Clonal Dynamics of Refractory Aplastic Anemia in Patients Treated with Eltrombopag

Abstract Despite documented success of immunosuppressive therapy (IST) in the treatment of AA, a minority of patients remain refractory, most responses are incomplete, and use of hematopoietic cell transplantation (HCT) is limited in older patients or those with significant comorbidities. While the introduction of the cMpl agonist eltrombopag (EPG) as salvage therapy or in conjunction with IST has revolutionized treatment for refractory AA. It may be effective in improving primary response rates to IST, engaging growth factor receptors with agonistic therapeutics (such as EPG) and also has the potential to promote evolution/expansion of mutant clones, thereby increasing the rate of progression to secondary myelodysplastic syndromes (MDS), a serious complication of AA occurring in 10-20% of patients. Clonogenic somatic mutations typical of MDS in patients with AA and PNH may increase the risk of progression to MDS. DNA from marrow samples of primary refractory AA patients was subjected to analysis before and after initiation of EPG to evaluate clonal expansion or evolution using a targeted multi-amplicon deep NGS panel of all ORFs of the top 60 most commonly mutated genes in MDS. In addition to the EPG treatment group, a case control cohort matched for age and duration from AA diagnosis to last clinical follow up (who did not receive EPG), was studied. Among 210 AA patients treated at Cleveland Clinic, we identified 26 who were treated with EPG for IST-refractory AA; median duration of treatment was 56 wks. The overall response rate after 12 weeks of therapy was 58% (15/26), while 31% of patients (8/26) showed stable disease with intermittent transfusions (one of whom underwent HCT). In 3 non-responders, one developed PNH, one had refractory AA/PNH, and one progressed to AML (see below). Expansion of PNH granulocytes after EPG treatment was observed in 23% of patients (6/26). In addition, 15% (4/26) had atypical subclonal chromosomal abnormalities. Prior to EPG, at least a single somatic event was found in 31% of patients (8/26), with 2 patients harboring 2 mutations. Events included CEBPA, EZH2, BCOR/BCORL1, ASXL1, U2AF1/2, TET2, and DNMT3A mutations. Following EPG therapy, acquisition of new somatic mutations was observed in 23% of cases, including RUNX1, U2AF1, BCOR, RIT1, and CEBPA. In cases with pre-existing clones, 6 clones expanded (e.g., BCOR or ASXL1 from VAF of 8 to 21% and 9 to 29%, respectively) despite clinical hematologic response, while in 2 cases clones disappeared (e.g., U2AF2 and BCORL1). In 54% of cases (14/26), we found detectable levels of a PNH clone at the time of diagnosis. Six of those cases had PNH clonal expansion post-EPG treatment, of which two developed clinically significant PNH clonal burden requiring eculizumab therapy. In the case-control cohort, 26 AA patients who received IST but were not treated with EPG, were followed for comparable time periods, and no evidence of progression to MDS was recorded. One patient was noted to have trisomy 15 on cytogenetics at diagnosis. "MDS type" molecular mutations were present in 10 patients similar to EPG cohort. Among these patients, 3 had persistent clones of U2AF1, DNMT3A, and STAT3 over one year without acquisition of any new molecular mutations. . PNH granulocytes expanded in 50% of AA cases, decreased in 30% and stayed stable in 20%. Thus, we did not observe any difference in expansion of PNH clones between those treated and untreated with EPG (p=0.73). Unlike for PNH clones, accounting for both new evolution and expansion of preexisting molecular mutations, the frequency of these clonal events was significantly higher in the EPG treated group (p=0.009). In conclusion, we observed occasional expansion of clones with potentially leukemogenic mutations during treatment with EPG in pts with AA. While higher rates of MDS evolution were not observed in this cohort of EPG treated patients, we found that serial evaluation of somatic mutations can inform clonal evolution and can potentially be used as abiomarker for evaluation of risk for post-AA MDS. Continued use of EPG in such patients should be judicious. Disclosures Carraway: Celgene: Research Funding, Speakers Bureau; Baxalta: Speakers Bureau; Incyte: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees; Novartis: Membership on an entity's Board of Directors or advisory committees. Sekeres:Millenium/Takeda: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees.

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Impact of Eltrombopag on Expansion of Clones with Somatic Mutations in Refractory Aplastic Anemia

Blood ◽

10.1182/blood.v126.23.300.300 ◽

2015 ◽

Vol 126 (23) ◽

pp. 300-300 ◽

Cited By ~ 1

Author(s):

Bhumika J. Patel ◽

Bartlomiej Przychodzen ◽

Michael J. Clemente ◽

Cassandra M. Hirsch ◽

Tomas Radivoyevitch ◽

...

Keyword(s):

Aplastic Anemia ◽

Board Of Directors ◽

Deep Sequencing ◽

Somatic Mutations ◽

Clonal Evolution ◽

Clonal Expansion ◽

Quantitative Detection ◽

Sequencing Analysis ◽

Advisory Committees ◽

Before And After

Abstract Despite documented success of immunosuppressive therapy (IST) in the treatment of aplastic anemia (AA), a significant minority of patients remain refractory, most responses are incomplete, and allogeneic stem cell transplantation is not available for older patients or those with significant comorbidities. Until introduction of the cMpl agonist eltrombopag, anabolic steroids were the most commonly used salvage drugs. At least theoretically, engaging growth factor receptors with eltrombopag has the potential to promote the evolution or expansion of mutant clones and thereby increase the rate of progression to secondary MDS, a feared complication of AA occurring in 10-20% of patients. Recently we and others reported detection of clonogenic somatic mutations typical of MDS in patients with AA and PNH. Subsequent study demonstrated that mutations characteristic of sMDS can be found in some patients at presentation of AA and may constitute risk for subsequent progression to MDS. As the risk of MDS evolution was a prominent concern when filgrastim was more widely used in management of AA, now similar questions have been raised regarding use of eltrombopag, be it as salvage therapy or to complement IST. Recently, one of our primary refractory patients receiving eltrombopag progressed to AML. This clinical observation led to investigation of the impact of eltrombopag on evolution and clonal expansion using deep sequencing of a cohort of patients with AA. DNA from bone marrow cells was sequenced before and after initiation of eltrombopag to evaluate clonal expansion or evolution using a targeted multi-amplicon deep sequencing panel of the top 60 most commonly mutated genes in MDS. Among 208 AA patients treated at Cleveland Clinic, we identified 13 patients (median age 68 yrs.) who were treated with eltrombopag for IST-refractory AA; median duration of treatment was 85 wks. The overall response rate, defined as sustained improvement in blood counts and transfusion independence after 12 weeks of therapy, was 46% (6/13), while 38% (5/13) of patients showed stable disease with intermittent transfusions (one of whom underwent HSCT). Among the two non-responders, one patient developed a PNH clone and another progressed to AML (see below). Expansion of PNH granulocytes after eltrombopag treatment was observed in 2 patients. Two patients had chromosomal abnormalities at initial diagnosis, one with t (10; 18) in 2 metaphases, and one with an extranumeral Y chromosome. Use of next generation sequencing (NGS) allows for the quantitative detection of clonal events. We hypothesized that serial analysis by NGS before and after eltrombopag therapy may provide clues as to potential effects of this drug on clonal evolution. Sequencing analysis before eltrombopag treatment revealed the presence of a sole clonal mutational event in 3/13 cases, including CEBPA, EZH2, and BCOR. In the patient with a CEBPA mutation, the mutation persisted during treatment with minimal clonal expansion evidenced by a change in VAF from 53% to 65%. In the second patient, NGS results revealed the initial presence of an EZH2 mutation. A post eltrombopag sample clearly identified acquisition of additional clonal events in genes highly associated with advanced disease and clonal evolution (RUNX1 and U2AF1), as well as slight expansion of a persistent EZH2 clone from 2 to 8%. The third patient harbored a BCOR mutation which expanded markedly, increasing from 8% to 21%, and was accompanied by a hematological response. Sequencing results after eltrombopag treatment revealed the acquisition of new somatic mutations in 5/13 (38%) cases: 2 new CEBPA mutations, 1 new BCOR mutation, and, as discussed, one case with an initial EZH2 mutation in which RUNX1 and U2AF1 mutations were later discovered. In the 5th patient, evolution to AML was observed and accompanied by a large DNMT3A and U2AF1 clone that was absent on initial evaluation. In conclusion, we did observe occasional expansion of clones with potentially leukemogenic mutations during treatment with eltrombopag. At our institution a case control study of patients with refractory aplastic anemia without treatment with eltrombopag is ongoing; ideally a prospective trial would be needed to confirm results. Our results suggest that the initial detection of certain somatic mutations (CBL, SETBP1 and RUNX1) associated with post-AA MDS may contraindicate use of eltrombopag in AA. Disclosures Sekeres: Celgene Corporation: Membership on an entity's Board of Directors or advisory committees; Amgen: 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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Association of MHC Class I Chain-Related Gene a (MICA) Polymorphisms with Allogeneic Hematopoietic Cell Transplantation Outcomes in Acute Myeloid Leukemia

Blood ◽

10.1182/blood-2018-99-112745 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 2075-2075

Author(s):

Sagar S. Patel ◽

Betty K. Hamilton ◽

Lisa Rybicki ◽

Dawn Thomas ◽

Arden Emrick ◽

...

Keyword(s):

Board Of Directors ◽

Binding Affinity ◽

Myeloid Leukemia ◽

Research Funding ◽

Somatic Mutations ◽

Hematopoietic Cell Transplantation ◽

Advisory Committees ◽

Post Transplant ◽

Transplant Outcomes ◽

Nkg2d Receptor

Abstract Background MHC class I chain-related gene A (MICA) is a polymorphic ligand of the natural killer (NKG2D) receptor on immune effector cells. The activating NKG2D receptor controls immune responses by regulating NK cells, NKT cells and γδ-T cells. Dimorphisms at sequence position 129 of the MICA gene confers varying levels of binding affinity to NKG2D receptor. MICA previously has been associated with post-allogeneic hematopoietic cell transplantation (alloHCT) outcomes including graft-versus-host-disease (GvHD), infection, and relapse. However, it is unclear how MICA interacts with cytogenetic and somatic mutations in regards to these outcomes in acute myeloid leukemia (AML). Methods We conducted a single center, retrospective analysis of adult AML patients in first or second complete remission (CR1, CR2), who underwent T-cell replete matched related or unrelated donor alloHCT. Analysis was limited to those who had MICA data available for donors and recipients. In addition to cytogenetic risk group stratification by European LeukemiaNet criteria (Döhner H, et al, Blood 2016), a subset of patients had a 36-gene somatic mutation panel assessed prior to alloHCT by next-generation sequencing. Dimorphisms at the MICA-129 position have previously been categorized as weaker (valine/valine: V/V), heterozygous (methionine/valine: M/V), or stronger (methionine/methionine: M/M) receptor binding affinity. Fine and Gray or Cox regression was used to identify the association of MICA and outcomes with results as hazard ratios (HR) and 95% confidence intervals (CI). Results From 2000 - 2017, 131 AML patients were identified meeting inclusion criteria. Median age at transplant was 54 years (18-74), with 98% Caucasian. Disease status at transplant included 78% CR1 and 22% CR2. Cytogenetic risk stratification showed 13% of patients as favorable, 56% as intermediate, and 31% as adverse-risk. The five most common somatic mutations were FLT3 (15%), NPM1 (14%), DNMT3A (11%), TET2 (7%), and NRAS (6%). 60% of patients had a related donor. A myeloablative transplant was performed in 84% of patients and 53% had a bone marrow graft source. The most common conditioning regimen used was busulfan/cyclophosphamide (52%). 12% of patients were MICA mismatched with their donor. The distribution of donor MICA-129 polymorphisms were 41% V/V, 53% M/V, and 6% M/M. In univariable analysis, donor-recipient MICA mismatch tended to be associated with a lower risk of infection (HR 0.49, CI 0.23-1.02, P=0.06) and grade 2-4 acute GvHD (HR 0.25, CI 0.06-1.04, P=0.06) but was not associated with other post-transplant outcomes. In multivariable analysis, donor MICA-129 V/V was associated with a higher risk of non-relapse mortality (NRM) (HR 2.02, CI 1.01-4.05, P=0.047) (Figure 1) along with increasing patient age at transplant (HR 1.46, CI 1.10-1.93, p=0.008) and the presence of a TET2 mutation (HR 6.00, CI 1.77-20.3, P=0.004). There were no differences between the V/V and the M/V+M/M cohorts regarding somatic mutational status, cytogenetics and other pre-transplant characteristics and post-transplant outcomes. With a median follow-up of 65 months for both cohorts, 45% vs. 49% of patients remain alive, respectively. The most common causes of death between the V/V and the M/V+M/M cohorts was relapse (38% vs. 62%) and infection (31% vs. 8%), respectively. Conclusion While previous studies have demonstrated associations of somatic mutations and cytogenetics with survival outcomes after alloHCT for AML, we observed mutations in TET2 and the V/V donor MICA-129 polymorphism to be independently prognostic for NRM. Mechanistic studies may be considered to assess for possible interactions of TET2 mutations with NK cell alloreactivity. The weaker binding affinity to the NKG2D receptor by the V/V phenotype may diminish immune responses against pathogens that subsequently contribute to higher NRM. These observations may have implications for enhancing patient risk stratification prior to transplant and optimizing donor selection. Future investigation with larger cohorts interrogating pre-transplant AML somatic mutations with MICA polymorphisms on post-transplant outcomes may further elucidate which subsets of patients may benefit most from transplant. Disclosures Nazha: MEI: Consultancy. Mukherjee:Pfizer: Honoraria; Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Projects in Knowledge: Honoraria; BioPharm Communications: Consultancy; Bristol Myers Squib: Honoraria, Speakers Bureau; Takeda Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees; LEK Consulting: Consultancy, Honoraria; Aplastic Anemia & MDS International Foundation in Joint Partnership with Cleveland Clinic Taussig Cancer Institute: Honoraria. Advani:Amgen: Research Funding; Pfizer: Honoraria, Research Funding; Glycomimetics: Consultancy; Novartis: Consultancy. Carraway:Novartis: Speakers Bureau; Balaxa: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Jazz: Speakers Bureau; FibroGen: Consultancy; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Amgen: Membership on an entity's Board of Directors or advisory committees; Agios: Consultancy, Speakers Bureau. Gerds:Apexx Oncology: Consultancy; Celgene: Consultancy; Incyte: Consultancy; CTI Biopharma: Consultancy. Sekeres:Celgene: Membership on an entity's Board of Directors or advisory committees; Opsona: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Opsona: Membership on an entity's Board of Directors or advisory committees. Maciejewski:Apellis Pharmaceuticals: Consultancy; Ra Pharmaceuticals, Inc: Consultancy; Alexion Pharmaceuticals, Inc.: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Ra Pharmaceuticals, Inc: Consultancy; Alexion Pharmaceuticals, Inc.: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Apellis Pharmaceuticals: Consultancy. Majhail:Incyte: Honoraria; Anthem, Inc.: Consultancy; Atara: Honoraria.

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Patterns of Clonal Evolution Assessed By Whole Exome Sequencing during Progression from MDS to AML Are Related to Therapy

Blood ◽

10.1182/blood.v128.22.4309.4309 ◽

2016 ◽

Vol 128 (22) ◽

pp. 4309-4309

Author(s):

María Abáigar ◽

Jesús M Hernández-Sánchez ◽

David Tamborero ◽

Marta Martín-Izquierdo ◽

María Díez-Campelo ◽

...

Keyword(s):

Board Of Directors ◽

Research Funding ◽

Clonal Evolution ◽

Clonal Expansion ◽

Driver Mutations ◽

Advisory Committees ◽

Disease Evolution ◽

Mutational Burden ◽

Whole Exome ◽

Leukemic Phase

Abstract Introduction: Myelodysplastic syndromes (MDS) are hematological disorders at high risk of progression to acute myeloid leukemia (AML). Although, next-generation sequencing has increased our understanding of the pathogenesis of these disorders, the dynamics of these changes and clonal evolution during progression have just begun to be understood. This study aimed to identify the genetic abnormalities and study the clonal evolution during the progression from MDS to AML. Methods: A combination of whole exome (WES) and targeted-deep sequencing was performed on 40 serial samples (20 MDS/CMML patients evolving to AML) collected at two time-points: at diagnosis (disease presentation) and at AML transformation (disease evolution). Patients were divided in two different groups: those who received no disease modifying treatment before they transformed into AML (n=13), and those treated with lenalidomide (Lena, n=2) and azacytidine (AZA, n=5) and then progressed. Initially, WES was performed on the whole cohort at the MDS stage and at the leukemic phase (after AML progression). Driver mutations were identified, after variant calling by a standardized bioinformatics pipeline, by using the novel tool "Cancer Genome Interpreter" (https://www.cancergenomeinterpreter.org). Secondly, to validate WES results, 30 paired samples of the initial cohort were analyzed with a custom capture enrichment panel of 117 genes, previously related to myeloid neoplasms. Results: A total of 121 mutations in 70 different genes were identified at the AML stage, with mostly all of them (120 mutations) already present at the MDS stage. Only 5 mutations were only detected at the MDS phase and disappeared during progression (JAK2, KRAS, RUNX1, WT1, PARN). These results suggested that the majority of the molecular lesions occurring in MDS were already present at initial presentation of the disease, at clonal or subclonal levels, and were retained during AML evolution. To study the dynamics of these mutations during the evolution from MDS/CMML to AML, we compared the variant allele frequencies (VAFs) detected at the AML stage to that at the MDS stage in each patient. We identified different dynamics: mutations that were initially present but increased (clonal expansion; STAG2) or decreased (clonal reduction; TP53) during clinical course; mutations that were newly acquired (BCOR) or disappearing (JAK2, KRAS) over time; and mutations that remained stable (SRSF2, SF3B1) during the evolution of the disease. It should be noted that mutational burden of STAG2 were found frequently increased (3/4 patients), with clonal sizes increasing more than three times at the AML transformation (26>80%, 12>93%, 23>86%). Similarly, in 4/8 patients with TET2 mutations, their VAFs were double increased (22>42%, 15>61%, 50>96%, 17>100%), in 2/8 were decreased (60>37%, 51>31%), while in the remaining 2 stayed stable (53>48%, 47>48%) at the AML stage. On the other hand, mutations in SRSF2 (n=3/4), IDH2 (n=2/3), ASXL1 (n=2/3), and SF3B1 (n=3/3) showed no changes during progression to AML. This could be explained somehow because, in leukemic phase, disappearing clones could be suppressed by the clonal expansion of other clones with other mutations. Furthermore we analyzed clonal dynamics in patients who received treatment with Lena or AZA and after that evolved to AML, and compared to non-treated patients. We observed that disappearing clones, initially present at diagnosis, were more frequent in the "evolved after AZA" group vs. non-treated (80% vs. 38%). By contrast, increasing mutations were similar between "evolved after AZA" and non-treated patients (60% vs. 61%). These mutations involved KRAS, DNMT1, SMC3, TP53 and TET2among others. Therefore AZA treatment could remove some mutated clones. However, eventual transformation to AML would occur through persistent clones that acquire a growth advantage and expand during the course of the disease. By contrast, lenalidomide did not reduce the mutational burden in the two patients studied. Conclusions: Our study showed that the progression to AML could be explained by different mutational processes, as well as by the occurrence of unique and complex changes in the clonal architecture of the disease during the evolution. Mutations in STAG2, a gene of the cohesin complex, could play an important role in the progression of the disease. [FP7/2007-2013] nº306242-NGS-PTL; BIO/SA52/14; FEHH 2015-16 (MA) Disclosures Del Cañizo: Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Jansen-Cilag: Membership on an entity's Board of Directors or advisory committees, Research Funding; Arry: Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Membership on an entity's Board of Directors or advisory committees, Research Funding.

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Molecular Characterization of Leukemia Evolving from Paroxysmal Nocturnal Hemoglobinuria

Blood ◽

10.1182/blood-2019-131918 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 2499-2499

Author(s):

Hassan Awada ◽

Shafia Rahman ◽

Cassandra M Kerr ◽

Jibran Durrani ◽

Vera Adema ◽

...

Keyword(s):

Board Of Directors ◽

Incidence Rate ◽

Molecular Characterization ◽

Clonal Evolution ◽

Cleveland Clinic ◽

Clinical Manifestations ◽

Monogenic Disease ◽

Advisory Committees ◽

Myeloid Malignancies ◽

Pnh Clone

Myeloid malignancies can evolve from prior hematologic disorders, most commonly AML evolving from MDS. AA and PNH are not malignant conditions but they can evolve to myeloid malignancies with a lower frequency compared to MDS and other myeloid and myeloproliferative diseases. PNH can evolve to myeloid disorders with an incidence rate of 4-10%. Here we aim to revisit the subject of malignant evolution of PNH to myeloid disorders by analyzing the molecular background of PNH using modern NGS technologies. Clinical characteristics, demographics and mutational profiles of patients were collected at The Cleveland Clinic Foundation. In total a cohort of 243 patients evaluated for hemolytic PNH (n=83), AA (39) and AA/PNH (n=121) followed for a period of 22 years was evaluated. Inclusion criteria were: complete flow cytometric panels of PNH cells, patients without antecedent AA (pPNH, 45), patients evolving from AA with PNH clone >20% (sPNH, 38), karyotype (at diagnosis of PNH and transformation), clinical parameters including time to malignant progression, and molecular characterization resulting from NGS performed using various library preparation systems (TruSeq, TruSight, Nextera), comparison of molecular mutations with control cohorts (AA, 160; MDS, 835). The incidence rate of myeloid disorders in our PNH cohort was 3% (7/243). Among hemolytic PNH patients, 7 patients progressed to AML (n=1), MDS (n=5) or myelofibrosis (n=1). Median age was 48 yr (range, 24-80); M/F, 5/2. Median PNH clone size was 71% (range, 29-99). Three progressors were in the pPNH and 4 in the sPNH group. Time to malignant diagnosis was <1-22 yr: 4 yr for 3 patients, 5 yr for 1 patient, <1 yr for 2 patients and 22 years for 1 patient. At the time of transformation, combination of karyotypic abnormalities and molecular lesions showed that 4 cases had abnormal karyotype (+8, -7, del13q) and 5 cases carried myeloid mutations (ASXL1, BCOR, NPM1, TET2, U2AF1, WT1). Normal karyotype was seen in 3 patients with ASXL1+U2AF1, U2AF1 and BCOR+NPM1+WT. In 2 patients, del13q and -7 were associated with BCOR and TET2. In 2 others, del(13q) and +8 were the only detected aberrancies. A total of 45 somatic mutations equally distributed in the 2 groups (pPNH, 22; sPNH, 23) and with similar VAFAVG (pPNH vs. sPNH 38% vs. 33%) were found. PNH showed a higher proportion of individuals with mutations compared to AA/PNH+AA (42 vs. 22% of cases with ≥1 mutation; P=.002) with a median VAF percentage significantly higher in PNH vs. AA/PNH+AA (40 vs. 19%; P<.0001). FLT3 (n=2), JAK2 (n=1), LUC7L2 (n=1), NPM1 (n=1), SRSF2 (n=1) and ZRSR2 (n=2) were exclusively mutated in PNH with the presence of some of them (FLT3, NPM1) possibly representing an early onset of clonal evolution. BCOR/BCORL1 core was more mutated in PNH as compared to AA/PNH+AA patients (11 vs. 3%; P=.01) as did TET2 and U2AF1. This pattern of mutations had a strong similarity with that of MDS. VAF comparison between myeloid mutations and PIGA mutations showed that accessory mutations in patients with PNH were secondary hits, with PIGA mutations being the founder lesions. We then analyzed the clonal hierarchy of mutations using VAF-adjusted for X-chromosomal loci in males and inferred mutational rank (founder/ co-dominant) vs. secondary (sub-clonal). PIGA mutations were founder lesions in 70% of the cases, co-dominant in 2% and secondary in 28% suggesting that additional mutations represented mainly cooperative events without over representing PIGA. In fact, comparison of VAF and PNH clonal size showed that 70% of the hits were present in the same clone (VAFSUM >55), 17% were equivocal (possibly hits biclonal with a VAFSUM between 45-55), while 13% were more likely a result of clonal chimerism (hits present in different clones; VAFSUM <45). Clonal evolution of hemolytic PNH to MDS/AML is rare, but still occurs and it is accompanied by mutations in typical myeloid genes (BCOR, NPM1, TET2, U2AF1) which in permissive circumstances are capable to change the cell's fate favoring clonal evolution. Our results suggest that most PNH cases can carry additional mutations in the same clone and these mutations can be secondary hits, with PIGA mutations being the founder lesions. However even when mutations in myeloid genes are dominant, the phenotype of the patients is inferred by PIGA. This observation supports the nature of PNH as a monogenic disease with clinical manifestations resulting by PIGA mutations rather than by myeloid genes. Disclosures Sekeres: Syros: Membership on an entity's Board of Directors or advisory committees; Millenium: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees. Maciejewski:Novartis: Consultancy; Alexion: Consultancy.

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Karyotypic and Genetic Abnormalities Associated with Clonal Evolution in Paroxysmal Nocturnal Hemoglobinuria.

Blood ◽

10.1182/blood.v120.21.2371.2371 ◽

2012 ◽

Vol 120 (21) ◽

pp. 2371-2371

Author(s):

Hideki Makishima ◽

Kenichi Yoshida ◽

Michael J. Clemente ◽

Masashi Sanada ◽

Yasunobu Nagata ◽

...

Keyword(s):

Stem Cell ◽

Research Funding ◽

Somatic Mutations ◽

Chromosomal Abnormalities ◽

Clonal Evolution ◽

Clonal Expansion ◽

Novel Mutations ◽

Jak2 Mutation ◽

Myeloid Malignancies ◽

Whole Exome

Abstract Abstract 2371 PNH is a clonal stem cell disease. While nonmalignant, PNH shows certain similarities to MDS and other neoplasms affecting hematopoietic stem and progenitor cells, including persistence of an aberrant clone, clonal expansion, and phenotypic abnormalities. In a small proportion of patients, subtle chromosomal abnormalities can be found and cases of otherwise classical PNH due to microdeletions involving the PIG-A locus have been described, illustrating similarities to other malignant conditions. PIG-A gene mutations lead to defective biosynthesis of GPI anchors and are responsible for the PNH phenotype. Similarly, phenotypic features of stem cells affected by PIG-A mutations are believed to be responsible for the extrinsic growth advantage and clonal expansion in the context of immune mediated suppression of hematopoiesis. While this scenario is plausible, there are also observations suggesting that intrinsic factors may be also involved. For instance, PNH persists after successful immunosuppression, often for many years, suggesting activation of stem cell maintenance genes. Furthermore, PNH clones can also be encountered (albeit at a very low frequency) in healthy individuals, and PNH can present in a pure form without aplastic anemia. Such extrinsic factors may include additional, secondary genetic events such as somatic mutations. Supporting this theory, clonal rearrangement of chromosome 12, which leads to overexpression of the transcription factor HMGA2 gene, were found in cells with the PIG-A mutation from 2 PNH cases. Also, we recently reported 3 PNH cases with JAK2 V617F mutation, who presented with a MPN phenotype and thrombosis. We theorized that study of clonal architecture in PNH will reveal clues as to the pathogenesis of clonal evolution of the PNH stem cell. We applied next generation whole exome sequencing to detect somatic mutations in PNH cases (N=6). The subsequent validation set included 45 PNH cases. PNH and non-PNH cells were sorted using magnetic beads. DNA from both fractions was analyzed by whole exome sequencing and results of the non-PNH cells were subtracted from the results of the PNH clone. We found biallelic PIG-A mutations in 2 female cases and a single mutation in each male case. In an index female case with thrombosis, a novel somatic heterozygous mutation of NTNG1 (P24S) was detected, while the patient was negative for the JAK2 mutation. Allelic frequency with the NTNG1 mutation (53/160 sequence reads (33%)) was larger than that with a concomitant heterozygous PIG-A mutation (intron 5 splice donor site G<A) (78/333 reads (23%)). In this case, the size of the other heterozygous PIG-A mutation (G68E) was less (31/194 (16%)) than the other PNH clone. These findings suggest that there are 2 different PNH clones in one case and that the NTNG1 mutation might be acquired before PIG-A gene was mutated. Moreover, NTNG1 encodes a GPI-anchored cell membrane protein and the mutation (P24S) was located in the predicted signal peptide. All together, 3 novel mutations were discovered, including MAGEC1 (C747Y) and BRPF1 (N797S) mutations. Of note, BRPF1 mutations have been also reported in AML. Interestingly, BRPF1 encodes a component of MOZ/MORF complex, positively regulating the transcription of RUNX1. To screen pathogenic karyotypic lesions in PNH clonal expansions, we combined metaphase cytogenetics and single nucleotide polymorphism arrays. We detected 14 somatic chromosomal abnormalities in 13 out of 26 PNH cases (50%). Of note is that a microdeletion on 2q13 resulted in the loss of an apoptosis-inducing gene BCL2L11, suggesting a contribution to growth advantage. Somatic UPD lesions strongly suggest the presence of homozygous mutations, for example the SET nuclear oncogene, which is located in UPD9q32qter was observed in another PNH case. Overall, the discovery of these novel mutations, as well the previously described JAK2 mutation, indicates that the pathophysiology of PNH clonal evolution partially overlaps that of other myeloid malignancies. In sum, various novel somatic karyotypic abnormalities and mutations are frequently detected in PNH clones using technology with comprehensive and high resolution. Some of these aberrations play a similar role in the clonal evolution of myeloid malignancies. These results suggest new therapeutic strategies similar to those for other myeloid malignancies should be considered in PNH cases with addition mutations. Disclosures: Makishima: Scott Hamilton CARES Initiative: Research Funding. Maciejewski:NIH: Research Funding; Aplastic Anemia&MDS International Foundation: Research Funding.

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Clonal Evolution in a Murine CALM-AF10 Leukemia: Evidence of Functional Heterogeneity of Leukemia Stem Cells

Blood ◽

10.1182/blood-2021-154068 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 1158-1158

Author(s):

Niloofar Zandvakili ◽

Hui Mei Lee ◽

Rhea Desai ◽

Alyona Oryshchuk ◽

Peter J. Browett ◽

...

Keyword(s):

Stem Cells ◽

Board Of Directors ◽

Somatic Mutations ◽

Clonal Evolution ◽

Advisory Committees ◽

Genetic Changes ◽

Expression Levels ◽

Long Latency ◽

Marker Expression ◽

Secondary Leukemias

Abstract Myeloid leukemia is caused by acquired genetic changes in haematopoietic stem cells. The combination of stepwise acquisition of genetic changes together with selection of the fittest clones results in great genetic and clonal heterogeneity. We used a CALM-AF10-driven retroviral transduction murine bone marrow transplantation leukemia model (MBMTLM) to study clonal hierarchy and clonal evolution starting with a primary leukaemia (Fig 1: Leu7) which developed after 131 days and had B220 marker expression on 4% of its cells. Limiting dilution assays (LDAs) showed that the leukemia stem cell (LSC) frequency of Leu7 was 1:2339 (95% confidence interval: 1:794-1:6885). Whole exome sequencing (WES) and analysis of the variant allele fraction of somatic mutations revealed that Leu7 was composed of a main clone (Fig 1: grey) with two subclones (blue and red). Half a million leukemic cells from Leu7 were transplanted into 4 sublethally irradiated recipients, which all developed secondary leukemias after a latency of 19 days (Leu7Sec1 to 4). All secondary leukemias showed similar B220 expression levels to Leu7, and all showed an expansion of the blue subclone. When again half a million cells each of one of the secondary leukemias (Leu7Sec2) were transplanted into 4 recipients, the expansion of the blue subclone continued, the red subclone vanished and, surprisingly, the proportion of B220 expressing cells increased to between 16 to 26%. LDAs showed that the LSC frequency of Leu7Sec2 had not changed. However, several of the leukemias from the LDAs had greatly varying latencies (27 to 193 days) and B220 marker expression (2 to 85%). Four of these tertiary LDA leukemias (Leu7Sec2Ter5 to 8), which each arose from a single LSC, were analysed more closely using WES. Leu7Sec2Ter5 showed a similar latency (27 days) and B220 expression levels like Leu7SecTer1 to 4 and also had the expansion of the blue subclone. Leu7Sec2Ter6 had a long latency of 69 days and a very low B220 expression. Leu7Sec2Ter6 was driven by a new, third subclone (pink), and both the blue and the red subclone disappeared. Very interestingly, Leu7Sec2Ter7 and Leu7Sec2Ter8 had a very long latency of 193 days, and showed an expansion of a subclone (green) of the red subclone. The B220 expression was high (37%) to very high (85%) in these two leukemias. Taken together, these observations paint an interesting picture with the blue subclone outcompeting the red subclone, as leukemias arising from the red subclone only appear after a long latency and in leukemias initiated by a single LSC, when there is no blue subclone LSC present. As the four leukemias (Leu7Sec2Ter5 to 8), which each were derived from a single LSC, showed striking differences in latency and surface marker expression, it can be concluded that this variation in phenotype is an intrinsic property of an individual LSCs most likely a consequence of the distinct combination of somatic mutations present in the individual LSCs. These observations also suggest that distinct LSCs with different properties might be present in a single human leukemia. Figure 1 Figure 1. Disclosures Browett: Janssen: Membership on an entity's Board of Directors or advisory committees; MSD: Membership on an entity's Board of Directors or advisory committees; AbbVie: Honoraria.

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Mutations in Driver Genes and Changes in Clonal Dynamics Are Associated with Shorter Time to Treatment in MBL Cases

Blood ◽

10.1182/blood.v126.23.5264.5264 ◽

2015 ◽

Vol 126 (23) ◽

pp. 5264-5264

Author(s):

Santiago Barrio ◽

Juhi Ojha ◽

Charla Secreto ◽

Kari G. Chaffee ◽

klaus Martin Kortum ◽

...

Keyword(s):

Board Of Directors ◽

Research Funding ◽

Germ Line ◽

Clonal Evolution ◽

Clonal Expansion ◽

Driver Mutations ◽

Driver Gene ◽

Driver Genes ◽

Advisory Committees ◽

Recurrent Mutations

Abstract Introduction: Monoclonal B cell lymphocytosis (MBL) is an asymptomatic expansion of clonal CD19+/CD5+ B cells with less than 5x109/L cells in the peripheral blood and without other manifestations of chronic lymphocytic leukemia (CLL). Approximately 1% of MBL evolves to CLL requiring therapy per year; thus it is critical to develop more precise tools to identify which MBL will progress to CLL and require treatment. Patients and Methods: In this study, we performed targeted deep sequencing (TDS) on 49 high-count MBL individuals (median B-cell count 3.7x109/L; range 0.8-4.9x109/L) and explored the mutation status of 20 driver genes recurrently mutated in CLL. We analyzed the clonal evolution in 45 of these 49 MBLs by screening 2-4 sequential samples (average time between samples 56 months, range 10-119 months). At last follow-up, 19 cases (39%) had progressed to Rai>0, and 10 cases (20%) required treatment. Tumor and germ line DNAs were isolated from sorted CD5+/CD19+ and CD5-/CD19- cell populations, respectively. Overall, 154 samples from 49 MBL cases (105 tumor and 49 germ line) were screened using semiconductor sequencing technology. The latter genetic information was integrated with relevant clinical and biological parameters, and we evaluated the effect of driver mutations and clonal expansion on time to CLL progression and time to treatment (TTT). Results and Discussion: Our cohort consisted in 17 women and 32 men, with a median age of 66 years (range: 44-80). Five cases presented secondary diseases, including melanoma, lung and bladder cancer. Clinical and biological parameters were collected, including IGHV mutation status (mutated 66%, unmutated 34%), ZAP70 and CD49 expression (25% each). At presentation, 46% of cases had del(13q), 27% trisomy 12, 6% del(11q), and 4% del(17p). Overall, we found somatic non-synonymous mutations in 23 of 49 MBLs (47%) at the initial time point including 22% of cases with more than one mutated driver gene. The average depth of coverage was 730x, thus allowing the identification of small subclonal mutations. Recurrent mutations were found in most of the drivers: CHD2, DDX3X (8% of cases), FBXW7, NOTCH1, SF3B1 (6% each), ATM, BCOR, BIRC3, BRAF, KRAS, MED12, MYD88 and ZMYM3 (4% each). Furthermore, ITPKB, POT1, SAMHD1 and XPO1 were mutated in only one case, whereas no mutations were found in HIST1H1E, RIPK1 and TP53. In 4 individuals, we found two mutations in the same gene (BRAF, DDX3X, KRAS and SAMHD1). Genes that are known to be associated with disease progression in CLL were either mutated with significantly lower incidence (NOTCH1, SF3B1) or not mutated (TP53). Mutations were detected on average 45 months (range 9-73) prior to progression to CLL Rai>0 indicating the early origin of most driver gene mutations in the MBL/CLL continuum. The presence of driver mutations in MBL was associated with shorter TTT (median TTT: present: 96 months vs. not present: not reached, HR: 5.52, 95% CI: 1.2-26.2, P =0.015). Next, we looked at clonal expansion of driver mutations over time (defined as >2-fold change in the allelic frequency of driver mutations between time points). Of 20 MBLs with mutations at baseline who had sequential samples available, 10 cases showed clonal expansion. Seven out of 10 MBLs who required therapy showed clonal expansion, which was detected on average 15 months (range 6-30 month) prior to treatment. Finally, the detection of clonal expansion was significantly associated with reduced TTT (median TTT: clonal expansion: 21 months vs. no clonal expansion: 84 months, HR: 7.79, 95% CI: 1.94-31.3, P <0.001). Conclusion: We have confirmed the existence of recurrent mutations in most CLL putative driver genes at the premalignant MBL stage many years before progression to CLL. Furthermore, the early identification of driver mutations and its clonal expansion predicts a shorter TTT. Of note, clonal evolution under selective pressure has recently been linked to the onset of CLL progression after therapy. In this study, we characterized the clonal dynamics in the pre-malignant stages of the disease and underlined its impact on clinical outcome. Despite the relatively small size of the cohort, these findings suggest that the sequential monitoring of MBL individuals with a simple and reliable technique, such as TDS, will be at least of prognostic use and thus its incorporation in the disease stratification and clinical management should be further tested. Disclosures Fonseca: Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties, Research Funding; Applied Biosciences: Membership on an entity's Board of Directors or advisory committees; Sanofi: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties, Research Funding; Millennium: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties, Research Funding; Binding Site: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties, Research Funding; Onyx/Amgen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties, Research Funding; Bayer: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties, Research Funding; BMS: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties, Research Funding; Celgene: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties, Research Funding. Kay:Gilead: Membership on an entity's Board of Directors or advisory committees, Research Funding; Pharmacyclics: Research Funding; Tolero Pharma: Research Funding; Genentech: Research Funding; Celgene Corporation: Membership on an entity's Board of Directors or advisory committees, Research Funding; Hospira: Research Funding.

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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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The Biological Inferences from the Ranking of SF3B1 Mutations in the Clonal Hierarchy of Myeloid Neoplasia

Blood ◽

10.1182/blood-2019-128965 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 5411-5411

Author(s):

Hassan Awada ◽

Jibran Durrani ◽

Ashwin Kishtagari ◽

Vera Adema ◽

Cassandra M Kerr ◽

...

Keyword(s):

Board Of Directors ◽

Research Funding ◽

Chromosomal Abnormalities ◽

Clonal Evolution ◽

Data Monitoring Committee ◽

Advisory Committees ◽

Hematopoietic Stem ◽

Clonal Architecture ◽

Clonal Nature ◽

Myeloid Neoplasia

Chromosomal abnormalities can be founder lesions (e.g., t (8; 21), inv (16), inv (3)), initiate or advance disease progression (both founder and secondary hits e.g., ASXL1, TP53, RUNX1) or can be obligatory secondary hits (FLT3, NPM1). Hence, the rank of these mutations may determine the biological properties and clinical outcomes. However, while many mechanistic studies have been undertaken without identifying the key pathogenetic factors resulting from SF3B1 mutations, important biological clues can be derived from the consequences of SF3B1 alterations in the context of the clonal architecture of myeloid neoplasia (MN). SF3B1 mutant patients often have a homogeneous phenotype with isolated erythroid dysplasia, ring sideroblasts (RS) and favorable prognoses. Studies in primary MDS cells have suggested that SF3B1 mutations are initiating lesions and provide a marked clonal advantage to MDS-RS cells by propagating from rare lympho-myeloid hematopoietic stem cells. However, there is significant diversity of clinical phenotypes and outcomes including the observation that the disappearance of RS can be observed during the disease course of clonal MN and might suggest cellular shifts due to acquisition of additional hits. In such scenarios, the cell's fate in the context of SF3B1 mutations is pre-defined by the predominance of expanded hits. We took advantage of our detailed database of molecularly and clinical annotated cases with MN to study the SF3B1 mutatome and describe whether the clonal nature (ancestral vs. secondary) might change the clinical and phenotypic trajectories of MDS cells and whether the concatenation of mutations decreases the competitiveness of SF3B1 clones, leading to the dominance of other driver genes and subsequently to clonal evolution. The clonal hierarchy was resolved using our in-house designed VAF-based bioanalytic method and confirmed by the PyClone pipeline, which showed a high level of concordance. We first assigned clonal hierarchy to SF3B1 mutations by using VAFs (adjusted for copy number and zygosity) and classifying the mutations into dominant (if a cutoff of at least 5% difference between VAFs existed), secondary (any subsequent sub-clonal hit) and co-dominant hits (if the difference of VAFs between two mutations was <5%). In total, we identified 140 dominant (SF3B1DOM), 121 secondary (SF3B1SEC) and 74 co-dominant SF3B1 mutations. For the purpose of this study, we set aside co-dominant SF3B1 mutations. Focusing on SF3B1DOM and SF3B1SEC, SF3B1DOM were often associated with a normocellular bone marrow compared to SF3B1SEC (n=42 vs. 26; P=0.02) and were less likely enriched in multi-dysplastic myeloid cells (29% vs. 53%; P=0.01). As such, SF3B1DOM tended to be more frequently detected in lower-risk MDS (P=0.05) in the subtypes of MDS-RS and MLD-RS (RS≥15%: 67% vs. 41%; P=0.01) compared to other disease subtypes. Twenty-three percent of patients with SF3B1SEC had secondary acute myeloid leukemia (sAML) (P=0.03). SF3B1SEC patients tended to have a lower median platelet count than patients with SF3B1DOM (97 vs. 130 x 109/L; P=0.05). SF3B1SEC was also more associated with bi-cytopenia compared to SF3B1DOM (52% vs. 36%; P=0.01). No specific association was found between SF3B1 clonal nature and cytogenetic abnormalities, suggesting that additional mutations might be the main contributors in the evolution of MDS to AML. Of note, patients with SF3B1SEC had half OS compared to patients with SF3B1DOM (SF3B1SECvs. SF3B1DOM: 15.9 mo. vs. 39.7 mo., P= 0.0001), suggesting that in cases evolving to AML, expanding hits might have dramatically skewed the favorable nature of SF3B1 mutations. Indeed, mutations preceding SF3B1 mainly affected lineage-restricted genes associated with repression of erythroid programs (RUNX1, 23%), terminal monocytic differentiation (TET2, 9%), transcriptional corepressors (BCOR/L1, 8%) and development of leukemia (DNMT3A, 8%). In conclusion, our study of the clonal architecture of SF3B1 mutations highlights that clonal progression of cases with MN harboring SF3B1 mutations might be inferred by the rank of additional genetic lesions cooperating with SF3B1. Disclosures Meggendorfer: MLL Munich Leukemia Laboratory: Employment. Advani:Abbvie: Research Funding; Macrogenics: Research Funding; Pfizer: Honoraria, Research Funding; Amgen: Research Funding; Glycomimetics: Consultancy, Research Funding; Kite Pharmaceuticals: Consultancy. Nazha:Tolero, Karyopharma: Honoraria; Novartis: Speakers Bureau; MEI: Other: Data monitoring Committee; Daiichi Sankyo: Consultancy; Jazz Pharmacutical: Research Funding; Incyte: Speakers Bureau; Abbvie: Consultancy. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Sekeres:Syros: Membership on an entity's Board of Directors or advisory committees; Millenium: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees. Maciejewski:Alexion: Consultancy; Novartis: Consultancy.

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Haploinsufficiency and Deletions of G3BP1 on Chromosome 5q Result in Induction of TP53

Blood ◽

10.1182/blood.v124.21.784.784 ◽

2014 ◽

Vol 124 (21) ◽

pp. 784-784

Author(s):

Naoko Hosono ◽

Mahfouz Reda ◽

Bartlomiej P Przychodzen ◽

Chantana Polprasert ◽

Latifa Zekri ◽

...

Keyword(s):

Growth Inhibition ◽

Board Of Directors ◽

Cell Lines ◽

Lower Risk ◽

Chromosomal Instability ◽

Somatic Mutations ◽

Clonal Evolution ◽

Loss Of Function ◽

Advisory Committees ◽

Low Expression

Abstract Interstitial deletion of the long arm of chromosome 5 (del(5q)) is the most common chromosomal abnormality in MDS. The extent of individual defects vary, which may account for observed clinical diversity. Del(5q) pathogenesis has been related to haploinsufficiency of genes contained in the common deleted regions (CDR), including RPS14, miR-145/146a and SPARC. Driver mutations or pathogenic microdeletions were not identified for these genes, suggesting that multiple genes must function in combination to promote clonal evolution and phenotypic heterogeneity. Hence, we performed a comprehensive analysis of somatic mutations in genes located on chromosome 5 (chr5), both in patients with diploid 5q and in those with del(5q), to clarify the role of germline and somatic mutations in disease pathogenesis. In parallel, expression analysis was performed to correlate haploinsufficiency with the frequency of mutational events, in particular for diploid 5q cases. Applying SNP-array karyotyping to samples from 146 patients with del(5q), the lesion was identified in 5q31.1q33.1. Two retained regions (CRRs) were also observed in q11.1q14.2 (CRR1) and q34qter (CRR2). Lower-risk MDS is frequently affected by CDR, while in higher-risk MDS and secondary AML CRR1/2 are commonly co-involved. Using whole exome sequencing, we identified 11 hemizygous mutations located within the deleted area in del(5q) (N=59), while in cases diploid for 5q (N=330), 243 heterozygous mutations were found. One of the mutations discovered on chr5q afflicted a gene G3BP1 (5q33.1), located within the CDR and present in 2 patients. Both were missense mutations (one heterozygous and the other homo/hemizygous). A mutant case showed good responses to lenalidomide even though diploid 5. In addition, other somatic mutations of driver genes including TET2, CUX1 and EZH2 were concomitantly observed. Whole transcriptome sequencing demonstrated hemizygous loss of G3BP1 resulting in haploinsufficiency. G3BP1 was haploinsufficient in 48% of RAEB as well as low-risk MDS cases with del(5q). Overall, defective G3BP1 is associated with shorter overall survival (P<.001) in AML, consistent with the reports that del(5q) is a worse prognostic factor in myeloid neoplasms with aggressive phenotype. G3BP1 is a nuclear RNA-binding protein and is ubiquitously expressed in bone marrow, CD34+ progenitors and leukemic cell lines. Furthermore, G3BP1 binds to TP53 and its expression leads to the redistribution of TP53 from the nucleus to the cytoplasm. Similar to RPS14, haploinsufficient of G3BP1 resulted in TP53 up-modulation. Moreover, low expression of G3BP1 in diploid 5q cases was indeed associated with higher TP53 expression. Next, we generated haploinsufficient G3BP1 cell lines using shRNA transduction. Decreased expression of G3BP1 led to growth inhibition and impaired colony formation by transduced cells lines and hematopoietic progenitor cells, respectively. Knockdown of G3BP1 in K562 cell line increased TP53 in the nucleus, and when treated with CPT11, DNA-damaged induced G1-arrest was more prominent in knockdown cells. Furthermore, after knockdown of G3BP1 in TP53-null HL60 cells, we observed increased aneuploidy, suggesting that the loss of function of G3BP1 and TP53 may result in chromosomal instability. Most significantly, G3bp1-/+ mice showed lower blood counts and defective, dysplastic hematopoiesis, similar to lower-risk MDS. As previously described, TP53 defects are associated with advanced disease but recently it became apparent that TP53 may be one of the most common somatic lesions found in the context of del(5q). We stipulate that loss of TP53 function might overcome TP53 tumor suppressor effects and induce leukemic evolution in the defective G3BP1 status. In our cohort, TP53 mutations were more frequently present in high-risk phenotype with G3BP1 haploinsufficient expression. In conclusion, novel somatic mutations of G3BP1 suggest that it could be a candidate gene associated with the clonal evolution of del(5q). Loss of function or low expression of G3BP1 has been shown to up-modulate TP53 and result in dysplasia and growth inhibition, hallmarks of early stages of MDS. Additional events constitute loss of function of TP53, resulting in chromosomal instability, which is associated with leukemogenesis. 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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