Kdm6a deficiency restricted to mouse hematopoietic cells causes an age- and sex-dependent myelodysplastic syndrome-like phenotype

Kdm6a/Utx, a gene on the X chromosome, encodes a histone H3K27me3 demethylase that has an orthologue on the Y chromosome (Uty) (Zheng et al. 2018). We previously identified inactivating mutations of Kdm6a in approximately 50% of mouse acute promyelocytic leukemia samples; however, somatic mutations of KDM6A are more rare in human AML samples, ranging in frequency from 2–15% in different series of patients, where their role in pathogenesis is not yet clear. In this study, we show that female Kdm6aflox/flox mice (with allele inactivation initiated by Vav1-Cre in hematopoietic stem and progenitor cells (HSPCs) have a sex-specific phenotype that emerges with aging, with features resembling a myelodysplastic syndrome (MDS). Female Kdm6a-knockout (KO) mice have an age-dependent expansion of their HSPCs with aberrant self-renewal, but they did not differentiate normally into downstream progeny. These mice became mildly anemic and thrombocytopenic, but did not develop overt leukemia, or die from these cytopenias. ChIP-seq and ATAC-seq studies showed only minor changes in H3K27me3, H3K27ac, H3K4me, H3K4me3 and chromatin accessibility between Kdm6a-WT and Kdm6a-KO mice. Utilizing scRNA-seq, Kdm6a loss was linked to the transcriptional repression of genes that mediate hematopoietic cell fate determination. These data demonstrate that Kdm6a plays an important role in normal hematopoiesis, and that its inactivation may contribute to AML pathogenesis.

IL7R Targeting Using OSE-127 Shows Robust Anti-Leukemic Activity in B-Cell Precursor Acute Lymphoblastic Leukemia Xenografts

Despite the favorable prognosis of B cell precursor acute lymphoblastic leukemia (BCP-ALL), relapse remains a clinical challenge. Antibody-based immunotherapies like Blinatumomab have improved BCP-ALL outcome, yet these can quickly turn ineffective due to CD19 antigen escape. Therefore, novel targeted immunotherapy options are urgently needed. We previously showed that high IL7R expression associates with adverse outcome in BCP-ALL patients and that IL7R targeting using laboratory-grade blocking antibodies significantly reduced leukemic burden in E2A-PBX1 and BCR-ABL patient derived xenografts (PDX) (Alsadeq et al., Blood, 2017; Abdelrasoul et al., Nat. Commun., 2020). Here we used the humanized monoclonal antibody OSE-127, a full IL7R antagonist which is not internalized by target cells and prevents IL7R heterodimerization and subsequent downstream signaling (Belarif et al., Nat. Commun. 2018, Belarif et al. JCI, 2019). Importantly, OSE-127 has recently been positively evaluated in a phase 1 study conducted in 63 healthy volunteers receiving either a single dose or two doses two weeks apart (EUDRACT 2018-001832-22). OSE-127 demonstrated an excellent safety and tolerability profile showing no signs of lymphopenia, cytokine release syndrome or T-cell compartment alterations. Based on these preclinical and clinical results, we investigated the anti-leukemic efficacy of OSE-127 immunotherapy in PDX models of BCP-ALL. First, to identify patients that may benefit from IL7R-immunotherapy, we measured IL7R surface expression in diagnostic BCP-ALL patient samples of different cytogenetic subgroups via flow cytometry. We detected IL7R-positivity (defined as ≥10% IL7R + BCP-ALL cells) in 52% (49/94) of patient samples including BCR-ABL + (25%; 5/20), TEL-AML1 + (41%; 7/17) and B-other (40%, 8/20) samples. Particularly high numbers of IL7R + patients were found in the E2A-PBX1 + and MLL-rearranged (MLLr) BCP-ALL subgroups (79%; 19/24 and 85%; 11/13 IL7R + patient samples, respectively). Next, we tested the efficacy of OSE-127 in NSG mice injected with PDX cells from two different E2A-PBX1 + patients (63.0% and 89.6% IL7R-positive blasts, respectively) modelling an MRD-situation by starting treatment one day after injection of PDX cells. While 100% of control animals developed overt leukemia, 0% of the OSE-127-treated animals developed the disease, with 10/10 and 7/10 mice per PDX-group being MRD-negative by the time of sacrifice. Of note, OSE-127-therapy was also effective in corresponding PDX models when therapy was initiated upon detection of 1% BCP-ALL cells in the peripheral blood, modelling an overt leukemia situation (P<0.0001 in both cases). To investigate the efficacy of OSE-127 in a variety of BCP-ALL samples, we conducted a preclinical phase II-like study using PDX from different cytogenetic patient subgroups (8E2A-PBX1 +, including 1 matched diagnostic/relapse sample, 1 BCR-ABL, 1 MLLr and 1 ETV6-NTRK3). Two mice per PDX were injected, randomly assigned to control or OSE-127 treatment groups and therapy was initiated when >1% blasts were detected in the peripheral blood. Response to OSE-127 was detected in 9/11 (82%) PDX samples in vivo, including BCR-ABL +, MLLr and E2A-PBX1 +-relapse samples. Accordingly, OSE-127 immunotherapy led to a significant increase in median overall survival (85 days versus 55 days; P=0.0122). Of note, OSE-127 therapy response associated with IL7R expression levels on BCP-ALL cells and no significant downregulation of the IL7R antigen was observed upon OSE-127 treatment. Taken together, our data demonstrate that IL7R-targeting using OSE-127, which has already demonstrated a good safety profile in healthy volunteers, is an efficient approach for BCP-ALL immunotherapy and may be particularly beneficial for patients with high IL7R-expression and/or relapsed/refractory disease after CD19-directed therapy. Disclosures Lenk: OSE Immunotherapeutics: Research Funding. Baccelli: OSE Immunotherapeutics: Current Employment, Other: Author of patents related to anti-IL7R antibodies. Corallo: OSE Immunotherapeutics: Current Employment. Schrappe: SHIRE: Other: research support; JazzPharma: Honoraria, Other: research support; Servier: Honoraria, Other: research support; Novartis: Honoraria, Other: research support; SigmaTau: Other: research support; Amgen: Other: research support; Servier: Honoraria; Novartis: Honoraria; JazzPharma: Honoraria. Cario: Novartis: Other: Lecture Fee. Brüggemann: Incyte: Other: Advisory Board; Amgen: Other: Advisory Board, Travel support, Research Funding, Speakers Bureau; Janssen: Speakers Bureau. Poirier: OSE Immunotherapeutics: Current Employment, Other: Author of patents related to anti-IL7R antibodies. Schewe: OSE Immunotherapeutics: Research Funding; Bayer: Other: Advisory Board; SOBI: Other: Advisory Board; Jazz Pharmaceuticals: Other: Advisory Board.

ETV6/RUNX1 fusion gene and its active role

Recent investigation successfully identified a pre leukemic ETV6/RUNX1-positive clone in the healthy twin of a patient diagnosed with ETV6/RUNXI-positive acute lymphoblastic leukemia (ALL) and also some studies with ETV6/RUNX1 knock in mice showed that the expression of the fusion gene is not sufficient for the invivo induction of ALL. Taken together, these data indicate that ETV6/RUNX1-positive leukemia is .generated through a multi-step mechanism, and that accumulation of additional genetic changes is necessary for the development of overt leukemia. Hence, to understand fully the genetic evolution of this disorder, identification of the complete spectrum of genetic changes that accompany the ETV6/RUNX1 fusion gene is necessary. Moreover, critical patho genetic insights may be gained from studying the correlation pattern of the different copy number changes.

Kdm6a Deficiency Restricted to Mouse Hematopoietic Cells Causes an Age- and Sex-dependent Myelodysplastic Syndrome-Like Phenotype

Kdm6a/Utx , a gene on the X chromosome, encodes a histone K27me3 demethylase that has an orthologue on the Y chromosome ( Uty ). We previously identified inactivating mutations of Kdm6a in approximately 50% of mouse acute promyelocytic leukemia samples; however, somatic mutations of KDM6A are more rare in human AML samples, ranging in frequency from 2-15% in different series of patients, where their role in pathogenesis is not yet clear. In this study, we show that female Kdm6a flox/flox mice (with allele inactivation initiated by Vav1 -Cre in hematopoietic stem and progenitor cells (HSPCs) have a sex-specific phenotype that emerges with aging, with features resembling a myelodysplastic syndrome (MDS). Female Kdm6a -knockout (KO) mice have an age-dependent expansion of their HSPCs with aberrant self-renewal, but they did not differentiate normally into downstream progeny. These mice became mildly anemic and thrombocytopenic, but did not develop overt leukemia, or die from these cytopenias. ChIP-seq and ATAC-seq studies showed only minor changes in H3K27me3, H3K27ac, H3K4me, H3K4me3 and chromatin accessibility between Kdm6a -WT and Kdm6a -KO mice. Utilizing scRNA-seq, Kdm6a loss was linked to the transcriptional repression of genes that mediate hematopoietic cell fate determination. These data demonstrate that Kdm6a plays an important role in normal hematopoiesis, and that its inactivation may contribute to AML pathogenesis by altering the epigenetic state of HSPCs .

Towards prevention of childhood ALL by early-life immune training

B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most common form of childhood cancer. Chemotherapy is associated with life-long health sequelae and fails in approximately 20% of cases. Thus, prevention of leukemia would be preferable to treatment. Childhood leukemia frequently starts before birth, during fetal hematopoiesis. A first genetic hit (e.g. the ETV6-RUNX1 gene fusion) leads to the expansion of pre-leukemic B-cell clones, which are detectable in healthy newborn cord blood (up to 5%). These pre-leukemic clones give rise to clinically overt leukemia in only about 0.2% of carriers. Experimental evidence suggests that a major driver of conversion from the pre-leukemic to the leukemic state is exposure to immune challenges. Novel insights have shed light on immune host responses and how they shape the complex interplay between (A) inherited or acquired genetic predispositions, (B) exposure to infection, and (C) abnormal cytokine release from immunologically untrained cells. Here, we integrate the recently emerging concept of "trained immunity" into existing models of childhood BCP-ALL and suggest future avenues towards leukemia prevention.

Cell cycle corruption in a preleukemic ETV6-RUNX1 model exposes RUNX1 addiction as a therapeutic target in acute lymphoblastic leukemia

SummaryETV6-RUNX1 is the most common translocation in pediatric B-acute lymphoblastic leukemia (B-ALL), shown to arise in utero and to initiate a clinically silent pre-leukemic state. Here, we integrate chromatin immunoprecipitation sequencing (ChIP-seq) and RNA-sequencing (RNA-seq) to characterize the authentic ETV6-RUNX1 regulome and explore its interplay with the native RUNX1 as a substrate for preleukemia. We show that preleukemic initiation is primarily mediated through competition for RUNX1 binding sites and transcriptional repression of the RUNX1 program. Using mass cytometry we functionally demonstrate that as a “first-hit” ETV6-RUNX1 induces a cell cycle impairment in a human pluripotent stem cell (hPSC) model, antagonizing RUNX1-mediated cell cycle regulation. Strikingly, in overt leukemia, genetic perturbation of native RUNX1 protein or its co-factor CBFβ leads to cell death of pediatric and adult B-ALL cells. We demonstrate that RUNX1 addiction can be therapeutically exploited by pharmacological inhibition using an allosteric CBFβ inhibitor.

Prodromal / Pre-Leukemic Acute Leukemia of B-Lymphoblasts in 7 Adult Patients

Background: Prodromal/pre-leukemic acute leukemia is rare, mostly described in childhood B-lymphoblastic leukemia (B-ALL), with its initial presentation confused with aplastic anemia (AA). Findings reported in pediatric prodromal/pre-leukemic B-ALL include female preponderance, bone marrow (BM) fibrosis and uniform hypocellularity, and transient recovery. Reports in adults are rarer still. We conducted a retrospective review of adult patients we diagnosed with B-ALL and mixed phenotype acute leukemia with B-lymphoid and myeloid components (MPAL-B/myeloid) with prodromal/pre-leukemic manifestations. We sought to identify common clinical features, peripheral blood (PB) and BM morphology, diagnostic considerations, and clinical follow-up (whenever available) to aid in improved recognition in the adult setting. Methods: Patients with unusual presentations preceding overt acute leukemia were identified from pathology and clinical records from our institution from 2010-2020. These include (a) incidental PB blasts and partial BM-based disease, followed by spontaneous, transient regression (STR); (b) pancytopenia with rare to absent PB blasts and unexpected detection of BM-based blasts (10% or lower), compatible with aleukemic prodrome (AP) cases; (c) pancytopenia without PB blasts yet unexpected excess BM-based blasts (50% or greater) followed by marked reduction of BM-based blasts (compared to initial BM) despite absence of treatment (AP-->SR). BM pathology during prodromal/pre-leukemic phases were reviewed to identify key morphologic features. Results: Seven patients were identified (4 M, 3 F; age range 20-75 years), including one previously described by our group (Table 1). All were of Hispanic ethnicity. They displayed a broad range of symptoms including fatigue, fevers, throat pain, and weight loss. Initial presentations were STR in 3, AP in 2, and AP-->SR in 2. Although variably cellular, all BM trephine biopsies in prodromal/pre-leukemic phase had at least focal hypocellularity with stromal damage, characterized by granular to fibrillary stroma, striking cellular dropout, and multiloculated fat cells with fibrinoid appearance. Relative erythroid hyperplasia was seen in 4, while dyserythropoiesis and dysmegakaryocytopoiesis were both observed in 2 cases, raising concern for myelodysplastic syndrome (MDS). AA and MDS were, in some cases, seriously considered in the initial differential diagnosis. Because of low level BM blasts at initial presentation in most (5/7), definitive lineage designation was sometimes challenging. Furthermore, flow cytometric data was limited and IHC stained only a sparse number of immature B-cells; thus normal precursor B-cell (hematogone) hyperplasia was a strong possibility. Workup in 2 cases during low numbers of BM-based blasts or spontaneous blast reduction (cases #6 and #7, respectively) revealed T-cell clones on PCR/NGS testing. In STR and AP cases, the disease proceeded from initial presentation to overt leukemia within a fairly short interval (range 1.5 - 7.0 months; median 2.5). Final diagnosis in the majority of cases (6/7) was B-ALL, with one case of MPAL-B/myeloid. Conclusion: Herein we describe a series of 7 adult prodromal/pre-leukemic cases of B-lymphoblasts (6 B-ALL; 1 MPAL-B/myeloid) with a variety of clinical presentations. In contrast to the female-predominant pediatric prodromal B-ALLs, most of our adult cases occurred in males. Given pancytopenia, relatively low numbers, and difficulty in assigning blast lineage, diagnostic considerations initially included MDS, AA, and hematogone hyperplasia with marrow regeneration. Key morphologic features that favored a prodromal/pre-leukemic case of B-lymphoblasts over MDS or AA were profound stromal damage and expansion (albeit low numbers) of immature B-cells - findings that would be unusual in low-grade MDS and AA. Intriguingly, in 2 of our cases, T-cell clones detected on PCR testing during low blast levels may indicate an immunologic role of T-cells in transiently reducing blasts in prodromal acute leukemia, as previously suggested by Zimmermannova and colleagues (Haematol2017;102:e225-228). Regardless of whether patients experienced STR, AP, or AP-->SR, close clinical follow-up is advised, as progression to overt leukemia occurs within a relatively short time frame (median of 2.5 months in our series). Disclosures No relevant conflicts of interest to declare.

Co-Targeting of CD38 and CD47 in T Cell Acute Lymphoblastic Leukemia

Antibody application is a promising therapy in hematological malignancies including acute lymphoblastic leukemia (ALL). Unlike for B-cell precursor (BCP-ALL), immunotherapeutic interventions in T-cell ALL (T-ALL) are practically non-existent. Most T-ALL patient samples show substantial surface expression of CD38. Moreover, mice bearing T-ALL patient-derived xenograft (PDX) samples treated with daratumumab (Dara) monotherapy displayed prolonged survival and MRD-negativity in 50% of cases as opposed to animals treated with chemotherapy (Vogiatzi et al., Blood, 2019). Besides CD38, elevated surface expression of CD47 has been described in T-ALL (Chao et al., 2011). CD47 acts as a "don't-eat-me" signal protecting cancer cells from macrophage-dependent phagocytosis. In this study, we explored the efficacy of Dara and a CD47 blocking antibody (Fc-modified version of Hu5F9-G4, termed Hu5F9-IgG2σ) alone or in combination in T-ALL. In vitro phagocytosis assays with M-CSF derived M0 (CD64+, CD80-, CD163+) macrophages from healthy donors were evaluated in T-ALL cell lines. Cells labelled with a pH-dependent dye became fluorescent upon engulfment by macrophages and formation of the acidic phagolysosome, which was automatically measured as an absolute cell count. The highest count was set as 100% in each experiment and all other values expressed as percentages relative to that. Treatment of MOLT-13 cells with Dara or Hu5F9-IgG2σ increased median phagocytosis from 5% in control to 23% and 27%, respectively (p=0.008 for both, Figure 1A). However, combined treatment resulted in a maximal increase of median phagocytosis in MOLT-13 cells (p=0.004 compared to Dara and p=0.008 compared to Hu5F9-IgG2σ, Figure 1A). Similar results were obtained in HSB-2 and P-12 cells (p=0.037/0.004 for HSB-2, p=0.011/0.001 for P-12). In addition, phagocytosis was determined in 12 PDX samples from random T-ALL patients. Hu5F9-IgG2σ alone showed a modest increase in median phagocytosis compared to control (19% vs. 6%, p<0.001) and Dara increased phagocytosis to 43% (p<0.001). Combination therapy, however, led to a maximal rise of median phagocytosis in all samples (p<0.001 compared to all others). Phagocytosis was also determined in 16 relapsed/refractory (r/r) T-ALL-PDX samples, in which a maximal median phagocytosis upon combination of Dara and Hu5F9-IgG2σ was also observed (2% in control, 37% in Dara and 14% in Hu5F9-IgG2σ, p<0.001/p=0.02/p=0.02, respectively). The extent of phagocytosis correlated with CD38 and CD47 surface expression on T-ALL cells and, in part, also with expression of signal regulatory protein α (SIRPα) on macrophages, the interacting partner of CD47. A maximal increase in phagocytosis was also observed when applying Hu5F9-IgG2σ in 1/10 of the concentration of Dara, confirming its high efficacy. The effects of the Dara/ Hu5F9-IgG2σ combination were also examined in vivo in phase II-like preclinical trials containing different patients in one experiment. Six random T-ALL-PDX samples were injected into NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice and subjected to therapy with Dara and Hu5F9-IgG2σ alone or in combination. In order to mimic minimal residual disease (MRD), antibody therapy was started one day post injection. Mice subjected to Dara displayed prolonged survival in 4/6 (67%) animals compared to control (p=0.007), whereas animals treated with Hu5F9-IgG2σ showed significantly prolonged survival in all cases (p=0.007, Figure 1B). Interestingly, mice not responding to Dara benefitted from Hu5F9-IgG2σ monotherapy and the combination had no further survival advantage in this MRD model. In a second approach, eight r/r T-ALL PDX samples were used, and the same therapy was started upon overt leukemia (1% human blasts in peripheral blood). Compared to control, mice treated with Dara in this overt leukemia and r/r setting showed no survival benefit, while animals subjected to Hu5F9-IgG2σ showed a trend towards a prolonged survival (5/8 cases, 63%, p=0.08). Most importantly, the combination of both agents resulted in a statistically significant survival prolongation in 7/8 cases (88%, p=0.010, Figure 1C). Altogether, we show that combining Dara with CD47 blockade increases phagocytosis in vitro in three T-ALL cell lines and 28 PDX samples. Our in vivo data suggest that this combination is a highly promising therapeutic strategy, especially in the relapsed/refractory setting. Figure Disclosures Cario: Jazz Pharmaceuticals: Consultancy, Other: travel support; Novartis: Consultancy, Other: travel support. Kulozik:bluebird bio, Inc.: Consultancy, Honoraria; Novartis: Consultancy, Honoraria. Bourquin:Servier: Other: Travel Support. Schewe:Sobi: Other: was an advisory board member; Bayer: Other: was an advisory board member; Jazz: Other: was an advisory board member; OSE pharmaceuticals: Research Funding.