The BCL-2 inhibitor venetoclax has transformed the treatment of acute myeloid leukemia (AML), but relapse due to resistance of leukemic stem cells (LSCs) remains a major challenge. By molecular and functional profiling of LSCs from >150 patients, we identify four LSC subtypes. These mirror distinct hematopoietic lineage stages, which determine the expression ratio between the venetoclax target BCL-2 and resistance-inducing proteins MCL-1 and BCL-xL (MAC-score). Longitudinal analyses reveal that venetoclax resistance mostly arises in LSCs through plasticity toward a megakaryocytic/erythroid-progenitor (MEP)-LSC state that switches survival dependency from BCL-2 to BCL-xL. In rare cases, mature monocytic/dendritic (MoDe)-LSCs, found within LAMP5+ monocytic AMLs, drive venetoclax resistance. LSC subtyping improves genetic risk stratification and provides subtype-specific therapies: venetoclax-resistant MEP-LSCs respond to BCL-xL inhibitors, whereas MoDe-LSCs are sensitive to MEK1/2 inhibition. Our findings reveal four distinct LSC types with unique vulnerabilities and propose biomarker-guided treatment strategies that complement genetic profiling to overcome venetoclax resistance.

Chromosomal instability is a major driver of intratumoral heterogeneity (ITH), promoting tumor progression. In the present study, we combined structural variant discovery and nucleosome occupancy profiling with transcriptomic and immunophenotypic changes in single cells to study ITH in complex karyotype acute myeloid leukemia (CK-AML). We observed complex structural variant landscapes within individual cells of patients with CK-AML characterized by linear and circular breakage-fusion-bridge cycles and chromothripsis. We identified three clonal evolution patterns in diagnosis or salvage CK-AML (monoclonal, linear and branched polyclonal), with 75% harboring multiple subclones that frequently displayed ongoing karyotype remodeling. Using patient-derived xenografts, we demonstrated varied clonal evolution of leukemic stem cells (LSCs) and further dissected subclone-specific drug-response profiles to identify LSC-targeting therapies, including BCL-xL inhibition. In paired longitudinal patient samples, we further revealed genetic evolution and cell-type plasticity as mechanisms of disease progression. By dissecting dynamic genomic, phenotypic and functional complexity of CK-AML, our findings offer clinically relevant avenues for characterizing and targeting disease-driving LSCs.

Book Citations: Authors, Title, HemaSphere, 2023;7(S3):pages. The individual abstract DOIs can be found at https://journals.lww.com/hemasphere/pages/default.aspx. Disclaimer: Articles published in the journal HemaSphere exclusively reflect the opinions of the authors. The authors are responsible for all content in their abstracts including accuracy of the facts, statements, citing resources, etc. 3406 for the development of novel predictive biomarkers for standard chemotherapy regime. HemaSphere | 2023;7(S3) EHA2023 Hybrid Congress Copyright Information: (Online) ISSN: 2572-9241 © 2023 the Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the European Hematology Association. This is an open access Abstract Book distributed under the Attribution-NonCommercial-NoDerivs (CC BY-NC-ND) which allows third parties to download the articles and share them with others as long as they credit the author and the Abstract Book, but they cannot change the content in any way or use them commercially. Abstract Book Citations: Authors, Title, HemaSphere, 2023;7(S3):pages. The individual abstract DOIs can be found at https://journals.lww.com/hemasphere/pages/default.aspx.Book Citations: Authors, Title, HemaSphere, 2023;7(S3):pages. The individual abstract DOIs can be found at https://journals.lww.com/hemasphere/pages/default.aspx. Disclaimer: Articles published in the journal HemaSphere exclusively reflect the opinions of the authors. The authors are responsible for all content in their abstracts including accuracy of the facts, statements, citing resources, etc. 3407

Topic: 3. Acute myeloid leukemia - Biology & Translational Research Background: Acute Myeloid Leukemia (AML) is a highly aggressive adult leukemia with a high incidence of relapse and mortality. AML hijacked the hierarchical organization of normal hematopoiesis with Leukemia Stem Cells (LSCs) at the top of the differentiation tree and differentiated and highly proliferating myeloid blast at the bottom. Similar to normal hematopoietic stem cells (HSCs), LSCs have been originally identified as CD34+CD38- cells. However, this strategy to isolate LSCs is particularly challenging in NPM1 mutated AMLs, since expression of CD34 on leukemic cells is low or absent altogether. Aims: In this study, we aimed to establish a novel sorting strategy to isolate LSCs independently of CD34 surface marker in both CD34positive and CD34negative AMLs. Methods: Using a genetically highly homogeneous cohort of 46 AML patients carrying DNMT3A and NPM1 mutations, we established a novel isolation strategy to enrich for LSCs even in CD34negative AMLs by additionally including a positive selection for GPR56 and a negative selection for mature markers such as NKG2DLigandss. Results: By combining functional in vivo data, mutational analyses on xenografts and transcriptomic data, we found that CD34+GPR56+NKG2DL- subpopulations can contain along with LSCs also normal and/or pre-leukemic (HSCs). In contrast, no such residual normal or pre-leukemic HSCs were detected in CD34-GPR56+NKG2DL- subpopulations. Finally, we show that naïve AML patients who retain a relevant reserve of normal and/or preleukemic HSCs, able to reconstitute immunocompromised mice at time of diagnosis, have significant longer relapse-free and overall survival compared to patients without engrafting HSCs. Summary/Conclusion: These data suggest that the presence of normal and/or preleukemic HSCs with multilineage engrafting potential in the bone marrow of naïve patients is associated with good response to standard chemotherapy, providing a basis for the development of novel predictive biomarkers for standard chemotherapy regime. Keywords: DNMT3A, AML, Leukemic stem cell, Stem cell marker

Background: Despite typically high response rates to initial chemotherapy, the rate of mortality in acute myeloid leukemia (AML) remains high due to frequent and hard to control relapses. Persistence of therapy resistant Leukemic Stem Cells (LSCs) harboring clonal outgrowth capacity and present within Minimal Residual Disease (MRD) during complete remission stage are thought to be the origin of relapse. However, identifying the exact cellular composition of MRD in patients during remission has been notoriously difficult due to the exceedingly low number of resistant leukemia cells in MRD stage hiding within the vast majority of healthy blood cells. Thus, the molecular and cellular mechanisms responsible for the functional maintenance of LSCs in patient MRD remains poorly understood. Aims: Clinical MRD sample analysis is limited by the difficulty of accessing such samples in a longitudinal manner. Therefore, we established and characterized an MRD human xenograft mouse model to circumvent the difficulty to analyze the MRD fractions of AML patients. Based on the knowledge attained, precise strategies targeting or preventing the appearance of resistant persister leukemic cells including LSCs will be developed. Methods: A unique set of four longitudinally collected triplet samples (diagnosis, remission, and relapse) were used for this analysis. Established in vivo patient derived xenograft (PDX) models from the longitudinally triplet samples were treated with combination chemotherapy (Cytarabine and Daunorubicin) in order to mimic the MRD state in the clinical setting. Using flow cytometry and RNA-seq, we analysed MRD fractions in both primary samples and the corresponding PDX models. Results: First, we determined the in vivo regimen and the optimum sub-lethal dose of Cytarabine (AraC) + Daunorubicin. Administration of AraC 30mg/kg/day for 4 consecutive days combined with 2 days of Daunorubicine 2.5mg/kg/day was determined as the most efficient treatment to observe a significant reduction in total AML cell tumor burden in the bone marrow and spleen at day 8. Additionally, we determined week 2 as the optimal time point to observe tumor regrowth mimicking the clinical MRD state. Our data show that this combination treatment (4 + 2) is well tolerated in NSG mice at a dose and schedule analogous to the clinically used 7 + 3 AML patient treatment regime, and thus allowing us to study mechanisms involved in drug resistance. Importantly, PDX generated from diagnosis samples, but not from MRD or relapse samples, displayed sensitivity to chemotherapy. Moreover, the residual AML-MRD cells surviving chemotherapy in PDX mice from diagnostic samples displayed a higher OxPhos metabolism compared to untreated controls, as we observed a higher mitochondrial membrane potential and mitochondrial mass as assessed by FACS assays TMRE and MTG respectively. In addition, MRD cells expressed higher level of the myeloid chemokine receptors. Collectively, these data correlate with the clinical data of the analysed longitudinal triplet samples as both primary patient and PDX MRD samples were enriched on High OxPhos signature and presented a higher gene expression of the myeloid chemokine receptors compared to the respective diagnosis samples. Summary/Conclusion: Taken together, we have established PDX mouse models that recapitulates the metabolic properties and the phenotypic features that we identified at the clinical MRD state. Single-cell multi-omics technologies will now be applied to gain novel insights into the cellular identity, heterogeneity, and molecular mechanism of therapy-resistant LSCs in AML. Keywords: Acute myeloid leukemia, Minimal residual disease (MRD), Chemoresistance

Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of relapse and mortality. Current chemotherapies whilst successful in eradicating blasts, are less effective in eliminating relapse-causing leukemic stem cells (LSCs). Although LSCs are usually identified as CD34+CD38- cells, there is significant heterogeneity in surface marker expression, and CD34- LSCs exist particularly in NPM1mut AMLs. By analyzing diagnostic primary DNMT3AmutNPM1mut AML samples, we suggest a novel flow cytometry sorting strategy particularly useful for CD34neg AML subtypes. To enrich for LSCs independently of CD34 status, positive selection for GPR56 and negative selection for NKG2D ligands are used. We show that the functional reconstitution capacity of CD34- and CD34+ LSCs as well as their transcriptomes are very similar which support phenotypic plasticity. Furthermore, we show that although CD34+ subpopulations can contain next to LSCs also normal and/or preleukemic hematopoietic stem cells (HSCs), this is not the case in CD34-GPR56+NKG2DL- enriched LSCs which thus can be isolated with high purity. Finally, we show that patients with AML, who retain at the time of diagnosis a reserve of normal and/or preleukemic HSCs in their bone marrow able to reconstitute immunocompromised mice, have significantly longer relapse-free and overall survival than patients with AML in whom functional HSCs are no longer detectable.

Poly(A) binding protein nuclear 1 (PABPN1) is known for its role in poly(A) tail addition and regulation of poly(A) tail length. In addition, it has been shown to be involved in alternative polyadenylation (APA). APA is a process regulating differential selection of polyadenylation sites, thereby influencing protein isoform expression and 3ʹ-UTR make-up. In this study, we generated an inducible Pabpn1flox/flox mouse model using crRNA-tracrRNA:Cas9 complexes targeting upstream and downstream genomic regions, respectively, in combination with a long single-stranded DNA (ssDNA) template. We performed extensive in vitro testing of various guide RNAs (gRNAs) to optimize recombination efficiency for in vivo application. Pabpn1flox/flox mice were generated and crossed to MxCre mice for validation experiments, allowing the induction of Cre expression in the bone marrow (BM) by poly(I:C) (pIC) injections. Validation experiments revealed successful deletion of Pabpn1 and absence of PABPN1 protein. Functionally, knockout (KO) of Pabpn1 led to a rapid and robust depletion of hematopoietic stem and progenitor cells (HSPCs) as well as myeloid cells, suggesting an essential role of Pabpn1 in the hematopoietic lineage. Overall, the mouse model allows an inducible in-depth in vivo analysis of the role of PABPN1 and APA regulation in different tissues and disease settings.

Haematopoietic stem cells (HSCs) are characterized by their self-renewal potential associated to dormancy. Here we identify the cell surface receptor neogenin-1 as specifically expressed in dormant HSCs. Loss of neogenin-1 initially leads to increased HSC expansion but subsequently to loss of self-renewal and premature exhaustion in vivo. Its ligand netrin-1 induces Egr1 expression and maintains quiescence and function of cultured HSCs in a Neo1 dependent manner. Produced by arteriolar endothelial and periarteriolar stromal cells, conditional netrin-1 deletion in the bone marrow niche reduces HSC numbers, quiescence and self-renewal, while overexpression increases quiescence in vivo. Ageing associated bone marrow remodelling leads to the decline of netrin-1 expression in niches and a compensatory but reversible upregulation of neogenin-1 on HSCs. Our study suggests that niche produced netrin-1 preserves HSC quiescence and self-renewal via neogenin-1 function. Decline of netrin-1 production during ageing leads to the gradual decrease of Neo1 mediated HSC self-renewal. Haematopoietic stem cells (HSCs) are characterized by their self-renewal potential and associated dormancy. Here the authors show that niche produced netrin-1 preserves HSC quiescence and self-renewal via neogenin-1, and that decline of netrin-1 production during ageing leads to decreased Neo1 mediated HSC self-renewal.

The long non-coding RNA (lncRNA) Maternally Expressed Gene 3 (Meg3) is encoded within the imprinted Dlk1-Meg3 gene locus and is only maternally expressed. Meg3 has been shown to play an important role in the regulation of cellular proliferation and functions as a tumor suppressor in numerous tissues. Meg3 is highly expressed in mouse adult hematopoietic stem cells (HSCs) and strongly down-regulated in early progenitors. To address its functional role in HSCs, we used MxCre to conditionally delete Meg3 in the adult bone marrow of Meg3(mat-flox/pat-wt) mice. We performed extensive in vitro and in vivo analyses of mice carrying a Meg3 deficient blood system, but neither observed impaired hematopoiesis during homeostatic conditions nor upon serial transplantation. Furthermore, we analyzed VavCre Meg3(mat-flox/pat-wt) mice, in which Meg3 was deleted in the embryonic hematopoietic system and unexpectedly this did neither generate any hematopoietic defects. In response to interferon-mediated stimulation, Meg3 deficient adult HSCs responded highly similar compared to controls. Taken together, we report the finding, that the highly expressed imprinted lncRNA Meg3 is dispensable for the function of HSCs during homeostasis and in response to stress mediators as well as for serial reconstitution of the blood system in vivo.

In Extended Data Fig. 1a of this Letter, the flow cytometry plot depicting the surface phenotype of AML sample DD08 was a duplicate of the plot for AML sample DD06. Supplementary Data 4 has been added to the Supplementary Information of the original Letter to clarify the proteome data acquisition and presentation. The original Letter has been corrected online.