5q Deletion Research Articles

Overall Survival Outcomes in Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma Patients with High-Risk Molecular-Cytogenetic Features Treated with 1L Ibrutinib: A Comparative Effectiveness Study Using the Flatiron Health Data

Introduction: In individuals diagnosed with chronic lymphocytic leukemia (CLL)/small lymphocytic lymphoma (SLL), high-risk features are associated with an unfavorable outcome. Evidence is lacking in comparing the overall survival (OS) of a high-risk group (HRG) vs. a non-high-risk group (NHRG). This large retrospective cohort study, using data from the Flatiron Health CLL Core Registry electronic medical records (EMR), included 1,242 CLL/SLL patients treated with first-line (1L) single-agent ibrutinib. This study compared the OS of patients from the HRG (presence of deletion 17p [del(17p)], or deletion 11q [del(11q)], or unmutated immunoglobulin heavy-chain variable region gene [IGHV]) with that of patients from the NHRG (del[17p] absence, del[11q] absence, and mutated IGHV). This study also included a sensitivity analysis with an alternative high-risk definition and a subgroup analysis for Medicare patients. Methods: The Flatiron Health EMR data includes patients with confirmed CLL/SLL diagnosis using both diagnosis code and chart abstraction. Patients aged ≥18 years were included if they initiated single-agent ibrutinib 28 days before index date (1L initiation+28 days) between 04 March 2016 and 31 January 2023. Patients were excluded if there was missing or incomplete information on their first systemic therapy or on the genetic variables of interest, or if they had other malignancies (≥2 diagnosis codes ≥30 days apart) within the prior 12 months before 1L initiation. OS (the time interval between the index date and all-cause mortality date) was assessed using Kaplan-Meier survival estimators, censoring patients without mortality information at the last activity date. COX proportional hazard model was used for pairwise comparison analysis, treating NHRG as the reference group. Potential confounders (including baseline covariates such as gender, age, race, stage, ECOG PS, comorbidities, practice type, disease type, and other biomarkers) were adjusted using inverse probability of treatment weighting (IPTW). The Medicare subgroup included patients with Medicare as the single payer or one of the multiple payers at ibrutinib initiation, which serves as a proxy for the elderly group (aged ≥65 years). A sensitivity analysis was conducted by defining HRG as those with del(17p) presence and/or unmutated IGHV and NHRG as those with del(17p) absence and mutated IGHV. Flatiron Health mortality data were obtained from multiple sources including EMR, the U.S. Social Security Death Index, obituaries, funeral homes, which had been benchmarked against the U.S. National Death Index, demonstrating 87-92% sensitivity, 94%-99% specificity, and 96%-98% positive predictive value. Results: Of the 1,242 patients included, 969 were from HRG and 273 from NHRG, with mean age of 70.0 vs 70.8 years. For HRG and NHRG, 36.2% vs 43.6% were female, 72.0% vs 74.7% were White, 37.5% vs 39.6% were Medicare patients (due to data limitation, 18.5% and 19.8% patients had missing data for payer type, respectively), 91.6% vs 93.8% were from the community setting, 48.8% vs 53.1% were between Rai stage 0 and II, 74% vs 70.1% had ECOG ≤ 2, 47% vs 63% had deletion 13q presence, 23.5% vs 24.2% had trisomy 12 presence, respectively. Mean (Standard Deviation) time from diagnosis to 1L initiation was 35.0 (48.0) vs 64.4 (73.2) months for HRG and NHRG. Within the HRG, 32.9%, 36.7%, and 58.7% of the patients had the presence of del(17p), del(11q), and unmutated IGHV, respectively. After applying IPTW with trimming, OS hazard ratio (HR; 95% confidence interval [CI]) was 1.09 (0.79, 1.51) and median OS was not reached for either group (Figure 1). Median follow up (interquartile range [IQR]) was 32 (17, 48) months and 31 (19, 44) months, for HRG and NHRG, respectively. The HRG sensitivity analysis showed similar results to the main analysis, with OS HR (95% CI) being 1.19 (0.86, 1.64) and median OS not reached for either group. Within the Medicare subgroup, OS HR (95% CI) was 0.98 (0.63, 1.53), and median OS was not reached for either group (Figure 2). Conclusions: In this real-world study using a large community healthcare dataset, CLL/SLL patients with high-risk molecular-cytogenetic features (del[17p], or del[11q], or unmutated IGHV) treated with 1L ibrutinib had similar OS compared to patients without high-risk features. Importantly, similar findings were observed in the high-risk sensitivity analysis and the Medicare subgroup.

Mosaic Chromosomal Alterations and Monoclonal B-Cell Lymphocytosis: Relationship and Risk of Hematologic Malignancies

Background: Monoclonal B-cell lymphocytosis (MBL) is a precursor condition to chronic lymphocytic leukemia (CLL) characterized by the presence of circulating monoclonal B-cell populations in the peripheral blood of otherwise healthy individuals. MBL increases risk of several adverse clinical outcomes, including development of hematological malignancies. Mosaic chromosomal alterations (mCAs) are a form of clonal hematopoiesis which affect large segments of DNA and include gains, losses, and copy number neutral loss of heterozygosity events. mCAs can be detected from SNP-array genotyping. Prior work has suggested mCAs as a potent risk factor for hematological malignancies. However, the nature of the relationship between mCAs and MBL is unknown. We sought to determine 1) the association between mCAs and MBL and 2) their combined effect on risk of hematological malignancies, in a large, prospectively collected, and well-annotated cohort of individuals with known MBL, mCA, and clinical outcomes. Methods: We examined the prevalence of mCA in a cohort of individuals from the Mayo Clinic Biobank who were screened for MBL using a sensitive eight-color flow cytometry assay. We classified MBL by the size of the clone relative to total B-cells, with high count (HC) defined as those individuals who had a percent clonal B-cell count ≥85% out of total B-cell count and low-count (LC) otherwise. Autosomal mCAs were detected from whole blood DNA collected at the time of MBL screening using a SNP-array-based assay. The MoChA pipeline was used to identify mCA events. Logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CIs). To examine incident hematological cancers, we identified and validated all hematological cancers through medical record abstraction using the International Statistical Classification of Diseases codes. Cox regression was used to calculate hazard ratios (HR) and 95% CIs, stratified by MBL status or autosomal mCA status. All models were adjusted for age and sex. Results: We evaluated the prevalence of autosomal mCA in 3,764 individuals (792 individuals with MBL of whom 64 had HC-MBL and 2,972 without MBL). The prevalence of autosomal mCA was 7.7% ( n=288) with a median mCA cell fraction of 0.09 (range 0.01-1). Among those with and without MBL overall, the prevalence of mCA was 15.5% ( n=123) and 5.6% ( n=165), respectively (Figure 1). Compared to those without an autosomal mCA, individuals with an autosomal mCA were 2.4-fold more likely to have MBL (95% CI 1.9-3.2; P =2.0x10 -11; Figure 1). CLL-associated mCA (i.e., those commonly altered in CLL including trisomy 12 and deletion of 6q, 11q, 13q, and 17p) were present in 42 individuals, of whom 38 (90.5%) had MBL overall and 30 (71.4%) individuals had HC-MBL. Compared to those without a CLL-associated mCA, individuals with a CLL-associated mCA were 539.39-fold more likely to have HC-MBL (95% CI 190.3-1975.9; P <2.0x10 -16) and 6.7-fold more likely to have LC-MBL (95% CI 2.0-26.5; P =0.0031; Figure 1). Next, we evaluated the relationship between MBL and mCA with risk of developing a hematologic malignancy in 3,009 individuals with follow-up data (median 10 years). Forty-one individuals developed an incident hematological malignancy (68.3% lymphoid). When we evaluated the effect of autosomal mCA stratified by MBL status we observed elevated but non-significant risk of hematological malignancies (Figure 2). When we evaluated the effect of MBL stratified by autosomal mCA status we observed elevated and significant increased risk of developing a hematological malignancy (Figure 2). Conclusions: We found that the presence of an autosomal mCA is highly associated with having MBL. In particular, >90% of CLL-associated mCA carriers had MBL with ~7- and ~540-fold increased association for LC- and HC-MBL, respectively. These results suggest that almost all individuals in large biobanks with CLL-associated mCAs have undiagnosed MBL. However, not all individuals with MBL have an mCA. When evaluating risk of hematological malignancies, we found autosomal mCAs had >2-fold elevated but non-significant effects when stratified by MBL status while MBL remained a significant risk factor regardless of autosomal mCA status. Collectively these results support that MBL remains an important risk factor and suggests that mCAs hold potential to identify a subgroup of individuals at greater risk of developing a hematological malignancy.

Impact of Typical and Atypical Complex Karyotype Subgroups on Outcome of AML Patients Undergoing Allogeneic Stem Cell Transplantation

Introduction Acute myeloid leukemia (AML) with a complex karyotype (CKT) confers an adverse prognosis, even within the subgroup of patients (pts) with adverse risk according to European LeukemiaNet 2022 (ELN22) risk stratification. Mrózek et al. further characterized CKT pts according to distinct mechanisms of leukemogenesis into balanced (presence of ≥1 balanced rearrangement), and unbalanced CKT (CKT ub, exclusively unbalanced cytogenetic abnormalities). Considering the high incidence of deletions (del) of 5q, 7q, and 17p in CKT, CKT ub were further divided in typical CKT ub (with latter abnormalities present), and atypical CKT ub (with exclusively other abnormalities). In the context of consolidating chemotherapy, typical CKT ub was associated with shorter event-free survival (EFS) and overall survival (OS) compared to atypical CKT ub. However, we lack data in the context of allogeneic hematopoietic stem cell transplantation (HSCT) which remains the preferred treatment in eligible pts. Here we aimed to investigate this classification in CKT AML pts consolidated by HSCT. Methods We analyzed 263 pts with AML who were classified as ELN22 adverse risk and underwent an allogeneic HSCT. 105 had a CKT, while 158 fulfilled other ELN22 adverse risk criteria. Of the pts harboring a CKT, median age at HSCT was 61 (range 20 - 76) years. Remission status at HSCT was first complete remission with or without count recovery (CR/CRi, 62%) or refractory AML (38%). Conditioning intensity according to EBMT criteria were myeloablative (19%), reduced intensity (31%) or non-myeloablative (50%). Donors were matched related (16%), haploidentical (2%) or matched (65%) or mismatch unrelated (17%).Cytogenetic analyses at diagnosis were performed using standard techniques of banding and in situ hybridization. Pretreatment genomic DNA was screened for genes recurrently mutated in myeloid malignancies using next generation sequencing. Median follow-up alive was 1.3 years. Results Pts with a CKT had a significantly shorter EFS ( P<.01) and OS ( P<.01) than other ELN22 adverse risk pts. Of all pts harboring a CKT, 17% had a balanced CKT, and 83% a CKT ub. Among CKT ub, 85% were classified as typical (67% with del(5q), 49% with del(7q), 26% with del(17p), Figure 1). Comparing typical and atypical CKT ub, pts with typical CKT ub more often had a monosomal karyotype ( P<.01), had more cytogenetic abnormalities (in typical CKT ub median 8 [range 3-39] vs atypical CKT ub median 6 [range 3-9], P=.04), more often TP53 mutations ( P=.02), less often RUNX1 mutations ( P=.03) and a lower LDH at diagnosis ( P=.03). They also had a higher expression of the leukemic stem cell markers CD34+/CD38- ( P=.01) and GPR56 ( P<.01). However, after allogeneic HSCT, EFS ( P=.50) and OS ( P=.50) did not differ between pts with typical and atypical CKT ub (Figure 2). Next, we looked for other adverse prognostic factors within CKT pts receiving HSCT, which in univariate analyses were the presence of a del(5q) (EFS P<.01 and OS P=.03), a del(17p) (EFS P=.10 and OS P=.02), the presence of ≥5 vs <5 cytogenetic aberrations (EFS P=.03 and OS P=.06), a concomitant TP53 mutation (EFS P=.01 and OS P=.01), and a higher age at HSCT (≥60 years, EFS P=.04 and OS P=.08). In contrast, neither the presence of a del(7q) nor a monosomal karyotype impacted EFS or OS within pts with a CKT. In multivariate analyses for CKT pts, the presence of ≥ 5 cytogenetic aberrations (Hazard Ratio. [HR] 1.7, 95% Confidence Interval [CI] 1.0-3.0, P=.05), higher age at HSCT (HR 1.6, 95% Ci 1.1-2.5, P=.02), and no CR/CRi at HSCT (HR 1.7, 95% CI 1.1-2.7, P=.01) were adverse factors for EFS, while the presence of a del(17p) (HR 2.0, 95% CI 1.2-3.4, P=.01), higher age at HSCT (HR 1.8, 95% CI 1.1-3.0, P=.02), and no CR/CRi at HSCT (HR 1.8, 95% CI 1.1-2.9, P=.02) were adverse factors for OS. Conclusion The presence of a CKT retains its negative prognostic impact after HSCT and differentiates within the ELN22 adverse risk group. However, in contrast to chemotherapy consolidation alone, the subgroup of pts harboring a typical CKT ub did not perform worse than pts with an atypical CKT ub, indicating a potential immune-mediated beneficial effect of HSCT. Within pts with a CKT receiving HSCT, we identified additional prognostic factors including the presence of ≥5 cytogenetic aberrations. These pts are in urgent need for novel post HSCT approaches.

Data-Driven Harmonization of 2022 Who and ICC Classifications of Myelodysplastic Syndromes/Neoplasms (MDS): A Study By the International Consortium for MDS (icMDS)

Background. The inclusion of gene mutations and chromosomal abnormalities in the 2022 WHO and ICC Classifications of MDS has enhanced diagnostic precision and is expected to improve clinical decision-making process. Although these two systems share similarities, clinically relevant discrepancies still exist and potentially cause inconsistency in their adoption in a clinical setting. In this study on behalf of the International Consortium for MDS (icMDS), we adopted a data-driven approach to provide a harmonization roadmap between the 2022 WHO and ICC classification for MDS. A modified Delphi Process consensus approach is currently ongoing among icMDS experts to finalize a harmonized MDS classification scheme. Methods. We analyzed retrospective international cohorts of patients with a diagnosis of MDS (n=7017) and AML (n=1002) according to WHO 2016 criteria. Hierarchical Dirichlet Processes were applied to define clusters capturing broad dependencies among all gene mutations and cytogenetic abnormalities. To investigate the features of importance and their impact on the clustering process, we employed the SHapley Additive exPlanations approach (SHAP). This allowed to define harmonized labels for each clinical entity. The clinical relevance of the unsupervised clustering was assessed through the analysis of phenotypic features and outcomes among each group. ( Blood 2022;140: 9828-9830) Results. Patients' characteristics are summarized in Table 1. We identified 9 clusters, defined by specific genomic features. The cluster of highest hierarchical importance was characterized by biallelic inactivation of TP53 (biTP53). According to SHAP analysis, bi TP53 was defined as 2 or more TP53 mutations, or 1 mutation with copy number loss or cnLOH. Most patients assigned to bi TP53 cluster had TP53 VAF>10% (77.9%) and complex karyotype (70.1%). Assignment to bi TP53 cluster was irrespective of blast count. Patients with monoallelic TP53 mutation segregated into other clusters. Hierarchically, the second cluster included patients with del(5q). SHAP analysis highlighted 5q deletion alone, or with one other chromosomal abnormality other than -7, and absence of bi TP53, as the most relevant features. Most of these patients had blast counts <5% (88.1%). The third distinct cluster included patients with SF3B1 mutations (in the absence of concurrent del(7q), abn3q26.2, complex karyotype or RUNX1 mutation). Most patients with MDS and SF3B1 mutation had <5% blasts (94.2%). Common co-mutated variants in the SF3B1 cluster included mutant DNMT3A (25.2%) and TET2 (38.3%). Morphologically defined MDS cases (i.e., not meeting criteria for bi TP53, del(5q) or SF3B1) were preferentially assigned to the following additional clusters: SF3B1 and concurrent higher-risk mutations (e.g., RUNX1 and ASXL1); SRSF2 and concomitant TET2 mutations; U2AF1 mutations with del(20q), del(7q) or -7; SRSF2 with TET2 mutations and co-mutational patterns including RUNX1 and ASXL1; and AML-like genomic signatures. Our analyses suggest that morphologically defined MDS is characterized by a large heterogeneity in terms of mutation profiles, not entirely captured by the presence of unilineage versus multilineage dysplasia, percentage of bone marrow blasts, and presence of hypocellularity and fibrosis. To better investigate the continuum between high risk MDS (i.e., patients with ≥10% blasts) and AML, an exploratory comparison was made using a cohort of AML (defined according to WHO 2016) patients analyzed using the same statistical methods. Only a partial overlap in genetic signatures was observed between MDS with ≥10% blasts and AML. However, similarities were observed between the AML-like MDS clusters (characterized by mutant NPM1, bZIP CEBPA, and Core Binding Factor abnormalities) and AML clusters defined by the same genetic signature, thus supporting the classification of these entities as AML, irrespective of blast count. Conclusion. Our study demonstrated the utility of a data-driven approach based on advanced statistical methods to generate a harmonized classification for MDS. Table 2 shows a provisional, hierarchical classification algorithm. Further refinement of entity labels and classification criteria is the subject of the ongoing modified Delphi Process consensus approach among icMDS experts.

A Potential Link between hnRNP K and Cebpα: Implications for Ribosomal Dysfunction in Acute Myeloid Leukemia (AML)

Deletion of the long arm of chromosome 9, del(9q), is a recurrent genetic abnormality involving the haploinsufficient loss of the RNA binding protein hnRNPK and is often associated with poor treatment responses in AML. In addition to reduced hnRNP K expression, other critical proteins, not localized to this locus, are also aberrantly expressed in del9q AML. One protein of critical interest is CEBPα, a well-established myeloid differentiation transcription factor. Recently, CEBPα was discovered to have a novel role in ribosomal RNA (rRNA) synthesis. However, as opposed to CEBPα, hnRNP K's role in RNA stability, rRNA processing, and ribosomal functions is already firmly rooted. Collectively, these results suggest that del(9q) AML dysregulations in hnRNP K and CEBPα expression may have a multi-faceted influence on ribosomal biogenesis and protein translation. Previously, we used animal models and patient samples to demonstrate that Hnrnpk haploinsufficiency alters CEBPa expression, suggesting that reduced hnRNP K expression contributes to decreased CEBPα levels and activity. These findings led us to hypothesize that these distinct, yet interconnected proteins, play a cooperative role in regulating rRNA synthesis in two major ways. Firstly, hnRNP K directly governs rRNA processing and ribosomal loading. And secondly, via hnRNP K's mediated regulation of the nucleolar-localized isoform of CEBPα (p42 isoform), which was recently shown to enhance recruitment of RNA polymerase I to rRNA genes. To explore these relationships, we used AML patient samples, Hnrnpk haploinsufficient animal models, si- and sh- HNRNPK AML cell lines, and biochemical analyses. Initially, RPPA, CyTOF, and western blot analyses were used to investigate how reduced hnRNP K levels affect proteins involved in ribogenesis and protein translation. Here, we observed a direct correlation between hnRNP K expression and defects in proteins and pathways involved in protein translation, such as mTOR, phos-S6, and eEF- and eIF-family members, and CEBPa (log 10pAdj < .0001). Subsequently, we performed polysome assays that revealed 40S and 60S subunit formation was impaired in AML cell lines with reduced hnRNP K levels. Across multiple cell lines, reduced hnRNP K expression directly led to a significant increase in monosomes (unbound/inactive ribosomes; p < 0.01) and a significant decrease in polysome-bound RNA (p < 0.05) . Critically, HNRNPK haploinsufficiency and si- and sh- HNRNPK knock down experiments disrupted the abundance and processing of the 47S transcript (p < 0.05). To understand the impact that hnRNP K has on CEBPα in the context of rRNA biology, we performed co-immunoprecipitation of hnRNP K followed by RNA-seq (RIP-Seq) in human AML cell lines KG-1 and KG-1a. 1076 interacting RNAs were identified, which were strongly enriched in transcription factors implicated in myeloid biology, including CEBPA (log 2pAdj < .0001). Biochemical analyses of sequence-specific motifs conferred direct and functional interactions between hnRNP K and the 5‘ and 3‘ UTRs of the human CEBPA. These interactions support our in vivo findings that del9q AML and Hnrnpk haploinsufficiency lead to reduced CEBPA expression, specifically in the p42 isoform, potentially impacting its role in nucleolar localization and rRNA transcription regulation. Currently, we are evaluating the significance of these interactions at both the biological and translational levels. Using biochemical and cell-based assays, we are evaluating the direct effect that Hnrnpk haploinsufficiency has on rRNA abundance and on the processing of ITS products in the context of CEBPA. Through the use of viability screens, we are examining the efficacy of inhibitors of protein translation, translation initiation, and RNA Pol I on leukemic cells with 9q deletions of reduced hnRNP K expression. Altogether, these findings identify an uncharacterized relationship between del9qAML ( HNRNPK haploinsufficiency), CEBPα expression, and ribogenesis, providing valuable insight towards mechanisms driving this subtype of leukemia. Collectively, these data also suggest that del9q AML represents a novel and currently uncharacterized ribosomopathy.

UBA1 Mutations Identify a Rare but Distinct Subtype of Myelodysplastic Syndromes

Background Mutations in UBA1 are associated with VEXAS (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) syndrome, an adult-onset inflammatory disorder (Beck DB et al. NEJM 2020). Approximately 40% of VEXAS patients are also diagnosed with myelodysplastic syndromes (MDS). We previously profiled UBA1 p.M41 mutations in a select subset of the International Working Group for MDS (IWG-PM) cohort (Bernard E et al. NEJM Evid 2022) including 375 male patients lacking disease-defining mutations or established disease classification by WHO guidelines, and identified 28 patients (7%) with UBA1 p.M41T/V/L mutations (Cohort A, Sirenko M et al. Blood 2022). However, the prevalence and characteristics of UBA1 mutations in MDS have not been systematically evaluated in a representative MDS population. Methods We used targeted next-generation sequencing of the full UBA1 locus to profile 2027 diagnostic and treatment-naive MDS samples (Cohort B, 61% male) ascertained through the IWG-PM (Figure 1). Clinical associations of UBA1 mutations were evaluated and clinical history was reviewed for inflammatory conditions when available. Results In Cohort B, 35 UBA1 mutations in 34 (1.7%) patients were identified, of which 20 (0.97%) had likely pathogenic variants and 14 had variants of unknown significance (VUS). Likely pathogenic variants included 13 p.M41T/V/L mutation (variant allele fraction [VAF] range 0.013-0.94), and 7 non-p.M41 mutations where 6/7 had VAF>0.35: 2 with p.S56F (VAF 0.87 and 0.93), 2 p.A478S (VAF 0.72 and 0.80), 2 p.S621C (VAF 0.80 and 0.82) and 1 p.Y55H (VAF 0.025). Three VUS were in female patients. 204 cases were profiled by both assays and of those, all 8 ddPCR positive cases were identified by NGS with concordant VAF (R2=0.999 p<0.0001). Integration of Cohort A and B (n=2,198) yielded 40 patients (all male, median age 72; range 44-89 years) with pathogenic UBA1 variants. The WHO 2016 classification (available for n=38 of 40) was MDS-SLD/MLD (25), MDS-EB1 (4), MDS-U (3), CMML (2), MDS-RS-MLD (1), aCML (1), MDS/MPN-RS-T (1), MDS/MPN-U (1). Patients had a median of 1 myeloid gene mutation in addition to UBA1 (range: 0-4) with most frequent co-occurring events in TET2 (n=12), DNMT3A (n = 10), ASXL1 (n=3), SF3B1 (n=3) and loss of the Y chromosome (n=5). In 8 patients with pathogenic UBA1 > 2% VAF and co-occurring DNMT3A mutations, DNMT3A and UBA1 VAF were correlated (slope = 0.88, r = 0.87, p = 0.0005), suggesting that co-mutation may lead to clonal expansion. Conversely, TET2 co-mutations were either subclonal (n=4) or clonal (n=8) to UBA1. Among patients with pathogenic UBA1 variants, the majority had IPSS-M Very-Low/Low risk (73% 27/37). In contrast, patients with VUS were more likely to have Moderate or High risk (64% 7/11). Partial clinical history was available for 33 cases with pathogenic UBA1 variants. 50% (9/18) had inflammatory-rheumatic disease (IRD) including psoriatic arthritis, relapsing polychondritis, Sweet syndrome, bronchiolitis obliterans with organizing pneumonia, ear chondritis, and rosacea. 3 patients had more than one IRD. 8 were treated for IRD with steroids (n=6) or methotrexate (n=2). 4 patients had MGUS. Other manifestations included vacuoles (4/8), thromboembolic disease (5/16), non-infection fever (5/14), weight loss (4/14), ocular symptoms (5/15), arthralgia (3/16), chondritis (5/15), and other inflammation (6/14). IRD diagnosis usually preceded MDS (average time 0.28 years; range 16.5 years prior to 1.4 years after). Three patients transformed to acute myeloid leukemia (AML). One patient had a low VAF UBA1 p.M41V (0.0002 by ddPCR) and TET2, SF3B1, FLT3, and ASXL2 co-mutations at baseline. The second had UBA1 p.S56F (VAF 0.868) and a Chr 7q deletion. The third had VUS UBA1 p.R869L (VAF 0.222) and IRF1, NFE2 and RRAS co-mutations. Among the other UBA1-mutant patients that died or were censored after 1 year (n=37), none transformed to AML. Conclusion Within the large, representative, diagnostic and well-characterized IWG-PM MDS cohort, we find likely pathogenic UBA1 mutations in 1% of patients, with enrichment in male patients with few or no mutations in myeloid driver genes (7%). UBA1-mutant patients were predominantly IPSS-M low risk with a median of 1 additional mutation, usually in DNMT3A or TET2. UBA1 mutations may define a distinct subset of MDS and its recognition in future guidelines will improve the management of patients with MDS/VEXAS overlap.

Prediction of Time-to-First Treatment (TTFT) in Favorable-Risk Chronic Lymphocytic Leukemia (CLL) Patients Using a Novel Stratification through Transcriptome Risk Scoring

Background: CLL is the most prevalent adult leukemia with a highly heterogenous genetic landscape leading to extremely varied clinical outcomes. Previously, CLL patients with immunoglobulin heavy chain variable region ( IGHV) mutated status and presence of deletion 13q14 [del(13q)] were identified as favorable-risk with most patients remaining on lifetime observation. However, other intrinsic factors contributing to CLL disease progression and leading to treatment initiation remain unknown. Our goal was to identify patients at high-risk of progression with added predictive value (APV) beyond IGHV-status and presence of del(13q). Methods: Flow cytometry was used to sort CD19+CD5+ malignant cells in peripheral blood from CLL patients at Huntsman Cancer Institute at University of Utah and triple sequencing generated (tumor whole transcriptome and paired tumor-normal whole exome data). We used SPECTRA, a novel dimension reduction transcriptome approach, to derive a set of independent, intrinsic, quantitative transcriptome tumor variables from 249 CLL patients with quality-controlled transcriptome sequence data. From this set, 182 treatment-naïve (TN) patients with quality-controlled clinical variables were used as a discovery cohort set to derive a SPECTRA-based risk score for TTFT using multivariable Cox proportional hazards modeling. Event time was date of patient specimen acquisition to initiation of frontline therapy with patients censored at last follow-up or death. Gaussian mixture modeling (GMM) was performed to identify evidence for distinct risk groups within the quantitative risk score. GMM-risk groups, and further stratifications by IGHV mutational and del(13q) status, were used in hazard ratios (HR) and to illustrate differences in Kaplan-Meier time-to-event curves. An independent publicly available dataset of 548 TN CLL patients with clinical and transcriptome data for CD19+ enriched cells was used for replication. Results: SPECTRA produced 19 quantitative spectra variables to describe most of the expression variation across the 249 CLL patients. In multivariable Cox modeling for TTFT, 7 spectra were significant and retained in a final model, which GMM separated into a bi-modal distribution and defined high (N=83) and low-risk (N=99) groups (HR=5.7, 95% confidence interval [CI] 3.4-9.7). In a post-hoc model including IGHV mutational and del(13q) status, the spectra-risk score showed significant APV beyond both factors (p<0.001 for both). The discovery study timeframe was 6.3 years (y) and included 109 IGHV-mutated and 75 del(13q) patients. In the IGHV-mutated patients, median TTFT (mTTFT) was significantly shorter for spectra-high risk patients (3.1y) vs. spectra-low risk patients (median not reached [NR]; p<0.001). Similarly, in the del(13q) patients, mTTFT was significantly shorter in high-risk patients (3.3y) compared to median NR for spectra-low (p<0.001) ( Figure). Importantly, stratification of patients into low- and high-risk SPECTRA scores provided significant additional information for prediction of TTFT than IGHV mutational and del(13q) status ( Figure). For validation, we applied the same spectra-risk score to the independent data set containing 301 IGHV-mutated and 278 del(13q) CLL patients. In the replication set, the mTTFT in the IGHV-mutated patients who were spectra-high was 3.3y vs. 11.2y in spectra-low (p<0.001). Similarly, in the replication set of del(13q) patients, spectra-high-risk patients had a mTTFT of 2.7y vs. 10.7y for spectra-low (p<0.001). Conclusion: A transcriptome risk score utilizing novel SPECTRA variables identified a substantial subset of CLL patients with IGHV-mutated status and presence of del(13q) who have uncharacteristically short TTFT, but who would be classified as favorable risk under current best practice stratification. Future directions include validating our results with external patient cohorts from Mayo Clinic and investigating the genetic and transcriptomic profile of SPECTRA low- and high-risk cohorts to determine targetable pathways for treatment.

Salvage Autologous Peripheral Blood Stem Cell Transplantation after the Development of tMDS or AML in Multiple Myeloma Patients

Multiple Myeloma (MM) patients are often treated with high-dose chemotherapy and autologous stem cell transplantation (ASCT) for disease control. Lenalidomide is typically used as maintenance but results in an estimated 3.3% chance of developing a therapy-related myeloid neoplasm (TMN) typically myelodysplastic syndrome (MDS) or acute myelogenous leukemia (AML). This complication is often devastating with a median survival for those with a TMN of just 13 months. Over the past 6 years, 4 patients with multiple myeloma who developed a TMN were treated with a salvage ASCT using banked stem cells collected prior to their initial ASCT and before lenalidomide maintenance. None of these patients qualified for an allogeneic transplant. Melphalan 140 - 200 mg/m2 was used as conditioning prior to infusion of the peripheral blood stem cells, resulting in successful MDS/AML disease control. Case 1 = 61-year-old man with MM initially treated with CyBorD then transplanted in 2010. Post transplant treatment included lenalidomide maintenance, followed by a variety of salvage regimens over the next 7 years including thalidomide, carfilzomib, daratumumab and pomalidomide. He developed cytopenias evaluated by bone marrow biopsy in May 2017. This showed tMDS (Karyotype 47-48, XY, der (5)t(5:20)(q11.1;q11.1), +19, der(21:22)(q10:q10),+2~3mar[cp11]/46-48,idem,-der(5),+20[cp5]/46,XY[4]. FISH confirmed deletion 5q in 76% and loss of chromosome 5 in 6.5% of cells. NGS showed a frame shift mutation of TP53 at a variant allele frequency of 92.5%. He underwent a second ASCT in Aug 2017 and recovered normal hematopoiesis within three weeks. Unfortunately, he developed an aggressive relapse of his multiple myeloma 9 months later and succumbed from refractory multiple myeloma 14 months after the salvage transplant, without evidence of MDS. Case 2 = 72-year-old man with MM initially treated with CyBorD then an ASCT in May 2015. Lenalidomide maintenance was continued until October 2017 when he developed severe thrombocytopenia and circulating blasts. A bone marrow biopsy showed tMDS EB-1. Cytogenetics 46, XY t(3:21) (q26.2,q22) [18]/46, XY[2]. He received a second ASCT after melphalan 140 mg/m2 in Oct 2017 followed by recovery of normal blood counts. Bone marrow biopsy showed complete remission. He remains in remission from both the multiple myeloma and MDS almost 6 years later without any further therapy. Case 3 = 65-year-old man with MM treated with bortezomib + dexamethasone followed by ASCT in Aug 2012. He received maintenance lenalidomide for 4 years but then progressed. In Jan 2018 he developed pancytopenia and bone marrow biopsy demonstrated MDS with ringed sideroblasts. Cytogenetics were normal but NGS showed mutations of ASXL1, RUNX1, SF3B1, SETBP1 and DNMT3A. He underwent a second ASCT using his banked stem cells after melphalan 140 mg/m2 in Jan 2018 followed by full hematopoietic recovery. A repeat bone marrow biopsy in March 2022 showed persistent MDS harboring ASXL1, SF3B1, and DNMT3A mutations, but no detectable RUNX1 or SETBP1 abnormalities. His multiple myeloma remains in remission >5 years later. He receives only intermittent erythropoietin to maintain a Hgb of 11. Case 4 = 58-year-old man with MM initially treated with CyBorD followed by an ASCT in May 2014. He received lenalidomide maintenance but relapsed multiple times after 4 years ultimately complicated by renal failure requiring permanent dialysis. In March 2022 he developed pancytopenia. Bone marrow biopsy showed 15% blasts harboring del(5q), del(17p) and trisomy 8 by FISH. NGS demonstrated a mutation of ASXL1, and a copy number loss of TP53. Six months of decitabine did not improve his blood counts. In Dec 2022 he underwent a second ASCT after melphalan 140 mg/m2. A repeat bone marrow biopsy in Feb 2023 showed a complete morphological remission with a normal NGS. He is off all treatment 8 months post-transplant other than erythropoeitic support due to ongoing dialysis-dependent renal failure. The development of TMN is an uncommon but devastating event in patients with multiple myeloma after ASCT and lenalidomide maintenance. These patients responded well to a salvage ASCT using banked stem cells. This approach was well tolerated and provided durable hematopoietic recovery. Second ASCT using banked autologous stem cells should be considered in such patients who are not otherwise candidates for allogeneic transplantation.

Cytogenomic features of Richter transformation

BackgroundRichter transformation (RT) is the development of aggressive lymphoma in patients with chronic lymphocytic leukemia (CLL) or small lymphocytic lymphoma (SLL). This rare disease is characterised by dismal prognosis. In recent years, there has been a deeper understanding of RT molecular pathogenesis, and disruptions of apoptosis (TP53) and proliferation (CDKN2A, MYC, NOTCH1) has been described as typical aberrations in RT.ResultsA single-institution cohort of 33 RT patients were investigated by karyotyping, fluorescence in situ hybridization and single nucleotide polymorphism/copy number (CN) arrays. Most of RTs were typically manifested by diffuse large B-cell lymphoma, not otherwise specified, among the remaining cases one was classified as high-grade B-cell lymphoma with 11q aberrations. The most frequent alterations (40–60% of cases) were represented by MYC rearrangement/gain, deletions of TP53 and CDKN2A, IGH rearrangement and 13q14 deletion. Several other frequent lesions included losses of 14q24.1-q32.33, 7q31.33-q36.3, and gain of 5q35.2. Analysis of 13 CLL/SLL-RT pairs showed that RT arised from the CLL/SLL by acquiring of 10 ~ 12 cytogenetic or CN lesions/case, but without acquisition of loss of heterozygosity regions. Our result affirmed the higher genetic complexity in RT than CLL/SLL and confirmed the linear features of RT clonal evolution as predominant.ConclusionsCytogenomic profile was concordant with the literature data, however the role of IGH rearrangement, 14q deletion and 5q35.2 gain need to be explored. We anticipate that further characterization of RT lesions will probably facilitate better understanding of the RT clonal evolution.

Loss of DDX3X Function Promotes CLL Progression By Facilitating NOTCH1 mRNA Translation

A variety of driver genes are present in chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), and those with high mutation frequencies include SF3B1, NOTCH1, and TP53, which are involved in the development of CLL/SLL and are associated with poor prognosis. The biological significance of some driver genes, such as DDX3X, has not yet been elucidated. DDX3X is located on the X chromosome. As one of the members of the DEAD-box helicase family, it is expressed ubiquitously in human tissues and participates in many biological processes. Here, we described the mapping of the DDX3X abnormalities and demonstrated its clinical significance in CLL/SLL. We also explored the effect and mechanism of DDX3X dysregulation on tumorigenesis and development of CLL by in vitro experiments. To examine the mutational landscape of DDX3X, we performed next-generation sequencing on 402 CLL/SLL patients, and 17 patients (4.2%) had DDX3X mutations. Six patients were frameshift mutations and 2 were nonsense mutation, which caused truncation of DDX3X. Among the 7 cases of missense mutations, 4 cases involved the ATP-binding or C-terminal domain, which may affect the function of DDX3X. The remaining two cases are deletion mutation and splicing mutation. Next, we evaluated the clinical significance and prognostic role of DDX3X mutation. The patients with DDX3X mutations are mostly male (94.1% vs 66.5%, P=0.017), and had more adverse prognostic indicators: unmutated IGHV (88.2% vs 48.6%, P=0.002), 17p deletion (42.9% vs 11.4%, P=0.041), and 11q deletion (46.7% vs 15.7%, P=0.006). DDX3X mutation was an independent risk factor for disease specific survival of CLL/SLL in the competing-risk regression. Also, we found all (14/14) the mutated patients and 15.2% (5/33) of the non-mutated patients had low expression of DDX3X in bone marrow samples by immunohistochemistry. Overall, these results indicates that dysregulation of DDX3X are common in CLL/SLL and may contribute to its progression. To delineate the functional consequences of DDX3X loss in CLL, we used CRISPR/cas9 system to construct stable DDX3X knockout (DDX3X-KO) MEC-1 and JVM-3 cells. DDX3X-KO cells showed significantly increased proliferation and reduced spontaneous apoptosis compared to vector control. Additionally, DDX3X-KO cells showed higher rates of cell viability and reduced apoptosis after treatment of ibrutinib or venetoclax. We further found that DDX3X-KO cells had higher expression level of phosphorylated BTK and MCL-1, which may explain the resistance to ibrutinib and venetoclax, respectively. Moreover, DDX3X-KO cells showed increased expression level of CXCR4 and enhanced chemotaxis in response to CXCL-12. In summary, loss of DDX3X function promotes progression of CLL by mediating more invasive biological behaviors of CLL cells. To evaluate the mechanisms by which DDX3X deletion affects CLL, we detected key signaling pathways in the tumorigenesis and development of CLL in DDX3X-KO and control cells. We found increased expression of NOTCH1 and its downstream target proteins in DDX3X-KO cells (Figure 1), indicating that loss of DDX3X activated the NOTCH1 pathway. Considering that DDX3X is an RNA-binding protein and mainly regulates translation, we speculated that DDX3X may regulate the translation of NOTCH1. We performed RNA binding protein immunoprecipitation assay and found that DDX3X directly interacted with NOTCH1 mRNA (Figure 2A, B). Dual-luciferase reporter assay showed enhanced activity of NOTCH1 5‘ UTR in DDX3X-KO cells (Figure 2C), further suggesting that DDX3X may regulate translation of NOTCH1 mRNA through binding to the 5‘ UTR. Finally, polysome profiling demonstrated that DDX3X knockout resulted in increased NOTCH1 mRNAs in polysome fractions (Figure 2D), confirming that loss of DDX3X function facilitates NOTCH1 mRNA translation. In conclusion, DDX3X abnormalities are common in CLL and associated with poor prognosis. DDX3X dysregulation is involved in the progression of CLL by facilitating NOTCH1 mRNA translation through binding to the 5' UTR.

The Transcriptional Impact of 5q Deletion in MDS at Single Cell Resolution

Introduction: Myelodysplastic syndromes with 5q deletion (del(5q) MDS) are characterized by two commonly deleted regions (CDRs): 5q31 and 5q32-33. Although several genes within these CDRs have been associated with disease pathophysiology, the molecular basis underlying its origin is still unknown. Lenalidomide represents the first therapeutic approach for del(5q) MDS, but patients experience loss of responsiveness within 2-3 years, highlighting the need of characterizing the mechanisms impairing treatment response. While previous studies have identified dysregulated genes and pathways in the disease, they overlooked that the hematopoietic system of these patients is composed of a mixture of cells with and without the deletion (del(5q) and non-del(5q) cells), which hampers the ability to unravel the real transcriptional impact of the deletion. Methods: We isolated by FACS and performed single-cell RNA sequencing (scRNAseq, 10XGenomics Chromium platform) of CD34+ cells from 4 untreated patients, 2 patients treated with lenalidomide (partial (PCR) and complete (CCR) cytogenetic responders), and 3 healthy elderly donors. To identify del(5q) and non-del(5q) cells, the copy number alteration (CNA) inference methods CopyKat and CaSpER were applied. To unveil the transcriptional alterations prompted by the deletion, differential expression (DE), gene regulatory network (GRN) and cell-to-cell communication (CCC) analyses were performed (Figure 1). Results: CNA methods robustly identified del(5q) cells and non-del(5q) cells, which was consistent with the del(5q) percentage obtained by karyotyping. At diagnosis, del(5q) cells were detected in all hematopoietic progenitors, including the hematopoietic stem cells (HSC), suggesting that the deletion occurs in the earliest stages of hematopoietic differentiation. Although the distribution of del(5q) cells was highly heterogeneous among patients (Figure 2), a positive enrichment of del(5q) cells was detected in erythroid progenitors, underscoring the role of this genetic lesion in the anemia characterizing del(5q) MDS. To delve into the transcriptional mechanisms differentiating del(5q) and non-del(5q) cells, we performed DE and GRN analyses. Only 7 genes were downregulated in del(5q) cells; however, most play a key role in MDS and other tumors, such as PRSS21, MAP3K7CL, and CCL5. GRN analyses identified regulons JARID2, IRF1 and KAT6B, known to be key for proper hematopoietic differentiation, showing less activity in del(5q) cells. Likewise, the regulons RERE and KDM2A, which downregulated genes involved in ribosomal processes, were more active in del(5q) cells, supporting the concept that cells harboring the deletion may have a more prominent role in promoting altered hematopoiesis. However, comparisons against healthy donor cells suggested that non-del(5q) cells could share similar, albeit attenuated, abnormal behavior to del(5q) cells. In line with these results, CCC analyses identified minimal differential interactions in del(5q) cells with respect to non-del(5q) cells, indicating that the deletion does not confer a differential communicative potential to the cells. Importantly, several interactions present in MDS cells were absent in healthy cells, such as the AGTRAP-RACK1, whose members have been postulated as potential therapeutic targets for promoting proliferation in other cancers. After lenalidomide, del(5q) and non-del(5q) cells from PCR and CCR patients showed higher protein degradation and erythropoietin signaling, as well as higher activity of the PD-L1/PD-1 pathway, suggesting a potential immunosuppressive mechanism of these cells after treatment. Even if several transcriptional alterations detected at diagnosis were reverted after lenalidomide, ribosomal translation processes were still altered, even at time of CCR. These results evidence that, after lenalidomide, non-del(5q) progenitor cells revert some of the transcriptional alterations that present at diagnosis, while maintaining other lesions that could be relevant for abnormal hematopoiesis, and potentially, for the future relapse of the patients. Conclusions: This study provides the first characterization of del(5q) and non-del(5q) cells at the single-cell resolution and reveals previously unknown transcriptional alterations that could contribute to disease pathogenesis or less responsiveness to lenalidomide.

A Proposal for a Classification of Ccus, MDS and AML Primarily Based on Genetic Abnormalities Considering the Biological Continuum of These Entities

Background: According to the 5 th edition of the WHO classification (WHO 2022) and the International Consensus Classification (ICC) the main parameters used for the definition of CCUS, MDS and AML are cytopenias, dysplasia, blast count and distinct genetic abnormalities. These entities represent a disease continuum as CCUS can progress to MDS and MDS to AML. Thus, we asked the question whether this continuum can be reflected in a proposed comprehensive classification system. Methods: We evaluated 222 CCUS, 718 de novo MDS and 751 de novo AML. The diagnosis was established following WHO 2022. Bone marrow samples were analyzed by cytomorphology, chromosome banding analysis, targeted NGS panel sequencing (median coverage 1500x) and WGS (median coverage 100x). Overall survival (OS) was available for 1552/1691 patients. Median follow-up with respect to OS was CCUS: 1.7 years, MDS: 9.3 years, AML: 6.7 years. Results: In the WHO 2022 classification a subset of AML entities (AML with defining genetic abnormalities (DGA)) is defined by fusions ( PML:: RARA, RUNX1:: RUNX1T1, CBFB:: MYH11, DEK:: NUP214, RBM15:: MRTFA other defined genetic alterations/ ODGA), rearrangements ( KMT2A, NUP98, MECOM) and distinct mutations ( NPM1, CEBPA). These well-established distinct entities were kept in the classification proposal. 511 AML cases (67%) were classified as AML DGA (Figure 1). The remaining 240 AML cases classified as AML myelodysplasia-related and AML defined by differentiation according to WHO 2022 were combined with MDS and CCUS cases and categorized hierarchically into 5 distinct groups based on the presence of the following genetic abnormalities (GA group): 1. 5q deletion, 2. SF3B1 mutation, 3. other spliceosome mutations (SP: SRSF2, U2AF1, ZRSR2), 4. IDH1/2 or DNMT3A or TET2 mutations (I/D/T), 5. None of these (NO) (Figure 1). Next, within these GA groups the presence of progression markers (PM) was evaluated: PM subset A: presence of a) biallelic TP53 alterations ( TP53bi), or b) mutations in RUNX1 or ASXL1 and mutations in RAS pathway genes or KMT2A-PTD (R/A+RAS/PTD); PM subset B: presence of a) complex karyotype without TP53bi (complex), or b) RUNX1,or ASXL1 mutations (R/A), or RAS pathway mutations or KMT2A-PTD (RAS/PTD); PM subset C: absence of these PM. The assignment into GA groups and PM subsets differed substantially between CCUS, MDS and AML. With respect to GA group CCUS, MDS and AML cases were assigned into GA groups del(5q): CCUS (0%), MDS (76%), AML (24%); SF3B1: CCUS (4%), MDS (91%), AML (5%); SP: CCUS (16%), MDS (55%), AML (29%); I/D/T: CCUS (45%), MDS (30%), AML (25%); NO: CCUS (27%), MDS (62%), AML (11%). With respect to PM subsets CCUS, MDS and AML cases were assigned into A: CCUS (1%), MDS (43%), AML (56%); B: CCUS (10%), MDS (54%), AML (36%); C: CCUS (27%), MDS (69%), AML (4%) (Figure 1). Next, OS was evaluated. Median OS for PM subsets A (n=168), B (n=301) and C (n=572) was 0.7, 2.0 and 6.8 years ( p<0.001), respectively and thus were named acute myeloid neoplasm (MN), high risk MN and low risk MN. Median OS in years in each GA group in acute MN was del(5q): 0.3, SF3B1: 0.7, SP: 1.1, I/D/T: 0.9 and NO: 0.3. The respective data for high risk and low risk MN were: 1.9, 3.3, 2.0, 1.5, 1.3 and 6.4, 7.4, 6.9, 5.8, and 6.8 years (Figure 1). Conclusions: The proposed classification aims at reflecting the biological continuum of CCUS, MDS and AML and allows reclassification during the course of the disease without changing the disease entity following the concept of MPN with chronic phase and blast phase. Further, the classification reflects prognosis and also directly indicates potential therapeutic targets. It is flexible as new genetic markers can easily be added without changing the overall concept.

CD34+ Megakaryocytes Associate with Myelodysplastic Syndromes and Related Cytogenetic Abnormalities, but Not Other Hematological Disorders

Background: CD34 is a transmembrane phosphoglycoprotein that is a marker of hematopoietic stem cells and is used clinically to aid in enumeration of blast cells for identification of advanced myeloid neoplasms. Megakaryocytes are differentiated cells from the myeloid lineage that reside in the bone marrow and generally stain negative for CD34 (CD34-). However, CD34 positive (CD34+) megakaryocytes have been observed in hematological disorders such as myelodysplastic syndrome, myeloproliferative neoplasms, and acute leukemias. CD34+ megakaryocytes are proposed to be relatively specific for malignant hematologic conditions and have been reported to associate with a worse prognosis. However, the general clinical, biochemical, and cytogenic characteristics for bone marrow cases of CD34+ megakaryocytes versus CD34- megakaryocytes remains unclear. Objective: We sought to determine the clinical, biochemical, and cytogenetic characteristics associated with finding CD34+ megakaryocytes on bone marrow biopsies. Methods: We identified 281 independent, index bone marrow biopsy cases between 2011-01-01 and 2017-12-31 from Vancouver General Hospital, Canada that underwent CD34 immunohistochemistry at clinical request. The clinical, biochemical, and cytogenetic characteristics of patients were compared based on megakaryocytes being CD34+ vs CD34- on immunohistochemistry. Cases of CD34+ megakaryocytes were defined as having >5% of megakaryocytes staining CD34+, but sensitivity analyses were performed using different percentage cut-offs of 10, 30, and 50%. Results: Out of 281 cases, 134 had CD34+ megakaryocytes (58.2% male sex; mean age = 64.1 years [SD = 15.2 years]) and 147 had CD34- megakaryocytes (57.1% male sex; mean age = 60.0 years [SD = 16.6 years]). There was a significant difference in the distribution of diagnostic categories observed between cases of CD34+ versus CD34- megakaryocytes: myelodysplastic syndromes 35.1% (n=47) versus 21.8% (n=32), acute myeloid leukemias 20.9% (n=28) versus 21.1% (n=31), non-diagnostic etiology 17.9% (n=24) versus 14.3% (n=21), and myeloproliferative neoplasms 10.4% (n=14) versus 19.7% (n=29) (Figure A; Chi-square p-value=0.0004). Sensitivity analyses using different percentage cut-offs to define cases of CD34+ from CD34- megakaryocytes yielded similar results. The differences in biochemical characteristics between cases of CD34+ versus CD34- megakaryocytes were generally unremarkable. The median (IQR) for biochemical parameters between cases of CD34+ and CD34- megakaryocytes were hemoglobin 99 (28) versus 100 (34) g/L, mean corpuscular volume 94 (14) versus 93 (10) fL, neutrophil count 2.20 (3.68) versus 2.46 (3.63) x10 9/L, platelet count 98 (158) versus 112 (194) x10 9/L, and bone marrow blasts 7 (4) versus 3 (14)%. Lastly, there were notable trends in cytogenetic results associated with 90 cases with CD34+ versus 84 cases with CD34- megakaryocytes including: complex karyotypes for 15.6% (n=14) versus 6.0% (n=5), isolated deletion 5q for 7.8% (n=7) versus 1.2% (n=1), and/or isolated trisomy 8 for 5.6% (n=5) versus 2.4% (n=2). Similar cytogenetic results were observed when cases were restricted to only cases of CD34+ versus CD34- megakaryocytes with a diagnosis of myelodysplastic syndrome (Figure B). Conclusion: The presence of CD34+ megakaryocytes is more common in cases of myelodysplastic syndrome relative to other neoplastic hematologic disorders, but does not appear to help with discriminating between neoplastic and non-neoplastic hematological disorders ( e.g. non-diagnostic etiology). Cases with CD34+ megakaryocytes tend to associate with complex karyotype and deletion 5q abnormalities relative to cases with CD34- megakaryocytes.

Hidac Consolidation Cycles May Impede Stem Cell Transplant Planning for High-Risk Acute Myeloid Leukemia Patients

Background Acute myeloid leukemia (AML) is a clonal aggressive hematologic neoplasm characterized by arrested myeloid maturation, resulting in the accumulation of myeloid blasts in bone marrow, blood, and other tissues. Cytogenetic and molecular characteristics further stratify AML into favorable, intermediate, or high-risk classifications; with high-risk including DEK-NUP214, KMT2A-rearrangement, BCR-ABL1, GATA2, MECOM, deletion 5q, abnormal 17p, complex or monosomal karyotype, wild type NPM1 and FLT3-ITD, or mutated: RUNX1, ASXL1, or TP53. In fit and eligible patients, therapy for high-risk AML patients involves induction therapy, and response evaluation at count recovery. If remission is confirmed, it is ideal that the patient proceed straight to hematopoietic stem cell transplantation (HSCT). HSCT remains the only curative therapy currently available. The logistics of proceeding to transplant might necessitate consolidation chemotherapy usually involving high dose cytarabine (HiDAC). Methods We performed a retrospective cohort analysis and evaluated outcomes for high-risk AML patients treated at our transplant institution, the Georgia Cancer Center, who were diagnosed and received HiDAC consolidation therapy between November 2003 and December 2020. High-risk AML was defined as those patients, whose AML was positive for one (or more) of the following FLT3, monosomy 5,7 and/or complex cytogenetics (CG) defined as having greater than or equal to 3 CG changes). For those not transplanted, we reviewed the complications, if any, that would preclude a HSCT. Results A total of 93 patients diagnosed with high-risk AML were evaluated at our center from 2003 to 2020. Males comprised 46.2% (n=43) and females comprised 53.8% (n=50) of the cohort. Of these patients, the median age of the patient cohort was 61.5 years. 40.8% (n=38) received HiDAC consolidation. Among patients who received HiDAC consolidation and proceeded to undergo HSCT, the median age was 47.6 years. In contrast, patients who received HiDAC consolidation but were unable to undergo HSCT had a median age of 61.3 years. Among the patients who were unable to undergo HSCT due to death, the median age was 41.8 years. For patients who received HiDAC consolidation but did not undergo HSCT due to reasons other than death, the median age was 53.4 years. 55.3% (n=21) went on to HSCT, and others did not proceed to HSCT. Of the patients who did not receive HSCT, 76.4% (n=13), underwent HLA-typing, indicating consideration for transplantation. Of these 17 patients (44.7%, n=9) did not proceed to transplant due to infectious complications, the remaining 8 had noninfectious reasons for non-transplant. Of the 9 patients without HSCT due to infection, four had an infection that prevented them from receiving a transplant and five patients passed away prior to transplant due to septic shock or multi-organ failure. Infections included bacteremia from Klebsiella, E. Coli, Proteus, group B strep, vancomycin resistant E. Faecalis, and coagulase negative staph, pneumonia from Klebsiella, urinary tract infections from extended spectrum beta-lactamase resistant E. Coli, Klebsiella, and proteus mirabilis, fungal sinusitis, and Clostridium difficile colitis. Other reasons that prevented HSCT included neutropenic fever with an unknown cause, substance abuse, disease progression, and lack of follow-up. Conclusion The data from our study and the literature on this topic over the past 30 years suggest starting the process of HSCT during the induction admission. HSCT is the sole curative option for high-risk AML patients, and the concept of bridging the period between induction and HSCT with HiDAC consolidation appears to offer no additional benefit compared to IDAC. Moreover, this approach prevents a subset of this population from being fit enough to receive HSCT.

Investigating the Influence of Germline ATM Variants on Susceptibility to Chronic Lymphocytic Leukemia and Other Malignancies

Introduction: Chronic lymphocytic leukemia (CLL) patients (pts) face an increased susceptibility to secondary cancers. Furthermore, the hereditary predisposition to CLL is influenced by factors that have yet to be fully elucidated by GWAS-identified common variants. Among the hereditary cancer risk mutations observed, germline Ataxia-telangiectasia mutated ( ATM) aberrations are among the most prevalent. Rare germline ATM variants are detected in 24% of CLL pts, surpassing the frequency observed in other hematologic neoplasms and the general population. In CLL, loss of ATM via 11q23 deletion is linked to an unfavorable prognosis and a shortened progression-free survival. The extent to which germline ATM variants predispose CLL pts to other malignancies remains unclear; to examine this potential risk we conducted a retrospective study to assess the influence of germline ATM variants on the predisposition to secondary neoplasms in CLL pts and their relatives. Methods: Five hundred and eighty-five pts seen at Dana-Farber Cancer Institute and who had NGS performed to evaluate germline ATM status, either through direct germline sequencing of saliva or by inference according to the hierarchical algorithm we have previously published (Lampson, 2022), were mailed a questionnaire that investigated: demographics; personal and family history of any cancer; non-medical radiation and Agent Orange exposure; and Ataxia-Telangiectasia syndrome (AT). Of these, 333 replied (57%). Information collected from our CLL database included FISH, IGHV status and treatment status. European ancestry was categorized based on the United Nations geoscheme (UNSD, 2019). Pt characteristics are in Table 1. Pts were stratified into 4 groups, based on ATM mutational status and del(11q): Group-1, ATM germline variants alone (N=63); Group-2, ATM germline with somatic ATM mutation and/or del(11q)(N=22); Group-3, ATM somatic aberration alone (including del(11q))(N=41); and Group-4, no ATM aberration (N=207). Results: Of the 333 pts in our cohort, baseline demographic and clinical characteristics among the 4 groups were balanced, except for unmutated IGHV status. Nineteen (86%) and 36 (86%) pts of groups 2 and 3, carrying somatic ATM aberrations, had unmutated IGHV, compared to 21 (33%) and 76 (37%) of groups 1 and 4, without somatic ATM aberrations(p<0.01). Regarding treatment, 60% of our cohort had received at least one line of therapy (median: 1 (1-7)). Among the 164 pts (49%) with history of an additional non-CLL neoplasm, 221 cancers were reported. Excluding pts with only non-melanoma skin cancers, the incidence is reduced to 31% (104 pts). The median number of second cancers per pt is 1 (1-4). Of the 134 pts with available age of onset data for the secondary malignancy, 80 (60%) were diagnosed with the secondary cancer after CLL. Comparing pts with germline ATM variants (N=85) to the ones without germline ATM variants (N=248), no significant difference in the incidence of secondary cancer was found (p=0.73). The median age of secondary cancer onset was also similar between the groups (median: 63 and 64 years in germline ATM present vs absent, p=0.28). Of the whole cohort, 283 pts (85%) reported at least one relative with a cancer history (median 2 relatives affected (1-17)). The incidence of B-cell lymphoproliferative disorders was significantly higher (p=0.02) in pts with germline ATM variants (32%) compared to those without germline ATM variants (21%), including familial CLL (25% vs18%) (p=0.04). Familial CLL was also strongly associated with Ashkenazi Jewish ethnicity (39% incidence in Ashkenazi pts vs 16% in non-Ashkenazi, p=0.004). No difference in the incidence of other hematologic or solid malignancies was found between the relatives in the two groups. No pts reported a familial or personal history of AT. Compared to pts without any ATM aberration, time to first treatment (TTFT) was shorter in pts harboring somatic ATM events, while no difference was observed between pts with germline ATM variants (median TTFT: 82, 59, 52, 90 months for group 1, 2, 3 and 4 respectively, p=0.01) (Figure 1). Conclusions: Our results suggest a higher incidence of B-cell lymphoproliferative disorders, including familial CLL, in the relatives of CLL pts carrying germline ATM variants. The presence of these germline variants did not impact TTFT, compared to pts harboring somatic ATM mutations.

A Phase 2 Study of Acalabrutinib, Umbralisib, and Ublituximab (AU2) in Treatment-Naïve and Relapsed or Refractory Chronic Lymphocytic Leukemia (CLL)

Background Targeting the B-cell receptor (BCR) signaling pathway is highly effective for the treatment of CLL. However, attainment of undetectable minimal residual disease (uMRD) is infrequent with current BCR targeting strategies. Here, we report results of a phase 2 study testing time-limited dual BCR inhibitor therapy with a BTK inhibitor acalabrutinib and a PI3Kδ inhibitor umbralisib. With the goal of enhancing depth of remission, a glycoengineered anti-CD20 antibody ublituximab was initiated during Cycle (C) 7. Methods In this investigator-sponsored trial, eligible patients with treatment-naïve (TN) or relapsed or refractory (RR) CLL received up to 24 cycles of AU2 (NCT04624633). Each cycle was 28 days. Daily oral doses of acalabrutinib (100mg BID) and umbralisib (800mg QD) began on C1 Day (D) 1. Ublituximab IV began on C7 for 6 cycles (D1, 2, 8, and 15 of C7, D1 of C8-12). Treatment was stopped after C12 if patients achieved complete response (CR) by IWCLL criteria, while all others continued acalabrutinib and umbralisib until C24. In March 2023, umbralisib was withdrawn from drug development, and those who were receiving study therapy at the time continued acalabrutinib alone until C24. The primary endpoint was the CR rate after C24. MRD was assessed in peripheral blood (PB) and bone marrow (BM) using multi-color flow cytometry at 10 -4. Results The study enrolled 29 patients from December 2020 to January 2022. The median age at enrollment was 63 years (range 40-77). Most patients were male (62%), had TN CLL (72%), and had unmutated IGHV (79%). RR CLL patients had a median of 1 prior line of therapy, most frequently (88%) with chemoimmunotherapy. Genetic alterations were commonly observed at study enrollment, including deletion 17p or TP53 mutation (21%), deletion 11q or ATM mutation (38%), trisomy 12 (24%), and mutations of NOTCH1(45%), SF3B1 (24%), and RAS/RAF pathway (21%). 7% had complex karyotype defined as ≥3 abnormalities. At a median follow-up of 23 months (range 2-29), with 7 patients still receiving therapy prior to reaching C24, there were no deaths, Richter's transformations, or CLL progression events on the study. The rates of CR, BM uMRD, and PB uMRD at best response were 30%, 44%, and 67%, respectively (Table 1). There were no statistically significant differences in CR and uMRD rates between TN and RR groups at best response. CR and BM uMRD rates improved during the second year of therapy (CR rate: 11% after C12, 28% after C24; BM uMRD rate: 22% after C12, 39% after C24). PB uMRD occurred earlier than BM uMRD, and the rate (44%) remained unchanged between C12 and C24. After completion of study therapy, PB MRD was monitored every 3 months. Five patients had MRD conversion at the end of therapy or shortly after treatment cessation. Median time from the last uMRD to detectable MRD (dMRD) in PB was 3 months (range 3-6). Most (80%, n=4/5) patients with MRD conversion had partial response or dMRD in BM at best response. Two patients stopped treatment early (due to the diagnosis of second cancer and G4 transaminitis, in 1 patient each). In addition, 7 (24%) patients stopped umbralisib between C15-19 due to discontinuation of drug supply; these patients remained on acalabrutinib monotherapy until C24. All others completed up to 24 cycles of treatment including 3 (10%) patients who stopped therapy per protocol after C12 once CR was achieved. Dose reduction of umbralisib (38%) was more common than acalabrutinib (7%) and was most frequently due to diarrhea (21%) and transaminitis (14%). Only 2 (7%) patients required temporary dose reduction of acalabrutinib to avoid drug-drug interaction. Notable adverse events included diarrhea or colitis (76%, 10% Grade 3 or higher [G≥3]), bruising (69%, 0% G≥3), transaminitis (62%, 17% G≥3), COVID-19 infection (55%, 7% G≥3), hypertension (52%, 10% G≥3), rash (24%, 0% G≥3), and pneumonitis (7%, 3% G≥3). One (3%) patient had Pneumocystis jirovecii pneumonia while being off of mandatory prophylaxis due to non-compliance. None had atrial fibrillation. Conclusions Dual inhibition of the BCR signaling pathway with up to 2 years of AU2 provided a time-limited treatment option for TN and RR CLL patients. Immune-related adverse events were frequently observed and required dose reduction of umbralisib in 38% of the patients but most were then able to stay on therapy. Longer follow-up is required to determine durability of remission off therapy.

Early Initiation of Oral Therapy with Cyclosporine and Eltrombopag for Treatment Naïve Severe Aplastic Anemia: Interim Results of a Phase II Trial

Introduction: Severe aplastic anemia (SAA), a life-threatening bone marrow failure disease, is treated with allogeneic bone marrow transplantation or immunosuppression (IST). Pancytopenia meeting “Camitta” criteria and an empty bone marrow (<30% cellularity) establish the diagnosis of SAA. However, neither diagnosis nor therapeutic interventions are straightforward, resulting in delays of therapy. SAA must be differentiated from hematologic malignancy, and constitutional forms should be excluded by functional or genetic testing. Administration of IST usually occurs at a tertiary care center, and in younger patients' evaluation for BMT is first required. Ongoing immune mediated destruction of stem cells further depletes marrow reserve and increases regenerative stress with such delays. In this phase II study, we tested the feasibility and safety of early initiation of cyclosporine (CSA) to block T cells and eltrombopag (EPAG) to stimulate hematopoiesis followed by standard of care therapies to expedite treatment (NCT04304820). Methods: Twenty-six patients with treatment-naive SAA were enrolled since 2020. Patients were 3 years or older and median age was 35 years. Exclusion criteria included a diagnosis or high clinical suspicion for inherited disease or evidence of myeloid neoplasm. To ensure rapid initiation of therapy, enrollment was not dependent on pending specialized tests (telomere length, chromosomal breakage, cytogenetics, or genomics). Lower dose CSA (2mg/kg) and full dose EPAG were initiated after confirming eligibility. Upon completion of evaluation and confirmation of acquired SAA diagnosis, all subjects received standard IST (horse ATG, CSA, and EPAG; Figure 1A). Primary feasibility endpoint assessed a composite measure of misdiagnosis, non-compliance, and treatment-related serious adverse events (TRSAE) during oral therapy. Secondary endpoints were efficacy at 6 months, relapse, clonal evolution, and overall survival. Results were compared to a historical cohort of 139 patients treated with hATG, CSA, and EPAG initiated the same day (NCT01623167). Results: All patients completed the protocol-defined treatment period, with median time on oral therapy of 17 days (range 0 - 86 days). All subjects ultimately were confirmed to have acquired SAA (no misdiagnoses), all tolerated oral treatment well without any TRSAE, and patients were compliant with local and study-site follow-up. Thus, there were zero events for the primary feasibility endpoint. A single SAE during oral treatment occurred in subject #1, enrolled at the height of the COVID pandemic and was severely ill with persistently positive COVID-19 PCR and recurrent ileitis requiring hospitalization care; his time to standard IST was the longest (86 days). There was significant increase in absolute neutrophil count (ANC; median 0.315x10 3/mL vs 0.570, p=0.041) in a brief interval of oral therapy prior to receiving hATG. There was also a trend towards improvement in absolute reticulocyte count (29x10 3/mL vs. 35.8) and a decrease in absolute lymphocyte count (1.5x10 3/mL vs. 1.3; Figure 1B). Compared to historical cohort, less patients (19% vs 52%) had very SAA (ANC <200 K/uL); age, sex, race, and pre-treatment blood counts were similar in two cohorts. Hematologic response occurred in 68% at 6 months with 45% complete responses, rates similar to the historical cohort (80% and 40%, respectively). Time to platelet and red blood cell transfusion independence was 43 and 51 days, respectively. Only age (18-40 years) was predictive for 6 month response. With median follow-up of 396 days, the cumulative incidence of relapse at 2 years was 17%, lower than in the historical cohort (27%). Clonal evolution to secondary myeloid malignancy was not increased compared to historical cohort; one subject had myelodysplastic syndrome with excess blasts 1 with deletion 20q, and two had transient trisomy 8 without dysplasia. Overall survival was 96.2%; no deaths occurred during study treatment period of oral medications only. Conclusion: Early initiation of CSA and EPAG is a feasible and safe approach to rapidly treat patients with SAA as a bridge to standard therapies and it may lead to improved blood counts, in turn, decreasing early infectious complications. Hematologic response was comparable to our historic cohort. Rates of long-term complications need to be confirmed in a larger cohort with ongoing study enrollment.

STAG2 Somatic Mutations Are Associated with Specific Dysplastic Megakaryocytic and Myeloid Cell Features in Myelodysplastic Syndrome

Introduction: Although myelodysplastic neoplasms/myelodysplastic syndromes (MDS) are driven by genetic mutations, their diagnosis relies on morphologic evaluation of abnormal hematopoiesis in the bone marrow. Only a small number of genetic abnormalities define bone marrow morphologic features in MDS, such as those harboring SF3B1 mutations and deletions of chromosome 5q. We hypothesized that there are additional genetic alterations and dysplastic morphologic features in MDS that have not been well-described in the literature. We assessed genetic morphologic associations between 50 commonly mutated genes and 10 morphologic features in a cohort of MDS bone marrows with a high degree of dysplasia. We validated and extended these findings in an independent cohort of myeloid neoplasms. STAG2 mutations were strongly associated with specific dysplastic megakaryocytic and myeloid cell features in both cohorts. Methods: We reviewed bone marrow core biopsies and aspirates from 272 MDS clinical cases (2013-2014) and selected 89 for further study based on the presence of prominent dysplastic features. Each case was independently evaluated by two pathologists for the following dysplastic features: small hypolobated megakaryocytes, widely separated megakaryocyte nuclei; abnormal myeloid nuclear segmentation, myeloid hypogranulation, Auer rods; ring sideroblasts, erythroid binucleation, irregular erythrocyte nuclei, erythroid nuclear cytoplasmic dyssynchrony, and erythroid karyorrhexis. Targeted next generation sequencing was performed using a 50 gene panel comprising the most common somatic myeloid mutations. For each dysplastic feature, univariate risk analysis was used to identify genetic mutations for use in multivariable analysis. Significant associations were validated through blinded morphologic review in an independent cohort of 155 bone marrow biopsies of myeloid neoplasms, comprised of 83 myelodysplastic syndromes, 33 myelodysplastic/myeloproliferative neoplasms and 39 acute myeloid leukemias, diagnosed between 2014 and 2019 and selected for mutations identified in the initial discovery cohort ( STAG2, RUNX1, SRSF2, ASXL1 and SETBP1) . Results: Pairwise analyses demonstrated broad patterns of genetic associations with myeloid/megakaryocytic dysplasia versus erythroid dysplasia (Panel 1). In multivariable analysis, STAG2 and SRSF2 mutations were significantly associated with megakaryocytes with widely separated nuclei ( STAG2, OR = 25.5, 95% CI [4.17, 493.5], P = 0.003; SRSF2, OR = 10.1, 95% CI [2.07, 75.0], P = 0.008). Mutations in STAG2 and SETBP1 were significantly associated with abnormal myeloid nuclear segmentation ( STAG2, OR = 7.08, 95% CI [1.94, 28.0], P = 0.003; SETBP1, OR = 12.2, 95% CI [1.29, 267.4], P = 0.04). Furthermore, STAG2 mutations were significantly associated with myeloid cell hypogranulation (OR = 12.7, 95% CI [3.10, 86.3], P = 0.002). Because this initial cohort was relatively small, which led to wide confidence intervals suggesting estimation instability, we validated and extended these findings in an independent cohort of myeloid neoplasms. In the validation cohort (enriched for mutations in STAG2, SRSF2, and SETBP1), STAG2 mutations were significantly associated with separated megakaryocyte nuclei (univariate OR = 4.18, 95% CI [1.98, 8.80], P = 0.0002), abnormal myeloid nuclear segmentation (univariate OR = 3.47, 95% CI [1.47, 8.22], P = 0.008), and myeloid cell hypogranulation (multivariable OR = 5.28, 95% CI [2.18, 13.4], P = 0.0003) (Panel 2). In contrast, morphologic associations with SRSF2 and SETBP1 mutations were not validated. Conclusion: STAG2 genetic alterations are strongly associated with the presence of separated megakaryocyte nuclei, abnormal myeloid nuclear segmentation and myeloid cell hypogranulation in MDS. Our data suggest that STAG2 may affect pathways involved in nuclear shape control and secondary granule formation. Panel 1: Pairwise associations between gene mutation and bone marrow morphology in MDS. N, number. Panel 2: Multivariable (black) and univariate (white) analysis in two independent cohorts showing significant gene associations with megakaryocytes with separated nuclei, abnormal myeloid nuclear segmentation, and myeloid cell hypogranulation. CI, confidence interval.

Late B Cell-Specific Dis3-Knockout Mice Do Not Develop Plasma Cell Neoplasm

Recent advances in next-generation sequencing have unveiled genetic abnormalities associated with multiple myeloma (MM). Of note, DIS3 mutations have been observed in ~10% of MM patients, and 13q deletion including the DIS3 gene locus are present in ~40% of MM patients. Furthermore, DIS3 mutations/deletions have been shown to be associated with poorer prognosis in MM. Regardless of high incidence of DIS3 mutations/deletions and their relation to adverse outcome, the roles of DIS3 in hematopoiesis and myelomagenesis remains incompletely understood. Here we show that Dis3 is required for normal hematopoiesis and Dis3 deficiency is not sufficient for the development of plasma cell neoplasm in mice. We first explored DIS3 functions in hematopoiesis by generating Dis3 conditional knockout (KO) mice (Dis3 fl/fl;Mx-Cre). To avoid possible effects of Dis3 deficiency on nonhematopoietic cells, we transplanted bone marrow (BM) cells from Dis3 fl/fl;Mx-Cre mice into lethally irradiated CD45.1 + recipient mice. Four weeks after transplantation, we knocked out Dis3 by inducing Cre recombinase via an intraperitoneal injection of Poly(I:C). The deletion of Dis3 in BM cells was confirmed by genotyping and quantitative real time PCR. Importantly, loss of Dis3 in hematopoietic cells resulted in severe pancytopenia at 2 weeks after Dis3 deletion. Consistent with this observation, Dis3 KO mice showed reduced BM counts with relative preservation of mature lymphocytes. A flow cytometric analysis of the BM exhibited lower frequencies of Lin -Sca-2 +c-Kit + (LSK), hematopoietic stem, and multipotent progenitor cells in Dis3 KO mice compared with wild-type (WT) mice. Dis3 KO mice also exhibited lower frequencies of common myeloid progenitors, granulocyte/macrophage progenitors, and megakaryocyte/erythroid progenitors compared with WT mice. A frequency of common lymphoid progenitors (CLPs) was comparable between WT and Dis3 KO mice, whereas absolute numbers of CLPs were significantly reduced in Dis3 KO mice than in WT mice. These results indicate that Dis3 is indispensable for normal hematopoiesis, and LSK and myeloid progenitor cells are more dependent on Dis3 than lymphoid progenitor cells. We next examined whether loss-of-function of Dis3 drives plasma cell neoplasm. To do so, we crossed Dis3 fl/wt or Dis3 fl/fl mice with Cgamma1-Cre mice and generated late B cell-specific Dis3 KO mice by activating Cre recombinase via immunizing with NP-CGG in these compound mice. However, these mice did not develop any B cell malignancies and shorten the survival compared with WT mice. In the samples of MM patients, the frequency of DIS3 mutations is significantly higher in t(14;16) samples than in those without t(14;16) (Walker et al. Blood 2018). We therefore utilized t(14;16) model mice (c-Maf TG) (Morito et al. Cancer Res 2011) and generated c-Maf TG; Dis3 fl/wt;Cgamma1-Cre and c-Maf TG; Dis3 flfl;Cgamma1-Cre mice. As reported (Morito et al. Cancer Res 2011), a small fraction of mice with c-Maf TG developed B cell lymphoma after a long latency. However, the addition of Dis3 KO did not increase the frequency of B cell lymphoma and shorten the survival compared with c-MAF TG mice. These results indicate that only Dis3 deficiency and the combination of c-Maf overexpression and Dis3 deficiency do not develop plasma cell neoplasm and suggest that additional oncogenic events are necessary for myelomagenesis. Further investigations are required for elucidating the mechanisms of how loss-of-function of DIS3 is involved in the development of MM.

Characterizing ATM Aberrations in Chronic Lymphocytic Leukemia (CLL): Prognostic Implications and Sensitivity to PARP Inhibition

Introduction ATM mutations (muts) frequently occur in CLL, yet their influence on ATM protein function and DNA break repair is poorly elucidated. Our prior study demonstrated functional hypomorphism of the rare germline variant L2307F in ATM and a higher occurrence of 11q deletions (del(11q)) with ATM germline variants in CLL (Lampson et al, JCO 2023). However, the role of other ATM germline variants in association with del(11q) or somatic muts remains unknown. Here, we analyzed the characteristics of CLL patients (pts) with ATM aberrancies and evaluated ATM function in primary CLL cells. Methods We retrospectively analyzed 278 CLL pts with ATM aberrancy, evaluated by clinical targeted sequencing from 2014 to 2019, as per our recent study (Lampson et al, JCO 2023). ATM, KAP1, and H2AX phosphorylation levels were examined after etoposide or irradiation (IR) exposure, by western blot or flow cytometry, in primary CLL cells with or without ATM aberrancy. We assessed the inhibitory effect of talazoparib, a PARP inhibitor, on CLL proliferation over 14 days using flow cytometry and Cell Trace Violet dye. Results We identified 294 ATM variants, 146 unique (germline N=74, somatic N=72). In CLL pts, 58 had dual ATM allele loss (biallelic group), including del(11q) together with only germline ATM variant(s) (N=29), only somatic mut(s) (N=18), or both (N= 11). 168 pts had ATM muts or variants without del(11q), including only germline (N=137), somatic (N=19), or both (N=12) ( ATM group), and 52 pts had del(11q) alone (11q group). Complex karyotype increased with ATM allele deficiency, particularly with 5+ abnormalities (complex karyotype 5+, biallelic vs 11q vs ATM: 22.6% vs 10.6% vs 5.8%, P=0.002). Unmutated IGHV was significantly higher in the groups with del(11q) versus ATM alone (biallelic vs 11q vs ATM: 85.1% vs 87.8% vs 53.9%, p<0.001). Interestingly, when we compared IGHV status in the ATM alone group with or without somatic ATM muts, unmutated IGHV significantly increased in those with somatic muts ( ATM-somatic vs ATM-germline alone, 81.8% vs 43.6%, p<0.001), and karyotypic complexity tended to be higher in the somatic ATM mut group (P=0.077). This might suggest that pts with ATM somatic muts have clinical characteristics and pathogenicity more similar to del(11q) as compared to those with germline muts. SF3B1 muts were more common in those with del(11q) (biallelic vs 11q vs ATM: 20.7% vs 26.9% vs 12.5%, P=0.036). For functional evaluation, we compared the five groups of primary CLL samples: del(11q) with somatic ATM mut with/without germline (11q+ ATM-S), del(11q) alone with no ATM muts (11q), somatic ATM muts without del(11q) with/without germline ( ATM-S), germline ATM muts alone ( ATM-G), and no ATM aberrancies (wild type, WT). Western blot demonstrated significantly lower phosphorylated protein levels (pATM, pKAP1, γH2AX) in response to DNA damage with etoposide in ATM aberrancy groups compared to WT (WT vs 11q, vs ATM-S, vs 11q+ ATM-S, all P<0.001 except for WT vs 11q in γH2AX, P<0.05) (Figure 1A). Flow cytometry also showed significantly lower phosphorylation levels of ATM after IR in 11q, ATM-S and 11q+ ATM-S groups compared to WT, while ATM-G group didn't show significance. To assess ATM deficient cell sensitivity to talazoparib, we compared proliferation inhibition across groups cocultured with talazoparib for 14 days. The 11q+ ATM-S group exhibited significantly greater sensitivity to talazoparib at lower dosage compared to the WT (talazoparib 0.1 μM, P<0.05; 0.5 μM, P=0.098) (Figure 1B). The monoallelic ATM deficient groups (del11q and ATM-G) tended to have lower proliferation, but not significantly. Higher concentrations of talazoparib (2.5μM) strongly inhibited proliferation of all CLLs including WT. Conclusions Pts with ATM somatic aberrancy including del11q had worse associated prognostic factors including unmutated IGHV and complex karyotype. Somatic events showed greater functional impact than some germline variants. CLL cells with ATM aberrancies had ATM pathway dysfunction, and those with biallelic ATM aberrancies were more sensitive to the PARP inhibitor, talazoparib, than WT. This work could potentially lead to additional avenues for treatment based on differential sensitivities of CLLs with ATM aberrancy. Further studies are needed to characterize specific ATM germline variants with or without somatic ATM events.