WT1 Mutations Research Articles

Ubtf tandem Duplications Define a Novel Subtype of Acute Myeloid Leukemia Associated with Younger Age, WT1 Mutations and HOXA9 Marked Overexpression

Background Upstream Binding Transcription Factor ( UBTF) gene plays an important role in ribosomal RNA transcription. UBTF tandem duplications (TD) have been recently described as a recurrent genetic lesion in acute myeloid leukemia (AML). UBTF-TDs appear to be mutually exclusive with other class-defining lesions in AML and display a unique comutational signature. UBTF-mutated AML affects predominantly younger patients and is associated with trisomy 8, internal tandem duplication of FLT3 ( FLT3-ITD), mutations in WT1 and poor prognosis. Moreover, HOX and MEIS genes seem to be overexpressed in AML with UBTF-TD similarly to NPM1-mutated ( NPM1m) or KMT2A-rearragend ( KMT2Ar) AML, suggesting potential sensitivity to menin inhibitors. In this study we sought to characterize UBTF-TDs in our AML cohort. Methods We studied 456 adult patients (median age 54 years; range 18-70) diagnosed with de novo AML and included in AML-12 protocol from CETLAM group. All patients from the 2012-2017 period (n=403) were consecutively studied and we also selected 53 cases of WT1-mutated AML from the 2017-2020 period, given the strong association with UBTF-TD. Screening for UBTF-TD was performed on bone marrow (BM) or peripheral blood (PB) genomic DNA samples. Exon 13 of UBTF gene was amplified and analysed by Polymerase chain reaction (PCR) and subsequent fragment length analysis by capillary electrophoresis. Mutated samples were confirmed through Sanger sequencing. Further, RNA from 9 UBTF-TD cases was available and HOXA9 and MEIS1 gene expression analysis was performed by Real-Time Polymerase Chain Reaction (RT-qPCR). Clinical and biological data were obtained from CETLAM registry. Results UBTF-TD was found in 13 patients from our cohort whose characteristics are detailed in Table 1. UBTF-TDs range from 45 base pairs (bp) to 365 bp, being the 48 bp the most recurring size. As described, although small UBTF-TDs are in frame insertions, the largest ones are not multiple of 3. Notably, most UBTF-TDs presented small insertions and deletions among the duplication. Presence of UBTF-TD was associated with younger age (36 vs 55 years; p<0.001) and BM dysplastic changes (80% of U BTFMUT). UBTF-TD was particularly frequent (8.9% of all cases) in patients below 40 years, compared to other lesions as CEBPA mutations (1.1%). Eleven (85%) U BTFMUT patients presented intermediate cytogenetics, being trisomy 8 (5), normal karyotype (3) and 9q deletion (2) the most recurrent findings. Two cases of adverse karyotype with MECOM-rearrangements were found. As previously described, there was a strong association between UBTF-TD and of FLT3-ITD (38.5%). Other recurrent genetic lesions in AML like NPM1 and CEBPA mutations or core-binding factor (CBF) rearrangements were exclusive of UBTF wild type patients. Further, we found that UBTFMUT leukemias showed marked overexpression of HOXA9 compared with other AML subtypes (22.1-fold vs 5.0-fold; p<0.001; Fig. 1) and similar to NPM1m AML (22.3-fold). On the other hand, MEIS expression did not differ significantly among groups. Conclusions In our cohort of adult AML patients, UBTF-TDs are found in 1.8% of cases and are especially frequent in younger individuals in absence of other class-defining genetic lesions. The presence of UBTF-TD is strongly associated with cytomorphological dysplasia and co-occurrence of FLT3-ITD and WT1 mutations, while NPM1 and CEBPA mutations and CBF rearrangements appear to be mutually exclusive. HOXA9 upregulation could be a leukemogenic event in UBTF-TD AML, as described in NPM1-m and KMT2A-r AML, suggesting potential utility of menin inhibitors in this subset of patients. Screening for UBTF-TD is going to be incorporated in our molecular diagnostic panel for new AML cases.

Mutational and Cytogenetic Dynamics at Diagnosis and Relapse in Acute Myeloid Leukemia: Influence of Intensity and Type of Treatment

Introduction: Cytogenetic and molecular aberrations are common at diagnosis in patients with acute myeloid leukemia (AML) and may have significant prognostic impact. Relapse after prior response is associated with a poor outcome. The dynamics of cytogenetic and molecular abnormalities at relapse and their impact on outcome is less well studied. Methods: This is a retrospective single center study including patients with AML diagnosed from April 2017 to October 2022 who relapsed after achieving a prior response. Mutations were detected using a targeted 81-gene NGS panel and cytogenetics were assessed using conventional karyotyping and FISH testing. To assess disappearance, maintenance or appearance of cytogenetic and molecular aberrations, they were evaluated at diagnosis and relapse and differences in incidence were evaluated with the Chi-square and Fisher test. Results: The cohort includes164 patients who had relapsed after achieving remission. The median age at diagnosis and relapse was 67 years (range, 20-94) and 68 years (range, 21-95). 53% were male. Patients received intensive treatment (IT; 40% of patients, 41% of whom with the addition of venetoclax) or low intensity therapy (LIT; 60% of patients, 72% with venetoclax). The median time from diagnosis to relapse was 8.9 months (range, 2.2-52). According to the ELN 2022 risk classification, 15%, 15% and 70% had favorable, intermediate and adverse risk, respectively. At diagnosis, the most frequent mutations were DNMT3A (32%), TP53 (31%), RUNX1 (19%), TET2 (18%), SRSF2 (17%) and NPM1 (17%). At relapse, the most frequent mutations were DNMT3A (35%), TP53 (35%), TET2 (24%), RUNX1 (20%) and SRSF2 (17%). The median number of mutations per patient at diagnosis and relapse was 3 (0-12) and 3 (0-14), respectively (p=0.07). Most frequent karyotypes at diagnosis were diploid (34%), complex (32%), chromosome 5 abnormalities (29%) and chromosome 7 abnormalities (26%). At relapse, the most frequent karyotypes included complex (36%), chromosome 7 abnormalities (31%), chromosome 5 abnormalities (30%) and diploid karyotype (27%). When analyzing each mutation individually, the rate of mutation clearance from diagnosis to relapse was higher for FLT3-ITD (58%, p=0.01), FLT3-TKD (83%, p<0.001), KIT (88%, p=0.003), NF1 (71%, p=0.004) and WT1 mutations (71%, p=0.004), compared to other remaining mutations (32%). Conversely, ASXL1 (95%, p=0.01), DNMT3A (84%, p=0.006), SRSF2 (89%, p=0.01), TET2 (84%, p=0.02) and TP53 mutations (86%, p=0.002) persisted more frequently at relapse compared to other mutations (66%). At relapse, WT1 mutations were more frequently acquired (77%, p=0.001), compared to other mutations (36%). Diploid karyotype changed more frequently than other cytogenetic abnormalities (33% vs 5%, p <0.001), whereas complex karyotype persisted at relapse (98% vs 87%, p=0.04) more frequently. Chromosome 7 abnormalities were more frequently acquired at relapse (23%), compared to other cytogenetic abnormalities acquired at relapse (11%, p=0.04). We then compared mutational dynamics from diagnosis to relapse between patients receiving IT and LIT. NRAS mutations disappeared more frequently from diagnosis to relapse in patients treated with IT (73%), compared with patients treated with LIT (27%, p=0.01) whereas TP53 mutations were acquired more frequently in IT treated patients (67% vs 10%). Patients treated with IT acquired chromosome 7 abnormalities more frequently than patient treated with LIT (60% vs 14%, p=0.007). No significant differences were found regarding disappearance, maintenance or appearance of mutations when comparing patients treated with or without Venetoclax. Conclusion: The number of mutations does not vary significantly from diagnosis to relapse, and most mutations persist, suggesting maintenance of leukemic clones as the cause of relapse. Overall, genes involved in signaling pathways tend to disappear more frequently at relapse whereas chromatin and histone modifiers as well as TP53 mutations tend to persist. NRAS mutations disappear more frequently at relapse with IT, whereas TP53 mutations are acquired more frequently.

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

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

Influence of Co-Mutational Patterns in Disease Phenotype and Clinical Outcomes of Chronic Myelomonocytic Leukemia

Introduction: Chronic myelomonocytic leukemia (CMML) is characterized by recurrent somatic mutations in a conserved number of genes and functional pathways. Although specific genomic events are associated with disease phenotype and prognosis, identification of genomically-defined disease subgroups based on common recurrent cooperative genomic patterns is needed to refine disease classification and identify disease subsets with unique clinical behavior. Methods: To evaluate if CMML is defined by recurrent co-mutational profiles defining unique clinicopathologic subgroups we evaluated a cohort of 296 patients (pts) with newly diagnosed CMML. Whole bone marrow DNA was subject to 81 gene targeted next-generation sequencing analysis. Akaike information criterion (AIC) method was applied to evaluate mixture model components defining clusters based on mutational profile. Expectation-maximization (EM) algorithm was used for mixture model fitting to multivariate binary data. Unsupervised cluster membership was chosen as a function of the component with the highest weight for any individual, and we examined means of cluster centers. Cox proportional hazards models, regressing overall survival (OS) and leukemia-free survival (LFS), were fit on cluster in some cases and normalized cluster weights in other cases, with and without adjustment for age and sex. Two degree of freedom likelihood ratio tests was performed on cluster and cluster weight in all models regardless of covariate adjustment. Results: Median age of the population was 70 years [range 30-71]; 160 (54%) pts had myeloproliferative CMML (MP-CMML) and 152 (51%) had CMML-2 by WHO classification. Most frequent mutations included TET2 (51%), ASXL1 (48%), SRSF2 (40%), RUNX1 (22%), NRAS (18%), CBL (14%) and KRAS (14%) all present in >10% of pts. Based on frequency and co-occurrence of mutations, AIC optimization identified 3 unique clusters. Clusters based on mutation landscape are shown in Figure 1A. Unsupervised clustering allowed attribution of individual patients to specific clusters. Cluster 1 (C1, n=107), was characterized by near universal presence of ASXL1 mutations (86%), with lower frequency of TET2 mutations, and enrichment of RUNX1 (35%), NRAS (28%) and U2AF1 (18%) mutations. SETBP1 and EZH2 mutations were nearly exclusively observed in C1 (16% and 20% of C1 pts, respectively). All pts with ETV6 mutations belonged to this cluster. Cluster 2 (C2, n=135) was defined by universal presence of TET2 mutations (93%) with frequent SRSF2 co-mutation (56%) and lower frequency of ASXL1 (34%), RUNX1 (15%) or NRAS (12%) mutations. Despite their overall low frequency, BRAF mutations were restricted to C2, while CBL mutations were observed at similar frequencies in C1 and C2. This suggests that co-mutation profiles and genomic context differs among genes involved in RAS pathway signaling. Cluster 3 (C3, n=54) included a minor and more genomically heterogenous group enriched for SF3B1 (25%), KRAS (24%), DNMT3A (22%) and TP53 (15%) mutations, with absence of ASXL1 mutations, and low frequency of TET2 (12%) mutations. All BCORL1 and WT1 mutations and most ASXL2 and CEBPA mutations were in C3. RUNX1 mutations not only were more frequent among C1 but appeared at higher median VAF compared to other clusters (C1: 40%, C2: 11%, C3: 25%, p=0.003). Mutations in U2AF1 had higher median VAF in C3 compared to cluster 1 (49% vs 43%, p=0.017). C1 was enriched for MP-CMML (C1: 64%; C2: 48%; C3: 52%, p<0.001) and had higher frequency of del(7q)/-7 (C1: 11%; C2 0%, C3: 6%, p<0.001) and trisomy 8 (C1: 15%, C2: 7%, C3: 6%, p=0.05). Complex karyotype (C1: 1%, C2: 1%, C3: 22%, p<0.001) was nearly exclusive of C3, while C2 was more likely to be associated with a normal karyotype (C1: 59%; C1: 73%; C3: 41%, p<0.001) and higher median hemoglobin (C1: 9.8g/dL; C2: 12.1g/dL, C3: 9.7g/dL, p<0.001). In total 66% of pts received therapy with hypomethylating agents with no differences in response, median time to or duration of response between clusters. Use of Cox proportional hazards model identified that, when corrected by age and sex, patients on C1 and C3, based on attributed cluster weights, had significantly worse LFS (p=0.02, Figurer 1B) and OS (p=0.05) than those in C2. Conclusions: These data suggest that somatic mutations in CMML have unique patterns of clustering that define disease phenotype and influence disease outcomes.

Characterization of the Molecular Landscape of Pediatric Acute Myeloid Leukemia: A Retrospective AIEOP AML2013/01 Study

Background. Advances in genomic techniques have recently shed light on leukemia biology, recognizing that pediatric acute myeloid leukemia (AML) is a highly genetically heterogeneous disease. In the last two decades, genetic and cytogenetic abnormalities contributed to the stratification of patients in different classes of risk, where children receive a risk-adapted therapy. In the recently concluded AIEOP-AML2013/01 clinical trial, 371 Italian pediatric AML patients were allocated into three risk groups that were largely based on measurable residual disease at the end of induction therapy and on recurrent molecular markers with a recognized impact on children's outcome. Methods and Results. We screened by RT-PCR, RQ-PCR, capillary electrophoresis and Sanger sequencing 41 genetic markers on 371 RNA and DNA samples, identifying a molecular marker at diagnosis for 247 cases out of the 371 enrolled (67%). As far as gene mutations detected are concerned, we identified 24/371 cases harboring a mutation in exon 12 of NPM1 gene (6.5%), 16/371 a FLT3-ITD mutation (4.3%), and 7 harboring both NPM1 and FLT3-ITD mutations (2%). Moreover, we also found 2 cases having a partial tandem duplication affecting KMT2A gene (2/371, 0.5%), one of them occurring together with a FLT3-ITD mutation. For chromosomal aberrations, we confirmed that t(8;21) RUNX1::RUNX1T1 and inv(16) CBFB::MYH11 are recurrent translocations in pediatric AML, being found in 13.5% (50/371) and 12% (44/371) of cases respectively. Sixty-four (17,3%) AML cases were characterized by a KMT2A fusion with different partner genes, with the t(9;11) KMT2A::MLLT3 being the most recurrent (24/371, 6.5%), followed by t(10;11) KMT2A::MLLT10 (21/371, 5.7%), t(6;11) KMT2A::AFDN (10/371, 2.7%), t(11;19) KMT2A::ELL (6/371, 1.6%). In 14 patients, we found a NUP98 translocations (3.8%), and, in particular, 9 cases harbored the t(5;11) NUP98::NSD1 (2.4%, 5 of them together with a FLT3-ITD mutation), 4 the t(11;12) NUP98::KDM5A (1%) and only one case the t(2;11) NUP98::HOXD13 (0.3%). Other chromosomal aberrations were rarer in our cohort, with t(16;16) CBFA2T3::GLIS2 accounting for 2.4% of cases (9/371), t(6;9) DEK::CAN 1.3% (5/371, co-occurring with FLT3-ITD in 3/5 cases), t(1;22) RBM15::MKL1 1.1% (4/371), t(3;5) NPM1::MLF1 0.5% (2/371, one concomitant with FLT3-ITD), t(16;21) FUS::ERG 0.5% (2/371), t(16;21) RUNX1::CBFA2T3 0.3% (1/371), del(9) SET::NUP214 0.3% (1/371), t(8;16) KAT6A::CREBBP 0.3% (1/371), t(9;22) BCR::ABL1 0.3% (1/371). In addition, we retrospectively evaluated the incidence and prognostic relevance of mutations at specific loci of KIT, FLT3, ASXL1, WT1 and CEBPA genes. As concerns the KIT gene, we identified mutations at exon 8 or 17 in 16/371 AML (4.3%). Of note, all the 16 cases had a concomitant core-binding factor (CBF) rearrangement, and in particular 10/16 the t(8;21) RUNX1::RUNX1T1 translocation and 6/16 the inv(16) CBFB::MYH11, with a relative occurrence of 17% in the CBF-r AML subgroup (16 KIT mutated AML/94 CBF-r) and a slight, but not significant, impact on outcome. As regards exon 13 of ASXL1 gene and the tyrosine-kinase domain of FLT3 gene ( FLT3-TKD), our study confirmed a low prevalence of these mutations, which occurred in 2.5% and 3.4% of AML respectively. On the contrary, WT1 mutations (exons 6-9) occurred in a consistent portion of AML (45 mutated cases, 13.2%)did not affect the outcome of FLT3-ITD mutated AML. Conversely, by screening both at bZIP and NTD domains of the CEBPA gene, we identified 18 double-mutated patients (4.8%), and notably all these patients had no other molecular marker detected at diagnosis, reducing the proportion of negative cases from 33% to 28%. We found that CEBPA mutated cases are characterized by a favorable outcome (EFS 93% vs 58% for CEBPA wt, p=0.008), this finding corroborating the indication to allocate these patients to the standard risk group. Conclusion. Overall, in the prospective AIEOP AML2013/01 trial, we described the frequency of different molecular lesions and improved the genetic landscape of AML. The future use of NGS-based screenings could further optimize the characterization of the genetic landscape of childhood AML, thus refining the risk class patients stratification and modulation of treatment approaches.

Sex-associated differences in frequencies and prognostic impact of recurrent genetic alterations in adult acute myeloid leukemia (Alliance, AMLCG)

Clinical outcome of patients with acute myeloid leukemia (AML) is associated with demographic and genetic features. Although the associations of acquired genetic alterations with patients’ sex have been recently analyzed, their impact on outcome of female and male patients has not yet been comprehensively assessed. We performed mutational profiling, cytogenetic and outcome analyses in 1726 adults with AML (749 female and 977 male) treated on frontline Alliance for Clinical Trials in Oncology protocols. A validation cohort comprised 465 women and 489 men treated on frontline protocols of the German AML Cooperative Group. Compared with men, women more often had normal karyotype, FLT3-ITD, DNMT3A, NPM1 and WT1 mutations and less often complex karyotype, ASXL1, SRSF2, U2AF1, RUNX1, or KIT mutations. More women were in the 2022 European LeukemiaNet intermediate-risk group and more men in adverse-risk group. We found sex differences in co-occurring mutation patterns and prognostic impact of select genetic alterations. The mutation-associated splicing events and gene-expression profiles also differed between sexes. In patients aged <60 years, SF3B1 mutations were male-specific adverse outcome prognosticators. We conclude that sex differences in AML-associated genetic alterations and mutation-specific differential splicing events highlight the importance of patients’ sex in analyses of AML biology and prognostication.

Genetic and Functional Characterization of NUP98-Rearranged Leukemia

NUP98 rearrangements ( NUP98r) are recurrent alterations in pediatric acute myeloid leukemia (AML) and are associated with dismal outcomes (PMID:21813447). These structural variantsresult in fusion oncoproteins comprised of the N-terminus of NUP98 and the C-terminus of fusion partners. Among more than 30 fusion partners discovered so far, the associations between NUP98::NSD1 with myeloblastic AML and NUP98::KDM5A with acute megakaryocytic/erythroid leukemia (AMKL/AEL) have been appreciated, which often harbor distinct cooperating mutations (e.g., NUP98:: NSD1 with FLT3-ITD and WT1 mutations). In contrast, other fusions, such as NUP98:: RAP1GDS1 or NUP98:: HOXA9 can be found also in myelodysplastic syndrome (MDS) or T-cell acute lymphoblastic leukemia (T-ALL) (PMID:32766874). However, how these fusions and cooperating mutations contribute to the specific phenotypes of NUP98r leukemias is poorly understood. To investigate the genetic background of NUP98r leukemia, we collected RNA-seq, WGS, and WES data for 91 pediatric cases from St. Jude (n=71),AEIOP (n=3), and the TARGET study (PMID:29227476, n=17; Panel.A), which included AML (n=82), MDS (n=4), and T-ALL (n=5). NUP98::NSD1 (n=47, 51.6%) and NUP98::KDM5A (n=26, 28.6%) were the most common fusions, in line with previous observations. NUP98::RAP1GDS1 (n=6, 6.6%), an understudied NUP98 fusion, was the third most common fusion in this study. We also confirmed frequent mutations of WT1 and FLT3-ITD in NUP98::NSD1 AML and entire or partial chromosome 13 loss involving RB1 locus in NUP98::KDM5A AMKL, while we observed frequent mutations in RAS or epigenetics-related genes, CCND2/3, and RUNX1 preferentially in cases without alterations of WT1, FLT3 or RB1 loss. NUP98:: RAP1GDS1 and NOTCH1 mutations were strongly enriched in T-ALL. These findings suggest that fusions and cooperating alterations both contribute to the disease phenotypes. To study how NUP98 fusion oncoproteins (FOs) drive leukemogenesis and specific phenotypes, we applied Cleavage Under Targets and Release Using Nuclease (CUT&amp;RUN) to determine NUP98 FO binding for a primary sample (myeloblastic with NUP98::NSD1), CHRF-288-11 cell line (megakaryocytic with NUP98::KDM5A), and HA-tagged CD34 NUP98::KDM5A model (Panel.B-top). CUT&amp;RUN using antibodies against the N-terminus NUP98 and histone modifications (H3K4me3, H3K27ac) revealed that these models shared NUP98 FO binding sites at the HOXA/B and RUNX1 loci, together with active histone marks. In contrast, binding patterns at differentiation-related gene loci were heterogenous. NUP98::NSD1 uniquely binds to CEBPA, which encodes a master regulator of myeloid differentiation, contrary to NUP98::KDM5A binding to GFI1B encoding regulator of erythromegakaryocytic differentiation . These data indicate that NUP98 FOs directly and uniquely regulate differentiation-related genes. We also performed CUT&amp;RUN in AML cells with RUNX1::RUNX1T1 or UBTF tandem duplications, in which the N-terminus NUP98 antibody did not show any detectable peaks, confirming the specificity of the N-terminus NUP98 signals in NUP98r AML models. Experiments using a HA antibody in HA-tagged NUP98::KDM5A CD34 models confirmed that fusion oncoproteins are binding to these target regions. However, the C-terminus NUP98 antibody also detected similar signals as the N-NUP98 antibody, suggesting that wild-type NUP98 is also recruited to NUP98 FO target genes, possibly by a heteromer formation with NUP98 FOs and other NPC components. To understand the possible association between somatic mutations and the genomic binding of NUP98 FOs, we next investigated chromatin immunoprecipitation sequencing (ChIP-seq) data from the ENCODE study (PMID:22955991) for RB1, WT1, and STAT5 (downstream FLT3-ITD). Binding peaks of these proteins partly coincided with NUP98 peaks on representative target genes (Panel.B-bottom), suggesting that frequent mutations in NUP98r leukemia converge on the genomic interaction of NUP98 FOs. In conclusion, genomic characterization of NUP98r leukemia showed the association among fusion partners, cooperating mutations, and disease phenotypes. Epigenetic profiling revealed that NUP98 FOs directly regulate target genes in a fusion and differentiation-specific manner and provide a basis for further study to investigate how NUP98 FOs and cooperating partners drive leukemogenesis and disease phenotypes.

Ubtf- Tandem Duplications Are Recurrent Somatic Genetic Events in Adult AML and Associate with Additional Structural Variants and a Distinct Gene Expression Profile (Alliance)

Background The gene upstream binding transcription factor ( UBTF ) encodesa nucleolar protein that is a key regulator of the epigenetic status of ribosomal DNA and RNA transcription. Tandem duplications (TDs) of the UBTF gene have been initially identified in pediatric patients (pts) with acute myeloid leukemia (AML) and were recently also reported as relatively rare, but recurrent genetic events in adult AML based on targeted re-sequencing efforts (1.2%-3%). Their presence was associated with dysplastic bone marrow features, and co-occurrence of select genetic features, including FLT3-internal tandem duplications (ITDs) and WT1 mutations, and inferior outcome. However, associated biologic features and affected pathways have not yet been thoroughly investigated, and may provide further insights into leukemogenesis and identify potentially targetable vulnerabilities. Thus, we set out to assess the frequency of UBTF-TDs in a large cohort of adult AML pts (n=807) treated on frontline protocols of the Alliance for Clinical Trials in Oncology with complete RNA sequencing data, comprehensive targeted mutation profiling, centrally reviewed cytogenetic data and clinical information available, and to gain further insights into UBTF-TDs via comprehensive integrated genomic profiling. Methods UBTF-TD detection was performed via the RNAseq-based RNAmut and EnFusion algorithm. To gain insights into associated molecular features, all UBTF-TD + pts underwent paired tumor-normal whole-exome sequencing. To understand associated pathways and downstream effects, differential gene expression (DGE) and gene set enrichment analyses (GSEA) were performed. Results UBTF-TDs were detected in 6/807 pts (0.7%). In line with previous studies, these 6 UBTF-TD + pts were young, with a median age of 35y (range: 19-59y). Three pts had extramedullary disease, 2 with skin and 1 with gingival involvement. All but 1 of the 6 pts were cytogenetically normal. Clinically, pts did poorly after treatment with intensive chemotherapy induction, with a CR rate of only 33%. No pt was alive 2.5 y after diagnosis. In paired tumor/normal exome sequencing, UBTF-TD + pts had a median mutation burden of 21 non-synonymous variants in coding genes (range: 17-27), with a notable presence of larger insertions/deletions (indels), loss of heterozygosity (LOH) or TDs as co-occurring somatic genetic lesions (median: 4, range: 2-5). There was a 100% co-occurrence of UBTF-TDs with FLT3-ITDs. In addition, pts harbored larger indels in WT1 (n=2), BPTF, CEBPA, Corf53, KRTAP5-7, NFE2, PTPRN2, RNF144B, SOWAHC and ZCCHC14. Also, analysis of copy-number variations and LOH revealed LOH in 5 pts, in chromosomes 13 (n=3), 15 (n=1) and 18 (n=1), suggestive of a propensity to the acquisition of structural variants. In unsupervised clustering analysis of the RNAseq data, UBTF-TD + pts clustered with FLT3-ITD + pts but formed a relatively distinct subcluster in principal component and t-distributed stochastic neighbor embedding analyses. In supervised clustering comparing 6 UBTF-TD +/ FLT3-ITD + and 196 UBTF-TD -/ FLT3-ITD + pts, 2 UBTF-TD - pts clustered together with the UBTF-TD +/ FLT3-ITD + group, suggesting either presence of an undetected TD or genetic phenocopy. UBTF expression was higher in UBTF-TD pts. DGE analysis of UBTF-TD +/ FLT3-ITD + and UBTF-TD -/ FLT3-ITD + pts (Fig 1) showed distinct upregulation of the locus of the stem cell and chemoresistance marker ALDH1A3, including the associated long non-coding RNAs AC015712.7/AC015712.2 in UBTF-TD + pts, which was confirmed by a comparison of those pts to AML pts who had neither TD (n=605). GSEA indicated a downregulation of inflammation pathways and several metabolic pathways of UBTF-TD +/ FLT3-ITD + compared to FLT3-ITD + pts (Fig 2). Conclusions UBTF-TDs are rare, but recurrent genetic events in adult AML, associated with high chemotherapy resistance. Our results highlight a susceptibility of those pts to the acquisition of structural variants and suggest a distinct associated biology, with upregulation of ALDH1A3 as possible contributing resistance mechanism. Support: U10CA180821, U10CA180882, U24CA196171; Clinicaltrials.gov Identifiers: NCT00048958 (CALGB 8461), NCT00899223 (CALGB 9665), NCT00900224 (CALGB 20202); https://acknowledgments.alliancefound.org

DNA Damage Response Constrains Cell Growth and Drives Clonal Hematopoiesis in Telomere Biology Disorders

Telomere biology disorders (TBD) are inherited diseases caused by genetic defects in telomere maintenance. Patients with TBD have critically shortened telomeres, leading to bone marrow failure (BMF) and an increased risk of myeloid neoplasms (MN). We conducted a study to understand the genetic changes driving clonal evolution in TBD patients and their distinct mechanisms compared to normal aging and sporadic myelodysplastic syndrome (MDS). We analyzed acquired genetic alterations in hematopoietic cells from 105 TBD patients. The diagnosis of TBD was made using a combination of clinical history, germline mutation status, and telomere length. Germline mutations were identified in 84% of patients, a family history consistent with TBD was seen in 46%, and 76% of patients had lymphocyte telomere lengths (TL) &amp;lt;1st %ile for their age, while 22% fell between the 1st and 10th %ile. Complications observed in our cohort included BMF (42%), myeloid neoplasms (17%), solid tumors (17%), cirrhosis (14%), and interstitial lung disease (34%). Clonal hematopoiesis was detected in 44 of 105 patients (42%), including 8 of 27 (30%) patients 18 years or younger. Somatic genetic alterations primarily involved the DNA damage response (DDR) pathway, with ATM and TP53 being the most frequently mutated genes (11 ATM mutations in 5 of 80 patients; 5 TP53 mutations in 4 of 84 patients; Fig. 1). Mutations typical of age-related clonal hematopoiesis were seen in 4 patients (3 ASXL1, 1 TET2). Somatic reversion of TBD germline lesions was found in 7 patients. Additionally, 11 somatic mutations were detected in genes involved in DDR, telomere maintenance, and cell senescence, including KAT6B, PALB2, TELO2, TOP1, and RTEL1. MDS-associated gene mutations were found in 15 patients (18%), 8 in the setting of MN. The most common mutations affected spliceosome genes with U2AF1 p.S34F and SF3B1 being most notable, including 1 U2AF1 S34F identified in a 15-year-old. Mutations in NPM1, RUNX1, WT1, SF3B1, and FLT3 were identified only after malignant transformation. Acquired cytogenetic changes were observed in 16 of 87 evaluable patients (18%), 8 in the setting of MN, and included gain of 1q in 5 patients (5.7%). Two patients with TP53 mutations developed a complex karyotype (Fig 1). To understand selective pressures contributing to clonal hematopoiesis development in TBD, we analyzed transcriptional changes in bone marrow (n=2) and peripheral blood (n=1) mononuclear cells (MNCs) of 3 TBD patients with different germline lesions using single cell RNA sequencing (scRNASeq). MNCs from TBD patients exhibited significant differences compared to healthy controls, showing downregulation of MYC targets, reduced translation, cell cycle arrest, and upregulation of ATM-dependent DDR pathway and FAS pathway (Fig 2). We hypothesized that mutations in DDR pathway genes, particularly somatic ATM loss, enable TBD hematopoietic stem and progenitor cells to overcome telomere-induced DDR induction and premature senescence. Consistent with our hypothesis, low dose ATM inhibition in TBD patients' fibroblasts significantly enhanced growth rate of TERC-mutated and DKC1-mutated cells, whereas control fibroblasts were unaffected. Somatic mutations in ATM in our cohort were typically observed in patients with TERC-mutated TBD (3 of 5, 3 of 34 with TERC-mutated TBD), very low TL, and extra-hematopoietic manifestations. Of the 11 ATM mutations, 3 were predicted loss of function and 4 were missense kinase domain mutations, known or predicted to result in loss of kinase activity. Somatic ATM loss occurred both as heterozygous or compound heterozygous mutations. The development of ATM mutations alone was not causative of malignancy; however, 2 patients with somatic ATM mutations developed myeloid neoplasms after acquisition of additional mutations (subclonal mutation in NPM1 in one patient and clonal replacement with a TP53-mutant clone in another patient). In conclusion, our findings highlight the role of telomere dysfunction-induced DDR and cellular senescence in bone marrow failure and clonal selection in TBD. ATM loss selectively enhances growth of TBD cells by inhibiting DDR activation which may ameliorate marrow failure but has the potential to increase the risk of myeloid neoplasms after acquisition of additional genetic events. Future studies should explore the possibility of a therapeutic window involving very low doses of ATM inhibition in TBD.

Optimizing FLT3 Inhibitor Use in Adult Acute Myeloid Leukemia with FLT3 Mutations Using Proteomics

CONCLUSION FLT3 mutations are the most frequent genetic alteration in adult Acute Myeloid Leukemia (AML). The use of FLT3 inhibitors (FLT3I) has improved outcome among FLT3 mutant patients, but not all benefit. We developed a proteomic-based approach to stratify patients according to their response to FLT3I therapy. The expression of 429 proteins (339 total, 90 post-translational modified) was measured by Reverse Phase Protein Arrays (RPPA) in fresh samples from 805 newly diagnosed AML patients, with levels normalized to normal CD34+ cells. Of 137 with FLT3 ITD or D835 mutations, 54 who were treated with FLT3I (Sorafenib=22, Quizartinib=11, Midostaurine=6, Gilteritinib=4 and Crenolanib=1) combined with other agents (Hypomethylating agents (HMA)=23, HMA+Venetoclax (VTX)=5, Idarrubicin+Cytarabine (AraC)+Purine Analogs (IA+Pur)=19, IA+Pur+VTX=2, AraC=3, Fludarabine+AraC (FA)=1, none=1) were selected for analyses. Proteins prognostic for Overall Survival (OS) and Complete Remission Duration (CRD) were identified using pairwise LogRank tests (p &amp;lt; 0.05) adjusted for False Discovery Rate, followed by unbiased hierarchical clustering. Continuous and categorial variables were compared with Wilcoxon, Kruskal-Wallis or Fisher's Exact test with simulated p-values (10000 replicates). Cox proportional hazards models (CoxPH) were developed for Uni-(UV) and Multi-variate (MV) analysis. Deep neural network analysis using random forest models identified proteins most predictive of cluster assignment. 28 proteins were individually prognostic for both OS and CRD and divided patients into 3 clusters (Fig. 1: C1=red, C2=blue, C3=green). The distribution of nearly all other clinical and molecular features did not differ between clusters, including: age, gender, race, cytogenetic risk and AML group. Co-occurrence with other mutations was not biased, except for FLT3+TET2 and FLT3+TET2+NPM1 mutants, more frequent in C1. OS was significantly longer (Fig. 2), in C1 (Median: C1&amp;gt;84mo, C2=14.8mo, C3=11.4mo; p&amp;lt;0.001) as was CRD (Median: C1&amp;gt;84mo, C2=8.6mo, C3=5.7mo; p&amp;lt;0.05). A similar OS pattern was observed for mutation combos, including with NPM1 or DNMT3a but not if IDH, CEBPa, TET2, or ASXL1 mutation were present. It was also seen when patients were divided by gender, age groups (except &amp;gt;70yo), primary, but not secondary AML, diploid karyotype and intermediary cytogenetic risk, and with Sorafenib or IA+PR therapies. In the UV CoxPH model for OS, C1, C2 and C3 were predictive (HR=1, 4.1, 7.5; p=ref., 0.037, 0.009), along with age, secondary AML, complex karyotype, Trisomy 6 and IDH1 mutation. In the MV model for OS, only C1, C2 and C3 (HR=1, 3.3, 4.8; p=ref., 0.011, &amp;lt;0.001), and age were predictive. In the CRD UV model, C1 and C3 (HR=1, 3.3, 4.8; p=ref., 0.072, 0.022), age, secondary AML, and mutations in ASLX1, PTPN11, RAS, TP53 and WT1 were predictive. Only C1 and C3 were predictive in the MV model for CRD (HR=1, 2.9, 6.3; p=ref., 0.16, 0.04). The predictive proteins, are biased towards specific cellular processes, mainly: proliferation and metabolism (RHEB, GSKA_B, SDHA, AKT1, AKT2 and TYRO3), cell cycle and DNA damage response (CDKN2A, DDB1, SIRT6, SLFN11 and WEE1), cellular adhesion and cytoskeleton organization (MYH9.pS1943, PAK4 and PXN), and apoptosis (AIFM1, BBC3 and BCL2L11). Key differences between clusters included: higher FOS in C1, and higher CDKN2A, MYH9.pS1943, PXN, PAK4, SDHA, BBC3 in both C2 and C3, with higher levels of these in C3. Since PAK4, PXN and MYH9 are connected to cellular motility/migration and inhibitors for those proteins are available, there is a therapeutic opportunity to overcome FLT3I resistance in C2/C3 patients. Moreover, we identified a set of 6 proteins (FOS, AKT1, PXN, SMARCA2, CDKN2A and DPF2) that predicted cluster assignment with 97.5% accuracy, making rapid patient stratification possible in the clinical setting. Protein profiling identified cohorts of FLT3 mutant patients that achieved the highest benefit from FLT3I addition, regardless of all other clinical or molecular characteristics. We identified targetable proteins that are elevated in adverse signatures, and hypothesized that these may be targets for modulation to improve FLT3I response. Moreover, a small set of 6 proteins accurately classifies patients and could be used clinically to triage patients for treatment recommendation.

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.

Clinical and Prognostic Implications of WT1 Mutations in De Novo and Relapsed Acute Myeloid Leukemia

Introduction Wilms Tumor 1 ( WT1) is integral to cell proliferation and survival and is mutated in up to 10-15% of patients (pts) with acute myeloid leukemia (AML). WT1 mutated ( WT1 m) AML frequently co-occurs with fms-like tyrosine kinase 3 ( FLT3) and nucleophosmin 1 ( NPM1) mutations, and is generally thought to impart poorer outcomes, however the impact of WT1 m remains incompletely understood. Methods We analyzed 307 pts with WT1 m AML, identified through next generation sequencing panels of recurrently mutated myeloid genes performed at two large academic cancer centers between 2015 - 2022. Of the 307 pts, 161 (52%) had WT1 m at AML diagnosis (ND) and 146 (48%) were identified at relapse (RR). Here we describe the baseline characteristics and outcomes in pts with WT1 m AML with emphasis on co-mutated FLT3 and NPM1. Results In pts with ND WT1 m AML, the median age was 59 years (range,22-87). Pts most commonly had intermediate (41%) or adverse (43%) risk disease by ELN 2022 criteria. 51% (n=82) had co-mutated FLT3 (ITD or TKD). Among pts with FLT3 mutated AML, 30% (37%) also had co-mutated NPM1. 10 (7%) pts had co-mutant NPM1 m without FLT3 m. Median OS in the ND cohort was 19.8 months. Variant allele frequency (VAF) ranges of WT1 m were 1-98 (median 27) and 1-97 (median 13) in the ND and RR cohorts respectively. OS was affected by mutational profile (table 1) with triple mutated NPM1/FLT3/WT1 exhibiting worse OS compared to others. 68% of ND pts received intensive chemotherapy (+/- venetoclax (VEN)) at time of diagnosis with mOS of 26.5 mos vs. 11.1 mos (p = &amp;lt;0.0001) for pts treated with lower intensity therapy (+/- VEN). Improved OS was observed in pts with ELN2022 favorable risk disease (mOS not reached (NR)) and in pts receiving an allogeneic hematopoietic stem cell transplant (SCT). Pts with ND AML and ELN2022 intermediate-risk disease who underwent SCT had significantly longer OS of 47.9 mos vs. 11.8 mos (p&amp;lt;0.0001, figure 1). In the ND cohort, pts had significantly improved OS if they underwent SCT after achievement of CR1 compared to SCT after first relapse, mOS NR vs. 38 months (p=0.00039), respectively. Notably, the median age of pts who received SCT was 50 (22-74) with 16% having secondary (s-AML) or therapy related (t-AML). Of those who did not undergo SCT median age was 63 (23-87) and had with 28% of pts with (s- or t-AML). Within the RR cohort, 44 (30%) pts acquired WT1 mutation post SCT. 56 (38%) were FLT3 m (25 pts with co-mutated NPM1) and 10 (7%) NPM1 m mutated (without FLT3 m). The mOS in the RR cohort (from time of WT1 m acquisition) was shorter in pts with co-mutated FLT3/WT1 without NPM1 (table 1). Pts who underwent SCT after WT1 macquisition had mOS of 25.7 mos (95% CI 23.8-38.7) compared to 18.3 mos (95% CI 13.2-21.2) (p=0.001) in those who did not undergo SCT. 28% of pts received intensive therapy (+/- VEN) as salvage after acquisition of WT1 mwithout difference in OS compared to those receiving low intensity therapy (66% with VEN). mOS (11.1 vs. 7.8 mos, p=0.12) . In pts ND AML and co-mutant NPM1/WT1, WT1 m was frequently (75%) subclonal to NPM1 m with a mOS NR. However, in pts who initially had NPM1 m disease and acquired a WT1 m at relapse, WT1 m was more clonally co-dominant with NPM1 mwith a mOS of 15.9 mos (p=0.11). Amongst both cohorts, there was no difference in survival based on sex. Conclusion WT1 mutations are enriched in intermediate and adverse risk AML, frequently acquired at relapse, and are associated with overall poor OS in the absence of SCT. Our data suggests that pts with WT1m AML benefit from high intensity induction regimens and SCT at CR1 should be considered in all WT1 m pts with ELN2022 intermediate or adverse risk disease. WT1 mutations should also be considered for inclusion into ELN risk stratification given poor overall survival without SCT.

Characteristics of FLT3-ITD and Efficacy of Sorafenib Treatment in Pediatric AML: A Report from AML-BFM Study Group

Introduction Internal tandem duplication (ITD) of FMS-related tyrosine kinase 3 ( FLT3) gene is one of the most common somatic mutations in acute myeloid leukemia (AML). We and others have previously shown that the prognostic significance of FLT3-ITD in children and young adults relies on its characteristics e.g., co-occurrence with WT1 mutationsand NUP98::NSD1 fusions (Niktoreh et al. 2019) or higher allelic ratio (AR) (Tarlock et al. 2018) lead to worse survival outcomes. Also, recent studies suggested that treatment with FLT3 inhibitors, including sorafenib, might be effective in children with FLT3-ITD positive AML. In this report, we summarize the characteristics of FLT3-ITD and outcomes of treatment with sorafenib in patients recruited in AML-BFM consecutive trials. Methods Patients aged 0-21 years old, diagnosed with FLT3-ITD positive de novo AML between Jan. 2004 and Dec. 2021 in Germany and recruited in AML-BFM 2004 and 2012 studies or the 2012 and 2017 registries were retrospectively analyzed. All patients with FLT3-ITD with high- or intermediate risk stratification (HR or IR) were recommended to receive 100 mg/m² sorafenib taken orally twice daily on days 7 to 21 of their induction and consolidation chemotherapy blocks, the final decision however was made by the treating physicians. Patient samples were examined in AML-BFM reference laboratory in Essen, Germany using standard methods. Patients with Down syndrome and AML-M3 were excluded from the current analysis and survival rates were calculated using Kaplan-Meier method and Log-Rank test (significance threshold p&amp;lt;0.05). Results In total, 137 patients (51% male) with median age of 7.78 (1.3-19, IQR=7.27) years at diagnosis were included. Most of the patients were initially stratified in IR group (70%, N=95) followed by HR (26%, N=35). FABs M2, M4 and M1 consisted 74% of all morphologic subtypes with 26%, 25% and 23% of patients, respectively and with a median of 64,000 (500 -700,400, IQR=53,178) x10 9/L, the majority of patients showed a leukocytosis at diagnosis. The median ITD length in the 107 patients with available data was 51 (9-111, IQR=39) bps and 54% of the 91 patients with available data had an AR above 0.5. WT1 mutations and NUP98::NSD1 were detected in 25% (N=34) and 7% (N=10) of patients, respectively and 4% (N=6), harbored both mutations simultaneously. The three-year probability of overall and event-free survival (3y-OS and 3y-EFS, respectively) in all FLT3-ITD patients were 68.8% (±4.3) and 47.6% (±4.5), respectively and although harboring ITDs longer than the median length had a tendency to worsen the 3y-OS (54.4% in ITD&amp;gt;51 bps vs. 73.3% in ITDs&amp;lt;51 bps, p=0.071), it did not influence the 3-y EFS (41.7% vs. 54.2%, p=0.204). Similarly, an AR higher than 0.5 did not affect the survival outcomes (3y-OS: 67.4% vs. 60.4%, p=0.744, 3y-EFS: 46.8% vs. 47%, p=0.618). In total, 36 patients (27%) were treated with sorafenib of which, 23 (63%) received a consecutive HSCT. We observed no survival advantage between sorafenib-treated and sorafenib-naive groups of patients (3y-OS: 73.7% vs. 67.3%, p=0.408, 3y-EFS: 48.3% vs. 47.5%, p=0.929). Patients with longer ITDs did not benefit from sorafenib treatment (3y-OS: 68% vs. 54.3%, p=0.279, 3y-EFS: 48.9% vs. 38.4 %, p=0.649) but higher AR, showed a tendency of improved survival outcomes when sorafenib treatment was implicated (3y-OS: 80.8 % vs. 61.9 %, p=0.159, 3y-EFS: 67.3 % vs. 39.9 %, p=0.131). Although the number of patients were limited, we observed a possible survival advantage in double or triple FLT3-ITD, NUP98::NSD1 and WT1 mutated patients who received Sorafenib: from 28 patients with WT1 mutations only, four patients received sorafenib three of which, are currently alive and in CR but contrarily, from the 24 untreated patients, 14 (58%) are deceased (78% due to relapse). Additionally, from 10 patients with NUP98::NSD1 (w/o WT1 mutations), two who were treated with sorafenib are alive and in CR, whereas from the remaining 8 patients, 6 (75%) experienced relapse and unfortunately did not survive. Conclusions Our preliminary analysis implicates that although addition of sorafenib to the intensive chemotherapy of children and adolescence with FLT3-ITD positive AML, did not improve the survival outcomes in allpatients; specific genetic subgroups might benefit from this treatment. These results must be validated in bigger cohorts of patients with longer follow-ups.

UBTF Tandem Duplications in Pediatric MDS and AML: Implications for Clinical Screening and Diagnosis

Recent genomic studies in adult and pediatric acute myeloid leukemia (AML) demonstrated recurrent in-frame tandem duplications (TD) in exon 13 of upstream binding transcription factor ( UBTF) (PMID: 35176137, PMID:37085611). UBTF-TDs are subtype-defining genomic alterations associated with poor outcomes that account for ~4.3% of AMLs in childhood and up to 3% in adult AMLs under the age of 60. UBTF-TD AMLs are characterized by HOXA/HOXB dysregulation, trisomy 8 or normal cytogenetics and frequent FLT3-ITD and/or WT1 mutations. A more comprehensive investigation into the clinicopathological features of UBTF-TD AMLs is needed to better understand disease features for appropriate diagnosis and to develop more effective therapies. Here, we present 94 unique pediatric cases harboring a tandem duplication in exon 13 of UBTF with a median size of 60bp (range 21-1173bp). Of these 94 cases, 6 (6.4%) were diagnosed with childhood MDS with increased blasts (WHO), suggesting that like in adults, UBTF-TDs are not only confined to AML. UBTF-TD AMLs are associated with an overall lower median white blood cell (WBC) when compared to other common HOXA/B dysregulated leukemias ( UBTF-TD median = 10.2x10 9/L, NPM1-mutation median = 21.8x10 9/L, NUP98-rearranged ( NUP98r) median = 97x10 9/L). Available immunophenotyping on 32 U BTF-TD tumors demonstrated positivity for HLA-DR (31/31; 100%), CD117 (28/29; 95%), and CD34 (26/30; 86%) with variable positivity for CD7 (17/30; 56%) and CD64 (13/25; 52%). A limited number of cases tested for CD123 (n=11) and CD11c (n=15) were all positive for the respective marker. Furthermore, morphologic assessment of these cases revealed pleomorphic blasts with occasional Auer rods and increased immature myeloid cells with salmon-colored granules, commonly with background multilineage dysplasia and increased erythroid precursors. At the transcriptional level, UBTF-TD leukemias are largely similar to NPM1-mutated and NUP98::NSD1 AMLs with the exception of UBTF-TD cases having marked increase in expression of histone genes (e.g., HIST1H4F and HIST1H2B1) and a subset of posterior HOXB cluster genes (e.g., HOXB9). Further inspection using UMAP (Uniform Manifold Approximation and Projection) of expression profiles across different pediatric AML cohorts revealed two unclassified cases of AML that clustered with the UBTF-TD subtype ( Figure 1). One case had a WT1p.S364* and the other a somatic GATA2 p.R338fs and FLT3-ITD, but did not contain an exon 13 duplication or other defining alterations. Upon closer inspection of the UBTF gene in these cases, we uncovered that each case had an in-frame tandem duplication in exon 9 of UBTF encoding a region between HMG box 2 and 3 with features similar to those in exon 13 ( Figure 2). We therefore postulated that exon 9 TDs ( UBTF-e9) could represent a functionally equivalent subgroup of UBTF-TDalterations. To test this hypothesis, cord-blood CD34+ (cbCD34+) cells were transduced to test the transforming potential of UBTF-e9 duplications. Like with UBTF-e13 duplications, cbCD34+ cells expressing UBTF-e9 duplications displayed increased proliferation compared to UBTF -WT and lentiviral empty vector control in liquid culture; and increased colony counts and replating capacity, increased CD117 expression, and a more blast-like morphology in CFU assays. Collectively, these data suggest that like TDs in exon 13, exon 9 TDs are also sufficient to promote leukemogenic phenotypes. In conclusion, we find that UBTF-TDs occur in both MDS and AML and are associated with lower WBC count, myelodysplasia, and stem cell-related surface marker expression. We have also expanded the spectrum of UBTFalterations in myeloid neoplasms through the identification of rare UBTF duplications in exon 9 that induce a similar transcriptional signature to exon 13 UBTF-TDs. The recent identification of UBTF-TDs in adult and pediatric high-risk myeloid neoplasms has highlighted the importance of understanding and appropriately diagnosing tumors with this genomic alteration, including a new class of alterations that will not be detected by PCR-based screening strategies that specifically target exon 13 of UBTF.

Wilms' tumor gene 1: lessons from the interface between kidney development and cancer.

In 1990, mutations of the Wilms' tumor-1 gene (WT1), encoding a transcription factor in the embryonic kidney, were found in 10-15% of Wilms' tumors; germline WT1 mutations were associated with hereditary syndromes involving glomerular and reproductive tract dysplasia. For more than three decades, these discoveries prompted investigators to explore the embryonic role of WT1 and the mechanisms by which loss of WT1 leads to malignant transformation. Here, we discuss how alternative splicing of WT1 generates isoforms that act in a context-specific manner to activate or repress target gene transcription. WT1 also regulates posttranscriptional regulation, alters the epigenetic landscape, and activates miRNA expression. WT1 functions at multiple stages of kidney development, including the transition from resting stem cells to committed nephron progenitor, which it primes to respond to WNT9b signals from the ureteric bud. WT1 then drives nephrogenesis by activating WNT4 expression and directing the development of glomerular podocytes. We review the WT1 mutations that account for Denys-Drash syndrome, Frasier syndrome, and WAGR syndrome. Although the WT1 story began with Wilms' tumors, an understanding of the pathways that link aberrant kidney development to malignant transformation still has some important gaps. Loss of WT1 in nephrogenic rests may leave these premalignant clones with inadequate DNA repair enzymes and may disturb the epigenetic landscape. Yet none of these observations provide a complete picture of Wilms' tumor pathogenesis. It appears that the WT1 odyssey is unfinished and still holds a great deal of untilled ground to be explored.

Chronic Mitochondrial Dysfunction Renders Acute Myeloid Leukemia Resistant to Multipronged Inhibition of Mitochondrial Metabolism

Acute Myeloid Leukemia (AML) is a genetically diverse and aggressive myeloid neoplasm that awaits novel therapeutics to improve patient survival. Targeting AML metabolic aberrations as a genotype-agnostic strategy has shown promise, evidenced by the clinical success of venetoclax and the rapid pre-clinical development of other mitochondrial (mt) metabolism targeted therapies. However, the mechanism of how AML develops resistance to drugs targeting key mt metabolic pathways is not fully understood. We previously identified sirtuin 5 (SIRT5), a deacylase that regulates several pathways of mt metabolism in AML including oxidative phosphorylation and glutamine metabolism. In AML, it functions as a master metabolic regulator that is necessary for leukemic stem cell survival. Genetic or pharmacological inhibition of SIRT5 leads to rapid AML cell apoptosis in vitro and disease regression in multiple AML mouse models. However, a subset of AML cell lines and primary samples can survive SIRT5 inhibition, indicating an unusual intrinsic resistance to mt dysfunction. To provide a mechanistic explanation, we first compared the molecular features between SIRT5-dependent and independent cases. Among the 25 primary AML samples we tested, NPM1c mutation, but not FLT3-ITD, TP53, WT1, NRAS, or IDH1 mutations, is significantly enriched in SIRT5-independent samples. Accordingly, among the panel of 22 AML cell lines we tested, the only NPM1 mutant cell line (OCI-AML3) sits at the most SIRT5-independent extreme of the spectrum. NPM1 mutant AML cells have increased cytoplasmic mitochondrial DNA (mtDNA) and fragmented mt morphology, indicating chronic mt damage (Wu H et al. Cancer Discovery. 2021). Because SIRT5 exerts its metabolic maintenance functions within the mt, we hypothesize that AML cells that can adapt to chronic, sublethal mt dysfunction will be capable of proliferation without SIRT5. To test this, we took three orthogonal approaches: (1) introducing NPM1c mutation, (2) using low concentrations of ethidium bromide (EtBr) to selectively block mtDNA replication, or (3) genetically inducing chronic mt dysfunction by silencing the essential mt transcription factor TFAM in 3 AML cell lines that are heavily dependent on SIRT5 - OCI-AML2, CMK, and SKM-1. SIRT5-dependent cells expressing ectopic NPM1c exhibit mt dysfunction as evidenced by decreased oxygen consumption rate (OCR) measured using the Seahorse metabolic flux assay. Also, the lethal effect of SIRT5 depletion is rescued in these cells. Pharmacologically blocking NPM1c nuclear export with selinexor in the typically SIRT5-independent OCI-AML3 cells sensitizes them to the lethal effect of SIRT5 depletion. After culturing in 100 ng/mL EtBr for 3, 5, or 11 days, cells had significantly decreased mt abundance as measured by mtDNA content relative to nuclear DNA and had significantly decreased OCR and extracellular acidification rate (ECAR). SIRT5-dependent cells cultured in EtBr survived shRNA-induced SIRT5 depletion, in contrast to the rapid lethality of cells not cultured in EtBr. Additionally, cells initially cultured in EtBr and allowed to recover in the absence of EtBr assume their original phenotype of SIRT5 dependence. However, inhibiting specific subunits of the mt using potent complex I and III inhibitors (rotenone and antimycin A) shows no effect on SIRT5 dependence. Together these data suggest that mt damage, rather than loss of function in one pathway, is needed to convert SIRT5-dependent cells to SIRT5 independence. TFAM, a nuclearly coded transcription factor for mtDNA, is necessary for the replication and transcription of mt genes. We used cas13d-mediated knockdown of TFAM to deplete mtDNA and induce mt dysfunction. Experiments that investigate how this method of inducing mt dysfunction affects OCR, ECAR, and SIRT5-dependent cell line proliferation are currently underway and will be presented at the ASH conference. In summary, we present a mechanism of how NPM1 mutation-associated or experimentally induced chronic sublethal mt dysfunction renders AML resistant to therapies targeting vital mt metabolic pathways, such as SIRT5 inhibitors, demonstrating AML's metabolic flexibility. Experiments are scheduled to validate these findings in primary samples and additional metabolomic and transcriptional studies will be done to deduce the mechanism for SIRT5 dependence in AML.

Features of the TCR repertoire associate with patients' clinical and molecular characteristics in acute myeloid leukemia.

Allogeneic hematopoietic stem cell transplant remains the most effective strategy for patients with high-risk acute myeloid leukemia (AML). Leukemia-specific neoantigens presented by the major histocompatibility complexes (MHCs) are recognized by the T cell receptors (TCR) triggering the graft-versus-leukemia effect. A unique TCR signature is generated by a complex V(D)J rearrangement process to form TCR capable of binding to the peptide-MHC. The generated TCR repertoire undergoes dynamic changes with disease progression and treatment. Here we applied two different computational tools (TRUST4 and MIXCR) to extract the TCR sequences from RNA-seq data from The Cancer Genome Atlas (TCGA) and examine the association between features of the TCR repertoire in adult patients with AML and their clinical and molecular characteristics. We found that only ~30% of identified TCR CDR3s were shared by the two computational tools. Yet, patterns of TCR associations with patients' clinical and molecular characteristics based on data obtained from either tool were similar. The numbers of unique TCR clones were highly correlated with patients' white blood cell counts, bone marrow blast percentage, and peripheral blood blast percentage. Multivariable regressions of TCRA and TCRB median normalized number of unique clones with mutational status of AML patients using TRUST4 showed significant association of TCRA or TCRB with WT1 mutations, WBC count, %BM blast, and sex (adjusted in TCRB model). We observed a correlation between TCRA/B number of unique clones and the expression of T cells inhibitory signal genes (TIGIT, LAG3, CTLA-4) and foxp3, but not IL2RA, CD69 and TNFRSF9 suggestive of exhausted T cell phenotypes in AML. Benchmarking of computational tools is needed to increase the accuracy of the identified clones. The utilization of RNA-seq data enables identification of highly abundant TCRs and correlating these clones with patients' clinical and molecular characteristics. This study further supports the value of high-resolution TCR-Seq analyses to characterize the TCR repertoire in patients.

Phenotype, genotype, and clinical outcome of Taiwanese with congenital nephrotic syndrome

Congenital nephrotic syndrome (CNS) is one of the important causes of end-stage kidney disease in children. Studies on the genotype, phenotype, and clinical outcome in infants with CNS caused by genetic mutations are scarce. We analyzed the genetic background, clinical manifestations, treatment response, and prognosis of pediatric patients with CNS in Taiwan. Fifteen infants with CNS were enrolled, and 11 patients of median age 21 (interquartile range 3∼44) days caused by genetic mutations from 10 unrelated families were included in the study. Of the eleven patients, 9 had extra-renal manifestations including microcephaly, facial dysmorphism, and skeletal anomalies. More than two-thirds of the patients had disease onset before 1 month of age. Diffuse meningeal sclerosis was the most common histological characteristic. Whole exome sequencing followed by direct Sanger sequence revealed mutations in OSGEP (R247Q), WT1 (R366H and R467Q), LAMB2 (Q1209∗ and c. 5432-5451 19 bp deletion), NUP93 (D302V), and LAGE3 (c.188+1G>A). Three of the variants were novel. Corticosteroids and/or immunosuppressants were administered in 2 patients, but both were refractory to treatment. During the mean 3.5 years of follow-up, all but two died of uremia and sepsis. The two survivors reached end-stage kidney disease and required peritoneal dialysis, and one of them underwent uneventful renal transplantation. The majority of patients with CNS in Taiwan were caused by OSGEP followed by WT1 mutation. R247Q is the hotspot mutation of OSGEP in Taiwan. CNS patients in Taiwan suffer from significant morbidity and mortality.

Characteristics and Outcome of FLT3-ITD-Positive Pediatric Acute Myeloid Leukemia-Experience of Polish Pediatric Leukemia and Lymphoma Study Group from 2005 to 2022.

The FMS-like tyrosine kinase 3 (FLT3) gene mutated in 10-15% of pediatric acute myeloid leukemia (AML) is associated with an inferior outcome. The aim of the study was to analyze the outcome and characteristics of FLT3-ITD-positive pediatric AML. We retrospectively analyzed the nationwide pediatric AML database from between 2005 and 2022. FLT3-ITD was found in 54/497 (10.7%) patients with available analysis. Three consecutive treatment protocols were used (AML-BFM 2004 Interim, AML-BFM 2012 Registry, AML-BFM 2019 recommendations). Probabilities of 5-year overall (OS), event-free (EFS) and relapse-free survival were significantly lower in the FLT3-ITD-positive patients compared to FLT3-ITD-negative (0.54 vs. 0.71, p = 0.041; 0.36 vs. 0.59, p = 0.0004; 0.47 vs. 0.70, p = 0.0029, accordingly). An improvement in the outcome was found in the analyzed period of time, with a trend of better survival in patients treated under the AML-BFM 2012 and AML-BFM 2019 protocols compared to the AML-BFM 2004 protocol (5-year EFS 0.52 vs. 0.27, p = 0.069). There was a trend of improved outcomes in patients treated with FLT3 inhibitors (n = 9, 2-year EFS 0.67 vs. 0.33, p = 0.053) and those who received stem cell transplantation (SCT) (n = 26; 5-year EFS 0.70 vs. 0.27, p = 0.059). The co-occurrence of the WT1 mutation had a dismal impact on the prognosis (5-year EFS 0.23 vs. 0.69, p = 0.002), while the NPM1 mutation improved survival (5-year OS 1.0 vs. 0.44, p = 0.036). It seems that SCT and FLT3 inhibitors have a beneficial impact on the prognosis. Additional genetic alterations, like the WT1 and NPM1 mutations, significantly influence the outcome.

WT1-mutated acute myeloid leukemia is sensitive to fludarabine-based chemotherapy and conditioning regimens

We conducted a retrospective analysis of WT1-mutated acute myeloid leukemia (AML) patients who underwent allogeneic stem cell transplant. Thirty-seven patients with WT1-mutated AML were identified. Primary induction failure (40%) and early relapse rate (18%) after idarubicin/cytarabine (7 + 3) chemotherapy were observed. All patients with induction failure subsequently achieved CR with additional chemotherapy. There was no significant difference between outcomes after myeloablative vs. reduced intensity (Fludarabine/Melphalan [Flu/Mel]) conditioning regimens. RFS but not OS was significantly better in patients who received FLAG-IDA prior to transplant and/or a fludarabine-containing conditioning. In an independent ex vivo study, WT1-mutated AML samples exhibited greater sensitivity to fludarabine (p = 0.026) and melphalan (p = 0.0005) than non-WT1-mutated AML samples while there was no difference between sensitivity to cytarabine. Our data favor using a fludarabine-based induction for AML with WT1 mutation instead of 7 + 3. Fludarabine conditioning regimens for alloHCT showed better RFS but not OS.