Core Binding Research Articles

Acute myeloid leukemia with t(16;21)(q24;q22), CBFA2T3::RUNX1, in post-treatment setting, a case report

Abstract Introduction/Objective Acute myeloid leukemia (AML) with t(16;21)(q24;q22), CBFA2T3::RUNX1 is an uncommon entity that has been reported in both pediatric and adult patients as de novo AML or secondary to prior chemo/radiation therapy. CBFA2T3::RUNX1 AMLs share similar clinico-pathological features and gene expression profile with RUNX1::RUNX1T1 AML. Methods/Case Report We report a case of AML with CBFA2T3::RUNX1 in a 52 year old female who had history of small cell cervical cancer treated with chemotherapy (4 cycles of cisplatin and etoposide) and pelvic radiation therapy. About 17 months after completion of therapy, she presented with anemia and thrombocytopenia, normal WBC/neutrophil count, eosinophilia and increased blasts (up to 10%) in blood. Bone marrow biopsy shows AML with maturation (FAB-M2), erythropoiesis is present, whereas megakaryocytes are decreased. Flow cytometry analysis shows myeloblasts with aberrant CD19 and CD56 expression; in addition, increased CD117/tryptase positive cells are noted, mostly interstitial and more concentrated around bone trabeculae. By immunohistochemical stains, these cells are at least partially positive for CD25, negative CD2, CD30. Karyotype studies demonstrate t(16;21)(q24;q22) and trisomy 8 in all metaphases. FoundationOne heme NGS studies confirmed CBFA2T3::RUNX1 fusion, and no additional mutations were identified. Patient received induction chemotherapy with Idarubicin/Cytarabine plus GO (Gemtuzumab ozogamicin); day 14 bone marrow showed chemotherapeutic effect and she is now in morphologic remission 5 months after diagnosis. Results (if a Case Study enter NA) NA Conclusion Our case adds to the limited knowledge of CBFA2T3::RUNX1 AMLs. Our case shows morphological and immunophenotypic features similar to AML with RUNX1::RUNX1T1, with unusual presentation of peripheral eosinophilia, and increased CD117/tryptase positive cells in bone marrow, the latter has been reported occasionally in core binding factor AMLs. We emphasize the importance of comprehensive genetic studies in AML patients, lack of adverse genetic abnormalities in our patient indicates favorable risk category regardless of the post-treatment clinical setting.

Venetoclax and Azacitidine for Molecular Relapse during First Line Intensive Chemotherapy in Patients with NPM1 Mutated or Core Binding Factor (CBF) AML. a Study from the Dataml Registry

Introduction: Molecular follow-up (FU) for AML patients (pts) with NPM1 mutation, RUNX1::RUNX1T1 or CBFB::MYH11 fusion transcripts has been established over the last ten years. Real-time quantitative PCR (qPCR) is the gold standard for the evaluation of measurable residual disease (MRD) in pts undergoing intensive chemotherapy (IC). Failure to achieve a deep molecular response is a strong predictive factor of relapse and survival and may guide post remission therapy (Ivey A, NEJM 2016). Moreover, the ELN MRD working party recommended a schedule for molecular FU and recently established a definition of molecular relapse (Heuser M, Blood 2021). However, there is no therapeutic consensus for pts with molecular relapse before overt clinical relapse. Frontline allogeneic hematopoietic cell transplantation (alloHCT), salvage IC or even waiting for morphological relapse in order to screen molecular characteristics of the relapsing disease or propose a clinical trial, may be discussed with pts. Venetoclax with azacitidine (VEN/AZA) was recently approved in unfit AML pts and demonstrated a particular efficacy in NPM1-mutated AML. In this study, we thought to describe the safety and efficacy of VEN/AZA in pts with NPM1 mutated or CBF AML in molecular relapse after first line IC. Methods: Pts of the DATAML registry with the following criteria were included in this study : AML with NPM1 mutation, RUNX1::RUNX1T1 or CBFB::MYH11 transcripts, first line IC, morphological complete remission (CR), no alloHCT in first line, regular monitoring of MRD by qPCR in bone marrow (BM) and/or blood, molecular relapse defined according to ELN2021 guidelines on two successive samples, at least one cycle of VEN/AZA. Pts with molecular relapse followed by morphological relapse before VEN/AZA or those who relapsed after alloHCT were not included. Treatment: First line IC was cytarabine 200 mg/m² d1-7 with idarubicin 9mg/m²/d1-5 or daunorubicin 90mg/m²/d1-3 in pts 18-60y or cytarabine 100 mg/m² d1-7 with idarubicin 8mg/m²/d1-5 and lomustine 200 mg/m²/d1 in pts > 60y. Post remission therapy was intermediate or high dose cytarabine or mini-consolidations according to age and performance status. Midostaurin was added in FLT3-mutated pts. At time of molecular relapse, pts received off label venetoclax 400 mg/d (d1-14, d1-21 or d1-28 according to centers) with no ramp-up and azacitidine 75 mg/m²/d subcutaneously (d1-5, d8-9). Antifungal/antibiotic prophylaxis and G-CSF use were not systematically recommended. Results: Twenty-two pts treated with VEN/AZAfrom 21/09/2020 to30/03/2023 were included. Their characteristics at diagnosis were: female (n= 14), median age 55y (range 27-71), de novo AML (n=21), median WBC (68 giga/L, range 2.32-339.7), NPM1 mutation (n=20), CBFB::MYH11 (n=2), FLT3 mutation (n=13). All pts achieved first CR after one cycle of induction chemotherapy. Pts received a median of three consolidation cycles. All but three pts had negative MRD or low level MRD (LL-MRD) in blood and/or BM at the end of consolidation. The median time between CR1 and molecular relapse was 9.5 months (range, 1-50). The median time between molecular relapse and first VEN/AZA cycle was 51 days. During first cycle of VEN/AZA, 12, 5 and 5 pts received 14, 21 or 28 days venetoclax, respectively; 19 were treated as out-pts, 4 received posaconazole and GCSF was used in 11 pts. 12 and 3 pts had grade 3-4 neutropenia or febrile neutropenia (FN), respectively. Only 3 pts (14%) were hospitalized for FN. The median number of VEN/AZA cycles was 2 (range 1-12). After C1+/-C2, 10 (45%) and 11 pts (55%) had undetectable or LL MRD in blood, respectively (Fig1). 20 pts were bridged to alloHCT in morphological CR after a median of 2 cycles (range, 1-4). Only one pt had a molecular progression before transplantation after 2 cycles. Two pts died, one had a molecular relapse after 7 cycles and progress rapidly to frank relapse, the other one died of post-transplant complication while in CR with undetectable MRD. All other pts remained in CR at date of last news. With a median FU from D1C1 of 13.5 months, median OS wat not reached and 1y-OS was 86% (Fig2). Conclusion: In the setting of molecular relapse, VEN/AZA is safe, prevent overt relapse, and induce a high rate of molecular response before alloHCT. Molecular relapse becomes a major therapeutic challenge. Clinical trial endpoints should include the treatment of molecular relapse as an event for RFS and EFS estimation.

Assessment of 2022 European Leukemianet Risk Classification System in FLT3-ITD Positive Real-World Cohort from China

Background: The 2017 European LeukemiaNet (ELN-2017) risk classification system updated AML guidelines in 2022, adjusted FLT3-ITD mutated patients without core binding factor (CBF) or adverse risk markers to intermediate risk groups, according to the clinical trial results of midostaurin on patients with FLT3-ITD not NPM1 mutation and MRD in treatment decisions. However, midostaurin is not approved in mainland china; many patients in China are unable to receive FLT3 inhibitor due to highly cost yet. Methods: We include newly diagnosed de novo AML patients at our center from January 2017 to December 2021, regardless of the further treatment received. Patients with acute promyelocytic leukemia and AML with other previous myeloid neoplasms were excluded. All patients were diagnosed according to 2016 World Health Organization (WHO) criteria. Clinical data, chromosome and next-generation sequencing (NGS) results, treatment regimen and date of survival were included. Results: 408 patients were diagnosed as de novo AML (excluding M3) in our center, 364 patients have available cytogenetic and NGS data to access ELN-2022 risk classification. 137 (37.7%), 141 (38.8%) and 83 (23.5%) patients are classified into ELN-2022 favorable, intermediate and adverse risk groups, respectively, the median age of all patients at diagnosis is 52. 37 (10.2%) patients have a change in ELN risk classification compared with ELN-2017. In ELN-2017 favorable risk group, 19 patients whose FLT3-ITD allelic ratio <50% with NPM1 mutation are reclassified to ELN-2022 intermediate risk; in ELN-2017 intermediate risk group, five patients with CEBPA monoallelic bZIP mutation are reclassified to ELN-2022 favorable risk, 10 patients with MR gene mutations are reclassified to adverse risk; in ELN-2017 adverse risk group, 3 patients with FLT3-ITD allelic ratio >50% are reclassified to ELN-2022 intermediate risk. 323 (89.0%) patients received induction therapy: 271 (74.6%) patients received cytarabine-based chemotherapy, 52 (14.3%) patients unfit for intensive chemotherapy received hypomethylating agents (HMA)-based therapy, while 36 (9.9%) patients only received best supportive care, mainly due to early death during hydroxyurea treatment or did not want any therapy due to potential treatment costs. 211 (58.1%) patients received complete remission (CR), with CR rates in the ELN-2022 favorable, intermediate and adverse groups of 74.4%, 53.1% and 40.0%, respectively (p<0.001). After a median follow-up of 36.9 months, the median overall survival (OS) is 27.6 months, 10.6 months and 4.7 months in the ELN-2022 favorable, intermediate and adverse risk groups, compared to 21.9 months, 10.6 months and 4.8 months in the corresponding ELN-2017 risk groups. Patients in the ELN-2022 favorable group have a significantly better OS than those in intermediate and adverse group (p=0.002 and p<0.001), while there are no statistical differences between the intermediate and adverse groups (p=0.11), not significant as ELN-2017 (p=0.046). (Figure.1) 61 patients with FLT3-ITD mutations without adverse prognostic markers are classified as ELN-2022 intermediated risk. Among these patients, only 9 received FLT3 inhibitors (gilteritinib or sorafenib) due to late approval of FLT3 inhibitors in China; the remaining 52 patients received chemotherapy alone: 40 have FLT3-ITD allelic ratio <50%, 12 have allelic ratio ≥50%. These patients unable to receive FLT3 inhibitor did not achieve the same survival outcomes as other ELN-2022 intermediate risk patients (FLT3-ITD allelic ratio <50% group vs. intermediate risk group, p=0.046; FLT3-ITD allelic ratio >50% group vs. intermediate risk group, p=0.021); instead, both FLT3 mutated groups have no survival difference compare to the ELN-2022 adverse risk group. Moreover, for the ELN-2022 intermediate risk group without FLT3-ITD mutated patients, we find statistical difference to ELN-2022 adverse risk group on overall survival (median OS 17.6 months vs. 4.6 months, p=0.029), which is not achieved when FLT3-ITD mutated patients is included. (Figure.2) Conclusion: our real-world clinical data show that the ELN-2022 risk classification system is not superior to the ELN-2017 version in classifying patients in our center. For patients with FLT3-ITD mutation but unable to receive FLT3 inhibitor, their risk classification and treatment therapy should be considered as adverse risk group.

ZBTB7A Loss Promotes Synthesis of Lipids and Ketone Bodies in Myeloid Leukemia

Cancer cells reprogram their metabolism at many levels to meet the high demand for ATP and metabolites necessary for rapid tumor growth. We recently showed that inactivation of ZBTB7A, a transcription factor essential for lineage fate decision, causes upregulation of glycolysis culminating in increased energy supply in myeloid leukemia cells (Redondo Monte et al., 2020, Oncogene). ZBTB7A mutations are specifically associated with AML t(8;21), pointing toward cooperation with the RUNX1-RUNX1T1 fusion. However, the underlying mechanism is still not fully understood. Besides alteration of glycolysis, we found genes related to fatty acid metabolism upregulated in the K562 ZBTB7A knockout (KO) myeloid leukemia cell line. This led us to hypothesize that the loss of ZBTB7A could provide the cells with additional energy via increased fatty acid oxidation. To further investigate the role of ZBTB7A in fatty acid metabolism we performed metabolic flux (Seahorse, Agilent) and metabolic tracing experiments. In the palmitate oxidation assay, using a setting where the cells were cultivated in a substrate-limited medium overnight prior to the experiment and deprived of glutamine during the assay, the K562 ZBTB7A KO cells did not exhibit an advantage in oxidizing this substrate for ATP production. Moreover, in this context, the ZBTB7A KO cells responded negatively to the inhibition of the CPT1A enzyme by Etomoxir, suggesting that these cells are not dependent on fatty acid oxidation. Interestingly, RNA-seq revealed that in K562 ZBTB7A KO cells several genes from the electron transport chain (ETC) were downregulated, supporting the idea that these cells do not depend on OXPHOS metabolism. Metabolic tracing of the 13C6 glucose isotope by mass spectrometry confirmed that K562 ZBTB7A KO cells exhibit upregulated glycolysis and pentose phosphate pathways, as previously reported (Redondo Monte et al., 2020, Oncogene; Liu et al., 2014, Genes Dev.). Conversely, tricarboxylic acid cycle (TCA) metabolites were not different between control and knockout cells. We observed that upregulation of glycolysis resulted in high amounts of acetyl-CoA, which is not entering the OXPHOS metabolism but is used as a precursor for palmitate synthesis instead (Figure 1A). Of note, palmitate is required for the production of several complex lipids in cell membranes, which are highly demanded in cancer cells. Accordingly, the transcript level of FASN, the enzyme that catalyses palmitate synthesis, is upregulated in core binding factor (CBF) AML patients with mutation in ZBTB7A (Figure 1B). Remarkably, the K562 ZBTB7A KO cells preferentially produce acetoacetate (ketone bodies) from the additional acetyl-CoA and secrete it to the medium (Figure 1A). The genes HMGCS1 and ACAT1, encoding enzymes that enable ketone bodies reutilization in lipid synthesis, are downregulated upon ZBTB7A loss, indicating that these cells do not use the ketone bodies. Since ketone bodies not only serve as a substrate for ATP production but also act as signaling mediators, we hypothesize that ketone bodies might fuel the bone marrow microenvironment to support leukemia cells expansion. In summary, we have advanced the understanding of ZBTB7A loss in leukemia metabolism, showing increased lipid and ketone bodies synthesis at the metabolite level. Lipid synthesis enzymes, such as FASN, FADS1, and FADS2 are attractive drug targets for therapeutic applications, especially in combination with standard therapies and glycolysis inhibitors.

KIT exon 17 mutations are predictive of inferior outcome in pediatric acute myeloid leukemia with RUNX1::RUNX1T1.

Pediatric core binding factor acute myeloid leukemia (CBF-AML), although considered a favorable risk subtype, exhibits variable outcomes primarily driven by additional genetic abnormalities, such as KIT mutations. In this study, we examined the prognostic impact of KIT mutations in 130 pediatric patients with CBF-AML, treated uniformly at a single center over 4years (2017-2021). KIT mutations were detected via next-generation sequencing using a myeloid panel comprising 52 genes for most patients. Our findings revealed that KIT mutations were present in 31% of CBF-AML cases. Exon 17 KIT mutation was most commonly (72%) seen with notable occurrences at the D816 and N822 residue in 48% and 39% of cases, respectively. The 3-year cumulative incidence of relapse (CIR) and overall survival (OS) for patients with exon 17 KIT mutation were 36% and 40%, respectively, and was significantly worse in comparison to other site KIT mutations (3-year CIR: 11%; OS: 64%) and without KIT mutation (3-year CIR: 13%; OS:71%). Notably, the prognostic impact of KIT mutations was prominent in patients with RUNX1::RUNX1T1, but not in those with CBFB::MYH11 fusion. Additionally, a high KIT variant-allele frequency (VAF) (>33%) predicted for a higher disease relapse; 3-year CIR of 40% for VAF greater than 33% versus 7% for VAF less than 33%. When adjusted for site of KIT mutation and end-of-induction measurable residual disease, VAF greater than 33% correlated with poor OS (hazard ratio [HR]: 4.4 [95% CI: 1.2-17.2], p=.034). Exon 17 KIT mutations serve as an important predictor of relapse in RUNX1::RUNX1T1 pediatric AML. In addition, a high KIT VAF may predict poor outcomes in these patients. These results emphasize the need to incorporate KIT mutational analysis into risk stratification for pediatric CBF-AML.

Maintenance Therapy with Chidamide Decreases the Relapse in Fusion Gene-Positive AML Patients with MRD-Positive or ELN-High Risk

Purpose: Acute myeloid leukemia (AML) patients with fusion gene-positive including core binding factor (CBF), mixed-lineage leukemia (MLL) gene rearrangement have a high incidence of relapse if they are continious measurable residual disease (MRD)-positive or in ELN-high risk and could not be bridged to allogenetic heamatopoitic stem cell transplantation (allo-HSCT). As known histone deacetylase (HDAC) is abnormally recruited in these fusion gene-positive AML, also RUNX1 mutated AML, and could be a therapy target. Aim of this study is to assess the effect and safety of HDAC inhibitor chidamide as maintemance therapy in these AML patients. Methods: A multi-center retrospective study was performed. Patients with MRD-positive CBF-AML, MLL rearrangement or RUNX1 mutation AML, without being bridged to allo-HSCT were included. Maintemance with chidamide was started one to three months after consolidation for at least six months, at a dose of 10mg/day or 30mg twice a week. Results: Twelve patients were enrolled, included 8 with AML1-ETO-positive, 3 with RUNX1 mutation, 1 with MLL rearrangement. The median age was 33(16-62) years old. The ratio of male to female was 6 to 5. They previously experienced median 6(4-8) cycles of chemotherapy, included one with allo-HSCT, one with autologous-HSCT. They were all maintemanced with chidamide, except one with chidamide plus sorafenib. Eleven patients were available for outcome assessment. With a median follow-up of 14(2-67) months, among the 9 patients with MRD-positive, 6(66.7%) achieved MRD-negative, 1 stable disease, 2 relapsed and died. The median time to achieved MRD-negative was 2.5(1-12) months. The other 2 patients was contenious MRD-negative. The cumulative incidence of relapse was 2/11(18.2%). The rate of MRD-nagetive was 8/11(72.7%). The mortality rate was 2/11(18.2%). During the maintemance, 4 patients underwent bone marrow suppression, including 2 with grade 3, 2 with grade 1/2. One patients had an anorexia of grade 2. Conclusion: Maintenance therapy with chidamide might decrease the relapse in fusion gene-positive AML patients with MRD-positive or ELN-high risk, who could not take allo-HSCT, and prolong their survival, with a well toleration. Key words: chidamide, maintenance, fusion gene, acute myeloid leukemia

Genomic Analyses Unveil the Pathogenesis and Inform on Therapeutic Targeting in KMT2A-PTD AML

A partial tandem duplication (PTD) in the KMT2A gene is detected in approximately 5-10% of acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Previous studies revealed that HOX-genes are highly expressed in KMT2A-PTD AML similar to KMT2A-rearranged or NPM1-mutated AML. While the overexpression of HOX-genes is a convergent oncogenic pathway shared by these molecular subtypes of AML, the mechanism by which KMT2A-PTD induces high expression of the HOX-genes remains unclear and may be distinct from that mediated by balanced KMT2A-translocations, and NPM1 mutations. We stipulated that analysis of common molecular features of KMT2A-PTD will help identifying mechanistic intersections pointing towards possible targeted therapies. In a total of 5420 AML cases 1 including 793 cases from publicly available sources (Beat AML 2 and TCGA 3), we identified 254 cases of KMT2A-PTD. Somatic mutational screening and karyotype analysis showed co-occurrence with DNMT3A (31%), FLT3-ITD (32%), IDH1/2 (26%), RUNX1 (28%), TET2 (18%), SRSF2, STAG2, U2AF1 mutations and deletion 5q. Strong leukemic initiators such as KMT2A-rearrangement, CBFB-MYH11, PML-RARA, RUNX1-RUNX1T1, trisomy 8 and NPM1 mutations were mutually exclusive with KMT2A-PTD and did not rely on acquisition of additional mutations linked to secondary AML ontogenesis ( e.g., ASXL1, RUNX1, SRSF2, and STAG2) different from KMT2A-PTD. Next, we analyzed bulk mRNA-expression between mutually exclusive KMT2A-PTD, KMT2A-rearranged or NPM1-mutant high HOX-genes expressors. While several differentially expressed genes (DEG) between KMT2A-PTD and KMT2A-rearranged cases were detected, there were few DEG between KMT2A-PTD and NPM1-mutated cases. Compared to KMT2A-rearrenged cases, KMT2A-PTD had higher expression of CD34 and KIT in addition to some HOX-genes such as HOXB2 or NKX2-3. In contrast, expression of CD1D, CD14, and immune checkpoint genes including LILRB4, CD276, CD86, and SIGLEC7 was much higher in KMT2A-rearranged than KMT2A-PTD cases. These results prompted us to analyze the hematopoietic differentiation status. For this purpose, we defined three gene signatures along the HOX-targeted genes axis, termed as HOX-primitive, HOX-transient, and HOX-committed profiles. Differentiation analysis revealed almost all of KMT2A-PTD cases could be subclassified into HOX-transient stage while most of KMT2A-rearranged cases were HOX-committed. However, NPM1-mutated cases were interspersed in all the differentiation stages along the HOX-axis. We therefore assumed that there were a few DEG shared between KMT2A-PTD and NPM1-mutated cases as some NPM1-mutated AML clustered in the HOX-transient expression profile group. Intriguingly, DEG analysis was concordant with the hierarchical clustering based on the HOX-gens axis. Indeed, CD34 and KIT were highly expressed in the HOX-transient cases, and CD1D and CD14 in the HOX-committed cases, consistent with the enrichment of KMT2A-PTD and KMT2A-rearranged AML, respectively. We can conclude that the observed signatures were unique to the HOX-stages rather than the molecular abnormalities such as KMT2A-PTD and KMT2A-rearrangements. For example, CD34 upregulation was a feature shared transversally by all HOX-transient cases, including both KMT2A-rearranged and NPM1-mutated cases. As shown in Figure, KMT2A-rearranged, KMT2A-PTD, and NPM1-mutated cases were more clearly classified in HOX-profiles than molecular abnormalities. Additionally, among the cases which molecular subtypes were not clear, those with high HOX-genes expression revealed higher MEN1 expression. In conclusion, despite molecularly different, KMT2A-PTD, KMT2A-rearranged, and NPM1-mutated AML have similar expression patterns defined by each HOX differentiation stage. Like core binding factor AML such as RUNX1-RUNX1T1 and CBFB-MYH11, AML with higher expression of HOX-genes should be classified in the same group, HOX-AML. Given the results obtained with menin inhibitors in KMT2A-rearranged and NPM1-mutated AML, our findings open an opportunity for exploiting a therapeutic vulnerability in all HOX-AML including KMT2A-PTD AML or AML with high MEN1 expression. Since HOX-AML highly express genes according to the HOX differentiation profile, stage-specific surface proteins coded by these genes would be promising targets.

Concurrent BCR::-ABL1 and CBFB Rearrangement in De Novo Acute Myeloid Leukemia

Introduction Acute myeloid leukemia (AML) is known for its genetic heterogeneity. Several recurrent genetic variants have been characterized including AML-defining chromosomal rearrangements involving the core binding factor (CBF), such as inv(16)/t(16;16)/ CBFB:: MYH11. 1 Less common is a subset of AML characterized by the Philadelphia chromosome (Ph+), generating a BCR::ABL1 fusion protein. 2 The Ph+ AML subtype is associated with poor prognosis and treatment resistance. 3,4 Co-occurrence of CBFB rearrangement and BCR::ABL1 fusion is rare, representing a subgroup with unique clinical and molecular features. To date, there have been less than 30 cases reported in the literature. 5-8 Case Description A 62-year-old male presented to hospital with headaches, visual changes, weakness, and a nodular rash on his back, with leukocytosis, thrombocytopenia, and 42.5% circulating blasts. A bone marrow (BM) aspirate and biopsy was diagnostic of AML with 56% myeloblasts. RT-PCR was positive for an e19a2 BCR::ABL1 fusion transcript coding for p230 kDa fusion protein (p230) and CBFB: :MYH11 fusion gene transcript. Cytogenetics identified a complex karyotype with an inv(16) and a Ph chromosome (46,XY,t(1;14)(p32;q24),t(9;22)(q34;q11.2),inv(16)(p13.1q22)[10]), consistent with concurrent BCR::ABL1 and CBFB::MYH11 rearrangements within the same clonal population of cells. Treatment consisted of hydroxyurea for cytoreduction, 7+3 induction, one cycle of low dose cytarabine consolidation, and oral azacytidine maintenance, in combination with dasatinib. He did not receive Gemtuzumab ozogamicin (GO) given patient preference and comorbidities. Post-induction course was complicated by febrile neutropenia due to Enterococcus Faceium bacteremia, pre-renal acute kidney injury, and dasatinib-related complications including rash and transaminitis. These issues resolved by holding dasatinib for 15 days. Complete morphologic remission (CR) was obtained by Day 33 post-induction and no fusion gene transcripts were detectable by nested RT-PCR from BM aspirate on day 49 post-induction, nor day 76 post-consolidation The patient was ineligible for an allogeneic stem cell transplant given his poor performance status. At present, the patient remains alive and well, continuing on maintenance with oral azacytidine and dasatinib. Discussion We present the only case, to our knowledge, of a concurrent BCR::ABL1 p230 isoform and CBFB::MYH11 with de novo AML. Based on our literature search, 26 cases have been reported. BCR::ABL1 and CBFB::MYHII rearrangements in de novo AML potentially confers an intermediate to favorable prognosis with outcomes comparable to those of CBF-AML. Studies suggest that this entity may be more akin to AML with inv(16) rather than CML-BP with inv(16), thereby retaining favorable prognosis. 5,9-11 There are no formal guidelines for management of de novo AML with concurrent BCR::ABL1 and CBFB rearrangements. Traditional chemotherapy treatment strategies for Ph+ AML are often ineffective in these cases. The presence of BCR::ABL1 fusion transcript raises the possibility of utilizing TKIs targeting the BCR::ABL1 kinase domain. In our case, the patient achieved rapid CR with induction chemotherapy and dasatinib, but experienced multiple complications, precluding further intensive chemotherapy and allogeneic stem cell transplantation. This case raises a number of questions, including the optimal timing, combination, and duration of TKI therapy in the context of dual rearrangement de novo AML. This patient subgroup may benefit from intensive chemotherapy regimens and TKIs. Prospective monitoring of these cases is warranted to assess outcomes in comparison to Ph+ AML without coinciding CBFB rearrangement. This case report underscores the importance of comprehensive genetic profiling in Ph+ AML to determine the genetic landscape and individualize therapeutic strategies.

Data-Driven Harmonization of 2022 Who and ICC Classifications of Myelodysplastic Syndromes/Neoplasms (MDS): A Study By the International Consortium for MDS (icMDS)

Background. The inclusion of gene mutations and chromosomal abnormalities in the 2022 WHO and ICC Classifications of MDS has enhanced diagnostic precision and is expected to improve clinical decision-making process. Although these two systems share similarities, clinically relevant discrepancies still exist and potentially cause inconsistency in their adoption in a clinical setting. In this study on behalf of the International Consortium for MDS (icMDS), we adopted a data-driven approach to provide a harmonization roadmap between the 2022 WHO and ICC classification for MDS. A modified Delphi Process consensus approach is currently ongoing among icMDS experts to finalize a harmonized MDS classification scheme. Methods. We analyzed retrospective international cohorts of patients with a diagnosis of MDS (n=7017) and AML (n=1002) according to WHO 2016 criteria. Hierarchical Dirichlet Processes were applied to define clusters capturing broad dependencies among all gene mutations and cytogenetic abnormalities. To investigate the features of importance and their impact on the clustering process, we employed the SHapley Additive exPlanations approach (SHAP). This allowed to define harmonized labels for each clinical entity. The clinical relevance of the unsupervised clustering was assessed through the analysis of phenotypic features and outcomes among each group. ( Blood 2022;140: 9828-9830) Results. Patients' characteristics are summarized in Table 1. We identified 9 clusters, defined by specific genomic features. The cluster of highest hierarchical importance was characterized by biallelic inactivation of TP53 (biTP53). According to SHAP analysis, bi TP53 was defined as 2 or more TP53 mutations, or 1 mutation with copy number loss or cnLOH. Most patients assigned to bi TP53 cluster had TP53 VAF>10% (77.9%) and complex karyotype (70.1%). Assignment to bi TP53 cluster was irrespective of blast count. Patients with monoallelic TP53 mutation segregated into other clusters. Hierarchically, the second cluster included patients with del(5q). SHAP analysis highlighted 5q deletion alone, or with one other chromosomal abnormality other than -7, and absence of bi TP53, as the most relevant features. Most of these patients had blast counts <5% (88.1%). The third distinct cluster included patients with SF3B1 mutations (in the absence of concurrent del(7q), abn3q26.2, complex karyotype or RUNX1 mutation). Most patients with MDS and SF3B1 mutation had <5% blasts (94.2%). Common co-mutated variants in the SF3B1 cluster included mutant DNMT3A (25.2%) and TET2 (38.3%). Morphologically defined MDS cases (i.e., not meeting criteria for bi TP53, del(5q) or SF3B1) were preferentially assigned to the following additional clusters: SF3B1 and concurrent higher-risk mutations (e.g., RUNX1 and ASXL1); SRSF2 and concomitant TET2 mutations; U2AF1 mutations with del(20q), del(7q) or -7; SRSF2 with TET2 mutations and co-mutational patterns including RUNX1 and ASXL1; and AML-like genomic signatures. Our analyses suggest that morphologically defined MDS is characterized by a large heterogeneity in terms of mutation profiles, not entirely captured by the presence of unilineage versus multilineage dysplasia, percentage of bone marrow blasts, and presence of hypocellularity and fibrosis. To better investigate the continuum between high risk MDS (i.e., patients with ≥10% blasts) and AML, an exploratory comparison was made using a cohort of AML (defined according to WHO 2016) patients analyzed using the same statistical methods. Only a partial overlap in genetic signatures was observed between MDS with ≥10% blasts and AML. However, similarities were observed between the AML-like MDS clusters (characterized by mutant NPM1, bZIP CEBPA, and Core Binding Factor abnormalities) and AML clusters defined by the same genetic signature, thus supporting the classification of these entities as AML, irrespective of blast count. Conclusion. Our study demonstrated the utility of a data-driven approach based on advanced statistical methods to generate a harmonized classification for MDS. Table 2 shows a provisional, hierarchical classification algorithm. Further refinement of entity labels and classification criteria is the subject of the ongoing modified Delphi Process consensus approach among icMDS experts.

Molecular Characterisation and Outcomes of 363 Adolescent and Young Adults with AML in Saudi Arabia Risk Stratified By PCR and NGS-Based Testing

Introduction Acute Myeloid Leukaemia (AML) is characterised by cytogenetic (CGN) abnormalities and or mutations in one or more of a number of genes that allow risk stratification and guide treatment. The mutational landscape of patients from Saudi Arabia, which has a young population, has not been well characterised. One study indicates a higher rate of core binding factor and monosomies. Mutational analysis by Next generation sequencing (NGS) has not had widespread utilisation hampering the risk stratification of AML in the country. The more recent introduction of NGS panels has allowed more risk stratification. Here we analysed patients and characterised the CGN and molecular abnormalities. Methods Data were collected from 363 patients, and their cytogenetic and molecular results were reviewed. Patients were divided into 2 cohorts: Cohort A only had PCR-based testing diagnosed or treated at King Faisal Specialist Hospital and research centre - Riyadh. PCR testing included mutation analysis for FLT3, NPM1, CEBPA, c-KIT, IDH1, IDH2, WT1, DNMT3A, and JAK2; quantitative PCR for RUNX1-ETO in a subset of patients. Cohort B had PCR-based mutation testing in addition to the Next-Generation Sequencing (NGS) myeloid panel, which was Illumina-based or Ion Torrent. The panel comprises 23 hotspot genes, 17 entire genes, 29 fusion drivers, and five expression genes associated with haematological malignancies. We risk-stratified patients according to the most recent testing method available. Cohort A and Cohort B were risk-stratified, according to ELN risk classification 2017. Survival analysis for these patients was conducted. Results The median age for all patients was 39 years (13-89). PCR testing included mutation analysis for FLT3 (93.4%), NPM1 (90.4%), CEBPA (69.7%), c -KIT (54.3%), IDH1 (57%), IDH2 (57.9%), WT1 (61.2%), DNMT3A (54.5.5%), JAK2 (4.7%) and quantitative PCR for RUNX1- ETO fusion (13.2%). Cohort A comprised 262 (72.7%) patients who underwent PCR-based mutation testing only. Cohort B consisted of 101 (27.8%) patients who underwent PCR-based mutation testing in addition to NGS myeloid panel analysis. In the entire cohort of 363 patients, we found FLT3-ITD mutations in 85 patients (23.4%) and NPM1 mutations in 68 (18.7%). 36 patients (9.9%) harboured both FLT3-ITD and NPM1 mutations together. In Cohort A, FLT3-ITD detected 26.7% of patients, and 20.2% had NPM1 mutation, while 40% had no detectable mutations by conventional PCR. On the other hand, FLT3-ITD was detected in 14.9% of patients by both NGS and conventional PCR and in 14.9% of patients with NPM1. When comparing Cohort A and Cohort B, Cohort B had more mutations in genes that play an important role in myeloid malignancies, which might have better risk stratification and precision, including TP53 in 13.9% of patients and RUNX1 in 18.8% of patients and ASXL1 in 9.9% of patients. Moreover, NGS pick up more mutations in CEBPA, c-KIT, WT1, IDH1 and JAK2 genes compared to conventional PCR. Within cohort A, 9.2% of patients had normal cytogenetic testing results with no detectable mutations, whereas in cohort B, only 1% of patients had normal karyotype and molecular testing. Furthermore, six mutations were detected only by NGS but not PCR in FLT3-ITD, CEBPA, c-KIT, IDH2, WT1 and DNMT3A in 5.9% of patients. Cohorts A and B were also categorised into ELN risk groups using PCR, sequencing, and cytogenetics testing. It was found that patients at adverse risk had shorter overall survival compared to those at intermediate or favourable risk in both cohorts, with p-values of 0.030 and 0.0007, respectively (Figure 1). The use of NGS was found to be more effective than conventional testing in identifying patients with adverse risk, with a hazard ratio for death of 0.22 (95% CI, 0.08989-0.5732) compared to a hazard ratio of 0.66 (95% CI, 0.4352 -1.031) for conventional PCR testing. Conclusion In this study, we present the mutational profile of AML in young Saudi patients and identify certain frequent mutations in this population. The study presents the largest molecular profiling to our knowledge of this population. The study emphasises the need for integration of NGS to enhance risk stratification and precision, enable better characterisation of high-risk patients, and improve the potential for targeted treatments.

Intensification of Therapy and Pharmacogenetic Personalization Mitigate Racial Disparities in Pediatric Acute Myeloid Leukemia Outcomes

Introduction Recent reports have highlighted disparities in outcomes for black children, adolescents, and young adults with acute myeloid leukemia (AML) compared to their non-Hispanic white counterparts. An analysis of pediatric AML patients treated from 1996-2013 revealed that black race was associated with inferior event-free survival (EFS) and overall survival (OS) (Conneely 2021). In a study of adolescent and young adult patients with AML, black race was a predictor of poor outcome, particularly among patients 18-29 years old (Larkin 2022). Addressing these outcome disparities and developing treatment strategies to overcome them is crucial. In this study, we evaluated the interactions between outcomes by race and cytarabine pharmacogenomics in pediatric AML patients treated on two multi-institutional clinical trials. Methods Pediatric patients with newly diagnosed AML treated on AML02 (NCT00136084) or AML08 (NCT00703820) were included. Patients received high-dose cytarabine, daunorubicin, and etoposide (HDAC), low-dose cytarabine, daunorubicin, and etoposide (LDAC), or clofarabine and cytarabine (Clo/AraC) as initial therapy. The pharmacogenomics ACS10 scores, derived from combination of 10 single nucleotide polymorphisms, were calculated as reported (Elsayed 2022). Results Overall, 86 patients were black and 359 were white; 68 had other or unknown racial backgrounds and were not included in this analysis. Complete remission rates after two courses of induction therapy did not differ between black and white patients (92.6% vs 95.0%, p=0.63), nor did the rates of MRD negativity after one course of therapy (55.8% vs 55.4%, p=0.85). The EFS rates of black and white patients were nearly identical, with 5-year estimates of 58.3% (95% CI = 48.8%-69.8%) and 58.2% (95% CI = 53.2%-63.6%; p=0.89, Fig 1). Likewise, OS did not differ between black and white patients (63.8%; 95% CI = 54.3%-74.8% vs 69.4%; 95% CI = 64.7%-74.5%; p=0.24). The cumulative incidence (CI) of relapse did not differ by race (26.0% vs 26.1%, p=0.99), nor did the CI of treatment-related mortality (7.0% vs 6.8%, p=0.78). The prevalence of core binding factor (CBF) leukemia was higher in black patients as compared with white patients (30% vs 19%, p=0.04), but we did not find differences in EFS between black and white patients with or without CBF AML. We recently showed that low ACS10 scores were associated with worse outcomes in patients treated with low-dose cytarabine-based induction. In the present study, there was a significant difference in the distribution of ACS10 scores according to race, with low scores occurring in 73% of black patients compared with 30% of white patients (p<0.001). When patients on all treatment regimens were considered, there were no differences in EFS between black and white patients with low (p=0.88) or with high ACS10 scores (p=0.72). However, black patients with low ACS10 scores had significantly better outcomes after treatment with Clo/Ara-C induction compared with LDAC induction (p=0.01 for EFS and p=0.04 for OS, Fig 2). In multivariable model adjusting for age, risk group, and leukocyte count, Clo/Ara-C induction was identified as the best treatment option for black patients with low ACS10 scores (EFS: HR = 0.2, p=0.03). Discussion Our findings contrast with recent reports, as we did not observe significant outcome differences between black and white patients in terms of complete remission rates, EFS, OS, CI of relapse, or CI of treatment-related mortality. The higher prevalence of low ACS10 scores in black patients compared with white patients likely contributes to outcome disparities observed among patients treated with LDAC in the present study and those in the literature, which have included patients who almost exclusively received low-dose cytarabine-based induction therapy. In the present study, black patients with low ACS10 scores had significantly worse outcomes compared to those with high scores when treated with LDAC. However, these differences in outcome were eliminated by the use of HDAC or Clo/Ara-C induction. By contrast, black patients with high ACS10 scores did not appear to benefit from HDAC or Clo/Ara-C induction. Our results suggest that pharmacogenomics differences between black and white patients should be considered when tailoring induction regimens to improve outcomes of black patients and bridge the racial disparity gap in AML treatment.

CPX-351 with Venetoclax in Patients with Relapsed/Refractory Acute Myeloid Leukemia: Results of a Phase Ib Study

Introduction: Relapsed/refractory acute myeloid leukemia (rAML) remains a significant challenge, with low response to therapy and poor long-term survival. Treatments focusing on achieving a response and, in eligible patients (pts), proceeding with an allogeneic stem cell transplantation (alloSCT) offer the best prospect for improved survival. CPX-351 is a liposomal fixed-ratio formulation of cytarabine and daunorubicin, which has demonstrated higher response rates and reduced early mortality in some subsets of AML and has also been shown to be active in rAML. The BCL2 inhibitor venetoclax (Ven) has demonstrated efficacy in AML in combination with other agents, such as hypomethylating agents, low dose cytarabine, and intensive chemotherapy. We conducted a Phase Ib/II dose-finding study to evaluate the combination of CPX-351 with Ven in AML. Herein we present the results of CPX-351 plus Ven in the cohort of rAML pts treated on study (NCT03629171). Methods: The study was designed with a safety lead-in phase to establish the safe dose and schedule in R/R AML, followed by 2 expansion cohorts to explore efficacy in (1) R/R AML and (2) frontline AML. Prior Ven use was allowed for pts with R/R AML. The dose of CPX-351 was fixed : daunorubicin 44 mg/m2 and cytarabine 100 mg/m2 IV on days 1, 3 and 5 of induction, and daunorubicin 29 mg/m2 + cytarabine 65 mg/m IV on days 1 and 3 during consolidation. The starting effective dose of Ven was 300mg (at the -1 dose level) on D2-21 for the safety lead-in cohort with appropriate dose adjustment for concomitant CYP3A inhibitors. First, interruption of Ven after D14 was implemented if a D14 bone marrow was hypocellular and without evidence of leukemia. However, a second de-escalation was required (-2 dose level) with Ven given on day 2-8 of each cycle, and daunorubicin dose reduced to 22 mg/m2 during consolidation. This was found to be the recommended phase 2 dose. Results: Between 11/2018 to 1/2022, 33 pts were enrolled. The median age was 53 yrs (range, 26-72) and 61% were female. Diploid karyotype was present in 7 pts (21%), core binding factor rearrangements in 2 (6%), MECOM rearrangement in 2 (6%) and 13 (39%) had a complex karyotype. The most frequent mutations were DNMT3A (37%), TP53 (21%) and NRAS (21%). 8 (24%) pts had secondary AML including 4 (12%) with prior HMA exposure; the median number of prior lines of myeloid-directed therapies was 1 (1-7), including 58% of them with a previous exposure to Ven. Pts received a median of 1 cycle (1-4), and the median number of cycles to first response was 1 (1-2). The ORR was 45% (15/33), with 5 patient (15%) achieving CR, 8 (24%) achieving CRi and 2 (6%) achieving MLFS. The ORR was higher in those pts with only one prior line of therapy (59%) compared to those with 2 or more previous therapies (31%). The ORR for pts with prior exposure to Ven was 37% (7/19) vs 57% (8/14) for those not previously exposed to Ven (p=0.4). The 4- and 8-week mortality was 9 and 21%. 9/15 pts (60%) underwent alloSCT including 14 with CR/CRi/MLFS and 1 pt with an aplastic bone marrow insufficient for response assessment. The most frequent grade 3 or more adverse events were infections (45%, 30% of them pulmonary), febrile neutropenia (24%), and mucositis/stomatitis (6%). Three deaths occurred on study (2 due to sepsis and 1 due to cardiac arrest), all after one cycle of therapy. Other grade 3-4 events registered included rash (6%), cerebrovascular accident (6%), and intracranial hemorrhage (3%). After a median follow-up time of 20.7 months, the OS at 12 and 24 months was 34% and 25%, respectively. The median OS was 6.4 months. The EFS at 12 and 24 months was 26% and 19%, respectively. The median EFS was 2.8 months. For those who achieved response, the 2-year cumulative incidence of relapse and death without relapse were 41% and 28%, respectively. For those who underwent alloSCT, the median OS after alloSCT was 24 months, with 4 deaths after alloSCT, all following disease relapse. Conclusion: In this phase Ib dose escalation study, standard dose CPX-351 combined with 7 days of Ven was found to safe and tolerable in pts with rAML. The combination produced encouraging response rates in a poor risk population, including those with prior Ven treatment, allowing a significant proportion to undergo allo-SCT and extended survival. The RP2D is being studied in pts with newly diagnosed and less heavily pretreated AML.

Cohesin Haploinsufficiency Promotes Reduced Latency in Inv(16) Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a cancer of the bone marrow that affects 20,000 adults in the United States alone, with global rates increasing over the last 30 years (Heimbruch et al. 2021, Dong et al. 2020). Approximately 15% of adult AML patients harbor the chromosomal aberrations t(8;21) or inv(16), which affect the core binding complex members RUNX1 and CBFB, respectively. Together, RUNX1 and CBFB function as a transcription factor that regulates key lineage genes and proliferation in hematopoietic cells (Pulikkan and Castilla 2018). t(8;21) and inv(16) result in the expression of the fusion proteins AML1-ETO and CBFB-SMMHC, both of which have dominant negative effects on native RUNX1 as well as novel transcriptional roles (Surapally et al. 2021). Although both t(8;21) and inv(16) result in AMLs with similar characteristics, they differ in the number and type of co-occurring mutations (Opatz et al. 2020). More mutations per clone are observed in t(8;21) vs. inv(16) AMLs. Additionally, several studies have highlighted a difference between the rates of mutation of cohesin genes and t(8;21) vs. inv(16) (Faber et al. 2016, Opatz et al. 2020, Duployez et al. 2016, Jahn et al. 2020, Qin et al. 2022). Cohesin is comprised of the subunits SMC3, SMC1A, RAD21, and STAG2. The complex has a prominent role in hematopoietic cells in chromatin organization and DNA looping events that regulate gene expression and self-renewal (Heimbruch et al. 2021). Cohesin mutations are found in approximately 10% of AML cases (Ley et al 2013). Interestingly, cohesin mutations are found in 18-27% of t(8;21) AMLs, but in 0-4% of inv(16) AMLs (Faber et al. 2016, Opatz et al. 2020, Duployez et al. 2016, Jahn et al. 2020, Qin et al. 2022). The low rate of co-mutation between inv(16) and cohesin genes suggests potential synthetic lethality. However, it is also possible that cohesin mutations occur at a higher rate than reported due to biases in the age, ethnicity, or treatment status of the patients included in genome/exome sequencing studies. To test if cohesin mutations and inv(16) are synthetic lethal, we used an inv(16) knock-in mouse model ( Mx1-Cre;inv(16)) combined with a cohesin-deficient mouse ( Mx1-Cre; Smc3 fl/+) (Kuo et al. 2006, Viny et al. 2015). We followed inv(16);Smc3wt and inv(16);Smc3 -/+ animals post-Cre activation and monitored mice for leukemic development. We found that inv(16);Smc3 -/+ mice developed AML with reduced latency compared to inv(16);Smc3wt mice, suggesting cooperativity rather than synthetic lethality. To determine the mechanism by which Smc3 haploinsufficiency accelerates inv(16) leukemias, we performed ATAC sequencing and single cell RNA sequencing on hematopoietic stem and progenitor cells (HSPCs). ATAC-seq revealed a large increase in open chromatin in promoter regions in inv(16);Smc3 -/+ vs. inv(16);Smc3wt HSPCs. These open regions were enriched for binding motifs of the Ets family member Fli1. Increased expression of Fli1 was observed by western blotting in inv(16);Smc3 -/+ HSPCs. Interestingly, CBFB-SMMHC binding sites commonly contain Ets motifs (Mandoli 2014), suggesting that the increased Fli1 expression and binding site accessibility in inv(16);Smc3 -/+ may drive the observed decrease in latency. scRNA-seq revealed cluster-specific differences between inv(16);Smc3wt and inv(16);Smc3 -/+ cells. In several clusters, inv(16);Smc3 -/+ cells showed a loss of expression of genes involved in apoptosis and differentiation. Of particular interest is Gata2, as loss of Gata2 generates a more aggressive phenotype in AML (Saida et al. 2020). Therefore, Smc3 haploinsufficiency may result in Gata2 deregulation, thereby impacting disease latency. Currently, we have two potential explanations for the observed phenotype: Deregulated binding of Fli1 and its downstream transcriptional pathways and decreased expression of Gata2 in sub-populations of inv(16);Smc3 -/+ cells. Which of these mechanisms mediates the reduced latency in inv(16);Smc3 -/+ animals is an area of active investigation. Collectively, our studies show that a lack of observed co-mutation does not necessarily indicate synthetic lethality. We propose that cohesin mutations may be more common in inv(16) leukemias than has been reported and suggest that a careful consideration of age, ethnicity, and treatment status may be warranted when evaluating rates of co-mutation.

Influence of Pre-Treatment Features and Therapy Choice By Physicians on Overall Survival in Older Adults with Acute Myeloid Leukemia: A Report from the Beat AML Master Trial

Background: Acute myeloid leukemia (AML) therapy in older patients (age ≥ 60) has undergone a transformation with the introduction of multiple targeted therapies, which has allowed more patients to receive therapy than before. The most successful has been the combination of venetoclax + azacitidine (VA) which generated higher overall complete response rates in phase 2 studies than would be expected with azacitidine alone, leading to accelerated FDA approval on 21Nov2018. The VIALE-A phase 3 study confirmed the improved overall survival (OS, median 14.7 versus 9.6 months) of VA, leading to full FDA approval for marketing. This retrospective analysis provides real world data on the impact of baseline clinical and genomic markers of individuals receiving intensive chemotherapy versus VA. Methods: The precision medicine Beat AML Master Trial (NCT03013998) assigns patients to biomarker specific sub-study treatments based on targeted DNA sequencing and cytogenetics. However, a large subset of patients did not enroll on a sub-study, but were followed for off-study treatment and OS. From this subset, patients enrolled onward from 21Nov2018, when VA received accelerated approval, were examined for differences in clinical/genetic characteristics and OS in those receiving venetoclax + hypomethylating agent (V/HMA), any form of intensive chemotherapy (IC), alternative non-intensive therapy (NIT), or no therapy. The genetic mutations identified in this study are characterized by a variant allele frequency of 20%+, as defined in the trial for determining the dominant clone. The method of Kaplan-Meier was used to estimate OS, and the Cox model was fit to associate patient characteristics with OS. Results: From 21Nov2018, a total of 468 AML patients consented to the Beat AML trial and did not enroll to a sub-study. Treatment was chosen by the investigator based upon available clinical and genomic data. Of these 468 patients, 62 did not receive treatment, 2 had treatment data missing, 226 were treated with V/HMA, 112 with IC, and 66 with NIT. Demographics for all patients include median age 71 (60-90), 40% female, performance status (PS) (0-20%; 1-55%; 2-22%; 3-3%), median white blood cell (WBC) 4.1 (range 0.3-298.6), complex karyotype (CK) 20.6%, core binding factor (CBF) 7.8%, KMT2A-rearranged 3.6%, NPM1-mutated (m) 15.6%, IDH2m 14.6%, TP53m 13.2%, FLT3-ITD/TKD 12.9%, and NRASm/ PTPN11m/ KRASm/ NF1m/ CBLm 23.6%. Demographics that were significantly different (p<0.01) among the three groups (V/HMA, IC, and NIT) include age (younger in IC), PS (worse in NIT), AST/ALT (worse in NIT), CBF (more in IC), CK and TP53m (less in IC). Of the 404 patients who underwent treatment with V/HMA, IC, or NIT, 208 have died with those surviving having a median follow-up of 22.3 months. Figure 1 summarizes the OS of each treatment group. The median OS (95% CI) from time of initiating therapy is 13.6 (10.9-16.8) for V/HMA, 33.8 (20.7-not reached) for IC, and 11.6 (5.2-21.3) months for NIT. Univariable analysis for OS was significant at p<0.05 for increased age, WBC, PS, hemoglobin, CBF, CK, NPM1m, TP53m, TET2m and IC versus V/HMA. Multivariable analysis was significant at p<0.05 (hazard ratio) for increased age (1.14), PS (1.83), WBC (1.08), hemoglobin (0.91), and select genomic aberrations including CBF (0.37), NPM1m (0.35), and TP53m (2.1). Conclusions: These results from a large cohort of older AML patients treated with V/HMA, IC, or NIT show that their outcome is best defined by pre-treatment clinical features previously identified including age, performance status, WBC and hemoglobin along with limited genomic characteristics including CBF, NPM1m, and TP53m. While univariate analysis of OS favored IC over V/HMA and NIT, multivariable analysis supports that this advantage was most likely due to the favorable clinical and genomic features. The OS of V/HMA patients in this cohort is similar to that in the VIALE-A registration study of VA, providing further justification for this treatment for older AML patients deemed ineligible for intensive chemotherapy. Additionally, this data supports use of the patient cohort in this study for ongoing work in understanding and/or validating biomarkers associated with survival with V/HMA.

Standardization of Molecular MRD Levels in AML Using an Integral Vector Bearing ABL and the Mutation of Interest.

Quantitative PCR for specific mutation is being increasingly used in Acute Myeloid Leukemia (AML) to assess Measurable Residual Disease (MRD), allowing for more tailored clinical decisions. To date, standardized molecular MRD is limited to typical NPM1 mutations and core binding factor translocations, with clear prognostic and clinical implications. The monitoring of other identified mutations lacks standardization, limiting its use and incorporation in clinical trials. To overcome this problem, we designed a plasmid bearing both the sequence of the mutation of interest and the ABL reference gene. This allows the use of commercial standards for ABL to determine the MRD response in copy number. We provide technical aspects of this approach as well as our experience with 19 patients with atypical NPM1, RUNX1 and IDH1/2 mutations. In all cases, we demonstrate a correlation between response and copy number. We further demonstrate how copy number monitoring can modulate the clinical management. Taken together, we provide proof of concept of a novel yet simple tool, which allows in-house MRD monitoring for identified mutations, with ABL-based commercial standards. This approach would facilitate large multi-center studies assessing the clinical relevance of selected MRD monitoring.

Core binding factor subunit β plays diverse and essential roles in the male germline.

Much of the foundation for lifelong spermatogenesis is established prior to puberty, and disruptions during this developmental window negatively impact fertility long into adulthood. However, the factors that coordinate prepubertal germline development are incompletely understood. Here, we report that core-binding factor subunit-β (CBFβ) plays critical roles in prepubertal development and the onset of spermatogenesis. Using a mouse conditional knockout (cKO) approach, inactivation of Cbfb in the male germline resulted in rapid degeneration of the germline during the onset of spermatogenesis, impaired overall sperm production, and adult infertility. Utilizing a different Cre driver to generate another Cbfb cKO model, we determined that the function of CBFβ in the male germline is likely limited to undifferentiated spermatogonia despite expression in other germ cell types. Within undifferentiated spermatogonia, CBFβ regulates proliferation, survival, and overall maintenance of the undifferentiated spermatogonia population. Paradoxically, we discovered that CBFβ also distally regulates meiotic progression and spermatid formation but only with Cbfb cKO within undifferentiated spermatogonia. Spatial transcriptomics revealed that CBFβ modulates cell cycle checkpoint control genes associated with both proliferation and meiosis. Taken together, our findings demonstrate that core programs established within the prepubertal undifferentiated spermatogonia population are necessary for both germline maintenance and sperm production.

Fever with Significant Procalcitonin Increase Following Gemtuzumab Ozogamicin Infusion in Hematologic Malignancy Patients without Evidence of Infection

In patients diagnosed with hematologic malignancies, including acute myeloid leukemia (AML), infections remain a major cause of non-relapse mortality. The accurate detection and management of infections during the treatment of these diseases are crucial for successful outcomes. Procalcitonin (PCT) has been proposed as a valuable tool for identifying severe bacterial infections, even in patients with hematologic malignancies. Gemtuzumab ozogamicin (GO), a humanized anti-CD33 monoclonal antibody conjugated to calicheamicin, is used in certain subsets of AML patients, such as core binding factor (CBF) leukemia and AML with favorable-risk, as well as in cases of refractory AML. However, GO administration comes with its own set of risks, including liver dysfunction, veno-occlusive disease (VOD), bone marrow suppression, bleeding, and infusion reactions. Among these reactions, those causing high fever and shivering can be particularly challenging to differentiate from sepsis or severe infections. Nevertheless, there have been no reports evaluating the utility of PCT in discriminating infections during GO-induced infusion reactions. To shed light on the impact of GO administration on PCT levels, we undertook a retrospective analysis. Over the period between 2014 and 2022, we administered GO (3.0 mg/sqm per dose) to 42 patients with hematologic malignancies, a total of 97 times (median 2 doses per patient, range 1-6 doses per patient). Of the recipients, 23 had undergone allogeneic stem cell transplantation, while 19 were non-transplant patients. Prior to GO administration, all patients received premedication comprising corticosteroids, antihistamines, and acetaminophen. Among the 97 instances of GO administration, 40 (41.2%) resulted in fever (≥37.5 ℃) within 24 hours. For 19 cases, we conducted a complete set of PCT measurements and blood cultures within 24 hours of GO administration and analyzed the PCT levels and clinical parameters. These 19 cases corresponded to 19 individual patients, of whom nine had CBF leukemia, including t(8;21) AML or inv(16) AML, and ten had non-CBF leukemia. Out of these patients, 12 experienced fever (≥37.5 ℃), while seven did not. The findings indicated that patients with fever (≥37.5 ℃) exhibited significantly higher PCT levels compared to afebrile patients (p=0.018). Furthermore, PCT levels showed a significant positive correlation with C-reactive protein levels (p=0.003). However, among the 19 patients, only one patient with a positive PCT result had a documented infection identified through blood cultures or imaging studies.Other factors, such as patient gender (p=0.467), underlying disease (p=0.224), disease remission status at GO administration (p=0.492), transplant status (p=0.556), and the number of GO administrations (p=0.906), did not significantly influence PCT levels. It is essential to acknowledge that this analysis is based on a limited number of cases from a single institution. Nevertheless, approximately 40% of patients experienced fever within 24 hours of GO administration, despite receiving premedication.Furthermore, the presence of fever after GO administration was associated with a significant increase in PCT levels, even in the absence of identifiable infection. This raises the possibility of false positives for PCT in the context of GO-induced infusion reactions, underscoring the need for cautious interpretation of PCT values for infection differentiation in patients undergoing regimens that include GO. Further research with larger patient cohorts is warranted to validate these findings and improve our understanding of the implications of PCT measurements in this clinical setting.

Unmet Medical Needs Amongst Older Patients Aged ≥60 Years with Newly Diagnosed Acute Myeloid Leukemia Receiving Intensive Chemotherapy: Experience from a Predominately United States Community Setting

Background: Venetoclax (Ven) in combination with hypomethylating agents is approved for treatment in patients (pts) with newly diagnosed (ND) acute myeloid leukemia (AML) who are ≥75 years old or unfit for intensive chemotherapy (IC), based on the longer median overall survival (OS) with Ven+azacitidine (Aza) compared with Aza in combination with placebo in the Phase III VIALE-A study (NCT02993523). Several studies are now evaluating Ven-based regimens in pts eligible for IC, for example Ven+Aza compared with IC (NCT04801797). Additionally, Ven in combination with cladribine (CLAD) and low-dose cytarabine (LDAC) is currently under investigation in a Phase II single-arm study (NCT03586609) amongst older pts (aged ≥60 years) with ND AML. An interim analysis of this trial evaluated 60 pts where complete remission (CR) and CR with incomplete count recovery (CRi) was observed in 93% of pts, and the median OS, overall and by transplant status, was not reached; 1-year OS was 72.9% and 2-year OS was 63.5% (Kadia et al. J Clin Oncol 2022). The aim of this study is to better understand treatment outcomes amongst older pts (aged ≥60 years) with ND AML receiving IC in a routine clinical care setting in the United States (US). Methods: This was a retrospective cohort study using the Flatiron Health electronic health record-derived, US nationwide, de-identified database. Pts aged ≥60 years with ND AML who initiated IC within 60 days of AML diagnosis (Dx) between January 1, 2014, and November 30, 2022, with ≥2 visits recorded within 3 months of AML Dx, and ≥3 months of follow-up before study end date (February 28, 2023) were included. Clinical trial participants and pts with acute promyelocytic leukemia or core binding factor were excluded. Descriptive analysis on patient characteristics was conducted. The proportion of pts who achieved real-world response (defined as <5% bone marrow [BM] blasts), real-world CR/CRi (defined as <5% BM blast with either platelet count <100 x 10 9/L or absolute neutrophil count <1000 x 10 9/L) and received a stem cell transplant (SCT) post-remission were reported. Thirty-day mortality, 60-day mortality, 1-year real-world OS (rwOS), and 2-year rwOS were evaluated using Kaplan-Meier (KM) analyses. The starting points for KM analyses were IC treatment initiation (all pts), SCT (pts who underwent SCT post-remission), and remission (pts who did not undergo SCT post-remission). Pts were censored at the last activity date or SCT date (whichever occurred earliest) for the overall patient cohort, and the last activity date for pts with or without SCT post-remission. Results: A total of 1105 pts met the study criteria. The median (IQR) age was 67 (64-71) years, 57% were male, 27% had secondary AML, 48% had BM blast >50% at Dx, and 66% were treated in the community setting. Excluding 340 pts with unknown cytogenetic and molecular data, 19%, 32%, and 48% of pts had European LeukemiaNet 2017 favorable, intermediate, and adverse risk, respectively. At a median (IQR) follow-up of 13 (6-28) months from AML Dx, 74% (n=821) of pts achieved real-world response, including 66% (n=724) who achieved real-world CR/CRi. For all pts, the 30-day mortality was 3%, 60-day mortality was 6%, 1-year rwOS was 58%, 2-year OS was 34%, and the median rwOS was 14.3 months ( Figure A). A total of 37% (n=306/821) of pts underwent SCT post-remission; 98% (n=300/306) underwent allogeneic-SCT and 2% (n=6/306) underwent autologous-SCT. The median rwOS was 40.4 months for pts undergoing SCT post-remission, and 13.8 months for pts without SCT post-remission ( Figure B). Conclusions: In this large real-world data study, we observed older pts (aged ≥60 years) with ND AML receiving IC treatment had a median OS of <14 months and <35% of pts remained alive 2 years after IC initiation. Findings from this study suggest the need for other novel treatment options, including Ven based regimens, to improve OS in older pts (aged ≥60 years) with ND AML who are eligible for IC. Future studies are warranted to conduct randomized controlled trials to comparatively evaluate IC vs other novel treatment options in older pts (aged ≥60 years) with ND AML, or conduct the appropriate statistical adjustment to minimize confounding in indirect treatment comparisons from different studies.

Residual Mast Cells Can Explain Persistent Molecular Positivity in Difference from Normal Flow Cytometric-Defined MRD Negative Core Binding Factor AML

Introduction: Core binding factor acute myeloid leukemia (CBF-AML) accounts for 30% of pediatric and 15% adult AMLs and is defined by fusions involving RUNX1 or CBFB. RT-PCR is commonly used to monitor measurable residual disease (MRD) in patients with CBF-AML. However, it has been reported that these fusions can be detected in patients during complete remission (CR) or after hematopoietic cell transplant (HCT). This raises the question of if these patients should be considered MRD positive, given they appear otherwise disease free. We utilized flow cytometric cell sorting and fluorescent in situ hybridization (FISH) to determine the source of persistent CBF fusions. Methods: Flow cytometry was used to isolate mast cells (CD117 bright/CD34 negative) from 13 patients with CBF-AML fusions (8 RUNX1:: RUNX1T1 and 5 CBFB:: MYH11) alongside progenitor cells (CD34+/CD117 heterogeneous, 12 patients) and T cells (CD3+, 11 patients) as available for FISH analysis. These patients were fusion positive by RT-PCR but had no evidence of MRD by difference from normal multidimensional flow cytometry (ΔN), the gold standard for determination of residual disease in Children's Oncology Group-sponsored clinical trials for AML. Cells were sorted from 6 additional patients with a history of RUNX1:: RUNX1T1 CBF-AML who were MRD negative by ΔN but without RT-PCR results available. Results: In 11/13 patients, the mast cell fraction was positive for the CBF fusion but all other sorted cell fractions tested were negative. In the remaining two specimens, all cell fractions were negative, likely due to FISH sensitivity compared to RT-PCR. Both CBF fusions exhibited the same pattern, with fusions detected only in the mast cell fractions (7 RUNX1:: RUNX1T1 and 4 CBFB:: MYH11). The additional 6 patients who were MRD negative by ΔN but without RT-PCR data followed the same pattern, with RUNX1:: RUNX1T1 detected by FISH in the mast cells (6/6 patients) and not in other sorted populations (5/6 patients sorted for progenitor and T cells). Two patients had a clinical history of CBF-AML and systemic mastocytosis (SM). ΔN revealed no evidence of residual AML but showed abnormal mast cells with expression of CD2 and CD25, consistent with abnormalities associated with SM. FISH analysis of sorted mast cells revealed the presence of the RUNX1:: RUNX1T1 fusion, while progenitor and T cells were both negative. In all other patients the mast cells showed no phenotypic abnormalities, demonstrating that CBF fusions can be detected in both phenotypically normal and abnormal mast cells in patients who are free of residual AML. Two patients with CBFB:: MYH11 fusions had specimens evaluated by FISH on sorted cells over a month apart where the fusion persisted only in the mast cells. Two patients with RUNX1:: RUNX1T1 fusions had serial specimens analyzed at 4 different timepoints. One patient had fusion positive mast cells for over 8 months after residual disease was last detected by ΔN. The other patient, who had previously undergone HCT, harbored fusion positive mast cells for 13 months. Both patients remained MRD negative by ΔN over the course of testing. Discussion: These data demonstrate that in CBF-AML, fusions can be detected exclusively in the mast cells of otherwise leukemia-free patients, resulting in positive RT-PCR results in the absence of any other disease pathology. These mast cells can be normal or abnormal and can persist after successful HCT. Given that these patients are free of disease by other measures, these fusion positive mast cells do not appear to contribute to AML pathogenesis. Additionally, this post-HCT fusion positive persistence demonstrates a potential clinical implication: if patients such as reported here are assessed pre-transplant using RT-PCR on unsorted specimens alone, they may not be considered candidates for HCT even though the fusion is confined to terminally differentiated cells and successful transplant can be achieved. For these reasons, while RT-PCR is a specific and accurate assay, caution is required for CBF-AML patients. Flow cytometry and cell sorting in combination with genetic testing, in this case FISH, protect against these mast cell driven positive results and provide an accurate assessment of disease status. These data highlight the importance of considering AML biology and combining multiple testing methods to monitor AML patients comprehensively and accurately.

AML1-ETO and CCND2 Overexpression Cooperate to Drive AML Initiation and Progression

Objectives: The translocation between chromosome 8 and 21, resulting in the AML1-ETO fusion gene, is one of the most common cytogenetic abnormalities observed in acute myeloid leukemia (AML). However, AML1-ETO alone is insufficient to cause leukemia, additional secondary events are required for leukemogenesis. CCND2 gene, a key member of the CyclinD2-CDK4/6 complex, plays a crucial role as a cell cycle regulator. In hematopoietic malignancies, CCND2 mutations (particularly with a conserved mutated hotspot on Thr280) have been found in AML, particularly in core binding factor leukemias. The mutated CCND2 protein exhibits greater stability and resistance to proteasomal degradation. Previous research had shown that CCND2 was a transcriptional target of AML1-ETO, indicating that AML1-ETO can promote CCND2 expression. However, it remains unclear whether mutated CCND2 can cooperate with the AML1-ETO to drive leukemia initiation and progression. Methods: In our previous study, a conditional AML1-ETO knock-in mouse model was developed, in which the AML1-ETO fusion gene was tagged with m-Cherry. To investigate the role of CCND2 in this model, the coding sequences of both CCND2 wt (wild-type) and CCND2 mut (mutant with Thr280Ala substitution) were cloned into the retroviral vector MSCV-IRES-EGFP. Subsequently, the fetal liver cells (embryonic day=12.5) from AML1-ETO mice were infected with the corresponding retroviruses. Results: Four months post AML1-ETO induction, the percentage of m-Cherry + GFP + cells of the mice in CCND2 wt and CCND2 mut groups began to increase. The results revealed a substantial upregulation of CCND2 mRNA and protein expression in these groups compared to that of the Vec group. Additionally, the CCND2 mut group exhibited even higher CCND2 protein expression due to impaired protein degradation. Moreover, the shortened survival time and pathological findings in mice from the CCND2 wt and CCND2 mut groups confirmed that they were succumbed to leukemia infiltration. To assess the stemness of leukemia stem cells (LSCs), extreme limiting dilution analysis (ELDA) was conducted, and it showed a significant increase in LSC frequency in the CCND2 wt and CCND2 mut groups compared to that of the Vec group. Notably, transplanting AML1-ETO cells alone didn't confer any competitive advantage in sublethally irradiated mice, while the overexpression of CCND2 provided them with the ability to survive. Transcriptome analysis indicated that compared to the Vec group, CCND2 wt and CCND2 mut groups exhibited notable enrichment in OXPHOS, E2F, and G2M gene sets. Interestingly, the mTORC1 signaling pathway was particularly enriched in the CCND2 mut group compared to the other two groups. To verify this speculation, phosphorylated S6 and total S6 protein levels were assessed through Western blotting. The results showed that compared to Vec group, the p-S6/total S6 ratio show a gradual increase in the CCND2 wt and CCND2 mut groups, indicating activation of the mTOR pathway by CCND2 protein. Everolimus, a selective inhibitor of mTOR, was administered to CCND2 wt and CCND2 mut mice at a dose of 5mg/kg via oral gavage (three times a week) for three consecutive weeks. The Everolimus-treated mice exhibited reduced leukemic burden and fewer number of LSCs compared to that of the vehicle-treated group. Additionally, Everolimus restored the non-leukemic cells and extended their survival time in CCND2 wt and CCND2 mut group mice. Conclusion: In our study, a leukemia mouse model with co-expression of AML1-ETO and CCND2 mutation was successfully established, which demonstrated that the introduction of the CCND2 gene into the existing AML1-ETO model can trigger the development of leukemia. It was also confirmed that CCND2 overexpression results in the upregulation of the mTOR pathway, which drove the progression of leukemia. Everolimus effectively improved the outcome of mice with CCND2 wt or CCND2 mut, suggesting its potential as a therapeutic agent for this subtype of leukemia.