Del 5q Research Articles

Ibrutinib, Fludarabine, Cyclophosphamide and Obinutuzumab (iFCG) for Firstline Treatment of Patients with CLL with Mutated IGHV and without Del(17p)/ TP53 Mutation: Six-Year Follow-up Analyses

Background Patients (pts) with IGHV-mutated ( IGHV-M) CLL have favorable long-term outcomes after receiving first-line FCR (fludarabine, cyclophosphamide and rituximab). We designed an investigator-initiated, phase II trial with ibrutinib, fludarabine, cyclophosphamide, and obinutuzumab (iFCG) for previously untreated pts with IGHV-M CLL (NCT02629809), and we report here an updated analysis with a median follow-up of 72 months. Methods Inclusion criteria included diagnosis of previously untreated CLL/SLL needing treatment per iwCLL criteria, age ≥18, IGHV-M, absence of both del(17p) and TP53 mutation. Pts received 3 courses of iFCG. Pts achieving CR/CRi with undetectable MRD (U-MRD) in bone marrow (BM) (4-color flow-cytometry, sensitivity 10 -4) after 3 courses of iFCG received ibrutinib with obinutuzumab (iG) for 3 cycles, followed by ibrutinib monotherapy for 6 months. All other pts received iG for 9 cycles (C4-12). Pts with U-MRD (CR/CRi or PR) at end of Cycle 12 stopped all therapy, including ibrutinib. Response assessment was per 2008 iwCLL criteria with BM and CT scans every 3 months during the first year. After completion of all therapy, pts were followed by clinical examination, blood counts and peripheral blood MRD every 6 months. Results Between March 2016 and August 2018, 45 pts initiated treatment. Data cutoff was July 15, 2023. Baseline characteristics are shown in Table 1. All pts per study inclusion criterion had IGHV-M; however, 1 enrolled pt was later reclassified as IGHV-unmutated. A total of 69% pts had del(13q). After three cycles of iFCG, 39/45 (87%) pts achieved marrow U-MRD. Responses improved with continued therapy with 40/45 (89%) and 41/45 (91%) achieving marrow U-MRD after Cycles 6 and 12, respectively. Overall, 44/45 (98%) pts achieved marrow U-MRD as best response at any time during the study. Median follow-up duration is 72 months. 41/45 pts completed 12 cycles of treatment (4 pts came off study prior to Cycle 12). All 41 pts achieved marrow U-MRD and per protocol, discontinued ibrutinib. After a median follow-up of 61 mos post-discontinuing ibrutinib, 8 pts had MRD recurrence (defined as 2 consecutive values of ≥0.01% in peripheral blood by flow cytometry) at a median of 32 mos (range, 20-67 mos) after stopping all therapy. Of the 8 pts with MRD recurrence, 2 pts had clinical relapse (described below); remaining 6 pts are being monitored with no clinical progression or active therapy. The 6-year PFS and OS are 92.2% (95% CI= 77.7-97.4) and 97.7% (95% CI= 84.9-99.6), respectively. Two pts had clinical progression: one pt had IGHV 3-21; MRD recurred 28 mos after discontinuing ibrutinib, with clinical relapse 59 mos after discontinuing ibrutinib; this pt is now in remission with venetoclax-based therapy; the second pt with clinical relapse had IGHV-unmutated CLL, MRD recurred 24 mos after discontinuing ibrutinib, with clinical relapse 48 mos after discontinuing ibrutinib; this pt has not yet required therapy for relapse. No pt had progression to Richter transformation. One pt developed therapy-related myelodysplastic syndrome; this pt is being monitored for 58+ months without any active therapy for MDS with normal blood counts. One pt died from congestive heart failure during month 9 of the study. Conclusions iFCG regimen with only three cycles of combination chemotherapy achieves U-MRD rates of 98% in bone marrow on an intent-to-treat analysis and a 6-year PFS of 92% in IGHV-M CLL. These results are favorable compared to the 5-year PFS of approximately 65% with FCR (CLL10 trial) for the same genomic subgroup. Additionally, these results also appear favorable to the current targeted therapy regimens (such as BTKi, BCL2i+CD20 antibody) for IGHV-M CLL. With the caveat that the role of chemoimmunotherapy in CLL has significantly declined, the iFCG regimen provides for a very high rate of durable remissions among a chemo-sensitive subgroup of pts with CLL.

Loss of Mir-221/222 Cluster Expression Results in Short-Term Disease Progression and Poor Post-Treatment Outcome in Multiple Myeloma

Despite the notable progress that has been achieved in the realm of MM treatment, the persistence of elevated relapse rates and therapy resistance remain a substantial hindrance to effective management of the patients. Therefore, the development of modern tools to ameliorate patients' prognosis and predict treatment outcome is of first clinical priority. MicroRNAs (miRNAs) have emerged as powerful post-transcriptional regulators of gene expression, while recent advances in high-throughput sequencing techniques have unveiled their prognostic utility in numerous pathologies. Herein, using a miRNA-seq we have investigated miRNA profiles in association with Revised International Staging System (R-ISS), aiming to reveal potential MM-related miRNAs able to improve patients' risk stratification. Bone marrow (BM) aspiration samples were collected from 120 MM patients at diagnosis (screening cohort). Mononuclear cells were isolated using Ficoll-Paque, while CD138 + plasma cells were positively selected using anti-CD138 mAbs magnetic beads. miRNA-seq was performed in CD138 + cells from 8 R-ISS I, 8 R-ISS II and 8 R-ISS III MM patients. Following 3‘-end polyadenylation of total RNA, miR-221/222 levels were quantified in our screening cohort by RT-qPCR. Disease progression (relapse and/or death) and patients’ mortality were assessed as clinical endpoint events, while internal validation was accomplished by bootstrap Cox proportional regression analysis. Aash et al. 2023 (n=86) and Kruykov et al. 2016 (n=149) served as external validation cohorts. miRNA-seq revealed miR-221/222 to be concurrently downregulated in R-ISS III versus R-ISS I/II MM patients (miR-221: FC=0.356; miR-222: FC=0.357; Fig.1B,C). The analysis of our screening cohort documented that CD138 + miR-221/222 loss is significantly associated with higher risk for short-term disease progression ( p=0.010; Fig.1D) and poor survival ( p=0.001; Fig.1E) of MM patients. Furthermore, the analysis of the two independent validation cohorts (Aass et al. cohort A, p=0.019; and Kryukov et al. cohort B, p=0.013) clearly confirmed the worse treatment outcome of the patients with miR-221/222 loss (Fig.1F,G). Moreover, miR-221/222-fitted multivariate models demonstrated the ability of miR-221/222 cluster to ameliorate the clinical routine of the established MM prognostic markers, including “R-ISS stage”, “high-risk cytogenetics” [+1q21, t (4;14) del(17p13), t(14;16), t(11;14), del(13q)] and “response to 1 st line therapy” (IMWG guidelines). In this context, the evaluation of CD138 + miR-221/222 levels significantly improved the risk-stratification of MM patients, resulting in the advanced positive prediction of patients' poor treatment outcome within R-ISS III (PFS: p=0.006, OS: p=0.019; Fig.2A,B) and high-risk cytogenetics groups (PFS: p=0.025, OS: p=0.022; Fig.2C,D). Finally, focusing on patients' response to 1 st line therapy stratification, loss of miR-221/222 could efficiently define optimal (sCR/CR/VGPR) and poor (PR/SD/PD) responders' subgroups (PFS: p<0.001, OS: p<0.001; Fig.2E,F). In conclusion, we identified miR-221/222 loss in CD138 + plasma cells as a powerful independent predictor of patients' risk for disease progression and poor treatment outcome, while miR-221/222-fitted multivariate prognostic models resulted to improved patients' risk-stratification and prediction of MM treatment outcome.

A Phase II Study of Intermittent Duvelisib Dosing in Patients with Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma (CLL/SLL)

Background. Targeting phosphatidylinositol 3-kinase (PI3K) has emerged as an efficacious approach for treatment of chronic lymphocytic leukemia (CLL) and non-Hodgkin lymphoma (NHL). However, toxicities of the PI3K inhibitors are an important concern limiting their use. Duvelisib is a potent oral inhibitor of both the PI3K-δ and PI3K-γ isoforms with proven efficacy in CLL/SLL. Here we report the results of a phase 2 study evaluating efficacy and safety of duvelisib with intermittent dosing in patients with relapsed/refractory CLL/SLL Methods. This open-label, single arm, phase 2 study enrolled patients with CLL/SLL treated with at least 1 prior line of therapy with active disease as defined by the iWCLL 2008 criteria. Duvelisib was given at a dose of 25 mg PO BID for 28-day cycles for a total of 12 weeks during the induction phase, followed by 75 mg PO BID 2 days on and 5 days off for repeated 28-day cycles during the maintenance phase until death, intolerance or disease progression. The primary endpoint was progression free survival (PFS) at 12 months; secondary endpoints were safety and clinical benefit. The trial was originally planned to enroll 27 patients but was stopped early due to difficulties with enrollment following changing FDA guidance for the use of PI3K inhibitors. Results. Fifteen patients were enrolled. Median age was 74 (59-82) years, 8/15 (53%) were female; patients were primarily Caucasian (13/15; 87%); performance status was 0-1, with 27% (4/15) ECOG 0 and 73% (11/15) ECOG 1. This was a heavily pre-treated patient population with a median of 3 prior lines of therapy (1-6). Among patients where results were available, 79% (11/14) had abnormal FISH results including 36% with TP53 gene loss, 27% del(13q), and 18% del(11q). Sixty-seven percent (8/12) had unmutated IGHV. Of the 15 patients treated, 4 were not evaluable for efficacy due to coming off study early for toxicity (2), development of MDS unrelated to study drug (1) or death due to complications from COVID-19 infection (1). Among the 11 efficacy-evaluable patients, 82% achieved PR, and 18% had stable disease. The 12-month PFS was 43% (95%CI: 18%-66%) and the median PFS was 9.9 months (95% CI: 5.5-NA). Among the 9 responders, the median duration of response (DOR) was 5.3 months (95%CI: 1.9-NA) and 12-month DOR was 22% (95%CI:3%-51%). Five patients (33%) discontinued therapy due to adverse events, which occurred during the induction phase in 4/5 of the patients. Five patients (33%) discontinued due to progressive disease - all during the maintenance phase of treatment. Additionally, 2 patients discontinued due to MD decision; one patient developed MDS which was unrelated to duvelisib; one patient died during treatment due to complications from COVID-19. Treatment was generally well tolerated with the most common grade 3 or higher adverse events being leukocytosis (20%), alanine aminotransferase (ALT) increase (13%), aspartate aminotransferase (AST) increase (13%), oral mucositis (13%) and colitis (13%). The adverse events leading to treatment discontinuation occurred primarily during induction. The most common adverse events of any grade included fatigue in 5 patients (33%), leukocytosis, vomiting, ALT increase, AST increase, diarrhea, and elevation of alkaline phosphatase, which occurred in 4 patients each (27%). Conclusions. We report the results of an open-label, phase 2 study utilizing a continuous dosing induction phase followed by an intermittent dosing maintenance phase of the PI3K inhibitor duvelisib in patients with relapsed/refractory CLL/SLL. Patients who received duvelisib on an intermittent schedule achieved some clinical benefit, however, the desired 12-month PFS goal of 50% was not reached. Adverse events in general were manageable and mainly related to gastrointestinal and liver toxicity, and patient died during treatment from complications from COVID-19 pneumonia. After an initial 12 weeks of continuous duvelisib treatment, the incorporation of intermittent dosing appears to be a viable option for patients with previously treated CLL/SLL.

Comparison of Venetoclax Based Treatments for Patients with Relapsed/Refractory Chronic Lymphocytic Leukemia

Background: Venetoclax (Ven) is a BCL-2 inhibitor that produces deep responses with high rates of undetectable minimal residual disease (uMRD) for patients (pts) with chronic lymphocytic leukemia (CLL) (Al-Sawaf et al. 2020). Currently, ven is FDA approved as either monotherapy (mono) or in combination (combo) with rituximab (R) In patients with relapsed/refractory (R/R) CLL (Seymour et al. 2018). However, the optimal ven based treatment (tx) for pts with R/R CLL either as mono, or in combo with anti-CD20 monoclonal antibody (mab), or bruton tyrosine kinase inhibitor (BTKi) is uncertain. We performed a single institution retrospective analysis of pts with R/R CLL treated with ven based regimens evaluating efficacy of different ven based txs. Methods: 98 pts with R/R CLL treated between the years of 2012 and 2023 were evaluated. Ven based treatment consisted of ven mono or in combo with R, obinutuzumab (G), or ibrutinib (BTKi) with standard ven dose ramp up to a maximum dose of 400mg daily. R and G were administered per FDA standard dosing. Ibrutinib was administered as 420mg daily, as either fixed or continuous duration tx. Response assessment was performed using iwCLL criteria. Minimal residual disease (MRD) was assessed by multi-parametric peripheral blood flow cytometry with a sensitivity of 10 -4. Time-to-event analyses were performed with the Kaplan-Meier method, with log-rank test used to assess statistically significant differences between variables. Hazard ratios (HR) were calculated by use of Cox proportional modelling. Results: The pts had a median age of 68 years (range; 46-89). Rai stage at time of tx initiation with ven: I 14.2%; II 36.3%; III 8.8%; Stage IV 40.7%. The median number of previous txs was 4 (range; 1-14). Pts harbored the following cytogenetic abnormalities: del(13q) 50.5%; del(11q) 18.5%; trisomy 12 15.5%; normal 15.5%; del(17p)/TP53 mutation 24.7%; and complex in 33%. Seventy percent of pts harbored an unmutated immunoglobulin heavy chain. 25.5% of pts had genomic complexity, with ≥ 5 gene mutations. 43.9% of pts were treated with ven mono; 19.4% were treated with venR; 25.5% of pts were treated with venG; and 11.2% of pts were treated with ven + BTKi. The median number of months of ven based tx was 16.3 (range; 0.9-118.6). 14.3% of pts currently remain on ven. 60.8% of pts had progression after ven based tx; with 62.2% requiring additional tx. 15.3% of pts developed Richter's Transformation. The best overall response for the cohort was: CR 67%; PR 24.5%; SD 1.1%; and PD 7.4%. The best MRD response for the whole cohort was uMRD 76.8%; low MRD 19.5; and high MRD 3.6%. uMRD as best MRD response occurred in 66.7% of ven mono; 82.4% of venR; 86.4% of venG; and 70% of ven + BTKi treated pts. With a median follow-up of 52 months (mo), the median progression-free survival (PFS) for the whole cohort was 67.8 mo. Ven combo had superior PFS to ven mono; median PFS 76.6 vs 58.9 mo (p = 0.04; HR 0.5037; 95% CI 0.2583 - 0.9635). Among the combination treatment approaches, there was a trend for improved PFS for venG compared to ven mono; median PFS not reached (NR) vs 58.9 mo (p = 0.08; HR 0.4385; 95% CI 0.1608 - 1.0240). Similarly, there was also a trend to improved PFS for ven + BTKi compared to ven mono; median PFS NR vs 58.9 mo (p = 0.07; HR 0.2895; 95% CI 0.0462 - 0.9950). Both the presence of del17p/TP53 mutation; and the presence of MRD (+MRD) 12 months after stopping ven based tx were associated with inferior PFS. The median PFS for pts without del17p/TP53 mutation vs with del17p/TP53 mutation was 118 vs 39.7 mo (p < 0.0001; HR 0.2242; 95% CI 0.0533 - 0.8366). Median PFS for pts with uMRD vs +MRD 12 months after ven was NR vs 42.8 mo (p = 0.0001; HR 0.0689; 95% CI 0.0037 - 0.3810). Conclusions : In a high-risk population of pts with R/R CLL, we found that ven based tx leads to durable remissions, with high rates of uMRD. Combo approaches with the addition of either an anti-CD20mab or BTKi led to improved PFS. While venR is the current FDA approved combo regimen for pts with R/R CLL, we found that there was a trend for improved PFS with either venG or ven + BTKi compared to ven mono. Both the presence of a del17p/TP53 mutation and the presence of MRD 12 months after stopping ven based tx significantly adversely affected PFS. However, pts who maintained uMRD 12 months after completing ven, had exceptionally durable long-term remission. This has possible implications for employing MRD adapted txs for pts with CLL.

Association Vs Causation: Epidemiologic Clues As to the Autoimmune Pathogenesis of MDS

Multiple clinical associations of MDS and autoimmunity have been described, but the pathogenesis and cause-effect relationship are likely diverse and possibly intertwining. Telomeropathies, while increasing risk of bone marrow failure, can be also associated with liver or lung fibrosis and therapies for Wegener's granulomatosis can predispose to MDS. Moreover, clonal hematopoiesis (CH) seems to be more prevalent in some autoimmune diseases 1 (AD) perpetuating a process that may ultimately lead to increased risk of MDS. Reverse scenarios are also possible and AD can be a result of MDS as a form of paraneoplastic syndrome. The recently established relationship of somatic UBA1 mutations and MDS with autoimmune manifestations exemplifies such a scenario e.g., VEXAS syndrome 2. This remarkable configuration prompted us to systematically investigate the relationships between autoimmune symptomatology and MDS including genomic features such as UBA1 mutations, pathomorphological phenotypes, and demographics. We have investigated 1,903 MDS patients for the presence and the anamnestic evidence of AD. A total of 197 patients (about 10%) had a concurrent well-defined AD (5.3%) or positive inflammatory/autoimmune markers (4.9%; fibromyalgia and chronic fatigue syndrome invoked 0.3% of MDS cases and were not counted). Of those, polymyalgia rheumatica, systemic lupus erythematosus and rheumatoid arthritis were most common accounting for 13%, 5.5% and 19% of MDS cases with autoimmunity. The remaining 60% involved the presence of serological markers such as ANA, anti-RNP and anti-SSA among others (45%, 4%, 2%, respectively) without fulfilling the criteria for specific autoimmune entities. The gender distribution of cases with MDS/autoimmune features was similar to the general MDS demographics and cases without autoimmune conditions. A similar distribution was seen among males and females in both groups, with males representing 84% of each subgroup and females accounting for 16%. When stratified by risk criteria, 58% of patients with MDS/AD were found to have low risk disease (<5% of blasts) compared to patients without AD (46%; p= .74), while intermediate to high risk (HR) categories were seen in 42% and 52% (p= .74), respectively. While trisomy 8 and complex karyotype were underrepresented in MDS with AD (15% vs 22%, 4.5% vs 10%), del(11q), del(12q) and del(20q) were more common among patients with AD (10% vs 5.8%). When we screened the genomic landscape of AD/MDS, we found more mutations in TET2 (24 vs 13%, p= .004), SF3B1 (14 vs 8%, p= .026), BCORL1 (5 vs 1.5%, p= .026), DNMT3A (13 vs 6%, p= .003), IDH1 (3 vs 0.8%, p= .01), and CEBPA (3 vs 0.8%, p= .04) compared to patients without AD ( Fig.1) With a median follow up of 19 months, female patients with AD showed better 1-year survival rate of 89% vs 65% in cases without AD, (p= .044). A similar trend was seen for transformation to AML. However, such differences were not found among males. Next, we determined the etiologic fraction of the MDS/AD clinical dyad explained by the presence of VEXAS by screening UBA1 mutation in our cohort. We found mutations in 0.5% of MDS/AD vs 0.05% of the total cohort (p=0.1). To further expand on MDS association with AD, we investigated other potential autoimmune syndromes and found 0.5% of MDS with co-associated LGL with 1/3 of them presenting with RA. Notably, in the hypocellular MDS subgroup (n=175), 9.7% had concomitant AD (p= .89). Similarly, 0.3% of evaluable patients had Sweet syndrome, of which 16% associated with autoimmune conditions. Finally, since AD appear to be frequent in MDS, we queried whether in our internal cohort of CHIP patients (n=115), their prevalence could be analogous. Indeed, AD were present in a fraction similar to that of manifest MDS (around 5%). Moreover, in all of these patients, similar to those with MDS, the autoimmune diagnosis preceded that of CHIP with the caveat that, unlike MDS, CHIP may have evolved much sooner than the original diagnosis but was not screened. Our study provides valuable insights into the intricate relationship between MDS and AD. Our findings demonstrate that MDS and autoimmunity are linked through diverse mechanisms, with potential cause-effect relationships existing in both directions. Figure 1. Frequency of mutations Graph shows frequency of mutations among patients with autoimmune diseases (AD) in MDS versus those without AD.* p<0.05, **p<0.001.

Del(20q) As a Somatic Gene Rescue in Adult Patients: Can Germline Mutations Other Than SBDS be Found in Affected Patients?

Deletions involving chromosome 20 (20q-) are present in up to 5-8% of myeloid neoplasms (MN) and have been associated with either myelodysplastic (MDS) or myeloproliferative (MPN) features, chiefly myelofibrosis. Theoretically, any chromosomal deletion may result in haploinsufficient expression of tumor suppressor genes (TSGs) or in loss of a protective allele in heterozygous carriers of germline (GL) variants or heterozygous somatic (SM) mutations. However, deletions have also been implicated as a maladaptive somatic gene rescue (SGR) event in carriers of GL bone marrow failure (BMF) genes such as SAMD9 and SBDS. The latter is found in Shwachman-Diamond syndrome whereby the upregulated EIF6 gene, responsible for hematopoietic dysfunction, is clonally removed by SM 20q deletion event. We identified an interesting 35-years-old patient with mild cytopenia and 20q- in which a cryptic homozygous SBDS c.A148T GL mutation was found. This prompted us to search in other adult patients with 20q deletion for: i) other cases with SBDS gene alteration (both hetero and homozygous), ii) other GL variants which could be clonally relieved by compensatory 20q- or, iii) disease-prone GL variants on 20q, whereby either disease-prone suppressive allele is included in the deleted region. Within a cohort of 5,308 cases with various MN, 215 patients with 20q- were identified. WES results were available for 350 patients. We applied a stringent bioanalytic algorithm to identify unique GL alterations (not deposited in SM databases) in genes expressed in hematopoietic tissues and involved in BMF and cancer, and a population allelic frequency of <1% which were classified as pathogenic (P), likely pathogenic (LP), and VUS with particular level of clinical suspicion (sVUS). In 76 of 215 patients with 20q-, 346 GL mutations in genes of potential interest were identified and further analyzed. No P/LP variants were detected on genes within commonly deleted region on chr.20q, and no additional carriers of SBDS variants were found. However, we identified 9 pathogenic GL variants in potentially pertinent genes including GL alterations in DDX41, STAG2 and TP53 which have been described in the context of MN. However, these gene variants were also present in patients with diploid 20q. The remaining 6 variants included heterozygous P/LP GL alterations in 3 different Fanconi anemia genes ( FANCA, FANCM, FANCD2), SUZ12, and TINF2. The latter, TINF2, a telosome gene, known to be mutated in dyskeratosis congenita (DC), carried an LOF c.605-1G>A in a patient with MDS/MPN with a family history of cancer who later developed 20q-. The patient did not show any symptoms of DC-like features, which usually present at an early age. Since FANCA LOF with SGR via overepression of EIF6 has previously been described 1, we investigated and did not identify any cases in our cohort of EIF6 SGR resultant overexpression. While occasional patients with no previously diagnosed SBDS can be found among MDS with 20q-, screening for SBDS genes demonstrates that such a genetic configuration among adult patients with 20q is very rare. In addition, only 9 out of 215 patients with 20q- carried other pathogenic GL variants in non-recurrent genes which appear to be likely coincidental. This suggests that del20q is not a SGR in response to a GL mutation, but rather a SGR due to other aforementioned mechanisms, which are currently being explored in our cohort of patients.

Clonal Hematopoiesis Is Associated with Severe COVID-19 Enhancing Inflammatory Responses in Myeloid Cells

Background Clonal hematopoiesis (CH) is prevalent among aged populations and highlighted because its association with not only hematological malignancies but various benign diseases (e.g. cardiovascular diseases). Of particular interest among these diseases is COVID-19. To date, the association between severe COVID-19 and CH-related gene mutations or mosaic chromosomal alterations (mCAs) was examined using biobank samples taken long before the pandemic and the association has not been tested in a sufficiently large cohort of patients on the basis of CH evaluated at the time of COVID-19 diagnosis. Moreover, no study examined the joint effect of gene mutations and mCAs. The mechanism of the association between severe COVID-19 and CH has not been addressed either. Methods To address these issues we enrolled a total of 4,541 patients with COVID-19, of whom 54% had a severe infection. We performed targeted-capture sequencing of 42 CH-related genes and SNP-array analysis to detect CH-related mutations and mCAs. We also performed RNA-seq (n=987) of whole blood samples and plasma proteomic analysis (n=1,200) using the Olink technology to investigate the effect of biological consequence of CH, which was applied to understand the underlying mechanism of sever COVID-19. Results We identified gene mutations and mCAs in 16.3% and 6.2% of COVID-19 patients, respectively. They coexisted in 2.4% patients. As reported in CH in normal individuals, most frequent alterations included mutations in DNMT3A (7.6%), TET2 (4.1%), ASXL1 (1.4%), PPM1D (1.7%), and mCAs such as 14qUPD, and del(20q). To evaluate the risk of severe COVID-19 conferred by CH, we compared the age-stratified frequencies of CH between severe and non-severe COVID-19 patients (Figure, a). Focusing on CH in ≧10% clonal fractions, CH was significantly enriched in severe COVID-19 in elderly patients, we detected a significant enrichment of cases with both gene mutations and mCAs and isolated gene mutations, but not that of isolated mCAs, in severe cases. Multivariable logistic regression analysis with adjustment for age and sex revealed the significant association of CH defined either CH-mutations or mCA with severe COVID-19 with an odds ratio (OR) of 1.34 [95%CI=1.03-1.84] in patients aged ≥65 years. Particularly, CH defined by combined gene mutations and mCAs conferred a remarkable increase in the risk of severe COVID-19 [OR=12.1, 95%CI=1.61-90.6], suggesting the presence of their synergistic impact on severe COVID-19. To elucidate the underlying mechanism of the observed association between severe COVID-19 and CH, we next evaluated the transcriptomic/proteomic features of severe COVID-19 and CH (Figure, b). In severe COVID-19, multiple inflammatory pathways including IFN-α/γ, TNF-α, and IL-6 responses were consistently up-regulated in both transcriptomic and proteomic analysis. Similar to these features of severe COVID-19, CH was also associated with inflammatory response and IFN-α/γ responses in RNA expression while the impact of CH on protein expression was not prominent. To further clarify the transcriptomic features of severe COVID-19 and CH, we performed deconvolution analysis of gene expression to estimate the fraction of each cell component and cell-type-specific expression profiles. Severe COVID-19 was characterized by elevated fractions of neutrophils, activated dendritic cells (DCs), and decreased fractions of several types of lymphocytes, while only a marginal increase of activated DCs was observed in CH. Cell-type-specific pathway analysis revealed up-regulations of inflammatory responses and IL-6/TNF-a signaling in neutrophils/monocytes were associated with both severe COVID-19 and CH independently, suggesting that CH might be involved in the development of severe COVID-19 through the augmentation of inflammatory responses in these myeloid cells, which are further augmented by increased neutrophils induced by COVID-19 independent of CH. Conclusion CH was significantly associated with an increased risk of severe COVID-19, particularly when the patients had both gene mutations and mCAs, where the augmented inflammatory responses by myeloid cells can be a mechanism of severe COVID-19 risk conferred by CH. Our findings highlight the link between the mechanism of severe COVID-19 and the biological effects of CH.

Orelabrutinib, Fludarabine, Cyclophosphamide, and Obinutuzumab (OFCG) for First-Line Treatment of Chronic Lymphocytic Leukemia: A Multicenter, Investigator-Initiated Study (cwCLL-001 Study)

Background: A phase II trial has shown, first-line treatment with iFCG (ibrutinib, fludarabine, cyclophosphamide, and obinutuzumab) led to a bone marrow (BM) undetectable minimal residual disease (uMRD) rate of 98% (44/45) as best response in treatment-naïve patients with chronic lymphocytic leukemia/small lymphocytic leukemia (CLL/SLL). But this study[1] does not include patients with unmutated immunoglobulin heavy⁃chain variable region gene ( IGHV) and/or del(17p)/ TP53 mutation, and ibrutinib was the first generation BTK (BTKi) which had relatively high off-target adverse effects (AEs). Our study has demonstrated the efficacy and safety of the second generation BTKi orelabrutinib in patients with relapsed/refractory CLL [2]. Therefore, we used orelabrutinib (O), and initiated the phase II OFCG trial in younger, fit patients with previously untreated CLL/SLL unrestricted by IGHV mutation status and del(17p)/ TP53 aberrations (cwCLL-001 study, NCT05322733). Methods：This is a multicenter, open-label, non-randomized phase II study for previously untreated patients with CLL/SLL without restriction by del(17p)/ TP53 aberrations and/or IGHV mutation status. A 7-day lead-in period with single-agent oral orelabrutinib（150 mg daily）was given in all patients, followed by OFCG regimen which consisted of orelabrutinib, intravenous Obinutuzumab, fludarabine and cyclophosphamide for up to three 28-day cycles. MRD was detected by 8 multi-color flow cytometry (FCM) at 10 -4 sensitivity and cloneSEQ using NGS (next generation sequencing) assay with a sensitivity of up to 10 −6. If the patients could achieve undetectable MRD in BM, they will discontinue FC and receive 3 cycles of OG (orelabrutinib and obinutuzumab). Otherwise, the patients will receive another 3 cycles of OFCG. Patients will discontinue obinutuzumab if they achieve BM uMRD after 6 cycles and continue six additional cycles of orelabrutinib; all other patients will receive six cycles of OG. Patients who achieved BM uMRD after 12 cycles discontinue all treatments, otherwise will continue orelabrutinib for up to additional 1 year (Fig. 1). The primary endpoint is the percentage of uMRD in BM after 6 cycles by FCM (at 10 -4 sensitivity). The secondary endpoint is the percentage of uMRD in BM and peripheral blood (PB) at other key time points by FCM, best overall response rate (ORR), complete response rate (CRR), progression-free survival (PFS), 2- and 3-year PFS rate, duration of response (DOR), overall survival (OS), 3-year OS rate as well as safety. The percentage of uMRD by NGS is an exploratory endpoint. Results：From 30 May 2022 to 30 Jun 2023, 25 patients were enrolled. Median age was 49 years old (range, 23-62). Unmutated IGHV, TP53 mutation/del(17p) and del(11q) were detected in 56.5% (13/23), 16.0% (4/25), and 24.0% (6/25) of patients, respectively. At data cut off (30 Jun 2023), 19 patients completed 3 cycles of OFCG and were evaluable. 75% (15/20, 1 patient who off study was assessed at the end of C2 cycle) of patients achieved PB uMRD and 57.9% (11/19) achieved BM uMRD by FCM, ORR and CR/CRi rate was 100% (18/18) and 38.9% (7/18) (Fig. 2). One patient died after cycle 3 due to COVID-19 infection. 16 patients completed 6 cycles, 14 of them were evaluable and achieved deeper response irrespective of different strategies during cycle 4 to 6, PB uMRD and BM uMRD was 100% (14/14) and 85.7% (12/14) by FCM, and the ORR and CRR was 100% (14/14) and 57.1% (8/14), respectively. In IGHV unmutated subgroup, ORR was 100% (10/10) with 50% (5/10) CRR, 87.5% (7/8) patients achieved BM uMRD by FCM after cycle 6. The results of MRD response by NGS assay will be presented in the formal report. 91.7% patients experienced at least one treatment emergent AE at the data cutoff. Most AEs were mild and tolerable. The most frequent AEs (≥10% of any grade) were neutropenia, leukopenia and thrombocytopenia. No bleeding or cardiovascular AEs greater than grade 3 occurred in these patients. Overall, OFCG demonstrated a favorable safety profile. Conclusion：This is the first clinical trial exploring the efficacy and safety of the second generation BTKi plus chemoimmunotherapy in patients with CLL. The OFCG regimen shows a rapid and deep molecular remission with a pleasant safety profile in the TN CLL patients including the ones with unfavorable factors.

Extended Follow up of a Phase 2 Study of Early Intervention with Lenalidomide in Patients with High-Risk Chronic Lymphocytic Leukemia

CONCLUSIONS Lenalidomide (LEN) is an effective therapy for chronic lymphocytic leukemia (CLL) and has immunomodulatory effects that were hypothesized to improve immune function in patients (pts) with untreated early stage CLL. A NCI/CTEP sponsored phase 2 study (NCT01351896) randomized asymptomatic pts with high-risk CLL to receive LEN either concurrent with or delayed from (3 months after 1st dose) two doses of 13-valent protein-conjugated pneumococcal vaccine (PCV13). The primary endpoint was the proportion of pts who achieve an antibody response to the 2nd PCV13 vaccine and was not significantly different between groups (Thangavadivel et al., Clinical Cancer Research 2020). Despite this, many pts experienced effective CLL disease control with LEN. Here we report long-term results from this trial to examine the impact of LEN early treatment on CLL disease course, complicating infections (INF), and second neoplasms (SN). Pts ≥18 and <80 years-old who had CLL with a high-risk feature, defined as FISH positive for del(17)(p13.1) and/or del(11)(q22.3), complex karyotype (≥3 abnormalities), or unmutated IGHV status, no prior treatment, and no iwCLL 2008 criteria for treatment were eligible. LEN was started at 2.5mg daily and increased to 5mg as tolerated. Data on INF and SN was determined from study adverse events and graded (gr) using CTCAE v4.0 and 5.0. Overall survival (OS) and progression-free survival (PFS) were calculated from the start of LEN and discontinuation of LEN, and analyzed using the Kaplan-Meier method. Time to next therapy (TTNT) was calculated from start or discontinuation of LEN to the initiation of next therapy treating death without new therapy as a competing risk. Data cut for analysis was 6/12/2023. A total of 49 pts were enrolled between 11/2011 and 7/2014. The median age was 59 (range 40-70) years, 69% were men, and 96% were Caucasian. In terms of CLL features, 94% (46/49) were IGHV unmutated, 47% (23/49) had complex karyotype, 14% (7/49) had del(17)(p13.1), and 31% (15/49) had del(11q)(q22.2). The median follow-up from LEN start was 4.6 (range 0.4-11.2) years and median time on LEN treatment was 3.7 (range 0.02-10.1) years with 2 pts remaining on LEN at 9.7 and 10.1 years. The median PFS after starting LEN was 5.7 (95% CI: 3.2-6.4) years with an estimated 8-year PFS of 25.9% (95% CI: 13.9%-39.6%) (Figure). Eleven pts had progressive disease (PD) at the time of LEN discontinuation and their median time from first dose of LEN to PD was 3.7 (range 0.3-6.0) years. For those who discontinued without PD, the median PFS from discontinuation was 1.5 (95% CI: 0.6-2.6) years. For those who initiated a subsequent therapy, the median TTNT from starting LEN was 4.4 (range 0.3-9.1) years and from discontinuing LEN was 1.1 (range 0.1-7.8) years. There were 7 deaths, and the median OS was not reached with an estimated 8-year OS of 73.9% (95% CI: 51.6%-87.2%). There were 217 episodes of INF that occurred in 88% (43/49) of pts. Patients experienced multiple INF: 24 (49%) pts had 1-3 INFs and 19 (39%) had ≥3 INFs with 5 of those having >10 INFs. The most frequent INFs were upper respiratory (n=71), sinus (n=37), skin and soft tissue (n=27), and lower respiratory (n=22) (Table). INFs were gr 1-2 in 95% of cases. Gr ≥3 INF were experienced by 18% (9/49) of patients with 10 events. There were 9 gr 3 INFs (lower respiratory tract n=4, kidney n=1, urinary tract n=1, appendix n=1, joint n=1, meninges n=1) and 1 gr 5 COVID-19 INF which occurred in a pt who discontinued LEN >2 years prior. The rate of gr ≥3 INF was 3.8 (95% CI: 1.8-7.0) per 100-person-years. SN were experienced by 8 pts who had 19 SNs. The most common SN were non-melanoma skin cancers (n=15). Other SN were lung adenocarcinoma (n=2 in 1 pt), melanoma in situ (n=1), and squamous cell carcinoma in a parotid lymph node from a skin SCC (n=1). The rate SN was 7.2 (95% CI 4.3-11.3) per 100-person-years. There were no cases of acute leukemia. In this population of pts with CLL with high-risk disease features predictive of need for earlier treatment, LEN resulted in a prolonged time to subsequent therapy, even in cases of LEN discontinuation. The incidence of gr ≥3 INFs and SN were as expected for this population supporting that LEN does not increase risk for these complications.

Telomere Length and DNA Methylation Epitype Both Provide Independent Prognostic Information in CLL Patients; Data from the UK CLL4, Arctic and Admire Clinical Trials

The presence of TP53 aberrations ( TP53ab) and/or unmutated IGHV genes (U-CLL) helps select initial treatment for CLL patients (Hallek 2018 & Walewska 2022). However, many other biomarkers identified in recent years have failed to impact clinical decisions due to their coexistence with poor-risk indicators and uncertainty in their predictive abilities, often without suitable validation in long-term Phase II/III trials with comprehensive molecular analysis. We evaluated the clinical significance of two biomarkers, DNA methylation-based epitype (DME) and telomere length (TL), in (immuno-)chemotherapy clinical trials using samples from UKCLL4 (n=304) and ARCTIC/ADMIRE (ARC/ADM) (n=215). To our knowledge, DME and TL have not been assessed in a single study. Therefore, we utilized previously published DME (Wojdacz, 2019) and TL data (Strefford, 2015 & Norris, 2019), supplemented with new MMQ-PCR data (n=60). TL cut-offs of short (TL-S, <2.92kb), intermediate (TL-I, 2.92-3.57kb), and long (TL-L, >3.57kb) and DME classifications of n-CLL (naive B-cell-like), i-CLL (intermediate B-cell-like) and m-CLL (memory B-cell-like) were employed. 73% of m-CLL and 50% of n-CLL patients harboured TL-L and TL-S, respectively (p<0.001, Figure 1). Additionally, n-CLL and TL-S were associated with poor-risk indicators, such as TP53ab and del(11q) (p<0.05, Figure 1). We then assessed the impact of 10 clinico-biological features, including DME, TL, age and treatment arm, on progression-free survival (PFS) and overall survival (OS) in CLL4 and ARC/ADM cohorts using univariate analysis (UA). The n-CLL group exhibited the shortest PFS and OS in the ARC/ADM cohort (PFS hazard ratio (HR):4.47, 95% confidence interval (CI):2.56-7.82 & OS HR:3.95, CI:1.66-9.35, p<0.01), greater than the presence of TP53ab (PFS HR:4.39, CI:2.69-7.17 & OS HR:3.77, CI:1.94-7.33, p<0.001). In CLL4, whilst TP53ab was the strongest predictor of PFS and OS (PFS HR:3.61, CI:2.39-5.44 & OS HR: 3.66, CI:2.4-5.57, p<0.001), both n-CLL (PFS HR:1.96, CI:1.32-2.9 & OS HR:2.8, CI:1.81-4.34, p<0.001) and TL-S (PFS HR:2.36, CI:1.7-3.29 & OS HR:2.66, CI:1.87-3.76, p<0.001) were in the top five predictors of PFS and OS along with U-CLL and biallelic ATM inactivation ( biATM). Next, we performed Kaplan-Meier subgroup analysis, investigating DME in TL subgroups and vice versa. Examination of both biomarkers in the opposing subgroups in the ARC/ADM cohort, showed that TL could further stratify the i-CLL subgroup, with TL-L predicting longer PFS (median:6.12 years) compared to TL-S (HR:5.78, CI:2.34-14.33, median:3.8 years, p<0.001) or TL-I (HR:3.29, CI:1.4-7.76, median:4.35 years, p<0.01). As this pairwise analysis suggested that DME and TL may differentially contribute to outcome, we performed a multivariate cox regression, whilst controlling for confounding variables such as TP53ab and U-CLL. Covariates that were significant in UA were included in a stepwise backwards elimination process until a final model was reached. The CLL4 models were based on 246 subjects with 221 PFS and 205 OS events, ARC/ADM models were based on 138 and 176 subjects with 86 and 45 events for PFS and OS, respectively. For PFS models, TL-S emerged as significant (CLL4 HR:2.14, CI:1.39-3.3, p<0.001 & ARC/ADM HR:2.18, CI:1.17-4.05, p<0.01) with a HR lower than TP53ab (CLL4 HR:3.38, CI:2.13-5.37 & ARC/ADM HR:4.94, CI:2.58-9.48, p<0.001). DME emerged as significant for PFS in the CLL4 cohort (n-CLL HR:2.35, CI:1.37-4.05, p<0.01), along with SF3B1 mutation and treatment arm (Figure 2). In ARC/ADM, U-CLL, TP53ab, TL-S, del11q and biATM emerged as significant predictors of PFS (Figure 2). For OS, in both cohorts, TP53ab (CLL4 HR:2.77, CI:1.74-4.4, p<0.001 & ARC/ADM HR:3.28, CI:1.64-6.55, p<0.001) and DME (CLL4 HR:2.07, CI:1.15-3.73, p<0.05 & ARC/ADM, HR:3.4, CI:1.14-10.12, p<0.05) were found to predict shorter survival (Figure 2). Currently, we are integrating additional IGHV/IGLV data into our analysis, including the presence of IGLV3-21R110. In conclusion, by assessing the individual contribution of DME and TL to disease survival, we found that both variables offer valuable independent prognostic information when included in statistical models with poor-risk genomic lesions. TL and DME could help identify IGHV-mutated patients destined to respond poorly to (immuno-)chemotherapy, that might be more favourably treated with targeted agents.

Phase 1 Study of SC291, a Hypoimmune, Allogeneic CD19-Directed CAR T Cell Therapy for Relapsed/Refractory B-Cell Malignancies (ARDENT) - Initial Clinical Data

ARDENT is a phase 1 study evaluating safety and tolerability of SC291, a hypoimmune (HIP), allogeneic, CD19-directed CAR T cell therapy in subjects with Non-Hodgkin's Lymphoma and Chronic Lymphocytic Leukemia (CLL). SC291 is derived from healthy donor CD4+ and CD8+ T cells that are genetically engineered to disrupt function of CD3 and HLA class I/II, overexpress CD47, and express a CD19-directed CAR. A primary obstacle for allogeneic CAR T cell approaches remains their immune recognition and rejection. Patient immune responses prevent durable allogeneic CAR T clinical responses despite the use of enhanced lymphodepletion (LD) regimens. We therefore developed hypoimmune CAR T cells that avoid immune recognition and have the potential to deliver clinical efficacy while using a standard LD chemotherapy regimen (as defined by approved autologous CAR T products). The HIP engineering approach involves the depletion of HLA class I/II to prevent adaptive immune rejection and the overexpression of CD47 to prevent innate immune rejection, which has previously demonstrated alloimmune protection in preclinical models ( Nat Biotechnol 2019;37(3):252-258; Proc Natl Acad Sci U S A 2021;118(28):e2022091118; J Exp Med. 2021;218(3):e20200839; Nat Biotechnol. 2023; doi: 10.1038/s41587-023-01784-x, and Nat Commun. 2023;14(1):2020). The initial patient, a 74-year-old male with CLL (unmutated IGHV, del(11q), BTK C481S mutation) and 3 prior lines of therapy (FCR, ibrutinib, venetoclax + rituximab), received a LD regimen of cyclophosphamide 500 mg/m 2 and fludarabine 24 mg/m 2 (daily for 3 days) followed by a starting dose of 60 million CAR+ SC291 cells (of which approximately 80% are fully HIP engineered cells). SC291 was well tolerated with no observed CRS or ICANS. The patient developed non-neutropenic fever after LD (prior to SC291 infusion). At the Day 28 visit post-SC291 infusion, the patient had a partial response (per iwCLL 2018 criteria), along with significant (99%) B-cell reduction and improvements in platelet levels. Analysis of cellular kinetics is ongoing. SC291 is a mixture of T cells, in which portions are partially or fully HIP-engineered. As such, we evaluated the initial patient's immune response against SC291 subpopulations using a panel of previously described in vitro assays. Blood samples from the patient were taken pre-treatment (Day -5) and at the Day 13 and Day 28 visits following SC291 treatment and were assessed for immune evasion. The patient's PBMCs were sorted into CD3+ T cells and CD3-CD56+ NK cells and incubated with the following subpopulations sorted from SC291 drug product (DP): (i) fully HIP engineered (CD19 HIP CAR T cells), (ii) HLA I/II negative T cells without CD47 overexpression (DKO), and (iii) HLA I/II positive CAR T cells overexpressing CD47 (WT CD19 CAR T cells). Patient serum from Day -5 and the Day 28 visit were used for donor-specific antibody analyses, complement-dependent cytotoxicity (CDC), and antibody-dependent cellular cytotoxicity (ADCC) against the DP subpopulations. At Day -5, T cell EliSpot assays showed no immune responses against any of the SC291 sorted subpopulations, but by Days 13 and 28, these assays produced high and increasing IFN-g spot frequencies against the WT CD19 CAR T cells. Similar results were shown with T cell cytotoxicity assays (Fig. 1B). In contrast, no T cell activation and no T cell killing was observed with DKO and CD19 HIP CAR T cells at any time point. As expected, patient NK cells vigorously killed DKO T cells at all time points but spared WT CD19 CAR T and CD19 HIP CAR T cells (Fig. 1B). No antibodies against any sorted subpopulation were detected at Day -5, but IgG antibody binding of the WT CD19 CAR T population was observed at Day 28. These antibodies did not bind to DKO or CD19 HIP CAR T cells, and there was no CDC or ADCC response against these subpopulations. Interestingly, with the LD regimen used, we observed a 95% and 99% reduction of CD19+ cells on Days 0 and 28, respectively, while T cells rebounded from an 88% reduction on day 0 to pretreatment levels on Day 28 (Fig. 1A). These data demonstrate the preliminary safety and tolerability of SC291 in the initial treated patient. Immune assays demonstrated that the CD19 HIP CAR T cell subpopulation effectively evades the host adaptive and innate immune responses and could overcome the allogeneic barrier in humans. Additional data from the ARDENT study will be presented at the time of the conference.

IGLV3-21 R110 Is a Prognostic Marker for Early Stage CLL Patients Under Ibrutinib Treatment or Watch & Wait: Results from the Double-Blind, Randomized, Placebo-Controlled GCLLSG CLL12 Trial

INTRODUCTION: IGLV3-21 R110 is a point mutation that can confer the ability for autonomous signaling to B cell receptors (BCR) using light chains encoded by the allele IGLV3-21 ∗ 01 or IGLV3-21 ∗ 04. Chronic lymphocytic leukemia (CLL) patients with IGLV3-21 R110 have a shorter time to first treatment and shorter overall survival, independent of their IGHV mutational status. However, outcomes of CLL patients using IGLV3-21 R110 have not been evaluated in clinical trials of BTK inhibitors. METHODS: The CLL12 trial was a prospective, double-blind, randomized phase 3 trial that compared ibrutinib (ibr, n=182) vs. placebo (pcb, n=181) in previously untreated Binet A CLL patients with intermediate to very high risk, while low risk patients were assigned to watch & wait (w&w, n=152). The primary endpoint of the study was event-free survival (EFS) (event defined as death, symptomatic progression or initiation of CLL treatment), while overall survival (OS) was a secondary endpoint. The IGLV3-21 locus was sequenced via amplicon-based targeted next generation sequencing (tNGS) in 514 of 515 samples collected at enrolment. IGLV rearrangements and point mutations were detected with ScanIndel as well as IgCaller and the results of the genetic analyses were correlated with outcome. RESULTS: IGHV was unmutated (U-IGHV) in 148 (28.3%) patients (w&w n=8, pcb n=70, ibr n=70) and 10 patients belonged to stereotyped B cell receptor (BCR) subset 2 (w&w n=2, pcb n=1, ibr n=7). IGLV3-21 rearrangement was found in 34 of 514 patients (6.6%) and was more frequent in the intermediate/high risk groups (pcb n=16, ibr n=13) than in the low risk group (w&w n=5). Twenty of 34 patients with IGLV3-21 rearrangement had an IGLV3-21 R110 mutation (w&w n=3/5, pcb n=10/16, ibr n=7/13). For 5 patients with IGLV3-21 (3 pcb, 2 ibr) the mutational status for IGLV3-21 R110 could not be determined by tNGS. In the total cohort, IGLV3-21 R110 often co-occurred with mutations in SF3B1 (odds ratio 8.54, p < 0.001), but not with mutations in TP53 or any of the other frequently mutated genes in CLL. Conversely, SF3B1 mutations were not enriched in subset 2 patients (p = 0.165). Also, there was no association of IGLV3-21 R110 or IGLV3-21 usage in general with IGHV mutational status. At a median follow-up of 69.3 months, there were 166 events for EFS and 32 for OS. CLL with IGLV3-21 had a shorter EFS in the pcb (HR 1.93, CI95% 1.05-3.55, p=0.033) and ibr (HR 3.71, CI95% 1.62-8.46, p=0.002) arm (Figure 1A). The estimated 5-year EFS rate was 51.0% without and 21.4% with IGLV3-21 rearrangementin the pcb group vs. 80.7% and 44.8% in the ibr group, respectively. Similarly, IGLV3-21 R110 associated with shorter EFS with ibr (HR 3.30, CI95% 1.17-9.31, p=0.024) while no impact was observed in the pcb group (HR 1.51, CI95% 0.66-3.46, p=0.332, Figure 1B). Patients with IGLV3-21 R110 mutation and ibr treatment had an estimated 5-year EFS rate similar to that of patients in the pcb group without IGLV3-21 R110 (50.0% vs. 49.8%). In low risk patients with w&w, both IGLV3-21 rearrangement and IGLV3-21 R110 were adverse markers for EFS (HR 4.99, CI95% 1.52-16.41, p=0.008 and HR 17.0, CI95% 4.99-58.13, p<0.001, respectively). For the full trial, we observed a prognostic impact of IGLV3-21 in the M-IGHV (HR 3.87, CI95% 2.14-6.99, p<0.001) but not in the U-IGHV (HR 1.61, CI95% 0.74-3.54, p=0.233) group. Multivariable analysis for the treatment arms including the IGLV3-21 R110 status and other variables associated significantly with EFS in univariate analyses (treatment arm, serum β2-microglobulin, IGHV status, del(17p), del(11q), +(12), mutations in XPO1, NOTCH1, SF3B1 and NFKBIE) revealed presence of IGLV3-21 R110 (HR 2.76, CI95% 1.32-5.80, p = 0.007) as an independent prognostic factor. OS was excellent in all genetic subgroups and in all arms of the trial. The estimated 5-year OS rate was between 92.9% and 95.8% for any of the 4 subgroups defined jointly by IGHV status and presence of IGLV3-21 R110. CONCLUSIONS: IGLV3-21 R110 was identified as an independent prognostic factor for shorter EFS in early stage CLL with intermediate/high risk score and was associated with reduced ibrutinib efficacy in the CLL12 trial.

A Single Center Real World Study of Outcome and Resistance of Bruton Tyrosine Kinase Inhibitors (BTKi) in Chinese Patients with Chronic Lymphocytic Leukeima/Small Lymphocytic Lymphoma

Introduction Acquired BTK/PLCG2 mutations remain to be the driver of Bruton Tyrosine Kinase inhibitor (BTKi) resistance. But the underlying mechanisms need to be further explored. In this study, we retrospectively analyzed clinical and biological characteristics of BTKi-treated CLL patients and report the outcome and resistance in our center (the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital). Method 262 patients treated with single BTKis continuously were collected and follow up the outcome in our center. Progression-free survival (PFS) was defined as from BTKi initiation to disease progression on BTKi. Next-generation sequencing (NGS) and High sensitivity droplet digital PCR (ddPCR) acquired at treatment initiation /or at the time of disease progression were used to describe mutational landscape. Kaplan-Meier method and the log-rank test were used for analysis. Results A total of 262 patients were enrolled from January 2014 to March 2023, and the median age was 63 (range 28-88) years. Ibrutinib, Zanubrutinib, Orelabrutinib were administered in 55.3%,18.3% and 17.9% of patients respectively, in addition to 6 patients with Acalabrutinib and one with Loxo-305, among them 47.7% (125/262) received BTKi as first line treatment. With a median follow up of 27.3 months, 208 patients were in durable remission while 54 patients relapsed, the median exposure of BTKi was 26.8 (range, 1-73.8) sand 27.7 (range, 3-69.8) months respectively. The median PFS was 5.8 years (5.0-NA, 95% CI) for the whole cohort. Clinical and biological characteristics of both cohorts at initiation of BTKi treatment were described and compared in Table 1. Higher proportion of bulky disease (50.0% vs 23.5%), IGHV unmutated status (84.3% vs 50.5%), del(17p) (44.7% vs 12.9%), TP53 mutation (37.8% vs 15.2%), TP53 aberrations (62.5% vs 24.3%) and complex karyotype (40.5% vs 21.1%) were shown in the BTKi relapsed cohort as compared to responsive cohort. Inferior PFS was observed in patients with TP53 aberration vs without TP53 aberration ( 45.6 mos vs not reached, p<0.0001), unmutated IGHV vs mutated IGHV (56.2 mos vs not reached, p=0.0005), with del(17p) vs without del(17p) (36.1 mos vs not reached, p<0.0001), with complex karyotype and without complex karyotype (69.8 mos vs not reached, p=0.0401), bulky disease vs no bulky disease (45.6 mos vs 69.8 mos, p=0.0006) and elevated LDH vs normal LDH (66.5 mos vs not reached, p=0.0083). Moreover, patients with del(11q) or BTKi given as second or greater line showed a tendency of inferior PFS ( p= 0.1963, p= 0.0735, respectively). Regarding the relapsed cohort, 43 patients displayed CLL progression while 11 patients displayed Richter transformation (RT, including 1 Hodgkin lymphoma [HL]) , the median time from initiation to progression were 33.7 months and 9.5 months, respectively（p<0.0001). BTK/PLCG2 mutations were the most common mutation at the timepoint of disease progression. By integrating NGS and ddPCR results, 54.9% (28/51) relapsed patients acquired BTK/PLCG2 mutation. BTKC481S mutation was the dominant hotspot mutation in all kinds of BTKi relapsed cases. Other mutations at the C481 site included C481R, C481Y, C481F. However, BTKT474 mutation was only detected in Orelabrutinib-resistant cases (Figure 1). 6 patients presented with multi-hit mutations. Treatment after disease progression on BTKis is still challenging. In our relapsed cohort, the median PFS was 5.7 months and poorer in RT as compared with CLL progression (3.0 months vs 6.7 months, p= 0.0874). Venetoclax-based regimen might be an effective salvage therapy which could showed a benefit trend in PFS as compared to other post BTKi therapy (10.1 months vs 3.1 months, p= 0.1818). Conclusion In our real world study, patients with IGHV unmutated status, TP53 aberrations, bulky disease and elevated LDH showed inferior PFS. Acquired BTK/PLCG2 mutations remained to be key drivers of BTKis resistance and BTKC481S mutation was the dominant mutation, while BTKT474 mutation was only detected in Orelabrutinib-resistant patients. The prognosis was rather poor for relapsed patients especially for RTs, treatment strategy after disease progression remains to be optimized.

Molecular Landscape of c-CBL Mutation in Adults' Myeloid Malignancies

Background: CBL proteins are a family of RING finger (RF) E3 ubiquitin ligases that regulate proliferative signals via ubiquitination and degradation of tyrosine-phosphorylated signaling protein ( e.g., FLT3, JAK2, MPL). Thus, the loss of CBL activity due to hypomorphic or loss of function (LOF) mutations functionally may result in oncogenic effects. However, simple LOF does not explain the high rates of c-CBL (most abundant CBL isoform, located on chromosome 11)missensemutations affecting a canonical position in the RF domain, catalytic region responsible for ubiquitin ligase activity. We hypothesized that studying the molecular and clinical associations of c-CBL mutations will help clarifying the consequences of its mutations and conceptualize innovative treatment strategies. Methods: We analyzed molecular and clinical features of a cohort of 11036 patients with myeloid neoplasia (MN; 63% AML, 29% MDS, 5% MPN/MDS, 3% MPN) from The Cleveland Clinic Foundation and public series. Clonal burden of c-CBL was analyzed to infer clonal hierarchy and to establish founder vs secondary mutations based on our previously described criteria. Results: Overall, c-CBL mutations were detected in 2.4% (270/11036) of the patients. The most common c-CBL mutations were missense (80%) and mainly occurred in the RF domain and linker region (83% of mutations, Fig1). c-CBL mutations were found in 2% of both primary AML (pAML; 3% of CBF) and sAML/HR-MDS and 8% of CMML. Among CMML patients, mutations were associated with low-risk features (7% of CMML2 vs. 13% of CMML1). The most frequent co-associated mutations were TET2 (22%) and RUNX1 (19%) in all AML, ASXL1 (50%), SRSF2 (25%) and TET2 (25%) in MDS, and ASXL1 (50%), SRSF2 (44%) and JAK2 (28%) in MPN and MPN/MDS. In terms of associations with tyrosine kinase receptors ( FLT3, c-KIT, CSF3R, c-MPL), we found that 18% of c-CBL mutants carried at least one mutation in one the four receptors, contrarily to what expected from previously reported results of c- CBL/FLT3 mutational exclusivity. In most of the cases, c-CBL mutations were subclonal (53%), arguing against its primary driver/initiator function. Indeed, we observed c-CBL mutations as the only lesion in 7% of the cases with no specific disease association (66%, AML; 25%, LR-MDS; 8%, CMML). There was no difference in MN phenotypes between carriers of canonical vs non canonical c-CBL mutations; however, we found that non canonical mutations were more often ancestral or the only founder lesion detected compared to canonical mutations (46 vs 31%, P = 0.031). Del(11q) or monosomy 11 were found in 8 patients, without association with c- CBL VAF >50%. Furthermore, c-CBL VAF>50% was not associated with marrow blast infiltrate, WBC or shorter survival. We then analyzed the effect of c-CBL in cooperation with RAS genes ( NRAS, KRAS, PTPN11, NF1) and found that, in AML, the effect of c-CBL with 2 RAS genes (5 patients, 3%) showed some trends toward higher blast count ( P = 0.079), higher WBC ( P = 0.076) and lower rates of normal cytogenetics compared to the effect of the remaining c-CBL mutant (0 vs 48%, P = 0.061). Conclusions: In sum, our study of the molecular landscape of c-CBL mutations highlights that these lesions occur mainly during disease development with majority of the cases carrying subclonal hits with a weaker effect on disease phenotype and prognosis. Such mutations can be present in both primary and secondary AML (in contrast with previous reports) and additive effects can be observed when c- CBL mutationsco-occur with more than one RAS gene in these disease groups. In some cases, especially in non-canonical mutations, c- CBL could also act as ancestral event and as an independent leukemic driver.

Similar Efficacy of Ibrutinib Arms across ALPINE and ELEVATE-RR Trials in Relapsed/Refractory Chronic Lymphocytic Leukemia: A Matching-Adjusted Indirect Comparison

Background: Bruton tyrosine kinase inhibitors (BTKi) are currently widely used for the treatment of patients with chronic lymphocytic leukemia (CLL). Ibrutinib, the first BTKi approved for the treatment of CLL, was followed by the second-generation BTKi, acalabrutinib, and recently the next-generation BTKi, zanubrutinib. Both zanubrutinib and acalabrutinib were compared to ibrutinib in phase 3 randomized controlled trials in relapsed/refractory (R/R) CLL. In the ALPINE trial (NCT03734016), zanubrutinib demonstrated a superior progression-free survival (PFS) when compared with ibrutinib in the all-comer R/R CLL population with hazard ratio (HR)=0.65, whereas the ELEVATE-RR trial (NCT02477696) showed noninferior PFS of acalabrutinib vs ibrutinib in R/R CLL patients with the presence of del(17p) or del(11q) with HR=1. Recent attempts to compare the efficacy results of the ibrutinib arm across trials omitted some patient characteristics that are critical for appropriate cross-trial comparisons. This study aimed to compare the efficacy of the ibrutinib control arm across ALPINE and ELEVATE-RR trials using a comprehensive matching-adjusted indirect comparison (MAIC). Methods: Individual patient data from the ibrutinib arm of ALPINE were adjusted to match the published population-level profile from the ibrutinib arm of ELEVATE-RR. To obtain comparable populations for MAIC, a subgroup of patients from ALPINE was included in the analysis. An unanchored MAIC was conducted to adjust for all relevant treatment effect modifiers (EM). The following were considered for population adjustment: IGHV status, del17p, del11q, TP53 status, serum β2-microglobulin, number of prior therapies, and Binet stage. Additional prognostic factors (PF) were also adjusted in sensitivity analyses. ALPINE data cutoff of August 2022 was used given the availability of both independent review committee (IRC) and investigator (INV) assessed data, and the possibility of a comparison vs other recently published MAICs (median follow-up: 29.6 months). Efficacy of ibrutinib in ALPINE was compared with efficacy of ibrutinib in ELEVATE-RR (median follow-up: 40.9 months). After population adjustment, HR obtained by weighted Cox proportional hazard model was applied to assess PFS and overall survival (OS) outcomes. PFS was analyzed as per IRC and INV. As the ALPINE trial was conducted during the COVID-19 pandemic and ELEVATE-RR was not, sensitivity analysis was conducted by adjusting the ALPINE PFS and OS for COVID-19 impact by censoring the patients who died due to COVID-19 at the most recent disease assessment prior to death or at the death due to COVID-19. Results: The high-risk population in ALPINE included 123 patients in the ibrutinib arm, which were matched against 265 patients in the ibrutinib arm of the ELEVATE-RR trial. After population adjustment, no statistically significant differences were observed in ALPINE-ibrutinib vs ELEVATE-ibrutinib with regards to PFS-IRC (HR=0.80 [0.49-1.28], P=0.3485) (Figure 1), PFS-INV (HR=1.18 [0.75-1.86], P=0.4827) (Figure 2), and OS (HR=0.91 [0.50-1.65], P=0.7539). Sensitivity analysis with COVID-19 adjustment yielded similar results as the main analysis. Scenarios matching for both EM and PF also generated results consistent with the main analysis. Conclusion: Using a comprehensive list of matching variables, this MAIC compares the performance of ibrutinib across ALPINE and ELEVATE-RR trials and demonstrates no evidence of a difference. Comparing the common comparator arms of 2 trials (ibrutinib vs ibrutinib) instead of the different investigational arms (zanubrutinib vs acalabrutinib) allows for eliminating some of the residual confounding that is inherent in MAICs. Despite decreased estimated sample size due to considering a comprehensive list of variables in the adjustment, results were consistent across multiple scenarios tested. While MAIC provides a basis for testing hypotheses with regards to treatment efficacy across trials, the ultimate evidence of relative efficacy must be sought within randomized controlled trials.

Whole-Genome Sequencing for Copy Number Abnormalities in Multiple Myeloma Supersedes Karyotype Analysis and Fluorescent in Situ Hybridization

Whole-Genome Sequencing for Copy Number Abnormalities in Multiple Myeloma Supersedes Karyotype Analysis and Fluorescent in Situ Hybridization Jiali Li 1, Shaobing Gao 2, Zhenling Li 3, Yinyin Chang 4, Xiangxiang He 4, Yuexin Cheng 5, Manqian Li 4, Chunxiao Yao 4, Shiyong Li 6, Dandan Zhu 4, Shichun Tu 4, Mao Mao 6,7, #, Xi Zhang 1, #, Li Gao 1, # 1 The Xinqiao Hospital of Third Military Medical University, Chongqing 214426, China 2The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou 450003, China 3China-Japan Friendship Hospital, Beijin100029,China 4Clinical Laboratories, Shenyou Bio, Zhengzhou 450000, China 5Yancheng No. 1 People's Hospital, The Yancheng Clinical College of Xuzhou Medical University, Yancheng 224006, China 6Research & Development, SeekIn Inc., Shenzhen 518000, China 7Yonsei Song-Dang Institute for Cancer Research, Yonsei University, Seoul 03722, Korea Corresponding authors. Tel.: +86-15601973722(Maomao); 13808310064(Xi Zhang) 13228686076(Li Gao) Corresponding authors Email: mao_m@yahoo.com (Maomao); zhangxxi@sina.com (Xi Zhang); gaotiantiantiger@163.com (Li Gao) Introduction Prognosis and management of multiple myeloma (MM) relies on risk stratification based on copy number abnormalities (CNA) detection results. CNA is conventionally evaluated by cytogenetic methods including karyotyping and flurescence in situ hybridization (FISH), both limited by the invasiveness, low proliferative activity of plasma cell and the low plasma cell count. LeukoPrint is a novel shallow whole-genome sequencing (sWGS) based approach to profile CNA in bone marrow cells and/or circulating cell-free DNA (cfDNA). We compared the CNA detection results by LeukoPrint, karyotyping and FISH using bone marrow or plasma samples from multiple myeloma patients. Methods A total of 128 patients were enrolled in this study. Karyotyping and FISH were performed by conventional approaches. CNA was detected by sWGS in genomic DNA from bone marrow aspiration samples and CD138+ enriched plasma cells as well as in plasma cfDNA. CNA degree was measured by log R ratio. Significant mutational peak region was identified by GISTIC2. Risk stratification was performed following the Mayo Stratification of Myeloma and Risk-adapted Therapy (mSMART) criteria. Results In this study, 908 CNAs were identified by sWGS in 96 (75.0%, 96/128) patients, while the positive rate of CNA detected by karyotyping and FISH was 7.9% and 56.7% , respectively. A total of 368 whole chromosome aberration events were identified by sWGS, 66.0% (243/ 368) of which were trisomy that defined 39.6% (38/96) of patients as hyperdiploidy and the remaining 60.4% (58/96) as non-hyperdiploidy. The most frequently mutational CNA peak region were amp(1q21), del(1p), del(6q), del(8p), del(13q14) and del(14q). The concordance rate between sWGS and FISH in detecting the four conventional loci (1q21 gain, 13q14 del, 13q14.3 del, and 17p13 del) was 81.8%. Comparing to the conventional approaches, sWGS provided new CNA information for 75.0% of the patients, and redefined the risk stratification for 17.2% of patients according to mSMART criteria. CNA detection results using paired bone marrow aspiration samples and enriched plasma cell samples from 8 patients were compared. We found that more CNAs (81 vs 58) and higher Log R ratio of CNAs were detected using enriched plasma cells than that using bone marrow aspiration samples. The concordance rate of the CNA detection results by sWGS between paired bone marrow genomic DNA and plasma cfDNA from another 9 patients was 83.3%. Conclusions LeukoPrint is an automated, convenient and cost-effective approach to depict CNA profile in genomic DNA or cfDNA. This method is superior to conventional approaches when used for CNA testing, and the practice of this method could improve prognostic stratification of MM patients.

Influence of Co-Mutational Patterns in Disease Phenotype and Clinical Outcomes of Chronic Myelomonocytic Leukemia

Introduction: Chronic myelomonocytic leukemia (CMML) is characterized by recurrent somatic mutations in a conserved number of genes and functional pathways. Although specific genomic events are associated with disease phenotype and prognosis, identification of genomically-defined disease subgroups based on common recurrent cooperative genomic patterns is needed to refine disease classification and identify disease subsets with unique clinical behavior. Methods: To evaluate if CMML is defined by recurrent co-mutational profiles defining unique clinicopathologic subgroups we evaluated a cohort of 296 patients (pts) with newly diagnosed CMML. Whole bone marrow DNA was subject to 81 gene targeted next-generation sequencing analysis. Akaike information criterion (AIC) method was applied to evaluate mixture model components defining clusters based on mutational profile. Expectation-maximization (EM) algorithm was used for mixture model fitting to multivariate binary data. Unsupervised cluster membership was chosen as a function of the component with the highest weight for any individual, and we examined means of cluster centers. Cox proportional hazards models, regressing overall survival (OS) and leukemia-free survival (LFS), were fit on cluster in some cases and normalized cluster weights in other cases, with and without adjustment for age and sex. Two degree of freedom likelihood ratio tests was performed on cluster and cluster weight in all models regardless of covariate adjustment. Results: Median age of the population was 70 years [range 30-71]; 160 (54%) pts had myeloproliferative CMML (MP-CMML) and 152 (51%) had CMML-2 by WHO classification. Most frequent mutations included TET2 (51%), ASXL1 (48%), SRSF2 (40%), RUNX1 (22%), NRAS (18%), CBL (14%) and KRAS (14%) all present in >10% of pts. Based on frequency and co-occurrence of mutations, AIC optimization identified 3 unique clusters. Clusters based on mutation landscape are shown in Figure 1A. Unsupervised clustering allowed attribution of individual patients to specific clusters. Cluster 1 (C1, n=107), was characterized by near universal presence of ASXL1 mutations (86%), with lower frequency of TET2 mutations, and enrichment of RUNX1 (35%), NRAS (28%) and U2AF1 (18%) mutations. SETBP1 and EZH2 mutations were nearly exclusively observed in C1 (16% and 20% of C1 pts, respectively). All pts with ETV6 mutations belonged to this cluster. Cluster 2 (C2, n=135) was defined by universal presence of TET2 mutations (93%) with frequent SRSF2 co-mutation (56%) and lower frequency of ASXL1 (34%), RUNX1 (15%) or NRAS (12%) mutations. Despite their overall low frequency, BRAF mutations were restricted to C2, while CBL mutations were observed at similar frequencies in C1 and C2. This suggests that co-mutation profiles and genomic context differs among genes involved in RAS pathway signaling. Cluster 3 (C3, n=54) included a minor and more genomically heterogenous group enriched for SF3B1 (25%), KRAS (24%), DNMT3A (22%) and TP53 (15%) mutations, with absence of ASXL1 mutations, and low frequency of TET2 (12%) mutations. All BCORL1 and WT1 mutations and most ASXL2 and CEBPA mutations were in C3. RUNX1 mutations not only were more frequent among C1 but appeared at higher median VAF compared to other clusters (C1: 40%, C2: 11%, C3: 25%, p=0.003). Mutations in U2AF1 had higher median VAF in C3 compared to cluster 1 (49% vs 43%, p=0.017). C1 was enriched for MP-CMML (C1: 64%; C2: 48%; C3: 52%, p<0.001) and had higher frequency of del(7q)/-7 (C1: 11%; C2 0%, C3: 6%, p<0.001) and trisomy 8 (C1: 15%, C2: 7%, C3: 6%, p=0.05). Complex karyotype (C1: 1%, C2: 1%, C3: 22%, p<0.001) was nearly exclusive of C3, while C2 was more likely to be associated with a normal karyotype (C1: 59%; C1: 73%; C3: 41%, p<0.001) and higher median hemoglobin (C1: 9.8g/dL; C2: 12.1g/dL, C3: 9.7g/dL, p<0.001). In total 66% of pts received therapy with hypomethylating agents with no differences in response, median time to or duration of response between clusters. Use of Cox proportional hazards model identified that, when corrected by age and sex, patients on C1 and C3, based on attributed cluster weights, had significantly worse LFS (p=0.02, Figurer 1B) and OS (p=0.05) than those in C2. Conclusions: These data suggest that somatic mutations in CMML have unique patterns of clustering that define disease phenotype and influence disease outcomes.

Absence of BTK, BCL2, and PLCG2 Mutations in Chronic Lymphocytic Leukemia Relapsing after First-Line Treatment with Fixed-Duration Ibrutinib plus Venetoclax.

Mutations in BTK, PLCG2, and BCL2 have been reported in patients with progressive disease (PD) on continuous single-agent BTK or BCL2 inhibitor treatment. We tested for these mutations in samples from patients with PD after completion of first-line treatment with fixed-duration ibrutinib plus venetoclax for chronic lymphocytic leukemia (CLL) in the phase II CAPTIVATE study. A total of 191 patients completed fixed-duration ibrutinib plus venetoclax (three cycles of ibrutinib then 12-13 cycles of ibrutinib plus venetoclax). Genomic risk features [del(11q), del(13q), del(17p), trisomy 12, complex karyotype, unmutated IGHV, TP53 mutated] and mutations in genes recurrently mutated in CLL (ATM, BIRC3, BRAF, CHD2, EZH2, FBXW7, MYD88, NOTCH1, POT1, RPS15, SF3B1, XPO1) were assessed at baseline in patients with and without PD at data cutoff; gene variants and resistance-associated mutations in BTK, PLCG2, or BCL2 were evaluated at PD. Of 191 patients completing fixed-duration ibrutinib plus venetoclax, with median follow-up of 38.9 months, 29 (15%) developed PD. No baseline risk feature or gene mutation was significantly associated with development of PD. No previously reported resistance-associated mutations in BTK, PLCG2, or BCL2 were detected at PD in 25 patients with available samples. Of the 29 patients with PD, 19 have required retreatment (single-agent ibrutinib, n = 16, or ibrutinib plus venetoclax, n = 3); 17 achieved partial response or better, 1 achieved stable disease, and 1 is pending response assessment. First-line fixed-duration combination treatment with ibrutinib plus venetoclax may mitigate development of resistance mechanisms associated with continuous single-agent targeted therapies, allowing for effective retreatment. See related commentary by Al-Sawaf and Davids, p. 471.

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.

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.