scholarly journals TP53 Mutations, Deletions, and CN-LOH: Comparison of TP53 single Hit and Double Hit Events and Their Impact on Prognosis in Hematological Malignancies

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 2224-2224
Author(s):  
Anna Stengel ◽  
Heiko Müller ◽  
Manja Meggendorfer ◽  
Wencke Walter ◽  
Constance Baer ◽  
...  
Keyword(s):  
Hematological Malignancies ◽  
Neutral Loss ◽  
Complex Karyotype ◽  
Aim Analysis ◽  
High Frequencies ◽  
Lymphoid Malignancies ◽  
Total Cohort ◽  
Myeloid Neoplasms ◽  
Impact On Survival ◽  
Double Hit

Abstract Background: TP53 is altered in ~50% of human cancers. Alterations mainly include mutations and/or deletions, but also copy-neutral loss of heterozygosity (CN-LOH) was reported. Frequently, both TP53 alleles are altered (by mutation + deletion, mutation + CN-LOH or ≥2 mutations), leading to a "double hit" event. Aim: Analysis of TP53 aberrations using WGS in 4646 cases with 29 different hematological malignancies, comparing (1) the frequencies of TP53 alterations, (2) occurrence of single hit vs. double hit, (3) correlation with complex karyotype and (4) impact on survival. Methods: Whole-genome sequencing (WGS) was performed for all 4,646 patients (median coverage 100x). 151bp paired-end reads were generated on NovaSeq 6000 and HiSeqX machines (Illumina, San Diego, CA). As no sample specific normal tissue was available, a so-called Tumor/Unmatched normal (TUN) workflow was used to reduce technical artefacts and germline calls. All reported p-values are two-sided and were considered significant at p<0.05. Results: In the total cohort of 4,646 cases, in 582 (13%) at least one alteration (alt) involving TP53 was detected (comprising mutations (mut), deletions (del) and CN-LOH (LOH); Fig 1A,B). Cases were categorized as follows: cases with (1) 1 TP53 mut only (n=166), (2) del only (n=100), (3) LOH only (n=15), constituting the single hit events. Further, (4) cases with mut+del (might include 1 or more mut, n=211), cases with mut+LOH (≥1 mut, n=41), cases with ≥2 mut only (without del or LOH, n=49), resulting in double hit events (Fig 1B). Regarding the respective entities, high frequencies of TP53 alt were mainly detected in lymphoid malignancies (e.g. HGBL, MPAL, vHZL, MZL, MCL), whereas they were infrequent or absent in many myeloid malignancies (e.g. aCML, MPN, CMML, CML, MLN_eo; Fig 1A). For further analysis, only entities in which >10 cases showed TP53 alt events were used. Comparison of single hit vs. double hit revealed that T-NHL, MM, MPN and MDS predominantly showed a single hit, whereas the double hit was frequent in MPAL, MZL, MDS/MPN-U, CLL and MCL cases (Fig 1A). However, the type of double hit differed between myeloid and lymphoid malignancies, as myeloid neoplasms showed a high frequency of cases with ≥2 mut only, whereas in many lymphoid malignancies the double hit was predominantly generated by mut+del (Fig 1A,C). All TP53-associated events (mut, del, LOH and the respective combinations) were found to be associated with a complex karyotype in the total cohort (LOH: 14% complex karyotype in cases without TP53 alt vs. 59% in cases with TP53 alt, p<0.001). This association was also detected for most of the selected entities (exceptions: MZL, T-NHL). Regarding overall survival (OS), in the total cohort, all events involving TP53 impact on OS (TP53 alt: 22 months vs. 84 months, p<0.001; TP53 mut: 20 vs. 82 months, p<0.001; TP53 del: 20 vs. 79 months, p<0.001; TP53 LOH: 20 vs. 75 months, p<0.001). Moreover, although the single hit already impacts on OS, the double hit leads to an even inferior outcome (no hit vs. single hit vs. double hit: 84 vs. 39 vs. 14 months, p<0.001). In the selected entities, an influence of TP53 alt on OS was detected for all malignancies except HGBL, MZL and T-NHL, for which also the presence of a double hit did not show an effect on OS. For the majority of the other entities, the double hit leads to a shorter OS than the single hit (as observed for the total cohort), with the exceptions of MCL and MPAL: in these entities, the single hit did not impact on OS, but only a double hit is associated with inferior outcome. Conclusions: (1) Frequency of TP53 alterations and of double hit vs. single hit differs markedly between entities. (2) The kind of TP53 complexity differs between both lineages (double hit in myeloid neoplasms: often ≥2 mut only; in lymphoid malignancies: predominantly mut+del). (3) In 7% (41/582) of cases with TP53 alt, CN-LOH transforms a single hit into a double hit. (4) In the total cohort and in the majority of selected entities (except MZL and T-NHL), TP53 alt are associated with complex karyotype. (5) In the total cohort, all events involving TP53 impact on OS; cases with double hit show an inferior outcome compared to single hit. (6) Regarding OS, the selected entities can be divided into three categories: (i) no influence of TP53 alt (HGBL, MZL, T-NHL); (ii) double hit required for impact on OS (MCL, MPAL); (iii) influence of both single hit and double hit with inferior outcome of double hit (all other). Figure 1 Figure 1. Disclosures Kern: MLL Munich Leukemia Laboratory: Other: Part ownership. Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership. Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership.

Mutational Patterns and Correlation to Chip-Related Mutations in Hematological Malignancies - a Study on Mutation Frequencies of 122 Genes in 28 Entities Including 3096 Cases

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 37-38
Author(s):  
Anna Stengel ◽  
Constance Baer ◽  
Wencke Walter ◽  
Manja Meggendorfer ◽  
Wolfgang Kern ◽  
...  
Keyword(s):  
Hematological Malignancies ◽  
Nk Cell ◽  
Conflicts Of Interest ◽  
Broad Distribution ◽  
High Frequencies ◽  
Lymphoid Malignancies ◽  
Total Cohort ◽  
Myeloid Neoplasms ◽  
Age Related ◽  
Cell Neoplasm

Background: Acquired somatic mutations are crucial for the development of the majority of cancers. In hematological malignancies, some molecular mutations are very specific for certain entities (e.g. BRAF in HCL, MYD88 in LPL), while others were detected in a variety of malignancies (e.g. mutations in TP53, TET2, DNMT3A, RUNX1). Moreover, mutations in genes related to CHIP (clonal haematopoiesis of indeterminate potential; ASXL1, TET2,DNMT3A) were detected in an age-related manner. Aim: (1) Analysis/comparison of mutation frequencies of 122 selected genes in 3096 cases with 28 different hematological malignancies for identification of "mutation-driven" entities. (2) Correlation of CHIP-related mutations with mutational landscapes. Methods: Whole-genome sequencing (WGS) was performed for all 3096 patients. For this, 151bp paired-end reads were generated on NovaSeq 6000 and HiSeqX machines (Illumina, San Diego, CA). The Illumina tumor/unmatched normal workflow was used for variant calling. All reported p-values are two-sided and were considered significant at p<0.05. Results: Entities with the highest numbers of mutations (median n=4) and thus potentially with the largest impact of mutations on pathogenesis comprised aCML (range: 1-7), CMML (1-6), MDS/MPN-U (2-5) and s-AML (2-8), whereas the lowest numbers (median n=0) were observed for CML (0-3), MGUS (0-2), MLN_eo (0-3), NK cell neoplasm (0-3) and PPBL (0-2). In the total cohort of 3096 cases, the most frequently mutated genes were TET2 (14%), ASXL1 (13%), TP53 (10%), SF3B1 (9%), DNMT3A (9%) and SRSF2 (9%). Entities with high frequencies of specific mutations (> 50%) comprised: aCML (ASXL1, 86%), BPDCN (TET2, 67%), BL (TP53, 60%), CMML (TET2, 67%; ASXL1, 58%), FL (KMT2D, 87% and CREBBP, 73%), HCL (BRAF, 100%), LPL (MYD88, 98%; CXCR4, 51%), MDS/MPN-U (ASXL1, 60%), MPN (JAK2, 68%), B-NHL (TP53, 50%) and T-NHL (STAT3, 52%). Mutations enriched in distinct entities included SETBP1 (26% in MDS/MPN overlaps), CSF3R (30% in MDS/MPN-U), STAT3 (only in T-NHL and NK cell neoplasm, 52% and 23%), NOTCH1 and PHF6 (T-ALL, 38% and 30%) and MYC and ID3 (almost exclusively in BL, 30% each). Genes predominantly mutated in myeloid neoplasms comprised e.g. SF3B1 (with the exception of CLL), JAK2, NPM1, RUNX1, IDH2, CEBPA, STAG2, NF1 and GATA2. By contrast, mutations in KMT2D, MYD88, ARID1A, ATM, CXCR4, BIRC3 and CD79B were detected almost exclusively in lymphoid malignancies. A broad distribution across entities was observed for mutations in TET2, ASXL1,DNMT3A, TP53, BCOR and ETV6. Thus, the first three, i.e. CHIP-related genes were also mutated with a high frequency in lymphoid neoplasms. In line with this, gene mutations found in the largest number of entities comprise DNMT3A (n=23 entities), TET2 (n=21), ASXL1, TP53, NRAS (n=19, respectively), KRAS and BCOR (n=17, respectively). Further, we compared the mutational patterns of cases with at least one CHIP-associated mutation (n=920 cases in the total cohort, "CHIP+") with cases without such mutations (n=2176, "CHIP-") to decipher CHIP-correlated mutation patterns. Significant differences with respect to accompanying mutations were mainly detected for myeloid neoplasms (MDS, mutations in n=12 genes significantly different in CHIP+ vs. CHIP- without CHIP genes themselves; AML, n=7; MPN, n=4; aCML, n=2; CMML, n=1) but also for MPAL (n=3), T-ALL (n=2), B-ALL, FL and LPL (n=1, respectively). Mutations in TP53 were found significantly enriched in CHIP- cases in 4 different entities, moreover mutations in KRAS, WT1 and SF3B1 were more abundant in CHIP- cases (in CMML, AML and aCML, respectively). By contrast, CHIP+ cases were characterized by high frequencies of mutations in RUNX1 (in n=4 entities), SRSF2, IDH2, NRAS (n=3) and EZH2 (n=2). Conclusions: (1) Certain mutations showed a broad distribution within or even across the myeloid/lymphoid lineage, including CHIP-related mutations frequently detected also in lymphoid malignancies. (2) The median numbers of mutations were low in entities that are defined by chromosomal fusions (CML, MLN_eo) or in entities that are regarded as "pre-malignant" (MGUS, PPBL), while especially MDS/MPN overlap cases seem to be mutation-driven (high number of mutations). (3) We deciphered different mutation patterns in CHIP+ (RUNX1, SRSF2, IDH2, NRAS, EZH2) and CHIP- (TP53, KRAS, WT1, SF3B1) cases across all entities, suggesting differences in pathophysiology. Disclosures No relevant conflicts of interest to declare.

Ring chromosome in myeloid neoplasms is associated with complex karyotype and disease progression

2017 ◽  
Vol 68 ◽  
pp. 40-46
Author(s):  
Matthew W. Rosenbaum ◽  
Olga Pozdnyakova ◽  
Julia T. Geyer ◽  
Paola Dal Cin ◽  
Robert P. Hasserjian
Keyword(s):  
Disease Progression ◽  
Ring Chromosome ◽  
Complex Karyotype ◽  
Myeloid Neoplasms

scholarly journals Place of cytology in the diagnosis of systemic mastocytosis: A case report

2021 ◽  
Vol 7 (2) ◽  
pp. 01-05
Author(s):  
W. Quiddi ◽  
H. Boumaazi ◽  
S. Ed-dyb ◽  
H. Yahyaoui ◽  
M. Aitameur ◽  
...  
Keyword(s):  
Mast Cells ◽  
Hematological Malignancies ◽  
Systemic Mastocytosis ◽  
Bone Marrow Involvement ◽  
Acute Leukemias ◽  
Activating Mutations ◽  
Myeloid Neoplasms ◽  
Organ Systems ◽  
Cutaneous Mastocytosis

Mastocytosis is a heterogeneous group of rare diseases related to the clonal, neoplastic proliferation of morphologically and immunophenotypically abnormal mast cells, that accumulate in one or more organ systems. Their pathophysiology is dominated by activating mutations in C-Kit (Stem Cell Factor receptor). Several pathological forms have been described ranging from isolated cutaneous mastocytosis affecting mainly children, to aggressive systemic mastocytosis described mainly in adults with bone marrow involvement. According to the WHO 2016 classification of hematological malignancies, systemic mastocytosis appear as a new entity of "myeloid neoplasms and acute leukemias" that combines cytology (abnormal mast cells) with other genetic and molecular criteria. We describe through this observation the practical side of hematological cytology in the diagnostic orientation of this serious, rare and underestimated pathology.

Impact of Expression of BAALC, CDKN1B, ERG, EVI1, and MN1 on Prognosis and Their Association with Karyotype, FLT3-ITD, NPM1 and MLL-PTD Status In Adult AML: A Comprehensive Study on 286 Cases

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 953-953
Author(s):  
Claudia Haferlach ◽  
Alexander Kohlmann ◽  
Sonja Schindela ◽  
Tamara Alpermann ◽  
Wolfgang Kern ◽  
...  
Keyword(s):  
Molecular Genetic ◽  
Normal Karyotype ◽  
Genetic Alterations ◽  
Complex Karyotype ◽  
Employment Equity ◽  
Aberrant Expression ◽  
Cox Regression Analysis ◽  
Total Cohort ◽  
Equity Ownership ◽  
Low Expression

Abstract Abstract 953 Introduction: The WHO classification in 2008 listed for the first time aberrant expression of genes as molecular genetic alterations affecting outcome in AML. High expression of BAALC, ERG and MN1 were shown thus far to be associated with unfavorable outcome in normal karyotype AML (AML-NK). In addition high EVI1 expression was suggested to predict poor outcome. Recently, our group identified low expression of CDKN1B as a favorable prognostic marker. The aim of this study was to evaluate the expression of BAALC, CDKN1B, ERG, EVI1 and MN1 in AML comprising all cytogenetic risk groups with respect to their association with distinct cytogenetic and known molecular genetic subgroups and their impact on prognosis. Patients/Methods:: Expression levels of BAALC, CDKN1B, ERG, EVI1 and MN1 were determined by oligonucleotide microarrays (HG-U133 Plus 2.0, Affymetrix) in 286 AML (t(15;17) n=15; t(8;21) n=16; inv(16) n=7; normal karyotype n=99; 11q23/MLL-rearrangements n=10; complex karyotype n=51; other abnormalities n=88). Patients were further analyzed for mutations in NPM1, FLT3-ITD, CEPBA and MLL-PTD. Results: Expression of BAALC, CDKN1B, ERG, EVI1 and MN1 varied significantly between genetic subgroups: While t(15;17), t(8;21) and 11q23/MLL-rearrangements were associated with low CDKN1B expression, AML-NK and NPM+ cases showed a higher CDKN1B expression. Lower BAALC expression was observed in AML with t(15;17), 11q23/MLL-rearrangement and AML-NK as well as in FLT3-ITD+ AML and in NPM1+ AML, while in AML with other abnormalities a higher BAALC expression was observed. ERG expression was lower in AML with 11q23/MLL-rearrangement and normal karyotype, while it was higher in AML with complex karyotype. Low EVI1 expression was observed in AML with t(15;17), t(8;21), inv(16) and AML-NK, while it was higher in AML with 11q23/MLL-rearrangements. Low MN1 expression was associated with t(15;17), t(8;21) and AML-NK, while it was increased in cases with inv(16) or other abnormalities. Next, Cox regression analysis was performed with respect to overall survival (OS) and event free survival (EFS). In the total cohort high BAALC and ERG expression as continuous variables were associated with shorter OS and EFS while CDKN1B, EVI1 and MN1 had no impact. Furthermore the cohort was subdivided into quartiles of expression for each gene. After inspection of the survival curves the cut-off for high vs low expression was set as follows: BAALC: 75th percentile, CDKN1B: 25th percentile, ERG and MN1: 50th percentile. For EVI1 expression pts were separated into expressers (n=44) and non-expressers (n=242). Low CDKN1B expression was associated with longer OS and EFS in the total cohort (p=0.005, not reached (n.r.) vs 14.9 months (mo); p=0.013, 31 vs 9.7 mo). High BAALC expression had no impact on OS, but was associated with shorter EFS in the total cohort as well as in AML with intermediate cytogenetics and AML with other abnormalities (p=0.032, 6.2 vs 13.0 mo; p=0.027, 5.1 vs 11.3 mo; p=0.006, 2.3 vs 14.8 mo). High ERG expression was significantly associated with shorter OS and EFS in the total cohort (p=0.002, 12.5 mo vs n.r.; p=0.001, 8.1 vs 15.7 mo) as well as in AML-NK (p=0.001, 11.3 mo vs n.r.; p=0.010, 7.2 vs 22.1 mo). OS was also shorter in AML with unfavorable karyotype (p=0.048, median OS 9.3 mo vs n. r.). With respect to MN1 high expressers had a significantly shorter OS and EFS in the total cohort (p=0.004, 12.3 mo vs. n.r.; p=0.001, 8.1 vs 16.7 mo) as well as in AML-NK (p=0.001, 9.7 mo vs n.r.; p=0.001, 5.1 vs 22.1 mo). In a multivariate analysis including CDKN1B, ERG and MN1 all parameters retained their impact on OS as well as on EFS, while BAALC lost its impact on EFS. Adding MLL-PTD, NPM1+/FLT3-ITD-, favorable and unfavorable karyotype into the model demonstrated an independent significant adverse impact on OS for MLL-PTD (p=0.027, relative risk (RR): 2.38) and ERG expression (p=0.044, RR: 1.59) only. In the respective analysis for EFS only favorable karyotype showed an independent association (p=0.002, RR: 0.261). Conclusion: 1) Expression of BAALC, CDKN1B, ERG, EVI1 and MN1 varies significantly between cytogenetic subgroups. 2) BAALC as a continuous variable and CDKN1B, ERG and MN1 as dichotomized variables are independently predictive for OS and EFS in AML. 3) ERG expression even retains its independent prediction of shorter OS if cytogenetic and other molecular genetic markers are taken into account. Disclosures: Haferlach: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Kohlmann:MLL Munich Leukemia Laboratory: Employment. Schindela:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Schnittger:MLL Munich Leukemia laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

Jumping Translocation of Homogeneously Staining Region Hsr(11q) in An Erythroid Leukemia: Identification of Amplified Regions by Fluorescence Hybridization, M-FISH and M-Banding.

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 4890-4890
Author(s):  
Catherine Helias ◽  
Carine Gervais ◽  
Eric Jeandidier ◽  
Bruno Lioure ◽  
Laurent Mauvieux
Keyword(s):  
Hematological Malignancies ◽  
Conflicts Of Interest ◽  
Erythroid Cell ◽  
Specific Gene ◽  
Complex Karyotype ◽  
Chromosome 11 ◽  
Hematological Neoplasms ◽  
Selective Growth Advantage ◽  
Blast Cells ◽  
Conventional Cytogenetics

Abstract Abstract 4890 Gene amplification is a mechanism whereby a tumor cell can increase the copy number of specific gene sequences and gain a proliferative advantage. Although amplifications are common in solid tumors, they are relatively rare in hematological neoplasms. We report here on a patient with an acute erythroid leukemia and a jumping translocation of a hsr(11q) in a complex karyotype, without MLL amplification. The patient was 40 years old when he was admitted for asthenia, peripheral blood showing pancytopenia (Hb=111G/L; neutrophils= 0.23 G/L; platelets 92 G/L), without circulating blast cells. Bone marrow was hypercellular with the presence of more than 50% of erythroid precursors and more than 20% of myeloid blast cells in non-erythroid cell population, leading to the diagnosis of erythroblastic acute leukemia. A marked dysgranulopoiesis was also detected. Conventional cytogenetics showed a complex karyotype with a del(5q), a unbalanced t(7;17) leading to partial 7q deletion and homogeneously staining regions (hsr). Fluorescence in situ hybridization confirmed the del(5q), and showed that TP53 was not deleted in the t(7;17). Multi-FISH (M-FISH) pointed out that the hsr consisted of chromosome 11 and was implicated in 3 different translocations with 3 different partner chromosomes in 3 different clones. To further characterize the amplicon and determine which bands were implicated, we used a chromosome 11 m-band probe. It revealed that the bands implicated are the same on the der(3), der(12) and der(20) and are localized between 11q23.3 and 11q25. A series of BAC probes showed that different genes, present in these regions, were amplified: ETS1, FLI1, KCNJ5, NFRKB, SNX19, HNT, OPCM, but not MLL. Amplifications of chromosome 11q usually includes MLL, but more telomeric amplicons have also been reported in AML and myelodysplatic syndromes (MDS). A very close 11q amplification was identified in 3 AML/MDS cases (Crossen et al, 1999; Tyybäkinoja et al, 2006). Also, the ETS1 oncogene was found to be rearranged and 30-fold amplified in a case of acute myelomonocytic leukaemia, in which an hsr occurred on 11q23 (Rovigatti et al, 1986). The role of chromosomal amplifications in leukemia is unclear, but it has been suggested that they are associated with rapid disease progression and short survival. Jumping translocations are an unusual phenomenon and have been rarely reported in hematological malignancies. Whether jumping translocations play a role in tumor genesis or confer a selective growth advantage on tumor cells is unknown. The combination of hsr and jumping translocations as described here are very rare in hematological malignancies. The cases of the literature (Yoshida et al, 1999) and the one presented here suggest that the 11q24-q25 region may harbor new candidate oncogenes, together with unusual chromosomal mechanisms. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Comprehensive Genomic Profiling of Pediatric Therapy-Related Myeloid Neoplasms Identifies Mecom Dysregulation to be Associated with Poor Outcome

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1394-1394
Author(s):  
Jason R Schwartz ◽  
Jing Ma ◽  
Michael P Walsh ◽  
Xiaolong Chen ◽  
Tamara Lamprecht ◽  
...  
Keyword(s):  
Primary Tumor ◽  
Lymphoblastic Leukemia ◽  
Hematopoietic Cells ◽  
Fusion Partner ◽  
Genomic Profile ◽  
Complex Karyotype ◽  
Rna Seq ◽  
Primary Tumors ◽  
Expression Levels ◽  
Myeloid Neoplasms

Therapy-related myeloid neoplasms (tMN) occur in children secondary to cytotoxic therapies used to treat pediatric malignancies, are typically resistant to conventional chemotherapy, require hematopoietic cell transplantation as the only curative option, and have a dismal prognosis. The genomic alterations that drive tMN in children have yet to be comprehensively described, and it is unclear if particular genomic lesions hold prognostic value. We have characterized the genomic profile of 62 pediatric tMN cases (tMDS: n=23, tAML: n=39) obtained from the St. Jude Children's Research Hospital Tissue Bank from patients diagnosed between 1987 and 2018. These cases arose following treatment for a variety of primary tumors (hematological (74%), bone and soft tissue (23%), and brain (3%)). Acute lymphoblastic leukemia was the most frequent primary tumor (n=39, 63%). Conventional cytogenetics (n=60) showed a complex karyotype (≥3 structural alterations) in 19 (32%) cases, and 7 of these cases contained a deletion involving chromosome 7 (del(7)). Eleven (18%) other cases without complex karyotypes had del(7). Deletions of chromosome 5 were present in 9 (15%) cases, but only in the context of a complex karyotype. We hypothesized that the patients' younger age and the different spectrum of primary tumor types and chemotherapy would give rise to a mutational spectrum distinct from adult tMN. We used whole exome (WES), whole genome (WGS), and RNA sequencing (RNA Seq) to describe the mutational profile of our pediatric tMN cohort. WES was completed for 58 tumor/normal pairs using Nextera Rapid Capture Expanded Exome (Illumina). Fifteen cases were analyzed by WGS (11 also had WES). Normal comparator genomic DNA was obtained from flow-sorted lymphocytes. An average of 21 coding variants/patient (range: 1-131) was observed from the gene-coding region, and these include synonymous, non-synonymous, and splice site variants. Ras/MAPK pathway mutations were present in 44% of the cases (43 mutations in 27 cases). Canonical KRAS (n = 16), NF1 (n = 10), and NRAS (n = 7) mutations were the most frequent coding mutations. Eleven (18%) patients had either heterozygous deletion or a copy neutral loss of heterozygosity event involving chromosome 17p and the TP53 locus; 5 of these cases had concurrent TP53 missense mutations identified at allele frequencies near 100%. Unlike tMN in adults, mutations in PPM1D were not identified. RNA-Seq completed on 56 evaluable cases identified 28 (50%) cases with KMT2A rearrangement (KMT2Ar). MLLT3 was the most common fusion partner (n=13, 46%). In addition to KMT2A rearrangements, RNA-Seq also identified a RUNX1-MECOM fusion. Alterations involving the MECOM locus have been described in some myeloid neoplasms like tMN, and its overexpression is associated with a poor prognosis and some AMLs with KMT2Ar. MECOM expression levels were variable in this cohort (FPKM range: 0.004 - 38.4) with 24 cases (43%) having an FPKM>5 (MECOMHigh). In addition to the RUNX1-MECOM event, these 24 MECOMHigh cases included 18 with KMT2Ar (64% of KMT2Ar group) and 1 with a NUP98 fusion (NUP98-HHEX). The remaining 4 MECOMHigh cases demonstrate allele-specific MECOM expression, suggesting a cis-regulatory element is driving this expression. Two of these 4 cases have WGS and were found to contain a t(2;3)(p21;q26.2) involving MECOM on chromosome 3 and noncoding regions of chromosome 2 adjacent to ZFP36L2, a gene highly expressed in hematopoietic cells. ENCODE data supports that this region of the genome is an active enhancer in hematopoietic cells, suggesting a proximity effect in which this enhancer has been hijacked to drive high levels of MECOM expression. In our cohort, MECOM expression levels are predictive of a worse outcome (overall survival (OS) at 2 years: High=14.6% vs. Low=46.3%; log rank p<0.01). Although KMT2Ar was frequently present in our cohort and enriched in the MECOMHigh group (High=75% (18/24) vs. Low=31% (10/32); p<0.01), high MECOM expression did not confer a significant survival difference within the KMT2Ar group (OS at 2 years: High=16.7% vs Low=40%; log rank p=0.33). Further, the presence of a KMT2Ar or a complex karyotype did not significantly affect the OS in this cohort. In conclusion, we report the genomic profile of a large cohort of pediatric tMN cases and show that high levels of MECOM expression, a portion of which is driven by enhancer hijacking, predicts a worse outcome. Disclosures Gruber: Bristol-Myers Squibb: Consultancy.

Role of Bcl-2 Family in Lymphoid Malignancies

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. SCI-41-SCI-41
Author(s):  
Andreas Strasser ◽  
G. Kelly ◽  
S. Glaser ◽  
S. Grabow ◽  
A. Delbridge ◽  
...  
Keyword(s):  
Transgenic Mice ◽  
Hematological Malignancies ◽  
Cell Cycle Control ◽  
Family Members ◽  
B Lymphoma ◽  
Over Expression ◽  
Death Studies ◽  
Lymphoid Malignancies ◽  
Single Allele

Abstract Impaired apoptosis is considered one of the prerequisites for the development of most, if not all, cancers, but the mechanisms that guarantee the sustained survival of most cancer cells remain unknown. Members of the Bcl-2 family are key regulators of apoptosis and include proteins essential for cell survival and those required to initiate cell death. Studies with transgenic mice have shown that over-expression of Bcl-2 or related pro-survival family proteins, such as Bcl-xL or Mcl-1, can promote tumorigenesis, particularly in conjunction with mutations that deregulate cell cycle control, such as deregulated c-myc expression. It is, however, not known whether expression of pro-survival Bcl-2 family members under endogenous control is required to maintain the survival of cells undergoing neoplastic transformation. Using Eµ-myc transgenic mice, a well-characterized model of human Burkitt’s lymphoma, we investigated the role of endogenous Bcl-2 in lymphoma development. Bcl-2 was found to be dispensable for the development of Eµ-myc pre-B/B lymphoma. In contrast, loss of Bcl-xL and even, more remarkable, loss of a single allele of Mcl1 greatly impaired lymphoma development. Experiments with inducible knockout mice demonstrated that Mcl-1 but not Bcl-xL is essential for the sustained survival and expansion of Myc-driven malignant pore-B/B lymphoma. Remarkably, even loss of one Mcl1allele greatly impaired lymphoma growth. These findings were translated into using lymphoid malignancies by using inducible expression of selective antagonists of distinct pro-survival Bcl-2 family members. Such studies showed that Mcl-1 is also critical for the sustained survival and expansion of Burkitt Lymphoma, a Myc-driven malignancy. These observations indicate that (even relatively weak) targeting of Mcl-1 may be an attractive strategy for the treatment of Myc-driven hematological malignancies. Disclosures: Strasser: Genentech Inc: Consultancy.

Molecular and Clinical Characterization of Patients with Myeloid Neoplasms Carrying the 12p Deletion

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 2007-2007
Author(s):  
Vera Adema ◽  
Cassandra M. Hirsch ◽  
Bartlomiej P Przychodzen ◽  
Andrea Pellagatti ◽  
Jacqueline Boultwood ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Board Of Directors ◽  
Transcriptional Factors ◽  
Chromosome 12 ◽  
Complex Karyotype ◽  
Advisory Committees ◽  
Expression Levels ◽  
Myeloid Neoplasms ◽  
Mrna Expression Levels

Abstract Background: Cytogenetic abnormalities have been described in almost 50% of patients with MDS and area strong and independent risk factor for prognosis. The interstitial deletion in the short arm of the chromosome 12 [del(12p)], is a characteristic but rare abnormality in MDS patients. Del(12p) abnormality has been described in approximately 1-5% of patients as a sole anomaly and is also found in up to 4% of patients along with an additional cytogenetic alteration. Isolated del(12p) is classified as a good risk abnormality according to the Revised International Prognostic Scoring Systems (IPSS-R). The commonly deleted region between 12p12.2 and 12p13.1 encompasses the ETV6 gene. To date, besides mutations in the transcriptional factor ETV6 and in the cell signaling KRAS gene, no other molecular mutations have been associated with del(12p). Murine studies have highlighted a role of the transcriptional factors ETV6 and RUNX1 in the impairment of both erythroid and platelets maturation. Here we investigated the presence of alternative molecular factors associated with del(12p) possibly influencing clinical outcomes and disease phenotypes. Methods: We studied the molecular and clinical data of a total of 2834 patients with myeloid neoplasms and found that 3% (93/2834) had alterations in chromosome 12. The median age was 67 years (24-84), with a male: female ratio of 56:37. Del(12p) occurred in 71% of cases (66/93); among them 14% (9/66) had isolated del(12p), 9% (6/66) had del(12p) + 1 additional alteration and 77% (51/66) carried a complex karyotype. The additional alteration to del(12p) included -7/del 7q (N=3), del(5q) (N=1) and t(X;20) (N=1). Cases with del(12p) were also classified according to disease type (MDS=40, AML=16; MDS/MPN=10; P=.057) and according to MDS risk group [lower-risk (33%, 22/66) and higher-risk (45%, 30/66)]. We applied whole exome sequencing and a targeted deep sequencing panel of 64 most frequently mutated genes in myeloid neoplasms. The ETV6 (12p13.2) gene was deleted in 55% (36/66) of cases while the KRAS (12p12) gene was deleted in 32% (21/66) of cases. One-third (32%, 21/66) of patients had deleted both genes. Two patients were hemizygous for KRAS. Results: Comparing patients with del(12p) (isolated, +1 alteration) to patients without alterations in chromosome 12 (n=2741), those with del(12p) had lower hemoglobin levels compared to patients without 12p aberrations (9.2 g/dL (6-16) vs. 9.7 g/dL (3-17); P=.009) and lower platelets counts (47 x109/L (8-577) vs. 73 x109/L (2-2336); P=.04). We noted that patients with isolated del(12p) had a longer median OS compared to patients with del(12p) associated with a complex karyotype [14 months (1-27) vs. 7 months (5-8)] although this difference was not significant. We then analyzed the mutational profile of the del(12p) cohort (isolated, +1 alteration) and compared their mutational spectrum with that of cases diploid for 12p. The most recurrently mutated genes in cases with del(12p) compared to cases diploid for 12p included RUNX1 (27% vs. 7%; P=.01) and DNMT3A (27% vs. 9%; P=.04). When we analyzed all the cases with del(12p) abnormalities (isolated, +1 alteration and complex) the significantly mutated genes were the transcriptional factors TP53 (38% vs. 4%; P=.0001) and RUNX 1 (14% vs. 7%; P=.04) and the histone modifier ASXL1 (21% vs. 10%; P=.01) We then analyzed the gene expression profile of patients carrying the del(12p) abnormality and found that KRAS mRNA expression levels of patients with MDS with del(12p) had a 2-fold reduction compared to the levels of healthy subjects (P=.017). Similarly, we observed also a decrease in ETV6 mRNA expression levels in patients with del(12p) (P=.07). Conclusions: Patients with del(12p) had lower levels of hemoglobin and platelets counts compared to patients without this cytogenetic abnormality. Mutations in transcriptional factors such as RUNX1 were commonly detected in this cohort, suggesting a possible mechanism contributing to the role of ETV6 in the impairment of erythroid and megakaryocytic cell maturation. Disclosures Sole: Celgene: Membership on an entity's Board of Directors or advisory committees. Maciejewski:Alexion Pharmaceuticals Inc: Consultancy, Honoraria, Speakers Bureau; Celgene: Consultancy, Honoraria, Speakers Bureau; Apellis Pharmaceuticals Inc: Membership on an entity's Board of Directors or advisory committees.

Characterization of MDS Harboring TET2 Mutations and/or TET2 Deletions

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4288-4288 ◽  
Author(s):  
Claudia Haferlach ◽  
Anna Stengel ◽  
Manja Meggendorfer ◽  
Wolfgang Kern ◽  
Torsten Haferlach
Keyword(s):  
Overall Survival ◽  
Relative Risk ◽  
Molecular Genetic ◽  
Normal Karyotype ◽  
Prognostic Impact ◽  
Complex Karyotype ◽  
Wild Type ◽  
Employment Equity ◽  
Total Cohort ◽  
Equity Ownership

Background: TET2 mutations and deletions have been reported in MDS. A detailed analysis of the prognostic impact of TET2 deletions and their association to TET2 mutations is lacking. Aim: To characterize MDS with TET2 mutations (mut) and/or TET2 deletions (del) with respect to accompanying cytogenetic and molecular genetic abnormalities and their impact on prognosis. Patients and Methods: First 788 unselected MDS cases (cohort A) were evaluated. As in this cohort only 8 cases with TET2 deletion were detected, further MDS were screened for TET2 deletions. In total 77 MDS harboring a TET2 deletion were identified and included in cohort B. Both cohorts were analyzed by chromosome banding analysis, FISH, genomic arrays and mutation analysis of TET2. Cases from cohort A were also analyzed for mutations in ASXL1, ATM, BCOR, BRCC3, CBL, CTCF, DNMT3A, ETV6, EZH2, FBXW7, IDH1, IDH2, JAK2, KRAS, LAMB4, MPL, NCOR1, NCR2, NF1, NRAS, PHF6, PRPF8, PTPN11, RAD21, RUNX1, SETBP1, SF3B1, SMC3, SRSF2, STAG2, TET2, TP53, U2AF1 and ZRSR2. Results: In cohort A 248 cases (31%) with TET2mut were identified. TET2del and a normal karyotype were more frequent in MDS with TET2mut as compared to those with TET2 wild-type (wt) (3% vs 1%, p=0.006; 89% vs 78%, p<0.001). SF3B1 and ASXL1 were frequently mutated in both TET2mut and TET2wt MDS (32% and 34%, 22% and 18%, respectively). In MDS with TET2mut compared to MDS with TET2wt the following genes were less frequently mutated: ATM (0.5% vs 3%, p=0.05), DNMT3A (9% vs 15%, p=0.02), ETV6 (0.5% vs 3%, p=0.03), IDH1 (0.5% vs 3%, p=0.02), IDH2 (1% vs 5%, p=0.002), TP53 (2% vs 7%, p=0.004), U2AF1 (4% vs 9%, p=0.04), while the following genes were more frequently mutated: CBL (6% vs 2%, p=0.01), EZH2 (8% vs 2%, p<0.001), SRSF2 (27% vs 12%, p<0.001), and ZRSR2 (15% vs 3%, p<0.001). Overall spliceosome genes were more frequently mutated in TET2mut than in TET2wt MDS (77% vs 56%, p<0.001). In the total cohort A neither TET2mut nor TET2del had an impact on overall survival (OS). In TET2mut MDS and TET2wt MDS SF3B1mut were associated with favorable outcome, while TP53mut were associated with shorter OS in both subsets (table 1). However in TET2mut MDS mutations in RUNX1 (p<0.0001), CBL (p=0.001), and U2AF1 (p=0.03) were independently associated with shorter OS, while in TET2wt MDS mutations in KRAS (p=0.03), EZH2 (p=0.02), NRAS (p=0.02), SRSF2 (p=0.007), IDH2 (p=0.05), and ASXL1 (p=0.01) were independently associated with shorter OS. In cohort B 40/77 (52%) MDS with TET2del also harbored a TET2mut. The 4q deletion encompassing the TET2 gene was < 10 MB in size and thus cytogenetically cryptic in 77% of cases with TET2mut, while the TET2 deletion was cryptic in only 24% of cases without TET2mut. A normal karyotype was present in 37 cases (48%), a complex karyotype in 29 (38%) and other abnormalities in 11 cases (14%). TET2mut were frequent in cases with a normal karyotype (68% vs aberrant karyotype: 32%, p<0.001) and were rare in cases with a complex karyotype (13%). Relating the mutation load of TET2mut to the proportion of cells with TET2del as determined by FISH revealed in 60% of cases that both TET2 alterations were present in the main clone, while in 23% of cases the TET2mut was present in a subclone only and in 17% the TET2del was observed in a subclone only. In the subset of patients with TET2del in a subclone only, 83% showed a normal karyotype and none a complex karyotype, while in the subset of cases with TET2mut in a subclone only, 43% showed a normal and 29% a complex karyotype. In the total cohort B the presence of a TET2mut in addition to the TET2del had no prognostic impact, while the presence of a complex karyotype was associated with shorter OS (RR: 8.0, p=0.004). Conclusions: 1) TET2 deletions are rare in TET2 mutated MDS (3%). 2) TET2 mutations are frequent in MDS with TET2 deletion (52%). 3) TET2 mutations are highly correlated to a normal karyotype and are rare in complex karyotype. 3) Neither TET2 mutations nor TET2 deletions have a prognostic impact in MDS. 4) In TET2 mutated MDS mutations in RUNX1, TP53, CBL, and U2AF1 have the strongest negative independent impact on OS, which in TET2 wild-type MDS is the case for mutations in TP53, KRAS, EZH2, NRAS, SRSF2, IDH2 and ASXL1. Table The relative risk of parameters significantly (p<0.05) associated with overall survival are depicted in TET2 mutated and TET2 wild-type MDS Table. The relative risk of parameters significantly (p<0.05) associated with overall survival are depicted in TET2 mutated and TET2 wild-type MDS Disclosures Haferlach: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Stengel:MLL Munich Leukemia Laboratory: Employment. Meggendorfer:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

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