Non‐Coding NOTCH1 Mutations in Chronic Lymphocytic Leukemia Negatively Impact Prognosis

Abstract Background: We and others have reported on the impact of recurrent somatic mutations not only in the multistep pathogenetic process, but also in the clinical heterogeneity of chronic lymphocytic leukemia (CLL) patients. Immunophenotyping, as part of the diagnostic workout, is used for assessing clonality, as a differential diagnosis tool, and to examine the expression of molecules associated with a worse prognosis. Recently, NOTCH1 mutations have been linked to low CD20 levels in CLL and with a relative resistance to anti-CD20 immunotherapy in vitro. But to date, there is limited information on the correlation between cell surface marker expression and the presence of somatic mutations in CLL. The aim of this study was to evaluate potential associations between an extended phenotypic panel and the mutational status of 13 recurrently mutated genes in CLL detected by deep sequencing. Patients and Methods: To this end, we performed targeted NGS sequencing of blood samples, collected at diagnosis, from 131 CLL patients. Every patient underwent, at baseline, a flow cytometry characterization with a panel including (sIg)λ, (sIg)κ, CD19, CD5, CD11b, CD81, CD10, CD79b, CD29, CD38, FMC7, CD22, CD45, CD103, CD11c, CD25, ZAP70, CD11a, and CD24. We designed a TruSeq Custom Amplicon panel (Illumina, Inc. San Diego, CA, USA) containing 13 genes and covering 28.099 bases. The average amplicon size was 238 base pairs and ~ 99.1% of the regions were covered on both strands. Paired-end sequencing (2x250 bp) was performed with MiSeq v2.2 chemistry, and a mean depth of 998 reads/base within the regions of interest was obtained. Raw data were analyzed with IlluminaonJboard Real Time Analysis (RTA v.2.4.60.8) software and MiSeq Reporter. Results: With a median age of 68 y.o. (range, 33-95) and a slight male predominance, the median follow up time of our cohort was 43 months (24-104). We found that 47/131 (35%) patients harbored at least one mutation, with NOTCH1 (n = 13, 10%), ATM (n = 10, %), TP53 (n = 8, %), and SF3B1 (n = 8, 5.5%), as the most frequently mutated genes. Those patients with a NOTCH1 mutation showed a lower CD25 expression (25 mean fluorescence intensity units (MFIu)) than those without a mutation (45 MFIu), p=0.001. In addition, a higher expression of CD5 (265 vs. 219 MFIu, p= 0.02), of the monoclonal light chain (90.5 vs. 58.6 MFIu, p=0.03), and a higher percentage of CD38+ cells in the CD19+CD5+ compartment (37% vs. 19%, p=0.006) were significantly associated with the presence of, at least, one somatic mutation. We could not validate the recently reported association between the presence of NOTCH1 mutations and a low expression of CD20. In our cohort, the MFI expression in NOTCH1 mutated and non-mutated patients was 176 and 135 units, respectively (p=0.2) In the multivariate Cox analysis, the presence of a somatic variant in TP53 and a higher percentage of positive CD38 cells in the tumour population showed both a worse overall survival and shorter time to first treatment. The independence of these two variables was also supported by not finding a significative difference percentage of CD38 positive cells between TP53 mutated and non mutated cases (p=0.5). Conclusions: The associations described herein suggest potential pathogenic pathways in CLL, in particular the CD25-NOTCH1 axis, with a significative inferior expression of CD25 when activating NOTCH1 mutations are present. The relationship found between these two variables, with an inversed direction to that found in physiological conditions, has also been shown in the setting of NOTCH1-mutated acute lymphoblastic leukemia, emerging as a potential targetable pathway in this subset of CLL patients. Disclosures Maciejewski: Apellis Pharmaceuticals Inc: Membership on an entity's Board of Directors or advisory committees; Alexion Pharmaceuticals Inc: Consultancy, Honoraria, Speakers Bureau; Celgene: Consultancy, Honoraria, Speakers Bureau.

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Inhibition of the Notch1 Pathway in Chronic Lymphocytic Leukemia Promotes Apoptosis and Inhibits Proliferation

Blood ◽

10.1182/blood.v124.21.1972.1972 ◽

2014 ◽

Vol 124 (21) ◽

pp. 1972-1972 ◽

Cited By ~ 2

Author(s):

Josephine L. Klitgaard ◽

Reuma Magori-Cohen ◽

Reina Improgo ◽

Stacey M. Fernandes ◽

Bethany Tesar ◽

...

Keyword(s):

Chronic Lymphocytic Leukemia ◽

Expression Profiles ◽

Annexin V ◽

Receptor Activation ◽

Lymphocytic Leukemia ◽

Gamma Secretase ◽

Induced Apoptosis ◽

Notch1 Mutations ◽

Notch1 Receptor

Abstract In chronic lymphocytic leukemia (CLL), mutations in the NOTCH1 receptor occur in 4-10% of newly diagnosed patients and 15–20% of multiply relapsed patients. Using next-generation sequencing, our group previously reported NOTCH1 p.P2514fs mutations in 15 CLL patients (9.4%) in an initial cohort of 160 CLL patients in which NOTCH1 mutations were associated with IGHV unmutated (UM) CLL (p=0.0001). Further analysis using a three-group comparison (NOTCH1 mut, IGHV UM vs. NOTCH1 wild-type [wt] IGHV UM vs. NOTCH1 wt IGHV mut) showed that NOTCH1 mutations associated with both trisomy 12 (p=0.049) and 17p deletion (p=0.0008) and poor overall survival (HR 2.99, p=0.008). Given that targeting activating mutations has proven an effective therapeutic strategy in many cancers, we explored the therapeutic potential of a Notch1 inhibitor, PF-03084014, in CLL. Previous studies in T-cell acute lymphoblastic leukemia cells harboring NOTCH1 mutations have shown that gamma secretase inhibitors can induce apoptosis by blocking Notch1 receptor activation. When we tested the gamma secretase inhibitor (GSI) PF-03084014 in 18 CLL samples with NOTCH1 mutations, it consistently induced apoptosis of all CLLs after 48 hours in culture across all cytogenetic groups tested (13.3-47.2% death with 5 μM GSI, p<0.0001)(Figure A). The induction of apoptosis was similar (GSI vs. ibrutinib, p=ns) to that of ibrutinib (n=11,11.9-74.4% death with 5 μM ibrutinib, p<0.0001). In contrast, GSI treatment only induced apoptosis in some (n=10), but not all NOTCH1 wt CLLs (n=6) (p=0.0137). We next tested the effect of GSI PF-03084014 in the context of a stromal environment. Co culture of CLL cells with CD40L-expressing fibroblasts partially mimics the lymph node and bone marrow microenvironments, which are known sites of drug-resistance and proliferation of CLL in vivo. We tested whether the interaction with stromal cells protects CLL cells from Notch1 inhibitor-induced apoptosis, as seen with other drugs including ibrutinib. We found that co culture with CD40L-expressing 3T3s decreased GSI-induced apoptosis in NOTCH1 mutant CLLs (p=0.0006) and in the majority of the NOTCH1 wt CLLs that responded to the GSI (Figure A). Since NOTCH1 mutations have been reported to be an independent marker of aggressive disease in CLL, we tested whether CLL cells with NOTCH1 mutations were more proliferative in vitro compared to NOTCH1 wt CLL cells. We showed that CLL cells upregulate Ki67 expression in co culture with 3T3-CD40L cells and in a cohort of 10 NOTCH1 mutants and 11 NOTCH1 wt, we found the NOTCH1 mutants to be more proliferative than the NOTCH1 wt (median of 7.6% vs. 2.3%, p=0.015). To then address whether blocking of the Notch1 pathway decreases proliferation, we treated CLL cells in co culture with 3T3-CD40L cells with 5 μM GSI for 7 days. GSI treatment decreased the percentage of Ki67+ CLL cells in all but one NOTCH1 mutant (median decrease 28.3%, p=0.044) as wells as in the majority of NOTCH1 wt samples (median decrease 38.7%, p=0.037). Having established that inhibition of Notch1 can reduce proliferation and induce apoptosis in CLL cells in vitro, we were interested in determining the downstream genes that may be the effectors of this activity. We therefore compared the gene expression profiles (GEP) of NOTCH1 mut vs. NOTCH1 wt CLLs, and found upregulation of genes involved in the Notch1 pathway, in apoptosis and in chemokine signaling in the NOTCH1 mutants. Furthermore, comparing GEP of high Ki67 vs. low Ki67 expressing CLL cells revealed higher expression of a range of both upstream and downstream Notch1 pathway genes in high Ki67 expressing CLL cells. In conclusion, we show that PF-03084014 induces apoptosis and decreases proliferation in both NOTCH1 mutant and wt CLL cells. We find NOTCH1 mutant CLL cells to be more proliferative than NOTCH1 wt and show upregulation of Notch1 pathway genes in NOTCH1 mutants compared to wt CLL cells and in high Ki67 expressing compared to low Ki67 expressing CLL cells. Taken together, these results emphasize the important role of Notch1 signaling in CLL in general, perhaps particularly in proliferative compartments like lymph nodes, and demonstrate that Notch1 pathway inhibitors are worthy of therapeutic investigation in CLL. Figure A. GSI-induced apoptosis in NOTCH1 mut vs. wt CLL cells at 48 h. CLL cells naked or in co culture with 3T3-CD40L cells +/- 5 µM PF-03084014. Survival was assessed by CD19 and Annexin V/PI staining. Figure A. GSI-induced apoptosis in NOTCH1 mut vs. wt CLL cells at 48 h. CLL cells naked or in co culture with 3T3-CD40L cells +/- 5 µM PF-03084014. Survival was assessed by CD19 and Annexin V/PI staining. Disclosures No relevant conflicts of interest to declare.

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Prognostic Impact of NOTCH1 Mutations in Chronic Lymphocytic Leukemia (CLL): A Study On 538 Patients.

Blood ◽

10.1182/blood.v120.21.2873.2873 ◽

2012 ◽

Vol 120 (21) ◽

pp. 2873-2873

Author(s):

Sandra Weissmann ◽

Andreas Roller ◽

Vera Grossmann ◽

Claudia Haferlach ◽

Wolfgang Kern ◽

...

Keyword(s):

Chronic Lymphocytic Leukemia ◽

Deep Sequencing ◽

Cox Regression ◽

Clonal Evolution ◽

Lymphocytic Leukemia ◽

Published Data ◽

Prognostic Impact ◽

Mutational Burden ◽

Equity Ownership ◽

Notch1 Mutations

Abstract Abstract 2873 Background: Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults. Recurrent activating mutations of NOTCH1 have been reported, including the relevance of NOTCH1 mutations as independent negative prognostic marker (Rossi et al., Blood 2012). Aims: 1. Determine the frequency and prognostic impact of NOTCH1 mutations (NOTCH1 mut) in a large unselected cohort of adult CLL patients. 2. Evaluate the range of mutational burden by amplicon deep-sequencing. Patients and Methods: We investigated 538 patients (189 female, 349 male; median age: 66.1 years, range: 37.8 – 90.5 years) with untreated CLL by FISH and for NOTCH1 mut (Transcript ID ENST00000277541) using next-generation amplicon deep-sequencing (454 Life Sciences, Branford, CT). Additionally, TP53 (n=45 mut/523 screened, 8.6%) and IGHV mutation status were analyzed. IGHV status was unmutated in 39.2% (209/533) and mutated in 60.8% (324/533) cases. Since NOTCH1 mut in CLL are known to be located predominantly within the C-terminal PEST domain (Rossi et al., Blood 2012) we sequenced exons 33–34 (covering codons 2029 to 2556), represented by 7 distinct PCR reactions with a median amplicon length of 345 bp. In median, 608 bidirectional reads (range 140–2,117) were generated per amplicon, thereby allowing a sensitive detection of variants, i.e. at a cut-off value of 5% ∼30 independent reads were sequenced. Results: All patients were investigated by FISH: del(17p) (30/538, 5.6%), del(11q) (57/538, 10.6%), +12 (103/538, 19.1%), del(6q) (8/538, 1.5%), normal karyotype according to FISH (NK) (111/538, 20.6%) and del(13q) as sole abnormality (229/538, 42.6%). In total, 81 NOTCH1 mut were observed in 71/538 (13.2%) patients. The vast majority of mutations (98.8%) were found to be heterozygous, only 1/81 mutation (1.2%) was homozygous. We identified 23 point mutations (6 missense and 17 nonsense; 28.4%) and 58 frame-shift alterations (57 deletions and 1 indel; 71.6%). The most frequently occurring mutation was as previously described p.Pro2514ArgfsX4 (c.7541_7542delCT), which was identified in 51/81 (62.7%) variants. The median mutational burden as assessed by deep-sequencing read counts was 28% of sequence reads carrying the mutation (range: 2% - 69%). Of note, in 54/81 (66.7%) variations the detected mutation load was ≤20% and therefore would be below the detection level of Sanger sequencing. In detail, a mutational burden ≤20% was observed in 32/81 (39.5%) variations and ≤10% in 22/81 (27.2%) mutations. 10/71 (14.1%) NOTCH1 mut patients carried 2 mutations. In 9/10 patients a different mutational load between the 2 NOTCH1 mut was detected, indicating the presence of 2 independent clones or clonal evolution with acquisition of a second mutation in the initially NOTCH1 single mutated clone. Mutations mainly clustered in the C-terminal part, i.e. codons 2,385 to 2,555 of exon 34 where 72/81 (88.8%) alterations were located. Confirming published data, statistical analyses revealed NOTCH1 mut being associated with unmutated (unmut) IGHV status (unmut vs mut: 59/209, 28.2% vs 11/324, 3.4%; P<0.001), TP53 mut (mut vs unmut: 10/45, 22.2% vs 58/478, 12.1%, P=0.064) and +12 as sole cytogenetic aberration (+12 sole vs remainder: 23/64, 35.9% vs 48/472, 10.2%; P<0.001). We did not detect any difference in NOTCH1 mut frequency between cases harboring +12 sole and +12 with other aberrations (+12 sole vs +12: 23/64, 35.9% vs 13/45, 28.9%; P=0.54). In contrast, NOTCH1 mut were rare events in patients with del(13q) (del(13q) vs remainder: 24/296, 8.1% vs 47/240, 19.6%; P<0.001). No associations with other cytogenetic subgroups were detected. Univariable cox regression analyses revealed an adverse prognostic impact for NOTCH1 mut (P=0.056) and IGHV unmut (P<0.001). With respect to patients of the favorable prognostic risk group (IGHV mut, TP53 unmut, n=146), NOTCH1 mut patients (n=9) showed a significantly shorter time to treatment (TTT) than NOTCH1 wild-type cases (n=137) (median TTT n.r. vs. 9.4 years, P=0.042). Conclusion: 1. We present the first deep-sequencing study of NOTCH1 mutations in a large unselected CLL cohort and report an overall frequency of 13.2%. 2. The mutational burden of 66.7% of NOTCH1 mutations in CLL patients was ≤20%. 3. NOTCH1 mutations are an adverse prognostic parameter associated with shorter TTT and represent yet another novel important biomarker in CLL. Disclosures: Weissmann: MLL Munich Leukemia Laboratory: Employment. Roller:MLL Munich Leukemia Laboratory: Employment. Grossmann:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Equity Ownership. Kern:MLL Munich Leukemia Laboratory: Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Equity Ownership. Kohlmann:MLL Munich Leukemia Laboratory: Employment.

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High-Throughput Sequencing For The Identification Of NOTCH1 mutations In Early Stage Chronic Lymphocytic Leukemia: Biological and Clinical Implications

Blood ◽

10.1182/blood.v122.21.1622.1622 ◽

2013 ◽

Vol 122 (21) ◽

pp. 1622-1622

Author(s):

Marta Lionetti ◽

Sonia Fabris ◽

Giovanna Cutrona ◽

Luca Agnelli ◽

Carmela Ciardullo ◽

...

Keyword(s):

Chronic Lymphocytic Leukemia ◽

Allele Frequency ◽

Deep Sequencing ◽

Mutant Allele ◽

Sanger Sequencing ◽

Early Stage ◽

Lymphocytic Leukemia ◽

Mutant Allele Frequency ◽

Mutational Activation ◽

Notch1 Mutations

Abstract NOTCH1 mutations have recently emerged as new genetic lesions significantly correlated with survival in chronic lymphocytic leukemia (CLL). NOTCH1 c.7541_7542delCT is by far the most frequently observed NOTCH1 mutation in the disease. To estimate the prevalence and clonal evolution of NOTCH1 c.7541_7542delCT mutation, and prospectively investigate its clinical significance in early stage CLL and clinical monoclonal B cell lymphocytosis (cMBL), we analyzed by next generation sequencing (NGS) 384 cases at diagnosis enrolled in the GISL O-CLL1 multicenter trial. The patient cohort included 100 cMBL and 284 Binet stage A CLL cases, 48 of whom were also longitudinally investigated at progression or during follow-up (32 and 16, respectively) in absence of treatment. Deep sequencing of the NOTCH1 mutation hotspot was performed by Roche 454 pyrosequencing on the Genome Sequencer Junior instrument. NOTCH1 mutation was validated by an extremely sensitive PCR-based approach and Sanger sequencing. The association between NOTCH1c.7541_7542delCT and clinical, molecular and biological variables, as well as its impact on progression free survival (PFS), were tested. Deep sequencing analysis of NOTCH1 mutation hotspot in our cohort (median depth of coverage 1510x, ranging from 605 to 2842) revealed a mutant allele frequency ranging from 0.02% to 75% of total reads in 145 cases. The occurrence of the mutation was subsequently assessed by an extremely sensitive ARMS (ampliﬁcation refractory mutation system)-PCR, which allowed to confirm the presence of delCT in the 49 cases with frequency of mutated sequencing reads greater than 0.7%, specifically in 11% of cMBL (11/100) and 13.4% of CLL patients (38/284). Furthermore, mutated samples were subjected to DNA Sanger sequencing: in line with the expected sensitivity of the method, the mutation was identified only in samples with higher mutation loads according to NGS (mutant allele frequency ≥ 7%, n=25). Our data revealed that often NOTCH1 mutational activation affected a neoplastic sub-clone, especially in cMBL patients. NOTCH1 mutated patients utilized unmutated IGHV genes more frequently, and had higher expression of CD38 and ZAP-70 (P=3.2e-11, P=2.6e-08, P=3.4e-05, respectively). Trisomy 12 was more frequent in this patient group (P=5.4e-04), whereas 13q14 deletion was less represented than in the NOTCH1 wild-type patients (P=2.8e-03). NOTCH1 mutation was associated with the occurrence of stereotyped HCDR3 (P=5.6e-03); in addition, compared with other major BCR subsets, CLL subset #10 was significantly enriched in NOTCH1 mutations (P=0.032). The prevalence of the analyzed dinucleotide deletion was not significantly different between cMBL and CLL patients, even if only Rai 0 cases (28/197 cases, 14.2% mutation frequency) were considered. The percentages of variant sequencing reads in NOTCH1-mutated cases were slightly higher in CLL (median 19.6%) than in cMBL (median 4.2%), a finding confirmed by a regression analysis that highlighted the association of the CLL presentation with higher percentages of NOTCH1 delCT reads (P=0.033). NOTCH1-mutated cases, both at sub-clonal and clonal levels, displayed a significant reduction in median PFS (P=0.0018), although NOTCH1 mutation prognostic value, in multivariate analysis, was not independent if 11q and/or 17p deletion, IGHV mutational status, and cMBL or CLL status were considered. Finally, sequential analyses in a representative fraction of cases of our dataset indicated that (i) NOTCH1 mutation did not occur during the course of the disease and that (ii) the mutational load in positive cases was stable over time. These findings highlight the importance of using high sensitive methods for an accurate detection of NOTCH1 mutation in cMBL/early stage CLL. This is required for a better prognostic stratification and also to obtain useful information for potential therapeutic approaches, since sub-clonal mutations in untreated CLL can possibly anticipate the dominant genetic composition of the relapsing tumor. Disclosures: No relevant conflicts of interest to declare.

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Functional Effects Of NOTCH1 Mutations In Chronic Lymphocytic Leukemia Patients

Blood ◽

10.1182/blood.v122.21.4117.4117 ◽

2013 ◽

Vol 122 (21) ◽

pp. 4117-4117

Author(s):

Francesca Arruga ◽

Branimir Gizdic ◽

Sara Serra ◽

Tiziana Vaisitti ◽

Davide Rossi ◽

...

Keyword(s):

Bone Marrow ◽

Chronic Lymphocytic Leukemia ◽

Signaling Pathway ◽

Lymphocytic Leukemia ◽

Mrna Levels ◽

Nuclear Staining ◽

Notch1 Signaling ◽

Notch1 Mutations

Abstract Chronic lymphocytic leukemia (CLL), is characterized by the expansion of mature B lymphocytes present in blood, bone marrow and lymphoid organs. Clinical behavior is highly heterogeneous, thus requiring timely identification of high-risk patients. NOTCH1 encodes a trans-membrane receptor acting as a ligand-activated transcription factor. NOTCH signaling initiates when the ligand, from either the Jagged or Delta families, binds to the receptor and induces successive proteolytic cleavages, resulting in the release and nuclear translocation of the NOTCH intra-cellular domain (NICD). Signaling is terminated by phosphorylation of the PEST domain of NOTCH1, triggering its ubiquitination and proteasomal degradation. Whole exome sequencing approaches have revealed NOTCH1 mutations in 5-10% newly diagnosed CLL cases, with their prevalence increasing to 15-20% in progressive or relapsed patients. The most frequent mutation is 7544-7545delCT frameshift deletion in exon 34, resulting in disruption of the C-terminal PEST domain. Truncation of the PEST domain is predicted to result in NOTCH1 impaired degradation, stabilization of the active NOTCH1, and deregulated signaling. The present study was undertaken with the aim to compare NOTCH1 expression and functional role in CLL patients harboring wild type (WT) or mutated (M) NOTCH1 gene. NOCTH1 mRNA and surface protein were expressed at comparable high levels in peripheral blood (PB) CLL cells obtained from NOTCH1 M and WT patients, consistent with a more general requirement of NOTCH1 signaling in this leukemia. However, at a variance of NOTCH1 WT cases, NOCTH1 M patients displayed remarkable accumulation of both the intermediate molecular species of the activated NOCTH1 receptor, as well as of the active NICD. Consistently, by gene expression profiling NOCTH1 M patients displayed significantly higher levels of HES1 and DTX1, the main NOTCH1 target genes. Overall, these data suggest a more active signaling pathway in NOTCH1 M CLL than in NOTCH1 WT cases. Expression of NOTCH1 and of its target gene (DTX1) varied across disease compartments, being higher in CLL cells obtained from the lymph nodes (LN), as compared to paired samples derived from the PB or the bone marrow (BM). By immunohistochemical analyses of primary LN tissue samples, NOTCH1 M CLL showed an intense nuclear staining as opposed to the more cytoplasmic distribution observed in NOTCH1 WT samples. These data suggest a more active NOTCH1 signaling in CLL residing in the LN microenvironment and confirm the functional effect of NOTCH1 mutations in vivo. When PB CLL cells were cultured in vitro in the absence of any supporting layer or stimulation, they showed a rapid down regulation of the NOTCH pathway, with complete loss of NICD after 24 hours paralleled by a sharp decrease in HES1 and DTX1 transcription. Consistently, levels of presenilin-1 (PSEN1), the catalytic subunit of the g-secretase complex, were also down-regulated offering a partial mechanistic explanation for the NICD loss. NOTCH1 mRNA levels remained unchanged, with accumulation of the receptor at the plasma membrane. These effects were independent of NOTCH1 mutation status and suggested the dependence of NOTCH1 signaling activation upon in vivo microenvironmental interaction, even in NOTCH1 M CLL. Within primary LN biopsies from CLL patients, the NOTCH1 ligand, was highly expressed on CD68+ elements of myeloid origin. This observation prompted the in vitro recreation of a lymphoid niche by co-culturing Jagged1+ nurse-like cells (NLC) with autologous CLL cells. Under these conditions, NOTCH1 activity in CLL cells was sustained over time, as shown by Q-PCR analyses of DTX1 and PSEN1. Moreover, NLCs protect NOTCH1 M CLL cells from fludarabine-induced apoptosis. This microenvironment-induced chemoresistance was prevented by pre-treatment of NOTCH1 M CLL cells with specific g-secretase inhibitors, to block NOTCH1 activation. Taken together, these results show that the 7544-7545delCT mutation in the PEST domain of NOTCH1 has a stabilizing effect on NOTCH1 signaling pathway. They also show that micro-environmental interactions are critical in activating NOTCH1 pathway both in the M and WT patients. Lastly, these results show that NOTCH1 signals micht create local conditions that favour drug resistance, thus making NOTCH1 a potential molecular target in CLL. Disclosures: No relevant conflicts of interest to declare.

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Subset-Specific Spectra of Recurrent Gene Mutations in Chronic Lymphocytic Leukemia with Stereotyped B-Cell Receptors

Blood ◽

10.1182/blood.v124.21.3320.3320 ◽

2014 ◽

Vol 124 (21) ◽

pp. 3320-3320

Author(s):

Lesley-Ann Sutton ◽

Emma Young ◽

Panagiotis Baliakas ◽

Anastasia Hadzidimitriou ◽

Karla Plevova ◽

...

Keyword(s):

Chronic Lymphocytic Leukemia ◽

B Cell ◽

High Frequency ◽

Gene Mutations ◽

Lymphocytic Leukemia ◽

B Cell Receptors ◽

Cell Receptors ◽

Recurrent Mutations ◽

Trisomy 12 ◽

Notch1 Mutations

Abstract Preliminary observations from essentially small patient series indicate that certain recurrent gene mutations may be enriched in subsets of chronic lymphocytic leukemia (CLL) with stereotyped B-cell receptors (BcR). On these grounds, it could be argued that differential modes of immune signaling, in the context of subset-biased antigen-immunoglobulin (IG) interactions, may be associated with the acquisition and/or selection of certain genomic aberrations within various stereotyped CLL subsets. With this in mind, we here sought to explore the genetic background of 10 major stereotyped subsets which collectively account for ~11% of all CLL and represent both IGHV unmutated (U-CLL) and/or mutated (M-CLL) cases. We focused on recurrent mutations within the NOTCH1 (entire exon 34 or targeted analysis for del7544-45), TP53 (exons 4-9), SF3B1 (exons 14-16), BIRC3 (exons 6-9) and MYD88 (exon 5) genes. Overall, 647 cases were analyzed, belonging to the following major subsets: (i) U-CLL: #1 (the largest within U-CLL, clinically aggressive), n=139; #3, n=39; #5, n=22; #6, n=48; #7, n=74; #8, n=46; #59, n=19 and #99, n=18; (ii) M-CLL: #4 (the largest within M-CLL, particularly indolent), n=78; and, (iii) subset #2 (the largest overall, variable mutational status and clinically aggressive), n=164. All cases were devoid of MYD88 mutations, which was not surprising given that our cohort was predominantly composed of U-CLL. Mutations within the BIRC3 gene were either absent (#2, #4, #6 and #59) or rare (#1, #3, #5, #7, #8 and #99; frequency 1.5%-7%) with no clear bias to any subset. BIRC3-mutant cases frequently co-existed with either del(11q) or trisomy 12. NOTCH1 mutations were more frequent in subsets #1, #6, #8, #59 and #99 (frequency, 22%-32%), sharply contrasting subsets #2 or #3 (4% and 7%, respectively) (p<0.0001). Of note, although NOTCH1 mutations tended to coincide with trisomy 12 in certain subsets e.g. #1 and #8, their co-occurrence differed significantly with only 33% of NOTCH1mut subset #1 cases carrying trisomy 12 compared to 75% of NOTCH1mut subset #8 cases (p=0.036). Moving to SF3B1, we noted that subsets harboring NOTCH1 mutations were either absent for or carried few SF3B1 mutations, while the inverse was also true i.e. very high frequency of SF3B1 mutations in subsets #2 and #3, 45% and 36%, respectively. Almost 80% of mutations observed in subset #2 were localized to two codons (p.K700E: n=44/76, 58%: p.G742D: n=15/76, 20%) within the HEAT domain of the SF3B1 protein; p.K700E accounted for only 29% (4/14) of all SF3B1 mutations detected in subset #3 while p.G742D was absent (p=0.043 and p=0.068 respectively). Thus, although the functional relevance of these mutations is currently unknown, their high frequency and striking bias to subset #2 bodes strongly for their critical role in the pathobiology of subset #2. Finally, TP53 mutations were: (i) enriched in subsets #3 (11%) and #7 (19%) and, in contrast, absent or rare in subsets #5 (0%) and #6 (4%), despite all utilizing the IGHV1-69 gene (p=0.02); (ii) enriched in subset #1 (15%) and subset #99 (33%), a less populated subset that is highly similar to subset #1; and, (iii) very rare in subsets #2 and #8 (2% in both), the latter known to display the highest risk for Richter's transformation among all CLL. In conclusion, we confirm and significantly extend recent observations indicating that different CLL stereotyped subsets display distinct genetic makeup. These findings imply that distinctive modes of microenvironmental interactions, mediated by certain stereotyped BcRs, may be associated with selection or occurrence of particular genetic aberrations, with the combined effect determining both clonal and clinical evolution, and ultimately disease outcome. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

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NOTCH1 mutations in chronic lymphocytic leukemia with trisomy 12

Genes Chromosomes and Cancer ◽

10.1002/gcc.21987 ◽

2012 ◽

Vol 51 (11) ◽

pp. 1063-1063 ◽

Cited By ~ 2

Author(s):

Ester M Orlandi ◽

Marianna Rossi

Keyword(s):

Chronic Lymphocytic Leukemia ◽

Lymphocytic Leukemia ◽

Trisomy 12 ◽

Notch1 Mutations

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TP53, SF3B1, and NOTCH1 mutations and outcome of allotransplantation for chronic lymphocytic leukemia: six-year follow-up of the GCLLSG CLL3X trial

Blood ◽

10.1182/blood-2012-11-469627 ◽

2013 ◽

Vol 121 (16) ◽

pp. 3284-3288 ◽

Cited By ~ 72

Author(s):

Peter Dreger ◽

Andrea Schnaiter ◽

Thorsten Zenz ◽

Sebastian Böttcher ◽

Marianna Rossi ◽

...

Keyword(s):

Chronic Lymphocytic Leukemia ◽

Disease Control ◽

Residual Disease ◽

Lymphocytic Leukemia ◽

Key Points ◽

Tumor Clone ◽

Minimal Residual ◽

Notch1 Mutations

Key Points This trial update shows that allotransplantation can provide long-term minimal residual disease–negative disease control in poor-risk chronic lymphocytic leukemia. Six-year survival is close to 60% and is independent of the presence of TP53, SF3B1, and NOTCH1 mutations in the tumor clone.

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