ZRSR2 Mutations Research Articles

Therapeutic strategies targeting aberrant RNA splicing in myeloid malignancies.

In recent years, large-scale sequencing efforts have identified targetable driver mutations in haematopoietic stem cells. These efforts have led to the development and approval of nine novel agents for relapsed or refractory acute myelogenous leukaemia (R/R AML). However, despite an expansion in targeted therapies, achieving a durable remission in AML and high-risk myelodysplastic syndrome (HR-MDS) remains a significant challenge, and there is an urgent need for new effective treatments. Modulation of aberrant RNA splicing has emerged as a novel therapeutic approach in myeloid diseases. Aberrant splicing drives dysregulated gene expression that promotes tumourigenesis through increased proliferation and metastatic potential, immune evasion, decreased apoptosis, and chemotherapy resistance. Mutations in spliceosomal components have been identified in numerous cancer subtypes, with mutations in RNA binding proteins SF3B1, SRSF2, U2AF1, and ZRSR2 occurring frequently in AML and in up to 60% of patients with MDS, as well as in chronic myelomonocytic leukaemia and in 10% of patients with chronic lymphocytic leukaemia. In this review, we explore therapeutic strategies targeting aberrant splicing and the potential of these approaches to drive clinical responses.

Characterisation and prognostic impact Of ZRSR2 mutations in myeloid neoplasms.

Characterisation and prognostic impact Of ZRSR2 mutations in myeloid neoplasms.

Abstract 2265: Distinct alternative splicing patterns in genetic subtypes of diffuse large B-cell lymphoma

Abstract Advances in sequencing techniques have made molecular subgrouping of Diffuse Large B-cell Lymphoma (DLBCL) based on DNA cahnges, which has led to the development of Lymphgen classification. By the way, although alternative splicing (AS) in cancer cells contributes to proliferation, invasion and metastasis, and immune escape, their role and association with DLBCL molecular subtypes are unknown. Therefore, we analyzed whole-exome sequencing (WES) and bulk RNA-Seq data paired in the public EGA dataset (EGAD00001003600) to explore the patterns of AS events that differ between Lymphgene subtypes. The WES data of 620 DLBCL samples that passed quality control were aligned to the reference using BWA-MEM, and variants were called with Mutect2. We used the information of copy number variants provided by cBioPortal. The RNA-Seq analysis was performed using the STAR-RSEM pipeline and differential splicing events were detected using rMATS to compare subtypes. Among 620 DLBCL samples, there were 19 MCDs, 95 EZBs, 22 BN2s, and 137 ST2s (50 samples with multiple genetic classes, and 291 samples unclassified). Mutations in spliceosome complex genes (ZRSR2 and SF1) were found in 14 and 27 samples, respectively. In BN2 and MCD subtypes, splicing events with significantly different exon inclusion levels were observed at a high frequency of 29 and 16 occurrences, respectively, compared to other subtypes. (P-value < 0.05). In contrast, retained intron is the only event observed in the EZB subtype (Table 1). Samples with mutations in ZRSR2 and SF1 showed four and two aberrant events, respectively, compared to samples without these mutations. Of note, rMATS detected an alternative 3’ splice site event in exon 6 of CD37 in the MCD. CD37 is involved in tumorigenesis in leukocytes and has been suggested as a potential biomarker in blood cancer, and its dysregulation may have influenced the poor prognosis of MCD. In summary, molecular subtypes of DLBCL had unique features in terms of alternative splicing. Functional consequences of these selective exon usages for each DLBCL subtype are being warranted. Citation Format: Sanyeowool An, Youngil Koh, Sung-Soo Yoon. Distinct alternative splicing patterns in genetic subtypes of diffuse large B-cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2265.

Clinical Factors but Not Somatic Mutations Predict for Survival in Patients with Myelofibrosis Undergoing Allogeneic Hematopoietic Cell Transplant: Analysis of the North American Myelofibrosis Transplant Outcome (NAMTO) Study

Introduction: Myelofibrosis (MF) is a clonal hematologic malignancy characterized by constitutive JAK-STAT activation and aberrant cytokine signaling. Allogeneic hematopoietic stem cell transplantation (allo-HCT) remains the only potentially curative therapy in MF. The contribution of disease-, patient- and donor-related factors to allo-HCT outcomes remains to be fully elucidated, as well as the presence of somatic mutations in genes such as ASXL1, EZH2, SRSF2, U2AF1 and IDH1/2 which are associated with worse prognosis in MF patients (pts). In this large multi- center retrospective analysis, we aimed to study the impact of clinical and molecular mutations on transplant outcomes. Methods: This analysis including 498 pts from 11 centers in North America and Canada. Univariate proportional-hazard Cox regression analysis stratified by center was used to assess the association of patient, transplant, and disease characteristics on overall survival (OS). Baseline patient demographic data and disease characteristics were selected as covariates in the multivariate analysis. Results: Pts transplanted between 2002-2021 were included in this analysis. Baseline and transplant characteristics are summarized in table 1. The 1- and 2-year OS was 77% (95% CI; 73-81) and 70% (95% CI; 66-74) and non-relapse mortality (NRM) 19% (95% CI: 17-21) and 23% (95% CI: 19-27), respectively. The cumulative incidence (CMI) of relapse at 1- and 2-years was 12% (95% CI; 10-14) and 16% (95% CI; 12-20). The CMI of acute graft versus host disease (aGVHD) grade II-IV was 31% (95% CI; 27-35) at 3 months and 42% (95% CI; 38-46) at 1-year post-transplant and grade was III-IV 13% (95% CI; 11-15) and 18% (95% CI; 14-22), respectively. The CMI of neutrophil engraftment at 1 and 3 months was 90% (95% CI: 87-93) and 97% (95% CI: 95-95) and for platelets 55% (95% CI: 50-59) and 80% (95% CI: 76-83). Univariate analysis included pts (age and gender), transplant (donor type and conditioning regimen intensity) and disease characteristics (DIPSS, mutations, cytogenetics (CG), blood counts, and spleen size). Hemoglobin > 10 g/dL (HR .5, 95% CI .34 -.73 p=3 x 10 -4) and platelets >50× 10 9/L (HR .59, 95% CI .42-.81, p=.0013) prior to transplant were associated with improved OS. High risk DIPSS was associated with decreased OS (p=0.0002). Mutations in ASXL1, EZH2, IDH1/2, U2AF1 and SRSF2 were not associated with decreased OS in this analysis (Figure 1). However, mutations in ZRSR2 were associated with inferior OS (HR 2.07, 95% CI 1.08-3.95, p=.0252). Lastly, JAK2 which had the most frequent mutations was not associated with OS (HR .0.93, 95% CI .65-1.31). There was no association between the CG risk groups and OS. Splenomegaly, measured radiographically, had no impact on OS but was strongly associated with engraftment (better engraftment defined as HR>1). For platelets, spleen size of 15.6-18.9 cm HR of 0.69 (95% CI .47-1, p=.0489) and size >18.9-22.5 cm HR of 0.48 ( 95% CI .33-.7, p=1x10^-4). For neutrophils, spleen size >19.9-22.5 cm had a HR of 0.68, (95% CI .48-.96, p=.0268) and size>22.5 cm had a HR of 0.65 (95% CI .46-.91, p=.0114). Mismatched unrelated (MMURD) and haplo identical donors had no impact on survival but were associated with delayed platelet engraftment; MMURD (HR .67, 95% CI .47-.96, p=.0298) and haploidentical donors (HR .56, 95% CI .39-.8, p=.0017). In a multivariate analysis adjusted for age, gender, highest DIPSS, donor type and conditioning regimen, platelets > 50× 10 9/L (HR .61, 95% CI .44-.87, p=.0053) hemoglobin >10 g/dL (HR .6, 95% CI .4-.9, p=.0244) and lower DIPSS at the time of transplant were associated with improved OS. Conclusions: In this large multicenter analysis only clinical variables; hemoglobin and platelets, were found to be associated with OS after allo-HCT in MF patients. Somatic mutations associated with poor prognosis were not associated with OS suggesting that transplant can overcome their negative impact. Splenomegaly was associated with delayed engraftment but not OS. Interestingly, using alternative donors (MMURD and haplo identical) didn't have a negative effect on OS, possibly reflecting the use of post-transplant cyclophosphamide for GVHD prophylaxis in recent years. These results highlight the importance of biologic factors in the prognostication of outcomes in MF pts undergoing allo-HCT independent of somatic mutations. Supported by the American Society of Hematology (ASH) and MPN Research Foundation

Clinical Outcomes and Mutational Profile Associated with Dysmyelopoiesis in Chronic Myelomonocytic Leukemia

Chronic myelomonocytic leukemia (CMML) is defined by absolute (≥ 0.5 x10 9/L) and relative (≥ 10%) monocytosis in peripheral blood. Presence of significant dysplasia in any of the three myeloid series, in particular dysgranulopoiesis, is an almost constant finding in CMML. In the absence of a clonal marker, a scenario very unlikely with the advent of next-generation sequencing (NGS), significant myeloid dysplasia becomes a crucial criterion for establishing the diagnosis. Although bone marrow dysplasia has demonstrated independent prognostic value in MDS, its significance in relation to CMML has never been assessed. The main interest of our work was to evaluate the genomic determinants of dysplasia and to assess its prognostic impact. We analyzed a series of 240 patients with CMML with clinical, morphological, immunophenotypic, cytogenetic and molecular information. Patients were diagnosed following WHO and ICC 2022 recommendations. As a novelty with respect to previous WHO classifications, the new definition of CMML includes those patients previously categorized as oligomonocytic CMML (OM-CMML). That is, myelodysplastic neoplasms (MDS) or unclassifiable myelodysplastic/myeloproliferative neoplasms with relative monocytosis and a monocyte count of 0.5 × 10 9/L to <1 × 10 9/L. A total of 167 (71%) patients were diagnosed with CMML-1 and 67 (29%) with CMML-2. Likewise, 193 (80%) patients were diagnosed with dysplastic CMML, 55 of whom would meet criteria for OM-CMML, and 47 (20%) were diagnosed with proliferative CMML. We assessed associations between dysmyelopoiesis and gene mutations by Spearman's rank correlation coefficient. Dysgranulopoiesis showed a significant positive correlation with NRAS, TET2 and ZRSR2 mutations; while a significant negative correlation with SETBP1 was observed. Dysmegakaryopoiesis showed a significant positive correlation with ASXL1 and TP53. Dyserythropoiesis showed a significant positive correlation with DNMT3A and SF3B1. The heatmap and matrix showing these correlations, as well as the differences in the degree of dysmyelopoiesis among these specific mutations are depicted in Figure 1-A & 1-B. Later, we wanted to assess the prognostic impact of dysgranulopoiesis, dyserythropoiesis and dysmegakaryopoiesis in terms of overall survival (OS) and leukemia-free survival (LFS) in our series. By applying the MaxStat package in R, it allowed us to detect the best cut-off points for dysgranulopoiesis (>75%) and dysmegakaryopoiesis (>20%) to separate our series into two groups with significantly different outcomes (Figure 1-C). We were unable to detect a significant cut-off point for dyserythropoiesis and the presence of multilineage dysplasia also showed no prognostic impact. CMML patients with dysgranulopoiesis above 75% showed a significant shorter median OS (34.4 vs 67.8 months; Hazard Ratio (HR): 1,99 [1.24-3.19]; P=0.0036) and LFS (33.4 vs 66.6 months; HR: 1,87 [1.17-3]; P=0.008). Likewise, patients with dysmegakaryopoiesis above 20% also showed a significant shorter median OS (30.2 vs 67.1 months; HR: 2.52 [1.63-3.88]; P<0.0001) and LFS (30.4 vs 66.6 months; HR: 2.76 [1.78-4.28]; P<0.0001). Remarkably, dysmegakaryopoiesis above 20% and dysgranulopoiesis above 75% were identified as independent prognostic factors for both OS and LFS after adjustment by multivariable Cox regression analyses by CMML-specific prognostic scoring system (CPSS) and Mayo Prognostic Model. Furthermore, the addition of dysmegakaryopoiesis above 20% and dysgranulopoiesis above 75% to these prognostic indices improved their prognostic accuracy in terms of OS as assessed by a C-index for right-censored data (Figure 1-C). In conclusion, our study has allowed us to detect mutations in genes related to dysmyelopoiesis. In addition, both dysgranulopoiesis and dysmegakaryopoiesis have demonstrated a negative prognostic impact on the survival of patients in our series that was not captured by the CPSS and Mayo prognostic model. Their worse prognosis could be partially justified by their association with poor prognostic mutations (e.g. NRAS, ASXL1, TP53), which allows us to visualize them as a good surrogate of poor prognostic molecular profiles.

Poor Prognosis of SRSF2 Gene Mutations in Patients Treated with Venetoclax-Azacitidine (VEN-AZA) for Newly Diagnosed Acute Myeloid Leukemia. a Multicentric Real-Life Study of 117 Patients

Introduction Spliceosomes are complexes composed of small nuclear RNA that remove introns in protein-encoding genes. Spliceosome mutations ( SRSF2, SF3B1, U2AF1, ZRSR2), are encountered in ∼50% of secondary AML cases. Splicing mutations (splice-mut), in particular SRSF2, correlate with inferior outcomes to standard induction therapy. A recent report in a cohort of 119 patients, of whom 33 had splice mutations and 24 were SRSF2 mutated, reported the lack of impact of splice-mut on prognosis of AML patients treated upfront with Hypomethylating agents (HMA) + VEN in clinical trials (Lachowiez, C. A. et al Blood Adv. 2021). Aims We aimed to assess the impact of splice-mut in a population of patients with newly diagnosed acute myeloid leukemia (ND-AML), treated with VEN-AZA. Methods We performed a retrospective multicentric study including patients treated in three French centers in Marseille (Institut Paoli-Calmettes, CHU La Conception) and Nice (Hôpital L'Archet). Inclusion criterias were ND AML adult patients treated with VEN (7 to 28 days per cycle) and AZA at conventional doses. Next Generation Sequencing (NGS) was performed at diagnosis and was available for all patients. Data were collected from patients' electronic medical records. Statistical analyses were performed using GraphPad Prism v9.5.1 Results We included 117 ND-AML patients (median age = 75 yo; range, 32-89) treated with VEN-AZA between October 2019 and March 2023. The five most frequently mutated genes in the whole cohort were TET2, ASXL1, TP53 and RUNX1in thirty-seven (32%), 36 (31%), 32 (27%) and 31 (26%) patients, respectively. Thirty-four patients (29%) had a mutation in at least one of the spliceosome genes (=Splice-mut), including 20 (17%), 11 (9%), 4 (3%) and 1 (1%) mutations in SRSF2, U2AF1, SF3B1 and ZRSR2, respectively (Fig.1). Median variant allele frequency (VAF) was 42%, 43% and 26% for SRFS2, U2AF1 and SF3B1 respectively. Secondary AML was found in 18 (53%) of the splice-mut AML and 21 (25.3%) of the splice-wt AML groups of patients. Prior HMA was given in seven (20.6%) patients in the splice-mut versus 6 (7.2%) in the splice-wt cohort. Complex cytogenetics was identified in 7 (20.6%) patients in the splice-mut cohort and 28 (33.7%) in the splice-wt cohort. We found a TP53 mutation in 17.6% and 31.3% of splice-mut and wt cohorts, respectively. Best overall response rate (= CR, CRi and MLFS) was 72.6%; with CR, CRi and MLFS observed in 63 (54%), 16 (14%) and 6 (5%) patients, respectively. We did not find any difference in response rate between the splice-mut (=73.5%) and splice-wt (72.3%) AML. Prior treatment with hypomethylating agents and TET2 mutation were the only factors significantly associated with lower response rates (42% vs 82%, p=0.004, and 64% vs 85%, p=0.025, respectively), while IDH2 mutation was predictive of a better response (100%vs 75%, p=0.037, OR: 9.9 [CI 95% 0.57-173]). Median overall survival (OS) and leukemia-free survival (LFS) for the whole cohort was 10.8 and 7.1 months, respectively. In multivariate analysis taking into account TP53 and/or del17p, NRASmut and/or FLT3-ITD, IDH2mut, complex karyotype, and SRSF2, the only factors predicting OS and LFS were mutations in TP53 and SRSF2 genes. Patients mutated for SRSF2 had a 4.8 months OS and a 5 months LFS compared to 11.3 and 8 months, respectively (p=0.034 and p=0.037), comparable with TP53mut AML patients ( Fig.2). Conclusions SRSF2mut seems to be predictive of a worse survival in ND AML treated with VEN-AZA. This finding warrants further exploration in larger cohorts.

What Is the Optimal Treatment Modality in Molecularly Defined Secondary AML? a Multicenter Cohort Study

Introduction Secondary ontogeny acute myeloid leukemia (AML), defined by the presence of mutations in ASXL1, BCOR, EZH2, SF2B1, SRSF2, STAG2, U2AF1 or ZRSR2 was recently integrated into both the ICC and WHO diagnostic criteria, as well as into the ELN 2022 risk classification as adverse risk. However, it is unknown whether cytarabine + anthracycline (7+3), liposomal cytarabine and daunorubicin (CPX-351) or hypomethylating agent + venetoclax (HMA+VEN) is the optimal frontline treatment for these patients (pts). We performed the largest multicenter retrospective cohort study to date, dedicated to pts with molecular-defined secondary ontogeny AML, comparing treatment modalities and assessing the impact of clinical and molecular characteristics on response and survival. Methods We included pts with newly diagnosed (ND) AML who were treated at 4 large academical centers with 7+3, CPX-351 or HMA+VEN. Secondary ontogeny was defined as absence of TP53 mutation and presence of at least one of the aforementioned mutations. Composite complete response (cCR) was defined as complete response (CR) + CR with incomplete count recovery (CRi). Logistic regression was fitted to evaluate odds ratio (OR) for cCR. Overall survival (OS) was compared between groups by log-rank test. COX regression for OS were fitted to evaluate effect of secondary/co-mutations within each treatment group, as well as the effect of treatment and allogeneic stem cell transplantation (SCT) as a time-varying covariate. Results Out of 1132 ND AML pts in the entire cohort, 401 (35%) were molecularly defined as secondary ontogeny and included in the final analysis. Initial treatment was 7+3 in 173 (43%), HMA+VEN in 162 (40%) and CPX-351 in 66 pts (17%). Pts in the HMA+VEN group were older (median age 74 years[yrs]; CPX351 66 yrs; 7+3 63 yrs, p<0.001), while pts in the CPX351 group were more likely to have prior myeloid neoplasm (n=52 [79%]; HMA+VEN n=72 [44%]; 7+3 n=48 [28%], p<0.001) and prior HMA exposure (n=27 [41%]; HMA+VEN n=23 [14%]; 7+3 n=28 [16%], p<0.001). The cCR rates were 56% (97/173), 56% (90/162) and 44% (29/66) in 7+3, HMA+VEN and CPX-351, respectively (p=0.21). In the 7+3 group, the presence of RUNX1 co-mutation was associated with lower cCR rate (OR 0.8, 95% confidence interval [CI] 0.7-0.95, p=0.01), while PTPN11 was associated with higher cCR rate (OR 1.4, 95% CI 1.1-1.8, p=0.011). In the HMA+VEN group, monosomal karyotype (OR 0.7, 95% CI 0.5-0.9, p=0.002), NRAS co-mutation (OR 0.6, 95% CI 0.5-0.8, p<.001) and SF3B1 mutation (OR 0.76, 95% CI 0.6-0.9, p=0.008) were associated with lower cCR rate and FLT3-TKD with higher cCR rate (OR 1.5, 95% CI 1.1-2.1, p=0.01). In the CPX-351 group, NRAS co-mutation was associated with lower cCR rate (OR 0.65, 95% CI 0.5-0.9, p=0.005). As most younger pts (aged ≤ 60 yrs, n=85) were treated with 7+3 (n=64) or CPX-351 (n=13) and almost exclusively older pts (age >75, n=78) were treated with HMA+VEN (n=74), we performed age-group based analyses. In pts aged > 60 yrs (n=318), the median OS (mOS) was comparable between groups (7+3: 16 months [mo], 95% CI 13-27; HMA+VEN 15 mo, 95% CI 13-19; CPX-351 11 mo, 95% CI 9-28 p=0.57). Similar results were seen in pts 60-75 yrs (n=238): 7+3 mOS 16 mo, 95% CI 13-27; HMA+VEN mOS 16 mo, 95% CI 13-26; CPX-351 mOS 10 mo, 95% CI 8-28, p=0.74. The effect of secondary/co-mutations on survival differ between groups: For 7+3 splicing mutations were associated with worse OS, whereas IDH1/2 were associated with improved OS ( Figure). Conversely, in HMA+VEN and CPX351 groups K/NRAS co-mutations were associated with worse survival. NPM1 co-mutation did not affect survival in any treatment group. In multivariable analysis, age, prior myeloid disease, K/NRAS co-mutations and monosomal karyotype were associated with worse OS ( Table). Conversely, BCOR mutation, IDH1/2 co-mutation and SCT were associated with improved OS. Treatment with HMA+VEN or CPX351 were not statistically different vs 7+3, although there was a trend for better OS with HMA+VEN vs 7+3 (HR 0.68, 95% CI 0.44-1.03, p=0.069). Conclusion In pts with ND secondary ontogeny AML the OS with HMA+VEN was at least comparable to 7+3 or CPX351 when adjusted for multiple covariates. The effect of co-mutations on response and OS differed between treatment modalities and may aid in optimal treatment selection in this population. Prospective trials should evaluate the potential superiority of HMA+VEN and effect of co-mutations in secondary ontogeny AML.

Pre-Transplant Somatic Co-Occurring Mutations (by next generation sequencing) in Acute Myeloid Leukemia: Frequency and Impact on Clinical Outcomes after Allogeneic Hematopoietic Cell Transplantation - a Large Study on Behalf of the EBMT Acute Leukemia Working Party

Background: Acute myeloid leukemia (AML) is a very heterogeneous hematological malignancy, which includes numerous genetically defined subsets. The genomic classification of AML with the identification of mutations in transcription factors, epigenetic modifiers, spliceosome, cohesin complex, and signaling pathways has led to a more accurate risk stratification model. The main genetic aberrations included in the European LeukemiaNet (ELN) 2022 classification are NPM1 (risk group according to karyotype and FLT3-ITD status), FLT3-ITD (intermediate risk), bZIP in-frame mutated CEBPA (favorable risk), and RUNX1, ASXL1, BCOR, EZH2, RUNX1, SF3B1, SRSF2, STAG2, U2AF1, ZRSR2 and TP53 mutations (all belonging to the adverse risk group). In the context of allogeneic hematopoietic stem cell transplantation (allo-HSCT), the frequency and prognostic value of different gene-gene interactions has not been studied and may differ from that of patients treated with chemotherapy alone. We aimed at evaluating, through the European Society for Blood and Marrow Transplantation (EBMT) database, the frequency and impact of different recurrent somatic mutations, either alone or in association, on prediction of relapse and survival in patients receiving allo-HSCT. Methods: This is a retrospective, registry-based, multicenter analysis from the EBMT with the approval of the EBMT Acute Leukemia Working Party. Adult patients aged more than 18 years with a diagnosis ofAML who received an allo-HSCT between 2013-2022, with an available genetic profile determined at diagnosis by next generation sequencing (NGS) were included. Results: We identified 836 allografted AML patients who had NGS performed at diagnosis. Most of these patients had de novo AML (88%), with a median age of 53 years (range: 18-78 years). Karyotype was favorable in 7%, intermediate in 69% and adverse in 24% of patients. At transplant, 74% of patients were in first remission (CR1) and 13% in CR2. The most frequent detectable mutations by frequency were DNMT3A (33%), FLT3 (29%), NPM1 (29%), TET2 (28%), NRAS (23%), RUNX1 (22%), WT1 (22%), BCOR (19%), ASXL1 (17%), IDH2 (17%), IDH1 (15%), SRSF2 (13%), STAG2 (12%), CEBPA (11%), TP53 (10%), KRAS (10%), and PTPN11 (10%) . By multiple correspondence analysis, two independent groups of co-occurring mutations were identified, the first group included DNMT3A, NPM1 and FLT3, the second group included ASXL1, SRSF2 and RUNX1. Outcome analysis was performed on the subset of 298 patients allografted in CR1 with available data for the aforementioned six genes ( DNMT3A, NPM1, FLT3, ASXL1, SRSF2 and RUNX1). Most of these patients had de novo AML (90%), with a median age of 53 years (range: 19-75 years). Patients received primarily reduced intensity conditioning (58%) and peripheral blood stem cells (93%) from matched sibling donors (35%), matched unrelated (28%), and haploidentical donors (21%). Seventy percent of these patients had intermediate-risk cytogenetics, while 27% were classified as adverse-risk. Median follow up calculated by the reverse Kaplan-Meier method was 2.5 years. Overall, the 2-year relapse incidence (RI), leukemia-free survival (LFS) and overall survival (OS) were 24%, 62% and 69%, respectively. When outcome analysis was performed according to the presence or absence of single mutations, none of the six mutations significantly affected RI or LFS. The 2-year OS was positively affected by the presence of NPM1 mutation (78% vs 66%; p=0.02) and FLT3 (79% vs 65%, p=0.01) but not significantly affected by the other 4 mutations. When mutations were investigated in groups, the 2-year RI, LFS and OS were 24%, 70% and 78%, respectively, for patients with NPM1 mutation regardless of other co-mutations, 35%, 56% and 69% for patients with FLT3-ITDand/or DNMT3A mutation, wild type NPM1, regardless of other co-mutations, 17%, 70% and 74% for patients with RUNX1 and/or ASXL1 and/or SRSF2 mutation without FLT3-ITD and with wild type NPM1 and wild type DNMT3A and 20%, 56% and 61% for patients with all six genes unmutated. Conclusion: NGS at diagnosis can be extremely useful in risk stratification of AML patients undergoing allo-HSCT, potentially allowing adequate post-transplant interventions. Notably, the 2-year LFS of 70% for patients harboring RUNX1 and/or ASXL1 and/or SRSF2 mutation indicates that allo-HSCT can overcome the adverse risk associated with these somatic mutations at diagnosis.

NGS Profile and the Mathematical Prediction Model for Venetoclax Combination Therapy in HM-Screen-Japan 02 Study

[Introduction] Azacitidine and venetoclax combination therapy (Aza/Ven) is a novel strategy for acute myeloid leukemia (AML). Although this regimen is widely used as a first line treatment not only for unfit/elderly patients but also for fit/young patients in the real-world situation, appropriate patient selection is an important issue. HM-SCREEN-Japan 02 (UMIN-CTR UMIN000046371) is a Japanese multicenter prospective observational study to evaluate the clinical utility of targeted sequencing. In this study, we performed the sub-analysis of newly diagnosed AML patients who received Aza/Ven as a 1 st line treatment to elucidate the genetic background of AML. Furthermore, we proposed a novel mathematical model to predict the response of Aza/Ven. [Methods] AmoyDx® Myeloid Blood Cancer Panel for acute myeloid leukemia was used for the targeted sequencing. We performed linear discriminant analysis to predict complete response patients by Aza/Ven based on clinical information before treatment. We utilized three clinical quantities for the analysis: Wilms Tumor-1 (WT1) mRNA expression level, the number of “favorable mutations”, and that of “unfavorable mutations”. Favorable and unfavorable mutations were defined as IDH1, IDH2, NPM1, and CEBPA mutations, and ASXL1, BCOR, EZH2, RUNX1, SF3B1, SRSF2, STAG2, U2AF1, ZRSR2 and TP53 mutations, respectively, based on the previous reports (NEJM 2019, Blood 2022). The data were standardized and utilized for the linear discriminant analysis. Statistical analyses were performed using R version 4.2.3 software (R Foundation for Statistical Computation, Vienna, Austria). [Results] Total 158 patients were enrolled in our study. Among 48 patients who received Aza/Ven as a 1 st line therapy, NGS analyses were performed prior to treatment in 38 patients. Their median age was 70.5 (39-92) years old. AML with myelodysplasia-related changes was the major subtype (71%) and 37 percent of the cases had high risk cytogenetic abnormalities at diagnosis. After 1 st line Aza/Ven treatment, complete remission (CR)/ CR with incomplete blood count recovery (CRi) was achieved in 63% of the cases while the remaining 37% were non-CR. There was a trend that patients with NPM1 and IDH1/2 mutations achieved CR/CRi, while patients with RUNX1 mutation were not tended to achieve CR (Figure 1). Next, we performed linear discriminant analysis of treatment response using three pretreatment clinical factors. Linear discriminant analysis found a linear combination of prognostic factors that best separates two classes in the group of patients. Thirty-seven patients were employed to determine the discriminant function D, given by D = 0.638 × x − 0.76 × y + 0.68 × z + 0.145. Here x, y, and z represented the WT1 quantity in peripheral blood, the number of “favorable mutations”, and that of “unfavorable mutations” after standardization, respectively. Using this model, 81.1% of cases were correctly classified, and so were 75.7% of cases with leave-one-out cross validation method (Table 1). [Discussions] As previously reported (NEJM 2019, Blood adv 2020), IDH1/2 and NPM1 mutations tended to be sensitive to Aza/Ven in our cohort. However, it would be hard to predict the response of Aza/Ven by a single gene mutation because multiple gene mutations were co-existed in most of the cases (Figure 1) and clinical factors including tumor markers might also affect the outcome. Our mathematical model, involving gene mutations and WT1, could efficiently predict the response of Aza/Ven, which may support the selection of 1 st line treatment. In conclusion, our study revealed the genetic landscape of real-world Aza/Ven therapy and provided a potential prognostic model.

Acute Myeloid Leukemia (AML) Patients with Myelodysplasia (MDS) Related-Gene Mutations in First Complete Remission (CR1) Found to Have Benefit from Allogeneic Hematopoietic Stem Cell Transplant (HCT)

Introduction: Acute myeloid leukemia (AML) with myelodysplasia-related gene mutations is a new disease entity introduced in the International Consensus Classification of Myeloid Neoplasms 2022 (ICC 2022). Myelodysplasia-related gene mutations include ASXL1, BCOR, EZH2, RUNX1, SF3B1, SRSF2, STAG2, U2AF1, or ZRSR2 . Allogeneic hematopoietic stem cell transplant (HCT) represents a curative option for subgroups of AML patients, but not for all. In a prior study (Song et al.) reported the survival benefit of allogeneic HCT in 59 patients with AML with secondary type mutations (STM) including SRSF2, SF3B1, U2AF1, ZRSR2, ASXL1, EZH2, BCOR, and STAG2. Allogeneic HCT could abrogate adverse prognosis in AML with STMs, and reduce its mortality risk by 58% (Song et al. BMT 2022). In the present study, we aim to evaluate the frequency of this new disease entity of AML with MDS-related mutations and evaluate the prognostic impact of allogeneic HCT in patients with MDS-related mutations achieving CR1. For comparison of the benefit from HCT, the mantel-Byar test was applied to take into account time-dependent covariate of HCT in CR1 to avoid immortal bias. Patients and Methods: We conducted a retrospective study that included 1,228 adult patients who were diagnosed with AML from January 1997 to January 2020and achieved CR1 in 5 centers (Toronto, Vancouver, and Montreal, Canada; Hwasun and Seoul, South Korea). Next-generation sequencing was performed as their standard clinical practice using targeted sequencing panel in each institution. As defined in ICC 2022, AML with myelodysplasia-related gene mutations was defined as the case of AML with ASXL1, BCOR, EZH2, RUNX1, SF3B1, SRSF2, STAG2, U2AF1, or ZRSR2 mutation(s). We considered allogeneic HCT in CR1 as a time-dependent covariate and used a Mantel-Byar test to avoid immortal bias. We identified 278 pts (22.6%) who had at least one MDS-related gene mutation at diagnosis. Relapse-free survival (RFS) at 2 years was selected for the primary endpoint, defined as the time from CR1 to relapse or death from any cause. EZR software version 1.41 was used throughout the study for statistical analysis. Results: The median follow-up duration among survivors after achieving CR1 was 16.5 months (mo) (Range: 1.3-217.9 mo). Between the HCT vs non-HCT group, there were no differences in sex, cytogenetic risk or other somatic mutation except NPM1 mutation which was more frequently detected in non-HCT group (p <0.001). As expected, younger pts were more frequently noted in HCT group, p=0.001). First, considering HCT as non-time dependent covariate, we have compared RFS and OS between HCT vs non-HCT groups. The 1 year RFS rate was superior in the HCT group (77.7%) to that in non-HCT group (49.9%, p<0.0001; Fig.1A). A similar trend was noted for the 1-year OS rate presenting higher OS rate in the HCT group (83.8%) than in the non-HCT group (72.7%, p=0.0003). Next, when HCT in CR1 was taken into account as a time-dependent (td) covariate, Mantel-Byar analysis showed a consistent finding of superior RFS in HCT group to non-HCT group: time dependent covariate of HCT in CR1 was found to be favorable (Hazard ratio [(HR) of 0.45, (95% C.I. [0.31-0.65]; p=0.00003)] as shown in Fig.1B which is a Simon-Makuch plot. In multivariate analysis (MVA) for RFS, time-dependent covariate of HCT in CR1 retained its statistical significance, thus concluding that HCT in CR1 is an independent prognostic factor for RFS (HR: 0.44, 95% CI [0.29-0.68], p =0.0002) together with other variables found to be adverse on RFS including monosomal karyotype (p=0.03), IDH1 mutation (p=0.01), and age > 60 years (p=0.002); while CEBPA (p=0.02) and NPM1 (p=0.049) mutations were found to be favorable on RFS in MVA. Conclusion: In our cohort of 1228 AML patients, we have identified 278 AML patients with myelodysplasia-related gene mutations (22.6%). We have confirmed that allogeneic HCT in CR1 is strongly recommended in a subgroup of AML with myelodysplasia-related gene mutations based on the favorable impact of HCT in CR1 on RFS from the present study. This result supports the urgent referral of this patient group for allogeneic HCT in CR1.

Molecular Classification of Chronic Myelomonocytic Leukemia: Results of the Analysis of an International Cohort of 2,471 Patients

Background. Chronic myelomonocytic leukemia (CMML) is a rare myeloid neoplasm that shares both dysplastic and proliferative features and includes patients with highly heterogeneous clinical manifestations and prognosis. Despite known co-mutation patterns that are suggesting of a CMML diagnosis such as TET2 and SRSF2 mutations, the current diagnosis and classification schemes rely solely on morphological criteria that fail to capture the genomic heterogeneity of the disease. Here we perform an unsupervised analysis using only genomic features to generate a novel classification schema of CMML patients with unique clinical features. Methods. A cohort of 2,471 CMML patients defined according to WHO 2016 criteria from European and US centers was analyzed. Bayesian network analysis and hierarchical Dirichlet processes were used to identify genomic associations and subgroups as a basis to define a molecular classification of CMML. Bayesian networks allow to infer the structure of conditional dependencies among mutations. Dirichlet processes were applied to define clusters capturing broad dependencies among all gene mutations and cytogenetic abnormalities. Multivariate logistic regression analysis was applied to compare clinical and hematological characteristics among different groups. ( JCO 2021 39:11, 1223-1233) Results. Baseline clinical and molecular characteristics are summarized in Table 1. We identified 11 clusters defined according to specific genomic features (Table 2). Two clusters were primarily defined by the presence of mutations in splicing genes SRSF2 and ZRSR2, frequently associated with TET2 mutations. Patients assigned to these clusters showed myelodysplastic features according to French American British (FAB) criteria, had a low rate of peripheral blood cytopenias, and low blast counts. Additionally, two clusters were characterized by the same mutations in splicing genes (i.e., SRSF2 or ZRSR2 with associated TET2), together with co-mutations in genes that correlate with a more aggressive phenotype ( RUNX1, ASXL1, EZH2). These groups showed overlapping myelodysplastic and myeloproliferative features by FAB, intermediate-risk per prognostic scores, and decreased survival as compared with the first 2 clusters. A distinct cluster was characterized by SF3B1 gene mutations (frequently associated with TET2 or DNMT3A). The SF3B1 cluster was marked by a dysplastic phenotype and more severe anemia (with a high rate of transfusion-dependence) with respect to the other genomic groups. Four clusters (27.8% of the overall population) were characterized by the presence of mutations in signal transduction and tyrosine kinase pathways genes ( NRAS/KRAS, CBL, JAK2 and SETBP1 often associated with ASXL1/TET2, respectively). Patients within these groups showed a mostly proliferative phenotype and intermediate survival. The presence of JAK2 mutations appeared to confer a better prognosis compared with other proliferative clusters. A minority of patients (4.6%) were assigned to two high-risk clusters, defined by TP53 mutations (often biallelic) with complex karyotype, and AML-like mutations ( NPM1, IDH1/2, FLT3), respectively. Patients in these clusters were predominantly dysplastic by FAB, had a high prevalence of severe cytopenias, higher blast counts, and a dismal outcome. Finally, we identified a cluster of patients defined by the absence of gene mutations and chromosomal abnormalities (4.5%). The majority of patients assigned to this cluster were characterized by a dysplastic phenotype, had low absolute monocyte counts, and favorable outcome. A subset of patients (18.9%) could not be assigned to a specified cluster in this preliminary analysis. An independent validation of this molecular classification is currently being conducted on a US prospective cohort (n=650). Conclusion. Our results provide proof of concept for a molecular classification of CMML based on the identification of homogeneous genomic signatures and associated clinical features. 15% of patients showed clear overlapping features with other myeloid neoplasms, thus providing the rational to refine the boundaries among different clinical entities. A molecular classification of CMML may provide a basis to define a next-generation prognostic tool and improve clinical decision-making.

CHIPping in: Clonal hematopoiesis clinics in community oncology.

499 Background: Clonal hematopoiesis of indeterminate prognosis (CHIP) is recently recognized as a pre-malignant condition and independent cardiovascular risk factor with doubled risk of coronary heart disease, cerebrovascular events, and worsened heart failure outcomes. Despite this recognition, multidisciplinary CHIP clinics are near-uniformly associated with tertiary centers where only a minority of oncology patients receive care. Tennessee Oncology is a large community oncology practice with over 200 providers at 35 sites of care throughout Tennessee and North Georgia. Here, we report the characteristics of two years of patients with common CHIP mutations as we prepare to launch our CHIP clinic. Methods: Patients with solid tumors who underwent either tissue- or blood-based comprehensive genomic profiling from May 2021 to May 2023 were reviewed. Patients with incidental discovery of DNMT3A, ASXL1, TET2, JAK2, IDH1/2, SRSF2, U2AF1, SF3B1, and ZRSR2 mutations are classified as having CHIP. High-risk mutation profile was defined as >1 mutation or a single mutation with variant allele frequency (VAF) of ≥10%. In patients sequenced >1x, only initial sequencing was used. The presence of cardiovascular disease or traditional risk factors was based entries into the patients’ “problem list” or use of medications commonly used to treat these conditions. Results: Over a two-year period, 3599 patients underwent sequencing and CHIP mutations were identified in 1069 (29.7%) patients. The median VAF was 1.58% and 585 patients had at least one mutation with a VAF of ≥2%. Median age at sequencing was 69.6 years. Distribution between males/females was similar. Lung cancer was the most common histology (n=328) followed by breast (n=122) and colon (n=121). DNMT3A mutations (n=829) were most frequently seen followed by TET2 (n=353), ASXL1 (n=335), SRSF2/U2AF1/SF3B1/ZRSR2 (n=147), JAK2 (n=138), and IDH1/2 (n=104). Nearly two-thirds of patients had a high-risk mutational profile with >1 mutation (n=479) or VAF ≥10% (n=185). Assessing traditional risk factors for cardiovascular and cerebrovascular disease, essential hypertension and type 2 diabetes were present in 56.4% (n=603) and 30.1% (n=322) of patients, respectively, and a minority of patients had established coronary disease (n=181) or heart failure (n=74). Twenty-three percent (245/1069) had no cardiovascular risk factors. Conclusions: In a large community practice, 29.7% of patients have common CHIP mutations – most of whom are considered high-risk based on current risk stratification criteria. Many patients also have traditional risk factors or established cardiac disease underscoring the strong association between CHIP and cardiovascular disease. A community-based, multi-disciplinary CHIP clinic would enhance these patients’ care and potentially lead to improved outcomes.

Clinical and prognostic profile of SRSF2 and related spliceosome mutations in patients with acute myeloid leukemia.

Mutations in splicing factor (SF) genes are frequently detected in myelodysplastic syndrome, but their clinical and prognostic relevance in acute myeloid leukemia (AML) have rarely been reported. A total of 368 newly diagnosed non-M3 AML patients were included in this study. Next generation sequencing including four SF genes was performed on the genomicDNA. The clinical features and survival were analyzed using statistical analysis. We found that 64 of 368 patients harbored SF mutations. The SF mutations were much more frequently found in older or male patients. SRSF2 mutations were shown obviously co-existed with IDH2 mutation. The level of measurable residual disease after first chemotherapy was higher in SF-mutated patients compared to that in SF-wild patients, while the complete remission rate was significantly decreased. And the overall survival of SF-mutated patients was shorter than that of SF-wild patients. Moreover, our multivariable analysis suggests that the index of male, Kit mutation or ZRSR2 mutation was the independent risk factor for overall survival. SRSF2mut was associated with older age, higher proportion of peripheral blasts or abnormal cell proportion by flow cytometry. SF mutation is a distinct subgroup of AML frequently associated with clinic-biological features and poor outcome. SRSF2mut could be potential targets for novel treatment in AML.

High BM plasma S100A8/A9 is associated with a perturbed microenvironmentand poor prognosis in myelodysplastic syndromes.

S100A8/A9 is a proinflammatory protein and plays an essential role in the pathogenesis of myelodysplastic syndromes (MDS) via the S100A8/A9-Toll-like receptors axis. While S100A8/A9 levels have been used as biomarkers in many inflammatory diseases, their clinical relevance has not been conclusively resolved in MDS. To address this, we used an enzyme-linked immunosorbent assay to quantify S100A8/A9 heterodimers in bone marrow (BM) plasma from 215 MDS patients and compared S100A8/A9 levels across patients with various disease risks and genotypes. S100A8/A9 levels correlated with ASXL1 variant allele frequencies significantly. Moreover, mutant ASXL1 with concurrent RUNX1, STAG2, ZRSR2, or EZH2 mutations was associated with higher S100A8/A9 levels. We further showed that higher S100A8/A9 independently predicted inferior leukemia-free survival and overall survival in MDS patients, irrespective of age, Revised International Prognostic Scoring System subgroups, and known detrimental mutations. Lastly, through deep-sequenced transcriptomic analysis, we demonstrated that higher S100A8/A9 in the BM intimated a perturbed microenvironment with enhanced myeloid-derived suppressor cell-mediated tumor immune escape signal, altered metabolism, and impairment in the functions and quantities of CD8+ T cells and NK cells. S100A8/A9 in the BM microenvironment may be a potential biomarker in the prognostication of MDS and target for novel therapy.

Significance of hypergammaglobulinemia in patients with chronic myelomonocytic leukemia.

Chronic inflammation is often indicated by arelative increase in the gamma globulin fraction in the serum electrophoresis. In aretrospective study, we analyzed the prevalence of relative hypergammaglobulinemia in 60patients with chronic myelomonocytic leukemia (CMML), its potential prognostic impact, and potential correlations with laboratory and molecular features. Relative hypergammaglobulinemia (> 20%) was found in 25/60 (42%) patients. The median survival of patients with relative hypergammaglobulinemia was significantly shorter than in patients without hypergammaglobulinemia (10vs. 24months, p = 0.018). There was no difference between the groups regarding leukocyte count, hemoglobin value, and platelet count, but ahigher prevalence of NRAS mutations and alower prevalence of ZRSR2 mutations in patients with hypergammaglobulinemia. Our results show that hypergammaglobulinemia is present in aproportion of CMML patients and that this abnormality is associated with poor overall survival. The role of chronic inflammation in the pathophysiology of CMML needs to be further investigated.

Genetic Landscape of BPDCN Arising in CML Remission

Background BPDCN (blastic plasmacytoid dendritic cell neoplasm) is a rare and highly aggressive hematologic malignancy which often affects skin lesion. BPDCN initially responds to traditional chemotherapy, but has a high relapse rate and a poor prognosis even after autologous or allogeneic stem cell transplantation (SCT). Almost all patients have CD123 positive tumor, and CD123 targeting therapies are being developed. BPDCN mainly develops de novo, however, up to 20% of BPDCN patients have prior history of other hematologic malignancies (CMML, AML, MDS). Some groups propose to classify BPDCN with PCHM (preexisting or concurrent hematologic malignancies) into a unique subtype based on the clinical course (Blood (2019) 134 (Supp.1): 2723). On the other hand, there are attempts to classify BPDCN according to molecular profile, and they defined two subclasses based on somatic mutations (Blood Cancer Journal (2022) 12:101). Thus substantial efforts are being made to classify BPDCN from various aspects, the classification is still under development due to insufficient number of cases. Herein we experienced a rare case of BPDCN arising in the course of CML as a history of PCHM. Unexpectedly, there have been no reports of BPDCN with preexisting CML, therefore, we report the clinical course and genetic background in our case. Case: 70 year old male Clinical course of CML: He was referred to our hospital at age 60 with elevated white blood cell count (93,550/ul, blast 1.0%). Diagnosis of CML (chronic phase) was made; Sokal score was 0.31 (low risk). With initial therapy of dasatinib 100 mg, his disease status achieved complete molecular response (CMR) at 24 months of treatment; achieved CMR (MR 4.5) at 43 months. Due to side effects (pleural effusion and cytopenia), dasatinib was discontinued at month 74 of treatment, and however, CMR has been maintained. Clinical course of BPDCN: At 48 months after completion of dasatinib treatment, multiple bruise-like skin lesions appeared on the head and abdomen. Skin biopsy revealed diffuse proliferation of blastic cells. Immunohistochemistry and flow cytometry were positive for CD4, CD56, and CD123, and a diagnosis of BPDCN was made. Bone marrow involvement (13%) was also observed. HyperCVAD/MA (cyclophosphamide, vincristine, doxorubicin, dexamethasone, methotrexate and arabinocytocine) was selected as induction therapy. The skin and bone marrow lesions rapidly improved and the patient achieved hematological remission, but a few CD123-positive tumor cells remained in the bone marrow. Considering autologous SCT, peripheral blood stem cell collection was performed. Unfortunately, the graft was contaminated with CD123-positive cells, and it was determined that autologous SCT was not expected. Allogeneic SCT was not planned due to age and regimen related toxicity. We are currently preparing to conduct a clinical trial of CD123-targeting agent. Molecular Analysis WES of peripheral blood and bone marrow samples was performed. At the hematological remission after 2 cycles of HyperCVAD/MA, high VAF mutations in the splicing factor ZRSR2 gene (p.Y292X (84.6-85.2% VAF)) as well as the histone modifiers ASXL1 (p.L743fs (40.6-43.1% VAF)) and TET2 (c.3955-2A>G (36.2-38.3% VAF), p.T1959fs (42.1-47.0% VAF)) were observed. ZRSR2 nonsense mutation site in our case was located 3 residues upstream of the previously reported site, which has not been reported in previous BPDCN cases (Cancer Discovery (2022) 12: 522-541). Although the tumor cell rate in each sample was less than 10%, the VAF of ZRSR2 mutation was high (84.6-85.2%), indicating that clonal hematopoiesis with ZRSR2 mutations underlies the development of BPDCN. Conclusion This is the first report of BPDCN with a history of CML as a preceding hematologic malignancy. Based on WES data at the remission of BPDCN, we confirmed that the patient had clonal hematopoiesis with not only ASXL1 and TET2 mutations, but also ZRSR2 mutation, a driver mutation characteristic of BPDCN. Despite the fact that clonal hematopoiesis with ASXL1 and TET2 mutations is occasionally observed after CML treatment with TKIs (Blood (2017) 129: 38-47), there were no case reports of BPDCN in patients with preexisting CML. These facts suggest that the presence of mechanism is essential for the development of BPDCN other than driver mutation in ZRSR2. Further investigation of BPDCN with PCHM would provide useful information on the pathogenesis of BPDCN. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Impact of Spliceosome Mutations on the Prognosis of Myelodysplastic Syndrome (MDS)

Introduction: More than half of patients with myelodysplastic syndrome (MDS) have spliceosome mutations (SM) including ZRSR2, U2AF1, SF3B1 and SRSF2. Splicing is fundamental for proper mRNA processing. Mechanistic descriptions of the after-effects of SM remain elusive as improperly formed mRNA quickly decays or changes are subtle and may lack observable effects. These mutations have been implicated in multiple biological alterations including myeloid proliferation through aberrant NF-kB signaling. SRSF2P95* has been consistently shown to provide the highest fitness advantage in the bone marrow environment. This study reports the characteristics, treatment outcomes, leukemia free and overall survival of MDS with spliceosome mutations. Patients and Methods: A retrospective review of patients diagnosed with MDS older than 18 for whom genomic data was available were included at a single institution. Patient characteristics and bone marrow data, including cytogenetic and next generation sequencing (NGS) information were assessed. Genomic DNA was extracted from whole bone marrow aspirate samples and subject to 81-gene target PCR-based sequencing using a NGS platform. The IWG 2006 response assessment criteria were used. Overall and leukemia-free survival were calculated, the latter as a composite of acute myeloid leukemia diagnosis or death from any cause, using the log-rank test for group comparison. Results: First, we compared patients with SM vs no SM. We identified 427 patients with SM and 658 patients with no SM from 2017 to 2022 (Table 1). Among patients with SM, 71% were male, median age was 71. SM patients had higher incidence of IPSS Low (33.3% vs 10.3%) and IPSS Int- 1 (35.6% vs 32.2%), and a higher incidence of diploid karyotype (45% vs 21%), compared to patients with no SM. There was no difference in treatment regimens, and 66.9% of patients with SM received hypomethylating agents (HMA) alone or in combination vs 60.3% in the group without SM. MDS with SM had a lower CR/CRi rate (27% vs 36%); however, they had higher hematologic improvement (HI) (23% vs 14%) and lower chance of disease progression or death at the time of response assessment (39% vs 31% (p = 0.01)). Leukemia-free survival was longer in patients with SM vs no SM (median 4.1 years vs 1.9 years (p<0.0001), this was independent of SF3B1 mutations. Median OS was 4.5 years vs 1.9 years in patients with SM and no SM, respectively (p <0.0001). We then compared outcomes between patients with specific SM mutations. These included SF3B1 (34%), SRSF2 (26%), U2AF1 (25%), and ZRSR2 (14%). Thirty-six percent were female. Median age was 71 (range 28-93). Median percentage of blasts was 3 (range 0-19). Most frequent diagnoses were MDS-EB (35%), MDS-RS (25%) and MDS-MLD (23%). IPSS was Low, Intermediate 1, Intermediate 2 and High in 33.3%, 35.6%, 17.1% and 4.2%, respectively. Fifty-seven percent were in the favorable cytogenetic risk group, 44% with diploid karyotype. Patients with a SM mutation did not share any other SM mutation (Table 2). There were no differences in therapy selected or response rate among SM mutations. Median LFS was not reached (NR), 5.7 years, 3.4 years, and 2.7 years for patients with SF3B1, ZRSR2, U2AF1, and SRSF2 mutations, respectively. Median OS was NR, 5.7 years, 3.6 years, and 2.7 years (p = 0.005) for the same groups, respectively. Conclusions: In our study, patients with SM had a lower rate of CR/CRi with HMA-based therapy, however, leukemia free and overall survival were markedly different for each mutated gene. SM mutations were significantly more prevalent in males. Compared to MDS with diploid cytogenetics, ZRSR2 and SF3B1 mutations have a similar median LFS and OS, but SRSF2 and U2AF1 mutations carry a significantly worse median LFS and OS. While it is convenient to group these mutations together, prognostication should be individualized to specific mutations and co-mutations. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Chronic Myelomonocytic Leukemia Diagnosis By Flow Cytometry: An Italian Center Experience

Chronic myelomonocytic leukemia (CMML) is a myeloid neoplasm characterized by dysplasia, abnormal production of monocytes, and an increased risk of leukemic evolution. According to WHO, CMML patients show a persistent (≥3 months) absolute PB monocytosis (≥1×109/L) and relative monocytosis (≥10% of PB leukocytes), with the exclusion of Chronic Myeloid Leukemia (CML), Myeloproliferative Neoplasms, and a blast cell count <20% in PB and/or BM. In addition, morphological and/or histopathological evidence for diagnostic dysplasia ≥1 of the three major BM cell lineages must be present. If dysplasia is absent or not diagnostic (<10%), the presence of cytogenetic or molecular alterations or flow cytometry (FC) abnormalities may be utilized as co-criteria for the diagnosis of CMML. FC is helpful in confirming the monocyte and blast cell counts. In addition, FC is useful for confirming the presence of distinct monocyte populations. Based on the expression of CD14 and CD16, monocytes are classified into classical (MO1) (CD14+/CD16−), intermediate (MO2) (CD14+/CD16+) and non-classical (MO3) (CD14-/CD16+). FC analysis of PB monocytes was proposed as a quick and efficient tool for distinguishing CMML from reactive monocytosis by highlighting an increase in the MO1 fraction above 94% and a decrease in the percentage of MO3. Using FC, we evaluated 25 patients with a confirmed diagnosis of CMML in BM and PB samples, as well as 11 patients with other malignancies (MPN-monocytosis), and 28 patients with reactive monocytosis only in PB samples. Among these patients, 21/25 (84%) of CMML patients displayed MO1 ≥94%, while in patients with reactive monocytosis, MO1≥94% was observed in 11/28 (39%) and 2/11 (18%) in patients with MPN-monocytosis. Then we analyzed the MO3 fraction, which was <1.13% in 18/25 (72%) CMML patients, only one patient with MO1 lower than 94% resulted in an M3 fraction >1.13%. The evaluation of SLAN positivity in this fraction MO3 was always lower than 1.7%. The patient with MO1<94% and MO3 > 1.13% had an active ureteral carcinoma and, at NGS evaluation, had TET2, JAK2, and ZRSR2 mutations. In BM and PB samples from MPN patients, the MO3 fraction was in 2/11 <1.13%, the same patients with MO1> 94%, the diagnosis was a CML in one patient and a PMF triple negative in the other patient. PB samples from reactive monocytosis MO3 fraction were in 11/28 (39%) <1.13%, the same patients with MO1> 94%. The evaluation of SLAN positivity in this fraction MO3 in MPN and reactive monocytosis was always superior at 1.7% (range 4.9-60%). BM samples from CMML and MPN patients reflected the percentage of MO1 and MO3 of PB. Commonly PB and BM monocytes in CMML display aberrant expression of CD56. Furthermore, it was detectable a fraction of non-maturing neutrophils (CD66b+/CD11b-) in nearly half of CMML patients. In conclusion, our real-life experience of routinely FC study on PB and BM CMML samples is similar to the studies described in the literature. It confirms the comparable percentages of monocyte subpopulations in both samples, suggesting that PB samples can be used for diagnostic FC in these patients.

Effect of Mutation Allele Frequency on the Risk Stratification of Myelodysplastic Syndrome Patients

Introduction Myelodysplastic syndrome (MDS) is a diverse group of clonal myeloid neoplasms. The accumulation of mutations in stem cell compartments is involved in MDS pathogenesis. Mounting evidences demonstrate that the addition of mutation data improves the prognostic stratification in MDS patients. In addition to mutational profiles, the variant allele frequency (VAF) of individual mutations also influence the prognosis in MDS patients. Materials and Methods A total of 698 primary MDS patients were recruited. The diagnoses were based on the 2016 World Health Organization classification. Patients with antecedent chemotherapy/radiotherapy or hematologic malignancies were excluded. TruSight myeloid sequencing panel (Illumina, San Diego, CS, USA) and the HiSeq platform (Illumina, San Diego, CA, USA) were adopted to analyze the gene alterations and mutant allele burdens. Because of the sequencing sensitivity issue, we verified CEBPA mutations and FLT3-ITD via Sanger sequencing. Results Exploration of the correlation between prognosis and VAF of individual genes showed that compared with wild-type genes, high VAF of mutations in 9 genes, including DNMT3A (cutoff value 40%, hazard ratio HR 1.67, p<0.001), TET2 (45%, HR 1.60, p<0.001), ASXL1 (20%, HR 1.48, p<0.001), E.ZH2 (40%, HR 1.45, p=0.037), SETBP1 (15%, HR 1.39, p=0.025), BCOR (80%, HR 1.57, p=0.045), SRSF2 (50%, HR 1.89, p=0.002), ZRSR2 (60%, HR 1.70, p<0.001) and TP53 (25%, HR 2.79, p<0.001) were significantly associated with shorter leukemia-free survival (LFS). With the exception of EZH2, SETBP1, and BCOR mutations, high VAF of all other six mutations were also associated with shorter overall survival (OS). In addition, the patients with SRSF2 and TP53 mutations, even at lower VAF, had poorer prognosis for both LFS and OS compared with those with wild-type genes. For other 7 above-mentioned mutations, only higher VAF conferred poorer outcomes; the patients with lower mutation VAF had outcomes similar to the patients with wild-type genes. In multivariable analysis (Table 1), female sex and receiving allogenic hematopoietic stem cell transplantation (HSCT) were independent favorable factors for both LFS and OS, while older age and higher-risk IPSS-R predicted shorter LFS and OS. Mutant IDH2 and CBL predicted both shorter LFS and OS, while U2AF1 mutation and DNMT3A and ZRSR2 mutations with high VAF were associated poorer OS. The mutation status and VAF levels of TP53 mutations could distinguish patients into three hierarchical groups with different prognoses. The presence of poor-risk mutations as identified in the multivariable Cox analysis could re-stratify the IPSS-R risk groups. Patients with these unfavorable mutations in each IPSS-R risk subgroup had survivals worse than other patients of the same risk but similar to or even worse than those in the next higher-risk subgroup (Figure 1). Considering OS, the incorporation of the molecular data in the IPSS-R could reclassify 8.9% (18/202) of IPSS-R very low/low-risk patients to intermediate-risk subgroup, 17.9% (33/184) of IPSS-R intermediate to high-risk subgroup, and 34.4% (54/157) of IPSS-R high to very high-risk subgroup. Patients harboring U2AF1 mutation had poorer LFS and OS if they were not treated with hypomethylating agents (HMA), but had similar LFS (wild-type vs. mutant-type, 14.3 vs. 15.5 months, p=0.537) and OS (wild-type vs. mutant-type, 22.2 vs. 40.1 months, p=0.450) compared with those with wild-type U2AF1 if they received HMA treatment. Moreover, patients with low TP53 mutant VAF got benefit from HMA treatment considering LFS. Conclusion We provide evidences that VAF is critical for risk stratification in MDS patients and should be considered in novel scoring systems. Our data fostered our understanding of the mutation burden of the diseases and provided future patient-tailored therapeutic avenues. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

The Adverse Effect of Myelodysplasia-Related Mutations in De Novo Acute Myeloid Leukemia Is Associated with Higher Variant Allelic Frequency (VAF): A Proposal for a Numeric Cutoff for Variant Allelic Frequency

Mutations in myelodysplasia-related genes ASXL1, BCOR, EHZH2, RUNX1, SF3B1, SRSF2, STAG2, U2AF1 and ZRSR2 (MRmut) are class-defining alterations in acute myeloid leukemia (AML) in the latest World Health Organization (WHO, with the exception of RUNX1) and International Consensus Classification (ICC) schemes and indicate adverse-risk per European Leukemia Net (ELN) 2022 guidelines, unless occurring in favorable-risk AML. The lower limit of detection (LOD) for most clinical-grade next generation sequencing (NGS) is ~1-2% variant allelic frequency (VAF); however, data on the prognostic significance of MRmut relative to VAF is lacking. No guidelines that provide a numeric cutoff for VAF are available for utilizing these mutations to classify AML. Our aim was to define a clinically meaningful VAF cutoff for MR mutations in de novo AML. We included patients (pts) with de novo, untreated AML with MRmut treated at our institution between 2017 to 2022. We excluded pts with acute promyelocytic leukemia, core binding factor AML, and other ELN adverse-risk categories (adverse karyotype and/or TP53 mutation). NGS at baseline was performed using a panel of 81 genes recurrently mutated in myeloid neoplasms (LOD ~1-2%). We performed a best fit classifier on individual MRmut to determine optimal VAF cutoffs using event-free survival (EFS) and overall survival (OS) as endpoints. VAF for MRmut involving X-linked genes was adjusted for men. Pts (n=145) included 92 (63%) men and 53 (37%) women with a median age of 68 years (range, 58-75). 85 (59%) pts had diploid karyotype AML, 51 (35%) had other intermediate-risk non-diploid karyotype AML, and 9(6%) had insufficient metaphases for analysis. 34 (23%) pts had ELN favorable-risk and 111(77%) had ENL adverse-risk AML. Pts were treated with low-intensity+venetoclax (VEN) (72/50%), low-intensity (26/18%), high-intensity (22/15%), and high-intensity+VEN (12/17%) regimens. Median follow-up was 26.9 months (range, 13.9 - 40.8). 72 (49%) pts had 1 MRmut; the remaining had 2-4 concurrent MRmut. MRmut had the following frequencies and VAFs: ASXL1 (28%; median VAF: 26%, [range 2-48%]); BCOR (18%; median VAF 37% [3-100%]); EHZH2 (9%; median VAF 7% [1-55%]), RUNX1 (32%; median VAF 47% [1-96%]), SF3B1 (9%; median VAF: 38% [1-55%]), SRSF2 (46%; median VAF: 37% [1-76%]), STAG2 (20%; median VAF: 44% [15-98%]), U2AF1 (12%; median VAF: 33% [2-43%]) and ZRSR2 (2%; median VAF: 94% [93-95%]). 34 (23%) pts had ELN favorable-risk AML including 28 (23%) with mutated NPM1 without FLT3-ITD and 6 (4%) with CEBPA bZIP mutations, respectively; in 12/34 pts NPM1 or CEBPA bZIP mutations were subclonal compared with clonal MR mutation(s). A summary of baseline genetic and treatment data is provided in Fig 1A. The overall composite remission rate (CR+CRi) was 88% (64% and 24%, respectively) Median OS was 30.3 months and estimated 12/24 month OS were 77%/60%. The median EFS was 24.6 months and estimated 12/24 month EFS were 65%/51%. Pts with ELN favorable-risk AML with MRmut had longer OS and EFS compared with the adverse-risk group (median OS 34.9 vs 27.5 months, median EFS 34.9 vs 22.9 months) but the difference was not significant (p=0.60 and 0.30, respectively). The VAF cutoff for MRmut associated with EFS and OS, respectively, was: ASXL1: 21%/21%, BCOR 25%/25% , EHZH2 15%/15%, RUNX1 25%/27%, SF3B1 31%/31%, SRSF2 32%/35%, STAG2 40%/21%, U2AF1 44%/44% and ZRSR2 47/47%.There was no significant difference in OS or EFS between pts with 1 MRmut vs those involving ≥2 MR genes. Pts treated with high-intensity, high intensity+ VEN and low intensity+VEN regimens had longer OS (Fig 1B) and EFS compared with pts treated with low intensity regimens without VEN (OS: not reached, 31.7 months, 31.4 months vs 8.9 months, respectively, p<0.001; EFS: not reached, 31.7 months, 29.6 months vs 3.7 months, respectively, p<0.001). Our data suggest that the poor prognostic effect of MRmut in de novo AML is associated with higher VAF and not a binary presence or absence of MRmut. The minimum VAFs associated with worse outcome for each MRmut ranged from 15-47%. Additional analysis to create predictive models is in progress to determine the optimal VAF cutoff when using MRmut to assign AML to the WHO/ICC MR categories and to ELN adverse-risk group. Importantly, our results suggest that pts with MRmut and non-adverse karyotype have significantly better outcomes when treated with high-intensity and/or venetoclax-based treatment regimens. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal