDM2 inhibition. This indicates that CRISPR-Cas9 mediated Trp53 mutations result in a loss of function. SgTrp53 mice recapitulated the evolution of leukemic transformation of MPN, showing a PV phenotype for 8 weeks post CreER activation, characterized by elevated hematocrit but normal leukocytes and platelet counts, consistent with the phenotype exhibited by the EV and sgCatsper1 recipients. Subsequently, after 12 weeks, this MPN phenotype transformed to acute leukemia. This disease progression was associated with significantly shortened survival of sgTrp53 recipients, compared to the sgCatsper1 or EV control groups. Histopathologic analysis further supported these findings, showing leukocytosis and the presence of immature blast cells in the PB, spleen and BM of sgTrp53 mice, whereas such cells were absent in the control groups. Notably, the frequency of blast cells was correlated with the frequency of Trp53 frameshift mutations, consistent with what has been reported in MPN patients. Additionally, CRISPR-Cas9 mediated Trp53-loss primarily affected the erythroid lineage, driving expansion of erythroblasts, megakaryocyte-erythroid progenitors (MEP), and Lineage -/low Sca1 -c-Kit + in sgTrp53 mice. The erythroblasts showed aberrant co-expression of CD41 and CD71. Through secondary transplants with unfractionated spleen cells, whole BM cells, or sorted MEP cell populations, we confirmed that the leukemia driven by CRISPR-cas9 mediated Trp53-loss in the Jak2 V617F-driven PV is transplantable, and that the MEP compartment in leukemic sgTrp53 mice contains the leukemia initiation population. In total, we used CRISPR-Cas9 to induce Trp53-loss in HSCs of Jak2 V617F mice, faithfully replicating the process of clonal expansion and evolution observed in the leukemic transformation of MPN. These mouse models of secondary AML are valuable for testing new therapies targeting disease initiating stem cells. Moreover, our models represent the distinct stages of MPN progression, offering a platform to evaluate preventive and therapeutic interventions at various stages of this disease.

Irf5 Expression in Macrophages Contributes to Iron Regulation within Erythromyeloblastic Islands

Erythroblastic islands (EBIs) classically consist of a central macrophage supporting surrounding erythroid precursors as they develop from CFU-Es to reticulocytes. More recently, it has been shown that, in the bone marrow, these structures also support granulopoiesis, expanding our understanding of the niche, and leading to the concept of erythromyeloblastic islands (EMBI). Under certain inflammatory conditions, there is an imbalance between erythropoiesis and granulopoiesis, eventually leading to anemia and increased neutrophil counts. The central macrophage has been proposed to play a role in regulating this balanced blood production; however, the molecular mechanisms remain unknown. Recently, we demonstrated that mice lacking the transcription factor interferon regulatory factor 5 ( Irf5 -/-) present iron deficiency anemia as they age, along with altered structures in the bone marrow EMBIs. Further, our CITEseq studies showed that Irf5 is specifically expressed by macrophages in the EMBIs. Therefore, we concluded that Irf5 is a regulator of the balance between erythropoiesis and granulopoiesis in the bone marrow erythromyeloblastic niche. To understand the mechanisms leading to iron deficiency anemia, as well as changes in the island, we first undertook a comprehensive analysis of hematopoietic progenitors. We measured the relative amounts of megakaryocytic-erythroid progenitors (MEP), granulocyte-monocyte progenitors (GMP) and common myeloid progenitors (CMP) in the bone marrow and observed decreased MEP (WT: 82.81% vs KO: 76.28%, p-value 0.011), increased GMP (WT: 14.94% vs KO: 22.16%, p-value 0.002) and unchanged CMP compared to wild-type (WT) as the mice aged. Given that Irf5 is expressed in both hematopoietic and non-hematopoietic cells, we generated Irf5fl/fl-Vav-iCre+ mice to evaluate the contribution of non-hematopoietic Irf5 to EMBI formation and composition. We observed a significant reduction in the number of EMBI, with overrepresentation of myeloid cells, suggesting that the phenotype observed in Irf5 -/- is mostly due to hematopoietic Irf5. However, when we measured the relative amounts of MEP and GMP in the Irf5fl/fl-Vav-iCre+ mice, these remained unchanged, suggesting that cell non-autonomous functions contribute to EMBI composition. scRNAseq analyses of EMBIs from 3 and 9 months-old littermate-matched WT and Irf5 -/-mice revealed that heme synthesis was the only downregulated pathway. In addition, central macrophages from Irf5 -/- EMBIs presented decreased expression of major iron regulatory proteins, including heme transporter Slc48a1 and Heme-Oxygenase-1 (HMOX1). Functional analyses using Calcein-AM staining and flow cytometry of freshly isolated central macrophages from enriched EMBIs of WT and Irf5 -/-mice revealed that the labile iron pool (LIP) of the central macrophage of Irf5 -/- EMBIs was significantly reduced (mean 14.0) compared to WT (mean 49.0, p-value 0.004). This apparent decrease in intracellular iron was concomitantly supported by significant decreases in serum iron (WT: 67.27 uM/L vs KO: 39.67 uM/L, p-value: 0.0059), increased serum EPO (WT: 108 pg/dL vs KO: 163.8 pg/dL, p-value: .0075), and Prussian blue staining of Irf5 -/-spleen indicating iron deposition in aging Irf5 -/- mice. Finally, these findings were conserved in Irf5fl/fl-Vav-iCre+ mice, highlighting a cell autonomous function for Irf5 in iron regulation within the island. Together, these data suggest that Irf5 may be a new regulator of iron scavenging, trafficking, and/or utilization within the central macrophage, potentially playing a major role in the red-cell production capacity of the EMBI.

Early Generation Telomerase Deficient Mice to Investigate Clonal Hematopoiesis in Aging

Clonal hematopoiesis is an age-associated condition characterized by the expansion of hematopoietic stem cell (HSC) pools with somatic mutations, observed in 10-30% of individuals older than 70 years. This phenomenon is primarily driven by mutations in transcriptional regulators such as DNMT3A, TET2, and ASXL1. While the clonal expansion of mutated HSCs is ubiquitous with age, it appears largely benign in the absence of strong selective pressures. These benign clones might compensate for the loss of regenerative HSC capacity during aging, and skew differentiation towards the myeloid lineage. Telomere erosion plays a significant role in this process. Telomeres normally prevent the activation of the DNA damage response (DDR) machinery. However, with each cell division, telomeres shorten until they reach a critical length, eventually leading to apoptosis or senescence. Previous studies have suggested a potential involvement of telomere attrition in the development of clonal hematopoiesis (Hinds et al. Blood 2016; Zink et al. Blood 2017). Late generation telomerase deficient (Terc-/- G5) mice develop premature bone marrow failure and mortality, however earlier generation Terc-/- G3 (3 homozygous crosses) have shortened telomeres but appear relatively normal. Importantly, inhibitors of telomerase have recently entered clinical trials for haematological malignancies and therefore understanding the long-term effects of telomerase inhibition is important. By studying the interplay between telomere attrition, HSC aging, and the development of CHIP, we aim to gain insights into the mechanisms underlying age-associated hematopoietic changes and their potential clinical implications. We examined young (age 8-10 week) and aged (10-12 month) Terc-/- G3 mice. Telomere lengths were significantly reduced in bone marrow cells from young Terc G3 (15 kb) when compared to wild-type mice (30 kb) with mild reduction in BM cellularity. Absolute long-term HSC numbers were reduced, as were megakaryocyte erythroid progenitors, but there was preservation of granulocyte macrophage progenitors and common myeloid progenitors. Spleen progenitor numbers were not affected. In comparison, aged (10-12 months old) Terc G3 mice showed enhanced differentiation skewing in the peripheral blood with significantly increased myeloid (n = 8 wt; n = 12 Terc ko; p = 0.0004) and concomitantly reduced B cell (p = 0.0002) and T cell (p = 0.0320) populations. There was marked mobilization of bone marrow progenitors to the spleen, most notably GMP (p = 0.0004) but also MEP and CMP in aged Terc G3. Furthermore, aged Terc G3 ko now exhibited marked reduction in bone marrow CMP (p < 0.0001) and MEP (p < 0.0001), but skewing towards GMP (p<0.001) resulting in normal total GMP numbers, but markedly reduced CMP and MEP numbers (p < 0.0001). Compared to young Terc G3 mice, the aged Terc G3 mice had relative expansion of the BM LT-HSC population, and therefore normal numbers of BM LT-HSC compared to aged matched controls. Aged Terc G3 BM LTHSC have been isolated for gene expression and clonality analysis. Together, these findings are consistent with accelerated aging in G3 Terc-/- mice, providing a model for examining clonal hematopoiesis. In order to assess the cell intrinsic function of Terc G3 LTHSC, we next performed non-competitive bone marrow transplantation experiments from Terc ko or wild-type donors into lethally irradiated young wild-type recipients (n = 9 per group), and analysed these at 4 months post-transplant. There was reduced, but stable reconstitution by Terc G3 cells, consistent with previous competitive bone marrow transplants in Terc G3 (Bruedigam et al. Cell Stem Cell 2014). We observed a similar reduction in bone marrow cellularity in Terc ko transplanted recipients (p = 0.003). Lineage skewing was less pronounced but CMP percentages were significantly reduced in Terc ko compared to wild-type conditions (p = 0.03). In contrast to primary mice, mobilization of progenitors to the spleen was not observed, suggesting that this finding was ameliorated by normal bone marrow and splenic supporting cells. The aged G3 Terc ko model faithfully recapitulates the haematopoietic phenotype of aging in humans and we propose to utilise this model to further our understanding of the mechanisms and physiological consequences of clonal hematopoiesis, to eventually help identify strategies to mitigate its clinical consequences.

High Mobility Group A1 Chromatin Regulators Drive Regenerative Capacity during Stress Hematopoiesis through Modulation of TNF-α and Aging Transcriptional Networks

Introduction: Chromatin structure and epigenetic modifications are key determinants of regenerative function and cell fate decisions, although mechanisms governing these properties in hematopoiesis are only beginning to emerge. The High Mobility Group A1 ( HMGA1) chromatin regulator gene is induced by growth factors and highly expressed during embryogenesis and in hematopoietic stem cells (HSCs), but silenced in differentiated tissues ( Cancer Res 2018,78:1890). In leukemia and solid tumors, HMGA1 is re-expressed where it activates enhancers that induce stem cell transcriptional networks, leading to aberrant proliferation and differentiation ( Blood 2022,139:2797; JCI 2023 133:e151601). HMGA1 also drives self-renewal by amplifying Wnt networks in intestinal stem cells ( Nature Comm 2017,8:15008). However, its role in normal hematopoiesis is unknown. We therefore sought to: 1) Define HMGA1 function in HSC, and, 2) Test the hypothesis that modulating HMGA1 epigenetic networks enhances regenerative function. Methods: First, we compared HMGA1 expression across hematopoietic stem and progenitor cells (HSPC) and differentiated progeny in humans and mice. Next, we generated mice with global Hmga1 knock-out ( Hmga1-KO) or Hmga1 deficiency confined to HSC (vav- Hmga1-KO) to assess HSPC function in clonogenic assays, competitive bone marrow transplantation (cBMT), and following irradiation. To elucidate underlying mechanisms, we performed single cell RNA sequencing (scRNAseq) of bone marrow (BM)-derived Lin -, Sca +, c-kit + (LSK) cells followed by pathway analysis. To assess HMGA1 function in human CD34 + cells, we used CRISPR to inactivate HMGA1. Results: HMGA1 is expressed in HSC, multipotent progenitors (MPP), and megakaryocyte-erythroid progenitors (MEP), with decreasing levels after differentiation, suggesting that HMGA1 functions in stem and progenitors. However, steady state hematopoiesis is unperturbed in both Hmga1-KO and vav- Hmga1-KO mice up to 18 months. By contrast, HSPC lacking Hmga1 show decreases in total colony forming units (CFU), but only after serial replating, suggesting that Hmga1 deficiency impairs long-term HSC (LT-HSC) regenerative function. Accordingly, in cBMT assays, Hmga1-KO HSC are outcompeted by HSC with both Hmga1 alleles, with most pronounced effects after serial transplantation. Serial cBMT from young donors (6 weeks) show decreases in LT-HSC, short-term HSC (ST-HSC), and progenitors from Hmga1 KO HSPC compared to control HSPC. Results were similar with older donors (4 months, 18 months). Following irradiation, vav- Hmga1-KO mice have impaired platelet recovery, although the frequency of HSPC in bone marrow were similar to controls. HSPC function in clonogenic assays is also impaired after irradiation, as evidenced by decreases in total CFU, GM-CFU and megakaryocyte (Mk)-CFU. To determine how HMGA1 modulates cell state, we compared scRNAseq in BM-derived LSK cells from adult mice (4 months old) with intact Hmga1 to those with Hmga1-KO. The transcriptomes in HSPC lacking Hmga1 were distinct from those with both Hmga1 alleles intact. The Hmga1 KO HSPC show a decrease in quiescent HSC (marked by high Procr expression), with a relative expansion in more proliferative HSC and early progenitors. In human CD34 + cells, CRISPR-mediated HMGA1 inactivation decreases total CFU, GM-CFU, and Mk-CFU. To elucidate underlying mechanisms, we applied gene set enrichment analyses to scRNAseq results which revealed that Hmga1 activates TNF-a signaling via NF-κB, a pathway that maintains HSC survival and regeneration following inflammatory stress. Hmga1 also represses aging-related transcriptional networks. Further, TNFa partially rescues HSC with Hmga1 deficiency in serial clonogenicity assays. Conclusions: HMGA1 deficiency impairs HSC regenerative capacity under conditions of stress hematopoiesis by depleting quiescent HSC. Mechanistically, HMGA1 induces transcriptional networks involved in survival signals, including TNFa -NF-κB networks, while repressing transcriptional networks activated with aging. Further, TNF-apartially rescues regenerative capacity in clonogenicity assays. Our findings highlight HMGA1 as a critical factor in stress hematopoiesis and suggest that modifying its function could enhance regenerative capacity and repress aging pathways following BMT or irradiation.

Mesenchymal Stromal Cells from Individuals with DNMT3A mut Clonal Hematopoiesis Instruct Young Healthy Hematopoietic Stem/Progenitor Cells Towards a Myeloid-Biased Aging Phenotype Resembling That of Patients with Clonal Cytopenia of Undetermined Significance (CCUS)

Clonal hematopoiesis of indeterminate potential (CHIP) describes the age-related acquisition of somatic mutations in hematopoietic stem/progenitor cells (HSPC) leading to clonal blood cell expansion and variable risk of progression to myeloid malignancy. DNMT3A is the most commonly mutated gene and while single mutations do not raise the likelihood of progression, high variant allele frequencies (VAF) and presence of co-mutations do. In myeloid diseases, the bone marrow (BM) microenvironment exhibits alterations promoting malignant transformation. However, it is unknown whether similar alterations exist in the pre-malignant niche. We set out to analyze whether human mesenchymal stromal cells (MSC) from CHIP individuals with a DNMT3A mutation ( DNMT3A mut) are altered and whether they are able to remodel the HSPC compartment in healthy hematopoiesis. From our published cohort of previously sequenced BM samples from hematologically healthy individuals undergoing hip replacement surgery, we selected samples with either an isolated DNMT3A mut at a low VAF (2.47-6.8%, n=4, median age 73.5y, termed low-risk CHIP), or DNMT3A mut samples with a high VAF (17.5-28.5%) and at least one co-mutation (n=5, median age 73y, termed high-risk CHIP) as well as 12 age-matched samples without any mutation (n=12, median age 72y). HSPC were isolated from 3 younger healthy donors (median age 50y). MSC were expanded by plastic adherence and subjected to multilevel characterization. Compared to age-matched healthy controls, MSC from DNMT3A mut BM samples (CHIP-MSC) exhibited higher proliferation rates, lower colony-forming-unit (CFU) fibroblast capacity, as well as reduced adipogenic and increased osteogenic differentiation potential. To understand how altered CHIP-MSC influence the hematopoietic compartment, younger healthy CD34+ HSPC were co-cultured with the different MSC subgroups for 42 hours in a low cytokine-containing medium, followed by bulk RNAseq on subsequently sorted cell populations (MSC: CD45-/CD90+; HSPC: CD45+/CD34+). We found 31 differentially expressed genes (DEG) (logFC±0.5, FDR<0.05) in CHIP-MSC compared to their age-matched counterparts. Functional analyses suggested an activation of communication towards HSPC via extracellular vesicles. Strikingly, differential gene expression of sorted young healthy HSPC after co-culture revealed 375 DEG (322 up-regulated, 53 down-regulated; logFC±0.5, FDR<0.05) in HSPC cultured with CHIP compared to non-CHIP age-matched MSC (Figure panel A). We then used gene set variation analysis (GSVA) to analyze HSPC compartment composition after co-culture. Based on enrichment scores, unsupervised clustering identified two distinctive profiles that correlated with HSPC cultured with either non-CHIP or high-risk CHIP-MSC, while those cultured with low-risk CHIP-MSC showed an intermediate phenotype (Figure panel B). Co-culture of HSPC with high-risk CHIP-MSC resulted in enrichment of hematopoietic stem cells (HSC) and multipotent progenitors (MPP), as well as myeloid skewing represented by higher scores for common-myeloid (CMP) and granulocyte-monocyte (GMP) progenitors. Conversely, in contrast to the control group, megakaryocyte-erythroid progenitors (MEP) were underrepresented. CFU capacity was increased in healthy HSPC cultured with CHIP-MSC and multiparameter flow cytometry analysis showed a trend towards increased CMP/GMP and decreased MEP numbers, consistent with the RNAseq data. Finally, we evaluated the BM HSPC compartment composition of a cohort of 49 CCUS patients with DNMT3A mut (VAF 1-49%, median age 76y) compared to 56 control BM samples using whole transcriptome sequencing data. Intriguingly, we observed the same profile with a myeloid shift in progenitor populations as in our healthy young HSPC exposed to high-risk CHIP-MSC. Taken together, our results indicate that MSC from individuals harboring a DNMT3Amutation are able to instruct young healthy HSPC and influence their fate, thereby promoting a differentiation bias that shifts the hematopoietic compartment toward that associated with an aged pre-malignant state, even in the absence of DNMT3A mut HSPC. These findings suggest that focusing on the interaction between MSC and HSPC is a promising therapeutic strategy to intercept disease progression. Functional analysis of identified deregulated pathways in DNMT3Amut CHIP is ongoing.

Cellular and Molecular Analysis of Hematopoietic Stem and Progenitor Cells in Shwachman-Diamond Syndrome

Shwachman-Diamond syndrome (SDS) is an inherited multi-organ disorder with bone marrow failure (BMF), which may include neutropenia, anemia, and thrombocytopenia, as well as a high risk of myelodysplasia and leukemia. Hematological complications are common causes of morbidity and mortality in SDS. Around 90% of SDS patients have biallelic mutations in the Shwachman-Bodian-Diamond Syndrome ( SBDS) gene, which plays an important role in ribosome biogenesis and hematopoietic cell survival. In a collaborative study led by Dr. John Dick (Science 2016) novel hematopoietic progenitor subsets were identified (noted as F1, F2 and F3), of which the abundance, clonal capacity, and function in disease states remain unknown. We hypothesized that cellular and molecular analysis of hematopoietic stem and progenitor cells (HSPC) including these novel progenitors would provide valuable insights into the pathogenesis of BMF in SDS. Using multiparametric flow cytometry we quantified the following HSPC populations: hematopoietic stem cells (HSC), multipotent progenitors (MPP F1-F3), common myeloid progenitors (CMP F1-F3), megakaryocyte-erythroid progenitors (MEP F1-F3) and granulocyte-monocyte progenitor (GMP) in 13 SDS patients with SBDS mutations and 10 normal control donors. We found a significant reduction in CD34+/CD38- and CD34+/CD38+ cells in SDS patients. It is particularly noteworthy that the sub-populations of CMPs (F1 and F2), and MEPs (F2 and F3) were prominently decreased. These cells contribute to the production of myeloid, erythroid, and megakaryocytic cells with different proportions. Using single-cell colony-forming assays, we assessed the cloning efficiency of each HSPC, revealing that HSCs, MPPs and GMPs from SDS patients exhibited a significantly lower cloning efficiency compared to those from control subjects. Notably, the typical erythroid-committing progenitor cells (CMP F2, CMP F3, MEP F2, and MEP F3) in SDS collectively produced approximately 46% fewer erythroid cells per colony compared to control progenitors, while myeloid-committing progenitor cells (CMP F1, MEP F1) from these patients produced approximately 86% fewer myeloid cells, including neutrophils, per colony compared to the corresponding control cells. Further, HSCs and MPPs-F1 cells from SDS patients had a reduced cloning efficiency of approximately 22% and 27%, respectively, compared to control HSCs and MPP-F1 progenitors. These data suggest that multiple HSPC populations from SDS patients are characterized by reduced cell numbers, functional impairments, and dysregulation compared to normal subjects. Next, we performed transcriptome analysis of each HSPC by RNA sequencing. We revealed dysregulated pathways and genes with the potential to disrupt hematopoiesis and mediate BMF in SDS. Using KEGG pathway analysis, we found that downregulation of the ribosome pathway reached statistical significance in HSC, CMP F1 and MEP F3. Downregulation of the hematopoietic cell lineage pathway reached statistical significance in MEP F1-2 and MPP F1-2. Additionally, the TGF-beta signaling pathway was suppressed in CMP F1-3, MPP F1, and GMP, while the NF-kappa B signaling pathway, crucial for regulating the survival, activation and differentiation of innate immune cells and inflammatory T cells, was also found to be decreased in GMP. Interrogation of specific dysregulate genes, we found that the hematopoietic transcription factor, ZFP36 (ZFP36 ring finger protein) which involved in cellular response to cytokines and growth factors, was significantly downregulated in five subpopulations of SDS HSPCs, particularly noticeable in the four progenitors (CMP F1-3, MEP F2, and GMP) which produced substantially fewer colonies in SDS patients compared to controls. Additionally, we observed downregulation of TGFB2 and upregulation of NFKBIA and NFKBIB may inhibit the NF-kappa B signaling pathway in SDS patients. These alterations have the potential to influence the hematopoietic cell lineage pathway, leading to BMF. Functional assays are ongoing and aim to assess the impact of these dysregulated genes on formation and behavior of HSPCs. In summary, our data suggest that multiple SDS HSPC populations are characterized by reduced cell numbers and functional impairments. As well, we revealed dysregulated pathways and genes with the potential to disrupt hematopoiesis and mediate BMF in SDS.

TL-895, a Highly Selective, Covalent Inhibitor of Bruton's Tyrosine Kinase (BTK), Sensitizes Myeloproliferative Neoplasm (MPN)-Blast Phase Stem Cells to Navtemadlin By Targeting Intrinsic Dysregulated MDM2/p53 and NF-Κb Pathways and Disrupting the Protective Tumor Microenvironment (TME)

We recently reported that navtemadlin (nvtm), a potent, orally available, selective inhibitor of MDM2 (MDM2i), can deplete/eliminate TP53WT MPN-blast phase (BP) stem cells (SC) in an MPN-BP patient (pt)-derived xenograft (PDX) model (Wang EHA 2023). Single agent nvtm has demonstrated significant clinical activity in pts with advanced myelofibrosis (MF) (Vachhani EHA 2023, Verstovsek Future Oncology 2022). We hypothesized that effects of nvtm on MPN-BP, which is characterized by multiple SC subclones, could be enhanced by combination with agents that target additional MPN-BP SC vulnerabilities, such as hyperactivation of p65 subunit of NF-κB (Fisher Leukemia 2017; our unpublished data) and dependence on TME support. BTK and bone marrow (BM) kinase X-linked (BMX) are key Tec family members expressed in cells of myeloid origin. Here, we show BTK is constitutively activated in MPN-BP SC subpopulations relative to normal donor (ND) hematopoietic SCs (HSC) and progenitors [phospho (p)-BTK Y233 mean fluorescence intensity fold change (FC)]: CD34 +CD38 - cells: 1.34±0.18, HSC/multipotent progenitor (MPP): 1.50±0.23, multi-lymphoid progenitor (MLP): 1.59±0.59, megakaryocyte-erythroid progenitor (MEP): 1.56±0.49; p <0.05]. TL-895 is a highly selective, potent, orally available, second-generation covalent inhibitor of BTK and BMX, currently under clinical evaluation for treatment of pts with CLL (NCT02825836) and MF (NCT04655118). We used multi-modal single-cell analysis to study mechanistic effects of combination TL-895 + nvtm on dysregulated intracellular signaling pathways in primary MPN-BP SC, and investigated the combination in a PDX model of MPN-BP. In vitro treatment with TL-895 alone (100 nM-5 µM) did not affect growth of ND CD34 + cells [FC (TL-895 vs. vehicle, veh): 2.5 µM: 1.27±0.11, 5 µM: 0.97±0.14, n=3)] but modestly decreased growth of primary TP53WT MPN-BP CD34 + cells, in a dose dependent fashion [FC (TL-895 vs. veh): 2.5 µM: 0.88±0.11, 5 µM: 0.62±0.12, n=4. p<0.05). Addition of TL-895 (5 µM) to nvtm (400 nM) resulted in much greater reductions in MPN-BP CD34 + and CD34 +CD38 - cell numbers, along with increased apoptosis (n=6, p<0.05, TL-895 + nvtm vs. veh, TL-895, or nvtm alone). By contrast, at these doses, combination TL-895 + nvtm did not affect ND HSC subpopulations (n=3). We previously demonstrated that, multiple MPN-BP SC subclones contribute to the development of MPN-BP irrespective of clone size, and minor subclones may be responsible for clonal evolution and disease progression in most cases (Wang JCI insight 2022). Strikingly, single cell mutational profiling and epitope analysis of primary MPN-BP CD34 + cells treated with TL-895 + nvtm showed depletion of all 8 distinct MPN-BP SC subclones with differing variant allele frequencies, each containing 2-3 oncogenic mutations in WT1, ETV6 and/or KRAS. Combination TL-895 + nvtm treatment depleted 7 of 8 subclones to a greater degree than either agent alone (Fig. 1). Bulk RNA-seq and gene set enrichment analysis showed that combination TL-895 + nvtm synergistically upregulated p53 pathway gene transcription ( CDKN1 HDM2, DDB2, BTG2, GADD45A, FAS, FUCA1, S100A10, ATF3) in primary MPN-BP CD34 + cells. Mass cytometry analysis and intracellular flow cytometry of MPN-BP CD34 + cells treated with combination TL-895 + nvtm further revealed significant (p<0.05) upregulation of p53 and BAX proteins and decreases in the anti-apoptotic factors BCL-xL and activated NF-κB (p-p65), as well as significant reductions in DNA synthesis and protein markers associated with glycolysis (p-AMPK, MCT1). Downregulation of NF-κB activation might result from decreases in the upstream modulators p-S6 and p-4EBP1 (p<0.05, TL-895 + nvtm vs. veh). Treatment in vivo withTL-895 promoted dose-dependent egress of hCD45 +CD34 + cells from BM into the spleen and peripheral blood (PB) of MPN-BP PDX mice (Fig. 2). Furthermore, a limited course of combination TL-895 + nvtm treatment for 3 cycles led to clearance of hCD45 +CD34 + cells from the BM, spleen and PB of MPN-BP PDX mice (Fig. 2); neither treatment had this effect when administered alone. Our results indicate that BTKi therapy might increase susceptibility of MPN-BP SC to MDM2i therapy, by upregulating p53 activity and dampening NF-κB signaling, and also by disrupting protective TME interactions that sustain MPN-BP SC. This novel combination merits further clinical investigation in advanced phase MPN.

Single-Cell RNA-Seq Reveals Intermediate Cell States and Identifies Features Defining Cellular Heterogeneity in Inv(16) Acute Myeloid Leukemia (AML)

AML is an aggressive hematological malignancy with heterogeneous genetic abnormalities. One recurrent chromosomal translocation common in AML is chromosome 16 inversion, inv(16)(p13.1q22), which results in the leukemogenic fusion gene CBFB- MYH11. Using a conditional Cbfb-MYH11 (CM) knock-in mouse model to mimic the somatic expression of the CM fusion gene, we demonstrated that CM expression leads to impaired hematopoietic differentiation as well as accumulation of phenotypic hematopoietic stem cells (HSC) and pre-megakaryocyte/erythrocyte (Pre-Meg/E) progenitors, which are predisposed to leukemic transformation. Flow cytometry-based phenotypic analysis revealed that the transformed leukemic blasts are predominantly characterized as pre-granulocyte-macrophage progenitor (pre-GM) (Lin −cKit +Sca1 −CD16/32 -/loCD150 −CD105 −). However, cell type characterization via conventional surface markers is limited by known cell markers and is incapable of resolving pathologic heterogeneities. We previously reported that modeling AML in a continuum of differentiation states using single-cell RNA-seq (scRNA-seq) data predicts intermediate states of differentiation in AML. Herein, we utilized scRNA-seq to characterize CM leukemic blasts, and identified transcriptomic alternations and features that defined the leukemic cell states and heterogeneities. CM expression was induced by poly (I:C) and mice (n=3) were monitored for leukemia progression. At the leukemic end-stage (detection of >50% of circulating cKit + cells), we collected unfractionated and ckit + sorted peripheral blood mononuclear cells (PBMC) and bone marrow (BM) cells. Similarly poly(I:C)More than 105,000 cells harvested from the WT and CM leukemic mice were analyzed by scRNA-seq. We applied uniform manifold approximation and projection (UMAP) for dimensionality reduction and performed cell type annotation by SingleR. First, we mapped mature hematopoietic cell types in the WT PB and hematopoietic stem/progenitor cell populations (HSPC) in the WT BM, and in contrast, leukemic PB and BM were highly similar and showed distinct cell clusters compared to WT. To characterize HSPC subpopulations, we focused on cKit+ sorted WT and leukemic BM cells, visualized them via UMAP, and performed clustering and cell type annotation. The leukemic cKit+ cells were mostly identified as megakaryocytic-erythroid progenitor (MEP)-like HSC, revealing a discrepancy between flow cytometry-based phenotypic characterization and transcriptome-based cell type assignment. These leukemic MEP-like HSCs showed up-regulation of erythroid differentiation genes, including Hba-a1, Hba-a2, Hbb-bs, Hbb-bt and Sox6, together with decreased expression of granulocytic markers such as Elane, Prtn3, S100a8, S100a9 and Mpo. Comparison of leukemic MEP-like HSCs vs WT MEP clusters via gene set enrichment analysis (GSEA) with a threshold of nominal p-value ≤ 0.05 and FDR ≤ 0.05 in 50 hallmark gene sets (MSigDB) indicated dysregulated pathways, including up-regulation of “TNFα signaling pathway via NFκB”, “inflammatory response”, and “UV responsive downregulated genes”; and down-regulation of “MYC target V1”, “MYC target V2”, “E2F targets”, “G2M checkpoint”, and “oxidative phosphorylation”. Similarly, GSEA in Gene Ontology (GO) showed downregulation of pathways relevant to mitochondrial protein translation and ribosomal biogenesis/assembly in leukemic MEP-like HSCs, compared to WT MEP. In addition, cKit+ BM cells can be separated into 31 clusters (C0-C30), of which 9 leukemic clusters were identified. Through gene expression-based cell cycle scoring, single sample gene set enrichment (ssGSEA), and marker identification, these 9 leukemic clusters can be defined by several features, including high heme-metabolism (C0, C1, and C2), high proliferation (C1, C8), S phase (C4, C10), low oxidative phosphorylation (C2, C5, C17), high Cd9 (C10), high Egfl7 (C7, C8). Altogether, these data reveal intermediate differentiation cell states in inv(16) leukemic cells which are highly heterogeneous populations with distinct cell cycle stages, metabolic activities, and marker expression.

PDZD2 Is Required for Normal Erythropoiesis and Its 37-KDa Secreted Product, sPDZD2, Functions As a Soluble Tumor Suppressor in AML

PDZ domain-containing protein 2 (PDZD2) is expressed in normal hematopoietic stem and progenitor cells (HSPC), specifically HSC, MPP, and erythroid progenitors, however, it is almost universally lost through hypermethylation in acute myeloid leukemia (AML). PDZD2 encodes for a 300-kDa protein containing 6 PDZ domains. The full-length protein is cleaved in the cytoplasm in a caspase 3-dependent manner, and the C-terminal fragment containing PDZ domains 5 and 6 is secreted to the tissue microenvironment as a 37-kDa protein known as secreted PDZD2 (sPDZD2). sPDZD2 has been reported to function as a tumor suppressor in some solid tumors, including breast, prostate, and liver cancer. Thus, we hypothesized that PDZD2 is required for normal hematopoiesis and that sPDZD2 functions as a soluble tumor suppressor in the hematopoietic system. We first sought to determine if sPDZD2 is secreted to the bone marrow (BM) microenvironment. Using an ELISA to quantify sPDZD2 levels in BM plasma isolated from healthy donors (n=6) and primary AMLs (n=20), we confirmed its secretion by normal CD34+ HSPCs (NBM) and downregulation in AMLs (NBM: 169 ± 17.53 vs AML: 46.12 ± 6.70 ng/ml; p<0.0001). In addition, AML cell lines (n=7) secreted significantly lower levels of sPDZD2 into the culture medium than normal HSPCs (n=2) (NBM: 28.71 ± 1.76 vs AML: 4.62 ± 1.19 ng/mL; p<0.0001). Next, to study the role of PDZD2 in normal hematopoiesis we performed in vitro myeloid and erythroid differentiation and colony-forming unit assays in CRISPR-Cas9-edited human HSPCs. CD34+ cells from healthy donors were electroporated with recombinant Cas9-sgRNA ribonucleoprotein complexes targeting PDZD2 and editing confirmed by T7I endonuclease assay and Sanger sequencing. PDZD2-edited cells (PDZD2 KO) were plated either on methylcellulose or liquid differentiation cultures (n=6). PDZD2 KO resulted in decreased colony number of all types (Control: 172.5 ± 34.37 vs PDZD2 KO: 137.0 ± 18.25, p<0.05), indicating reduced colony-forming potential. In addition, loss of PDZD2 resulted in a delay in terminal erythroid differentiation with an accumulation of pro-erythroblasts (CD71+CD235a lowCD105 high, p<0.05) and late basophilic erythroblasts (CD71+CD235a highCD105 int, p<0.01) as well as decreased orthochromatic erythroblasts (CD71+CD235a highCD105 neg, p<0.01) in a tri-phasic liquid culture system. By contrast, PDZD2 KO had no impact on myeloid differentiation. To determine the role of Pdzd2 in vivo, we took advantage of a Pdzd2 Gt/Gt gene-trap (GT) mouse model and performed peripheral blood (PB) and BM analysis compared to wild-type (WT) controls. PB counts at 2 months of age (n=6-9 per genotype) showed anemia, with a significant decrease in both red blood cell counts (WT: 9.04 ± 0.26 vs GT: 7.58 ± 0.47 x10 6/mL; p=0.026) and hemoglobin levels (WT: 14.88 ± 0.46 vs GT: 12.30 ± 0.81 g/dL; p=0.036), an observation compatible with the impaired erythropoiesis seen in vitro after PDZD2 KO in human HSPCs. In addition, we observed a trend to decrease megakaryocyte-erythroid progenitors (MEPs) and short-term HSCs in the BM of 3 months-old mice (n=3), though the small size of the cohort prevented robust statistical analysis. Next, we sought to evaluate the tumor suppressor role of sPDZD2 in the context of AML. We treated a panel of AML cell lines (n=9) and primary human AML specimens (n=4) with recombinant sPDZD2 ( r-sPDZD2; dose: 100nM-300nM/day) for a period of 8 days. AML cells showed dose-dependent growth inhibition (CellTiter-Glo, p<0.05 for all) and increased expression of either CD11b or CD15 differentiation markers. Cell cycle analysis on day 8 revealed that AML cells treated with r-sPDZD2 were arrested at G0/G1 phase compared to control. In summary, our study is the first to shed light on a previously unrecognized role for PDZD2 in hematopoiesis. Loss of PDZD2 in HSPC resulted in impaired erythroid differentiation both in vitro and in vivo. Moreover, our findings validate a soluble tumor suppressor role for sPDZD2 in AML, similar to that seen in solid tumors. Importantly, we further demonstrate a potential role for r-sPDZD2 as a novel therapeutic approach for AML.

Targeting Venetoclax Resistance in TP53-Mutated Acute Myeloid Leukemia

Introduction: The combination therapy of Venetoclax (Ven) and Azacitidine (Aza) has shown remarkable improvements in the treatment of acute myeloid leukemia (AML) patients not eligible for chemotherapy. Nevertheless, patients with TP53-mutated AML are more prone to have a refractory disease or develop rapid resistance. A recent study indicated that a combined expression ratio of BCL-2, BCL-XL and MCL-1 proteins in leukemic stem cells predicts clinical response to Ven+Aza (Waclawiczek et al. 2023). Furthermore, our previous work has demonstrated that erythroid and megakaryoblastic leukemia blasts are more dependent on BCL-XL than BCL-2 (Kuusanmäki et al. 2023). Emerging evidence suggests that the erythroid-biased differentiation and gene signature is enhanced in many TP53-mutated patients (Rodriquez-Meira et al. 2022). Here we hypothesized that in TP53 -mutated AML, leukemic blasts correspond more closely to megakaryocyte-erythroid progenitors (MEPs) leading to an unfavorable BCL-2 family expression ratio, which can be associated with poor responses to Ven. Consequently, we aimed to identify novel compounds targeting this specific patient subgroup. Methods: We utilized flow cytometry to analyze the mean fluorescent intensity (MFI) of BCL-2 family proteins (BCL-2, BCL-XL, MCL-1) in the CD34+ blast cells of 16 bone marrow-derived AML samples taken before Ven+Aza therapy ( TP53mut n=8, TP53wt n=8). Ex vivo drug testing was performed with eight compounds and blast-specific drug responses were analyzed after 48 hours with flow cytometry. RNA sequencing was performed on CD34+ or CD117+ cells enriched from 35 pre-Ven+Aza treatment samples. To assess erythroid signature scores, we calculated the mean expression of six different erythroid genes ( GATA1, KLF1, ZFPM1, GATA2, GYPA, TFRC) for each patient, following the approach by Rodriquez-Meira et al. 2022. The expression levels of 19 intracellular proteins, including BCL-2, BCL-XL, MCL-1, were quantified from the corresponding cell population of the samples by mass cytometry (CyTOF). Results: In the comparison of BCL-2 family protein expression and treatment responses, BCL-XL levels were significantly higher (p=0.03) in the treatment-resistant group, while no differences were found in BCL-2 or MCL-1 ( Figure 1A). In the TP53-mutated blasts, a trend of decreased BCL-2 was identified compared to the TP53 wild-typeblasts (p=0.08), but no difference in BCL-XL or MCL-1 levels was noted. However, all three Ven+Aza-refractory TP53-mutants exhibited high BCL-XL expression compared to the treatment-responsive TP53-mutated patients. Next, we assessed whether an erythroid-like phenotype was associated with TP53 mutation status by computing the erythroid gene signature scores from the RNAseq data of enriched blasts. Erythroid scores were increased among TP53-mutated samples (p=0.04), and interestingly, a higher erythroid score was linked to lower BCL-2 protein expression, regardless of TP53 mutation status ( Figure 1B). Finally, we assessed the drug efficacy of eight pre-selected compounds, including BCL-2 family inhibitors. As expected, Ven was ineffective in the TP53-mutated samples. In contrast, the TP53-mutated blasts showed higher ex vivo sensitivity to Navitoclax (BCL-2/BCL-XL inhibitor) (Nav IC50=90nM, Ven IC50>1000nM). Additionally, LCL-161 (IAPs inhibitor) demonstrated notable efficacy in the TP53-mutants and was significantly more effective compared to the wild-type controls (LCL-161 IC50=300nM, Ven IC50>1000nM). Discussion: Here, we show that increased BCL-XL protein expression is associated with clinical resistance to Ven+Aza. Furthermore, the link between erythroid gene signature and BCL-2 expression suggests that especially those AML blasts harboring TP53 mutations might have impaired BCL-2 expression due to a closer resemblance to MEPs. The increased sensitivity of TP53-mutated AML cells to LCL-161 demonstrated in the study, highlights the potential of targeting extrinsic apoptosis pathway via inhibiting the inhibitors of apoptosis proteins (IAPs). Furthermore, co-targeting of BCL-2/BCL-XL might provide alternative therapeutic approach in Ven resistant TP53-mutated patients. These findings are currently being validated with a larger patient cohort.

Clinical and Hematopoietic Profiles Associated with Sustained Hydroxyurea Response for Patients with Sickle Cell Disease

Background: Hydroxyurea improves the lives of patients with sickle cell disease (SCD) by inducing expression of fetal hemoglobin (HbF). Higher HbF levels are associated with improved clinical outcomes. However, there is significant heterogeneity in long-term response to the drug. The impact of quantitative changes in hematopoietic stem and progenitor cells (HSPCs) during hydroxyurea treatment remains poorly characterized. Objectives: (1) Determine the prevalence and clinical impact of declining hydroxyurea response in pediatric patients with SCD; and (2) Characterize HSPC profiles associated with hydroxyurea response. Methods: We conducted a retrospective review of longitudinal clinical data from 760 pediatric patients with SCD seen at Texas Children's Hematology Center between 2010-2021. We selected patients consistently on hydroxyurea for >5 years for this study. We classified each subject according to their individual HbF response to hydroxyurea into: 1) Sustained-Response if the patient maintained an absolute HbF level >20% or 2) Decreased-Response if a patient's HbF levels decreased to <10% over time despite medication compliance. We obtained clinical and laboratory hydroxyurea treatment information for each individual. We isolated peripheral blood mononuclear cells (PBMCs) from whole blood collected from these patients during outpatient appointments. Patients were on a stable hydroxyurea dose without recent blood transfusions prior to collection. Flow cytometry was used to quantify the frequencies of ten HSPC populations in the PBMC samples. Results: In total, 208 children with HbSS or HbSβ 0-Thalassemia were included in our analysis: 148 individuals (71%) had a Sustained Response and 60 (29%) experienced a Decreased Response to hydroxyurea. Subjects with a Decreased Response had a median initial hydroxyurea induced HbF of 23.9% that decreased to 9.8% over time compared to stable values of HbF >20% in the HU-Sustained Response group (p<0.001). These differences were consistent after adjusting for age ( Figure 1). We found that patients who developed a Decreased Response to hydroxyurea experienced a significantly higher incidence of clinical complications, including number of visits to the emergency department (153.3 vs. 120.3 events per 100 patient-years), number of transfusions (37.4 vs. 11.9), and SCD-related hospitalizations (57.7 vs. 42.0). The causes of SCD-related hospitalizations included vaso-occlusive events requiring admission (27.7 vs 21.1 events per 100 patient-years), acute chest syndrome (13 vs 9.9), splenic sequestration (6.4 vs 3.5), and surgical procedures (7.47 vs 3.02). We also profiled HSPCs by flow cytometry using PBMCs collected from a subset of 40 patients (20 Sustained Response individuals vs. 20 Decreased Response). Individuals with a Sustained Response had increased numbers of hematopoietic multipotent cells (51.75% vs. 43%), hematopoietic stem cells positive for CD49F ++ (20.5% vs. 13.55%), and CD235a +/CD71 + cells (11.55% vs. 4.54%). In contrast, individuals with a Decreased Response had an increased percentage of unipotent hematopoietic progenitor cells (38.55% vs. 52.9%) and committed megakaryocyte erythroid progenitor cells (33.2% vs 46.2%; Figure 2). Conclusions: Nearly 30% of children with SCD taking hydroxyurea had a significant decline in their HbF levels after years of treatment and consequently suffered an increased number of clinical complications. While higher dosages of hydroxyurea may restore some HbF induction in these patients, we have quantified broad changes in specific HSPC levels that may be responsible for this decline in HbF. Patients with a Decreased Response had a lower percentage of multipotent progenitor cells that maintain self-regeneration capacity and increase numbers of committed erythroid progenitor cells. Although many stressors can impact quantitative and functional changes seen in HSPCs, these findings suggest that premature aging of the hematopoietic system plays an important role in long-term hydroxyurea response. Better understanding of why certain individuals are more susceptible to this phenomenon would enable the development of personalized strategies to enhance HbF induction and facilitate early selection of alternative treatments for these individuals with SCD.