The Complete Mutatome and Clonal Architecture of Del(5q)

Abstract Cytogenetic abnormalities are found in around half of MDS patients (pts) and have both clinical impact and may be subtype-defining, e.g. in 5q-syndrome. Interstitial deletion of the long arm of chr.5 [del(5q)] is the most common aberration (almost 20% of cases with abnormal cytogenetics). Del(5q) is heterogeneous, occurring as a sole abnormality or in combination, with the deleted region often truncated within or extended and/or beyond the CDR boundaries. Isolated del(5q) is frequently shorter and confers a more favorable prognosis with regard to survival and lenalidomide (LEN) responsiveness, while del(5q) in the context of a complex karyotype (CK) imparts a poor prognosis. In addition to chromosomal lesions, somatic mutations can contribute to the pathogenesis of MDS, including del(5q). We theorized that recognition of molecular defects in MDS with del(5q) may clarify the pathogenic mechanisms behind this lesion and help explain the clinical heterogeneity. We analyzed 225 pts with myeloid neoplasia and del(5q) using WES (n= 107 samples) and targeted multiplexed PCR (top 60 most frequently mutated genes) (n =133 samples); serial analysis was performed in 15 pts studied at ≥2 time points, 11 during LEN therapy and 4 upon relapse/progression. A total of 116 samples had a CK with other lesions such as -7/del(7q) found in 31% cases, and 18% had -17/del(17p). WES (average depth >60x) was followed by a bioanalytic pipeline, detecting ≥1 mutated gene in 71% of cases. Candidate somatic alterations were found in 357 genes and selected for further analysis. When focused on hemizygous mutations within the retained 5q allele, CSNK1A1 mutations were the most common, found in 4 pts, while other genes were only sporadically affected. Among heterozygous mutations on the non-deleted portion of del(5q) and other chromosomes (Chr), we found several novel mutations, in addition to TP53 (n=26), DNMT3A (n=8), PRPF8 (n =8), RUNX1 (n=5), TET2 (n=5), and ASXL1 (n=4), among others. Furthermore, LOH/haploinsuffciency of genes on 7q (e.g., LUC7L2, CUX1, EZH2 and MLL3) appears to be a common defect seen in pts with non-isolated del(5q), suggesting synergistic functional defects. When functionally grouping gene mutations, DNA methylation family (8 cases) and transcription factor mutations (29 cases) were associated with advanced disease (AD) and a CK. Heterozygous mutations in TP53 (34%) or deletions involving the TP53 locus (23%) resulted in total of 42% of cases carrying either TP53 LOH or mutation. TP53 lesions were more common in pts with AD vs. low risk. (21 vs. 5 p =.0008). In contrast, TP53 mutations are found in 8-10% of cases of MDS. A total of 34 pts were treated with LEN and subgrouped into responders (n=17) vs. refractory (n=9) with an overall response rate of 65%. When mutational profiles were compared, the presence of TP53 mutations did not preclude responsiveness to LEN. CK was present in 12% of responders vs. 67% of refractory pts. The most frequent Chr abnormalities were -7/7q (0% vs. 67% in responders vs. refractory) and 17p-(6% vs. 67% in responders vs. refractory) suggestive of their role in LEN resistance. In addition to cross sectional analysis, our WES study using paired Germline/tumor samples followed by deep sequencing facilitated analyses of clonal architecture by examining clonal dynamics over time. Assessment of del(5q) clone size by allelic imbalance combined with clonal burden by VAF allowed us to reconstruct the clonal hierarchy: in 73% of cases, del(5q) appeared to be the initial defect followed by subsequent mutations (e.g., TP53, DNMT3A, IDH2). In contrast, in 24% of cases, TP53, RUNX1, JARID2, were the primary defect followed by a subclonal del(5q) events. Serial samples collected before and after therapy demonstrated that responses were associated with decreased clonal burden for del(5q) but persistence of certain mutations. In refractory cases, persistent subclonal lesions and the appearance of new lesions were associated with progression. For example, pts with TP53, LAMB4, EPHA6 progressed and acquired additional lesions such as CSMD2 or KCND2, and did not see the disappearance of TP53 alterations upon treatment. In conclusion, no unifying somatic defect was found in pts with del(5q) regardless if the deletion event was primary or subclonal. Most commonly associated lesions were not present on the retained 5q alleles but rather other chr yet modified clinical behavior, including responsiveness to LEN. Disclosures Bejar: Celgene: Consultancy, Honoraria; Alexion: Other: ad hoc advisory board; Genoptix Medical Laboratory: Consultancy, Honoraria, Patents & Royalties: MDS prognostic gene signature. Sekeres:Celgene Corporation: Membership on an entity's Board of Directors or advisory committees; TetraLogic: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees.

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Analysis of Clonal Hierarchy Shows That Other Ancestral Events May Precede Evolution of Del(5q) in Myeloid Neoplasms

Blood ◽

10.1182/blood.v124.21.4605.4605 ◽

2014 ◽

Vol 124 (21) ◽

pp. 4605-4605

Author(s):

Naoko Hosono ◽

Hideki Makishima ◽

Bartlomiej P Przychodzen ◽

Thomas LaFramboise ◽

Chantana Polprasert ◽

...

Keyword(s):

Board Of Directors ◽

Tp53 Mutation ◽

Somatic Mutations ◽

Clonal Evolution ◽

Common Mutation ◽

Advisory Committees ◽

Tp53 Mutations ◽

Clonal Architecture ◽

Myeloid Neoplasms ◽

Associated Lesions

Abstract The molecular pathogenesis of myeloid neoplasms characterized by 5q deletion (del(5q)) has not been completely elucidated. While some pathomorphologic features including e.g., megakaryocytic and erythroid dysplasia, have been associated with specific genes within minimal common deleted regions (CDR), genes responsible for clonal advantage and expansion have not been identified. It is not clear if haploinsufficiency of one or multiple genes within del(5q) is responsible for clonal evolution or whether mutations in those genes or other genes located in other genomic areas are present. Moreover, with the recognition of intra-tumor diversity and hierarchical clonal architecture, it may be possible to establish whether del(5q) or other lesions, including common somatic mutations, constitute the ancestral event in the pathophysiologic cascade. We performed a comprehensive mutational screen in 124 patients with del(5q), including 59 patients studied by whole exome sequencing (WES) and 65 by targeted deep NGS of genes within the deleted area and the other most commonly mutated genes as previously determined in WES cohorts. To identify pathogenic genes, those most consistently found to be haploinsufficient in del(5q) were matched for the presence of mutations in diploid cases. For the purpose of this study haploinsufficiency was quantitated based on the number of cases with del(5q) showing <60% expression of the corresponding genes. E.g.,HDAC3 in 81%, PPP2CA in 62% and RPS14 in 14% of cases with del(5q). For all somatic mutations, we also describe the clonal composition based on deep sequencing in serial samples and analyses of variant allelic frequency. Finally, we compare the clonal size for individual mutations with that of del(5q). The latter was accomplished by calculation of clonal size based on allelic imbalance for informative SNPs present within deleted regions in heterozygous configurations in germ line samples. The average deviation from the ideal 50/50 distribution in tumor samples allowed for precise calculation of the proportion of cells in the sample affected by the deletion. Using this approach, there was a good correlation to the size of del(5q) clone by FISH (r=.94) Our results demonstrate that 10/14 genes were haploinsufficient within the CDR, but only 2 hemizygous somatic mutations were identified. However, 12 mutations in 7 genes (MATR3, SH3TC2, CSNK1A1, PDGFRB, CD74, FAT2 and G3BP1) were present with the area corresponding to the CDR in diploid cases. TP53 mutations were more commonly associated with del(5q) (73%, vs. 27% in diploid 5, p<.001) and were particularly frequent in patients affected with 2 commonly retained regions (CRR1;5q11.1-5q14.2 and CRR2; 5q34-qter), where they were found in 81% of cases (30/37) vs. 19% (7/30) among CDR deletions (p<.001). In lower-risk MDS, mutations were detected in 11% of deletion cases, whereas they were only found in 5% of diploid chr5 (p<.0001). In higher-risk MDS, TP53 mutation were found in 42% of del(5q) vs. 4% of diploid chr5 (p<.0001). Similarly, 45% patients with concomitant -7/del(7q) and del(5q) had TP53 mutations. The most common mutation associated with del(5q) was TP53, while mutations of FLT3, NRAS or TET2 were significantly mutually exclusive (p=0.03, 0.04 and 0.03; respectively). Next we determined the earliest somatic event by comparing of clonal size of the associated lesions. Del(5q) was present in 17-98% of tumor cells. We identified three theoretical possibilities as to the clonal architecture of del(5q) myeloid neoplasms: i) Tumors in which driver somatic mutations precede del(5q) (35%), ii) those in which del(5q) appears to precede any other somatic mutation (6%) and iii) the succession cannot be determined because of very expanded clones of similar size (“clonal saturation”) i.e., these cases were not informative. For cases in which del(5q) was a secondary lesion, TP53 was the ancestral event 64% of the time, and DNMT3A 27% of the time. The TP53 mutation was detected as a secondary event in 1 of 2 samples in which del(5q) was found to be ancestral. In sum, our results suggest that del(5q) is not universally an ancestral event. The TP53 mutation is the most common mutation in del(5q) and may also serve as ancestral event. While UPD17p and hemizygocity for TP53 can be found in 33% of TP53 mutant cases, most of the detected TP53 mutations were likely to heterozygous, and therefore the clonal size was not overestimated. Disclosures Sekeres: Celgene: Membership on an entity's Board of Directors or advisory committees; Amgen Corp: Membership on an entity's Board of Directors or advisory committees; Boehringer-Ingelheim Corp: Membership on an entity's Board of Directors or advisory committees.

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Determinants of Phenotypic Commitment and Clonal Progression--Conclusions from the Study of Clonal Architecture in CMML

Blood ◽

10.1182/blood.v126.23.2848.2848 ◽

2015 ◽

Vol 126 (23) ◽

pp. 2848-2848

Author(s):

Bhumika J. Patel ◽

Bartlomiej Przychodzen ◽

Michael J. Clemente ◽

Cassandra M. Hirsch ◽

Tomas Radivoyevitch ◽

...

Keyword(s):

Board Of Directors ◽

Clinical Features ◽

Germ Line ◽

Low Risk ◽

Molecular Heterogeneity ◽

Advisory Committees ◽

Cross Sectional ◽

Clonal Architecture ◽

Phenotypic Features ◽

Serial Samples

Abstract CMML is heterogeneous clinically (a varying degree of dysplastic or proliferative clinical features) and in terms of its molecular pathogenesis. Analysis of the spectrum of genomic lesions in CMML may contribute to understanding of the pathogenesis and help identify certain mutations as diagnostic biomarkers. Apart of the mere presence of a somatic lesion, phenotypic features may be shaped by initial hits. Conversely sub-clonal events may determine the phenotype or progression. Finally, initial hits may predetermine e.g., mutator phenotype, or differentiation block and therefore selecting for specific sub-clonal hits. We have selected a large CMML cohort to establish generalizable pathogenetic and clinical associations to account for molecular heterogeneity and serial samples have to be analyzed to assess clonal dynamics and hierarchy. The study group consisted of 242 patients, including 150 CMML cases (96 CMML-1, 27 CMML-2, 27 post CMML sAML) and JMML (N =92); 15 patients were studied serially. We also used comparison cohorts of M4/M5 AML (N =64) and advanced (N= 231) and low risk MDS (N= 199) serving as risk adjusted match for CMML subtypes. The CMML entity was further sub-classified based on clinical parameters and pathomorphologic features, 57% dysplastic (MD-CMML) and 43% proliferative form (MP-CMML). Analysis was performed using WES (paired germ line/tumor samples) and multiamplicon NGS targeting top 60 most commonly affected genes. For clonal architecture analysis, cross-sectional variant allelic frequency (VAF) concept based analysis was performed including assessment of affected genes by ranking of the corresponding clonal burden rather than the absolute cellular frequency. The results of this analysis were confirmed in serial samples to identify expanding, declining and stable subclones. Comparison of mutational spectra between the disease entity show profound differences in morphologically similar entities as particularly evident in comparison of CMML to JMML (TET2, ASXL1) or to lesser degree low risk MDS and CMML1 while progression in advanced cases was often associated with similar spectrum of additional subclonal events. However, the differences were more striking when clonal hierarchy was assessed to identify dominant/codominant and subclonal mutational events. We found that top 4 dominant/codominant clonal events, included TET2 (56%), SRSF2 (42%), ASXL1 (46%), DNMT3A (45% of patients), while in MDS corresponding frequency of these dominant events was TET2 (15%) SRSF2 (8%), ASXL1 (11%) and DNMT3A (8%), with most common ancestral events ranked SF3B1, TET2, ASXL1 etc. The clinical importance of these dominant events in CMML is highlighted by their impact on survival in KM analysis (p=.018). Our analysis also demonstrated that for certain founding events not pathognomonic for CMML either codominant or subsequent subclonal events determine the phenotypic features (1st generation) or progression (2nd generation). For instance initial TET2 in CMML was followed often by SRSF2 or in conjunction, RAS pathway mutations while MDS was driven by TET2, SF3B1, TP53, and many other events. Progression in our cohort was driven in both CMML and MDS by ASXL1, RUNX1, NPM1. When other common mutations were categorized by their role in individual patients 27% EZH2, 20% of CBL and 22% of SETBP1 were dominant. Serial analysis further qualified the cross-sectional analysis and allowed for categorization of subclonal events. For instance, CMML-1 cases initially presented with dominant TET2 followed by subtype specific subclonal SRSF2 and progression event IDH2 progressed to sAML with new NPM1 acquisition and expansion of IDH2 c lone. In our serial sample analysis we observed that increasing ASXL1 and RUNX1 clones correspond to clinical progression, ancestral events may remain stable (TET2, SRSF2, SETBP1), while non-permissive subclones can smolder or even decline. In sum, deep NGS allows for identification of specific ancestral events, which may determine the subsequent secondary mutational events in CMML. Classification of CMML based on ancestral events and subclonal events rather than on the global mutational spectrum correlates with clinical features and prognosis and may contribute to further clinical resolution of CMML based on the presence of specific founder mutations ultimately help establish therapeutic interventions. Disclosures Sekeres: Amgen: Membership on an entity's Board of Directors or advisory committees; Celgene Corporation: Membership on an entity's Board of Directors or advisory committees; TetraLogic: Membership on an entity's Board of Directors or advisory committees.

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Multicenter Analysis of Treatment and Outcomes for Patient with TP53 Mutated AML in the Era of Novel Therapies; Significant Impact of Allogeneic Stem Cell Transplantation on Survival

Blood ◽

10.1182/blood-2021-147639 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 797-797

Author(s):

Talha Badar ◽

Mark R. Litzow ◽

Rory M. Shallis ◽

Jan Philipp Bewersdorf ◽

Antoine Saliba ◽

...

Keyword(s):

Stem Cell ◽

High Risk ◽

Stem Cell Transplantation ◽

Board Of Directors ◽

Research Funding ◽

Univariate Analysis ◽

Advisory Board ◽

Novel Therapies ◽

Advisory Committees ◽

Tp53 Mutations

Abstract Background: TP53 mutations occur in 10-20% of patients with AML, constitute high-risk disease as per ELN criteria, and confer poorer prognosis. Venetoclax combination therapies and CPX-351 were recently approved for AML treatment and lead to improved outcomes in subsets of high-risk AML, however the most effective approach for treatment of TP53-mutated (m) AML remains unclear. In this study we explored the clinical outcome of TP53m AML patients treated over the last 8 years as novel therapies have been introduced to our therapeutic armamentarium. Methods: We conducted a multicenter observational study in collaboration with 4 U.S. academic centers and analyzed clinical characteristics and outcome of 174 TP53m AML patients diagnosed between March 2013 and February 2021. Mutation analysis was performed on bone marrow specimens using 42, 49, 199, or 400 gene targeted next generation sequencing (NGS) panels. Patients with an initial diagnosis of AML were divided into 4 groups (GP) based on the progressive use of novel therapies in clinical trials and their approvals as AML induction therapy during different time periods: 2013-2017 (GP1, n= 37), 2018-2019 (GP2, n= 53), 2019-2020 (GP3, n= 48) and 2020-2021 (GP4, n= 36) to analyze difference in outcome. Results: Baseline characteristics were not significantly different across different GP, as shown in Table 1. Median age of patients was 68 (range [R], 18-83), 65 (R, 29-88), 69 (R, 37-90) and 70 (R, 51-97) years in GP1-4, respectively (p=0.40). The percentage of patients with de novo AML/secondary AML/therapy-related AML in GP1-4 was 40/40/20, 36/29/24, 37.5/37.5/25 and 28/52/20, respectively (p=0.82). The proportion of patients with complex cytogenetics (CG) was 92%, 89%, 96% and 94% in GP1-4, respectively (p=0.54). The median TP53m variant allele frequency (VAF) was 48% (range [R], 5-94), 42% (R, 5-91), 45% (R, 10-94) and 60% (R, 8-82) in GP1-4, respectively (p=0.38). Four (11%), 13 (24.5%), 10 (21%) and 9 (25%) patients had multiple TP53 mutations in GP1-4, respectively (p=0.33). The proportion of patients who received 3+7 (30%, 16%, 6% & 8%; p=0.01), HMA only (11%, 18%, 2% & 8%; p=0.06), venetoclax-based (2.5%, 12%, 48%, & 61%; p <0.01) and CPX-351 induction (16%, 40%, 28% & 5%; p<0.001) were varied in GP1-4, respectively. The rate of CR/CRi was 22%, 26%, 28% and 18% in GP1-4, respectively (p=0.63). Treatment related mortality during induction was observed in 3%, 7%, 10% and 17% of patients in GP1-4, respectively (p=0.18). Overall, 28 (16%) patients received allogeneic hematopoietic stem cell transplantation (alloHCT) after induction/consolidation: 22%, 15%, 17% and 11% in GP1-4, respectively (p=0.67). In subset analysis, there was no difference in the rate of CR/CRi with venetoclax-based regimens vs. others (39% vs 61%, p=0.18) or with CPX-351 vs. others (25% vs 75%, p=0.84). The median progression-free survival was 7.7, 7.0, 5.1 and 6.6 months in GP1-4, respectively (p=0.60, Fig 1A). The median overall survival (OS) was 9.4, 6.1, 4.0 and 8.0 months in GP1-4, respectively (p=0.29, Fig 1B). In univariate analysis for OS, achievement of CR/CRi (p<0.001) and alloHCT in CR1 (p<0.001) associated with favorable outcome, whereas complex CG (p=0.01) and primary refractory disease (p<0.001) associated with poor outcome. Multiple TP53 mutations (p=0.73), concurrent ASXL1m (p=0.86), extra-medullary disease (p=0.92), ≥ 3 non-TP53m mutations (p=0.72), TP53m VAF ≥ 40% vs. < 40% (p=0.25), induction with CPX-351 vs. others (p=0.59) or venetoclax-based regimen vs. others (p=0.14) did not show significance for favorable or poor OS in univariate analysis. In multivariable analysis, alloHCT in CR1 (hazard ratio [HR]=0.28, 95% CI: 0.15-0.53; p=0.001) retained an association with favorable OS and complex CG (HR 4.23, 95%CI: 1.79-10.0; p=0.001) retained an association with dismal OS. Conclusion: We present the largest experience with TP53m AML patients analyzed by NGS. Although outcomes were almost universally dismal, alloHCT appears to improve the long-term survival in a subset of these patients. Effective therapies are warranted to successfully bridge patients to alloHCT and to prolong survival for transplant ineligible patients. Figure 1 Figure 1. Disclosures Badar: Pfizer Hematology-Oncology: Membership on an entity's Board of Directors or advisory committees. Litzow: Omeros: Other: Advisory Board; Pluristem: Research Funding; Actinium: Research Funding; Amgen: Research Funding; Jazz: Other: Advisory Board; AbbVie: Research Funding; Astellas: Research Funding; Biosight: Other: Data monitoring committee. Shallis: Curis: Divested equity in a private or publicly-traded company in the past 24 months. Goldberg: Celularity: Research Funding; Astellas: Consultancy, Membership on an entity's Board of Directors or advisory committees; Aprea: Research Funding; Arog: Research Funding; DAVA Oncology: Honoraria; Genentech: Consultancy, Membership on an entity's Board of Directors or advisory committees; Pfizer: Research Funding; Prelude Therapeutics: Research Funding; Aptose: Consultancy, Research Funding; AbbVie: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding. Atallah: BMS: Honoraria, Speakers Bureau; Takeda: Consultancy, Research Funding; Amgen: Consultancy; Abbvie: Consultancy, Speakers Bureau; Novartis: Consultancy, Honoraria, Research Funding; Pfizer: Consultancy, Research Funding. Foran: revolution medicine: Honoraria; gamida: Honoraria; bms: Honoraria; pfizer: Honoraria; novartis: Honoraria; takeda: Research Funding; kura: Research Funding; h3bioscience: Research Funding; OncLive: Honoraria; servier: Honoraria; aptose: Research Funding; actinium: Research Funding; abbvie: Research Funding; trillium: Research Funding; sanofi aventis: Honoraria; certara: Honoraria; syros: Honoraria; taiho: Honoraria; boehringer ingelheim: Research Funding; aprea: Research Funding; sellas: Research Funding; stemline: Research Funding.

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BCX9930, a Potent, Selective, Oral Factor D Inhibitor, Demonstrates Proof-of-Concept As Monotherapy in Patients with Paroxysmal Nocturnal Hemoglobinuria (PNH)

Blood ◽

10.1182/blood-2020-138838 ◽

2020 ◽

Vol 136 (Supplement 1) ◽

pp. 14-15

Author(s):

Austin Kulasekararaj ◽

Jacques Le Roux Malherbe ◽

Andrew McDonald ◽

Melanie Cornpropst ◽

Phil Collis ◽

...

Keyword(s):

South Africa ◽

Board Of Directors ◽

Research Funding ◽

Total Bilirubin ◽

Proof Of Concept ◽

Advisory Committees ◽

Clone Size ◽

The Past ◽

History Of ◽

Pre Treatment

INTRODUCTION: PNH, a rare, chronic, life-threatening disease, is characterized by hemolytic anemia due to uncontrolled activity of the complement alternative pathway (AP), bone marrow failure, and thrombosis. Inhibition of C5 by intravenously administered eculizumab and ravulizumab reduces intravascular hemolysis, but PNH red blood cells (RBCs) become opsonized and susceptible to extravascular hemolysis (Risitano et al, Blood 2009). Only approximately half of PNH patients become transfusion independent with eculizumab treatment (Hillmen et al, NEJM 2006). BCX9930 is a potent, selective, orally administered inhibitor of complement factor D. Inhibition of factor D may prevent both intravascular and extravascular hemolysis in PNH. In healthy subjects, BCX9930 showed linear pharmacokinetics and dose-related AP suppression, and was safe and generally well-tolerated over a wide dose range. Here we describe safety and laboratory data establishing proof-of-concept for BCX9930 monotherapy in PNH patients in Study BCX9930-101 (NCT04330534). METHODS: Ongoing Study BCX9930-101 includes an open-label, dose-ranging evaluation of BCX9930 in PNH subjects who may either be naïve to C5 inhibitors (and receive BCX9930 as monotherapy) or have an incomplete treatment response to eculizumab or ravulizumab (with BCX9930 added to existing treatment). Up to 4 sequential cohorts each use a forced titration design for the first 28 days (Figure 1). Subjects enrolled in South Africa can participate in an individualized 48-week extension if they derive benefit at Day 28. Clinical benefit from BCX9930 is evaluated using laboratory monitoring and symptom assessment. Safety and tolerability are evaluated via clinical and laboratory monitoring, causality of adverse events is assessed by investigators, and the study is overseen by an independent Data Monitoring Committee. Data from Cohort 1 through 28 days is reported; data from the extension and subsequent cohorts will be subsequently summarized as available. RESULTS: To date, four C5 inhibitor naïve PNH subjects in South Africa have enrolled in Cohort 1. These subjects had PNH for a median of 4.5 years; 2 subjects had a history of transfusions in the past year; 1 subject each had a history of aplastic anemia or major thrombosis. Pre-treatment lactate dehydrogenase (LDH), total bilirubin, hemoglobin (Hb), reticulocyte count, and RBC PNH Type III clone size ranged from 3.7-11.1 × ULN, 0.61-3.3 mg/dL, 6.1-11.6 g/dL, 0.13-0.29 × 106/µL, and 41.4%-88.6% respectively. Treatment over 28 days with 50 mg twice daily (BID; Days 1-14) and 100 mg BID (Days 15-28) of BCX9930 produced dose-dependent, clinically meaningful improvements across hemolysis biomarkers (Figure 2). Decreases were observed in LDH (4/4), reticulocytes (4/4), and total bilirubin (2/2 subjects with elevated pre-treatment values). Increases were observed in Hb (3/4) and PNH RBC clone size (4/4). One subject showed an initial response to BCX9930 50 mg BID, followed by worsening indicators of hemolysis temporally associated with an upper respiratory tract infection (URTI; onset on Day 7). With an increase in dose to 100 mg BID and resolution of the URTI, LDH and reticulocytes fell and Hb rose. All four subjects reported one or more PNH-associated symptoms, including hemoglobinuria, jaundice, fatigue, erectile dysfunction, headache and abdominal pain, prior to enrollment. With the exception of one subject with persistent hemoglobinuria, all symptoms resolved by Day 28 on BCX9930. Three subjects experienced moderate headache that resolved in < 3 days after initiating BCX9930. One subject developed a rash during treatment with amoxicillin for an URTI; the rash resolved while continuing BCX9930 dosing. One subject on concomitant chronic corticosteroids and azathioprine had an unrelated fatal serious adverse event of disseminated varicella during the study extension. Based on review of safety data, Cohort 2 opened at doses of 200 mg BID and 400 mg BID and, in the 3 subjects who continued into the extension, the dose was titrated to ≥ 200 mg BID. CONCLUSIONS: Oral BCX9930 elicited rapid changes in laboratory parameters indicative of reduced hemolysis and clinical benefit and was safe and generally well-tolerated over a 28-day dosing interval. These interim results establish proof of concept for monotherapy with BCX9930 in the treatment of C5-inhibitor naïve PNH patients and support evaluation of higher doses. Disclosures Kulasekararaj: Alexion:Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grants, Speakers Bureau;Ra Pharma:Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grants, Speakers Bureau;BioCryst Pharmaceuticals, Inc.:Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees;Apellis:Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grants, Speakers Bureau;Roche:Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau;Novartis:Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grants, Speakers Bureau;Celgene:Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grants, Speakers Bureau.Malherbe:Key Oncologics:Honoraria, Other: Conference sponsor;Novartis:Other: Conference sponsor;Astellas:Honoraria, Other: Conference sponsor;Takeda:Consultancy;Acino:Honoraria;Shire:Other: Conference sponsor;BioCryst Pharmaceuticals, Inc.:Consultancy;Janssen:Consultancy, Honoraria, Other: Conference sponsor;Roche:Honoraria, Other: Conference sponsor.McDonald:venetoclax advisory board in South Africa (in CLL context):Consultancy;Alberts Cellular Therapy:Current Employment.Cornpropst:BioCryst Pharmaceuticals, Inc.:Current Employment.Collis:BioCryst Pharmaceuticals, Inc.:Current Employment.Davidson:BioCryst Pharmaceuticals, Inc.:Current Employment.Chen:BioCryst Pharmaceuticals, Inc.:Current Employment.Tower:BioCryst Pharmaceuticals, Inc.:Current Employment.Gesty-Palmer:BioCryst Pharmaceuticals, Inc.:Current equity holder in publicly-traded company, Ended employment in the past 24 months.Sheridan:BioCryst Pharmaceuticals, Inc.:Current Employment.Risitano:Alexion:Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau;Alnylam:Research Funding;Novartis:Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau;Pfizer:Speakers Bureau;Achillion:Membership on an entity's Board of Directors or advisory committees;Apellis:Membership on an entity's Board of Directors or advisory committees, Speakers Bureau;Biocryst:Membership on an entity's Board of Directors or advisory committees;RA pharma:Research Funding;Amyndas:Consultancy;Samsung:Membership on an entity's Board of Directors or advisory committees;Roche:Membership on an entity's Board of Directors or advisory committees;Jazz:Speakers Bureau.

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Dose-Adjusted EPOCH and Rituximab (DA-EPOCH-R) Treatment in Dual Expressor Diffuse Large B-Cell and Double/Triple Hit Lymphomas: TP53 Mutations Influence on Clinical Outcome

Blood ◽

10.1182/blood-2019-124350 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 4116-4116

Author(s):

Anna Dodero ◽

Anna Guidetti ◽

Fabrizio Marino ◽

Cristiana Carniti ◽

Stefania Banfi ◽

...

Keyword(s):

High Risk ◽

B Cell ◽

Board Of Directors ◽

Research Funding ◽

Poor Prognosis ◽

Tp53 Mutation ◽

Advisory Committees ◽

Tp53 Mutations ◽

Travel Costs ◽

Large B Cell

Introduction: Diffuse Large B-Cell Lymphoma (DLBCL) is an heterogeneous disease: 30-40% of cases have high expression of MYC and BCL2 proteins (Dual Expressor, DE) and 5-10% have chromosomal rearrangements involving MYC, BCL2 and/or BCL6 (Double-/ Triple-Hit, DH/TH). Although the optimal treatment for those high-risk lymphomas remains undefined, DA-EPOCH-R produces durable remission with acceptable toxicity (Dunleauvy K, Lancet 2018). TP53 mutation is an independent marker of poor prognosis in patients (pts) with DLBCL treated with R-CHOP therapy. However, its prognostic value in poor prognosis lymphomas, receiving intensive therapy, has not been investigated yet. Methods: A series of consecutive pts (n=87) with biopsy proven diagnosis of DE DLBCL (MYC expression ≥40% and BCL2 expression ≥ 50% of tumor cells) or DE-Single Hit (DE-SH, i.e., DE-DLBCL with a single rearrangement of either MYC, BCL2 or BCL6 oncogenes) or DE-DH/TH (MYC, BCL2 and/or BCL6 rearrangements obtained by FISH) were treated with 6 cycles of DA-EPOCH-R and central nervous system (CNS) prophylaxis consisting of two courses of high-dose intravenous Methotrexate. Additional eligibility criteria included age ≥18 years and adequate organ functions. Cell of origin (COO) was defined according to Hans algorithm [germinal center B cell like (GCB) and non GCB)]. TP3 mutations were evaluated by next generation sequencing (NGS) based on AmpliseqTM technology or Sanger sequencing and considered positive when a variant allelic frequency ≥10% was detected. Results: Eighty-seven pts were included [n=36 DE only, n=32 DE-SH (n=8 MYC, n=10 BCL2, n=14 BCL6), n=19 DE-DH/TH] with 40 patients (46%) showing a non GCB COO. Pts had a median age of 59 years (range, 24-79 years). Seventy-three pts (84%) had advanced disease and 44 (50%) an high-intermediate/high-risk score as defined by International Prognostic Index (IPI). Only 8 of 87 pts (9%) were consolidated in first clinical remission with autologous stem cell transplantation following DA-EPOCH-R. After a median follow-up of 24 months, 73 are alive (84%) and 14 died [n=12 disease (n=2 CNS disease); n=1 pneumonia; n=1 suicide]. The 2-year PFS and OS were 71% (95%CI, 60-80%) and 76% (95%CI, 61%-85%) for the entire population. For those with IPI 3-5 the PFS and OS were not significant different for DE and DE-SH pts versus DE-DH/TH pts [64% vs 57% p=0.77); 78% vs 57% p=0.12)]. The COO did not influence the outcome for DE only and DE-SH [PFS: 78% vs 71% (p=0.71); 92% vs 86% (p=0.16) for GCB vs non -GCB, respectively]. Fourty-six pts (53%;n=18 DE only, n=18 DE-SH, n=10 DE-DH/TH ) were evaluated for TP53 mutations with 11 pts (24%) carrying a clonal mutation (n=6 in DE, n=3 in DE-SH, n=2 in DE-DH/TH). The 2-year PFS and OS did not significantly change for pts DE and DE-SH TP53 wild type as compared to DE and DE-SH mutated [PFS: 84 % vs 77%, (p=0.45); OS: 87% vs 88%, (p=0.92)]. The two pts DE-DH/TH with TP53 mutation are alive and in complete remission.Conclusions: High risk DLBCL pts treated with DA-EPOCH-R have a favourable outcome independently from high IPI score, DE-SH and DE-DH/TH. Also the presence of TP53 mutations does not negatively affect the outcome of pts treated with this intensive regimen. The efficacy of DA-EPOCH-R in overcoming poor prognostic genetic features in DLBCL should be confirmed in a larger prospective clinical trial. Disclosures Rossi: Daiichi-Sankyo: Consultancy; Roche: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees; Abbvie: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Jazz: Membership on an entity's Board of Directors or advisory committees; Astellas: Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria; Mundipharma: Honoraria; BMS: Honoraria; Sandoz: Honoraria. Carlo-Stella:Takeda: Other: Travel, accommodations; F. Hoffmann-La Roche Ltd: Honoraria, Other: Travel, accommodations, Research Funding; Rhizen Pharmaceuticals: Research Funding; Celgene: Research Funding; Amgen: Honoraria; AstraZeneca: Honoraria; Janssen Oncology: Honoraria; MSD: Honoraria; BMS: Honoraria; Genenta Science srl: Consultancy; Janssen: Other: Travel, accommodations; Servier: Consultancy, Honoraria, Other: Travel, accommodations; Sanofi: Consultancy, Research Funding; ADC Therapeutics: Consultancy, Other: Travel, accommodations, Research Funding; Novartis: Consultancy, Research Funding; Boehringer Ingelheim: Consultancy. Corradini:AbbVie: Consultancy, Honoraria, Other: Travel Costs; KiowaKirin: Honoraria; Gilead: Honoraria, Other: Travel Costs; Amgen: Honoraria; Celgene: Honoraria, Other: Travel Costs; Daiichi Sankyo: Honoraria; Janssen: Honoraria, Other: Travel Costs; Jazz Pharmaceutics: Honoraria; Kite: Honoraria; Novartis: Honoraria, Other: Travel Costs; Roche: Honoraria; Sanofi: Honoraria; Takeda: Honoraria, Other: Travel Costs; Servier: Honoraria; BMS: Other: Travel Costs.

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The Broad Spectrum of TP53 Variants in CLL: NGS Analysis of 573 Pathogenic TP53 Variants

Blood ◽

10.1182/blood-2019-130907 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 3021-3021

Author(s):

Gregory Lazarian ◽

Floriane Theves ◽

Myriam Hormi ◽

Virginie Eclache ◽

Stéphanie Poulain ◽

...

Keyword(s):

Tumor Progression ◽

Board Of Directors ◽

Research Funding ◽

Lymphocytic Leukemia ◽

Fish Analysis ◽

Snp Analysis ◽

Advisory Committees ◽

Exon 2 ◽

Tp53 Mutations ◽

Mutational Status

TP53 aberrations, including somatic mutations of TP53 gene or 17p deletion leading to the loss of the TP53 locus, are a major predictive factor of resistance to fludarabin based chemotherapy in chronic lymphocytic leukemia (CLL) and remain an adverse prognostic factor in the chemofree era. Therefore, detection of TP53 alteration before each new line of treatment is required for theranostic stratification. In order to better characterize the distribution and combination of the TP53 variants in CLL, we collected the TP53 sequencing data of 343 patients harboring TP53 mutations from centers of the French Innovative Leukemia Organization-CLL (FILO) and established a large data base of 573 TP53 mutations. Mutations were identified through NGS sequencing (covering exon 2 to 11) allowing the detection of low frequency variants down to 1% VAF. Several distinct low VAF mutations were orthogonally confirmed by digital PCR. TP53 variants were analyzed through UMD_TP53 data gathering 90 000 TP53 mutations from all type of cancers. IGHV mutational status and FISH analysis were available for 224 and 176 patients respectively. Using ACMG criteria from the UMD_TP53 database, we confirmed that 523 could be classified as pathogenic, 42 were likely pathogenic and 8 were VUS (Variants of Unknown Significance). As expected, the mutation distribution along the p53 protein exhibited a clustering of variants in the DNA binding domain of the protein. We also confirmed the presence of a specific hotspot at codon 234 (6%) which is noticeable in other CLL cohorts but absent in solid tumors. 431 TP53 variants led to the expression of a mutant protein whereas the remaining 142 led a TP53 null phenotype. For 8 patients without 17p deletion and a mutation VAF larger than 50%, SNP analysis indicate that these tumors had a copy number neutral loss of heterozygosis at 17p with a duplication of the mutant allele leading to homozygous mutations of TP53. When focusing on the allele burden of TP53 mutations, 264/573 (46%) variants had an allele frequency <10%. Even if they were predominantly found in polymutated cases, presence of only low VAF (<10%) mutations was evidenced in 74 (21%) patients (50 patients with a single TP53 mutation and 24 patients with more than one). All these cases would have been missed by conventional sequencing. Among the 343 patients, 113 (33%) were poly-mutated and harbored more than one pathogenic TP53 variants (2 to 11 variants per patient): 57 (16,7 %) had 2 variants, 32 (9,3%) had 3, 10 had 4 (3%) and 14 patients (4%) had 5 to 11 variants. Using both long range sequencing and in silico analysis, we could show that all these variants were distributed in different alleles supporting an important intratumoral heterogeneity and a strong selection for TP53 loss of function during tumor progression in these patients. Null variants were rarely found as single alteration: only 46 patients (13,4%) patients harbored a single null mutation. Null mutations were predominantly found in patients with multiclonal mutations (87% with 4 or more). Median size of variants significantly decreased with the number of mutations and most of low VAF (less than 10%) variants were found in multiclonal combinations. Multiclonal mutations were predominantly found in previously treated patients (41% treated versus 10 % untreated) but whether all these variants preceded treatment and were further selected is currently unknown. We observed that 71,5 % of patients were IGHV unmutated and multiclonal mutations were surprisingly more frequent in mutated IGHV cases than in unmutated ones. Only 50% of cases carried a 17p deletion, highlighting again the importance of testing for TP53 mutations in addition to FISH analysis. Presence or absence of 17p deletion was unrelated to the number of TP53 mutations. Taken together these observations suggest that the TP53 mutational landscape in CLL is very complex and can involve multiple mechanisms, converging to a total loss of TP53 function and tumor progression. NGS provides a powerful tool for detecting all these alterations including variants with low VAF and should become a standard for CLL screening prior to each line of treatment. Disclosures Leblond: Amgen: Honoraria, Speakers Bureau; Abbvie: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Janssen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Gilead: Honoraria, Speakers Bureau; Astra Zeneca: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Roche: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Letestu:Abbvie: Membership on an entity's Board of Directors or advisory committees, Other: speaker fee, expert contracts; Janssen: Membership on an entity's Board of Directors or advisory committees, Other: speaker fee, expert contracts; Roche: Membership on an entity's Board of Directors or advisory committees, Other: speaker fee, expert contracts; Alexion: Membership on an entity's Board of Directors or advisory committees, Other: speaker fee, expert contracts. Cymbalista:Abbvie: Honoraria; Roche: Research Funding; Sunesis: Research Funding; Gilead: Honoraria; Janssen: Honoraria; AstraZeneca: Honoraria.

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Clonal Architecture and Variant Allele Frequency Predict Clinical Outcomes and Drug Response in Acute Myeloid Leukemia

Blood ◽

10.1182/blood-2020-136477 ◽

2020 ◽

Vol 136 (Supplement 1) ◽

pp. 2-2

Author(s):

Brooks Benard ◽

Logan Leak ◽

Armon Azizi ◽

Daniel Thomas ◽

Andrew Gentles ◽

...

Keyword(s):

Board Of Directors ◽

Clinical Outcomes ◽

Drug Sensitivity ◽

Clonal Evolution ◽

High Risk Patient ◽

Variant Allele Frequency ◽

Clonal Heterogeneity ◽

Advisory Committees ◽

Clonal Architecture ◽

Linear Evolution

Introduction: AML is an aggressive cancer that develops from the sequential accumulation and clonal expansion of somatic mutations in hematopoietic stem and progenitor cells. Recent next-generation sequencing (NGS) studies of AML have correlated mutations with clinical outcomes and response to targeted therapies. Additionally, emerging reports have suggested that increased clonal heterogeneity and mutation burden tend to correlate with worse survival outcomes. However, due to previous cohort sizes, the architecture of clonal evolution and variant allele frequency (VAF) of recurrent mutations have yet to be robustly correlated with response to therapy or with more granular risk stratification. To address previous limitations, we combined available datasets of sequenced AML to model features of clonality and determine their correlations with clinical outcomes and drug sensitivity. Methods: A systematic literature review was performed to identify cohorts of clinically annotated and genetically profiled adult AML. Studies were included if: (i) their sequencing panel targeted at least 30 of the most commonly mutated genes, (ii) censored overall survival data was reported, and (iii) data were publicly available. An additional cohort of patients profiled at Stanford was also included. Leveraging statistical learning methods and robust clonal modeling algorithms (PyClone and ClonEvol), we performed a meta-analysis of the clonal architecture of mutations, their temporal relationships, sensitivity to drugs, and correlation with outcomes in AML. Results: A total of 12 studies were aggregated into a uniformly annotated database comprising 2,987 AML patient samples profiled with an array of DNA sequencing modalities (2,884 with VAFs) and ex vivo drug screening results (nsamples = 562; ndrugs = 122); survival outcomes were available for 2,606 patients. To investigate broad features of leukemia evolution, we used clonal modeling algorithms to infer clonal architecture. Interestingly, patients exhibiting linear evolution (sequential mutations in the same clone) displayed worse outcomes compared to those with branched architecture (distinct subclonal populations). Additionally, mutational burden and clonal heterogeneity only stratified patients with branched structure. These results motivated us to understand how the temporal acquisition of mutations might further stratify outcomes. Using dynamic VAF thresholds, we identified novel high-risk patient populations for 15 recurrently mutated genes. Greater VAF was associated with statistically significant improved survival in genotypes such as GATA2mut and WT1mut and with worse outcomes for patients with NRAS and NF1 mutations. Next, we leveraged VAFs to infer the temporal ordering of individual mutations and functional mutation categories. Patients where NRAS mutations occurred before GATA2 mutations showed a significant correlation with worse outcomes. We also observed that patients in which (i) DNA methylation mutations occurred before those in tumor suppressors and (ii) splicing factor mutations occurred before RTK/RAS signaling components showed significantly shortened overall survival. These results indicate that patients with the same genotype can be stratified by the timing of mutations in the clonal evolution of their leukemia. Finally, we used linear regression between drug sensitivity and VAF to identify several mutations which predict drug sensitivity exclusively in a VAF-dependent manner. Increased WT1 VAF correlated with sensitivity to ABT-737 and elevated FLT3-TKD VAF predicted sensitivity to cabozantinib, among other clinically notable drug-gene relationships. These results suggest potential biomarkers for clinical response to emerging targeted agents. Conclusions: We show that VAF can identify novel high-risk patient populations at the individual mutation level (e.g. BCOR and NF1) and can also be leveraged to stratify outcomes based on inferring the temporal ordering of mutations (e.g. NRAS and GATA2). Our observation that patients with leukemias exhibiting branched evolution showed improved survival compared to linear evolution was also striking and warrants further experimental and clinical validation. Incorporating these results with our findings of drug sensitivity validate the clinical utility of integrating clonal analysis into the molecular evaluation and treatment of AML. Disclosures Majeti: Zenshine Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Kodikaz Therapeutic Solutions Inc.: Membership on an entity's Board of Directors or advisory committees; Stanford University: Patents & Royalties: pending patent application on CD93 CAR ; Coherus BioSciences: Membership on an entity's Board of Directors or advisory committees; BeyondSpring Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Forty-Seven Inc.: Divested equity in a private or publicly-traded company in the past 24 months; Gilead Sciences, Inc.: Patents & Royalties: inventor on patents related to CD47 cancer immunotherapy; CircBio Inc.: Research Funding.

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TP53 Alterations Including Missense Mutations, Aberrant Exon-Junctions and Internal Intron Retentions Are Frequent and May Contribute to MDM2 Antagonist-Resistance in B-Acute Lymphoblastic leukemia

Blood ◽

10.1182/blood.v118.21.1484.1484 ◽

2011 ◽

Vol 118 (21) ◽

pp. 1484-1484

Author(s):

Ilaria Iacobucci ◽

Anna Ferrari ◽

Stefania Trino ◽

Annalisa Lonetti ◽

Cristina Papayannidis ◽

...

Keyword(s):

Dna Binding ◽

Board Of Directors ◽

Lymphoblastic Leukemia ◽

Binding Domain ◽

Dna Binding Domain ◽

Missense Mutations ◽

Advisory Committees ◽

Tp53 Mutations ◽

Mdm2 Antagonist ◽

Exon Junctions

Abstract Abstract 1484 MDM2, a p53-inducible phosphoprotein, binds to the N-terminus of the p53 and negatively regulates its transcriptional activity. New MDM2 antagonists, such as RO5045337 (Roche) and NSC-66811 (Merck), are now available for Phase I/II clinical development, but their activity is dependent on TP53 mutation status. Therefore, in order to efficiently treat B-progenitor acute lymphoblastic leukemia (ALL) patients with an MDM2 antagonist, we set up a sensitive assay to identify TP53 lesions. Deletions and uniparental disomy (UPD) involving TP53 were assessed on 146 DNA samples from Philadelphia-positive (Ph+)(n = 126) and Ph-negative (n = 20) ALL patients by Genome-Wide Human SNP 6.0 array (Affymetrix). No 17p UPD events were detected whereas losses were identified in 2% of cases. Mutations of TP53 were thereafter investigated in 67 samples including 60 Ph+ and 7 Ph-negative cases. Since the majority of the studies in leukemia were focused on genomic alterations and resulted in low rate of TP53 mutations, we aimed to identify RNA mutations and aberrant isoforms due to other mechanisms, such as RNA editing. To this purpose three overlapping shorter amplicons covering the entire coding cDNA sequence (GenBank accession number NM_000546.4) and the untranslated exon 1 [amplicon 1 (491 bp): exons 1–5; amplicon 2 (482 bp): exons 5–8; amplicon 3 (498 bp): exons 8–11)] and a longer amplicon (1,317 bp) starting from exon 1 and ending to exon 11 were sequenced by Sanger method. TP53 mutations were detected in only 6 cases (8.9%), suggesting that these alterations are apparently rare events in B-ALL. They included 4 missense point mutations in the DNA binding domain and in the carboxyl-terminal tetramerization and regulatory domain: C135Y (ex 5), A234T (ex 7), R290C (ex 8) and A347T (ex 10). Interestingly, in two cases we identified aberrant transcripts: 1) a TP53 isoform characterized by retention of introns 5–6–7 and predicted to encode for a truncated protein due a premature stop codon; 2) a TP53 isoform in which the DNA binding domain is lost due to an exon conjunction between the exon 4 and the 3' untraslated region (UTR)(ex4-3'UTR: 7579533–7572842, according to GRCh37/hg19). Next, in order to investigate if low rate of mutations were detectable, we also analyzed our whole transcriptome data obtained using next generation sequencing technology (Illumina/Solexa Genome Analyzer) on 3 Ph+ ALL patients. Curiously, all patients harbored clones ranging from 45% to 94% with TP53 mutations in the DNA binding and tetramerization domains: C182W (ex 5), T231A (ex 7), L330R (ex 9) in the first patient and Stop394S, D393V/H and G389Y/V (ex 11) in the second one. Moreover, in the first and third patient we detected 10 and 13 base exchanges, respectively, located in intron 6 within 7578166–7578142 region, suggesting a retention of this intron in the primary transcript and the dysfunction of the DNA-binding domain. The mechanism of intron retention (with or without mutations) was particularly intrigued since it could be a new mechanism of functional inactivation of TP53. To address this hypothesis we performed amplification of TP53 cDNA followed by single cell cloning and subsequent direct sequencing in 4 patients previously resulted wild-type by Sanger sequencing for TP53. By this approach, all patients showed cDNA alterations. In one case we identified the missense mutation S90P (ex 4) and an aberrant isoform lacking the DNA binding domain and caused by an exon-junction between exons 2 and 7 (ex2-7: 7579866–7577510). In a second patient the P190S (ex 6) and N235S (ex 7) missense mutations were detected. Moreover, an aberrant isoform lacking the DNA binding domain and characterized by an exon-junction between the first part of exon 4 and the last part of exon 7 (ex4-7: 7579581–7577532) was also identified. In the third patient the E285G (ex 8) was found associated with a 3'-UTR base exchange, which was also detected in the remaining fourth patient. In conclusion, we demonstrate for the first time that TP53 alterations at the RNA level, including missense mutations, aberrant exon junctions and internal intron retentions are highly frequent in B-ALL patients and that testing for TP53 mutations with sensitive assay based on RNA analysis is absolutely required. Supported by European LeukemiaNet, AIL, AIRC, Fondazione Del Monte di Bologna e Ravenna, FIRB 2006, PRIN 2009, Ateneo RFO grants, PIO program, Programma di Ricerca Regione – Università 2007 – 2009. Disclosures: Soverini: Novartis: Consultancy; ARIAD: Consultancy; Bristol-Myers Squibb: Consultancy. Baccarani:Pfizer Oncology: Consultancy; Novartis: Consultancy; BMS: Consultancy; Ariad: Consultancy; Novartis: Research Funding; Pfizer Oncology: Honoraria; Novartis: Honoraria; BMS: Honoraria; Ariad: Honoraria; Novartis: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees; Ariad: Membership on an entity's Board of Directors or advisory committees. Martinelli:Novartis: Consultancy, Honoraria; BMS: Consultancy, Honoraria; Pfizer: Consultancy.

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Transition of Chronic Myeloid Leukemia to Chronic Myelomonocytic Leukemia As a Tool to Observe Development of Chronic Myelomonocytic Leukemia

Blood ◽

10.1182/blood.v126.23.5223.5223 ◽

2015 ◽

Vol 126 (23) ◽

pp. 5223-5223

Author(s):

Jamshid S Khorashad ◽

Srinivas K Tantravahi ◽

Dongqing Yan ◽

Anna M. Eiring ◽

Hannah M. Redwine ◽

...

Keyword(s):

Board Of Directors ◽

Myeloid Leukemia ◽

Research Funding ◽

Clonal Evolution ◽

Chronic Myelomonocytic Leukemia ◽

Imatinib Treatment ◽

Advisory Committees ◽

Clonal Architecture ◽

Myelomonocytic Leukemia

Abstract Introduction. Development of abnormal Philadelphia (Ph) negative clones following treatment of chronic myeloid leukemia (CML) patients with imatinib has been observed in 3 to 9% of patients. Here we report on a 77 year old male diagnosed with CML that responded to imatinib treatment and subsequently developed chronic myelomonocytic leukemia (CMML). He achieved major cytogenetic response within 3 months but this response coincided with the emergence of monocytosis diagnosed as CMML. Five months after starting imatinib treatment the patient succumbed to CMML. We analyzed five sequential samples to determine whether a chronological order of mutations defined the emergence of CMML and to characterize the clonal evolution of the CMML population. Materials and Method. Five samples (diagnostic and four follow up samples) were available for analysis. CMML mutations were identified by whole exome sequencing (WES) in CD14+ cells following the onset of CMML, using CD3+ cells as constitutional control. Mutations were validated by Sequenom MassARRAY and Sanger sequencing and quantified by pyrosequencing. Deep WES was performed on the diagnostic sample to determine whether the mutations were present at CML diagnosis. To determine the clonal architecture of the emerging CMML, colony formation assays were performed on the diagnostic and the next two follow-up samples (Samples 1-3). More than 100 colonies per sample were plucked for DNA and RNA isolation. The DNA from these colonies were tested for the presence of the confirmed CMML mutations and the RNA was used for detection of BCR-ABL1 transcript using a Taqman real time assay. Results. Four mutations were identified by Sequenom and WES throughout the patient's time course [KRASG12R, MSLNP462H, NTRK3V443I and EZH2I669M ]. Sequenom did not identify these at diagnosis while deep WES did. Clones derived from colony formation assay revealed three distinct clones present in all samples analysed. Clone 1 had only KRASG12R, clone 2 had KRASG12R, MSLNP462H, and NTRK3V443I, and clone 3 had all four mutations. All clones containing any of these four mutations were BCR/ABL1 negative. Analysis of clonal architecture indicated that KRASG12R was acquired first and EZH2I669M last, while MSLNP462H and NTRK3V443I were acquired in between. These CMML clones increased proportionately as clinical CML metamorphosed into clinical CMML after initiation of imatinib therapy. Consistent with the colony data, pyrosequencing revealed that the ratio between the mutants remained largely stable throughout the follow up period. Conclusion. This case illustrates how targeted therapy impacts clonal competition in a heterogeneous MPN. While the CML clone was dominant in the absence of imatinib, it was quickly outcompeted by the CMML clones upon initiation of imatinib therapy. The clonal architecture analysis, in combination with in vivo kinetics data, suggest that the KRASG12R mutation alone was able to produce a CMML phenotype as clones with just KRASG12R remained at a relatively stable ratio during follow up. Unexpectedly, acquisition of additional mutations, including EZH2I669M as the last mutational event identified in this patient, did not increase clonal competitiveness, at least in the peripheral blood. These data show that clonal evolution may not invariably increase clonal fitness, suggesting that factors other than Darwinian pressures contribute to clonal diversity in myeloproliferative neoplasms. Disclosures Deininger: Gilead: Research Funding; Bristol-Myers Squibb: 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; Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees; Incyte: Consultancy, Membership on an entity's Board of Directors or advisory committees; Ariad: Consultancy, Membership on an entity's Board of Directors or advisory committees.

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Clonal Evolution of Multiple Myeloma in Patients from Diagnosis to First Relapse, Who Were Treated in Subsequent Clinical Trials

Blood ◽

10.1182/blood-2019-130086 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 1798-1798

Author(s):

Mark van Duin ◽

Annemiek Broijl ◽

Jasper Koenders ◽

Sonja Zweegman ◽

Monique C. Minnema ◽

...

Keyword(s):

Board Of Directors ◽

Survival Data ◽

Research Funding ◽

Complete Response ◽

Allelic Frequency ◽

Braf Mutations ◽

Advisory Committees ◽

Kras Mutations ◽

Clone Size ◽

Paired Samples

Background Treatment of Multiple Myeloma (MM) has reached a point at which cure for a subset of patients becomes feasible. Still, resistance to therapy is a major challenge in the management of MM patients. Underlying resistance are the emergence of subclones, different to those found at diagnosis. Assessing the mutation status of recurrently mutated genes in MM can assist in tracking those subclones. In this study, we aimed to estimate the clonal composition by performing next generation sequencing in a set of samples from newly diagnosed patients included in a transplant-eligible trial (EMN02, Cavo et al., Blood 2017 130:397), and repeating this analysis in paired samples obtained at relapse when these patients were treated with Carfilzomib/ Pomalidomide/ Dexamethasone in the EMN11 trial (Sonneveld et al., Blood 2018 132:801). Materials and methods Panel-Seq was performed for a subset of most frequently recurring genes in MM (NRAS, KRAS, BRAF, DIS3, FAM46C and TP53). For 21 patients, DNA from bone marrow derived MM cells was available at diagnosis (EMN02/HOVON-95) and at relapse (EMN11/HOVON-114). For an additional 24 patients material at relapse was available (EMN11); survival data were available of 38/45 EMN11 cases. Endpoints were response, progression-free survival (PFS) and overall survival (OS). Response categories were stringent complete response (sCR), complete response (CR), very good partial response (VGPR), partial response (PR) and stable disease (SD). All samples had a sample purity > 53% (median 98% (53-100%)). Results Using an allelic fraction of more than 1%, NRAS mutations were found in 48% of diagnostic samples, and in 43% of relapse samples (Figure 1). Overall, KRAS mutations were less frequent at relapse compared to diagnosis (24% vs 43% at diagnosis). In contrast, mutations in TP53 were found more frequently at relapse compared to diagnosis (in 2 patients at relapse (10%), compared to none at diagnosis). BRAF mutations were found in 4 patients at diagnosis and 2 at relapse (19% vs 10%). An allelic fraction of 40% or higher may be used to indicate clonality, i.e. all cells in the tumor are affected. For NRAS, this was observed at diagnosis and at relapse, in 5/10 and 5/9, and for KRAS, in 4/9 and 3/6, respectively. In 9 out of 21 patients with paired samples identical NRAS mutations were detected at both time points. In 4 of these cases the estimated clone size of the NRAS mutation had increased at the time of relapse, while in 5 cases the clone remained similar in size. Four out of 6 cases with a stable clone size or diminishing NRAS clone had achieved sCR/CR with first-line treatment whereas all cases with increasing NRAS clone size were VGPR or worse (p=0.08). Interestingly, out of 19 cases with known survival data in the EMN11 trial, 2 out of 3 cases with an increase of 40% or more in NRAS clone size demonstrated an OS of less than 6 months, compared to only 1 out of 16 remaining cases. Four cases demonstrated both NRAS and KRAS mutations at diagnosis. In three of these cases, the KRAS mutation was not detected at relapse. In total, 5 pairs showed KRAS mutations at diagnosis and relapse. BRAF mutations were found in 4 cases at diagnosis; in two of these, both V600E, the mutation was also detected at relapse. None of the clonal shifts in genes other than NRAS demonstrated an association with PFS, OS or response. Of the 45 patients analysed at entry in the EMN11 trial with an variant allelic frequency of 1% or higher, KRAS mutations were found in 36% of cases, followed by NRAS (29%), FAM46C (16%), BRAF (11%), TP53 (7%) and DIS3 (4%). Clonal NRAS mutations at baseline EMN11 cases were associated with worse OS but not PFS (median OS of clonal NRAS patients: 5 months compared to not reached for remaining patients; log rank p<0.05). Conclusion Although limited in patient size and number of genes studied, this unique cohort of homogeneously treated patients through 1st ánd 2nd line treatment allowed clinical analysis of mutations detected with high sensitivity to a variant allelic frequency of 1%. Sequential sequencing analysis has limited predictive value for 2nd line response, PFS and OS. Only an increase in NRAS clone size may be associated with worse survival, which requires validation in different datasets. In RRMM, clonal NRAS mutations may represent an additional risk factor. Disclosures Broijl: Takeda: Honoraria; Amgen: Honoraria; Janssen: Honoraria; Celgene: Honoraria. Zweegman:Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Takeda: Membership on an entity's Board of Directors or advisory committees, Research Funding; Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding. Minnema:Celgene Corporation: Honoraria, Research Funding; Amgen: Honoraria; Servier: Honoraria; Gilead: Honoraria; Jansen Cilag: Honoraria. Boccadoro:Celgene: Honoraria, Research Funding; Amgen: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; Novartis: Honoraria, Research Funding; Bristol-Myers Squibb: Honoraria, Research Funding; AbbVie: Honoraria; Mundipharma: Research Funding; Sanofi: Honoraria, Research Funding. Sonneveld:Amgen: Honoraria, Research Funding; BMS: Honoraria; Celgene: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; Karyopharm: Honoraria, Research Funding; Takeda: Honoraria, Research Funding; SkylineDx: Research Funding.

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