Clinical Impact of Clonal and Subclonal TP53 Mutations in Chronic Lymphocytic Leukemia

Abstract Introduction. The clinical course of patients with chronic lymphocytic leukemia (CLL) is highly heterogeneous. The deletions/mutations of 17p/TP53 are predictors of chemorefractoriness, and for this reason, in the management algorithm of CLL patients, when present, indicate treatment with with chemo-free regimens also in the context of first-line therapy. Recent studies based on ultra-deep-next generation sequencing (NGS) have shown that TP53 mutations can be present at very low clonal abundance in tumor cell populations, although whether these mutations may have a detrimental clinical impact on disease course is still to be established. Aim. To investigate the presence of clonal and subclonal mutations of TP53 in a large cohort of CLL cases using an ultra-deep NGS strategy, and determined their clinical relevance for patients outcome. Methods. The study includes 590 CLL patients characterized for the deletion at chromosome 17p13 (FISH analysis) and TP53 mutations in samples before treatment. In all cases, analyses were carried out on DNA extracted from nearly pure (>90%) tumor cells. TP53 mutational status was investigated by NGS with an amplicon based strategy. Sequencing reads analysis was made by the Burrows-Wheeler Aligner-MEM algorithm and by SAMtools. Variant calling was performed using the entire pipeline established on the MiSeq Reporter software. Results were expressed as percentage of mutated DNA. The minimal allelic fraction for mutation calling was set at 1%. Synonymous variants and polymorphisms described in the Single Nucleotide Polymorphism Database (dbSNP138) were removed. Outcome variable was overall survival (OS). Clinical correlations were made using Kaplan-Meier plots and log-rank test. Results. FISH and mutational analyses were performed in samples within 2 years from diagnosis in 92% of the cases (Figure 1A). A total of 125 TP53 mutations (Figure 1B) were found in 96 patients (11.7%). Subclonal mutations have similar molecular characteristics as their respective high frequency allele mutations supporting a comparable pathogenic effect (Figure 1B). According to a 15% cutoff of variant allele frequency (VAF), 78 cases were considered clonal and 18 subclonal (Figure 1C) for TP53 mutations (1% < VAF < 15%). In this context, cases with subclonal and clonal TP53 mutations experienced significant shorter OS than TP53 wild-type (wt) cases, without differences between clonal and subclonal cases (Figure 1E). Accordingly, ROC analysis on the same cohort identified a cutoff of >0% for the clinical impact of TP53 mutations (Figure 1E inset). Deletion of chromosome 17p was found in 180 out of 574 patients (31.3%), and using a 10% cutoff, 61 patients presented a percentage of deleted nuclei above the cutoff (Figure 1D). Using only 17p deletion data and considering the above mentioned cutoff, patients with 17p13 deletion ≥10% experienced shorter OS than wt cases, while patients with 17p13 deletion <10% experienced OS superimposable to wt cases (Figure 1F). These data were confirmed by ROC analysis that selected >9% of deleted nuclei as optimal cutoff for OS discrimination (Figure 1F inset). Given the frequent co-occurrence of TP53 mutations with 17p deletions, we also evaluated the impact of isolated TP53 mutations and 17p deletions. By using the ROC cutoffs for the definition of mutated/deleted cases, 466 cases (81.1%) presented no TP53 disruption (TP53 mutations and deletion), 47 cases (8.2%) were TP53 mutated only, 15 cases (2.6%) were 17p deleted only and 46 cases (8.1%) presented a concomitant TP53 mutation and 17p deletion. Kaplan-Meier curves demonstrated comparable significant shorter OS intervals for TP53 mutated and/or deleted CLL cases respect to wt cases, while no differences were observed between these three groups (Figure 1G). Conclusion. By using a highly sensitive NGS approach, we have detected small subclones of TP53 in a relative high proportion of patients. TP53 mutations conferred a significant shorter OS irrespectively of VAF percent, while deletion of chromosome 17p impacted on OS only when detectable in more than 10% of nuclei. These cutoffs, once validated by prospective studies, may be employed in daily practice for the clinical management of CLL patients. Disclosures Zaja: Novartis: Honoraria, Research Funding; Abbvie: Honoraria; Celgene: Honoraria, Research Funding; Amgen: Honoraria; Janssen: Honoraria; Takeda: Honoraria; Sandoz: Honoraria.

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Clinical Impact of Clonal and Subclonal TP53 Mutations and Deletions in Chronic Lymphocytic Leukemia: An Italian Multicenter Experience

Blood ◽

10.1182/blood-2019-124647 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 480-480 ◽

Cited By ~ 3

Author(s):

Riccardo Bomben ◽

Francesca Maria Rossi ◽

Tiziana D'Agaro ◽

Tamara Bittolo ◽

Filippo Vit ◽

...

Keyword(s):

Research Funding ◽

Roc Analysis ◽

Validation Cohort ◽

Advisory Board ◽

Clinical Impact ◽

Lymphocytic Leukemia ◽

Training Cohort ◽

Tp53 Mutations ◽

Scientific Advisory Board ◽

Scientific Advisory

Background. TP53 mutations (TP53mut) along with 17p13 deletion (del17p) are strong predictors of poor survival and refractoriness to chemo-immunotherapies (CIT) in chronic lymphocytic leukemia (CLL), and their analyses should be always performed before treatment. Studies based upon ultra-deep-NGS have shown that TP53mut can be present at very low level in CLL cell populations, although their detrimental clinical impact in this setting is still matter of debate (Rossi, Blood 2014), and ERIC recomendations discourage to report TP53 mutations if subclonal Malcikova, Leukemia 2018). Aim. To investigated the presence and clinical relevance of clonal/subclonal TP53 aberrations in a large CLL cohort. Methods. The study includes 1,058 out of 1,613 CLL patients (509 treated with standard CIT) diagnosed between 1991 and 2018, and consecutively referred to a single institution for del17p analyses by FISH (167-kb 17p13 orange probe, MetaSystems), and TP53mut by ultra-deep NGS (MiSeq Illumina; median coverage >2,000X with an amplicon-based strategy covering exons 2-11 using 40ng DNA/test) in CD19-purified (>85% pure) CLL samples, collected before treatment (as per ERIC recommendations). For TP53mut analyses, FASTQ files were aligned to the Hg19 reference with Burrows-Wheeler Aligner-MEM algorithm, and allele variants called by FreeBayes (Garrison & Marth, arXiv 2102) with non-stringent parameters. To calculate random/systematic errors we generated a specific database with all the variant allele frequencies (VAF) observed in a subset of TP53 wild type (wt) subjects (n=362). TP53mut were accepted if: i) validated by Fisher exact test after Bonferroni correction (p<0.01); ii) with a VAF at least 2.75 standard deviations from the mean of the transformed distributions. The minimal allelic fraction for TP53mut calling was 0.4%. TP53mut cases with less than 2% VAF were tested twice. Outcome was overall survival (OS) from the date of exam. Results. A total of 248 TP53mut (Fig.A) were found in 154 patients (13.5%, Fig.B) with a median mutations/patient of 1.65 (range 1-11). According to the 12.5% VAF cutoff for TP53mut (Nadeu, Blood 2016), 87 cases were clonal (at least one clone > 12.5%) and 67 subclonal (all clones <12.5%; Fig.AB). Clonal and subclonal TP53mut have similar molecular characteristics (Fig.C), supporting the idea of comparable pathogenic effects. In fact, cases bearing clonal and subclonal TP53mut experienced comparably OS, shorter than TP53-wt cases (Fig.D). Accordingly, ROC analysis identified a cutoff of VAF >0.4% for the clinical impact of TP53mut (Fig.D), and the c-index of combined clonal/subclonal TP53mut (0.645) was significantly higher than the c-index of clonal TP53mut alone (0.602; P<0.001). Del17p was found in 178 patients (16.8%; Fig.E). In keeping with a ROC analysis (Fig.F, inset), the 64 cases with del17p in >10% of nuclei had significantly shorter OS than cases with del17p in <10% or without del17p (Fig.F). By combining del17p and TP53mut according to ROC cutoffs, 891 cases (84.2%) presented no TP53 aberrations, 13 cases (1.2%) were del17p only, 103 cases (9.7%) were TP53mut only, and 51 cases (4.8%) were del17p/TP53mut. Compared to TP53-wt cases, similar shorter OS were observed for TP53mut and del17p/TP53mut cases (Fig.G). Same results were obtained in the context of treated patients when OS was computed from the date of treatment (Fig.H). The "yes/no effect" of TP53 mutations on CLL outcome was verified dividing our cohort in a training cohort of 630 CLL cases, and in a validation cohort of 428 CLL patients. These two cohorts presented similar OS, and the same proportion of TP53 mutated cases and 17p deletion. ROC analysis on training cohort based on TP53 mutation variables, identified >0.5% as the best cutoff. In keeping with this cutoff, TP53 mutated patients experienced a significantly shorter OS than wt patients. Again cases with clonal and subclonal mutation experienced the same OS (Fig.I). Importantly, the cutoff found in the training cohort was able to reproduce the very same results also in the validation cohort both in term of mutation per se and in terms of clonal and subclonal TP53 mutations (Fig.J). Conclusion. i) By applying ERIC recommendations and a rigorous pipeline of analysis, TP53mut impacted on OS also with VAF <1%; ii) del17p associated with short OS only when detectable in >10% of nuclei. These cutoffs may be employed for the clinical management of CLL patients. Figure Disclosures Di Raimondo: Takeda: Consultancy; Amgen: Consultancy, Honoraria, Research Funding. Rossi:Gilead: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Abbvie: Honoraria, Other: Scientific advisory board; Janseen: Honoraria, Other: Scientific advisory board; Roche: Honoraria, Other: Scientific advisory board; Astra Zeneca: Honoraria, Other: Scientific advisory board.

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Clinical Impact of Clonal and Subclonal TP53, SF3B1, BIRC3, and ATM Mutations in Chronic Lymphocytic Leukemia

Blood ◽

10.1182/blood.v126.23.4138.4138 ◽

2015 ◽

Vol 126 (23) ◽

pp. 4138-4138

Author(s):

Ferran Nadeu ◽

Julio Delgado ◽

Cristina Royo ◽

Tycho Bauman ◽

Tatjana Stankovic ◽

...

Keyword(s):

Chronic Lymphocytic Leukemia ◽

Allele Frequency ◽

Lymphocytic Leukemia ◽

Molecular Characteristics ◽

Prognostic Impact ◽

Driver Genes ◽

Germline Variants ◽

Tp53 Mutations ◽

Mutational Status ◽

The Impact

Abstract Genomic studies have provided a complete profile of somatic mutations in chronic lymphocytic leukemia (CLL). These comprehensive approaches have revealed a relatively large number of mutated genes, the adverse prognostic value of some of which has been demonstrated in a number of reports. Recent studies have shown the clinical relevance of TP53 mutations at very low allele frequency. The presence and prognostic impact of minor mutated clones of other CLL driver genes and their clonal dynamics in the evolution of the disease is not well known. The goal of this study was to explore the presence of clonal and subclonal mutations of TP53, SF3B1, BIRC3, and ATM using an ultra-deep next-generation sequencing (NGS) strategy, to define the evolution of these subclones in different time-points of the disease, and to determine their influence in the outcome of the patients. Samples from 363 untreated CLL cases were included in this study. Copy number alterations were investigated by high density SNP-arrays or by quantitative PCR in 341 and 16 cases, respectively. Targeted ultra-deep NGS of TP53 (exons 4-10), ATM (exons 2-63), BIRC3 (exons 2-9), and SF3B1 (exons 14-16 and 18), including splicing sites, was performed using the Access-Array system (Fluidigm) and sequenced in a MiSeq equipment (Illumina). This methodology combined with a robust bioinformatic analysis based on well-known available tools allowed the identification of mutations down to 0.3% of variant allele frequency (VAF). Results obtained were fully verified by orthogonal techniques. Twelve per cent of VAF was used as threshold for the classification of clonal or subclonal mutations since 12% was the cut-off for detection of mutations by Sanger sequencing. Deletions of 11q comprising ATM or BIRC3 were found in 7% of the cases and were associated with mutations of the other ATM allele in 19/26 (73%) cases and BIRC3 in 3/23 (13%). Deletions of 17p were found in 19 (5%) cases and co-existed with TP53 mutations in 15 (79%) of them. Regarding the mutational status of the studied genes, TP53 mutations were present in 11.6% of patients (7.2% clonal, 4.4% subclonal), ATM mutations in 10% (7% clonal, 1% subclonal, 2% germline mutations considered pathogenic), SF3B1 mutations in 12% (7% clonal, 5% subclonal), and BIRC3 mutations in 4% (2% clonal, 2% subclonal). These subclonal mutations had similar molecular characteristics to their respective high-allele frequency mutations supporting a comparable pathogenic effect. In this regard, clonal and subclonal SF3B1 mutations were associated with shorter time to first treatment (TTT) independently of IGHV mutations. Clonal and subclonal TP53 mutations predicted for shorter overall survival (OS) together with the IGHV mutational status, although the impact of isolated TP53 mutations (i.e. without 17p deletion) on OS was not so evident, as has been the case in other studies. In addition, the outcome of patients with clonal and subclonal BIRC3 mutations showed a similar significant shorter OS. Regarding ATM, the effect of isolated subclonal ATM mutations could not be evaluated because of their low number, but ATM mutations as a whole had a significant impact on TTT even in the absence of 11q deletions. This study also reinforces the need to study the germline of the patients to fully characterize the ATM mutations observed in the tumors. Of note, germline variants previously described as pathogenic were associated with 11q deletions, confirming the hypothesis already suggested that these germline variants may influence disease progression through loss of the otherallele. Clonal dynamics was examined in longitudinal samples of 45 CLL patients. We confirmed the expansion of most TP53 mutated clones after therapy. However, both TP53 and SF3B1 mutations expanded also before any therapy in some patients, indicating that progressive dynamics of these clones is not only dependent on therapy selection. On the contrary, small ATM mutated clones seemed to be more stable. Although the number of cases is limited, we observed that clonal evolution in longitudinal samples had an unfavorable impact on OS. In conclusion, this study shows the presence of a high number of subclonal mutations of different driver genes in CLL and provides insights on the impact of these mutations on the outcome of the patients. These findings suggest that the characterization of the subclonal architecture may be relevant for a better management of CLL patients. Disclosures No relevant conflicts of interest to declare.

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CD49d Is The Strongest Flow Cytometry-Based Predictor Of Overall Survival In Chronic Lymphocytic Leukemia

Blood ◽

10.1182/blood.v122.21.672.672 ◽

2013 ◽

Vol 122 (21) ◽

pp. 672-672 ◽

Cited By ~ 1

Author(s):

Pietro Bulian ◽

Tait D Shanafelt ◽

Chris Fegan ◽

Antonella Zucchetto ◽

Lilla Cro ◽

...

Keyword(s):

Flow Cytometry ◽

Overall Survival ◽

Chronic Lymphocytic Leukemia ◽

Research Funding ◽

Early Stage ◽

Cox Model ◽

Univariate Analysis ◽

Lymphocytic Leukemia ◽

Bivariate Analysis ◽

The Impact

Abstract Purpose Although CD49d is an unfavorable prognostic marker in chronic lymphocytic leukemia (CLL), definitive validation evidence is lacking. A worldwide multi-center analysis was performed using published and unpublished CLL series to evaluate the impact of CD49d as overall survival (OS) and treatment free survival (TFS) predictor. Patients and Methods A training/validation strategy was chosen to find the optimal CD49d cut-off. The hazard ratio (HR) for death and treatment imposed by CD49d was estimated by pooled analysis of 2,972 CLL, and Cox analysis stratified by center and stage was used to adjust for confounding variables. The importance of CD49d over other flow cytometry-based prognosticators (CD38, ZAP-70) was ranked by recursive partitioning. Results Patients with ≥30% of neoplastic cells expressing CD49d were considered CD49d+. The decrease in OS at 5 and 10-years among CD49d+ cases was 7% and 23% (decrease in TFS 26% and 25% respectively). The pooled HR of CD49d for OS was 2.5 (2.3 for TFS) in univariate analysis. This HR remained significant and of similar magnitude (HR=2.0) in a Cox model adjusted for clinical and biological prognosticators. Hierarchical trees including all cases, or restricted to early stage or patients ≤65 years, always selected CD49d as the most important flow-cytometry-based biomarker, with negligible additional prognostic information added by CD38 or ZAP-70. Consistently, by bivariate analysis, CD49d reliably identified patients' subsets with poorer outcome independent of CD38 and ZAP-70. Conclusions In this analysis of ∼3000 patients, CD49d emerged as the strongest flow cytometry-based predictor of OS and TFS in CLL. Disclosures: Shanafelt: Genentech: Research Funding; Glaxo-Smith-Kline: Research Funding; Cephalon: Research Funding; Hospira: Research Funding; Celgene: Research Funding; Polyphenon E International: Research Funding. Burger:Pharmacyclics: Research Funding.

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Bone Marrow Hematopoietic Dysfunction in Untreated Chronic Lymphocytic Leukemia Is Partially Mediated By Exposure to Constituents of the Leukemic Microenvironment

Blood ◽

10.1182/blood-2018-99-118916 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 3132-3132

Author(s):

Bryce Manso ◽

Kimberly Gwin ◽

Charla R Secreto ◽

Henan Zhang ◽

Wei Ding ◽

...

Keyword(s):

Bone Marrow ◽

B Cells ◽

Chronic Lymphocytic Leukemia ◽

Board Of Directors ◽

Research Funding ◽

Lymphocytic Leukemia ◽

Healthy Controls ◽

Advisory Committees ◽

The Impact

Abstract Peripheral immune dysfunction in B-Chronic Lymphocytic Leukemia (CLL) is well-studied and likely relates to the incidence of serious recurrent infections and second malignancies that plague CLL patients. However, the current paradigms of known immune abnormalities are not able to consistently explain these complications and it is not easy to correct CLL patient immune status. Here, we expand on our preliminary reports that demonstrate bone marrow (BM) hematopoietic dysfunction in early and late stage untreated CLL patients. We found reduced short-term functional capacity of hematopoietic progenitors in BM using colony forming unit assays (Figure 1A-C) and flow cytometry revealed significant reductions in frequencies of hematopoietic stem and progenitor cell (HSPC) populations (exemplified by Lin-CD34+ HSPCs, Figure 1D). We further report that protein levels of the transcriptional regulators HIF-1α, GATA-1, PU.1, and GATA-2 are overexpressed in distinct HSPC subsets from CLL patient BM, providing molecular insight into the basis of HSPC dysfunction. Interestingly, sustained myelopoiesis, evaluated by limiting dilution analysis in long-term culture-initiating cell (LTC-IC) assays maintained for five weeks, revealed no difference between healthy controls and CLL patients. These new data indicate that when HSPCs are removed from the leukemic microenvironment for ample in vitro culture time, they recover the ability to sustain myelopoiesis. To further assess the impact of the CLL microenvironment on HSPC biology, isolated HSPCs (CD34+ BM cells) from healthy controls were exposed in vitro to known leukemic microenvironment constituents. Exposure to TNFα, a cytokine constitutively produced by CLL B cells, resulted in rapid increases in PU.1 and GATA-2 proteins (Figure 2A-D). Similarly, addition of TNFα to the LTC-IC assay resulted in a striking ablation of myelopoiesis, even at the highest input cell concentration. Further, overexpression of PU.1 and GATA-2 were observed in HSPCs following co-culture with CLL B cells, a result that was not recapitulated when cells were exposed to IL-10, another cytokine constitutively produced by CLL B cells. These findings indicate specific components of the leukemic microenvironment are involved in HSPC modulation. Together, these findings expand on our previous observations of BM hematopoietic dysfunction in untreated CLL patients and offer new molecular insights into the contribution of the leukemic microenvironment on immunodeficiency in CLL. Disclosures Ding: Merck: Research Funding. Parikh:Pharmacyclics: Honoraria, Research Funding; MorphoSys: Research Funding; Janssen: Research Funding; Abbvie: Honoraria, Research Funding; Gilead: Honoraria; AstraZeneca: Honoraria, Research Funding. Kay:Morpho-sys: Membership on an entity's Board of Directors or advisory committees; Agios Pharm: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Acerta: Research Funding; Infinity Pharm: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees; Tolero Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees, Research Funding; Cytomx Therapeutics: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; Pharmacyclics: Membership on an entity's Board of Directors or advisory committees, Research Funding.

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Genomic Mechanisms of 17p / TP53 Loss in Primary “ultra High-risk” and Refractory Chronic Lymphocytic Leukemia: Results from the CLL2O Trial

Blood ◽

10.1182/blood.v124.21.2184.2184 ◽

2014 ◽

Vol 124 (21) ◽

pp. 2184-2184

Author(s):

Veronica Teleanu ◽

Jennifer Edelmann ◽

Claudia Haferlach ◽

Stefan Ibach ◽

Eugen Tausch ◽

...

Keyword(s):

High Risk ◽

Chronic Lymphocytic Leukemia ◽

Research Funding ◽

Tp53 Mutation ◽

Lymphocytic Leukemia ◽

Chromosome 17 ◽

Tp53 Mutations ◽

Ultra High Risk ◽

Treatment Naïve ◽

Donor Chromosome

Abstract Background: Unraveling the cytogenetic background helped to decipher the molecular basis of many hematologic cancers and to develop specific therapies. Recently, using chromosome banding analysis (CBA), jumping translocations were identified as a cause of 17p loss in multiple myeloma, providing new insights into the origin of clonal evolution and copy number alterations (CNA) (Sawyer et al, Blood 2014). In chronic lymphocytic leukemia (CLL) the genomic mechanisms leading to 17p loss are not fully understood. Aims: Characterization of underlying mechanisms of 17p loss using CBA and correlation with other clinicobiological features in “ultra high-risk” CLL. Methods: Samples from 112 patients (pts.) with refractory and/or 17p- CLL enrolled in the multicenter CLL2O trial were screened for CNAs by Affymetrix 6.0 SNP array analysis of CD19 sorted CLL cells and for chromosomal abnormalities by CBA using CpG oligonucleotide and interleukin-2 stimulation. Results: Considering both CBA and SNP data, 728 aberrations resulted in a mean of 6.5/case. 89 (79%) pts. had 17p deletion and 83 (74%) TP53 mutation. Regarding the origin of 17p/TP53 loss, 6 distinct types of rearrangements could be delineated: 1) whole arm translocations (WAT) 2) jumping translocations (JT) 3) dicentric chromosomes (DC) 4) cytogenetically balanced translocations (CBT) 5) other unbalanced translocations and 6) interstitial 17p deletions. WAT were identified in 33/112 (30%) cases and 30/33 (91%) involved chromosome 17 leading to 17p loss. Chromosomes involved ≥ 2 times in an unbalanced WAT were der(17;18)(q10;q10) (8, 24%), der(8;17)(q10;q10) (5, 15%), der(15;17)(q10;q10) (4, 12%), i(17)(q10) (4, 12 %), der(17;22)(q10;q10) (2, 6%). JT were identified in 11 (10 %) cases, 6 showing jumping WAT with 17q as donor chromosome, 1 case with breakpoints located in the pericentromeric regions of chromosome 17p11 (donor chromosome) and the receptor chromosomes 4p14 and 16p11. In 4 cases, initially a WAT involving 17q occurred and subsequently the partner chromosome “jumped off” leaving a 17p deletion behind. DC were detected in 19 pts., 8 with breakpoint in 17p11, 7/8 with TP53 mutation. Of note, all cases had the breakpoint on chromosome 17 in 17p11 indicating a fragile site affecting the pericentromeric region. Interestingly, of a total of 382 translocations observed by CBA, only 32 were CBT and except for those involving the IGH and IGK/L loci (n=6) all were random. 17p involvement in CBT was detected in 4 cases, 3 had TP53 deletion and all were TP53 mutated. Of the unbalanced translocations, der(17)t(8;17) was identified in 5 pts. simultaneously generating 8q gain. Nevertheless, breakpoints on chromosome 17p covered cytobands 17p11-13 and on chromosome 8, 8q11-22, one case having the breakpoint telomeric to the TP53 locus and no TP53 mutation, pointing to other putative candidate genes on 17p. In 36/112 (32%) cases, 17p deletion was induced by random rearrangements. Interstitial 17p deletions were identified in only 9/112 (8 %) cases. According to the inclusion criteria of the trial, 36/112 (32%) pts. had 17p deletion and were treatment-naïve while 76/112 (68%) were relapsed or refractory to fludarabine or bendamustine based therapy, 53/76 (70%) having a 17p deletion. Treatment naïve pts. had a mean of 7.36 aberrations/case and pretreated pts. 6.09/case. Focusing on WAT and JT, 18/33 (54%) pts. with WAT and 7/11 (63%) pts. with JT were pretreated whereas 57/78 (73%) pts. in the other cytogenetic subgroups had prior therapy exposure. Considering other genomic features, WAT and JT occurred almost exclusively within complex karyotypes (≥3 chromosomal aberrations), 31/33 WAT and 10/11 JT, were IGHV unmutated, 30/33 WAT and 11/11 JT and harbored TP53mutations, 29/33 WAT and 10/11 JT. Conclusions: “Ultra high-risk” CLL pts. are characterized by a high genomic complexity as compared to standard risk treatment-naïve CLL pts. (CLL8 trial with 1.8 CNAs/case). Previous genotoxic therapy had no influence on the total number of aberrations or the underlying mechanism, suggesting an intrinsic genomic instability of the tumor cells with TP53 alterations. WAT and JT emerged as nonrandom aberrations involved in 17p loss. Given the strong association of TP53 deletion with TP53 mutations of the remaining allele, one may speculate that TP53 mutations precedes TP53 deletion by disrupting the normal DNA repair mechanisms permitting incorrect recombinations. Disclosures Stilgenbauer: Amgen: Honoraria, Research Funding; Genzyme: Honoraria, Research Funding.

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NOTCH1 Stabilization By PEST Mutations Enhances IgM-Mediated Activity in Chronic Lymphocytic Leukemia

Blood ◽

10.1182/blood-2018-99-118064 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 1832-1832

Author(s):

Francesca Arruga ◽

Valeria Bracciamà ◽

Alison Yeomans ◽

Annalisa D'Avola ◽

Marta Coscia ◽

...

Keyword(s):

Cell Growth ◽

Chronic Lymphocytic Leukemia ◽

Board Of Directors ◽

Research Funding ◽

Target Genes ◽

Mrna Translation ◽

Lymphocytic Leukemia ◽

Advisory Committees ◽

Protein Levels ◽

The Impact

Abstract BACKGROUND. Mutations in NOTCH1 PEST domain (NOTCH1-M) are present in ~10% of Chronic Lymphocytic Leukemia (CLL) patients, result in accumulation of more stable NOTCH1 protein, and associate with poorer prognosis. NOTCH1-M are enriched in unmutated (U) immunoglobulin gene heavy-chain variable region (IGHV) CLL, which show high surface IgM (sIgM) expression and signaling capacity. mRNA translation is a prominent response to B cell receptor (BCR) engagement, increased in U-CLL, and for which therapeutic inhibitors are under active development. In CLL, c-MYC is an essential mediator of BCR-driven translation and direct target of NOTCH1, suggesting the impact of NOTCH1 on anti-IgM-mediated cell growth via MYC. AIMS AND METHODS. Our aim was to investigate the functional role of NOTCH1-M on anti-IgM-mediated signaling, compared to wild-type (WT) NOTCH1. The impact on global mRNA translation was studied using a flow cytometry-based O-propargyl-puromycin (OPP) incorporation assay and polysome fractionation assays. The effects of stabilized vs WT NOTCH1 were measured after 24-hour cultures of CLL cells, when data demonstrate differences in the expression of the two forms. Two cohorts of U-CLLs were compared: i) a subset of samples carrying NOTCH1-M [variant allele frequency (VAF) ≥30%, n=21] and ii) a cohort of samples with WT NOTCH1 (VAF<1%, n=23). In both subsets no additional cytogenetic lesions other than 13q deletion were present. RESULTS. sIgM levels and signaling capacity (measured by anti-IgM mediated iCa2+ mobilization) were higher in NOTCH1-M than in -WT samples, consistent with previous observations (1). Conceivably, anti-IgM-mediated phosphorylation of PLCg2 and ERK1/2 was stronger in M than in WT CLLs. In keeping with these results, expression of downstream targets as MYC and CCL3 was also induced at higher levels in M samples. Interestingly, inhibition of NOTCH1 with g-secretase inhibitor (DAPT) significantly decreased BCR target genes induction in M cells, reducing the differences with WT samples, and further enhanced the effects of ibrutinib when used in combination. In order to investigate the impact of NOTCH1 on IgM-mediated CLL cell growth, anti-IgM-induced global mRNA translation was compared in the two cohorts. Consistent with the higher MYC mRNA and protein levels, anti-IgM led to higher global mRNA translation in NOTCH1-M than in -WT cells. DAPT inhibited it in both CLL subsets, while ibrutinib led to complete inhibition of mRNA translation only in the -WT subset, suggesting a major contribution of NOTCH1 to the process. Consistently, the combination of DAPT+ibrutinib abrogated the difference between M and WT CLL cells. Importantly, MYC (but not translation initiation factors eIF4G, eIF4A or eIF3b) was already induced at 6 hours following anti-IgM stimulation and was maintained at high levels at 24 hours, while up-regulation of eIF4G, eIF4A and eIF3b was evident only at 24 hours, supporting the hypothesis of a direct MYC-dependent regulation of the translation machinery (2). NOTCH1 itself was post-transcriptionally regulated upon BCR ligation, as we observed increased NOTCH1 mRNA in polysome-enriched actively translated fractions and increased protein levels on the surface of anti-IgM stimulated cells, specifically inhibited by ibrutinib. Consequently, NOTCH1 pathway was significantly more activated upon anti-IgM stimulation in M than WT cells, as determined by qPCR of NOTCH1 target genes. Both Ibrutinib and DAPT significantly prevented NOTCH1 activation upon BCR triggering, with the drug combination being the most effective treatment. Moreover, in line with data showing NOTCH1-dependent regulation of a B cell gene signature, expression of BTK, LYN and BLNK was significantly increased in anti-IgM activated NOTCH1-M samples, an effect prevented by DAPT. CONCLUSIONS. These data indicate that NOTCH1 stabilization associates with stronger IgM signaling capacity and suggest an interplay between BCR and NOTCH1 pathway, with the former promoting NOTCH1 expression and activation. The evidence that NOTCH1 pathway inhibition reverts this difference suggests a direct effect of NOTCH1 on IgM signaling. In this scenario, stabilizing NOTCH1 mutations may enhance BCR signaling by boosting translation through MYC induction and by directly regulating expression of BCR cascade elements. NOTES. SD and FF share senior authorshipD'Avola, Blood 2016Ruggero, Cancer Res 2009 Disclosures Coscia: Abbvie, Gilead, Shire: Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen, Karyopharm: Research Funding. Gaidano:Janssen: Consultancy, Honoraria; AbbVie: Consultancy, Honoraria; Morphosys: Honoraria; Amgen: Consultancy, Honoraria; Gilead: Consultancy, Honoraria; Roche: Consultancy, Honoraria. Allan:Genentech: Membership on an entity's Board of Directors or advisory committees; AbbVie: Membership on an entity's Board of Directors or advisory committees; Sunesis: Membership on an entity's Board of Directors or advisory committees; Acerta: Consultancy; Verastem: Membership on an entity's Board of Directors or advisory committees. Furman:Gilead: Consultancy; AbbVie: Consultancy; Verastem: Consultancy; Janssen: Consultancy; Genentech: Consultancy; Incyte: Consultancy, Other: DSMB; Loxo Oncology: Consultancy; TG Therapeutics: Consultancy; Sunesis: Consultancy; Acerta: Consultancy, Research Funding; Pharmacyclics LLC, an AbbVie Company: Consultancy. Packham:Aquinox: Research Funding. Deaglio:iTeos therapeutics: Research Funding; VelosBio inc: Research Funding; Verastem: Research Funding. Forconi:Abbvie: Consultancy; Janssen-Cilag: Consultancy.

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Lenalidomide Inhibits Proliferation Of Chronic Lymphocytic Leukemia Cells Via a Cereblon/p21WAF1/Cip1-Dependent Mechanism

Blood ◽

10.1182/blood.v122.21.4139.4139 ◽

2013 ◽

Vol 122 (21) ◽

pp. 4139-4139

Author(s):

Jessie-Farah Fecteau ◽

Laura G Corral ◽

Diahnn Futalan ◽

Svetlana Gaidarova ◽

Ila Bharati ◽

...

Keyword(s):

Cell Cycle ◽

Cell Proliferation ◽

Chronic Lymphocytic Leukemia ◽

Research Funding ◽

Lymphocytic Leukemia ◽

Dependent Manner ◽

Direct Effects ◽

P53 Expression ◽

The Impact

Abstract Lenalidomide has demonstrated clinical activity in patients with chronic lymphocytic leukemia (CLL). However, its mechanism of action is not fully elucidated. Lenalidomide is not directly cytotoxic to CLL cells in vitro, but can alter the capacity of CLL cells to interact with cells in its microenvironment. This has led to the speculation that its primary activity is indirect, although direct effects on CLL cells have been observed. In this study, we examined the direct effects of lenalidomide on CLL cells. We performed transcriptome analysis on primary CLL cell samples exposed to lenalidomide in vitro for 6 and 24hrs and found a significant upregulation of the cyclin-dependent kinase inhibitor p21WAF1/Cip1 (p21), which was also confirmed at the protein level. Since p21 can inhibit the progression of cells from G1 to S phase of the cell cycle, this suggests that lenalidomide may render CLL cells less responsive to proliferation stimuli from the microenvironment. To test this hypothesis, we induced CLL cells to proliferate in vitro using accessory cells made to express CD154 and media containing human interleukin (IL)-4 and IL-10. We monitored for proliferation of CLL cells cultured with and without lenalidomide using carboxyfluorescein succinimidyl ester (CFSE). In repeated experiments, we observed that lenalidomide consistently and significantly inhibited the proliferation of CLL cells in a dose-dependent manner, at concentrations that are achieved in treated patients. Evaluation of the DNA content of CLL cells using propidium iodide and flow cytometry also revealed that lenalidomide significantly decreased the fraction of CLL cells in S and in G2/M phases of the cell cycle and concomitantly increased the percentage of CLL cells in G0/G1 phases. This block in cell proliferation also was accompanied by the upregulation of p21, and the extent of which correlated with the degree to which leukemia-cell proliferation was inhibited. In additional studies, we used small interfering RNA (siRNA) to silence p21 in CLL cells and measured the effect of silencing on cell proliferation in the presence of lenalidomide. We observed that the ability of lenalidomide to inhibit CLL cell proliferation was significantly reduced in CLL cells silenced for p21 compared to CLL cells transfected with control siRNA, supporting a role for p21 expression in mediating the proliferation block induced by lenalidomide. We did not however observe the induction of p53 expression following lenalidomide exposure, suggesting that lenalidomide may upregulate p21 via a p53-independent mechanism. Cereblon (CRBN) is the only known molecular target of lenalidomide. To functionally interrogate the potential role of CRBN in lenalidomide activity on CLL cells, we used siRNA to silence CRBN in primary CLL cells and monitored the impact of silencing on the ability of lenalidomide to upregulate p21 and to inhibit proliferation. We observed lower levels of p21 expression in CRBN-silenced cells exposed to lenalidomide compared to cells transfected with non-specific siRNA, suggesting that CRBN may play a role in p21 upregulation. Furthermore, we observed that CRBN silencing significantly abrogated the anti-proliferative effect of lenalidomide. These results indicate the involvement of CRBN in the anti-proliferative activity of lenalidomide, which is mediated, at least in part, by p21. This study demonstrates that lenalidomide inhibits the proliferation of CLL cells in a CRBN/p21-dependent manner. This direct effect of lenalidomide on CLL cells may account in part for the highly infrequent observation of disease progression in patients receiving long-term maintenance therapy with this agent (Blood, 2013, PMID:23801633). Disclosures: Fecteau: Celgene: Research Funding. Corral:Celgene: Employment. Gaidarova:Celgene: Employment. Cathers:Celgene: Employment. Lopez-Girona:Celgene: Employment. Messmer:Celgene: Research Funding. Kipps:Celgene: Membership on an entity’s Board of Directors or advisory committees, Research Funding.

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Population Level Outcomes of Chronic Lymphocytic Leukemia in the Era of Targeted Agents- Analysis of Surveillance Epidemiology and End Results (SEER) Database

Blood ◽

10.1182/blood-2019-130211 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 1757-1757

Author(s):

Ravi Kishore Narra ◽

Ehab L. Atallah ◽

Mehdi Hamadani ◽

Guru Subramanian Guru Guru Murthy

Keyword(s):

Chronic Lymphocytic Leukemia ◽

Research Funding ◽

Population Level ◽

Lymphocytic Leukemia ◽

Rank Test ◽

Seer Database ◽

Targeted Agents ◽

Kaplan Meier ◽

Treatment Paradigm ◽

Cox Proportional Hazard Regression

Background: The treatment paradigm of chronic lymphocytic leukemia (CLL) has changed significantly in the last decade with approval of multiple new targeted agents. Small molecule drugs such as ibrutinib, venetoclax, idelalisib and other targeted agents have improved the outcomes of patients with CLL treated in clinical trials. However, it is unclear if the population level outcomes of CLL have improved since the first approval of bruton tyrosine kinase (BTK) inhibitor Ibrutinib in February,2014. Methods: Using SEER database, we identified patients aged ≥ 20 years with pathologically confirmed CLL (ICD-0-3 code 9823/3) diagnosed between 2011-2016 and actively followed. Patients were divided into two groups by the period of diagnosis - 2011-2013, 2014-2016, reflecting the period pre-and post-ibrutinib approval. Overall survival (OS) was compared between the two groups using Kaplan-Meier method and log rank test. Cox proportional hazard regression method was used to determine the influence of period and demographic factors on OS. Statistical analysis was performed with significant two-sided p< 0.05. Results: A total of 30701 patients with a median age of 69 years (range 21-104) were included. Males (60.9%) and White race (80.8%) contributed to the majority as summarized in table 1. Median OS was not reached. OS at 30 months was significantly higher for patients diagnosed from 2014-2016 (83.3%) compared to those diagnosed from 2011-2013 (81.7%) (p=0.004) (figure 1). On multivariate analysis, diagnosis from 2014-2016 (HR 0.90, 95% CI 0.85-0.96, p: 0.002) and females (HR 0.74, 95% CI 0.70-0.78, p< 0.001) had lower mortality risk, whereas, increasing age (HR 1.07, 95% CI 1.07-1.08, p< 0.001), Hispanics (HR 1.18, 95% CI 1.05-1.32, p< 0.004), Non-Hispanic blacks (HR 1.41, 95% CI 1.28-1.54, p< 0.001) had higher risk of mortality. Conclusions: Survival of patients with CLL at the population level is improving since approval of Ibrutinib. Non-biological factors such as age, gender and race/ethnicity continue to influence the survival even in the era of novel agents, highlighting the need for continued research to address these discrepancies. Disclosures Atallah: Jazz: Consultancy; Jazz: Consultancy; Novartis: Consultancy; Pfizer: Consultancy; Helsinn: Consultancy; Helsinn: Consultancy; Takeda: Consultancy, Research Funding. Hamadani:Janssen: Consultancy; Merck: Research Funding; ADC Therapeutics: Consultancy, Research Funding; Pharmacyclics: Consultancy; Takeda: Research Funding; Celgene: Consultancy; Sanofi Genzyme: Research Funding, Speakers Bureau; Medimmune: Consultancy, Research Funding; Otsuka: Research Funding. Guru Murthy:Cardinal Health Inc.: Honoraria.

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TP53 Mutation and Survival in Chronic Lymphocytic Leukemia

Journal of Clinical Oncology ◽

10.1200/jco.2009.27.8762 ◽

2010 ◽

Vol 28 (29) ◽

pp. 4473-4479 ◽

Cited By ~ 343

Author(s):

Thorsten Zenz ◽

Barbara Eichhorst ◽

Raymonde Busch ◽

Tina Denzel ◽

Sonja Häbe ◽

...

Keyword(s):

Chronic Lymphocytic Leukemia ◽

High Performance ◽

Tp53 Mutation ◽

Prospective Trial ◽

Progression Free Survival ◽

Complete Response ◽

Lymphocytic Leukemia ◽

Prognostic Impact ◽

Tp53 Mutations ◽

The Impact

Purpose The precise prognostic impact of TP53 mutation and its incorporation into treatment algorithms in chronic lymphocytic leukemia (CLL) is unclear. We set out to define the impact of TP53 mutations in CLL. Patients and Methods We assessed TP53 mutations by denaturing high-performance liquid chromatography (exons 2 to 11) in a randomized prospective trial (n = 375) with a follow-up of 52.8 months (German CLL Study Group CLL4 trial; fludarabine [F] v F + cyclophosphamide [FC]). Results We found TP53 mutations in 8.5% of patients (28 of 328 patients). None of the patients with TP53 mutation showed a complete response. In patients with TP53 mutation, compared with patients without TP53 mutation, median progression-free survival (PFS; 23.3 v 62.2 months, respectively) and overall survival (OS; 29.2 v 84.6 months, respectively) were significantly decreased (both P < .001). TP53 mutations in the absence of 17p deletions were found in 4.5% of patients. PFS and OS for patients with 17p deletion and patients with TP53 mutation in the absence of 17p deletion were similar. Multivariate analysis identified TP53 mutation as the strongest prognostic marker regarding PFS (hazard ratio [HR] = 3.8; P < .001) and OS (HR = 7.2; P < .001). Other independent predictors of OS were IGHV mutation status (HR = 1.9), 11q deletion (HR = 1.9), 17p deletion (HR = 2.3), and FC treatment arm (HR = 0.6). Conclusion CLL with TP53 mutation carries a poor prognosis regardless of the presence of 17p deletion when treated with F-based chemotherapy. Thus, TP53 mutation analysis should be incorporated into the evaluation of patients with CLL before treatment initiation. Patients with TP53 mutation should be considered for alternative treatment approaches.

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Impact of Individual Comorbidities on Treatment Outcomes in Chronic Lymphocytic Leukemia

Blood ◽

10.1182/blood-2018-99-113917 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 4848-4848

Author(s):

Max J. Gordon ◽

Michael C Churnetski ◽

Hamood Alqahtani ◽

Xavier Issac Rivera ◽

Adam Kittai ◽

...

Keyword(s):

Random Forest ◽

Chronic Lymphocytic Leukemia ◽

Board Of Directors ◽

Research Funding ◽

Cox Model ◽

Lymphocytic Leukemia ◽

Advisory Committees ◽

Risk Of Death ◽

Oncology Research ◽

The Impact

Abstract Introduction: Chronic lymphocytic leukemia (CLL) is a common leukemia which tends to occur late in life. Comorbidities are common, and the iwCLL guidelines recommend their assessment in patients (pts) enrolled on clinical trials. The Cumulative Illness Rating Scale (CIRS) is a rigorous tool designed to evaluate the burden of comorbidities, which has been employed in therapeutic studies. Our group and others demonstrated that CIRS score predicts survival in pts with CLL treated with either chemo-immunotherapy (CIT) or novel kinase inhibitors (KI; ibrutinib) (Manda et al, 2016 & Gordon et al, 2018). However, CIRS has not become part of common clinical practice, in part due to complexities in scoring. It is also unknown whether all of the 14 organ systems included in the score carry equal weight to determine prognosis. Here we report the impact of specific comorbidities from a multicenter retrospective cohort of CLL pts treated with either CIT or KI. Methods: We conducted a retrospective analysis of pts with CLL treated at five US academic medical centers between 2000 and 2017. CIRS score was calculated as in Salvi et al, 2008. Random forest (RF) was used to assess specific comorbidities' impact on overall survival (OS) and event-free survival (EFS, defined as time to new therapy, disease progression or death). We adapted two separate approaches to investigate the RF variable selection process: variable Importance (VIMP), a property related to variable misspecification, and Minimal Depth (MD), a property derived from the construction of trees within the forest. Best variables were those selected consistently as top 3 in both VIMP and MD on the 500 RF repetitions. Because hepatic and renal comorbidities were rare they were excluded. OS and EFS were assessed by Kaplan-Meier estimates and Cox proportional hazard model adjusted for performance status and age. Significance was assessed with log-rank test. Results: 398 pts were included in the final analysis. The median age was 63 years (range, 30-93). 50% of pts (n=198) had a high CIRS score (≥7). 184 pts (46%) had comorbidities assessed in relapsed setting. For all pts, the most common treatments included ibrutinib (n=145; 37%), fludarabine-containing regimens (n=104; 26%) and bendamustine (n=39; 10%). Complex karyotype was observed in 3.5% (n=14) and 10.6% (n=42) of pts had del(17p). Pts with comorbidities (CIRS ≥7) demonstrated shortened survival following therapy, with 5-year OS of 64% vs 89% (p<0.0001) and median EFS of 24 vs 49 months (p<0.0001). Pts treated with CIT had lower CIRS scores compared pts on KIs (6.5 vs 8.7, p<0.001), however there was no difference in CIRS between pts treated with high vs. low intensity CIT (e.g. FCR/BR vs chlorambucil/rituximab [n=59]; CIRS 6.8 vs 6.6, p=0.78), indicating comorbidities are not consistently taken into account when selecting therapy. Random forest variable selections identified vascular comorbidities (e.g. DVT/PE) as the most influential risk factor for OS with CIT treatment, while HEENT and cardiac comorbidities were most impactful to OS for patients treated with KI. For EFS, the most influential comorbidities were cardiac and vascular for the CIT treatment group and endocrine and HEENT for patients treated with KI. Across EFS and OS, the most frequently selected variables in CIT were cardiac, hypertension, vascular and neurologic. We constructed a simplified scoring system assigning 1 point for each category. Comparing scores of 0, 1 and 2-4 (n=100, n=82, n=60), 5-year OS was 87%, 82% and 66%, respectively (p<0.0001). In an adjusted Cox model OS decreased between risk groups (HR=1.78; 95% CI, 1.2-2.6; p=0.004). Cardiac, vascular, HEENT and endocrine were the most frequently selected in pts receiving KI. Comparing scores of 0, 1 and 2-4 (n=50, n=51, n=55), 2-year OS was 98%, 87% and 81%, respectively (p=0.034). There was a trend towards increased risk of death in the adjusted cox model (HR=1.63; 95% CI, 0.80-3.34; p=0.19). Conclusion: Comorbidities impact survival in CLL whether treated with CIT or KI. Which comorbidities are most prognostic may vary by treatment type. Vascular and cardiac comorbidities appear to be the most relevant in CLL pts treated with CIT. Meanwhile, cardiac, endocrine and HEENT had greater impact when pts were treated with KI. A simplified CIRS score is predictive of outcomes in both treatment subgroups. Disclosures Choi: Gilead: Speakers Bureau; AbbVie, Inc: Consultancy, Speakers Bureau; Pharmacyclics: Consultancy, Research Funding, Speakers Bureau; Rigel: Consultancy; Genentech: Speakers Bureau. Cohen:Takeda: Research Funding; Pharmacyclics: Consultancy, Membership on an entity's Board of Directors or advisory committees; Infinity Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees; Millennium: Consultancy, Membership on an entity's Board of Directors or advisory committees; Seattle Genetics: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Janssen: Research Funding; AbbVie: Consultancy, Membership on an entity's Board of Directors or advisory committees; Bristol-Myers Squibb: Research Funding; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; BioInvent: Consultancy. Persky:Genentech: Honoraria; Morphosys (IDMC): Consultancy; Spectrum: Research Funding; Merck: Research Funding. Danilov:Aptose Biosciences: Research Funding; Verastem: Consultancy, Research Funding; Astra Zeneca: Consultancy; Gilead Sciences: Consultancy, Research Funding; Takeda Oncology: Research Funding; Genentech: Consultancy, Research Funding; TG Therapeutics: Consultancy; Bayer Oncology: Consultancy, Research Funding.

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