Citations

Abstract Introduction: The 5th edition of the World Health Organization (WHO-5) and the International Consensus Classification (ICC) recognize TP53-mutated myeloid neoplasms (MN) as a distinct disease category, reflecting their uniformly dismal outcomes and the urgent need for novel therapeutic strategies. However, both classifications do not include TP53-non-mutatedcases with 17p (TP53 locus) loss, despite emerging evidence that such lesions may confer biologic and clinical behaviour similar to TP53-mutated disease. Our preliminary work demonstrated that 17p loss without TP53 mutation in therapy-related MN (t-MN) is associated with poor survival, approximating that of TP53-mutated cases (Hiwase et al., Blood 2023). Yet, the true frequency and prognostic impact of 17p loss in TP53-non-mutatedMN remains largely undefined, representing a critical gap in current disease classification and risk stratification. To address this critical knowledge gap, we aim to define the frequency and prognostic impact of 17p loss across the TP53 locus in TP53-non-mutatedMN, including both myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Finally, we compared the survival outcomes of this cohort with those of TP53-mutated MN. Method This international collaborative study was designed to evaluate the frequency and prognostic significance of 17p loss in TP53-non-mutatedMN. We included MDS and AML patients who had conventional cytogenetic analysis and did not have TP53-mutation(TP53-non-mutated)by next-generation sequencing (NGS) with sensitivity of ≥2% variant allele frequency (VAF). These cases were systematically reviewed for 17p loss using karyotype data, and where available, fluorescence in situ hybridization (FISH) and SNP array were used to confirm the 17p/TP53 locus deletion. To assess the clinical impact, we compared the overall survival (OS) of TP53-non-mutatedcases with 17p loss against a reference cohort of TP53-mutated MNs with VAF ≥2% (n=603) (South Australian Myeloid Neoplasm Registry (SA-MN) and Mayo Clinic, Rochester, USA). Results We screened 8876 cases of TP53-non-mutatedMN cases across an international cohort comprising the SA-MN (Australia; n=1046), the Düsseldorf MDS Registry (Germany; n=545), Munich Leukaemia Laboratory (Germany; n=5785), and King's College Hospital, (United Kingdom; n=1500). We identified 85 (1%) cases with 17p loss across the TP53 locus, representing the largest international cohort to define the frequency of 17p loss in TP53-non-mutatedMN. Complex karyotype was present in 40% (n=34) of cases, frequently co-occurring with del(5q) and del(7q). Clinically, most cases were MDS (n=69; 81.2%), including MDS-IB1 (n=19), MDS-IB2 (n=15), MDS-LB (n=16), t-MDS (n=8), MDS/MPN overlap (n=3), CCUS (n=1), or unspecified MDS (n=7), while AML accounted for 16 cases (18.8%). Among evaluable cases, the majority were male (78.6%) and had a median age of 66.5 years at diagnosis. The most frequent cytogenetic abnormality causing 17p loss across the TP53 locus was monosomy 17 (39%), followed by i(17q) (29%), add (17p) (14%), derivative chromosome 17 from unbalanced translocations (11%), and del(17p) (7%). The majority represented de-novo MN (60%), with t-MN in 40% of cases. Median OS of evaluable 17p loss in TP53-non-mutatedcases (n=28; 10.2 months) was poor and comparable to TP53-mutated MN (n=603, 8.7 months; P=0.42). Similarly, survival censored for a stem cell transplant was also equally poor (10.4 vs. 8.7 months; P=0.34) in both groups. Complex vs. non-complex karyotype (7.7 vs. 10.7 months; P=0.68) did not significantly influence the OS of 17p loss. Median OS of MDS cases tended to be longer compared to AML (16.7 vs. 9.1 months; P=0.11), although not statistically significant. Conclusion: In this largest international study, 1% of TP53-non-mutatedMNs harbor 17p loss across the TP53 locus, displaying poor survival equivalent to TP53-mutated disease. Exclusive reliance on NGS to identify TP53 mutations misses these high-risk structural TP53 abnormalities, which are readily detectable by conventional karyotyping. These findings provide compelling evidence to include TP53-non-mutatedcases with 17p loss in the next revision of the classifications, enabling accurate prognostication and equitable access to curative and clinical trials of novel therapies.

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 Background: Mutations in ethanolamine kinase-1 (ETNK1) have been identified in a wide range of myeloid neoplasms (MN), but their clinical significance remains poorly defined. Key gaps remain, including the true prevalence, variant- and disease-specific co-mutation patterns, cytogenetic patterns, and prognostic impact, highlighting the need for broader multi-institutional studies to refine our understanding and risk stratification. We present findings from an ongoing multi-institutional study of ETNK1-mutated (ETNK1mut) MN. Methods We analyzed 106 patients with ETNK1mut MN across the Mayo Clinic Comprehensive Cancer Center (Minnesota, Arizona, and Florida), H. Lee Moffitt Cancer Center (Tampa, FL), Massachusetts General Hospital (Boston, MA), and University of Milano-Bicocca (Monza, Italy), integrating clinical, hematologic, cytogenetic, and next-generation sequencing (NGS) data. Appropriate IRB approval was obtained. Diagnoses were assigned by the 5th edition of the World Health Organization and 2022 European LeukemiaNet criteria. A clone was considered dominant if it had the highest variant allele frequency (VAF) or VAF within 5% of the highest co-mutation. Overall survival (OS) was assessed by Kaplan-Meier. Comparison cohorts for OS included 83 ETNK1 wild-type (ETNK1wt) myelodysplastic syndrome (MDS) and 415 ETNK1wt acute myeloid leukemia (AML) patients without TP53 mutations. GraphPad Prism v10 was used for statistical analysis. Results Median age at diagnosis was 70 years (range 30.4-90), with a male predominance of 72.6% (n=77). ETNK1mut were identified in MDS (n=47, 44.3%), myelodysplastic/myeloproliferative neoplasms (MDS/MPN; n=23, 21.7%), myeloproliferative neoplasms (MPN; n=13, 12.3%), AML (n=12, 11.3%), clonal cytopenia of undetermined significance (CCUS; n=5, 4.7%), and other entities (n=6, 5.7%) including atypical chronic myeloid leukemia (n=1) and systemic mastocytosis (n=1). Over a median follow-up of 33.6 months (IQR 15-91.8), 49.1% (n=52) patients died and 19.4% (n=18 of 93 at risk) progressed to AML. Cytogenetics were available in 103 patients; 57.3% (n=59) had a normal karyotype, while 30.1% (n=31) had abnormal and 12.6% (n=13) had complex karyotypes. None harbored classical MDS-associated deletions such as del(5q), del(7q), or del(20q). The most frequent cytogenetic abnormalities included translocations (n=17), monosomy 7 (n=9), and trisomy 8 (n=8). Of 17 translocations, 8 (47%) involved chromosome 1, two of which (11.8%) involved der(1;7)(q10;p10). The most common ETNK1 mutation was N244S (n=70, 66.0%), followed by K378N (n=12, 11.3%) and G245 variants (n=9, 8.5%), including G245V and G245D. VAF data were available for 103 patients; the median ETNK1 VAF was 31.4% (range 2.0-54.8%). High VAF (≥40%) was observed in 27.2% (n=28) of patients. ETNK1 was the dominant mutation in 33% (n=34) of cases, shared equal dominance with a co-mutation in 13% (n=14), and was a subclone in 56% (n=58). Co-mutations were detected in 77% (n=82) of patients, with a median of 4 (range 0-13) co-mutated genes. A third of patients (n=37, 35%) had ≥5 co-mutations. The most frequently co-mutated genes were epigenetic regulators including ASXL1 (n=29, 27%), TET2 (n=17, 16%), EZH2 (n=12, 11%), and DNMT3A (n=12, 11%), followed by splicing factor genes including U2AF1 (n=13, 12%), SRSF2 (n=10, 9%), and ZRSR2 (n=10, 9%). Mutations in signaling genes (JAK2, NRAS, SETBP1) and transcription factors (RUNX1, BCOR) were also observed. High VAFs were seen in co-mutations of EZH2 (median 49%), TET2 (46%), and NRAS (46%). ASXL1 was most enriched in MDS/MPN (n=8, 35%) and MPN (n=3, 23%). Survival analysis showed better survival in ETNK1mut compared to ETNK1wt within AML (65 vs 19 months; p=0.2002) and MDS (107 vs 61 months; p=0.1993), although statistical significance was not reached. Conclusion ETNK1 mut frequently co-occur with mutations in epigenetic and splicing regulators, and demonstrate distinct molecular and cytogenetic features, including the absence of classic MDS-associated deletions and a high prevalence of translocations involving chromosome 1. ETNK1 was the dominant clone in a third of cases with a high co-mutation burden. Overall survival was better in ETNK1mut AML and MDS, but the difference was not statistically significant. These findings highlight the need for larger collaborative studies.

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 and Significance: Chronic myelomonocytic leukemia (CMML) is a clonal hematopoietic malignancy with overlapping dysplastic and proliferative features, a high risk of leukemic transformation, and no disease-modifying therapies. Patients with proliferative CMML often present with symptomatic monocytosis, leukocytosis, splenomegaly, and systemic inflammation, which contribute to shortened survival and impaired quality of life. Hydroxyurea (HU), the standard cytoreductive agent, provides transient control of leukocytosis but has no known disease modifying properties. In the phase 3 DACOTA trial (Itzykson et al., JCO 2022), decitabine modestly delayed leukemic transformation compared to HU but did not improve event-free or overall survival and was associated with increased early mortality. HU achieved a clinical benefit rate (CBR) of approximately 15% (excluding stable disease), highlighting the urgent need for safer and more effective therapies. Pacritinib is a potent and selective multikinase inhibitor with a kinome profile that targets key mediators of clonal proliferation and inflammatory signaling relevant to CMML. It inhibits JAK2 (IC₅₀ = 6 nM) and IRAK1 (IC₅₀ = 13.6 nM)—critical drivers of cytokine-mediated growth and monocytic skewing—while sparing JAK1, potentially reducing myelosuppressive toxicity. Pacritinib also inhibits CSF1R (IC₅₀= 39.5 nM) which is involved in monocytic differentiation. Preclinical models demonstrate that dual inhibition of JAK2 and IRAK1 suppresses CMML colony formation and prolongs survival in xenografts. Furthermore, CSF1R inhibition may reduce monocyte-lineage bias in leukemic clones. Clinically, pacritinib is FDA-approved for intermediate- or high-risk myelofibrosis with severe thrombocytopenia (platelets <50 × 10⁹/L) based on evidence of significant spleen volume and symptom reduction with limited hematologic toxicity. These mechanistic and clinical data provide a strong rationale for evaluating pacritinib in advanced proliferative CMML, a setting characterized by both cytokine-driven proliferation and treatment-limiting cytopenias. Study Design and Methods PROSPERA (NCT07033598) is a collaborative multicenter, open-label, randomized phase 2 trial. Sixty-six patients with WHO-defined CMML-1 or CMML-2 will be enrolled. Eligible patients must have proliferative features (WBC ≥13 × 10⁹/L) and advanced disease as defined by ≥5 cm palpable splenomegaly, symptom burden (Myeloproliferative Neoplasm-Symptom Assessment Form Total Symptom Score MPNSAF-TSS ≥20), or thrombocytopenia (platelets <100 × 10⁹/L). Prior JAK inhibitor therapy is not allowed. The trial will be conducted at approximately six sites across the United States and United Kingdom, with enrollment anticipated to begin by the end of 2025. Participants will be randomized 2:1 to receive either pacritinib (200 mg orally twice daily) or HU (dosed as per investigator discretion) for 48 weeks. Patients in the HU arm may cross over to pacritinib at Week 24 if, in the opinion of the treating physician, they are not deriving clinical benefit (after assessment of the primary endpoint). Randomization will be stratified by prior cytoreductive therapy (none vs. prior HU or hypomethylating agents). The primary endpoint is CBR at Week 24, defined by modified IWG MDS/MPN criteria incorporating hematologic improvement, spleen volume reduction, and symptom response. Secondary endpoints include CBR at any time, duration of response, event-free survival, leukemia-free survival, and overall survival. Correlative studies will assess treatment-related changes in clonal dynamics, cytokine signaling, and hematopoietic composition using longitudinal peripheral blood and bone marrow sampling. Single-cell transcriptomic and immunophenotypic profiling will be employed to characterize pacritinib's impact on both the malignant clone and the surrounding immune microenvironment.

Abstract Background and Significance: CMML is a myeloid neoplasm characterized by hematopoietic stem and progenitor cell (HSPCs) monocytic bias, leading to downstream monocyte expansion that plays a key role in disease maintenance and progression. Monocytes in CMML express high surface expression of the homing C-C chemokine receptor 2 (CCR2), which promotes malignant monocyte survival. Expansion of CCR2+ monocytic progenitors drives acute transformation in CMML and contributes to venetoclax resistance in AML. For these reasons, CCR2 is a potential novel therapeutic target in CMML and monocytic AML. The CyTAC platform was designed to enable targeting of cell surface antigens that demonstrate limited or ineffective binding to conventional therapeutic antibodies. A CyTAC is a heterobivalent small molecule that binds to both a target of choice and to a fully humanized monoclonal antibody. STX-0712 comprises a CCR2 CyTAC which potently binds to CCR2 on malignant cells, and a CyTAC humanized ADCC-enabling monoclonal antibody, which when combined eliminates target cells via enhanced effector-mediated killing in the presence of NK cells. We have demonstrated that treatment with STX-0712 ex vivo results in human target engagement and pharmacodynamic activity, and in vivo leads to depletion of CCR2 MO1 monocytes in a potent and dose-dependent manner in CMML and AML (ASH 2024). Therapeutic depletion of CCR2+ malignant monocytes presents a novel opportunity to develop a potential disease-modifying targeted therapeutic agent. We have designed a first-in-human, phase 1 clinical trial to evaluate the effect of CCR2 CyTAC in patients with refractory/resistant CMML, and relapsed/refractory monocytic or monocytic predominant AML. Study Design and Methods This is a phase 1, first-in-human, open-label, multicenter clinical trial based in the USA to evaluate STX-0712 as a monotherapy in patients with CMML and AML who have no remaining treatment options known to confer clinical benefit. STX-0712 will be administered as a single intravenous (IV) infusion every 3 weeks (additional regimen schedules may be explored) until evidence of disease progression, death, intolerance to study medication, or withdrawal of consent. The study consists of a dose-escalation and dose-expansion part and includes two cohorts: Cohort 1 (refractory/resistant CMML) and Cohort 2 (relapsed/refractory monocytic or monocytic predominant AML). Dose escalation will begin in participants with CMML using the Bayesian Optimal Interval (BOIN) design, with a minimum of three patients enrolled at each dose level. Backfilling of up to two cleared dose levels will be initiated once efficacious exposure levels are reached and at least one CMML participant has achieved a complete remission (CR) or a partial remission (PR), marrow response, or clinical benefit as defined by the MDS/MPN IWG 2015 criteria. In the AML cohort, backfilling may begin once at least one participant has achieved a response defined by ELN 2022 criteria. Dose expansion will occur upon completion of dose escalation in each cohort, using a Simon 2-stage adaptive design. Approximately 47 CMML and 58 AML patients may be enrolled in this phase 1 study. The primary objectives of the study are to evaluate the safety and tolerability of STX-0712 and to determine the minimal safe and biologically effective dose, recommended phase 2 dose (RP2D), and/or maximum tolerated dose (MTD), and to characterize dose-limiting toxicities (DLTs). Secondary objectives include evaluation of preliminary antitumor activity, pharmacokinetic (PK) parameters, and pharmacodynamic effects of STX-0712 on CCR2+ malignant cells in blood and bone marrow. Key exploratory endpoints include: (1) assessment of changes in CCR2+ tumor cells following STX-0712 dosing, (2) evaluation of candidate biomarkers, (3) characterization of T cells, B cells and NK cells at baseline and over the course of treatment, and (4) to explore the effects of STX-0712 on patient-reported outcomes using the CMML Symptoms Assessment Tool (MPN-SAF-TSS scoring system) and the EuroQoL 5 Dimension 5 level (EQ-5D-5L) for AML. Enrollment for Cohort 1 (CMML) began in March 2025, and the study is ongoing. Clinical Trial Information: NCT06950034

Abstract BACKGROUND Whilst the broad clonal architecture of naturally progressing chronic lymphocytic leukemia (CLL) has been described, a comprehensive picture of how chemotherapy and targeted agents reshape that landscape is lacking. Here we integrate clone-specific growth kinetics with mutational profiles, transcriptomic subtypes, and CpG-methylation-based epigenetic classes to capture the multidimensional evolutionary responses of CLL under native conditions and during treatment. METHODS We previously reported a systematic whole-exome sequencing (WES) analysis of 417 leukemia–germline pairs from 169 treatment-naïve patients ≥ 65 y (Karisani et al., Blood 2024). The treatment arm comprised 83 patients who received ibrutinib and 39 who received chlorambucil in the RESONATE-2 trial (NCT01722487). Forty-seven age-matched “watch-and-wait” patients from the CLL Research Consortium served as untreated controls. Peripheral-blood samples were collected at baseline and again ~300 d and ~600 d after therapy initiation (or diagnosis in the watch-and-wait cohort), enabling longitudinal clonal tracking. WES data were processed with PhylogicNDT to reconstruct clonal architectures, define phylogenies, and identify significant clonal shifts. MutSig tools identified mutations enriched in expanding or contracting clones. Pretreatment RNA-sequencing profiles were grouped into transcriptional subtypes by consensus clustering based on the Louvain algorithm. Differentially methylated regions plus epitypes were called from reduced representation bisulfite sequencing data. RESULTS Across the 169 patients with WES, we resolved 579 subclonal clusters. Significant clonal shifts (defined as a distribution shift of cancer cell fraction in a subclone of >95% between two timepoints) were uncommon during watch-and-wait (36%) but markedly higher after therapy — chlorambucil 67% (q = 0.01), and ibrutinib 77% (q < 10-4). In ibrutinib-treated CLL, regressing subclones were enriched for KRAS (q<10-3) and SF3B1 mutations (q<10-3), whereas expanding subclones preferentially harboured mutations in BIRC3 (q<10-4), NOTCH1 (q <10-3), TP53 (q=0.02), and POT1 (q=0.098). In chlorambucil-treated patients, no specific mutations were found to be enriched in expanding or regressing subclones. Using the recently defined CLL expression clusters (ECs) in patients treated with chemoimmunotherapy as defined by Knisbacher et al. (Nat Genet 2022), we were unable to identify any relationship between ECs and outcomes. We therefore sought to identify de novo ECs with prognostic relevance in the context of BTK-inhibition (BTKi-ECs). We identified a transcriptionally defined patient subgroup (C4, n=20) associated with inferior progression-free survival (median PFS = 63 months, log-rank q=0.05), independent of known prognostic clinical and molecular features, including epitypes, in multivariate analysis (Cox HR=3.7, 95% CI: 1.6-8.6, q=0.02). Gene-set enrichment in this cluster highlighted TNF-ɑ signalling via NF-κB (REL, TNFAIP3, NFKB2) and G2M checkpoint pathways (SMC4, EZH2). We also identified a distinct transcriptionally defined patient subgroup (C3, n=18) that was enriched for patients harboring at least one contracting subclone and no expanding subclones (q=0.005). This cluster showed a relative depletion of mutations within the chromatin modification pathway (6% vs 50%, q<0.01). Gene-set enrichment in this cluster highlighted a downregulation of genes in the TNF-ɑ signalling via NF-κB pathway (SOCS3, ICOSLG, NFKB2). CONCLUSION BTK inhibition and chemotherapy drive distinct evolutionary trajectories in CLL. Multi-omics profiling reveals mutation-defined subclones with divergent sensitivity to targeted therapy and delineates two informative expression states: a high-risk NF-κB/inflammatory cluster (C4; poor PFS) and a cluster enriched with contracting subclones with depleted TNF-ɑ signalling via NF-κB (C3). Integrating clonal growth kinetics with genomic, transcriptomic, and methylation data can potentially identify patients likely to progress on BTK inhibitors and identify actionable pathways for adaptive or combination therapy.

Abstract Background: Venetoclax (VEN)+obinutuzumab (VO) is an effective therapy for CLL/SLL requiring regular monitoring for tumor lysis syndrome (TLS) during VEN ramp-up. The CLL14 trial of VO reported no TLS during VEN ramp-up; however, there are limited real-world data on monitoring practices and TLS outcomes for different dose levels and monitoring timepoints. This study assessed VEN initiation prophylaxis and monitoring outcomes for patients (pts) with CLL/SLL starting VO in first line (1L) in an outpatient, real-world setting. Methods This interim analysis relied onretrospective observational data from 4 US sites of the CLL Collaborative Study of Real-World Evidence (CORE). Adult pts with CLL/SLL were eligible if they: (1) started VO per-label outside of a clinical trial in 1L, or immediately after exposure in 1L to agents with different mechanisms of action (i.e., BTKi, anti-CD20 only) of <30 days; (2) prior to VEN start, had either (i) low physician-determined tumor burden (TB) (i.e., all lymph nodes [LN] <5 cm and ALC <25 x 109/L), or (ii) medium physician-determined TB (i.e., any LN ≥5-<10 cm or ALC ≥25 x 109/L) with creatinine clearance ≥80 mL/min; (3) had no strong CYP3A inhibitors or prophylactic rasburicase from 3 days prior to VEN start until end of VEN ramp-up; and (4) had VEN ramp-up in an outpatient setting. TB-related labs/imaging was assessed from 2 months prior to obinutuzumab initiation (i.e., index date) until VEN start. VEN characteristics (i.e., dosing, duration), prophylaxis measures (i.e., antihyperuricemics and IV hydration), and TLS-related monitoring and management (i.e., lab results and interventions received) were collected per ramp-up week and TLS monitoring timepoint. Results Of 128 pts in CORE who initiated VO in any line, 72 pts met inclusion criteria (low TB: 57 [79.2%]; medium TB: 15 [20.8%]). Median (IQR) age was 62 (56.0, 68.5) years, 58.3% were male, and 81.9% had ECOG grade ≤1. Among pts tested, 7/68 (10.3%) had del(17p)/TP53 mutation and 43/66 (65.2%) had unmutated IGHV. Median (IQR) time from index to VEN start was 23.0 (22.0, 30.0) days. Most pts completed ramp-up (98.6% [71/72]) and followed a per-label regular dosing schedule (93.1% [67/72]). Prior to VEN ramp-up, all pts received prophylactic antihyperuricemics (allopurinol: 71 [98.6%]; febuxostat: 2 [2.8%]) and prophylactic hydration. In the 2 days prior to a dose escalation for at least 1 week of ramp-up, prophylactic IV hydration was reported for 27 (37.5%) pts based on physician determination. One pt stopped VEN after week 2 due to neutropenia (grade 3+). During ramp-up (median [IQR] of 9 [8, 12] blood tests per pt), no lab or clinical TLS was reported. Of 21 (29.2%) pts who received an intervention following a lab assessment, most had low TB at VEN start (16 [76.2%]). All interventions were either prophylactic or non-TLS-related. Following a lab assessment for at least 1 week of ramp-up, prophylactic IV or escalated oral hydration intervention was reported in 17/21 pts (81.0%) based on physician determination (e.g., to manage impaired baseline renal function in those with low TB, patient request, or institutional practice) (IV hydration: 15 pts; escalated oral hydration: 2 pts). By per-label monitoring timepoints, hydration intervention was given prophylactically following pre-dose lab tests for 7 pts (across weeks 1-5), 6-8 hours post-dose for 5 pts (weeks 1-2), and 24 hours post-dose for 10 pts (weeks 1-2). By per-label monitoring timepoints, other non-TLS-related interventions (i.e., blood transfusion for anemia, insulin for hyperglycemia, and potassium for non-TLS-related hypokalemia) were given following pre-dose lab tests for 2 pts (weeks 1-5) and 24 hours post-dose for 4 pts (weeks 1-2). Conclusion Consistent with the CLL14 trial, no TLS was reported in this real-world, interim analysis of pts with mostly low TB and good renal function at 1L VO initation. All interventions during VEN ramp-up were prophylactic or non-TLS-related, with prophylactic hydration commonly given based on physician preference. These results suggest that VO initiation is manageable in an outpatient setting. Consideration should be given for simplified monitoring requirements including potential removal of 6-8 hour post-dose lab in this population and be further explored in prospective studies. Data collection for this study is ongoing to further contextualize real-world VEN initiation prophylaxis and monitoring outcomes in a larger cohort.

Abstract Introduction: Graft Failure (GF) is a rare but devastating outcome of HCT. Primary GF (PGF), defined as a failure of neutrophil recovery by Day+28, is straightforward to diagnose. Diagnosing secondary GF (SGF) is more challenging, with its broad time-range, multiple confounding diagnoses, and lack of predictive biomarkers. In BMT CTN1703/1801, we analyzed patients receiving RIC HCT for heme malignancies with either Tac/MTX (n=159) or PT-Cy (n=165) GVHD prophylaxis. SGF was defined as donor chimerism <5% after initial donor engraftment. With Tac/MTX, there were 3 PGF and 1 SGF diagnoses. With PT-Cy, there were 4 PGF and 6 SGF. Median SGF diagnosis was Day +64 (range: Day+28-215). There were too few Tac/MTX patients to analyze SGF, but sufficient events with PT-Cy. To identify PT-Cy SGF predictors, we leveraged lymphocyte, T, B, and NK cell reconstitution analysis. In SGF we found an early, profound deficit in the reconstitution of all major lymphocyte populations, including total lymphocytes, T, B, and NK cells, as early as Day+28. This enabled the modeling of a SGF risk classifier based on the Absolute Lymphocyte Count (ALC). Methods: Clinical ALC measurements were performed on all SGF patients (n=6) and on non-GF controls with ALCs available (146 of 155 non-GF patients). Flow cytometry was performed on all PT-Cy SGF patients (n = 6) and from a subset of non-GF controls (n = 18: controls were chosen as patients without relapse or severe GVHD, to reduce confounders introduced by immunologic interventions, and for whom all samples, including from the graft infusion, were available). T, B, and NK counts, as well as T cell subsets, were compared (using Welch's T test) on Days 7, 14, 21, 28, 42, 63, 98, 180, 270, 365, 730, with SGF patients censored on the day of GF diagnosis. To interrogate the optimal ALC cutoff, the cumulative incidence of SGF was computed at Days +28 and +42, with death without GF as a competing risk. Results: We have previously demonstrated that, compared to Tac/MTX, PT-Cy patients exhibited an early decrease in reconstitution of all T cell populations (with normal NK and B cell reconstitution). Here we focused specifically on PT-Cy patients with or without SGF. Graft CD34 counts/kg were not different between SGF patients and non-GF patients (mean CD34/kg = 1.38 x10e6 (SGF) vs 0.67 x10e6 (non-GF, p = 0.61) However, even amidst the overarching early suppression in T cell reconstitution with PT-Cy, SGF patients could be easily distinguished from the larger PT-Cy cohort, based on more profound deficits in ALC, T, B and NK cells reconstitution, measured using 2 strategies: (1) SGF patients demonstrated significant early (Day +28) quantitative defects in the reconstitution of the ALC (mean +/- SEM 262+/-32 cells/µL (non-GF) vs 60 +/- 25 (SGF, p<0.0001), CD4 T cells (62 +/- 12 cells/µL vs 19+/-15, p=0.048), CD8 T cells (15 +/-3 cells/µL vs 3.5 +/-1 p=0.0009), all CD8 T cell subpopulations, as well as NK cells (116+/-31 cells/µL vs 2.9+/-1.4 cells/µL, p= 0.002) and B cells (3.5 +/-1.4 cells/µL vs 0.16+/-0.07 p =0.03). (2) In SGF, there was a significant deficit in the rate of rise of all major lymphocyte populations between Days 28-42-60 vs non-GF, including CD4 T cells (p<0.0001), CD8 T cells (p = 0.0002), B cells (p<0.0001), and NK cells (p =0.048). These discoveries suggested that a classifier could be identified to risk-stratify patients for SGF. We explored an ALC cutpoint, amenable to standard clinical lab analysis. A statistically significant threshold was identified at both Days+28 and +42, with Day+42 being most predictive: A threshold of 120 cells/µL was identified as optimal, with landmark analysis documenting a SGF rate of 34.7% below the cutpoint, and SGF of 1% above it (HR = 45.9, 95% CI 5.7 - 366). Conclusions: Despite the small number of events, PT-Cy patients with SGF demonstrated a distinctive reconstitution trajectory that encompassed an early, substantial, and sustained deficit in all lymphocyte counts, as well as a lack of their longitudinal expansion. This enabled the discovery of a candidate ALC biomarker cutpoint at Day+42 that could distinguish patients who were more likely to develop SGF. If confirmed, these data could generate a predictive biomarker for SGF, which would enable the design of trials evaluating early interventions (e.g. CD34+ boosts, DLI, modification of immunosuppression) to improve outcomes for these patients.

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.