Mangaonkar, Abhishek A.

Background: There is an increased risk of second primary malignancies including second hematological malignancies (SHM) in multiple myeloma (MM) patients undergoing autologous stem cell transplant (auto-SCT) followed by lenalidomide maintenance. We analyzed the characteristics and outcomes of patients who developed SHM after an auto- SCT for MM. Methods: A retrospective study of all MM patients who underwent auto- SCT at Mayo Clinic, Rochester between January 1, 1990, and 31 August 2023 and later developed SHM. Demographic, clinical and pathologic data were collected retrospectively. Overall survival (OS) was calculated from the date of auto-SCT to the date of last follow up. Statistical analyses were performed using GraphPad prism 9.0. Chi-square test was used to calculate the difference between categorical variables. Kaplan Meier method and log rank test were used to estimate OS. Results: Among 3513 patients who underwent at least 1 auto-SCT, 104 (2.9%) developed a SHM at a median follow up of 59 (range, 0.2-265) months. Patients who developed SHM, more frequently received pretransplant alkylating agents (37.5 vs 24.2 %, odds ratio [OR], 1.87; P=0.003) and topoisomerase II inhibitors (anthracyclines/etoposide) (17.3% vs 10.4%, OR [1.79]; P=0.03) compared to a control group of MM patients without SHM. Further, exposure to lenalidomide (77.8% vs 57.6%, OR[2.59]; P <0.0001) and radiation therapy (32.6% vs 23.1%, [1.54]; P=0.04) were more often seen in the SHM cohort compared to control group. Among the 381 patients who underwent > 1 auto- SCT, 3.1% developed SHM. Therapy related myeloid neoplasms (t-MN) accounted for 90.3% of cases [n=94; t-myelodysplastic syndrome (t-MDS=64), t-acute myeloid leukemia (t-AML=12), t-MDS transformed to AML(n=16), chronic myeloid leukemia (n=1), MDS/myeloproliferative neoplasm overlap syndrome (n=1)]. Eight patients (7.6%) developed therapy related B- cell acute lymphoblastic leukemia (t-ALL); Philadelphia (Ph) negative ALL (n=7) and Ph- like ALL (n=1). One patient each developed mixed phenotype acute leukemia and acute leukemia, not otherwise specified. Sixty patients (57.6%) were males and the median age at diagnosis of SHM was 70 (range, 43-84) years. The median time from auto-SCT to diagnosis of SHM was 58.5 (range, 7-236) months. In a multivariate analysis, receiving an alkylating agent (hazard ratio [95% confidence interval]: 2.51 [1.54 to 4.01]; P = 0.0002) and/or topoisomerase II inhibitor as induction for MM (3.12 [1.59 to 5.88]; P = 0.0006), exposure to lenalidomide (7.08 [3.92 to 13.50]; P = <0.0001) and radiation therapy (1.60 [1.02 to 2.44]; P = 0.03) were independent predictors of developing SHM. At diagnosis, 57% (n=37) of t-MDS and 71% (n=20) with t-AML had high risk disease per R-IPSS and 2022 European Leukemia Net respectively. Clonal abnormality in chromosome 5 and/or 7 was present in 45% (n=42) of patients. Complex and monosomal karyotype was seen in 32% (n=30) with t-MN. The most frequently mutated genes based on next generation sequencing data included TP53 (n=33), DNMT3A (n=9), RUNX1 (n=5), TET2 (n=4) and CEBPA (n=4). In the t-MDS/AML cohort, 3 patients (3.1%) underwent second auto-SCT and 9 (9.5%) received allogenic SCT (allo-SCT) for SHM. After a median follow-up of 27.2 months, the median OS from t-MDS/AML diagnosis was 8.04 months (95%CI, 6.1-11.0 months) and there was no difference in median OS for allo-SCT recipients versus nonrecipients (9.1 vs 6.8 months, P =0.19). In the t-ALL (n=8) cohort, all of them received lenalidomide based induction and five received lenalidomide maintenance. Most of the t-ALL patients had adverse risk cytogenetics [IKZF1 deletion (n=2), complex karyotype (n=2), TP53 mutation (n=1) and P2RY8-CRLF2 fusion (n=1)]. Three patients with t-ALL underwent allo-SCT and the median OS for allo-SCT recipients versus non recipients were 8.3 vs 7.9 months respectively, P=0.50. Among patients with SHM, 92.3% (n = 96) have died with SHM (72%) being the most common cause of death. MM patients who developed SHM had an inferior OS when compared to those without SHM (median OS, 75 vs 90 months, P =0.006). Conclusion: SHM following auto-SCT tends to have aggressive disease biology with poor outcomes. Short term follow up underestimates the risk of SHM and the higher incidence noted in our study may be due to longer follow up. As the OS in MM patients continues to improve, SHM remains an important challenge in improving long term outcomes.

Background: Therapy-related myeloid neoplasms (t-MN) occur after exposure to DNA-damaging agentsincluding cytotoxic chemo and radiation therapy and are associated with dismal outcomes. TP53 and PPM1D (protein phosphatase Mn2+/Mg2+-dependent 1D) mutations (MT) disrupt the DNA damage response and repair (DDR) pathway, are often co-mutated (25-35%), and although enriched in t-MN (20%), can also be seen in age-related clonal hematopoiesis (CH) (5-10%). While progressive genomic instability with biallelic inactivation has been described as a mechanism of MN progression with TP53 MT, similar mechanisms remain to be elucidated for PPM1D MT. We conducted this study to assess the clinical phenotype and outcomes of TP53 and PPM1D co-mutated (PPM1DTP53m) versus PPM1D MT and wild type TP53 (PPM1DTP53wt) CH and MN. Methods: After approval from the Mayo Clinic IRB, the CH and MN databases were queried and 119 pts with PPM1D MT (CH= 26, clonal cytopenia of unknown significance [CCUS]= 64, myelodysplastic syndrome [MDS]=16, myeloproliferative neoplasm [MPN]=8, acute myeloid leukemia [AML]= 5) were identified. We analyzed baseline characteristics, karyotypic changes, somatic mutations, and survival outcomes between the PPM1DTP53m (n= 22) and PPM1DTP53wt (n= 97) groups (gp). Results: Baseline characteristics The median age in years (yrs) was 68.5 (range [R], 43-89) and 71 (R,30-92) in the PPM1DTP53m and PPM1DTP53wt gp (p= 0.65). 22% vs 18% (p=0.78), 58% vs 32% (p=0.03), 9% vs 32% (p=0.01), 7% vs 4.5% (p=>0.99) and 3% vs 14% (p=0.07) pts met criteria for CH, CCUS, MDS, MPN and AML in the PPM1DTP53wt and PPM1DTP53m gp, respectively. Similarly, 19% vs 18% (p=>0.99), 47% vs 32% (p=0.23), 7% vs 36% (p=0.001), 2% vs 0% (p=>0.99) and 2% vs 14% (p=0.04) of pts met criteria for t-CH, t-CCUS, t-MDS, t-MPN and t-AML in the PPM1DTP53wt and PPM1DTP53m gp, respectively. All PPM1D variants were truncating, located in exon 6 of the gene, with median variant allele frequency (VAF) (8% [R,1-64] vs 5.5% [R,2-24], p= 0.10) and number of PPM1D MT (1 [R,1-5] vs 1 [R, 1-3], p=>0.99) being similar between the two gp. While proportion of pts with t-MN were similar between the two gps (77% vs 86%, p= 0.40), cytogenetic (CG) abnormalities (67% vs 31%, p= 0.006), including monosomies (28% vs 2%, p= <0.001) and complex CG (53% vs 4%, p= <0.001) were more frequent in PPM1DTP53m gp compared to PPM1DTP53wt gp, respectively. The median TP53 MT VAF was 14% (R, 1-14); 50% had multi-hit TP53 MT. Somatic mutations in PPM1D MT myeloid neoplasm with and without TP53 MT Somatic co-mutations excluding TP53 were seen in 71% of pts; 73.5% in PPM1DTP53wt and 59% in PPM1DTP53m gp (p= 0.20). Apart from CBL (0% vs 9%,p=0.03), MT involving DNMT3A (20% vs 14%, p= 0.56), TET2 (15% vs. 14%, p= >0.99), IDH1 (6% vs 19%, p= 0.07), splicing factors (8% vs 14%, p=0.08), ASXL1 (11% vs 4.5%, p=0.46), and JAK2 (9% vs 0%,p=0.20) were comparable between PPM1DTP53wt and PPM1DTP53m gps, respectively. The proportion of pts with ≥ 2 somatic co-mutations excluding TP53 MT were numerically higher in PPM1DTP53wt gp (43%) compared to PPM1DTP53m gp (23%) (p= 0.09). In the PPM1DTP53wt gp, other somatic driver mutations included RUNX1 (n= 7 [7%]; CH [n=1], CCUS [n=2], MDS [n=3], MPN [n=1]), NRAS (n=1 [1%]; CCUS), BCOR (n=1 [1%]; CCUS), and PTPN11 (n=1 [1%]; CCUS). Leukemic transformation and survival With a median follow up of 6.43 months (mo) (R, 0.23-36.4), median overall survival (mOS) in mo among high-risk MDS/AML (16.4 vs 15.0, p= 0.66) and CHIP/CCUS pts (35.79 vs 26.28, p= 0.93) was similar between PPM1DTP53wt and PPM1DTP53m gps, respectively. CHIP/CCUS pts harboring multiple vs single PPM1D MT had an inferior mOS (23.9 vs 36.7 mo, p= 0.05). Three (2.5%) MDS pts underwent AML transformation; 1 (1%) and 2 (10%) in PPM1DTP53wt and PPM1DTP53m gp, respectively (p= 0.07). Conclusions In our study, 18% of pts had concurrent TP53 and PPM1D MT (82% t-MN), with the PPM1DTP53wt genotype being more frequent in CCUS, while the PPM1DTP53m genotype was more frequent in MN. The PPM1DTP53m genotype had a higher frequency of CG abnormalities, including complex CG. Survival outcome was inferior and comparable in PPM1D MT MN with or without TP53 MT. While 73.5 % of the PPM1DTP53wt gp had somatic driver MT and 31% had karyotypic abnormalities, 22% had no additional MT or CG changes (all CH/CCUS), underscoring the need to understand how PPM1D MT contribute to hematopoietic dysfunction and MN.

Background: The majority of patients with chronic myelomonocytic leukemia (CMML) harbor somatic mutations with the most frequent being TET2 (56%), SRSF2 (42%), and ASXL1 (41%) (Leukemia 2020;34:1407). The prognostic relevance of mutations in CMML has been studied extensively with consistent observations suggesting favorable survival impact from TET2 and unfavorable from DNMT3A, ASXL1, NRAS, and SETBP1 mutations. Among the latter, DNMT3A mutation stands out as being the strongest predictor of inferior overall (OS) and leukemia-free (LFS) survival (AJH 2017;92:56). The current study was inspired by observations from exploratory analyses of a large Mayo Clinic CMML cohort. Methods: The current retrospective study was conducted under an institutional review board approved minimum risk protocol that allowed retrospective collection and analysis of data from patient records (Mayo Clinic, Rochester, MN; Scottsdale, AZ; and Jacksonville, FL). Mutations were screened by multi-gene next-generation sequencing (NGS). Diagnostic criteria were according to the International Consensus Classification (Blood 2022; 140:1200). Conventional statistical methods were employed for comparisons of groups and survival analysis (JMP Pro 17.0.0 software SAS Institute, Cary, NC, USA). Results: Exploratory analysis of a well-characterized cohort of 398 Mayo Clinic patients with CMML suggested an unusually long median survival of 96 months for 7 patients harboring PHF6 mutation vs. 27 months for those without the mutation. A subsequent institutional database search focusing on PHF6-mutated CMML identified 20 more cases, expanding the total number of study patients to 418, including 27 PHF6-mutated cases. PHF6 mutations clustered with (co-mutation frequency) TET2 (93%) and less likely to be co-mutated with TP53 (0%), PTPTN11 (0%) and SF3B1 (0%) mutations. PHF6-mutated patients often presented with thrombocytopenia (platelet count <100 x 10(9)/L; 85% vs. 51% in PHF6 wild-type cases; p<0.01). Median time from initial presentation with thrombocytopenia to CMML diagnosis was 4 years (0-14 years). In order to isolate the prognostic impact of PHF6 mutation without associated DNMT3A mutation and independent of TET2 mutation, we considered 4 mutational categories: i) DNMT3A-mutated (N=19; 2 co-expressed PHF6 and 7 TET2 mutations), ii) PHF6-mutated with wild-type DNMT3A (N=25; 23 co-expressed TET2 mutation), iii) TET2-mutated without DNMT3A or PHF6 co-expression (N=169), and iv) wild-type for DNMT3A, TET2, and PHF6 (N=205). Compared to the other groups, PHF6-mutated patients with wild-type DNMT3A were less likely to display leukocytosis (p<0.01) or red cell transfusion need at presentation (p<0.01). At a median follow-up of 18 months, 302 deaths, 78 leukemic transformations, and 44 allogenic stem cell transplants were documented. Univariate analysis for OS disclosed superiority in favor of PHF6-mutated patients with wild-type DNMT3A (median OS 90 months) vs. the other three groups with median OS ranging from 10 months for DNMT3A-mutated patients (HR 20.7, 95% CI 8.1-52.7; p<0.01) to 40 months for TET2-mutated cases with wild-type DNMT3A (HR 3.5, 95% CI 1.7-7.6; p<0.01). Results were similar for multivariable analysis of LFS, where, remarkably, none (0%) of the 25 PHF6-mutated patients with wild-type DNMT3A experienced leukemic transformation vs. 15-30% risk of leukemic transformation in the other three groups (p<0.01). Multivariable analysis for both OS and LFS, which included other risk factors such as red cell transfusion need, leukocytosis (leukocyte count ≥13 x 109/L) and karyotype, confirmed the independent and favorable impact of PHF6 mutation/wild-type DNMT3A (p<0.01 in both instances). Finally, all-inclusive multivariable analysis of karyotype and mutations, in DNMT3A wild-type patients, confirmed the highly favorable and independent prognostic impact of PHF6 mutation (HR 0.18, 95% CI 0.09-0.37). Conclusion: The current study proposes a 2-gene genomic signature (PHF6 mutated and DNMT3A wild-type) to identify a unique subset of CMML patients who often present with thrombocytopenia and whose clinical course is characterized by a very low risk of leukemic transformation, resulting in superior overall survival. Additional studies are warranted to validate these findings and include the information in contemporary risk models.

Introduction Chronic myelomonocytic leukemia (CMML) is associated with a 15-30% risk for blast transformation (BT) over 3-5 years. Post-BT survival remains dismal with a median overall survival (mOS) of ~6 months (mo), even with intensive therapies. Although genetic drivers are identified in >40% of BT-CMML cases (Carr, 2021), mechanisms of BT remain to be elucidated. This multicenter study examines risk factors for BT in CMML and predictors of post-BT survival. Methods CMML patients at Mayo Clinic (n = 400, 47%) and MD Anderson Cancer Center (n = 449, 53%) were included with IRB approval. Analyses used clinical and molecular data at diagnosis or first referral in chronic phase (CP) and again at BT. Categorical variables were compared by Chi squared and continuous by Mann-Whitney U or Kruskal-Wallis tests. Multivariate analyses used Cox proportional hazards models with binarization via receiver operator curves. Kaplan-Meier analyses were censored at hematopoietic cell transplantation (HCT). P < 0.05 was considered significant. Calculations used BlueSky (v10.3.1) or Prism (v10.2.3). Results Of 849 CMML patients (median age 71 years, 32% female, 90% white) included in the study, 133 (16%) underwent BT. In comparison to CP-CMML without BT, those with BT were more likely (p < 0.05) to have had higher WBC counts (15.1 vs 11.4 x109/L), higher absolute monocyte counts (2.9 vs 2.2 x109/L), lower platelet counts (84 vs 102 x109/L), have circulating immature myeloid cells (52% vs 37%), and be classified as myeloproliferative (MP)-CMML (58% vs 44%) or CMML-2 (33% vs 17%) at diagnosis/first referral in CP. More mutations were detected in BT-CMML than in CP-CMML (mean 3.2 vs 2.8, p = 0.002). Mutations in RAS (NRAS, KRAS, BRAF, CBL, PTPN11; 51% vs 40%, p = 0.02) and signaling (CSF3R, FLT3, JAK2, SH2B3; 15% vs 7%, p = 0.004) pathway genes were more frequent in BT-CMML. Conversely, there were fewer BT-CMML patients with the favorable ASXL1WT/TET2MT genotype compared to CP-CMML (22% vs 33%, p = 0.004). Multivariate analysis identified MP-CMML (hazard ratio [HR] 1.5, p = 0.04), CMML-2 (HR 2.4, p < 0.001), and the presence of ≥4 somatic gene mutations (HR 1.8, p = 0.002) as risk factors for BT whereas the ASXL1WT/TET2MTgenotype was protective (HR 0.45, p = 0.002). The ASXL1WT/TET2MT genotype was also protective in the MP-CMML (HR 0.49, p = 0.04) and RAS-mutated (HR 0.35, p = 0.005) subgroups. Amongst BT-CMML cases, the median time to BT was 10 mo from diagnosis/referral. Compared to their CP assessment, patients in an overlapping Mayo Clinic BT-CMML cohort (n = 156, median age 69 years, 35% female) were more likely to have NPM1 (24% vs 3%, p < 0.001) and IDH2 (14% vs 1%, p = 0.01) mutations at BT. Amongst cases with paired molecular evaluations (n = 44), 7 (16%) acquired new mutations, including FLT3-ITD (n = 2) and NPM1 (n = 2). Conversely, 6 (14%) lost mutations, including TET2 (n = 3), SRSF2 (n = 2), CBL, NRAS, or PTPN11 (n = 1 each). There were no differences in variant allele fractions in driver genes present at CP and BT. Abnormal karyotypes were more prevalent at BT than in CP (60% vs 34%, p < 0.001), and 26 (25%) patients with a normal karyotype in CP acquired structural (65%) and/or numerical (69%) changes at BT, including 6 (23%) that acquired a complex karyotype. Acute myeloid leukemia defining translocations were seen in 4 (4%) cases: 2 with t(8;21) and 1 each with inv(3) and t(10;11)(KMT2A::TET1). After considering mutation and karyotype changes, only bone marrow blasts ≥30% (HR 1.7, p = 0.04) were independently prognostic for OS after BT (mOS 4 mo). Compared to supportive care (n = 50, mOS 1.3 mo), OS was improved by hypomethylating agents (HMA, n = 14, mOS 16 mo, HR 0.3, p < 0.001) or induction chemotherapy (n = 56, mOS 8 mo, HR 0.3, p < 0.001), but not by HMA + venetoclax (n = 11, mOS 6 mo, HR 0.7, p = 0.4). Allogeneic HCT (n = 28) improved mOS to 46 vs 3 mo (p < 0.001). Amongst 4 patients with paired whole genome sequencing before and after BT, 3 had increased copy number alterations (including 2 with loss of heterozygosity, 2 with gains, and 3 with deletions) while the 4th acquired novel likely pathogenic somatic mutations (MUC4, BAX, WNK2). Conclusions Survival in CMML after BT remains exceptionally poor. In this multicenter cohort, MP-CMML, CMML-2, and the presence of ≥4 somatic gene mutations were identified as risk factors for BT, with the ASXL1WT/TET2MT genotype being protective. Following BT, bone marrow blast burden ≥30% was an independent adverse predictor of survival.

Background: TP53-mutated (TP53mut) myeloid neoplasms (MN) have particularly poor survival. Discrepancies in defining TP53mut MN have impact on diagnostic work up, therapeutic decisions, and clinical trial enrolment. Methods: MN cases harboring TP53mut (variant allele frequency, VAF ≥2%) were classified based on bone marrow (BM) and peripheral blood (PB) blast % using the 4th revision of the WHO classification (WHO-4R). Biallelic loss was defined as (i) ≥2 mutations each with VAF ≥2%; (ii) single TP53mut VAF ≥2% plus 17p loss detected on karyotype, FISH, or SNP; or (iii) single TP53mut VAF ≥50%, whereas monoallelic loss was defined as single TP53mut VAF <50% without 17p loss. Primary endpoint was overall survival (OS) from diagnosis. Conditional Inference Trees (CIT) analysis was used to determine the true effect of a predictor. Results: We identified 580 cases including WHO-4R defined acute myeloid leukemia (AML, BM/PB blasts ≥20%, n=219, 37.8%), myelodysplastic syndrome (MDS) with excess blasts-2 (EB-2, BM 10-19% or PB 5%-19%, n=92, 15.9%), MDS with excess blasts-1 (EB-1, BM 5-9% or PB 2-4%, n=75, 12.9%), and the remaining were MDS with low blasts (-LB, BM <5% and PB ≤1%, n=194, 33.4%). Of the 578 cases evaluable for allelic status, 437 (75.6%) and 141 (24.4%) had biallelic and monoallelic TP53 loss, respectively. Higher frequency of biallelic loss was observed with increasing blasts. 63.2%, 73.3%, 78% and 86.3% of cases with MDS-LB, MDS-EB1, MDS-EB2, and AML had bi-allelic TP53 loss (P<0.0001). In a multivariable analysis, WHO-4R categories, VAF ≥10%, and biallelic loss were independent predictors of poor survival. CIT analysis further stratified the cohort into 4 groups with distinct survival: (1) MDS-LB (n=194, 33.4%); (2) MDS-EB1/EB2 and AML with VAF <10% (n=38, 6.6%); (3) MDS-EB1/EB2 with VAF ≥10% (n=149, 25.7%); and (4) AML with VAF ≥10% (n=199, 34.3%). MDS-LB cases could be further stratified based on allelic status and complex karyotype (CK): OS was poor for cases with biallelic TP53 loss and monoallelic TP53mut with CK compared to monoallelic TP53mut without CK, who had the most favorable survival (12.7 vs. 13 vs. 34.8 months, P<0.0001).MDS-EB1/EB2/AML with VAF<10% could also be stratified by CK: MDS-EB1/EB2/AML with VAF<10% cases without CK had the favorable survival compared to their counterparts with CK and MDS-EB1/EB2 with VAF ≥10% cases (26.2 vs. 5.6 vs. 6.3 months, P=0.003).MDS-EB1/EB2 with VAF ≥10% was a homogenous subgroup: Biological characteristics including the proportion of cases with biallelic TP53 loss, CK (P>0.9), monosomal karyotype (MK, P>0.9), del 5q (P=0.6), del 7q (P=0.4), and del 17p (P=0.2) were comparable between MDS-EB1 and -EB2 with VAF ≥10%. Importantly, median OS of MDS-EB1 and EB2 with VAF ≥10% was comparable (9.6 vs. 7.2 months, P=0.12). OS in this group was comparable regardless of the blast %, allelic status, or presence of CK.AML with VAF ≥10% had extremely poor survival: Median OS was 3.9 months. Survival of AML was equally poor irrespective of the mono- or biallelic (3.6 vs. 3.9, P=0.89) and non-CK vs. CK (1.8 vs. 3.9 months, P=0.09). Combined, our model would acknowledge poor survival of 514 (89.1%) cases. In contrast, retrospective application of the 5th edition of the WHO classification (WHO-5) and International Consensus Classification (ICC) would classify only 211 (36.4%) and 468 (80.7%) cases as biallelic/multi-hit TP53mut MN, respectively. Finally, the Harrell's c-index of the proposed model, WHO-5, and ICC was 0.66, 0.571, and 0.617, respectively. Conclusion: We provide evidence for subsequent refinements in classifying MN harboring TP53mut. Our salient findings include: (i) acknowledgement of CK as ‘biallelic equivalent’ in MDS-LB; as well as EB1/EB2/AML with VAF 2 to <10% cases; and (ii) demonstration of poor survival of MDS-EB1 and -EB2 with VAF ≥10% regardless of the allelic status. In conclusion, our proposed model acknowledged poor survival of a higher proportion of cases as TP53mut MN compared to the current models with a higher c- index.

Introduction: Somatic mutations in RAS pathway genes are present in ~30% of patients with chronic myelomonocytic leukemia (CMML) and are usually associated with myeloproliferative features. Whether mutations in distinct RAS pathway genes share similar genomic context and have similar implications remains unknown. Such an understanding might inform future studies evaluating genotype-specific therapies (RAS-codon specific and pan-RAS inhibitors) or cooperative leukemogenic mechanisms. This multicenter study examines the landscape of RAS pathway mutations (RASMT) in CMML. Methods: Newly diagnosed CMML patients evaluated at MD Anderson Cancer Center (n=449, 54%) and Mayo Clinic (n=383, n=46%) were included after IRB approval. Clonal relationships were tested using Pearson goodness-of-fit. Clones with the highest variant allele frequency (VAF), or with VAF close to 40% were defined as dominant, and those present at VAF <20% in the presence of another dominant clone were defined as subclonal. RASMT genes included NRAS, KRAS, BRAF, CBL, CBLC, PTPN11 and NF1. Standard statistical measures were applied. Results: Among 832 CMML patients (median age 71 years, 68% male) 387 (47%) had myeloproliferative (MP) and 445 (53%) had myelodysplastic (MD) CMML. A total of 350 (42%) patients had RASMT with higher prevalence among MP-CMML compared to MD-CMML (55% vs 31%, p<0.001). Among patients with RASMT, 262 (32%), 59 (7%), 20 (2%), 6 (<1%) and 3 (<1%) had 1, 2, 3, 4 or 5 distinct RASMT, respectively. Importantly, 17 patients harbored a RASmt as the only detectable somatic mutation, with KRASMT being the most frequent (n=10, 59%), including 3 (18%) patients with >1 RASMT. Among RASMT patients, a trend for higher hemoglobin (12.7 vs 10.8 g/dL, p=0.054) was observed in NF1MT CMML and lower WBC (14.4 vs 27.9 x109/L, p=0.067) values in CBLMT CMML. In total, 479 somatic mutations in RAS pathway genes were identified the most frequent involving NRAS (n=169, 35%) followed by CBL (n=120, 25%), KRAS (n=102, 21%), PTPN11 (n=38, 8%), NF1 (n=34, 7%), BRAF (n=11, 2%) and CBLC (n=5, 1%). Most frequently involved codons for each RAS pathway gene were as follows: G594 (n=3) for BRAF, R420 (n=22) and C404 (n=15) for CBL, G12 (n=41; G12D: 13, G12C: 3) and A146 (n=16) for KRAS, G12 (n=116; G12D: 74, G12C: 5) for NRAS and A72 (n=8) for PTPN11. CBLMT CMML had higher ASXL1 (58% vs 44%, p=0.011), BRAF (8% vs 4%, p=0.017), IDH2 (10% vs 4%, p=0.024), KIT (5% vs 1%, p=0.038), SRSF2 (54% vs 40%, p=0.004), TET2 (59% vs 47%, p=0.019) and ZRSR2 (10% vs 4%, p=0.014) co-mutation frequency. Of note, DNMT3A mutations were mutually exclusive of CBLMT CMML (0% vs 7%, p=0.007), and multihit TET2 was more common among TET2MT/CBLMT vs TET2MT/CBLWT CMML (82% vs 67%, p =0.039). CMML with NF1 mutations had higher BCORL1 (8% vs 0%, p=0.005), PTPN11 (15% vs 3%, p=0.014) and SETBP1 (23% vs 8%, p=0.022) mutational cooccurrences. NRASMT CMML was enriched for ASXL1 (53% vs 43%, p=0.042), ETNK1 (5% vs 1%, p=0.004), GATA2 (4% vs 1%, p=0.034) and STAG2 (4% vs 1 %, p=0.023) mutations but had lower JAK2 (1% vs 6%, p=0.036) and TP53 (1% vs 5%, p=0.022) mutational frequency. PTPN11 mutations were associated with higher NF1 (29% vs 7%, p=0.014), SETBP1 (27% vs 9%, p=0.01) and WT1 (6% vs <1%, p=0.014) mutational cooccurrences and lower SRSF2 (23% vs 42%, p=0.05) frequency. We evaluated RAS mutant clonal dominance in 253 (72%) RASMT patients. NRAS (63% vs 38%), KRAS (63% vs 38%) and CBL (65% vs 35%) mutations were more frequently observed as dominant clones while PTPN11 (44% vs 56%), BRAF (25% vs 75%) and NF1 (35% vs 65%) mutations were more frequently subclonal events, particularly of TET2, ASXL1 or SRSF2 mutant clones. Presence of a RAS pathway mutation was associated with shorter LFS (36 vs 53 months, HR 1.5, 95% CI 1.1-2.2, p=0.020), with presence of multiple RAS mutations shortening LFS further (53, 43, 27 months for 0, 1 and >1, p=0.017). PTPN11 mutations predicted for shorter OS (18 vs 39 months, HR 1.7, 95% CI 1.0-2.8, p=0.035) and LFS (14 vs 36 months, HR 1.9, 95% CI 1.2-2.9, p=0.008). Presence of >1 RAS pathway mutation was associated with shorter OS in ASXL1MT/TET2MT CMML compared to those with no RAS mutations (24 vs 53 months, HR 4.2, 95% CI 1.6-10.8, p=0.004). Conclusions: RAS mutations exhibit distinct genomic features and clonal hierarchy in CMML and cooperate with other somatic mutations to drive clinical outcomes. This study forms the foundation for assessment of novel RAS pathway inhibitors in CMML.

Background Venetoclax + hypomethylating agent (Ven-HMA) therapy results in favorable response rates (CR/CRi 66%) and overall survival (OS; median 14.7 months) in unfit patients with newly-diagnosed acute myeloid leukemia (ND-AML; N Engl J Med 2020;383). However, there is substantial heterogeneity in individual patient outcomes based on response to treatment. The objective of the current study was to develop a genetic risk model to predict survival outcome in treatment responders and non-responders, analyzed separately, and also account for allogeneic stem cell transplant (ASCT). Methods Treatment-naïve AML patients receiving Ven-HMA, outside of a clinical trial, at the Mayo Clinic, USA (MN, AZ, FL) were retrospectively recruited. Molecular studies (48-gene panel) were performed by next-generation sequencing. Response was assessed according to the 2022 European LeukemiaNet (ELN) criteria (Blood 2022;140). Standard statistical analyses were performed using JMP Pro (Version 17.0.0). Results 400 ND-AML patients (median age 73 years, 64% male, 60% de novo) received Ven-HMA. ELN cytogenetic risk included favorable 2%, intermediate 60%, or adverse 38%. Mutations involved TP53 in 26%, TET2 19%, RUNX1 19%, SRSF2 18%, ASXL1 18%, DNMT3A 15%, K/NRAS 13%, NPM1 12%, IDH2 12%, FLT3-ITD 10%, IDH1 7% and DDX41 in 4% of informative cases. 153 (38%) patients achieved CR, 94 (24%) CR with incomplete count recovery (CRi), resulting in CR/CRi in 247 (62%) patients. CR/CRi rates were higher with NPM1 (86% vs 59%), IDH2 (77% vs 60%), and DDX41 mutations (93% vs 61%) and lower with TP53 (45% vs 67%), FLT3-ITD (41% vs 64%), RUNX1 (49% vs 65%) mutations and adverse karyotype (48% vs 71%), with all retaining significance in multivariable analysis. CR/CRi rate was highest (87%) in 75 patients with one or more favorable mutations (NPM1, IDH2, DDX41) and no unfavorable mutation (TP53, FLT3-ITD, RUNX1). CR/CRi rate was lowest in 171 patients with at least one unfavorable mutation and no favorable mutation (44%; p<0.01). After a median follow up of 10.5 months (0.5-66), 105 relapses (43% of patients in CR/CRi), 248 (62%) deaths and 65 (16%) ASCT were documented. Univariate analysis for transplant-censored OS disclosed superior survival in patients achieving CR/CRi (median 21 vs 3.6 months; HR 5.4, 95% CI 4.1-7.1). Among patients achieving CR/CRi, IDH2 mutation was associated with superior (median not reached vs 20.5 months) and male gender (median 17.6 vs 29.2 months), TP53 mutations (median 11.9 vs 24.3 months) and adverse karyotype (median 12.6 vs 29.4 months) with inferior survival; multivariable analysis resulted in HRs (95% CI) of 2.1 (1.3-3.4) for male gender, 2.1 (1.2-3.8) for adverse karyotype, and 2.5 (1.1-5.7) for absence of IDH2 mutations. Male gender did not show an association with karyotype, or TP53 mutations (p>0.1). Accordingly, an HR-weighted genetic risk model was generated with assignment of one point each to male gender, adverse karyotype, and absence of IDH2 mutation: high risk = 3 risk factors (n=38; median 9.6 months; 3-year survival 0%); intermediate risk = 2 risk factors (n=129; median 22 months; 3-year survival 38%); and low-risk = ≤1 risk factor (n=78; median not reached; 3-year survival 69%; p<0.01). In patients bridged to ASCT (n=60), post-transplant survival was inferior in the presence of ≥ 2 risk factors (n=42; median 46 months) vs. ≤1 risk factor (n=18; median not reached; p=0.1). In patients not achieving CR/CRi, risk factors for OS included male gender (median 3.4 vs 6.1 months), adverse karyotype (median 3.3 vs 4.5 months) and TP53 mutation (median 3.1 vs 4.5 months) while those with IDH2 mutations lived longer (median 8.4 vs 3.4 months). In multivariable analysis, HRs (95% CI) were 1.9 (1.3-2.9) for male gender, 2.0 (1.4-2.9) for adverse karyotype, and 2.1 (1.1-4.3) for absence of IDH2 mutations. OS was shortest for non-responders harboring 3 risk factors (n=45; median 3 months; 1-year survival 0%) and longer for those harboring two (n=80; median 6 months, 1-year OS 15%) or ≤ 1 risk factor (n=25; median 14 months; 1-year OS 56%; p<0.01). Conclusion The current study describes a molecular profile for predicting response to Ven-HMA in ND-AML and also introduces a novel approach to survival prediction that considers treatment response as the starting point. In both responders and non-responders, male gender and adverse karyotype were identified as unfavorable and IDH2 mutation favorable risk factor for OS.

Introduction: Telomere biology disorders (TBD) are multisystemic accelerated aging syndromes due to abnormal telomere length (TL) shortening and increased cancer risk. Pediatric-onset TBD is characterized by severely shortened TL and specific associations with germline pathogenic variants mainly in DKC1, TINF2, PARN genes and characteristic clinical features [bone marrow failure (BMF), abnormal nail/skin/oral mucosa]. Adult-onset TBD is genetically distinct (predominantly, TERT, TERC, and RTEL1 mutations) with varied organ involvement [interstitial lung disease (ILD), BMF, cirrhosis, or bone disease] and heterogenous outcomes. In our previous study of predominantly adult patients with short telomeres, multiple organ involvement (Mangaonkar A et al. Blood Cancer J 2021) predicted poor overall survival (OS). We sought to validate these findings in a larger, well annotated adult cohort of TBD patients. Methods: Patients with suspected TBD underwent comprehensive clinical and molecular evaluation through our TBD-dedicated clinic after regulatory approval. TL was assessed through clinical flow cytometry fluorescence in-situ hybridization (FlowFISH).Clinical and laboratory features, including pulmonary imaging, lung volumes/function testing, hepatic imaging (MR elastography/fibroscan) and bone density assessments were retrospectively abstracted. Germline and somatic genetic testing was performed on peripheral blood through targeted panels for known TBD and myeloid genes respectively. Cox proportional hazard model was used to identify significant variables that also retained independent prognostic impact. Results: Overall, 122 patients met criteria for TBD as defined by lymphocyte TL (LTL) <=10th percentile and/or a presence of a germline-TBD variant; 34 patients LTL <1st percentile, 84 1st and the 10th percentile (27 with TBD-germline variants) and 4 with only TBD-germline variants. Median age at diagnosis was 56 (18-77) years, with 72 (59%) males. Clinical features included presence of ILD (n=81, 66%), BMF (n=39, 32%), cirrhosis/hepatic fibrosis (n=19, 38%), bone disease osteopenia/osteoporosis/fractures, n=53, 70%), MDS/AML (n=11, 9%), non-hematological cancer (n=38, 31%), and head and neck cancer (n=2). Germline pathogenic variants were detected in 22 (18%), most frequently in TERT (n=10), RTEL1 (n=7) and TERC (n=2), while variants of uncertain significance (VUS) were seen in 35 (29%) patients, especially in TERT (n=20), TERC/RTEL1(n=6), NAF1 (n=4). Somatic variants in hematopoietic cells were detected in 37 (30%) patients with frequent alterations seen in DNA damage response and repair (PPM1D/TP53, n=11), and splicing component (U2AF1/SF3B1/ZRSR2, n=9) genes. At last follow-up [median of 3 (0-18) years], there were 26 (21%) deaths (most commonly, progressive ILD-18, cancer of lung/breast/pancreas-3, transplant-related complications-2). After censoring patients at the time of any transplantation (lung transplant-26, liver transplant-5, bone marrow transplant-8), the Kaplan-Meier estimate of median OS was not reached. Univariate survival analysis found adverse OS predicted by older age at diagnosis (P=0.006), presence of ILD (P=0.0002), hepatic fibrosis/cirrhosis (P=0.02), and somatic DNA repair variants (P=0.03). Multivariate model analysis found that only presence of ILD retained independent prognostic impact (HR=2, P=0.02). Among radiographic ILD subtypes, UIP was the most common (51%), followed by NSIP (10%), and others (6%), with median FEV1 of 2L (range: 0.5-4.6), FVC 2.4L (0.7-6.2), and TLC 4L (1.9-7.4). TBD-ILD patients were older (P<0.0001) with a male preponderance (P=0.03), 52 (64%) with multi-organ involvement, and had a less severe hematological phenotype [lower incidence of BMF (P<0.0001) and fetal hemoglobin elevation (P=0.01)], more frequent bone disease (P=0.0009), relatively longer telomeres in lymphocytes (P=0.04), and no particular association with any germline or somatic genetic alterations. Conclusions: Presence of ILD is an independent and significant predictor of adverse survival in adult TBD. Within adult TBD, patients with ILD represent a unique clinical subtype without any obvious genetic or pathologic correlates. Focusing on definitive therapeutic measures in this subgroup of adult TBD has the best chance to alter natural history and improve outcomes.

Introduction: Chronic myelomonocytic leukemia (CMML) is a myeloid stem cell neoplasm with few effective therapies and poor prognosis. This disease is characterized by an expansion of malignant monocytes which express high and homogeneous levels of the homing chemokine receptor CCR2. We have developed a CCR2 targeting Cytotoxicity Targeting Chimera (CCR2-CyTAC, STX-0712), which potently binds CCR2 on cells, and when combined with the CyTAC platform antibody, eliminates target cells via enhanced effector mediated killing. We present here the characterization of CCR2 expression in CMML patient samples, ex vivo depletion of CMML cells via treatment with STX-0712, and the dose dependent depletion of MO1 monocytes (classical monocytes) in non-human primates, supporting CMML as a promising indication for STX-0712. Methods: IRB approval was obtained from Mayo Clinic for patient sample use. For CCR2 characterization and depletion experiments, we used bone marrow biopsy specimens and peripheral blood mononuclear cells (PBMCs) obtained from CMML patients and controls from healthy donors. CCR2 expression and monocyte depletion were evaluated via flow cytometry, as previously described. In vivo pharmacokinetic (PK) and pharmacodynamic (PD) studies were conducted in cynomolgus monkeys. Results: First, we evaluated CCR2 expression in peripheral blood and bone marrow in CMML samples by flow cytometry. In 6/6 (100%) peripheral blood samples CCR2 was highly expressed on >98% of the monocytes. Also, in 3/3 (100%) bone marrow samples, CCR2 was expressed on a subset of CD34+ progenitors, while low/no expression was observed in healthy controls. This progenitor subpopulation had characteristics of the inflammatory granulocyte-macrophage progenitor (GMP)-like cells. Next, STX-0712 was added to freshly isolated PBMCs from CMML donors and CCR2+ monocyte depletion, mediated by endogenous Fc gamma receptor 3a positive (FcγRIIIa) effector cells, was assessed. In 5/5 (100%) CMML patient samples, the drug selectively induced depletion of CD14+, CCR2+ cells with an average potency of 3nM and 66-91% target cell killing vs no drug control. Finally, we evaluated the effects of STX-0712 in cynomolgus monkeys to evaluate PK and PD effects on CCR2 MO1 monocytes in vivo. STX-0712 demonstrated PK supportive of dosing in man. In 9/9 (100%) animals, STX-0712 effectively depleted >95% of CCR2+ monocytes which returned after drug levels dropped below ~10ng/mL. All doses were well tolerated and the findings of comprehensive immunophenotyping were to be as expected, predictable and mechanism directed. Conclusion: These results demonstrate high and homogenous CCR2 expression on malignant monocytes, ex vivo human target engagement and pharmacodynamics, and in vivo depletion of CCR2 MO1 monocytes in a potent and dose dependent manner. Based on this data we plan a First in Human, phase 1 clinical trial for patients with relapsed/refractory CMML.

Introduction: VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) is an adult-onset autoinflammatory disorder defined by somatic UBA1 mutations in hematopoietic cells. VEXAS is associated with a high frequency of clonal hematopoiesis (CH- 60%); with the clonal landscape being dominated by DNMT3A mutations. In our prior study (Gutierrez-Rodrigues Blood 2023), we showed that DNMT3A mutations in VEXAS associated with increased mortality, but without a higher risk of MDS/AML. As DNMT3A is a critical epigenetic regulator, we conducted this study to define the epigenetic deregulation and impact on mortality of DNMT3Amt (mutant) CH in VEXAS. Methods: After IRB approval, 88 VEXAS patients from the Mayo Clinic and the NIH were retrospectively assessed, including 81 screened for CH by error-corrected DNA sequencing (ECS). DNA methylation changes were identified using the Illumina Infinium MethylationEPIC BeadChip on peripheral blood samples (PB). Cellular indexing of transcriptomes and epitopes (CITE)-seq was performed using the 10x Chromium 3' GEX platform; 16,600 pooled cells were subjected to UMAP dimensionality reduction, followed by Azimuth based cell identification. Genotyping of targeted loci with chromatin accessibility (GoTChA) was conducted on two PB DNMT3Amt samples from CCUS individuals (Izzo et al Nature 2024). Results: Patients' median age was 70 years (range: 56 - 89); 95% were white. Twelve out of 81 patients screened by ECS were found with a DNMT3Amt (15%), with a median variant allele fraction (VAF) of 42% (range: 6-46%). In this cohort, while the presence of any CH mutation did not impact survival, DNMT3Amt CH had an age-independent negative impact on mortality (5.5 years vs 8.7 years, p =0.005), without an increase in risk for MDS/AML. Changes in DNA methylation were profiled in 19 and 9 VEXAS patients without CH (Median Age: 68) or with DNMT3Amt CH (Median Age: 74), respectively. VEXAS samples with DNMT3Amt CH had >4,000 differentially methylated CpGs with 95% of the CpGs being hypomethylated compared to those without CH. Using the Roadmap Epigenomics project, we found that this hypomethylation was enriched at enhancer (Enh) sites and actively transcribed states (TxWk). Pathway analysis revealed that the hypomethylated sites were in or near genes involved in the development and differentiation of leukocytes, with IL-13 and IL-15 being identified as upstream regulators of the methylation changes. Bulk RNA-seq performed on PB of 2 and 3 VEXAS patients with and without DNMT3Amt, respectively, identified >1,500 differentially expressed genes in DNMT3Amt samples, 78% of these being overexpressed. Pathway analysis was enriched in gene pathways involved in the development of leukocytes, with IL-13 and IL-15 once again being identified as upstream regulators. Integration of methylation and transcriptomic data identified upregulation of several genes within the IL-13 and IL-15 pathways, with these regions correlating with a decrease in methylation. To assess if the epigenetic dysregulation is linked to DNMT3A mutations, we performed GoTChA-seq on two DNMT3Amt clonal cytopenia samples (CCUS). The comparison of the number of cutsites in DNMT3A wild type vs mt cells from the same individual demonstrated increased open chromatin within the IL-13 and IL-15 pathways in mt cells, both globally and in a genomic locus specific manner. CITE-seq performed on 3 VEXAS samples (2 DNMT3Amt CH vs 1 no CH) further showed that expression of genes involved in IL-13 and IL-15 pathway is significantly increased in CD4+ and CD8+ T cells from DNMT3Amt samples, suggesting a paracrine regulatory effect of T lymphocytes (mostly UBA1 and DNMT3A wild-type) in VEXAS. Pathway analysis of DEGs in these cells also revealed an enrichment of genes involved in inflammation and lymphocyte proliferation. Conclusions: Our study validates the age-independent, negative prognostic impact of DNMT3Amt CH on survival in VEXAS syndrome. DNMT3Amt mediates epigenetic and transcriptional priming associated with upregulation of IL-13/15 pathway in CD4/CD8 T cells, which are mostly DNMT3A and UBA1 wild-type, suggesting that the contribution of T lymphocytes to inflammation may be secondary to CH in the myeloid compartment.