Badar, Talha

Abstract Introduction: HMA monotherapy (HMAm) continues to be the standard of care for HR-MDS. While the addition of VEN to azacitidine (AZA) improved overall survival (OS) and complete remission (CR) rates among older pts with acute myeloid leukemia (AML) over AZA monotherapy, the recently completed phase III VERONA trial of AZA+/-VEN in HR-MDS failed to show an OS benefit for AZA/VEN over AZA monotherapy. Using the icMDS VALIDATE database, we compared outcomes of pts with HR-MDS treated with HMA or HMA/VEN as frontline therapy. Methods: The icMDS VALIDATE database includes over 4000 adult MDS pts who received HMA-based therapy from 32 international centers in 9 countries. For this analysis, we included pts with HR-MDS defined by International Prognostic Scoring System [IPSS] ≥1.5 or IPSS-revised [IPSS-R] ≥4 (at diagnosis or HMA initiation) and treated with HMAm or HMA/VEN as frontline therapy for HR-MDS. We assessed responses based on IWG 2023 criteria (Zeidan A et al, Blood 2023). Composite complete remission (cCR) was defined as CR+CRbi+CRuni+CRh+CRequivalent. We calculated OS from time of HMA initiation to date of death from any cause. Pts lost to follow-up were censored at the date they were last known to be alive. We used Kaplan-Meier methods to calculate OS and compared OS between different groups using the log-rank test. We used Cox and logistic regression models to adjust for baseline prognostic variables as appropriate. The study was funded by an independent grant from Abbvie. Results: A total of 1907 pts met eligibility and were included (1552 AZA, 221 decitabine, 134 HMA+VEN). 479 pts subsequently underwent allogeneic stem cell transplant (allo-SCT; 430 after HMAm [32.6%]; 49 after HMA/VEN [37.1%]). Our cohort was enriched for pts with adverse disease characteristics including complex karyotype (33.6%) and TP53 mutations (28.7%). Compared to pts treated with HMA/VEN, pts treated with HMAm were more likely to be male (p=0.012), have lower baseline platelet counts (p=0.037), peripheral blood (PB) blasts (p=0.004), or bone marrow blasts (p<0.001), and were less likely to have very high risk IPSS-M (p<0.001), TP53 mutations (p<0.001), or complex karyotype (p=0.020). In unadjusted analyses, the rate of cCR was significantly lower in HMAm treated pts compared to HMA/VEN treated pts (27.7% vs. 48.8%, p<0.001). However, CR rate was not significantly different (11.7% vs. 17.1% for HMAm and HMA/VEN, respectively, p=0.22). After adjusting for age, sex, and IPSS-M, pts treated with HMA/VEN were more likely to achieve cCR compared to HMAm with an odds ratio (OR) of 2.49 (95% CI: 1.56-3.96, p<0.001). When separated by TP53 mutation status, the OR for cCR for HMA/VEN vs HMAm was 4.17 (95%CI: 2.14-8.31; p<0.001) and 1.27 (95%CI: 0.54-2.86; p=0.57) for TP53 wild-type and TP53-mutant pts, respectively. In unadjusted analyses, median OS was 17.4 months for HMAm and 19.6 months for HMA+VEN, and OS did not differ significantly by treatment type (p=0.33). For HMAm treated pts, the OS rates at year 1, 2, 3 were 0.65 (95%CI: 0.63-0.67), 0.38 (95%CI: 0.36-0.40), and 0.27 (95%CI: 0.25-0.29), respectively. For HMA/VEN treated pts, the OS rates at year 1, 2, 3 were 0.64 (95%CI: 0.56-0.73), 0.45 (95%CI: 0.36-0.56), and 0.37 (95%CI: 0.27-0.51), respectively. In a multivariate analysis adjusting for age, sex, PB blast, IPSS-M and allo-SCT as a time-varying covariate, treatment with HMA/VEN vs HMAm did not significantly influence OS (hazard ratio (HR) of OS for HMA/VEN vs HMAm: 0.89, 95%CI: 0.69-1.13, p=0.33). When stratified by TP53 mutation status, HR of HMA/VEN vs. HMAm was favorable for TP53 wild-type (HR: 0.47; 95%CI: 0.29-0.74) but not TP53-mutant pts (HR=0.96; 95%CI: 0.66-1.41). Adjusting for other variables in the model, HR for pts who underwent vs. those who did not undergo allo-SCT were 0.65 (95% CI: 0.49-0.85) and 0.36 (95%CI: 0.24-0.53) in TP53 wild-type and mutant patients, respectively. Conclusion: In this large, international retrospective analysis from the icMDS VALIDATE database, HMA/VEN was associated with higher cCR rates—but not CR rates—compared to HMAm among pts with HR-MDS, though we observed no significant differences in OS. In our analysis, clinical benefit from the addition of VEN was most clear in TP53 wild-type pts, and allo-SCT was associated with improved OS regardless of baseline TP53 status. Our analysis was limited by the relatively small number of HMA/VEN-treated pts and heterogeneous real-world treatment patterns.

Abstract Background: Hypomethylating agent (HMA) with venetoclax (VEN) is used in clinical practice for frontline management of patients with myelodysplastic syndrome (MDS) based on encouraging data from phase 1 clinical trial (Garcia JS et al. Blood 2025). While the randomized clinical trial (VERONA-NCT04401748) did not show a survival benefit of azacitidine-VEN, the study had important differences such as exclusion of therapy related MDS and being conducted in several non-academic US centers. To better understand the impact of this regimen and its effects in subgroups, we conducted a real-world analysis of frontline MDS patients treated mainly at academic medical centers with HMA-VEN and compared to HMA monotherapy. Methods: This is a multicenter retrospective study of 19 US academic medical centers. We included contemporary cohorts of adults (age≥18 years) with MDS (intermediate, high or very high risk by IPSS-R) who were treated outside of clinical trials with either upfront combination of HMA-VEN or HMA monotherapy. Data on patient-related, disease-related and treatment-related variables were collected through chart review. Descriptive statistics were used for baseline characteristics. Overall survival (OS) and event free survival (EFS: progression, leukemic transformation, death as events) analysis was conducted using Kaplan-Meier method. Determinants of outcomes were analyzed using multivariable regression models. All analyses were conducted at a significance level of p<0.05. Results: Among 1198 patients with intermediate, high or very-high risk MDS, 313 patients received upfront VEN in combination with HMA [HMA-VEN] and 885 patients received HMA monotherapy. Median age was 70 (63-76) years and majority of patients had MDS with excess blasts-1 (34% overall, HMA-VEN=26%, HMA=37%) or MDS with excess-blasts-2 (41% overall, HMA-VEN=60%, HMA=34%). Disease risk by IPSS-R was intermediate (29% overall, HMA-VEN=18%, HMA=33%), high (30% overall, HMA-VEN=31%, HMA=30%) or very-high risk (41% overall, HMA-VEN=51%, HMA=37%, p<0.001). Therapy related MDS (t-MDS) was seen in 27% of patients (HMA-VEN=33%, HMA=25%, p=0.004), 34% had TP53 mutation (HMA-VEN=40%, HMA=32%, p=0.005) and 33% underwent allogeneic hematopoietic stem cell transplantation (AHSCT) (HMA-VEN=42%, HMA=30%, p<0.001). The most common mutations detected at baseline included TP53 (34%), ASXL1 (22%), DNMT3A (16%), RUNX1 (16%), TET2 (14%), SRSF2 (13%), and U2AF1 (11%). The response rate by IWG 2006 criteria was significantly higher with HMA-VEN than HMA monotherapy (overall 81% vs 39%, CR: 17% vs 9.6%; marrow CR: 56% vs 14%, p<0.001). In multivariable analysis accounting for upfront treatment, AHSCT, genomic mutations, baseline bone marrow blasts and t-MDS, patients treated with HMA-VEN in the upfront setting had significantly improved EFS (median EFS 10.7 vs. 7.8 mon, HR 0.83, 95%CI 0.72-0.96, p=0.01) and OS (median OS 22.4 vs. 18.1 mon, HR 0.79, 95%CI 0.64-0.97, p=0.02). In addition, TP53 mutation status (OS: HR 1.88, 95% CI 1.57-2.26, p<0.001, EFS: HR 1.43, 95% CI 1.23-1.65, p<0.001), subsequent AHSCT (OS: HR 0.34, 95% CI 0.27-0.41, p<0.001; EFS: HR 0.47, 95% CI 0.40-0.54, p<0.001), and therapy related MDS (OS: HR 1.20, 95% CI 1.00-1.44, p=0.04, EFS: HR 1.10, 95% CI 0.96-1.27, p=0.2) were significant predictors on multivariable analysis. When separately investigated in subgroups, an OS benefit of HMA-VEN over HMA was seen in patients undergoing subsequent AHSCT (median OS 40.6 vs. 30 mon, p=0.05), bone marrow blast 10-19% (median OS 25.1 vs. 17.4 mon, P=0.01), de novo MDS (median OS 30 vs. 20.1 mon, P=0.003) and absence of TP53 mutation (median OS 34.9 mon vs. 23.1 mon, p=0.004). The benefit of HMA-VEN over HMA was also seen across molecular mutations including presence of ASXL1 mutation (median OS 35.2 vs 20.9 mon, p=0.03). Conclusions: In this large multicenter retrospective analysis from US academic medical centers, we found that HMA-VEN therapy significantly improved OS in certain subsets of high risk MDS including patients with 10-19% blasts, denovo MDS, subsequent AHSCT and those without TP53 mutation. While our analysis is limited by its retrospective design, prospectively exploring subgroups of MDS patients who could benefit from HMA-VEN therapy is needed.

Abstract Background: Clonal cytopenia of undetermined significance (CCUS) is defined as clonal hematopoiesis in the absence of a hematologic neoplasm, along with unexplained cytopenia. While several studies have identified risk factors and developed scores to predict progression to overt myeloid neoplasms, the clinical and molecular features during the progression process remain poorly understood. Aim: Evaluate the clinical and clonal characteristics of patients with CCUS, with a focus on the longitudinal evolution of clonal and clinical parameters over time. Methods: After IRB approval, we retrospectively reviewed charts of patients with unexplained cytopenia (2015-2024), recording data at the time of CCUS diagnosis (WHO 2022 diagnostic criteria) and at time of follow-up bone marrow biopsy after diagnosis. Follow-up CBC and karyotype data were recorded for patients who had repeat bone marrow biopsies (n= 111), while follow-up clonal parameters and risk scores were calculated for those who underwent repeat NGS (n= 74). A reduction or expansion in clone size was defined as a change exceeding 5% (CE5%), or change exceeding 10% (CE10%) from the baseline value. Overall survival (OS) was calculated from diagnosis to last follow-up. For statistical analysis, we used BlueSky Statistics V10.3.1. Results: 214 CCUS patients (median age 73, 68% males) were included. At baseline, 30% of patients had abnormal cytogenetics, with del (20q) being the most common one (8%; n= 18), followed by trisomy 8 (6%; n= 13), and loss of chromosome Y (5%; n= 10). The median number of mutations was 2 (range, 1-5), with the most common mutations TET2 (38%), SRSF2 (21.5%), ASXL1 (21%), ZRSR2 (18.5%), DNMT3A (9.5%), and U2AF1 (9%). Most patients had high risk CHRS (60%), followed by intermediate (30%), and low risk (10%). On the other hand, 41% had high risk CCRS, 29% had intermediate risk, and 30% had low risk. After a median follow-up of 46 months, 62 patients died (median OS not reached). A decrease in the white blood cell (WBC) count from the time of diagnosis to follow-up was more frequently seen among CCUS patients who progressed to MN (70% vs 50%, p= 0.04), however, changes in hemoglobin and platelets did not differ between those who progressed and those who did not (p> 0.05). Although the frequency of abnormal karyotypes at diagnosis was similar between patients who eventually progressed (28%) and those who did not (31%) (p= 0.6), 4 (2%) patients with initially normal karyotypes acquired chromosomal abnormalities during follow-up, and all progressed to MDS. Among the 74 patients who had follow-up NGS, 31% acquired new mutations, clonal expansion of pre-existing mutations were seen in 54% using CE5% and 19% per CE10%, and 16% developed new variants of uncertain significance (VUS). Acquiring new pathogenic mutations was similar in patients who progressed to MN compared to those who did not progress (34% vs 28%, p= 0.6). On the other hand, clonal expansion was significantly more observed in patients who progressed compared to those who did not, using both CE5% (73% vs 31%, p = <0.001) and CE10% (27% vs 9%, p= 0.03). At follow-up, ASXL1 was the most commonly acquired mutation among patients who did not progress (4 cases), followed by TET2 (2 cases), and U2AF1, GATA2, DNMT3A, SF3B1, ZRSR2, TP53, and CBL (1 case each). On the other hand, SRSF2, SETBP1, CBL, JAK2, TET2, and RUNX1 were more frequently acquired among those who progressed to myeloid neoplasms (each appeared in 2 patients). When recalculating CCRS, CHRS, IPSS-M, and IPSS-R at follow-up for patients who had repeat NGS, there was no significant difference in score changes - either upward or downward - between those who progressed and those who did not (p> 0.05). Conclusion: In CCUS patients who progressed to myeloid neoplasms, WBC decline, clonal expansion (more frequent), and evolving chromosomal aberrations (less frequent) were observed, supporting the value of longitudinal genomic and clinical monitoring in CCUS.

Abstract Germline mutations in the RNA-helicase gene DDX41 cause predisposition to myeloid malignancies (MDS/AML) with a penetrance of 50% by age 90. DDX41 germline mutations are heterozygous and predominantly truncating variants, indicative of loss-of-function. More than half of DDX41-mutated carriers that develop MDS/AML will acquire a second-hit mutation in the other allele of DDX41, frequently causing the amino acid substitution p.R525H. Single-cell analysis from a biallelic DDX41-mutated MDS patient showed that the p.R525H mutation was highly enriched in dendritic cells (DCs) but less frequent in other cell types. We hypothesized that p.R525H causes the hematopoietic stem and progenitor cells (HSPCs) to differentiate preferentially into DC. To precisely model the germline of DDX41-mut patients, we generated human induced pluripotent stem cells (iPSC) with a frameshift mutation in exon 6 of one allele of DDX41, modeling the most common germline mutation. We attempted to modify the other allele of DDX41 to express the p.R525H mutation but could not derive viable cells. To circumvent potential lethality of the acquired mutation, we inserted a Doxycycline (DOX)-inducible wild-type DDX41 expression cassette in the AAVS1 safe harbor locus. Then we modified the endogenous allele to cause the p.R525H mutation in trans to the existing frameshift mutation. In this manner, we derived iPSCs that would model the most common configuration of DDX41 mutations (DDX41R525H/-) upon the withdrawal of DOX from the culture. In undifferentiated iPSC cultures, we observed profound defects in cell proliferation and survival upon DOX withdrawal. To determine the effect of the p.R525H mutation on hematopoietic cells, we differentiated the iPSCs into CD34+ HSPCs in the presence of DOX, and then withdrew DOX and studied the effect of the DDX41R525H/- genotype on HSPC function. In colony formation assays, DDX41R525H/- cells produced fewer and smaller myeloid and erythroid colonies after DOX withdrawal. In liquid culture, DDX41R525H/- cells showed cell cycle arrest by EdU incorporation assay and protein synthesis deficit by HPG assay. Thus, we conclude that DDX41 is required for proliferation and survival in iPSC and hematopoietic progenitor cells and that p.R525H lacks the essential function. Next, we tracked HSPC differentiation in liquid culture containing Flt3 ligand, stem cell factor and thrombopoietin with or without GM-CSF. Identification of DC subsets by flow cytometry was based on the literature (Sontag S, et al. Stem Cells 2017;35(4)). We observed reduced overall differentiation in DDX41R525H/- cultures, evidenced by maintenance of CD34 positivity. However, among the CD45+CD34- cells, DDX41R525H/- cells were 3-4 fold more likely to be identified as plasmacytoid DC (pDC) compared to control conditions (+DOX or DDX41+/- cells). Notably, in DDX41R525H/- CD45+CD34- cells, overall CD123 and CD304 expression were profoundly upregulated and CD11c was downregulated, indicative of increased pDC character. We used a similar DOX-inducible approach to generate Molm13 human AML cell line with DDX41R525H/- and homozygous knockout (DDX41-/-) genotype and found that these cells had profound survival defects. Both genotypes exhibited DC-like morphological change with extended multiple projections upon DOX withdrawal. In flow cytometry analysis, both genotypes exhibited upregulated Clec9a (conventional DC1 (cDC1) marker) and Clec10a and CD1c (cDC2 marker) upon DOX withdrawal. DDX41R525H/- cells specifically exhibited pDC features shown by upregulated CD123 by flow cytometry and increased IRF7 by western blotting, while DDX41-/- had decreased IRF7. Furthermore, we found that DDX41R525H/- cells specifically showed increased IRF9 and phosphorylated STAT1 and STAT2, which are downstream of interferon receptor activation, indicating that type-I interferon produced by DDX41R525H/- pDC activates interferon signaling in autocrine/paracrine manner. These results indicate that p.R525H promotes differentiation into pDC, which is not observed in DDX41-/- cells. In conclusion, DDX41 p.R525H mutation has bimodal functions in HSPC: loss-of-function for proliferation/survival and gain-of-function for skewed differentiation into pDC. Dysregulated DCs may contribute to the pathogenesis of DDX41-mutated MDS/AML, particularly in light of recent descriptions of AML with pDC differentiation and the broader role of DC dysregulation in MDS/AML.

Abstract Introduction TP53MT are associated with poor outcomes in MDS, especially in the context of biallelic MT. We have previously reported on outcomes of pts with HR-MDS with TP53MT who received HMA in the VALIDATE dataset (Kewan T et al, ASH 2023). Here we provide expanded analyses focusing on outcomes post allo-HCT, and we explore the prognostic significance of different classification methods for biallelic TP53MT. Methods The VALIDATE database includes 4,732 pts with MDS who received HMA-based frontline therapy from 32 international centers in 9 countries. For this study, only pts with HR-MDS with molecular data at time of diagnosis were included. Biallelic TP53MT status was assessed using three classification schemes: WHO 2022, ICC 2022, and a VAF-based Cleveland Clinic Foundation (CCF) method.1TP53 copy neutral loss of heterozygosity (CN-LOH) was evaluable in 386 pts (118 had TP53MT). Treatment responses were evaluated using IWG 2023 criteria (Zeidan A et al, Blood 2023). Composite complete remission (cCR) was defined as CR+CRbi+CRuni+CRh+CRequivalent. We calculated OS from time of HMA initiation to date of death or last follow up. Unsupervised clustering (MOSAIC framework) was applied to identify molecular subgroups within the TP53MT cohort. The study was funded by an independent grant from Abbvie. Results A total of 1,485 pts were included. Median age was 69 years (IQR: 62–76), with 66% male pts. Median bone marrow blast was 7%, and 28% had a complex karyotype. Treatment regimens included azacitidine (68%), decitabine (15%), HMA/Venetoclax (8%), and other HMA combinations (9%); 34% underwent allo-HCT. Overall, 392 (26%) had TP53MT with 430 TP53 mutations (missense: 316; truncating: 89). Biallelic TP53MT % varied by classification: 72% (WHO), 84% (ICC), and 85% (CCF). Compared to TP53 wild-type (TP53WT) pts, pts with TP53MT had worse OS (median: 11.5 vs. 23.9 months [mo], p< 0.001), were younger (68 vs. 70 years, p=0.039), and had lower counts at diagnosis. Complex karyotype (81% vs. 14%) and chromosomal abnormalities were more frequent in TP53MT pts. Pts with TP53MT also had fewer co-mutations in other genes. Response to HMA was evaluable in 1,094 pts: cCR and CR were 32% and 13%, respectively. TP53MT pts had higher cCR (39% vs. 29%, p=0.001) than TP53WT, but similar CR rates (16% vs. 12%, p=0.093). According to WHO 2022, biallelic TP53MT had higher CR rates than monoallelic TP53MT (18% vs. 8%, p=0.03), but similar cCR. ICC and CCF classifications did not differentiate response rates. Median OS did not differ by TP53MT allelic status using WHO or ICC definitions. However, using the CCF method, pts with biallelic TP53MT had shorter OS than monoallelic TP53MT (10.4 vs. 17.2 mo, p=0.038). In multivariable models adjusted for age, gender, and allo-HCT, only the CCF-defined biallelic TP53MT group had significantly worse OS (HR: 1.6; 95% CI: 1.1–2.4). TP53MT pts undergoing allo-HCT had improved OS regardless of allelic status. Median OS for TP53MT pts with allo-HCT was 18.9 vs. 9.2 mo without all-HCT. This benefit was observed across WHO, ICC, and CCF classifications. However, a TP53MT VAF ≥19% predicted worse OS even post allo-HCT (14.6 vs. 47.1 mo, p<0.001). At 1 year, the survival rate was 78% (95%CI: 69-89%) in TP53MT pts who underwent allo-HCT and had cCR vs. 68% (95%CI: 55-84%) in pts who did not have cCR. However, 1 year survival rate was significantly higher for pts with TP53MT who did not have allo-HCT and achieved cCR (60%, 95%CI: 48-76%) vs. no cCR (26%, 95%CI: 20-35%). Unsupervised clustering of 335 TP53MT pts identified 9 molecular clusters (MCs). MC2, characterized by low TP53MT VAF (median 17%), fewer co-mutations, and frequent del17p, was associated with significantly improved OS (17.9 mo) and predicted favorable outcome (HR for death: 0.6; 95% CI: 0.4–0.8). Other clusters were enriched for adverse features (e.g., high VAF, multi-hit TP53MT).Conclusions The CCF method appears to best classify biallelic TP53MT pts with worse survival in the absence of accurate assessment of LOH status. Treatment response per IWG 2023 for TP53MT pts was associated with OS only in non-transplanted pts. Allo-HCT improved survival across TP53MT subsets, but TP53 VAF ≥19% at diagnosis remained a strong negative prognostic factor. Integrative clustering revealed a less aggresive molecular subset among TP53MT pts, suggesting refined risk stratification may guide therapy in this high-risk population. Ref: 1.Bahaj et al. J Hematol Oncol 2023.

Abstract Introduction: Marrow complete remission (mCR) in 2006 IWG criteria for MDS (Cheson B et al, Blood 2006) reflects achieving bone marrow (BM) blast percentage below 5% but is frequently not associated with meaningful count recovery. While mCR + hematologic improvement (HI) does reflect wide ranges of count improvement or transfusion reductions, HI is difficult to measure accurately in routine clinical practice. The 2023 International Working Group (IWG) response criteria (Zeidan A et al, Blood 2023) eliminated the mCR category without meaningful count recovery and reclassified mCR associated with meaningful count recovery into specific “less-than-CR” categories. Still, many clinical trials continue to use mCR as a secondary efficacy endpoint or as a part of overall response rate (ORR). Within the icMDS VALIDATE database, we assessed the association of mCR with OS in hypomethylating agent (HMA)-treated higher risk (HR)-MDS patients among both (1) transplanted and (2) non-transplanted patients. Methods We included patients with HR-MDS (defined as IPSS ≥1.5 and/or IPSS-R >3.5) who received HMA-based therapies from the international icMDS VALIDATE dataset. We evaluated the best response by IWG 2006 criteria into CR, mCR, or no CR/mCR. We then reclassified patients with mCR per IWG 2023 criteria into either (A) having achieved a composite CR (cCR) defined as CR + CR equivalent (CRequ) + CR with bilineage count recovery (CRbi) + CR with unilineage count recovery (CRuni) + CR with partial hematologic recovery (CRh) or (B) not having achieved cCR (no cCR). OS was calculated from time of HMA initiation to date of death or last follow-up by using 6-month landmark analyses. We used Kaplan-Meier methods to estimate OS, and the Log-rank test to compare OS. VALIDATE is supported by an independent grant from AbbVie. Results A total of1049 patients met eligibility.Median age of patients was 69 (range 21-95), 64% were men. While 61% received azacitidine, 17% received decitabine, and 22% received HMA-based combination therapy. In total, 37% underwent subsequent allogenic stem cell transplantation (allo-HCT). Based on IWG 2006 criteria, 17%, 33%, and 50% achieved CR, mCR, and no CR/mCR as their best response, respectively. Patients achieving CR had superior median OS (25 months, 95% CI: 21-34 months) compared to those with mCR (16 months, 95% CI: 13-18 months; p=0.038) and no CR/mCR (15 months, 95% CI: 12-17 months; p=0.001). In patients who received a subsequent allo-HCT, the median OS for patients with mCR (30 months, 95% CI: 21-54 months; 1 year OS: 71%, 2 year OS: 55%) did not significantly differ compared to patients with CR (59 months, 95% CI: 25 months-not reached, p=0.80; 1 year OS: 73%, 2 year OS 62%) and patients with no CR/mCR (32 months, 95% CI: 21-45 months, p=0.46; 1 year OS: 69%, 2 year OS 54%). In contrast, in patients treated with HMA therapy alone without subsequent allo-HCT, median OS for patients with mCR (11 months, 95% CI: 9-15 months; 1 year OS: 46%, 2 year OS: 23%) did not significantly differ compared to patients with no CR/mCR (11 months, 95% CI: 9-14 months, p=0.85; 1 year OS: 47%, 2 year OS: 22%) but was significantly shorter compared to patients with CR (20 months, 95% CI: 17-28 months, p<0.001; 1 year OS: 69%, 2 year OS: 46%). Patients with mCR by IWG 2006 (N=347) were reclassified per IWG 2023 into having either achieved a cCR (N=219, 63%) or no cCR (N=128, 37%). Specifically, patients with mCR were reclassified per IWG 2023 into CR (4.9%), CRequ (0.6%), CRbi (26.8%), CRuni (29.4%), CRh (1.4%), PR (0%), HI (10%), no response (21.9%) and PD (4.9%). Patients with mCR who were reclassified into cCR had an improved median OS (16 months, 95% CI: 15-26 months; 1 year OS: 62%; 2 year OS: 43%) compared to patients reclassified into no cCR per IWG 2023 (13 months, 95% CI: 11-17 months, p=0.023; 1 year OS: 52%; 2 year OS: 31%). Conclusions Using the large icMDS VALIDATE dataset, we found that achievement of mCR by 2006 IWG criteria was not associated with improved OS compared to patients who did not achieve CR/mCR. Reclassification of mCR using IWG 2023 highlights the heterogeneity within the mCR group and suggests that IWG 2023 criteria stratifies outcomes in patients previously labeled as mCR by IWG 2006. IWG 2023 should be the standard used for ORR assessment in all future clinical trials involving patients with HR-MDS.

Abstract Background: TP53-mutated (TP53mut) myeloid neoplasms (MN) are a biologically and clinically distinct subgroup of blood cancers associated with extremely poor outcomes and limited response to conventional therapies. In some patients, MN are preceded by clonal cytopenia of undetermined significance (CCUS). Prior cytotoxic exposure (treatment related, TR) is an independent predictor for survival in CCUS (Li et al, Blood Adv. 2024). As TP53mut CCUS and MN are enriched in TR cases, the interaction between cytotoxic exposure and TP53mut status on the risk of progression and survival remains unclear. Methods: Adult patients with CCUS who were evaluated at the Mayo Clinic or South Australian myelodysplastic syndrome (MDS) Registry (Adelaide, Australia) were included. CCUS and MDS were defined according to the 5th edition of the WHO classification for MN (Khoury et al, 2022), except for the exclusion of cases harboring MDS-defining cytogenetics. Next-generation sequencing was performed using a targeted panel covering genes commonly mutated in MN. In cases with >1 TP53mut, VAFs were summed. Survival outcomes were assessed by Kaplan-Meier with log-rank testing. Univariate and multivariate analyses were estimated using Cox proportional hazards regression. Results: Of 320 CCUS cases, 50 (15.6%) harbored TP53mut (TP53mut CCUS), whereas 270 (84.4%) were wild-type (TP53wt CCUS). Median age at diagnosis was 71 years (range 16-99). TP53mut CCUS had a greater proportion of females (60% vs 33.7%, p<0.001) and TR (66% vs 23%, p<0.001) compared to TP53wt. Hematologic parameters including hemoglobin, red cell distribution width, mean corpuscular volume, white blood count, absolute neutrophil count, platelets, and bone marrow blasts were comparable between the two groups. Almost all TP53mut (n=48, 96%) were located in the DNA-binding domain and the median variant allele frequency (VAF) was 9% (range 2-46%). Five (10%) cases harbored 2 TP53mut. The distribution of TP53mut VAF among patients was as follows: ≤2.5% (n=2), 2.5-5% (n=10), 5-10% (n=19), 10-20% (n=11), and ≥20% (n=7). The proportion of cases with cytogenetic abnormalities was smaller in TP53mut compared to TP53wt CCUS(12% vs 25.9%, p=0.035). Both cohorts had a comparable median number of mutations: 2 (range 0-7) in TP53mut and 2 (range 0-5) in TP53wt. The most common co-mutations in TP53mut CCUS were TET2 (n=8, 17.8%), PPMD1 (n=7, 15.6%), DNMT3A (n=6, 13.3%), ASXL1 (n=6, 13.3%), and SRSF2 (n=4, 8.9%). At last follow up, the rate of progression was comparable between TP53mut and TP53wt CCUS (12% vs 22%, p=0.13). Median time to MN progression was not reached in TP53mut and 6.25 months in TP53wt CCUS (p=0.5197). A significantly higher proportion of TP53mut cases acquired complex cytogenetics compared to TP53wt cases (33% vs 2%, p=0.024) at MN progression. Of 20 deaths observed in the TP53mut cohort, non-myeloid hematologic malignancies (n=6, 30%), infections (n=5, 25%), and TP53mut MN (n=4, 20%) were the 3 most common causes. With a median follow-up of 4 years (IQR 1.2-4.8), median OS was longer in de novo (dn) cases (8.7 years for dn TP53wt; not reached for dn TP53mut) and shorter in TR cases (3.3 years for TR TP53wt; 4.8 years for TR TP53mut). Notably, TP53mut showed no independent prognostic impact in the entire cohort, or when stratified by TR vs dn CCUS. On multivariate analysis that included TP53mut status, factors independently associated with inferior OS included prior therapy (HR 2.21, 95% CI 1.41-3.45, p<0.001), anemia (HR 4.1, 95% CI 1.88-8.99, p<0.001), and thrombocytopenia (HR 2.38, 95% CI 1.43-3.95, p<0.001). Similarly, TR CCUS (HR 1.6, 95% CI 1.06-2.4, p=0.03) and anemia (HR 2.15, 95% CI 1.25-3.7, p=0.006) were independently associated with inferior progression free survival. Conclusion: TP53 mut in CCUS did not independently predict inferior survival or increase leukemic transformation. While TP53mut CCUS were less likely to harbor cytogenetic abnormalities at diagnosis, significantly more cases harbored genomic instability at leukemic transformation. The poor outcomes attributed to TP53mut CCUS were driven by prior cytotoxic exposure, cytopenia – particularly anemia, and non-leukemic causes of death. These findings suggest risk stratification in CCUS should prioritize clinical context over TP53mut status alone.

Abstract Background: Germline predisposition states (GPS), including inherited bone marrow failure syndromes (IBMFS) are seen in 5-10% of individuals with myeloid neoplasms (MN). Given overlap with somatic driver genes, blood, saliva, and buccal swabs are suboptimal specimens for GPS testing in MN; the latter two due to contamination with blood cells(Jerez, 2024). Skin biopsy with fibroblast culture-derived DNA remains the gold standard, but the process is expensive, takes 6-8 weeks to complete, and fibroblast culture failure can occur in some patients with telomere biology disorders. Given the need to rapidly screen donors for HSCT and adjust therapy/conditioning in certain IBMFS, we developed a rapid hematologic germline testing algorithm using hair follicle-derived DNA. Methods The study was conducted after IRB approval through the Mayo Clinic GPS/IBMFS clinic. To perform PCR-based hair follicle testing, we obtained 15-25 hair follicles (bulbs) per patient. The bulbs were placed in a microcentrifuge tube and subjected to a 24-hour digestion and extraction protocol using a modified version of the QIAGEN DNA Purification from Dried Blood Spots protocol. DNA quality was assessed by Nanodrop and Qubit.Testing included either validation of known or suspected germline variants (e.g., RUNX1, DDX41, ETV6), or panel testing (e.g., GPS or IBMFS). Pathogenic variants were validated by repeat testing in a CAP/CLIA certified lab prior to medical decision making. 23 patients underwent whole exome sequencing (WES) in a CAP/CLIA lab, and 13 patients had concurrent germline testing using alternate DNA sources (8 skin biopsies, 1 saliva, 4 buccal swabs). Results Ninety-three patients (49 male, 53%) underwent hair follicle-derived germline DNA testing (median age 63 years). Indications for germline testing included the presence of a suspected variant on somatic testing with variant allele frequency (VAF) between 35%-60% ( n= 66, 71%), patient age <50 years (n=26, 28%), antecedent thrombocytopenia (n=15, 16%), presence of syndromic features (n=4, 4%), patient history of multiple malignancies (n=4, 4%), and positive family history (n=15, 16%). Time to reporting variants after receipt of hair follicle-derived DNA was <14 days. There were zero complications associated with the procedure. DNA quality as assessed by Nanodrop revealed a median nucleic acid concentration of 25.64 ng/μL. The median A260/A280 ratio was 1.86 (range 0.701-2.133) and the median A260/A230 ratio was 1.27 (range -8.193-9.223). DNA quality was insufficient for chromosomal microarray (CMA) assessments. Of 93 patients evaluated, 67 (72%) had ≥1 germline variant, with 3 having >1 germline variant for a total of 72 variants. Pathogenic/likely pathogenic variants identified included: DDX41 (30, 41.7%), TP53 (4, 5.6%), ANKRD26 (4, 5.6%), RUNX1 (4, 5.6%), GATA2 (3, 4.2%), TERT (3, 4.2%), JAK3 (2, 2.8%), SAMD9/SAMD9L (2, 2.8%), ATM (2, 2.8%), and 1 each (1.4%) in BCL2, BCOR, BPGM, CDKN2A, CEBPA, CHEK2, CSF3R, CXCR4, DNMT3A, ETV6, GATA1, MPL, MPO, POT1, PTPN11, RPL5, and SH2B3. In the 13 patients that had concurrent germline testing, results were identical in all cases, except for 1 false negative in a buccal specimen (PTPN11) and 1 case of germline mosaicism, where the TP53 variant was identified in the blood and hair follicle DNA but not in skin fibroblast DNA. After testing, 30 (44.7%) patients had a change in their management plan: 8 (27%) with DDX41-GPS were observed due to known latency of DDX41-mutant MN, 6 (20%) were referred for HSCT based on the germline variant (CEBPA, DDX41, GATA1, GATA2, RPL5, TP53), 6 (20%) were placed on an enhanced surveillance plan for cancer screening (1 ANKRD26, 3 TERT, 2 TP53), 4 (13%) patients undergoing HSCT had related donors removed from consideration as they were carriers (2 DDX41, 1 ANKRD26, and 1 SAMD9), 2 (7%) patients with neutropenia and underlying germline variants (1 ATM, 1 DDX41) had G-CSF therapy discontinued due to concerns for clonal stimulation, and 1 (3%) patient with a germline CDKN2A mutation (hematological diagnosis- CMML) was recommended to avoid radiation therapy for prostate cancer. Conclusion In summary, we validate a rapid and simple hair follicle-derived DNA based germline assessment for patients with hematological disorders and demonstrate a positive impact on clinical care in 44% of patients. We are currently optimizing DNA quality so that germline copy number alterations can be better detected using CMA.

Abstract Heterozygous germline variants of DDX41 occur in 2-4% of adult Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML) cases, making them the most prevalent cause of inherited predisposition to these diseases. Homozygous deleterious variants are never observed in the germline, and loss of both DDX41 alleles causes apoptosis of proliferative cells, consistent with essentiality. Most disease-associated germline variants cause loss of full-length protein expression (truncating). However, 30-40% are missense (non-truncating) and their role in disease risk compared to truncating variants remains in question. Previous reports have shown that both truncating and non-truncating Pathogenic/Likely Pathogenic (P/LP) variants (defined by ACMG scoring) are associated with DDX41-specific disease features, including co-mutation of the contralateral allele of DDX41. In contrast, variants of unknown significance (VUS) are less associated with these features. Acquired co-mutations of DDX41, of which p.R525H accounts for 50-70%, are restricted to DDX41-mutated patients and are always missense. Our previous studies indicated that p.R525H lacks the essential DDX41 function and cannot support hematopoietic progenitor proliferation. However, the frequency with which this mutation occurs and the absence of acquired truncating mutations suggest that p.R525H has a specific effect on DDX41 function that is distinct from complete loss and promotes pathogenesis specifically in the context of existing P/LP DDX41 mutation. To understand how germline non-truncating variants predispose to disease, we characterized the effect of six recurrent non-truncating P/LP variants (p.G173R, p.R219H, p.P258L, p.Y259C, p.K331del, and p.I396T) and three VUS (p.K9E, p.Y33H, and p.M155H) on DDX41 function. We utilized a genetic complementation approach in murine lineage-negative (Linneg) bone marrow cells with inducible deletion of DDX41. We found that all non-truncating P/LP and VUS forms of DDX41 could fully rescue the colony forming potential of Ddx41-deficient cells to a similar level as wild-type protein, whereas the p.R525H variant completely failed to rescue. To determine the effect of the non-truncating variants on DDX41 function at endogenous expression levels, we utilized CRISPR to modify the DDX41 alleles in MOLM13 human AML cells. We produced viable, proliferating cell lines with homozygous mutations for all 3 VUS and 4/6 P/LP variants. For p.P258L and p.K331del, like p.R525H, we could not produce homozygous mutant cell lines despite screening hundreds of clones and finding several with heterozygosity. To further study the P/LP variants that were functional in the cell line, we generated C57Bl/6 mouse lines harboring p.G173R, p.Y259C, and p.I396T mutations in the endogenous Ddx41 alleles. Heterozygous mutant mice were phenotypically normal in all three strains. However, we could not obtain homozygous mutant mice for p.G173R or p.Y259C, indicating these cannot support embryonic/fetal development. In contrast, p.I396T-homozygous mutant mice were born at Mendelian ratios and were phenotypically normal until at least 15 months of age. Since p.R525H mutation is common in patients with non-truncating P/LP variants, we sought to model the combined effect of these mutations. We utilized the Linneg cells with inducible knockout of Ddx41, co-expressed each non-truncating variant with p.R525H by viral transduction, and monitored the colony formation potential. Remarkably, cultures expressing P/LP variants or M155I combined with p.R525H had dramatically reduced colony formation, while wild-type DDX41 and the other 2 VUS supported normal colony formation when co-expressed with p.R525H. Thus, we conclude p.R525H has a dominant-negative effect on certain non-truncating DDX41 variants. This is consistent with the emerging idea that the presence of an acquired hotspot DDX41 co-mutation is sufficient to classify a non-truncating DDX41 variant as pathogenic.Our results demonstrate that many DDX41 missense variants retain protein function when overexpressed. However, at endogenous expression levels, some P/LP variants are unable to support cell proliferation, indicative of hypomorphic effects on protein function. In patients, acquisition of the p.R525H mutation in the contralateral allele disrupts the functionality of P/LP variants through dominant-negative effects, leading to hematopoietic progenitor defects that are hallmark of the DDX41 pathogenesis.

Abstract Introduction: Leukemogenesis is driven by nucleophosmin 1 mutations(NPM1-m) or lysine methyltransferase 2A rearrangements(KMT2A-r) in ~35–40% of acute myeloid leukemia (AML) cases. Nearly half of AML patients will develop relapsed/refractory (R/R) disease within a year, with <20% expected response rate following venetoclax/azacitidine (Ven/Aza) and progressively poorer outcomes with each subsequent line of therapy. Ziftomenib–a potent, highly selective, oral, investigational menin inhibitor–has demonstrated clinical activity as both monotherapy and in combination for adults with R/R NPM1-m or KMT2A-r AML. KOMET-007 (NCT05735184) is an ongoing, open-label, ph1a/b study of ziftomenib in combination with standard chemotherapies in adults with newly diagnosed and R/R NPM1-m or KMT2A-r AML. Here we present updated safety and clinical activity in patients with R/R AML treated with the recommended ph2 dose (RP2D) of ziftomenib 600 mg in combination with Ven/Aza across ph1a/b. Methods: Adults (≥18y) with R/R NPM1-m or KMT2A-r AML enrolled independently into separate arms; patients in dose escalation (ph1a) and expansion (ph1b) were treated with oral ziftomenib 600 mg once daily (QD; continuously from C1D8 onward) plus standard doses of Ven/Aza. Primary endpoints: AEs, complete remission (CR; ELN 2022), dose limiting toxicities (DLT; ph1a only). Key secondary endpoints: composite CR (CRc; CR with full, partial or incomplete hematologic recovery), overall response, duration of response. Results: As of June 25, 2025, 80 patients (51 NPM1-m, 29 KMT2A-r) with R/R AML were enrolled (20 ph1a; 60 ph1b) and treated with ziftomenib 600 mg QD + Ven/Aza. Median age was 63y (range 19–85), 50% were female, 74% had ECOG PS 0–1; 22 (28%) had FLT3 co-mutations and 7 (9%) had IDH co-mutations. Median number of prior therapies was 1 (range 1–6); 18% (14/80) had prior stem cell transplant; 25 (49%) NPM1-m and 19 (66%) KMT2A-r patients had prior Ven exposure. 71 patients (89%) had Gr ≥3 treatment-emergent AEs, most commonly (≥20% of patients) febrile neutropenia (31%), decreased platelet count (28%), decreased white blood cell count (26%) and decreased neutrophil count (23%). Gr ≥3 ziftomenib-related AEs occurred in 30 patients (38%), most commonly febrile neutropenia (9%) and anemia (8%). 6% of patients discontinued ziftomenib treatment due to AEs. Differentiation syndrome (DS) occurred in 1 (1%) NPM1-m patient (Gr 3), which lasted 1d and successfully resolved with protocol-specified DS mitigation. No ziftomenib-related QTc prolongation was reported with the combination, and no DLTs were observed in ph1a. 70 patients (43 NPM1-m; 27 KMT2A-r) were response-evaluable (≥1 response assessment or death). Median follow-up was 18.0 wks for NPM1-m and 16.4 wks for KMT2A-r. Overall response rates (ORRs) were 65% (28/43) for NPM1-m and 33% (9/27) for KMT2A-r. CRc rates were 49% (21/43) for NPM1-m and 22% (6/27) for KMT2A-r after median time to first CRc of 4.9 wks (range 2.7–15.6) and 5.5 wks (range 2.6–18.9), respectively; measurable residual disease (MRD)-negativity rates (local) among tested CRc responders were 50% (9/18) for NPM1-m and 60% (3/5) for KMT2A-r after median time to first MRD-negativity of 5.9 wks (range 2.9–15.6) and 8.1 wks (range 7.7–18.9), respectively. During continuous ziftomenib administration in patients who achieved CRc, median time to neutrophil recovery (≥1×109/L) was 43d overall (43d for NPM1-m; 71d for KMT2A-r), and median time to platelet recovery (≥100×109/L) was 27d overall (27d for NPM1-m; 23d for KMT2A-r). As of the data cutoff, overall median duration of CRc was not estimable; median overall survival was not estimable for NPM1-m and 21.1 wks for KMT2A-r. In Ven-naive patients, CRc rates were 71% (15/21) for NPM1-m and 33% (3/9) for KMT2A-r; CR rates were 48% (10/21) and 11% (1/9); and ORRs were 81% (17/21) and 56% (5/9), respectively. The study is ongoing with 44% (19/43) of NPM1-m and 11% (3/27) of KMT2A-r patients still on treatment, with responses continuing to evolve.Updated data to be presented.Conclusions: In the ongoing KOMET-007 study, ziftomenib RP2D of 600 mg QD + Ven/Aza was well tolerated with robust clinical activity in patients with R/R NPM1-mor KMT2A-rAML. No ziftomenib-related QTc prolongation was reported. One case of DS (NPM1-m, Gr 3) successfully resolved with protocol-specified mitigation. These data support further investigation of ziftomenib-based combinations in R/R NPM1-mand KMT2A-rAML.