IGHV Unmutated Chronic Lymphocytic Leukemia Research Articles

Expression Pattern and Prognostic Significance of the Long Non-Coding RNA Metastasis-Associated Lung Adenocarcinoma Transcript 1 in Chronic Lymphocytic Leukemia.

Dysregulated expression of the long non-coding RNA MALAT1 has been implicated in the pathogenesis and progression of a variety of cancers, including hematological malignancies, but it has been poorly investigated in chronic lymphocytic leukemia (CLL). In this study, the expression of MALAT1 was measured using a quantitative reverse-transcriptase polymerase chain reaction in the peripheral blood mononuclear cells of 114 unselected, newly diagnosed CLL patients in order to analyze its association with clinical, laboratory, and molecular patients' characteristics at diagnosis, as well as its prognostic relevance. MALAT1 was found to be upregulated in CLL patients in comparison to healthy controls, and expression levels were not related to age, leukocyte, lymphocyte and platelet count, serum β2-microglobulin, and IGHV somatic hypermutational status. On the other hand, high MALAT1 expression was associated with several favorable prognostic markers (high hemoglobin, low serum lactate dehydrogenase, earlier clinical stages, CD38-negative status), but also with unfavorable cytogenetics. Furthermore, an association between high MALAT1 levels and longer time to first treatment and overall survival in IGHV-unmutated CLL subtype was observed. In summary, our results imply that high MALAT1 expression at diagnosis may be a predictor of better prognosis and point to MALAT1 expression profiling as a candidate biomarker potentially useful in clinical practice.

ZAP-70 augments tonic B-cell receptor and CCR7 signaling in IGHV–unmutated chronic lymphocytic leukemia

AbstractExpression of ZAP-70 in a subset of patients with chronic lymphocytic leukemia (CLL) positively correlates with the absence of immunoglobulin heavy-chain gene (IGHV) mutations and is indicative of a more active disease and shorter treatment-free survival. We recently demonstrated that ZAP-70 regulates the constitutive expression of CCL3 and CCL4, activation of AKT, and expression of MYC in the absence of an overt B-cell receptor (BCR) signal, bona fide functions of BCR activation. We, here, provide evidence that these features relate to the presence of a constitutive tonic BCR signal, exclusively found in IGHV-unmutated CLL and dependent on the ZAP-70–mediated activation of AKT and its downstream target GSK-3β. These findings are associated with increased steady-state activation of CD19 and SRC. Notably this tonic BCR signal is not present in IGHV-mutated CLL cells, discordantly expressing ZAP-70. Results of quantitative mass spectrometry and phosphoprotein analyses indicate that this ZAP-70–dependent, tonic BCR signal regulates CLL cell migration through phosphorylation of LCP1 on serine-5. Indeed, we show that CCL19- and CCL21-induced chemotaxis is regulated by and dependent on the expression of ZAP-70 through its function to enhance CCR7 signaling to LCP1. Thus, our data demonstrate that ZAP-70 converges a tonic BCR signal, exclusively present in IGHV-unmutated CLL and CCR7-mediated chemotaxis.

ZAP-70 Integrates Tonic B Cell Receptor and Chemokine Signaling in IGHV unmutated Chronic Lymphocytic Leukemia

The importance of B cell receptor (BCR) signaling for the progression of Chronic Lymphocytic Leukemia (CLL) has impressively been demonstrated through the clinical success of small molecule inhibitors interfering with this pathway, providing effective treatment options for a vast majority of patients. The scientific evidence which supported the development of drugs like BTK and PI3K inhibitors largely originate from studies of antigen-induced BCR-signaling. Notably, the presence of a constitutive, so-called tonic BCR-signal was long postulated to co-exist besides antigen-driven activation and is based on the identification of constitutively activated signaling molecules down-stream of the BCR. We here provide direct evidence for the presence of a tonic BCR-signal, which critically relies on the expression of the tyrosine kinase ZAP-70. We have previously established a method to inhibit ZAP-70 expression in primary CLL cells usingRNA-interference in combination with an extended co-culture system. Our previous work demonstrated that ZAP-70 is required for the constitutive gene expression of T cell chemokines CCL3 and CCL4 and contributes to the dysregulation of global protein synthesis and MYC expression in CLL ( Blood, 2021). Applying this method, we here provide evidence for the presence of a constitutive tonic BCR signal, which is dependent on ZAP-70 expression and exclusively found in IGHV unmutated CLL, but not in IGHV mutated cases discordantly expressing ZAP-70. We demonstrate that ZAP-70 is directly involved in the constitutive activation of AKT and GSK-3beta. Furthermore, ZAP-70 expression increases steady state activation of CD19 and the downstream kinase SRC, providing direct evidence for the existence of a ZAP-70 dependent tonic BCR signal in I GHV unmutated CLL only. To identify the underlying signaling events driving this signal, we performed mass spectrometry in combination with proximity ligation assays on CLL cells in the absence of an induced BCR-signal. Unexpectedly, we identified that the majority of ZAP-70 binding proteins do not related to BCR-signaling components, but to cytoskeleton organizing proteins involved in cell migration. Indeed, migration assays demonstrated that the loss of ZAP-70 directly and significantly impaired cell migration induced by CCL19 and CCL21, in keeping with previous data indication an association between ZAP-70 and cell migration. These results were confirmed using a switchable model of ZAP-70, which allowed us to toggle ZAP-70 expression on and off at any given time. To further define the mechanisms of ZAP-70 mediated cell migration, we studied CCL19 and CCL21 signaling in ZAP-70 proficient and deficient cells. Unexpectedly, we identified that ZAP-70 is required for chemokine-mediated activation of AKT. In summary, we here demonstrate that a tonic BCR-signal is present only in IGHV-unmutated CLL and dependent on the expression of ZAP-70. Furthermore, ZAP-70 converges two seemingly independent signaling events, namely chemokine- and tonic BCR signaling. Our data provide further explanations for the more aggressive clinical course of ZAP-70 positive CLL.

Fixed-Duration Pirtobrutinib Combined with Venetoclax ± Rituximab in Relapsed/Refractory Chronic Lymphocytic Leukemia: Updated Results, Including MRD Data, from the BRUIN Phase 1b Study

Background: Covalent (c) Bruton tyrosine kinase inhibitors (BTKi) have transformed the management of chronic lymphocytic leukemia (CLL). Recent clinical studies have evaluated the safety and efficacy of fixed-duration regimens with venetoclax and cBTKi. While these combinations are effective, their use may be limited by toxicity. Pirtobrutinib, a highly selective, non-covalent (reversible) BTKi, has shown promising safety and efficacy in heavily pretreated relapsed or refractory (R/R) CLL patients (pts). Here, we report the safety and efficacy of fixed-duration pirtobrutinib combined with venetoclax ± rituximab in pts with R/R CLL. Methods: Pts with R/R CLL were eligible for pirtobrutinib combined with venetoclax ± rituximab in the phase 1b portion of the multicenter phase 1/2 BRUIN study (NCT03740529). Prior cBTKi therapy was allowed, but not prior venetoclax. Pts were enrolled into sequential cohorts, first in the pirtobrutinib + venetoclax (PV) cohort and then the PV + rituximab (PVR) cohort. Pirtobrutinib 200 mg QD was started on cycle 1 day 1, and venetoclax was started on cycle 2 day 1 with the standard 5-week dose ramp to 400 mg QD target dose. PV was given for up to 24 cycles; each cycle was 28 days. For the PVR cohort, rituximab was given at 375 mg/m 2 on cycle 1 day 1 and then 500 mg/m 2 on day 1 of cycles 2-6. The primary endpoint was safety as assessed by treatment-emergent adverse events (TEAEs) graded according to CTCAE v5.0. Other key endpoints included overall response rate (ORR), progression-free survival (PFS), and minimal residual disease (MRD). Undetectable MRD (uMRD) was defined as less than 1 CLL cell/10,000 nucleated cells (<1x10 -4) in peripheral blood by ClonoSEQ® assay (Adaptive Biotechnologies, Seattle, WA). A data cut of May 5, 2023, was utilized. Results: Fifteen pts received PV, and 10 received PVR. Median age was 66 years (range, 49-77) for those who received PV and 69 (range, 39-78) for those who received PVR. Median prior lines of therapy was 1 (range, 1-2) for the PV cohort and 2 (range 1-4) for the PVR cohort. Most pts had received prior chemotherapy (PV=53%; PVR=60%), CD20 monoclonal antibody (73%; 70%), and cBTKi (73%; 60%). The majority of pts had IGHV unmutated CLL (PV=73%; PVR=89%). ORR was 93.3% (95% CI, 68.1-99.8) for the 15 pts receiving PV and 100% (95% CI, 69.2-100.0) for the 10 pts receiving PVR, with 10 complete responses (PV=7; PVR=3). Median duration of follow-up for PFS was 22.1 months (IQR, 20.1-25.7) for PV and 22.1 months (IQR, 20.7-22.1) for PVR; PFS at 18 months was 92.9% (95% CI, 59.1-99.0) for the 15 pts receiving PV and 80.0% (95% CI, 40.9-94.6) for the 10 pts receiving PVR. The overall uMRD rate at cycle 13 was 70.8% (PV=10; PVR=7) for the 24 evaluable pts, with 87.5% (PV=12; PVR=9) of pts achieving uMRD at some time during the trial and all but one pt sustaining uMRD during subsequent MRD assessments ( Figure). Twenty-two pts discontinued treatment (PV=14; PVR=8); of these, 14 completed all 24 cycles of therapy (PV=9; PVR=5) and 8 discontinued early because of progressive disease (PV=2), adverse events (PVR=2), protocol noncompliance (PV=1), death unrelated to treatment (PVR=1), or other reasons (PV=2). Three pts (PV=1; PVR=2) continue to receive treatment. The median relative dose intensity was similar in both cohorts (PV=97.9%; PVR=98.6%). The most common TEAE of any grade included nausea (PV=60.0%; PVR=40.0%), fatigue (53.3%; 50.0%), and diarrhea (46.7%; 60.0%). The most common grade ≥3 TEAE was neutropenia/neutrophil count decreased (PV=46.7%; PVR=60.0%). Grade ≥3 clinical tumor lysis syndrome occurred during venetoclax dose escalation (PV=2), including a grade 3 case that resolved spontaneously after 24 hours and a grade 4 case that resolved after short-term intravenous fluids. Treatment-related adverse events led to dose reductions in three pts (PV=1; PVR=2) and treatment discontinuation in two pts (PVR=2). Conclusions: Fixed-duration pirtobrutinib combined with venetoclax ± rituximab was well tolerated and demonstrated sufficiently promising efficacy to warrant further investigation in pts with R/R CLL. The BRUIN CLL-322 phase 3 trial comparing PVR vs VR in previously treated CLL is currently enrolling pts (NCT04965493).

Combined Ibrutinib and Venetoclax for First-Line Treatment of Patients with Chronic Lymphocytic Leukemia (CLL): 5-Year Follow-up Data

Background: Ibrutinib (IBR) and venetoclax (VEN) combination is an effective therapy for patients (pts) with CLL. We previously reported results of the first-line cohort of a phase II trial of combined IBR and VEN for high-risk pts with CLL (Jain, NEJM 2019, JAMA Oncology 2021). Here we report updated data for 120 pts (80 pts in the original published cohort and 40 pts in an expansion cohort) with a median follow-up of 61.5 months. Methods: Pts with previously untreated CLL meeting IWCLL treatment criteria were enrolled. All pts had at least one high-risk feature: del(17p), mutated TP53, del(11q), unmutated IGHV, or age ≥65 years. Pts received IBR 420 mg daily for 3 cycles followed by addition of VEN (weekly dose-escalation to 400mg daily). Combined therapy was given for 24 cycles (28 days/cycle). Pts with bone marrow (BM) undetectable MRD (U-MRD) (flow cytometry; sensitivity 10 -4) at 24 cycles of combined therapy discontinued both VEN and IBR; MRD+ pts continued IBR. A trial amendment allowed an additional 12 cycles of combined VEN and IBR for pts who remained BM MRD+ after Cycle 24. Response assessments included BM and CT studies (2008 IWCLL criteria). U-MRD was defined as <0.01%; low MRD+ 0.01% to <1%; high MRD+ ≥1%. Progression-free survival (PFS) was assessed as the time from the start of study drug to CLL progression, Richter transformation, or death from any cause. Blood MRD was monitored every 6 months after active therapy. Results: Between August 2016 and February 2019, a total of 120 pts were enrolled. Median age was 64.5 years (range, 26-88 years). 86% had IGHV-unmutated CLL. 23% had del(17p)/ TP53 mutation. The median follow-up is 61.5 months. Six pts came off study during 1 st 3 cycles of IBR monotherapy; 114 pts initiated VEN. After 12 cycles of the combination, 62/120 (52%) achieved BM U-MRD remission; 43/120 (36%) were BM MRD-positive (low MRD+, n=35; high MRD+, n=8). After 24 cycles of the combination, 77/120 (64%) achieved BM U-MRD remission; 24/120 (20%) were BM MRD+ (low MRD+, n=23; high MRD+, n=1). Overall, 86/120 (72%) achieved BM U-MRD as the best response. One pt had DLBCL transformation and 1 pt had CLL progression during the first 2 year of therapy (details below). The 5-year PFS is 90.1% and 5-year OS is 95.6% (Figure 1). The 5-year PFS for pts with del(17p)/ TP53 mutation (n=27) is 86.1%. Of the 77 pts who were BM U-MRD at the end of cycle 24 of the combination, 73 discontinued all therapy, 4 pts continued IBR per treating physician discretion. Among these 77 pts, with a median follow-up of 40 months post Cycle 24, 22 pts had recurrence of blood MRD (defined as MRD ≥0.01% in 2 consecutive visits). Of the 22 pts with MRD recurrence, 5 pt had CLL progression at a median of 18 months (range, 6-30 months) from MRD recurrence (details below); 16 are being monitored without any active therapy for CLL and without clinical disease progression; 1 pt died from mesothelioma. Among the 55 pts who remain in blood U-MRD remission, 53 remain in long-term follow-up in U-MRD remission; 1 pt had B-PLL transformation and 1 patient died (found unresponsive at home; was off therapy for 2 years). There were 24 pts who were BM MRD+ at the end of cycle 24 of the combination (low MRD+, n=23; high MRD+, n=1). The only pt with high-MRD+ at end of cycle 24 was noted to have Richter transformation at that time. The remaining 23 pts (all low MRD+ in BM, range 0.01-0.95%) continued IBR monotherapy. With a trial amendment, MRD+ pts after Cycle 24 could get 12 additional cycles of VEN; 18/23 pts have resumed VEN. 11/18 (61%) pts achieved U-MRD remission during the third year of combined therapy. Only 2/23 pts are still receiving IBR (remaining pts have d/c IBR; all pts have d/c venetoclax); none of these 23 pts had clinical relapse. A total of 6 pts had CLL progression (1 during the first 2 yr of therapy; remaining 5 during off-therapy phase). 3/6 had evaluation of BTK, PLGG2 and BCL2 mutations at the time of relapse and none were detected. 5 pts have started subsequent therapy (acalabrutinib, n=4; ibrutinib, n=1; all are clinically responding); 1 pt has not yet started therapy. Conclusions: We report long term follow-up of combined IBR and VEN in first-line CLL (n=120) with a 5-year PFS of 90.1%. The 5-year PFS for pts with del(17p)/ TP53 mutation is 86.1%. Retreatment with BTK inhibitor appears effective for pts with disease relapse.

Nucleosome repositioning in chronic lymphocytic leukemia.

The location of nucleosomes in the human genome determines the primary chromatin structure and regulates access to regulatory regions. However, genome-wide information on deregulated nucleosome occupancy and its implications in primary cancer cells is scarce. Here, we conducted a genome-wide comparison of high-resolution nucleosome maps in peripheral blood B cells from patients with chronic lymphocytic leukemia (CLL) and healthy individuals at single-base-pair resolution. Our investigation uncovered significant changes of nucleosome positioning in CLL. Globally, the spacing between nucleosomes-the nucleosome repeat length (NRL)-is shortened in CLL. This effect is stronger in the more aggressive IGHV-unmutated CLL subtype than in the IGHV-mutated CLL subtype. Changes in nucleosome occupancy at specific sites are linked to active chromatin remodeling and reduced DNA methylation. Nucleosomes lost or gained in CLL marks differential binding of 3D chromatin organizers such as CTCF as well as immune response-related transcription factors and delineated mechanisms of epigenetic deregulation. The principal component analysis of nucleosome occupancy in cancer-specific regions allowed the classification of samples between cancer subtypes and normal controls. Furthermore, patients could be better assigned to CLL subtypes according to differential nucleosome occupancy than based on DNA methylation or gene expression. Thus, nucleosome positioning constitutes a novel readout to dissect molecular mechanisms of disease progression and to stratify patients. Furthermore, we anticipate that the global nucleosome repositioning detected in our study, such as changes in the NRL, can be exploited for liquid biopsy applications based on cell-free DNA to stratify patients and monitor disease progression.

Integrating High-Throughput Dynamic BH3 Profiling and Molecular Phenotyping to Identify Therapeutic Vulnerabilities in CLL

Despite recent advances in chronic lymphocytic leukemia (CLL) therapy, such as the use of targeted agents including, Bruton's tyrosine kinase (BTK) inhibitor ibrutinib and the potent BCL-2 antagonist venetoclax, this disease remains incurable for most patients, who are refractory or become resistant to the novel agents. Thus, identifying new treatment regimens for CLL and building a precision medicine framework that can match CLL patients to the appropriate drugs are of high priority. To address this challenge, we optimized high-throughput dynamic BH3 profiling (HT-DBP), a functional assay that rapidly measures the initiation of apoptotic signaling after ex vivo exposure to drugs, for interrogation of CLL samples. The main advantages of this assay over other ex vivo assays are: (i) rapidity - under 24 hours, which is especially important in CLL, where cell viability substantially decreases after 24 hours; (ii) miniaturization - a very limited number of primary cells are required; and (iii) scalability - allowing to conduct hundreds of drug response tests in parallel on one 384-well plate. These features collectively maximize the information yield from a given patient sample. We recently identified prognostic genetic alterations and molecular subtypes of CLL, based on multi-omics profiling of >1100 CLL samples (Knisbacher et al., Nat Genet, in press). To determine if these molecular findings were associated with novel therapeutic vulnerabilities in CLL, we performed HT-DBP on 65 primary CLL samples previously characterized by exome, transcriptome and methylome profiling, using 42 FDA approved drugs that were selected for potential relevance to CLL biology. We isolated peripheral blood mononuclear cells (PBMCs) and cultured them in conditioned media derived from stroma cells to reduce spontaneous apoptosis. Target cells were treated with a drug for 20 hours followed by BH3 peptide exposure. Mitochondrial outer membrane permeabilization (MOMP) was then measured on digitonin-permeabilized cells in response to BH3-only synthetic peptides that mimic pro-apoptotic BCL-2 family proteins. Mitochondrial cytochrome c release was quantified as a measure of MOMP by flow cytometry, gating on CD19+ and CD5+ cells. This assay measures if the cell has moved closer to the threshold of apoptosis after drug treatment and thereby identifies drugs that enhance apoptosis priming. The peptides used in each experiment were derived from BIM or PUMA to measure increases in overall apoptotic priming, or BAD and MS1 peptides that identified BCL-2 and MCL-1 dependence, respectively. Our screen revealed differential drug-induced apoptotic priming for various drugs. As expected, venetoclax and ibrutinib were highly effective across CLL. Other drugs that demonstrated high priming included navitoclax (BCL-XL/BCL-2), nutlin-3 (MDM2), abexinostat (HDAC), gandotinib (JAK2), duvelisib (PI3K δ/γ), idelalisib (PI3Kδ) and cerdulatinib (SYK/JAK). The assay was robust, as indicated by an 0.92 median Pearson correlation across replicates. Additionally, the majority of drugs had greater effect on CLL samples than on healthy PBMCs (p<0.001, paired t-test), supporting their specificity. We focused our analysis on the differential drug effects among molecular subtypes of CLL. First, we found that IGHV-mutated CLLs (M-CLLs) became more primed to apoptosis than IGHV-unmutated CLLs (U-CLLs) across the panel of drugs (p<0.001, paired t-test) and significantly in response to fludarabine and umbralisib (FDR<0.1, t-test). Second, we compared drug-induced apoptotic priming among 8 CLL subtypes (i.e. RNA expression clusters (ECs); Knisbacher et al.). Notable among the many drug priming-EC relationships was that within M-CLL ECs, venetoclax was most effective in EC-m3 (high IL-10 expression) and least effective in EC-m2 (low IL-10 and enriched in trisomy 12). Interestingly, EC-m1, associated with high TFEC expression and poor outcome, was most sensitive to nutlin-3. For U-CLLs, EC-u1 was most sensitive to gandotinib and EC-u2 to navitoclax. EC-i, associated with the intermediate methylation subtype of CLL, was the most resistant EC to ibrutinib but was very sensitive to navitoclax, more than to any other drug. Altogether, we present a framework that links ex-vivo drug response with molecular features including expression subtypes to highlight new therapeutic opportunities in CLL.

Molecular Landscape of Chronic Lymphocytic Leukemia Using Targeted Gene Panel Sequencing

Introduction Chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease with various genetic abnormalities that can affect the treatment and survival of patients. Recently, by the advent of next-generation sequencing (NGS) techniques recurrently mutated genes have been described in CLL. Driver gene mutations such as NOTCH1, SF3B1, TP53, and MYD88 have been considered to have prognostic impact in CLL. The aim of this study was to detect pathogenic variants of commonly mutated genes in CLL patients and to explore their associations with IGHV mutational status and cytogenetic abnormalities. Patients and Methods The samples were collected from bone marrow or peripheral blood of 124 CLL patients. Genomic DNA was isolated using QIAamp Blood Mini kit. NGS analysis was performed using Twist Custom Panel and bidirectional sequencing with a minimum coverage of 1000x on Illumina NextSeq according to the manufacturers’ instructions. Data were analyzed by NextGene software. The following 27 recurrently mutated CLL genes were studied: PIK3CD, PIK3CA, SF3B1, MYD88, FBXW7, BRAF, NOTCH1, PTEN, BIRC3, PTPN6, MAP2K1, TP53, STAT5B, STAT3, CD79B, TCF3, MAPK1, DDX3X,ATM, BCL2, BTK, KRAS, NRAS, CARD11, CXCR4, PLCG2, POT1. Variants below 5% variant allele frequency (VAF) were filtered out from the analysis. Variants were considered subclonal with 5-10% VAF and clonal when VAF was >10%. Classification of variants were performed according to the American College of Medical Genetics and Genomics (ACMG) criteria. Results Our NGS study revealed a total of 96 variants in 124 CLL patients. Overall, 63/124 patients (50.8%) harbored at least one mutation, the majority of them (60/96, 62.5%) was clonal. In 36 patients only one pathogenic variant was detected, while 88 patients carried two or more (2-4) genetic alterations. The most frequently mutated gene was the NOTCH1, followed by TP53, SF3B1, FBXW7, and BRIC3. Subclonal variants were also detected in 36/124 patients (29%), particularly in NOTCH1,FBXW7, BIRC3, and PIK3CA genes. TP53 and NOTCH1 variants occured mostly in unmutated IGHV CLL cases. Patients with mutated IGHV harbored mainly FBXW7 and BIRC3 mutationss. FBXW7 variants were detected in 9/125 (7%) patients, that is a higher frequency compared to other studies. Fluorescence in situ hybridization (FISH) was performed in 113 cases. The majority of these patients (84 cases, 74%) had one or more cytogenetic abnormality. In this cohort, 13q deletion was the most common aberration (65%, 55/84 patients), followed by 11q deletion (26%, 22/84 patients) and 17q deletion (14%, 12/84 patients). Deletion of 17p co-occured with TP53 single nucleotide variants in 10 of 12 patients. SF3B1, NOTCH1, BIRC3 and TP53 variants occured with 11q deletion in 10 cases. Trisomy 12 was detected with NOTCH1, BIRC3 and FBXW7 variants, and showed negative association with unfavorable SF3B1 mutations. Conclusions Our results confirmed the presence of high number of clonal and subclonal variants in the most frequently mutated genes (NOTCH1, TP53, SF3B1, FBXW7, BIRC3). TP53, NOTCH1 and SF3B1 mutations were enriched with unfavorable biologic factors, as they were found to be associated with unmutated IGHV and cytogenetic aberrations, such as del17p, del11q and trisomy 12. Cases with NOTCH1 variants harbored all types of the investigated cytogenetic alterations (del13q, del11q, de17p, trisomy 12) and were associated exclusively with unmutated IGHV. TP53 variants occured mostly in unmutated IGHV CLL cases together with del17p. Patients with SF3B1 variants showed del11q, del13q and mostly unmutated IGHV. FBXW7 variants enriched in both of unmutated and mutated IGHV cases and harbored del13q, de17p and trisomy 12. FBXW7 and NOTCH1 pathogenic variants have the same biological consequences in CLL, therefore presence of FBXW7 mutations may have clinical relevance regarding anti-CD20 therapy. Taken together, these NGS results complemented with the study of IGHV mutational status and cytogenetic data can contribute to better prognostic workup and management of our CLL patients.

MER Signaling Axis: A Novel Therapeutic Target in Chronic Lymphocytic Leukemia

Chronic lymphocytic leukemia (CLL) is characterized by the accumulation of CD19+/CD5+/CD23+ monoclonal B-cells in peripheral blood, bone marrow and lymphoid tissues with a highly variable disease course. B-cell receptor (BCR)-signal inhibitors, specifically Ibrutinib which targets Bruton's tyrosine kinase (BTK) and Idelalisib which targets PI3Kδ, are effective in relapsed/refractory CLL patients. Despite BCR-signal-inhibitors are changing the management of CLL, these agents are not curative and resistance can develop, often leading to the transformation of CLL into more aggressive B-cell lymphomas limiting their therapeutics options. Thus, improved understanding of the nature and extent of other active receptor tyrosine kinase (RTK) signals in CLL cells is critical for development of additional therapies to treat these high-risk patients. Our recent discovery of MER, a RTK of the TAM (Tyro3, AXL, MER) family, in CLL cells may offer such an option. In order to analyze MER expression status in CLL cells from previously untreated CLL patients, we employed western blot, flow cytometry and qRT-PCR analyses. We detected low to high level expression of MER in CLL cells from ~50% of CLL patients as compared to normal, purified B cells. We also found that MER in CLL cells remained constitutively phosphorylated (active). Furthermore, our preliminary analysis suggested that MER expression in CLL cells may be positively associated with high-risk, unmutated IGHV CLL patients. In vitro ligation of Gas6 (growth arrest-specific gene 6), a specific ligand for all the TAM receptors, robustly activated MER as compared to AXL or Tyro3. Interestingly, activation of MER preferentially activated Erk1/2, NF-κB, and BTK of the BCR pathway in CLL cells. Partial depletion of MER in CLL cells using a specific-siRNA resulted in inhibition of P-Erk1/2, P-NF-κB and P-BTK, but not P-AKT, suggesting that MER may crosstalk with the BCR signaling pathway in CLL cells likely via interaction with CD79a, LYN or BTK. To address this hypothesis, we immunoprecipitated MER from CLL cell lysates and found a direct complex formation between MER and LYN. We also analyzed leukemic B cells from the Eµ-TCL1 transgenic mice which recapitulate highly aggressive human CLL for the expression of MER by western blot/flow cytometry. Results showed robust expression of MER in TCL1 leukemic B cells purified from mice with advanced CLL. Finally, treatment of CLL mice with a high-affinity MER inhibitor (UNC-2025) via oral gavage significantly reduced leukemic tumor burden. In total, our findings suggest that expression/activation of MER may potentiate CLL cell survival via a crosstalk with the BCR signal thus, could be an attractive therapeutic target for the progressive CLL patients.

High Cell Death Rates at Start of Ibrutinib Therapy Predict for Deeper Remissions in Patients with Chronic Lymphocytic Leukemia (CLL)

Introduction: The BTK inhibitor ibrutinib blocks B-cell receptor and other signaling pathways in CLL cells and has become a standard CLL therapy. Isotopic labeling with deuterated water (2H2O) to measure the effects of ibrutinib on CLL cell proliferation and death directly in patients revealed that ibrutinib profoundly inhibits proliferation and induces high rates of leukemia cell death (registered at clinicaltrials.gov as NCT01752426; Burger et al., JCI Insight, 2017). Here, we report a long-term follow-up of this trial in which we analyzed long-term outcomes and correlated CLL cell birth and death rates with depth of response over time. Methods: Thirty patients with previously untreated CLL/SLL enrolled in the study to receive continuous long-term ibrutinib monotherapy, after one month of labeling with deuterated water. For our analyses, we stratified patients in groups based on high or low CLL cell death rates in the peripheral blood (PB) or lymphatic tissues (lymph nodes, spleen), i.e. death rates above or below the median, assessed over the first months on therapy, as detailed in the original publication. Responses were assessed according to 2008 IWCLL guidelines, with the exception that lymphocytosis was not used as a sole criterion for progression. PB MRD was quantified by flow cytometry with a sensitivity 10-4. Results: The median age of the participants was 64 years (range, 48 - 78); 63.3% were male. Thirteen patients (43%) had advanced stage disease, 57% had unmutated IGHV genes, and 10% carried 17p deletion (del17p). Twenty-two patients (73%) completed 5 years of protocol treatment and subsequently continued treatment with commercial supply ibrutinib. The patients were followed for a median time of 107 months (range, 6 - 111). The reasons for eventual treatment discontinuation (n=21) were adverse events (n=8, 38%), progressive disease (n=4, 19%), change to another treatment (n=5, 24%), death (n=2, 7%) and other reasons (n=2, 7%). To date, nine patients are still receiving ibrutinib. Five patients (17%) achieved a complete remission, 24 (80%) achieved partial remission, and one patient (3%) had stable disease, resulting in an overall response rate of 97%. Median progression-free (PFS) and overall survival (OS) were not reached at a median follow-up of 107 months. Five-year PFS was 80.6%, and OS was 90%. PB MRD was measured in 18 patients after 5 years of ibrutinib (54 to 60 cycles); all patients had detectable MRD (median 11.8%, range, 0.06 - 47.30%). We found that CLL cell death rates in PB and tissues after treatment initiation inversely correlated with the level of PB MRD after 5 years (r=-0.5872, P=0.0104 and r=-0.4407, P=0.0672). MRD levels were significantly lower in patients with high CLL cell death rates in PB (7.03% ± 3.68% vs. 29.46% ± 5.53%, mean ± SEM, P=0.0056) and in tissues (9.73% ± 5.49% vs. 28.89% ± 4.42%, P=0.0155) as compared with patients with lower CLL cell death rates (Figure 1). Tissue CLL cell death rates were significantly higher in patients with IGHV-unmutated CLL compared to mutated (28.88% ± 2.75% vs. 13.16% ± 2.82%, P=0.0005), and MRD levels trended lower (IGHV-unmutated: 10.71% ± 5.39% vs. IGHV-mutated: 28.36% ± 6.02%, P=0.0878). No statistically significant correlation was found between CLL cell birth rate at baseline or after start of ibrutinib and MRD levels after 5 years of treatment. Conclusion: CLL cell death rates during early treatment correlated with achieving lower MRD levels. We found that CLL cell death rates are higher in IGHV-unmutated patients suggesting a higher dependency of IGHV-unmutated clones on BCR signaling and, therefore, resulting in deeper responses. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

S136: CONSTITUTIVE VLA-4 ACTIVATION IN CHRONIC LYMPHOCYTIC LEUKEMIA. THE OTHER SIDE OF BCR AUTONOMOUS SIGNALING.

Background: In chronic lymphocytic leukemia (CLL), CD49d, the alpha chain of the heterodimer CD49d/CD29 (VLA-4), is a strong negative prognosticator and key player of CLL microenvironmental interactions. The adhesive properties of VLA-4 can be rapidly inside-out activated by signals through the B-cell receptor (BCR), thus favoring the capability of the integrin to interact with its ligands. In CLL, beside the canonical antigen (Ag)-dependent mechanism, BCR signaling has been recently demonstrated to occur via an autonomous Ag-independent manner. Aims: To investigate the role of autonomous BCR signaling on constitutive VLA-4 activation state in CLL. Methods: VLA-4 activation/affinity was determined by flow cytometry (FC) using the conformation-sensitive anti-CD29 mAb HUTS21 and/or by “real-time” (FC) measuring the binding of the VLA-4 ligand LDV-FITC as reported (Tissino et al, J Exp Med, 2018) in: i) 1,984 consecutive CLL all with IGHV gene mutations/BCR features available; ii) sequential samples (0, 14, 30, 60 90 days) from CLL patients (n=26) treated in vivo with ibrutinib (IB) in real-world and from a clinical trial (NCT02827617). HUTS21 staining was also performed in the presence of: plasma depletion/replacement, soluble (s) VCAM-1, fibronectin (FN) and blocking anti-CD49d (HP1/2) mAbs. ELISA assays were used to quantify sVCAM-1 in plasma samples (n=122). BCR signaling were investigated by Ca++ influx assay in a 4-OH tamoxifen (4-OHT)-inducible murine TKO cell model (Dühren-von Minden M et al, Nature, 2012). Results: Out of 1,984 CLL, 1,070 (54%) expressed CD49d (cutoff 30%) and, among them, 250/1,070 (23%) were HUTS21+ (cutoff 20%), indicating an activated VLA-4 conformation. HUTS21 staining was: i) impaired by depletion of plasma from whole blood samples, and reconstituted by specific plasma components (sVCAM-1, FN); ii) impaired by pre-incubation with anti-CD49d HP1/2 blocking mAbs before addition of plasma, sVCAM-1 and FN. sVCAM-1 was higher in CD49d+ vs CD49d- CLL (p<0.0001); among CD49d+ cases, sVCAM-1 was lower in HUTS21+ (i.e. VLA-4 activated) cases (p=0.0096), suggesting ligand sequestration by activated surface VLA-4. CLL with mutated IGHV expressed higher levels of activated VLA-4 compared to unmutated IGHV CLL (p=0.001). Higher levels of activated VLA-4 were found in CLL using the IGHV3 and IGHV4 families, compared to cases using the IGHV1 family (p=0.043 and p=0.004). Finally, analysis of BCR stereotypy highlighted higher VLA-4 activation levels in CLL from subset#2 compared to CLL from subset#1 (p=0.02). To validate these data, murine TKO cells, expressing high VLA-4 levels, were transfected with different BCRs derived from 4 CLL with high level of constitutively activated VLA-4 (TKO-high) and 4 CLL with low level of constitutively activated VLA-4 (TKO-low). Compared to TKO-low cells, TKO-high cells showed a higher autonomous Ca++ influx (p=0.03), and consistently higher VLA-4 affinity (p=0.01). IB treatment impaired both BCR autonomous signaling and VLA-4 affinity. Notably, anti-IgM stimulation induced high Ca++ influx and high VLA-4 affinity state in both TKO-high and TKO-low, irrespective of IB treatment. According to TKO data, a decreased constitutive VLA-4 activation was observed in CLL cells collected at pre-treatment and at day 14, 30, 60 and 90 from patients on IB, confirming an IB-dependent impairment of VLA-4 activation via BCR signal. Summary/Conclusion: The presence of a constitutively activated form of VLA-4 is observed in a fraction of CD49d+ CLL, due to a continuous VLA-4 inside-out stimulation derived from autonomous BCR signaling.

Modeling the B-cell receptor signaling on single cell level reveals a stable network circuit topology between nonmalignant B cells and chronic lymphocytic leukemia cells and between untreated cells and cells treated with kinase inhibitors.

B-cell receptor (BCR) signaling is central for the pathomechanism of chronic lymphocytic leukemia (CLL), and inhibitors of BCR signaling have substantially improved treatment options. To model malignant and nonmalignant BCR signaling, we quantified five components of BCR signaling (ZAP70/SYK, BTK, PLCγ2, AKT, ERK1/2) in single cells from primary human leukemic cells and from nonmalignant tissue. We measured signaling activity in a time-resolved manner after stimulation with BCR crosslinking by anti-IgM and/or anti-CD19 and with or without inhibition of phosphatases with H2 O2 . The phosphorylation of BCR signaling components was increased in malignant cells compared to nonmalignant cells and in IGHV unmutated CLL cells compared to IGHV mutated CLL cells. Intriguingly, inhibition of phosphatases with H2 O2 led to higher phosphorylation levels of BCR components in CLL cells with mutated IGHV compared to unmutated IGHV. We modeled the connectivity of the cascade components by correlating signal intensities across single cells. The network topology remained stable between malignant and nonmalignant cells. To additionally test for the impact of therapeutic compounds on the network topology, we challenged the BCR signaling cascade with inhibitors for BTK (ibrutinib), PI3K (idelalisib), LYN (dasatinib) and SYK (entospletinib). Idelalisib treatment resulted in similar effects in malignant and nonmalignant cells, whereas ibrutinib was mostly active on CLL cells. Idelalisib and ibrutinib had complementary effects on the BCR signaling cascade whose activity was further reduced upon dasatinib and entospletinib treatment. The characterization of the molecular circuitry of leukemic BCR signaling will allow a more refined targeting of this Achilles heel.

Long-term outcomes for ibrutinib–rituximab and chemoimmunotherapy in CLL: updated results of the E1912 trial

AbstractHerein, we present the long-term follow-up of the randomized E1912 trial comparing the long-term efficacy of ibrutinib–rituximab (IR) therapy to fludarabine, cyclophosphamide, and rituximab (FCR) and describe the tolerability of continuous ibrutinib. The E1912 trial enrolled 529 treatment-naïve patients aged ≤70 years with chronic lymphocytic leukemia (CLL). Patients were randomly assigned (2:1 ratio) to receive IR or 6 cycles of FCR. With a median follow-up of 5.8 years, median progression-free survival (PFS) is superior for IR (hazard ratio [HR], 0.37; P < .001). IR improved PFS relative to FCR in patients with both immunoglobulin heavy chain variable region (IGHV) gene mutated CLL (HR: 0.27; P < .001) and IGHV unmutated CLL (HR: 0.27; P < .001). Among the 354 patients randomized to IR, 214 (60.5%) currently remain on ibrutinib. Among the 138 IR-treated patients who discontinued treatment, 37 (10.5% of patients who started IR) discontinued therapy due to disease progression or death, 77 (21.9% of patients who started IR) discontinued therapy for adverse events (AEs)/complications, and 24 (6.8% of patients who started IR) withdrew for other reasons. Progression was uncommon among patients able to remain on ibrutinib. The median time from ibrutinib discontinuation to disease progression or death among those who discontinued treatment for a reason other than progression was 25 months. Sustained improvement in overall survival (OS) was observed for patients in the IR arm (HR, 0.47; P = .018). In conclusion, IR therapy offers superior PFS relative to FCR in patients with IGHV mutated or unmutated CLL, as well as superior OS. Continuous ibrutinib therapy is tolerated beyond 5 years in the majority of CLL patients. This trial was registered at www.clinicaltrials.gov as #NCT02048813.

CD34+ cell of origin for immunoglobulin heavy chain variable region unmutated, but not mutated, chronic lymphocytic leukemia

The clinical course of chronic lymphocytic leukemia (CLL) is highly variable. Immunoglobulin heavy chain variable region (IgHV) mutation status is among the most important prognostic factors, with unmutated IgHV associated with inferior outcomes. CLL presumably arises from mature B cells. However, we hypothesized that IgHV unmutated CLL could arise early in B cell differentiation. We prospectively studied 29 patients with mutated and 88 with unmutated IgHV CLL for the presence of CD34+CD19+ cells harboring CLL chromosomal abnormalities. CD34+CD19+ cells were never detected in mutated CLL. In contrast, a small but distinct population of CD34+CD19+ cells harboring the CLL chromosomal abnormality was present in 86/88 patients with unmutated IgHV across all cytogenetic subtypes. Moreover, the CD34+CD19+ cells generated a 3.8 ± 0.7 fold CLL cell expansion over 3–4 weeks in cultures containing IL-3 and IL-2. Unmutated IgHV CLL appears to arise in CD34+ B cells, which perhaps contributes to its poorer prognosis.

Different Prognostic Impact of Recurrent Gene Mutations in IGHV-Mutated and IGHV-Unmutated Chronic Lymphocytic Leukemia: A Retrospective, Multi-Center Cohort Study By Eric, the European Research Initiative on CLL, in Harmony

Different Prognostic Impact of Recurrent Gene Mutations in IGHV-Mutated and IGHV-Unmutated Chronic Lymphocytic Leukemia: A Retrospective, Multi-Center Cohort Study By Eric, the European Research Initiative on CLL, in Harmony

The protein landscape of chronic lymphocytic leukemia

AbstractMany functional consequences of mutations on tumor phenotypes in chronic lymphocytic leukemia (CLL) are unknown. This may be in part due to a scarcity of information on the proteome of CLL. We profiled the proteome of 117 CLL patient samples with data-independent acquisition mass spectrometry and integrated the results with genomic, transcriptomic, ex vivo drug response, and clinical outcome data. We found trisomy 12, IGHV mutational status, mutated SF3B1, trisomy 19, del(17)(p13), del(11)(q22.3), mutated DDX3X and MED12 to influence protein expression (false discovery rate [FDR] = 5%). Trisomy 12 and IGHV status were the major determinants of protein expression variation in CLL as shown by principal-component analysis (1055 and 542 differentially expressed proteins, FDR = 5%). Gene set enrichment analyses of CLL with trisomy 12 implicated B-cell receptor (BCR)/phosphatidylinositol 3-kinase (PI3K)/AKT signaling as a tumor driver. These findings were supported by analyses of protein abundance buffering and protein complex formation, which identified limited protein abundance buffering and an upregulated protein complex involved in BCR, AKT, MAPK, and PI3K signaling in trisomy 12 CLL. A survey of proteins associated with trisomy 12/IGHV-independent drug response linked STAT2 protein expression with response to kinase inhibitors, including Bruton tyrosine kinase and mitogen-activated protein kinase kinase (MEK) inhibitors. STAT2 was upregulated in unmutated IGHV CLL and trisomy 12 CLL and required for chemokine/cytokine signaling (interferon response). This study highlights the importance of protein abundance data as a nonredundant layer of information in tumor biology and provides a protein expression reference map for CLL.

Genomic Complexity in Chronic Lymphocytic Leukemia Defined By Array-Based Analysis: Definitions, Associations with Other Biomarkers and Clinical Impact

Background: The advent of efficacious but also very expensive novel treatment regimens for high-risk chronic lymphocytic leukemia (CLL), has highlighted the need for accurate risk-stratification. Published evidence indicates that classic chromosome banding analysis (CBA) offers valuable complementary information to the routinely performed FISH analysis in CLL, potentially improving risk assessment. Indeed, recent studies identified complex karyotype (CK; defined as ≥3 abberations) as an independent predictive marker for refractoriness to ibrutinib and venetoclax, although for CLL, a precise evidence-based definition of genomic complexity (GC) is yet to be made. Array-based (CGH/SNP) analysis is capable of globally assessing the CLL genome, does not require in vitro mitogens, offers increased detection depth, and allows for easier standardization.Aims: 1. Determine a prognostic relevant definition of GC in CLL by array-based analysis. 2. Head-to-head comparison of the sensitivity of CBA versus array-based analysis.Methods: 1911 CLL and monoclonal B-cell lymphocytosis (MBL) patients (CLL=1895, 99% and MBL=16, 1%, respectively) were analyzed with CGH or SNP arrays mostly performed within the first year from diagnosis and before treatment administration (66% and 84%, respectively). For a subgroup (N=206) both CBA and array results were available (<1 year in between analyses). Main features of the studied cohort: median age: 60.7 years, males: 1252 (68%), Binet: A/B/C:623/324/141 (57%/30%/13%), IGHV-mutated CLL (M-CLL): 536/1082 (50%), del(13q): 1020/1910 (53%), del(11q): 353/1911 (19%), TP53 aberrations (TP53 abs, deletions and/or mutations of the TP53 gene): 205/1911 (11%). Recurrent chromosomal aberrations i.e. del(13)(q14), del(11)(q22.3) and del(17)(p13.1) defined by array were included in all analyses irrespective of size, while the cut-off for other aberrations are indicated.Results: First, analysis was performed using a size cut-off ≥5Mb according to Schoumans et al (Genes Chrom Cancer 2016). Applying the criteria ≥3 structural and/or numerical aberrations to define GC, 451/1911 cases (24%) displayed GC analyzed with CGH/SNP arrays. GC was significantly related (p<0.001) with advanced clinical stage (Binet B/C), IGHV-unmutated CLL (U-CLL), del(11q), del(13q) and TP53 abs. On univariate analysis, GC was associated with inferior OS (median: 10.0 vs 12.2 (p<0.001) years). GC cases were stratified into those with 3 (‘low-GC’, N=174, 39%), 4 (‘intermediate-GC’, N=103, 23%) and ≥5 (‘high-GC’, N=174, 39%) aberrations. High-GC cases differed significantly (p<0.05) from the other two subgroups, being enriched for U-CLL and TP53 abs (84% and 45%, respectively). The median OS was 5.8 years for the high-GC vs 10 years for the low- and 8.1 years for the intermediate-GC group (p<0.01). Only ‘high-GC’ remained significant (p<0.01) on multivariate analysis along with TP53 abs and IGHV status (see table).Lowering the array cut-off to 1Mb (N=353) resulted in detection of a higher number of aberrations (3.04 vs 2.34) compared to 5Mb cut-off (95% CI paired differences 0.475-0.924). Although a lower array cut-off resulted in upstaging of high risk GC (22 vs 12%), the median OS in the ‘high risk’ group was increased as compared to the cut-off of 5Mb (8.4 vs 5.5 years).Array-analysis (5Mb cut-off) showed a higher number of total detected aberrations as compared to CBA (2.35 vs 1.84, 95% CI paired differences 0.221-0.798). With array more patients were defined as GC with higher discriminatory power regarding survival (concordance index: 58 vs 55%) than with CBA. Prognostic impact of array vs CBA and of specific aberrations is currently being analyzed.Conclusion: According to this largest performed array-based analyses, current definitions for CK defined by the presence of ≥3 structural or numerical aberrations based on classical cytogenetic approaches may be suboptimal when applied for cases analyzed by array techniques. Instead, ≥5 aberrations detected by arrays were linked to high-risk disease, independent of clinical stage, IGHV and TP53 status. Since a lower array cut-off resulted in the detection of additional aberrations, without however been accompanied by the same dismal outcome as the 5Mb cut-off, further studies are warranted in order to define the actual prognostic relevance of smaller aberrations. [Display omitted] DisclosuresEldering:Roche: Research Funding; Gilead: Research Funding; Celgene: Research Funding. Ghia:Pharmacyclics LLC, an AbbVie Company: Consultancy; Janssen: Consultancy, Research Funding; Gilead: Consultancy, Research Funding, Speakers Bureau; Adaptive: Consultancy; AbbVie: Consultancy; Roche: Consultancy; Novartis: Research Funding. Stamatopoulos:Janssen Pharmaceuticals: Honoraria, Research Funding; Novartis SA: Research Funding; Gilead: Consultancy, Honoraria, Research Funding; Abbvie: Honoraria, Research Funding. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Strefford:Roche: Research Funding. Kater:Celgene: Consultancy, Research Funding; Johnson & Johnson: Research Funding; Abbvie: Research Funding.

Three-Year Follow-up from a Phase 2 Study of Combination Obinutuzumab, Ibrutinib, and Venetoclax in Chronic Lymphocytic Leukemia

Three-Year Follow-up from a Phase 2 Study of Combination Obinutuzumab, Ibrutinib, and Venetoclax in Chronic Lymphocytic Leukemia

Ibrutinib and Novel Oral Anticoagulants: Three Case Reports from a Single Center Real Life Experience

Background: Chronic Lymphocytic Leukemia (CLL) represents 7% of Non Hodgkin Lymphoma being the most common leukemia. Efficacy and safety data on Ibrutinib used as a single agent for treatment of previously treated CLL comes from RESONATE trial, which showed 6% of Overall incidence of grade 3 atrial fibrillation (AF).Another side effect of Ibrutinib is increased rate of bleeding. The 2019 long term follow-up of RESONATE 2 trial of Ibrutinib in previously untreated CLL reported major hemorrhage and grade 3 AF in 11% and 5% of patients on Ibrutinib arm, respectively; notably, 67% of patients who experienced Grade 3 Major hemorrhage were taking concomitant anticoagulation therapy. The use of Ibrutinib in patients with AF requiring anticoagulation therapy could be challenging, given that both the optimal starting dose of Novel Anti Coagulants (NOACs) and the specific NOAC to be used in patients taking ibrutinib have not been established yet. Here we describe the clinical history of three CLL patients affected by AF treated with ibrutinib associated with NOACs. Cases : 1. The first patient was a 72-year-old male affected by IGHV unmutaded CLL with no TP53 disruption relapsed five years after the achievement of first complete remission through 6 courses R-Bendamustine. He started full dose Ibrutinib on august 2019. When he started ibrutinib there were no bulky lesions, the biggest node diameter was 2.7 cm, spleen longest diameter was 18 cm, Hb was 9.3 g/dL, platelets were 166,000/µL, neutrophils 4,000/µL and ALC 129,000/ µL, b symptoms were absent. Since 2018 he suffered from chronic AF treated with Apixaban at the dose of 5 mg BID. He achieved partial response with no evidence of lymphadenopathy and lymphocytosis after 6 months of treatment with no occurrence of major bleeding. On April 2020 he came to our attention with minor bleeding consisting of small petechial macules. Neither epistaxis nor bruising were reported. Petechiae resolved on May 2020, at last follow-up clinical visit (July 2020) Ibrutinib and Apixaban are still well tolerated and signs and symptoms of both CLL and bleeding are absent. 2. The second patient was a 65-year-old male affected by IGHV unmutated CLL with no TP53 disruption, relapsed three years after a complete response achieved with first line treatment with 6 courses of R-Bendamustine. When he started full dose Ibrutinib (420 mg OD), Hb was 11.8 g/dL, neutrophils 5,100/ µL, lymphocyte 145,000/ µL and platelets 51,000/ µL. He achieved partial remission on May 2020. On April 2020, high rate AF was diagnosed, heart rate was 162 beats per min, systolic and diastolic blood pressure were 125 and 80 mmHg, respectively. The cardiologist prescribed bisoprolole 1.25 mg OD and after 24h heart rate became normal (60 beats per min). An Echocardiography was performed showing ejection fraction of 60% with all other parameters being normal. CHADS-VASc score was 3 and HAS-BLED score was 2, so he started Edoxaban at the dose of 30 mg OD, while Ibrutinib was never stopped. The patient now has neither signs and symptoms of CLL, nor those of AF and bleeding. 3. The last patient was a 81-year-old male affected by previously untreated IGHV mutated CLL with TP53 mutation and absence of del 17p. High rate AF was diagnosed on may 2020 and edoxaban 30 mg OD was started. He started reduced dose Ibrutinib (280 mg OD) on the first days of July 2020 due to risk of bleeding. Hb, neutrophils, lymphocyte and platelets were 10.8 g/dL, neutrophils 2,730/ µL, lymphocyte 195,000/µL and platelets were 116,000/µL. RAI and Binet where 3 and B, respectively. CLL-IPI was 8 (very high risk), neither bulky nodes nor B symptoms were present. After 1 month-follow-up there is no evidence of bleeding and AF is still asymptomatic. Conclusions: In our limited experience and according with literature, Ibrutinib could be safely used in patients with pre-existing or de novo AF in association with NOACs with no or minimal bleeding signs. Therefore, patients affected by AF might completely benefit from this highly effective therapy for CLL. Disclosures No relevant conflicts of interest to declare.

Abstract 1256: Widespread alterations of chromatin accessibility in chronic lymphocytic leukemia (CLL)

Abstract Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in western countries that has a strong genetic basis. Using data from both chromatin immunoprecipitation and sequencing (ChIP-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq), recent studies have uncovered alterations of chromatin landscape in CLL. However, the spectrum of epigenetic changes and the mechanisms of casualtyare only partially understood. In this study, we used ATAC-seq to profile chromatin accessibility across the two major CLL subtypes, IGHV-mutated (n=19) and IGHV-unmutated (n=22). DNA library of accessible chromatin regions was generated from purified CD5+/CD19+ leukemiacells. All libraries were assessed to have high data quality based on the ENCODE quality metrics. Additionally, publicly available ATAC-seq data (GSE118189 and GSE111015) from total (n=5), memory (n=6) and naïve B cells (n=6) were analyzed in parallel and used as normal reference. ATAC-seq peaks from CLL and normal B cells were merged to generate a consensus list of 107,928 high-confidence peaks that did not overlap ENCODE blacklisted regions, were present in at least two CLL or two normal B-cell samples, and had ≥1 counts-per-million in at least 10% of the samples. Raw read counts were Trimmed Mean of M-values normalized and log2 transformed. K-means clustering of differential peaks revealed an extensive reprogramming of chromatin accessibility landscape in CLL, with over 11,000 lost and nearly 9,000 gained open chromatin regions relative to normal B-cells. In particular, we identified two clusters comprising 1,401 regions that were largely open either in IGHV-mutated(571 peaks) or in IGHV-unmutated CLL (830 peaks). Open chromatin regions gained in IGHV-mutatedwere preferentially linked to genes in the B cell receptor signaling pathway and those in IGHV-mutatedto genes enriched in the interferon type I signaling pathway. These discriminatory regions are highly enriched with DNA binding motifs for transcription factors (TFs) with key roles in B cell development, such as PU.1, AP-1, c-Jun, BATF, and TCF family. In addition, 94% of the 1,401 peaks were located in distal regulatory regions, being ≥2.5 kb away from transcription start sites of genes; two-third of these distal regulatory regions overlapped H3K27ac peaks from CLL patients or immune cell types in the Roadmap reference epigenomes,indicating that enhancers are the prime sites of epigenetic differentiation between the two subtypes. Together, our analyses provide new insights into the global alterations of regulatory regions in CLL. Given the noticeable heterogeneity of chromatin landscape, further integration with histone modifications, TF binding, chromatin interaction, gene expression and genetic variation data are needed to understand the roles of epigenetic dysregulation and its interaction with genetic lesions in CLL pathogenesis. Citation Format: Huihuang Yan, Zhiquan Wang, Shulan Tian, Geffen Kleinstern, Nicholas Boddicker, Xing Li, Susan Slager, Esteban Braggio. Widespread alterations of chromatin accessibility in chronic lymphocytic leukemia (CLL) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1256.