Patnaik, Mrinal M.

Abstract Introduction Heterozygous germline pathogenic variants (PVs) in the 5' untranslated region of ANKRD26 cause inherited thrombocytopenia and predisposition to hematologic malignancy (HM). The estimated lifetime HM risk is ~10% based on families ascertained from an inherited thrombocytopenia cohort. However, the malignancy spectrum, molecular features, precursor states, and overall clinical outcomes remain poorly defined. Methods We established an international, multicenter cohort of individuals with ANKRD26-related thrombocytopenia diagnosed after undergoing genetic evaluation due to a personal and/or family history of thrombocytopenia and/or HM. Clinical, pathologic, and molecular data were collected for 27 individuals with germline ANKRD26 PVs from 21 unrelated families treated at 11 institutions across 5 countries. Statistical analyses were performed using R (v4.4.2). Results Patients were predominantly male (18/27) and white (25/27). Thrombocytopenia was typically identified in childhood (median age 10 years, range 0-48) with a genetic diagnosis made later (median age 53 years, range 2-80). The mean (+/- SD) pre-malignancy platelet count was 45 +/- 24 K/uL (range 5-87). ANKRD26 PVs observed in each family included: c.-126T>C (n=9), c.-128G>A (n=3), c.-134G>A (n=3), c.-116C>T (n=3), c.-118C>T (n=2), and c.-118C>A (n=1). Thirteen HMs were diagnosed in 11 of 27 (41%) patients, including myelodysplastic neoplasm/syndrome (MDS, n=5), acute myeloid leukemia (AML, n=3), chronic myeloid leukemia (CML, n=2), MDS/myeloproliferative neoplasm (MPN) overlap (n=2), and Langerhans cell histiocytosis (n=1). The median age at first HM diagnosis was 63 years (range 49-80). Recurrent somatic features in myeloid malignancies included complex karyotype (4/11, 36%) and TP53 mutations (5/10, 50%). Of the 3 patients with AML, 1 achieved a partial remission (PR) with venetoclax combined with cladribine, idarubicin, and cytarabine but relapsed, 1 achieved a PR with azacitidine but relapsed <100 days after haploidentical allogeneic stem cell transplantation (alloSCT), and 1 had primary refractory disease. Among 5 patients with MDS, 1 was refractory to decitabine, 1 underwent alloSCT but relapsed 2 years post-transplant, 1 remains in remission post-alloSCT with 1 year of follow-up, 1 is undergoing alloSCT evaluation, and 1 was lost to follow-up. Both patients with CML achieved durable major molecular remissions with imatinib. To better estimate HM risk, we assumed 100% penetrance of thrombocytopenia for ANKRD26 PV carriers and included family members with chronic thrombocytopenia who had not had germline genetic testing. In this expanded series (n=62), 16 individuals developed a HM (26%). Additional diagnoses included MDS with progression to AML (n=1), AML (n=1), CML (n=1), and leukemia of unknown type (n=2). Cumulative incidence of HM was 0% by age 40 years, 17% by age 60 years, and 60% by age 80 years. Somatic sequencing of peripheral blood was performed in 5 HM-unaffected ANKRD26 PV carriers. One individual was found to have clonal hematopoiesis driven by TET2 (c.1648C>T, p.Arg550*) with a variant allele frequency (VAF) of 9% at age 55. Bone marrow biopsy showed mild megakaryocytic atypia and 4% blasts without overt evidence of malignancy. To assess the prevalence of ANKRD26-related HM, we assessed the frequency of ANKRD26 PVs in 2 large MDS/AML cohorts. In the ARUP database (9662 AML, 6397 MDS), 2 individuals (0.01%) had an ANKRD26 PV with a VAF consistent with germline origin. In the MSK-IMPACT Heme Germline MDS/AML cohort (n = 284), no ANKRD26 P/LP variants were identified. Conclusions Germline ANKRD26 PVs underlie <1% of MDS/AML diagnoses but may represent a high-risk subtype characterized by complex karyotype, TP53 mutations, and high risk of relapse. Among our series, the incidence of HM was low early in life but increased substantially with age, reaching 60% by 80 years. This exceeds prior estimates, which were derived from individuals ascertained from thrombocytopenia-based registries. Together, our findings suggest that ANKRD26-associated HM may represent a high-risk clinical entity, and that age and family history should inform surveillance strategies. More studies are needed to define genetic and environmental modifiers of HM risk as well as precursor states to enable early detection and disease interception.

Abstract Introduction: DDX41 (DEAD-box helicase 41) mutations (mt) represent the most prevalent germline predisposition syndrome (GPS) in adult patients (pts) with myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). This molecular subtype is typically associated with late-onset disease, runs an indolent clinical course, with a relative absence of high-risk co-mutations. While several retrospective studies have reported favorable responses to venetoclax (VEN)-based therapies, anecdotal observations suggest variable outcomes. We aimed to evaluate the clinical characteristics and treatment outcomes of patients with DDX41-mt MDS/AML treated at the Mayo Clinic. Methods: We conducted a retrospective study of pts diagnosed with DDX41-mt germline predisposition syndrome with concurrent myeloid neoplasms at our institution. Germline testing was conducted under an IRB approved protocol (Mayo Clinic IRB# 16-004173; clinical-trials gov. Identifier: NCT02958462). Of 198 pts with DDX41-mt myeloid neoplasms, 77 had high-risk disease—43 with MDS with increased blasts (MDS-IB1, n = 11; IB2, n = 32) and 34 with AML (WHO 2022). We assessed how clinical, and disease features influenced outcomes in this subgroup. Among these pts, 69 (90%) pts had likely pathogenic/pathogenic variant (DDX41path) variants and 8 (10%) pts had variant of undetermined significance (DDX41VUS) according to variant classification criteria from the American College of Medical Genetics/ the Association of Medical Genetics/ the Association for Molecular Pathology (ACMG/AMP) guidelines. Results: The median age was 68 years (yrs) (range [R],34-92), 70% were male and the median bone marrow blast % was 15 (R,5-60). The most common DDX41 germlinevariants (> 5% cases) included p.D140fs (26%), p.M1I (22%), and p.P258L (6.5%). 74% had DDX41 truncating variants. Thirty-one (40%) acquired a somatic DDX41-mt (R525H [81%]) and 43 (56%) had other somatic mutations. Among these, the most frequent were ASXL1 (n= 9, 21%), TP53 (n= 8, 10%), splicing factor (n= 7, 9%), and DNMT3A (n= 5, 6%). Twenty-six, (34%), 26 (34%), 15 (19%) and 9 (12%) pts were treated with hypomethylating agents (HMA), HMA+VEN, intensive chemotherapy (IC) and active surveillance/supportive care, respectively. Overall, the composite complete remission rate (cCR) in high-risk MDS and AML was 56%. The cCR rates (41%, 59% and 68.7%, p= 0.10) and median duration of response (DOR; 43.7, 44.9 and 28.9 months [mo], p= 0.46) were not significantly different with HMA, HMA+VEN, and IC induction. Thirty-one (40%) pts received allogeneic stem cell transplantation (allo-HCT); 4 (36%), 15 (47%) and 12 (35%) in MDS-IB1, MDS-IB2 and AML groups, respectively (p= 0.56). With a median follow up of 34.7 mo (R, 0.7-136.7), the median overall survival (OS) from the time of diagnosis was 56.9 mo (95% CI, 50.7-63.0) and was not significantly (NS) different between MDS-IB1 (not reached, 70% at 3 yrs), MDS-IB2 (56.9 mo, 86% at 3 yrs) and AML (55.7 mo, 60% at 3 yrs) groups, p= 0.16). The median OS was NS different between DDX41path and DDX41VUS (58.6 vs 55.7 mo, p= 0.50), respectively. We conducted a multivariable analysis for OS using variables that showed significance or trend towards significance in univariable analysis. Concurrent splicing factor mutations (HR; 5.29, 95% CI: 1.29-21.6, p= 0.02) remained negatively prognostic, while there was a trend towards better survival outcomes with allo-HCT (HR; 0.48, 95% CI: 0.21-1.07, p= 0.07). Bone marrow blast ≥ 20% (HR; 1.87, p= 0.12) and TP53-mt (HR; 2.14, p= 0.12) did not retain significance. Conclusion: In our cohort of patients with germline DDX41-mt high-risk MDS and AML, VEN-based regimens were not superior to HMA alone or IC, in terms of response rates and outcomes. On multivariable analysis, the presence of concurrent splicing factor mutations independently and negatively impacted survival with a trend towards better outcomes with allo-HCT. These findings highlight the heterogeneity within DDX41-mt myeloid neoplasms and underscore the need for future studies in larger cohorts to better define predictors of response and survival.

Abstract Introduction: The DEAD-box helicase 41 (DDX41) gene, located on chromosome 5q35, is a tumor suppressor gene involved in RNA processing. Germline mutations in this gene can predispose patients to myeloid malignancies. Studies have suggested a more favorable prognosis in those with germline mutations in DDX41, with progression of disease being a frequently encountered cause of death. In this retrospective study, we explored the causes of death in a cohort of patients with pathogenic DDX41 mutations. Methods: This was a retrospective study of patients diagnosed with myeloid neoplasms between 2009-2024 and found to have DDX41 mutation (DDX41m) via next generation sequencing (NGS) at our institution. Myeloid NGS was obtained at or after the diagnosis of myeloid disease. Germline testing (when available) was performed through buccal/skin samples. Carriers of DDX41m without a myeloid neoplasm diagnosis and patients with only DDX41m VUS were excluded. Baseline characteristics at the time of myeloid neoplasm diagnosis included age at diagnosis, DDX41m variant allele frequency (VAF), blood counts (hemoglobin, white blood cell count, platelets), cytogenetics, bone marrow blast percentage, number of co-mutations, and treatment received. Unadjusted comparisons were made using continuous or categorical variables. Median overall survival (OS) was calculated from the time of diagnosis with myeloid neoplasm to the time of death, using BlueSky Statistics V.10.3.4. Results: Of the 112 patients identified to have pathogenic DDX41m, 29 (26%) patients were deceased at the time of data analysis. In this cohort of 29 patients (median age at diagnosis 72 years, 17 (59%) males), disease groups at initial diagnosis included 17 (59%) patients with MDS, 9 (31%) AML, and 3 (10%) MPN. Fourteen of the 17 (82%) of the patients with MDS were classified as MDS-EB1 or MDS-EB2. Seven of the 17 (41%) patients with MDS progressed to AML at the time of death, with 57% of the patients having more than 30% bone marrow blasts at time of progression. Blood counts at diagnosis in the cohort included a median hemoglobin of 9.8 g/dL, platelets of 83 x 109/L, and white blood cell count of 2.1 x 109/L. Twenty-one (72%) of patients had normal cytogenetics. Nine (31%) patients had both a pathogenic mutation and a variant of uncertain significance (VUS) in DDX41, with the remaining 20 patients harboring only a pathogenic DDX41 mutation. Eight (27%) patients underwent germline testing, with 7 confirmed to harbor a germline DDX41m. In the deceased cohort, 9 (31%) patients underwent HSCT. Three of the patients with AML and 1 patient with MDS were observed and did not undergo treatment. Median overall survival of the deceased cohort was 29 months. The median time to AML progression in the group with MDS was 14 months. Causes of death included infection in 11 (38%) patients, 9 (31%) with disease progression/relapse, 3 (10%) with acute gastrointestinal graft versus host disease (GVHD), and 1 (3%) from cerebral bleed. The cause of death was unknown in the remaining 5 (17.2%) patients. Infections included pneumonia, bacteremia, neutropenic enterocolitis, fungal, and unknown etiology. Of the 4 patients who were observed, 2 died from unknown cause and 2 died from disease progression. Of the 16 patients with AML at time of death, 9 (56%) died from disease progression or relapse, 3 (19%) from infection, 2 (13%) from GVHD, and 2 (13%) from unknown causes. Of the 10 deaths in the MDS group, 7 (70%) were from infection, 1 (10%) from GVHD, 1 (10%) from cerebral bleed, and 1 (10%) from an unknown cause. Three cases of infection in the MDS group occurred during remission. Infection was a more common cause of death in the MDS group compared to the AML group, where disease progression prevailed as a cause of death (70% vs 19%, p=0.01). Eight (80%) of the patients with MDS who died from infection were neutropenic prior to death, and 4 (50%) of those patients were on neutropenic antimicrobial prophylaxis. Conclusions: In this cohort of 29 deceased patients with a DDX41-mutated myeloid neoplasm, we characterized causes of death. Disease progression/relapse was a significantly more common cause of death in those with AML, compared to infection in patients with MDS. Our work underscores the need for additional studies looking into non-leukemic causes of death in patients with DDX41m myeloid diseases and potential strategies to mitigate infection-related mortality in this population.

Abstract Background: KMT2A-rearranged acute myeloid leukemia (KMT2Ar AML) is characterized by chromosomal translocation involving KMT2A gene at 11q23, resulting in fusion with variety of partner genes. It is usually associated with poor outcomes, high risk of relapses and suboptimal responses to conventional therapies. While NPM1-mutated (mt) AML is considered favorable risk, they are equally dismal in relapse refractory (RR) setting. Menin inhibitors have emerged as a promising therapeutic strategy, particularly in RR AML patients (pts) with KMT2Ar and NPM1-mt genotypes. While revumenib, a menin inhibitor approved for managing RR KMT2Ar acute leukemia, no menin inhibitor is currently approved for NPM1-mt AML. In this study, we evaluated clinical outcomes of adults with KMT2Ar AML and performed a comparative analysis of pts with RR KMT2Ar and NPM1-mt AML using data from the Mayo Clinic. Methods: After screening 102 AML pts with reported KMT2A abnormalities, we identified 33 adults with confirmed KMT2Ar diagnosed between 2012 and 2024 for retrospective analysis. Clinical and molecular/cytogenetics data, induction type (intensive chemotherapy [IC] vs non-intensive chemotherapy [NIC]), response, transplant use, and survival outcomes were reviewed. A separate analysis was performed comparing 20 RR KMT2Ar AML pts with 20 propensity score matched RR NPM1-mt AML pts from a pool of 125 NPM1-mt RR pts. Results: The median age was 50 years (yrs) (range [R], 19.0-75.0), and 60.6% were < 60 yrs. Most cases were de novo AML (64%), and the most frequent translocation was t(6;11)(q27;q23)/MLLT4 (27%), followed by t(10;11)(p12;q23)/MLLT10 (21%), t(9;11)(p21.3;q23.3)/MLLT3 (15%), and t(11;19)(q23;p13.1)/ELL (12%). Other KMT2A fusion partners were rare and collectively accounted for the remaining cases. The median follow-up was 57 months (mo) (R, 7.0-109.0). The overall response rate (ORR) was 91%, and composite complete remission (CRc, , including CR, CRi, and CRh) was 73%. The CRc rates were comparable between IC and NIC (80% vs 62%, p=0.24). CRc were not significantly different by disease type (de novo [71.4%] vs secondary [sAML] [75%], p= 0.82) or KMT2A fusion partner gene (60% for t[9;11]/MLLT3 vs. 57.1% for t[10;11]/MLLT10 vs 55.6% for t[6;11]/MLLT4, p=0.069). Seventeen (52%) pts received an allogeneic stem cell transplantation (allo-HCT). The median overall survival (mOS ) for the entire cohort was 16 mo (R, 11.0-34.0). In subset analysis, IC compared to NIC was associated with significantly longer mOS (30 vs 11 mo, p=0.014). The mOS was also superior in pts <60 vs ≥60 yrs (32 vs 8 mo, p=0.005). Similarly, de novo cases had better mOS than sAML (22.0 vs 9.5 mo, p=0.052). Among KMT2Ar subtypes, t(6;11)/MLLT4 showed the longest mOS (54 mo [R, 30.0-not reached (NR)]), while t(9;11)/MLLT3 had the shortest (11.0 mo, [R 9-NR]), but differences were not statistically significant (p=0.32). The mOS was significantly longer among allo-HCT pts (30 vs 11 mo, p=0.005). Among 29 pts who experienced RR disease, the median relapse free survival (RFS) was 3 mo (R, 2.0-10.0). First salvage therapy yielded a CRc of 43.8% in 16 evaluable pts. When compared to a propensity matched cohort of 20 RR NPM1-mt AML pts, the CRc rates was 57.9% vs 50% in RR NPM1-mt and KMT2Ar AML (p= 0.68). The mRFS was not significantly different between RR KMT2Ar and NPM1-mt AML, (3 vs 4 mo, p=0.9). However, KMT2Ar pts had inferior mOS compared to NPM-mt AML (12 vs 65 mo, p=0.004). We further compared survival between NPM1-mt and KMT2Ar pts stratified by allo-HCT status. Among those who underwent allo-HCT, NPM1-mt pts had longer mOS (NR vs 22 mo, p=0.037). Among non-allo-HCT pts, mOS was numerically higher in NPM1-mt vs KMT2Ar (19 vs 8 mo, p=0.11). Conclusions: This single institusion cohort of adult AML with KMT2Ar underscores the biological and clinical heterogeneity of this high-risk group. IC was associated with a survival benefit, particularly among younger and fit patients. However, the outcomes following relapse remained poor, highlighting the urgent need for improved post-remission and salvage therapies. Comparative analysis with matched RR NPM1-mt AML pts revealed similarly dismal survival outcomes. Emerging data from single-arm studies of menin inhibitors in both frontline and RR settings among pts with NPM1-mt and KMT2Ar AML are encouraging and may represent a paradigm shift in treatment.

Abstract Introduction: ASXL1-mutant (mt) Chronic Myelomonocytic Leukemia (CMML) is an aggressive myeloid neoplasm characterized by increased proliferation, resistance to epigenetic therapies, and poor survival. Epigenetic remodeling and up-regulation of leukemogenic driver genes are hallmarks of ASXL1mt CMML. Truncating mutations in ASXL1 activate enhancers that drive the expression of key leukemogenic driver genes such as HOXA9 and its co-factor MEIS1. Here, we investigate the chromatin accessibility of these leukemogenic enhancers by ASXL1 genotype at single-cell resolution (GoT-ChA-seq). Methods: After IRB approval, we performed bulk RNA-seq and ChIP-seq (H3K4me1, H3K4me3, H3K27ac, H3K27me3, H2AK119ub, H2BK20ac) on bone marrow (BM) mononuclear cells from 40 patients with CMML (19 ASXL1mt, 21 -wildtype/wt). After quality control, differential analyses of gene expression and histone modification occupancy between ASXL1mt and wt patients were conducted. A consensus peak calling framework was used to define genomic regions with ASXL1mt-specific histone modifications. Canonical enhancers were defined as genomic regions with a co-occupancy of H3K4me1 and H3K27ac. We then added regions marked by H2BK20ac to capture regulatory regions associated with p300 (Narita et al. Nat Genet 2023). We used an in silico prediction strategy to associate regulatory regions marked by strong histone modification occupancy with highly up-regulated leukemogenic driver genes (HOXA6-10, MEIS1). The ReMap database (Hammal et al. Nucleic Acids Res 2022) was queried for transcription factor binding in the genomic regions of interest. We then performed GoT-ChA-seq (Izzo et al. Nature 2024) to investigate chromatin accessibility for ASXL1mt (n=3) and wildtype BM single cells from CMML patients. In vitro colony forming assays were conducted on primary CMML BM cells (11- ASXL1mt and 9 wt CMML), assessing the efficacy of EP31670, a novel, oral, dual inhibitor of p300/BRD4. Results: This study included 40 patients with CMML, 19 ASXL1mt and 21 wt. The variant allele frequencies for ASXL1 were compatible with heterozygosity (median 0.41) and TET2 mutations were balanced between the two groups. We identified 149 candidate regulatory regions correlating with the expression of up-regulated target genes of interest (HOXA6-10, MEIS1) by bulk ChIP- and RNA-seq. Publicly available ChIP-seq data from myeloid cell lines demonstrated enrichment of p300 (in THP-1 cells, enrichment effect size +2.58, p=0.002) and BRD4 (in K-562 cells, enrichment effect size +1.58, p=0.045) in these candidate regulatory regions. Next, we interrogated the chromatin accessibility of ASXL1mt (n=13620) and ASXL1wt (n=24269) single cells from 3 CMML patients using GoT-ChA-seq. Differential accessibility analysis revealed 144 genomic regions, all of which were preferentially accessible in ASXL1mt cells compared to ASXL1wt cells (p<0.05 for all regions). Four of these preferentially accessible genomic regions (p<0.001 for all regions) overlapped with the previously identified candidate regulatory regions for MEIS1. The H3K27ac and H2BK20ac occupancy levels in these regions was strongly associated with the expression of MEIS1 (median Pearson r=0.73, p=1.16x10-7). These candidate regulatory regions were annotated in ENCODE as distal and proximal enhancers. Targeting this biology with the dual p300/BRD4 inhibitor EP31670 in progenitor colony forming assays led to a preferential therapeutic effect in ASXL1mt BM samples (median IC50 = 25nM) compared to in ASXL1wt samples (median IC50 = 74nM, p=0.03). Treatment with EP31670 was also associated with increased differentiation (increased blast forming units-erythroid; BFU-E) and organization of colonies in ASXL1mt vs wt CMML. Conclusions: ASXL1mt CMML is characterized by the up-regulation of several leukemogenic driver genes including HOXA9 and its co-factor MEIS1, secondary to the activation of genotype-specific enhancers. The preferential accessibility of these enhancers can be defined between ASXL1mt and ASXL1wt cells within patients. The enhancers of interest interact with p300 and BRD4 in myeloid cell lines and targeting them with the novel dual p300/BRD4 inhibitor, EP31670, induces therapeutic responses at low nanomolar drug concentrations in vitro, preferentially in ASXL1-mutant cells. These data solidify the biological rationale for targeting p300/BRD4 in ASXL1mt chronic myeloid neoplasms for therapeutic benefit (NCT05488548).

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: Protein truncating somatic ASXL1 mutations in CMML are associated with high-risk features and poor outcomes. We have previously demonstrated that ASXL1-mutant (mt) CMML is characterized by permissive chromatin states and overexpression of leukemia stemness genes (Binder et al. Nat Commun; 2022). DLK1 (delta-like homolog 1) is a pseudo-NOTCH like ligand that is maternally imprinted and paternally expressed and is physiologically not expressed beyond embryogenesis. Aberrant DLK1 expression has been associated with poor outcomes in solid tumors and we have shown differential overexpression in ASXL1mt versus wild-type (wt) CMML. Both the promoter and the last exon of DLK1 contain CpG islands that play a role in regulating DLK1. The CpG island within the fifth exon of DLK1, known as the DLK1-differentially methylated region (DMR) [chr14:100,726,892-100,738,224] is completely unmethylated on the maternal allele and partially methylated on the paternal allele. Previous work (Developmental Cell; 2021) has also identified a DLK1 imprinting control region (ICR) known as the IG-DMR [chr14:100,811,001–100,811,037]. DNA methylation state of the IG-DMR has been shown to impact the expression of MEG3 mRNA (lncRNA) which functions as a cofactor to direct PRC2 to the DLK1 promoter, suppressing DLK1 expression. Since the regulation of DLK1 in ASXL1mt CMML is not well understood, we conducted this multiomic analyses to define epigenetic mechanisms of DLK1 overexpression in ASXL1mt CMML. Methods: After IRB approval, we performed bulk RNA-seq, ChIP-seq (H3K4me1/me3, H3K27ac, H3K27me3) and Illumina MethylationEPIC array on bone marrow (BM) mononuclear cells of 40 CMML patients (19 ASXL1mt, 21 wt). scRNA-seq was conducted on 5 ASXL1mt and 3 wt cases. All libraries were sequenced on an Illumina NovaSeq instrument. We assessed these samples for differential gene expression (RNA-seq) and changes in histone modifications (ChIP-seq) between ASXL1mt and wt CMML, specifically at the DLK1-DMR and IG-DMRregulatory loci. We conducted ddPCR (digital droplet PCR) to determine allelic status of DLK1 in ASXL1mtand wt cases. Global and allele/sequence specific DNA methylation changes were determined using Biomodal's duet EvoC methodology (6 base sequencing, including 5mC and 5hmC) in 5 ASXL1mt and 5 wt CMML cases. Results: We validated the overexpression of DLK1 in 19 ASXL1mt versus 21 wt (log2 fold change +4.85, FDR 4.67e-13) CMML BM samples. scRNA-seq on 5 ASXL1mt versus 3 wt samples demonstrated that DLK1 is only expressed in mutant cases, with the expression being limited to HSPCs. ChIP-seq analysis at the DLK1 regulatory loci validated (a) reduced occupancy of H3K27me3, correlating with ASXL1mt associated disruption of the PRC2-complex, and (b) increased co-occupancy of H3K4me1 and H3K27ac in mt cases, validating a permissive chromatin state in ASXL1mt cases at the DLK1 regulatory regions. Through correlation analysis of RNA-seq and ChIP-seq, we defined the promoter for DLK1, characterized by high Pearson correlation coefficients (R > 0.5) and enrichment of H3K27ac and H3K4me3. Differential methylation analysis identified global hypomethylation around the DLK1-DMR and promoter regions. We observed a mean reduction of ~40% in methylation status at the DLK1 promoter in ASXL1mt versus wt cases, suggesting a loss of epigenetic silencing at this locus. This was corroborated by significant enrichment of 5hmC at the fifth exon of DLK1 indicating active DNA demethylation. Conversely, we observed a gain in methylation at the IG-DMR, suggesting loss of imprinting control through MEG3 silencing and DLK1 overexpression. To further determine the impact of imprinting deregulation on overexpression of DLK1 in ASXL1mt CMML, allele-specific methylation was profiled using the Biomodal whole genome methylation data. This demonstrated that the methylation patterns in ASXL1mt CMML cases were significantly deregulated at the DLK1-DMR, with >30% loss of methylation compared to GRCh38 reference alleles. Furthermore, ddPCR was able to confirm bi-allelic expression of DLK1 in ASXL1mt CMML, suggesting that the observed methylation dysregulation leads to loss of imprinting of the maternal allele. Conclusion: In summary, we demonstrate that ASXL1 mutations in CMML disrupt epigenetic pathways, promoting DNA demethylation, resulting in permissive chromatin states and an aberrant and oncogenic re-expression of maternal DLK1, due to loss of imprinting control.

Abstract Somatic mutations in hematopoietic stem and progenitor cells (clonal hematopoiesis) are known to alter the immune milieu and can result in autoimmune disorders including VEXAS (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) syndrome. There are currently no curative strategies for CH-linked autoimmune disorders besides allogenic hematopoietic stem cell transplantation. Recent work has shown a high prevalence of autoimmune syndromes among patients with IDH1/2 mutant myeloid neoplasms (MN). We thus hypothesized that IDH1/2-mutant CH might drive a subset of autoimmune disorders. To further characterize a possible association between IDH-mutant CH and autoimmune disease, we used data from two observational cohort studies, the UK Biobank (N=454,218) and All of Us (N=414,830). We observed 264 individuals with IDH1/2-mutant CH. IDH1/2 CH was associated with autoimmune disease (OR=1.8, p=4e-3), and, when compared to other CH genes with at least 100 carriers, showed the strongest effect size. When comparing autoimmune subtypes, we observed significant associations with polymyalgia rheumatica (OR=4.0, p=1e-3) and giant cell arteritis (OR=8.1, p=1e-6). IDH1/2 CH carriers had elevated CRP levels compared to other CH-carriers (p=1e-2) and non-carriers (p=8e-3). IDH1/2 CH was associated with lower neutrophil counts and higher monocyte counts. While most (68%) had blood counts outside the normal range, only a minority (11%) had severe cytopenias that met criteria for CCUS. Since IDH1/2 CH is associated with both autoimmune disease and blood count abnormalities, we sought to define the frequency, clinical presentation, and outcomes of IDH1/2-associated autoimmune disease among individuals with bone marrow biopsy confirmed CCUS. We used data from three CCUS cohorts: first, a multi-institutional cohort of CCUS patients with systemic autoinflammatory disease (SAID) who were UBA1-negative, second, a hospital-based cohort at Mayo Clinic, and third, a cohort of IDH1 carriers enrolled on a phase II clinical trial of ivosidenib (NCT05030441). Within 193 SAID patients who were free of myeloid neoplasm at the time of recruitment, IDH1/2 pathogenic variants were the most observed CH driver, occurring in 2% of individuals. These individuals (N=4) all had recurrent fevers and dermatologic manifestations, requiring chronic glucocorticoid treatment with 75% having inflammatory arthritis requiring multiple Disease-Modifying Antirheumatic Drugs (range 1-7, median=5). Within the Mayo Clinic cohort, 275 patients with CCUS were serially ascertained. Among those 8 (2.9%) were IDH1-mutant of whom 50% had autoimmune disease (three with seronegative rheumatoid arthritis and one with Sweet syndrome). At last follow up (median 16 months), 2 (25%) of 8 patients had progressed to MN. Within our open-label decentralized trial of ivosidenib (IDH1 inhibitor) in CCUS, we enrolled 20 patients, of whom 5 (25%) had a diverse array of pre-existing autoimmune disorders, including two cases of seronegative rheumatoid arthritis and one case each of Sweet syndrome, polymyalgia rheumatica, and Sjögren's syndrome. Underlying the clinical presentation of all five cases was episodic joint pain, with half also experiencing episodic dermatologic manifestations. The majority (58%, 11/19) of the IDH1mt-CCUS patients had an elevated hsCRP (>=5; range 6.91–46.2) including all four with co-occurring autoimmune disorders (range 7.97–46.2). Out of the 20 enrolled patients, 17 received at least 8 weeks of therapy, of which 9 had elevated hsCRP at baseline. Most of these (7/9) had normalization of hsCRP (falling below 5 mg/L) while on treatment (median time to hsCRP normalization of 58 days). Among the four patients with autoimmune disease, all had subjective improvement in their autoimmune symptoms following treatment with ivosidenib. In conclusion, we show that IDH1/2 CH is associated with autoimmune disorders and is particularly enriched among IDH1/2 CH carriers with co-occurring cytopenias. IDH1/2-associated autoimmune disease can range from classic rheumatic conditions such as rheumatoid arthritis to more severe VEXAS like presentations. IDH inhibition demonstrates efficacy for improving inflammatory manifestations within an ongoing clinical trial. Together these results nominate IDH mutant CH as a driver of autoimmune diseases with therapeutic implications.

Abstract Background: Paroxysmal nocturnal hemoglobinuria (PNH) is a clonal hematopoietic stem cell disorder caused by PIGA mutations, resulting in complement-mediated hemolysis. Myeloproliferative neoplasms (MPNs) are also clonal hematopoietic stem cell disorders driven by mutations in JAK2, CALR, or MPL, and include polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). Although the coexistence of PNH and and MPN is rare, both entities are associated with anemia and an increased risk of thrombosis. The main objectives of the current study were to characterize the clinical phenotype, and evaluate treatment outcomes, including response to complement inhibition in patients with treatment-requiring PNH and MPN. Methods A Mayo Clinic database search was conducted following Institutional Review Board approval to identify patients with PNH and MPN. Between January 2000 and June 2025, 11 patients had a pathologic diagnosis of MPN per the International Consensus Classification, and PNH requiring therapy. Clinical features, including hemolysis and/or thrombosis, and therapeutic interventions were recorded. Results The study cohort included 11 patients (median age 63 years; 73% male) with MPN (6 with PMF, 3 ET, 1 post-ET MF, 1 post-PV MF) in whom PNH was diagnosed concurrently (n=5), or at a median of 9 years (range: 2-15) after MPN diagnosis (n=6). In 9 of 11 patients (82%), PNH workup was initiated due to hemolytic anemia, while in 2 patients (18%), it was prompted by splanchnic vein thrombosis. Transfusion-dependent anemia was present in 6 patients (54%). PNH clone size [median (range)] was 0.58% (0–10.96%) in red blood cells, 18.82% (0–91.2%) in granulocytes, and 23.27% (0–98.8%) in monocytes. MPN driver mutations were evaluated in 8 cases and identified mutations in JAK2 (n=3), CALR (n=4), and MPL (n=1); two additional cases were negative for JAK2 mutations. Next-generation sequencing (NGS) was performed in 6 patients and identified ASXL1, ZRSR2, and SF3B1 mutations in one case each. Cytogenetic analysis (n =10) demonstrated an abnormal karyotype in 3 patients (30%), all of which were categorized as favorable risk. First-line treatment for PNH included complement inhibitors in 9 patients (82%), with eculizumab (n=8), or ravulizumab (n=1). Hemolysis was controlled in only 2 of 9 (22%) patients; one patient treated with eculizumab achieved durable anemia response for five years, while another patient achieved transfusion-independence within three months of eculizumab initiation. 3 patients underwent allogeneic stem cell transplant (ASCT); 2 achieved remission with follow up exceeding 5 years, while the third patient experienced PNH recurrence five months after transplant. The latter received donor lymphocyte infusions and eculizumab was re-initiated resulting in eradication of the PNH clone. Among patients treated with complement inhibitor and not transplanted, 4 of 6 (67%) were transfusion-dependent at last follow-up. Notably, one patient with PNH clone size of 91.19 % in granulocytes, had ongoing hemolysis despite dual complement blockade with ravulizumab and danicopan. Treatment for MPN included hydroxyurea (n=5), ruxolitinib (n=4), pacritinib (n=1), and erythropoiesis stimulating agents (n=4). Additionally, two patients each received antiplatelet therapy alone, anticoagulation alone, or a combination of antiplatelet and anticoagulation. During a median follow-up of 8.4 years (range, 0.6-19), 2 patients (18%) experienced venous thrombosis, and 1 patient (9%) had progression to myelodysplastic syndrome. 5 patients (45.5%) died, with sepsis as the cause of death in 3 cases. The incidence rate of thrombosis was 22 events per 1,000 person-years. Recurrent thrombosis was observed in a 68-year-old male with CALR-mutated MF and PNH clone size of 14.65% in granulocytes, with history of portal vein thrombosis. Despite treatment with eculizumab and low-molecular weight heparin, he developed thrombosis involving the inferior vena cava, common iliac, and hepatic veins. The second event occurred in a patient who developed deep venous thrombosis, while in remission and not on anticoagulation. Conclusion The current study represents the largest series of patients with treatment-requiring PNH and MPN. It reveals a predominance of MF patients, particularly among those harboring CALRmutations, and underlines suboptimal efficacy of complement inhibitor therapy in this patient population.