PAX5 Deletions Research Articles

Unraveling Copy Number Alterations in Pediatric B-Cell Acute Lymphoblastic Leukemia: Correlation with Induction Phase Remission Using MLPA.

Acute Lymphoblastic Leukemia (ALL) is the most common malignancy occurring in children. Copy number alterations (CNA) like PAX5, CDKN2A/2B, PAR1 Region, ETV6, IKZF1, BTG1, and RB1 gene deletion are important genetic events that define and prognosticate B-cell ALL. Thus, this study aimed to evaluate associations of CNA with induction phase remission status in childhood B-cell ALL. This study was observational with a cross-sectional design at the Dharmais Cancer Hospital, Harapan Kita Mother and Children Hospital, and Tangerang Regional Public Hospital. We evaluated 74 pediatric B-cell ALL cases with 1-18-year-olds. Genomic DNA was analyzed by Multiplex Ligation Dependent Probe Amplification Assay (MLPA). This study used the P335 ALL-IKZF1 panel kit, which contains several ALL-related genes. The patient's clinical and laboratory characteristics were collected from medical records from January to December 2019. We observed gene copy number alteration in children with B-Cell ALL. PAX5 was the most commonly observed gene deletion, followed by CDKN21/2B, ETV6, IKZF1, BTG1, RB1, and PAR1 Region. Based on gene mutations, only the PAX5 had a significant association with the remission status of pediatric B-cell ALL (p-value <0.05; OR = 3.91). It showed that patients with PAX5 gene mutations have 3.9 times the risk of no remission and/or relapse compared to those without PAX5 gene mutations. Patients with mutations in the PAX5 gene have a higher chance of not achieving remission and/or experiencing relapse than those without such mutations. The MLPA method can be utilized for examining copy number alterations, which is valuable for achieving more precise stratification in diagnosis.. Further research is needed to expand upon this finding.

IKZF1plus is a frequent biomarker of adverse prognosis in Mexican pediatric patients with B-acute lymphoblastic leukemia.

Recurrent genetic alterations contributing to leukemogenesis have been identified in pediatric B-cell Acute Lymphoblastic Leukemia (B-ALL), and some are useful for refining classification, prognosis, and treatment selection. IKZF1plus is a complex biomarker associated with a poor prognosis. It is characterized by IKZF1 deletion coexisting with PAX5, CDKN2A/2B, or PAR1 region deletions. The mutational spectrum and clinical impact of these alterations have scarcely been explored in Mexican pediatric patients with B-ALL. Here, we report the frequency of the IKZF1plus profile and the mutational spectrum of IKZF1, PAX5, CDKN2A/2B, and ERG genes and evaluate their impact on overall survival (OS) in a group of patients with B-ALL. A total of 206 pediatric patients with de novo B-ALL were included. DNA was obtained from bone marrow samples at diagnosis before treatment initiation. A custom-designed next-generation sequencing panel was used for mutational analysis. Kaplan-Meier analysis was used for OS estimation. We identified the IKZF1plus profile in 21.8% of patients, which was higher than that previously reported in other studies. A significantly older age (p=0.04), a trend toward high-risk stratification (p=0.06), and a decrease in 5-year Overall Survival (OS) (p=0.009) were observed, although heterogeneous treatment protocols in our cohort would have impacted OS. A mutation frequency higher than that reported was found for IKZF1 (35.9%) and CDKN2A/2B (35.9%) but lower for PAX5 (26.6%). IKZF1MUT group was older at diagnosis (p=0.0002), and most of them were classified as high-risk (73.8%, p=0.02), while patients with CDKN2A/2BMUT had a higher leukocyte count (p=0.01) and a tendency toward a higher percentage of blasts (98.6%, >50% blasts, p=0.05) than the non-mutated patients. A decrease in OS was found in IKZF1MUT and CDKN2A/2BMUT patients, but the significance was lost after IKZF1plus was removed. Our findings demonstrated that Mexican patients with B-ALL have a higher prevalence of genetic markers associated with poor outcomes. Incorporating genomic methodologies into the diagnostic process, a significant unmet need in low- and mid-income countries, will allow a comprehensive identification of relevant alterations, improving disease classification, treatment selection, and the general outcome.

Refining risk stratification in paediatric B-acute lymphoblastic leukaemia: Combining IKZF1plus and Day 15 MRD positivity.

This study investigates the potential utility of IKZF1 deletion as an additional high-risk marker for paediatric acute lymphoblastic leukaemia (ALL). The prognostic impact of IKZF1 status, in conjunction with minimal/measurable residual disease (MRD), was evaluated within the MRD-guided TPOG-ALL-2013 protocol using 412 newly diagnosed B-ALL patients aged 1-18. IKZF1 status was determined using multiplex ligation-dependent probe amplification. IKZF1 deletions, when co-occurring with CDKN2A, CDKN2B, PAX5 or PAR1 region deletions in the absence of ERG deletions, were termed IKZF1plus. Both IKZF1 deletion (14.6%) and IKZF1plus (7.8%) independently predicted poorer outcomes in B-ALL. IKZF1plus was observed in 4.1% of Philadelphia-negative ALL, with a significantly lower 5-year event-free survival (53.9%) compared to IKZF1 deletion alone (83.8%) and wild-type IKZF1 (91.3%) (p < 0.0001). Among patients with Day 15 MRD ≥0.01%, provisional high-risk patients with IKZF1plus exhibited the worst outcomes in event-free survival (42.0%), relapse-free survival (48.0%) and overall survival (72.7%) compared to other groups (p < 0.0001). Integration of IKZF1plus and positive Day 15 MRD identified a subgroup of Philadelphia-negative B-ALL with a 50% risk of relapse. This study highlights the importance of assessing IKZF1plus alongside Day 15 MRD positivity to identify patients at increased risk of adverse outcomes, potentially minimizing overtreatment.

Tyrosine kinase inhibitor resistance in de novo BCR::ABL1–positive BCP-ALL beyond kinase domain mutations

AbstractA better understanding of ABL1 kinase domain mutation–independent causes of tyrosine kinase inhibitor (TKI) resistance is needed for BCR::ABL1–positive B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Although TKIs have dramatically improved outcomes, a subset of patients still experiences relapsed or refractory disease. We aimed to identify potential biomarkers of intrinsic TKI resistance at diagnosis in samples from 32 pediatric and 19 adult patients with BCR::ABL1–positive BCP-ALL. Reduced ex vivo imatinib sensitivity was observed in cells derived from newly diagnosed patients who relapsed after combined TKI and chemotherapy treatment compared with cells derived from patients who remained in continuous complete remission. We observed that ex vivo imatinib resistance was inversely correlated with the amount of (phosphorylated) BCR::ABL1/ABL1 protein present in samples that were taken at diagnosis without prior TKI exposure. This suggests an intrinsic cause of TKI resistance that is independent of functional BCR::ABL1 signaling. Simultaneous deletions of IKZF1 and CDKN2A/B and/or PAX5 (IKZF1plus), as well as deletions of PAX5 alone, were related to ex vivo imatinib resistance. In addition, somatic lesions involving ZEB2, SETD2, SH2B3, and CRLF2 were associated with reduced ex vivo imatinib sensitivity. Our data suggest that the poor prognostic value of IKZF1(plus) deletions is linked to intrinsic mechanisms of TKI resistance other than ABL1 kinase domain mutations in newly diagnosed pediatric and adult BCR::ABL1–positive BCP-ALL.

Developmental trajectories and cooperating genomic events define molecular subtypes of BCR::ABL1-positive ALL

AbstractDistinct diagnostic entities within BCR::ABL1-positive acute lymphoblastic leukemia (ALL) are currently defined by the International Consensus Classification of myeloid neoplasms and acute leukemias (ICC): “lymphoid only”, with BCR::ABL1 observed exclusively in lymphatic precursors, vs “multilineage”, where BCR::ABL1 is also present in other hematopoietic lineages. Here, we analyzed transcriptomes of 327 BCR::ABL1-positive patients with ALL (age, 2-84 years; median, 46 years) and identified 2 main gene expression clusters reproducible across 4 independent patient cohorts. Fluorescence in situ hybridization analysis of fluorescence-activated cell-sorted hematopoietic compartments showed distinct BCR::ABL1 involvement in myeloid cells for these clusters (n = 18/18 vs n = 3/16 patients; P < .001), indicating that a multilineage or lymphoid BCR::ABL1 subtype can be inferred from gene expression. Further subclusters grouped samples according to cooperating genomic events (multilineage: HBS1L deletion or monosomy 7; lymphoid: IKZF1-/- or CDKN2A/PAX5 deletions/hyperdiploidy). A novel HSB1L transcript was highly specific for BCR::ABL1 multilineage cases independent of HBS1L genomic aberrations. Treatment on current German Multicenter Study Group for Adult ALL (GMALL) protocols resulted in comparable disease-free survival (DFS) for multilineage vs lymphoid cluster patients (3-year DFS: 70% vs 61%; P = .530; n = 91). However, the IKZF1-/- enriched lymphoid subcluster was associated with inferior DFS, whereas hyperdiploid cases showed a superior outcome. Thus, gene expression clusters define underlying developmental trajectories and distinct patterns of cooperating events in BCR::ABL1-positive ALL with prognostic relevance.

Molecular Subtypes in BCR::ABL1-Positive ALL Are Defined By Cellular Origins and Cooperating Genomic Events

Two developmental trajectories are acknowledged in BCR::ABL1-positive acute lymphoblastic leukemia (ALL) as distinct diagnostic entities by the ICC classification: ‘lymphoid-only’ with BCR::ABL1 restricted to the leukemic B precursor compartment vs. ‘multilineage’ with BCR::ABL1 involvement also in other hematopoietic lineages. Diagnostic standards for establishing this distinction are lacking and associated biological and clinical features are insufficiently characterized. To establish developmental trajectories, biological phenotypes, and clinical impact we analyzed n=277 BCR::ABL1-positive ALL patients (age: 2-84 years, median: 46) including our GMALL reference data set (n=113) and two independent validation cohorts (MLL: n=61; St Jude's: n=103; Gu Z, et al. Nat Genet. 2019). Unsupervised gene expression analysis (RNA-Seq: n=277) identified two major gene expression clusters with two further sub-clusters each (Figure A). This clustering was confirmed by a machine learning classifier trained on the GMALL data set which achieved similar grouping of samples in the external validation cohorts. BCR:: ABL1-FISH on FACS-sorted bone marrow/peripheral blood samples revealed the presence of BCR::ABL1 in leukemic as well as myeloid cells in n=18/18 samples from the 1 st major cluster (termed 'multilineage'). In the 2 nd major cluster ('lymphoid'), BCR::ABL1 was restricted to the lymphoid lineage in n=13/16 samples (p&amp;lt;0.001), with n=3/16 cases harboring BCR::ABL1-positive myeloid cells at lower frequencies compared to the multilineage cluster. In each cluster, two patients also harbored BCR::ABL1-positive mature B cells. T cells remained BCR::ABL1-negative. Diagnostic FACS data and analysis of proximity to normal human lymphoid gene expression confirmed more frequent myeloid co-expression and higher proximity to normal pro-B cells in the multilineage cluster, whereas lymphoid cases had increased lymphoid surface marker expression and a stronger proximity to normal pre-B I cells. Genomic profiling using WGS/SNParrays (n=160) revealed significant enrichment for genomic events in the four gene expression sub-clusters: focal deletions comprising exons 1 and 2 of HBS1-like translational GTPase ( HBS1L) or monosomy 7 were strongly enriched in the two multilineage sub-clusters ('delHBS1L'; n=20/27 vs. n=3/133 in remaining cohort or 'del7'; n=16/25 vs. n=10/135; p&amp;lt;0.001). Remarkably, a novel alternative HBS1L transcript with a putative TSS in intron 3 was highly expressed in both multilineage sub-clusters but not in BCR::ABL1 negative ALL cases or healthy B lymphoid progenitors, suggesting this transcript as novel cooperating event in multilineage BCR::ABL1-positive ALL. One lymphoid sub-cluster was enriched for homozygous deletions in IKZF1 ('IKZF1'; n=11/55 vs. n=4/105; p=0.008), whereas the other was enriched for homozygous CDKN2A/B deletions (n=21/53 vs. n=3/107; p&amp;lt;0.001) and PAX5 deletions (n=33/53 vs n=26/107; p&amp;lt;0.001; 'CDKN2A/PAX5'). Hyperdiploid karyotypes were exclusive to the lymphoid main cluster, mostly in CDKN2A/PAX5. We analyzed the clinical implications of these newly established BCR::ABL1-positive ALL subtypes in our homogenously treated GMALL adult patient cohort (n=98, first diagnosis 2014-2021) including TKI treatment combined with age-adapted chemotherapy, MRD monitoring and allo-SCT in 1 st CR (n=84/98, 86%). Overall survival (OS) at 3 years was uniformly high in multilineage and lymphoid cases (70%±6% vs. 70%±8%; p=0.890; Figure B). However, analysis of the sub-clusters revealed an inferior 3-years OS for the IKZF1 -/- enriched cluster in contrast to excellent outcome in hyperdiploid cases and intermediate outcomes in the remaining sub-clusters (Figure B). These data highlight that transcriptomic signatures in BCR::ABL1-positive ALL are driven by developmental disease origins (‘lymphoid’ vs. ‘multilineage‘) and specific patterns of corresponding genomic events. Novel molecular subtypes of BCR::ABL1-positive ALL have distinct outcomes in the context of current GMALL treatment protocols. Gene-expression based subtype definitions enable classification of BCR::ABL1-positive ALL according to ICC definitions based on RNA-Seq data alone. These definitions have been implemented in ALLCatchR - our freely available tool for ALL subtype allocation - to facilitate validation and application in clinical diagnostics.

Deciphering the Structural Variants in B Cell Acute Lymphoblastic Leukemia By Optical Genome Mapping

Introduction Structural variants (SVs) of the genome play a key role in the leukemogenesis and development of B cell lymphoblastic leukemia (B-ALL), including gene deletion, amplification, translocation, and other forms. Methods for analyzing SVs and CNVs include karyotype analysis, fluorescence in situ hybridization, gene chips, and high-throughput gene sequencing technologies. Optical genome mapping (OGM) is a novel ultra-long single-molecule DNA detection based high throughput SVs analysis technology, which has the characteristics of whole genome coverage, high detection incidence and sensitivity. There were few publications presenting technical concordance of SVs detection beween karyotyping and OGM, and there are no systematic studies comparing the concordance of OGM and RNA-seq in detecting gene fusion. This study aimed to compare the concordance of OGM and RNA-seq in the detection of fusion genes in B-ALL cases, and the additional findings using OGM technology. Methods Bone marrow aspirates of 70 patients with newly diagnosed or relapsed/refractory B-ALL were recruited into the study. All samples were conducted with both OGM and transcriptome sequencing (RNA-seq). Among these cases, 42 males and 28 females, 30 pediatric (&amp;lt; 18 years) and 40 adults (≥ 18 years) cases, ages ranged 4-60 years (median 16 years). Results Totally 50 gene fusions were reported in 48 cases, with 2 cases each carrying two fusion genes ( BCR::ABL1/ PAX5::ELK3 and P2RY8::CRLF2/ PAX5::GSE1, respectively) (Figure 1A). OGM and RNA-seq have complete concordance in reporting gene fusions, and OGM provides further insight into the genomic events that lead to gene fusion. A subtype of B-ALL characterized by UBTF microdeletion leading to UBTF::ATXN7L3 fusion and PAN3 downstream deletion-induced CDX2 aberrant expression has been reported recently, and has been accepted by the International Consensus Classification as a novel molecular subtype of UBTF/CDX2 of B-ALL. We performed the OGM investigation on 6 UBTF/CDX2 cases which were identified by RNA-seq. OGM identified both microdeletion events in all 6 cases, and further reported 1q amplification in 3 of them (Figure 1B, C). B-lymphocyte differentiation-associated transcription factor gene defects are common and important genetic abnormalities in B-ALL, often manifested as complete or partial deletion of genes. We focused on a panel including 30 genes in the OGM data and determined IKZF1 deletion in 35 patients, CDKN2A/B deletion in 32 patients, and PAX5 deletion in 25 patients (Figure 1 A). Follow-up data showed that patients with CDKN2A/B deletion had a worse prognosis than those without CDKN2A/B deletion ( P = 0.025). Conclusion This is the first B-ALL cohort to systematically compare OGM and RNA-seq in gene fusion detection, and the result showed complete consistency. RNA-seq has significant advantages in analyzing gene fusion transcripts, while OGM has technical advantages in analyzing SVs at the genome level. Combining the two technologies can accurately analyze gene fusion and other SVs in B-ALL, significantly improve the detection rate of SVs with important pathological/diagnostic classification significance, and may bring new discoveries on SVs and pathogenic mechanisms.

A Novel Germline PAX5 Single Exon Deletion in a Paediatric Patient with B-Cell Leukaemia

Germline predisposition underlies leukaemia development in children in 5-10% of the cases. Over the past years, several somatic drivers for leukaemia, including IKZF1, RUNX1, ETV6 and PAX5, have also been identified as leukaemia predisposing genes. For example, two germline PAX5 missense variants (p.Arg38His and p.Gly183Ser) have been identified in five families with a high incidence of B-cell precursor acute lymphoblastic leukaemia (BCP-ALL). The susceptibility to BCP-ALL in these patients is inherited in an autosomal dominant pattern with an incomplete but relatively high penetrance. The leukemic cells in the patients showed loss of the wild-type allele or a somatic mutation, suggesting a second hit is required for leukaemia development in this context. We present a boy who developed BCP-ALL at 5-years-old, with a father who was diagnosed with acute undifferentiated leukaemia at infancy. Because of his family history, germline testing of the patient and his parents was performed using SNP-based copy number analysis and whole exome sequencing (WES). This revealed a PAX5 exon 6 deletion in the child, which was absent in both parents. The PAX5 deletion causes a frameshift with premature stop in exon 7, resulting in a truncated protein with loss of the C-terminal transactivating and inhibitory domains. In contrast to what has been observed in patients with germline PAX5 missense variants, a second somatic hit in PAX5 was not observed. Genotype analysis, using heterozygous SNPs around the PAX5 deletion, revealed that the PAX5 deletion had occurred on the paternal allele. To test whether this deletion was present in (low) mosaic state in the father, we developed a sensitive breakpoint spanning PCR. Also with this method, the PAX5 deletion was not detected in DNA derived from blood and buccal cells of the father. Since we expected a causative germline variant to be inherited from the father, we re-analysed all sequence and copy number variants in the patient-parents' trio datasets for any other aberrations, but no plausible alternative candidates were identified. Since routine diagnostic analysis of PAX5 deletions is usually performed only in leukaemia samples, germline deletions could potentially be missed, particularly in isolated cases. To investigate the incidence of germline PAX5 deletions, we used a multiplex-ligated probe amplification (MLPA) dataset from 2041 ALL patients, from which we selected 303 cases with single-exon or partial (multiple exon) PAX5 deletion. Subsequently, we performed MLPA on 261 DNA samples from bone marrow or peripheral blood at time of remission. No additional case was found, suggesting that germline PAX5 deletions, if recurrent, are very rare. In conclusion, we present a boy with ALL carrying a de novo germline PAX5 exon 6 deletion leading to a truncated protein. Germline PAX5 deletions have not yet been described in ALL patients but since somatic PAX5 aberrations are common in ALL and germline PAX5 variants have been associated with ALL, we consider that this focal germline PAX5 deletion did contribute to leukaemia development in the boy.

Prognostic Significance of Chromosomal Genomic Array Testing in Adults with Newly Diagnosed Acute Lymphoblastic Leukemia

Introduction: As part of the diagnostic workup in newly diagnosed acute lymphoblastic leukemia (ND-ALL) in adults, chromosomal genomic array testing (CGAT) is frequently added to karyotype and fluorescence in situ hybridization (FISH) to enhance mutational profiling by allowing for more precise analysis of genomic copy number alterations (CNAs) and copy-neutral loss-of-heterozygosity that may impact genes of clinical significance. Despite its increasing use, the prognostic role of CGAT in ND-ALL in adults, and how to apply its findings to clinical decision making, is not well-established. Stanulla and others (JCO 2018) defined the IKZF1plus signature as IKZF1 deletions co-occurring with deletions in CDKN2A/B, PAX5, or PAR1 in the absence of an ERG deletion: this was based on CNAs and carries adverse prognostic significance in pediatric ALL. We hypothesized that by correlating CGAT results at the time of diagnosis with key demographic and outcomes data, we can enhance our ability to risk-stratify patients (pts) at the time of diagnosis. Methods: Eligible pts included those ≥18 years old diagnosed with ALL at our center between January 2012 and March 2022. We collected relevant demographic, laboratory, treatment, and outcome data. For CGAT, genomic DNA (gDNA) was processed on the CytoScan™ HD Array (ThermoFisher, MA), targeting a genome-wide region with 2.4 million markers for copy number and approximately 750,000 genotype-able small nucleotide polymorphisms (SNPs). The data were analyzed using Nexus Copy Number software with manual curation. Karyotype and FISH were performed in the conventional manner and classified per NCCN. The primary objectives were to characterize recurrent CGAT abnormalities and examine their correlation with survival. Results: We identified 196 pts with ND-ALL who had CGAT testing performed at diagnosis and received treatment at our center: 54 pts with available data comprised our initial discovery set (Table). CGAT among these pts disclosed large segmental CNAs frequently associated with ALL, such as gains of chromosome X, 1/1q, and 8q; and deletions of 7p, 9p, and 12p. Peak regions with CNAs were detected, which are regions with higher frequencies of aberrations compared with chromosomal segments on either side. We further investigated peak regions that showed aberrations in at least 15% of pts. After removing those that are entirely copy number variation (CNV), the following genomic loci were identified, in order of decreasing frequency: IKZF1 (55%; 17% homozygous loss), CDKN2A (50%), PAX5 (26%), ZCCHC7 (24%), LINC01619 (24%), RB1 (19%), ETV6 (17%), EBF1 (15%), ATP10A (15%), and SLX4IP (15%). The IKZF1plus signature was identified in 30% of pts. In pts without high-risk cytogenetics (n=17), 88% harbored aberrations in ≥1 of these genes: 29% had IKZF1 deletion and 18% had the IKZF1plus signature. Other commonly observed associations include IKZF1 deletion seen in 85% of Philadelphia-chromosome (Ph)+ pts (n=20) vs. 38% of Ph- (n=34) and CDKN2A deletion seen in 77% of pts with WBC >30K/µL (n=18) vs. 39% without (n=36). With a median follow-up of 2.1 years, there was no significant difference in median OS of the IKFZ1plus cohort (n=17; 4.1 yrs) vs. all IKZF1-deleted (including mono- and biallelic deletions) cohort (n=30; 4.1 yrs), vs. IKZF1 wild type (WT) (n=24, not reached) (p = 0.7). We next created univariate logistic regression models for mortality: statistically significant genomic loci included PAX5 deletion (OR 5.26, 95% CI 1.47-20.0), ZCCHC7 deletion (OR 4.34, 95% CI 1.17-16.67), and ETV6 deletion (OR 5.0, 95% CI 1.07-22.7). In a multivariable logistic regression model for mortality, the strongest associations were seen with PAX5 deletion (OR 4.0, 95% CI 1.0-16.39) and ETV6 deletion (OR 5.0, 95% CI 1.1-27.78): the median OS in the PAX5 deletion (n=14; 2.2 yrs) and the ETV6 deletion (n=9; 2.2 yrs) cohorts was inferior to the PAX5/ETV6 WT cohort (n=35; not reached) (p=0.035; Figure). Discussion: In this initial discovery-phase analysis of CGAT in ND-ALL in adults, we identified CNAs involving well-described genes (e.g. IKZF1), and lesser-described genes (e.g. LINC016919). Abnormal CGAT was seen in nearly all pts with otherwise normal or good cytogenetic risk. IKZF1plus was not associated with worse survival in this adult cohort, though deletions of PAX5 and ETV6 were. Analysis of additional pts to validate the significance of our findings will be presented. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Impact of IKZF1 Deletions in the Prognosis of Childhood Acute Lymphoblastic Leukemia in Argentina.

Simple SummaryAn association of deletions in the IKZF1 gene (IKZF1del) with poor prognosis in acute lymphoblastic leukemia (ALL) has been demonstrated. However, the co-occurrence of IKZF1del with deletions in other genes (IKZF1plus) seems to better define prognosis. Our aim was to analyze the influence of IKZF1del and/or IKZF1plus profiles on the survival of children with ALL. We analyzed 1023 eligible cases who were classified into three subsets: IKZF1not-del: IKZF1-not-deleted (n = 835), IKZF1del: IKZF1deleted (n = 94) and IKZF1plus: IKZF1del plus deletion of other genes (n = 94). Leukemia-free-survival probability (standard deviation) (LFSp(SE)) was 75 (2)% for IKZF1not-del, 51 (6)% for IKZF1del and 48 (6)% for IKZF1plus (p-value < 0.00001). The LFSp(SE) according to ALL-IC risk-group stratification showed a statistically significant difference within Intermediate-Risk patients, LFSp (SE) being 77 (2)% for IKZF1not-del, 61 (10)% for IKZF1del and 54 (7)% for IKZF1plus (p-value = 0.0005). The LFSp(SE) of the high-risk group was: 61 (4)% IKZF1not-del, 38 (8)% IKZF1del and 35 (9)% IKZF1plus (p-value = 0.0102). Thus, the IKZF1 status was shown to define a population of patients with a poor outcome, mainly in those with intermediate risk. However, not-significant differences were observed between the LFSp of IKZF1del versus IKZF1plus groups. The study of the IKZF1 status should be incorporated into the risk-group stratification of pediatric ALL.An association of deletions in the IKZF1 gene (IKZF1del) with poor prognosis in acute lymphoblastic leukemia (ALL) has been demonstrated. Additional deletions in other genes (IKZF1plus) define different IKZF1del subsets. We analyzed the influence of IKZF1del and/or IKZF1plus in the survival of children with ALL. From October 2009 to July 2021, 1055 bone marrow samples from patients with ALL were processed by Multiplex ligation-dependent probe amplification (MLPA). Of them, 28 patients died during induction and 4 were lost-in-follow-up, resulting in an eligible 1023 cases. All patients were treated according to ALLIC-BFM-2009-protocol. Patients were classified into three subsets: IKZF1not-deleted (IKZFF1not-del), IKZF1deleted (IKZF1del) and IKZF1del plus deletion of PAX5, CDKN2A, CDKN2B and/or alterations in CRLF2 with ERG-not-deleted (IKZF1plus). The LFSp and SE were calculated with the Kaplan–Meier calculation and compared with a log-rank test. From the 1023 eligible patients, 835 (81.6%) were defined as IKZF1not-del, 94 (9.2%) as IKZF1del and 94 (9.2%) as IKZF1plus. Of them, 100 (9.8%) corresponded to Standard-Risk (SRG), 629 (61.5%) to Intermediate-Risk (IRG) and 294 (28.7%) to High-Risk (HRG) groups. LFSp(SE) was 7 5(2)% for IKZF1not-del, 51 (6)% for IKZF1del and 48 (6)% for IKZF1plus (p-value < 0.00001). LFSp(SE) according to the risk groups was: in SRG, 91 (4)% for IKZF1not-del, 50 (35)% IKZF1del and 100% IKZF1plus (p-value = ns); in IRG, 77 (2)% IKZF1not-del, 61 (10)% IKZF1del and 54 (7)% IKZF1plus (p-value = 0.0005) and in HRG, 61 (4)% IKZF1not-del, 38 (8)% IKZF1del and 35 (9)% IKZF1plus (p-value = 0.0102). The IKZF1 status defines a population of patients with a poor outcome, mainly in IRG. No differences were observed between IKZF1del versus IKZF1plus. MLPA studies should be incorporated into the risk-group stratification of pediatric ALL.

Ponatinib and Chemotherapy in Adults with De Novo Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia. Final Results of Ponalfil Clinical Trial

Background and objective. The combination of HyperCVAD and ponatinib resulted in a high molecular response rate and survival in adults with Ph+ ALL, suggesting improved outcome compared with combinations of chemotherapy with first- or second-generation tyrosine kinase inhibitors (TKI) (Jabbour E, et al, Lancet Haematol. 2018;5:e618-e627). The Spanish PETHEMA group conducted the phase 2 PONALFIL trial, which incorporates ponatinib to the same chemotherapy as that of the ALL Ph08 trial that used imatinib as TKI (Ribera JM et al. Cancer 2019;125:2810-17). Final results of this trial are reported.Patients and method. PONALFIL trial (NCT02776605) combined ponatinib (30 mg/d) and induction chemotherapy (vincristine, daunorubicin, prednisone) followed by consolidation (high-dose methotrexate, high-dose ARA-C, mercaptopurine, etoposide) and allogeneic hematopoietic stem cell transplantation (alloHSCT). Ponatinib was scheduled after alloHSCT only for patients (pts) with persistence/reappearance of MRD. Response to therapy (complete morphological [CR], molecular [complete -CMR- or major -MMR-] after induction and before alloHSCT) (assessed by centralized BCR-ABL1/ABL1 ratio), disease-free survival (DFS), overall survival [OS]) and toxicity were analyzed. The following genetic studies were performed: 1. Additional gene abnormalities (Copy Number Alteration [CNA] analysis by SNP array Affymetrix 750K), 2. ABL1 mutation status at diagnosis (Sanger sequencing), 3. T315I mutation at diagnosis (allele-specific PCR). A propensity score comparison with the results of the ALL Ph08 trial was performed.Results. Median age was 49 (19-59) years (y), and 13/30 pts were female. One pt showed CNS involvement at diagnosis. ECOG score was <2 in 90% of pts. Median WBC count was 6.4 x10 9/L (0.6-359.3), Hb 90 g/L (63-145), platelets 38 x10 9/L (11-206). Immunologic phenotype was common in 26 cases, with p190 isoform in 20 pts (67%), p210 in 9 (30%) and p230 in 1 (3%). CR was attained in 30/30 pts, CMR in 14/30 (47%), MMR in 5/30 (17%) and no molecular response in 11/30 (37%). Two pts withdrew the trial during induction (thrombosis of central retina artery and severe intestinal infection, one case each). Consolidation was given to 28 pts, 2 pts withdrew the trial (physician's decision and lack of molecular response, one case each) and 26 pts received alloHSCT (20 in CMR, 6 in MMR). No relapses before HSCT were detected. One pt died by severe GVHD and two withdrew the trial (grade IV hepatic toxicity:1, protocol deviation after molecular relapse:1). One pt relapsed in BM after HSCT. Ponatinib was given after HSCT in 4/26 pts and dasatinib in 1/26 due to MRD reappearance, and 1/26 received dasatinib in CMR because of refusal to receive CNS prophylaxis, whereas 20/26 pts did not receive any TKI therapy after HSCT. Twenty-nine pts are alive (median follow-up 2.3y, range 1.3-4). 2y DFS and OS probabilities were 97% (91%-100%) and 97% (91%-100%) (Figure 1).Among 7/16 pts without CMR after consolidation and genetic material available, 4 showed IKZF1 deletion (IKZF1 plus in 2), 1 showed CDKN2A/B and PAX5 deletion and 2 did not show any CNA. Among 5/19 pts with molecular relapse, 3 showed IKZF1 deletion (1 being IKZF1 plus), and 2 pts did not show any CNA. No ABL1 mutations or T315I mutation at diagnosis were found.Propensity score with 1:1 matching identified 30 pts in each cohort (variables: age, gender, ECOG, WBC, CNS involvement, cytogenetic risk and BCR/ABL isoform). 2y DFS rates for PONALFIL and ALL Ph08 trials were 97% and 62%, (p=0.005), and 2y OS rates were 97% and 66% (p=0.001) (Figure 2).107 adverse events (AE) were registered in 20 pts (21 severe in 11 pts), prompting to withdrawn of the trial in 3 (thrombosis of central retina artery, severe bowel infection, grade IV hepatic toxicity). The most frequent AE were hematologic (28%), gastrointestinal (14%), hepatic (11%), infections (7%), and cutaneous (5%). Cardiovascular events occurred in 2 patients (angor pectoris and thrombosis of central artery of the retina).Conclusions. The results of the PONALFIL trial show a high antileukemic efficacy with acceptable toxicity profile and compare favorably with the same chemotherapy schedule and imatinib.Supported in part by grant 2017 SGR288 (GRC) Generalitat de Catalunya and “La Caixa” Foundation.Figure 1. OS (A) and DFS (B). PONALFIL.Figure 2. OS (A) and DFS (B). PONALFIL vs. ALL Ph08. [Display omitted] DisclosuresRibera: AMGEN: Consultancy, Research Funding, Speakers Bureau; NOVARTIS: Consultancy, Speakers Bureau; TAKEDA: Consultancy, Research Funding, Speakers Bureau; ARIAD: Consultancy, Research Funding, Speakers Bureau; SHIRE: Consultancy, Speakers Bureau; Pfizer: Consultancy, Research Funding, Speakers Bureau. Esteve: Novartis: Consultancy, Research Funding; Pfizer: Consultancy; Abbvie: Consultancy; Bristol Myers Squibb/Celgene: Consultancy; Novartis: Research Funding; Jazz: Consultancy; Astellas: Consultancy. Mercadal: Roche: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Gilead Sciences, Inc.: Honoraria, Speakers Bureau. Martínez-López: Roche, Novartis, Incyte, Astellas, BMS: Research Funding; Janssen, BMS, Novartis, Incyte, Roche, GSK, Pfizer: Consultancy. OffLabel Disclosure:This trial includes Ponatinib in off-label indication.

Genomic landscape of B-other acute lymphoblastic leukemia in an adult retrospective cohort with a focus on BCR-ABL1-like subtype

Introduction BCR-ABL1-like acute lymphoblastic leukemia (ALL) is a high-risk disease with a complex genomic background. Though extensively studied, data on the frequency and mutual associations of present mutations are still incomplete in adult patients. This retrospective study aims to map the genomic landscape of B-other ALL in a cohort of adult patients with a focus on the BCR-ABL1-like ALL subtype. Methods We analyzed bone marrow and peripheral blood samples of adult B-other ALL patients treated consecutively at three major Czech teaching hospitals. Samples were analyzed by cytogenetic methods, gene expression profiling, multiplex ligation-dependent probe amplification (MLPA), and next-generation sequencing (NGS). Results Fifty-eight B-other ALL patients (not BCR-ABL1, KMT2A-rearranged, ETV6-RUNX1, TCF3-PBX1, or iAMP21) were included in the study. Median follow-up was 23.8 months. Samples from 33 patients were available for a gene expression analysis, 48.9% identified as BCR-ABL1-like ALL. Of the BCR-ABL1-like ALL cases, 18.8% harbored IGH-CRLF2 and 12.5% P2RY8-CRLF2 fusion gene. We observed a higher MRD failure rate in BCR-ABL1-like than in non-BCR-ABL1-like ALL patients after the induction treatment (50.0 vs. 13.3%, p=.05). There was a trend to worse progression-free and overall survival in the BCR-ABL1-like group, though not statistically significant. Deletions in IKZF1 gene were found in 31.3% of BCR-ABL1-like cases. Patients with concurrent IKZF1 and CDKN2A/B, PAX5 or PAR1 region deletions (IKZF1 plus profile) had significantly worse progression-free survival than those with sole IKZF1 deletion or IKZF1 wild-type (p=.02). NGS analysis was performed in 54 patients and identified 99 short variants in TP53, JAK2, NRAS, PAX5, CREBBP, NF1, FLT3, ATM, KRAS, RUNX1, and other genes. Seventy-five of these gene variants have not yet been described in B-cell precursor ALL to date. Conclusion This study widens existing knowledge of the BCR-ABL1-like and B-other ALL genomic landscape in the adult population, supports previous findings, and identifies a number of novel gene variants.

A multicenter total therapy strategy for de novo adult Philadelphia chromosome positive acute lymphoblastic leukemia patients: final results of the GIMEMA LAL1509 protocol.

The GIMEMA LAL1509 protocol, designed for adult (≥18-60 years) de novo Philadelphia chromosome positive (Ph+) acute lymphoblastic leukemia (ALL) patients, was based on dasatinib plus steroids induction - with central nervous system prophylaxis - followed by dasatinib alone in patients in complete molecular response or by chemotherapy and/or allogeneic transplant in patients not reaching complete molecular response. Sixty patients (median age 41.9 years) were enrolled: 33 were p190+, 18 p210+ and nine p190/p210+. At the end of induction (day +85), 58 patients (97%) achieved complete hematologic remission. No deaths in induction were recorded. Eleven patients (18.3%) obtained complete molecular response. Among the incomplete molecular responders (n=47), 22 underwent an allogeneic transplant. Seventeen hematologic relapses occurred (median 7 months; range, 3-40.1): 13 during consolidation and four post-transplant. ABL1 mutations (five T315I, three V299L, one E281K and one G254E) were found in ten of 13 relapsed cases. With a median follow-up of 57.4 months (range, 4.2-75.6), overall survival and disease-free survival were 56.3% and 47.2%. A better disease-free survival was observed in patients who obtained a molecular response at day +85 compared to cases who did not. The presence of additional copy number aberrations - IKZF1 plus CDKN2A/B and/or PAX5 deletions - was the most important unfavorable prognostic factor on overall and disease-free survival (P=0.005 and P=0.0008). This study shows that in adult Ph+ ALL long-term survivals can be achieved with a total-therapy strategy based on a chemotherapyfree induction and, in complete molecular responders, also without further systemic chemotherapy. Finally, the screening of additional copy number aberrations should be included in the diagnostic work-up (clinicatrial gov. Identifier: EudraCT 2010-019119-39).

Prognostic Significance of IKZF1, PAX5, and CDKN2A Deletions in Patients with Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia Treated with Hyper-CVAD/MA with Dasatinib or Ponatinib

Prognostic Significance of IKZF1, PAX5, and CDKN2A Deletions in Patients with Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia Treated with Hyper-CVAD/MA with Dasatinib or Ponatinib

A novel PAX5 rearrangement in TCF3-PBX1 acute lymphoblastic leukemia: a case report

BackgroundChromosome translocations are a hallmark of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Additional genomic aberrations are also crucial in both BCP-ALL leukemogenesis and treatment management. Herein, we report the phenotypic and molecular cytogenetic characterization of an extremely rare case of BCP-ALL harboring two concomitant leukemia-associated chromosome translocations: t(1;19)(q23;q13.3) and t(9;17)(p13;q11.2). Of note, we described a new rearrangement between exon 6 of PAX5 and a 17q11.2 region, where intron 3 of SPECC1 is located. This rearrangement seems to disrupt PAX5 similarly to a PAX5 deletion. Furthermore, a distinct karyotype between diagnosis and relapse samples was observed, disclosing a complex clonal evolution during leukemia progression.Case presentationA 16-year-old boy was admitted febrile with abdominal and joint pain. At clinical investigation, he presented with anemia, splenomegaly, low white blood cell count and 92% lymphoblast. He was diagnosed with pre-B ALL and treated according to high risk GBTLI-ALL2009. Twelve months after complete remission, he developed a relapse in consequence of a high central nervous system and bone marrow infiltration, and unfortunately died.ConclusionsTo our knowledge, this is the first report of a rearrangement between PAX5 and SPECC1. The presence of TCF3-PBX1 and PAX5-rearrangement at diagnosis and relapse indicates that both might have participated in the malignant transformation disease maintenance and dismal outcome.

Comprehensive Genomic Analysis Identified Acute Lymphoblastic Leukemia in Down Syndrome Was Highly Heterogeneous with the High Prevalence of Ph-like Signature

BackgroundAcute lymphoblastic leukemia (ALL) in Down syndrome (DS) have uncommon genetic alterations such as mutations of JAK2, RAS, and overexpressions of CRLF2. These findings suggest DS-ALL may have unique biological features compared with non-DS-ALL. While recent studies implicated HMGN1 or DYRK1A in chromosome 21 were associated with molecular pathogenesis of DS-ALL, it remains to be elucidated what predispose DS children to develop ALL.Materials and MethodsWe performed whole transcriptome sequencing, targeted deep sequencing, and SNP array analysis in 25 DS-ALL samples, which included four ETV6-RUNX1 fusions and one high hyperdiploid. To compare with DS-ALL, we also performed whole transcriptome sequencing and whole exome sequencing to 118 non-DS-ALL samples, which included several subtypes such as ETV6-RUNX1 or BCR-ABL1. To cluster gene expression profiling, we applied the hierarchical clustering method. The detection of Ph-like signatures was performed by the hierarchical clustering by the gene set reported by Harvey.ResultsIn expression analysis, we identified 19 fusions in 25 DS-ALL samples. These fusions included 15 recurrent fusions in pediatric BCP-ALL and 4 novel fusions, which including SSBP3-DHCR24, PDGFA-TTYH3, and NIN-NDUFA6. In novel fusions, PDGFA-TTYH3 fusions were detected in two DS-ALL samples. The hierarchical clustering analysis (Figure 1) combining 25 DS-ALL with 123 non-DS ALL samples. In our cohort, we defined samples with PAX5 alteration only such as a mutation or fusion as PAX5-altered. This clustering revealed ALL samples were divided into six clusters (cluster E1 to E6). Among six clusters, DS-ALL samples were divided into four clusters. In these four clusters, chi-square test revealed the significant enrichment of DS-ALL in E6 cluster. Importantly, our expression analysis revealed DS-ALL samples were highly heterogeneous and had the same expression pattern corresponding to each subtype same as non-DS-ALL. Cluster E3 included most samples with PAX5 fusions. All samples with ETV6-RUNX1 fusions were classified into cluster E4. Most samples of high hyperdiploid were classified into cluster E5. Cluster E6 was characterized by BCR-ABL1 fusions and Ph-like signatures. We detected 21 samples had Ph-like signatures, which included seven DS-ALL samples and 14 non-DS-ALL samples. Though we also analyzed differentially expressed genes between DS-ALL and non-DS-ALL, no genes on chromosome 21 such as HNGN1 or DYRK1A was significantly expressed. To investigate a relation between expression and genomic status, we further searched mutational analysis and copy number analysis (Figure 2). In 25 DS-ALL samples, six samples revealed JAK2 mutations and CRLF2 fusions. Interestingly, all of these six samples had Ph-like signatures. In cluster E5, one non-DS-ALL sample revealed JAK2 mutation and CRLF2 fusion and this particular sample was expected to have the Ph-like signature. To detect other Ph-like samples, we performed hierarchical clustering of 143 ALL samples based on the genes with a significantly (adjusted P value <0.0001) high expression in already detected 21 Ph-like samples. This analysis revealed three additional samples (two DS-ALL and one non-DS-ALL) had Ph-like signatures. Intriguingly, Ph-like samples accounted for 36% in 25 DS-ALL samples. In contrast, because several subtypes in non-DS-ALL showed mutations of RAS pathway genes, mutations of RAS pathway genes are common drivers in pediatric BCP-ALL. Copy number analysis elucidated one DS-ALL sample in cluster E3 had a known focal amplification of chromosome 9 involving exon 2 to 5 of PAX5, which may result in dysfunction of PAX5. Though no report analyzed PAX5 status except for deletion in DS-ALL, DS-ALL had not only deletion of PAX5, but also miscellaneous aberrations such as amplification or fusion. One DS-ALL sample without ETV6-RUNX1 in cluster E4 had homozygous deletions of ETV6, implicating ETV6-RUNX1-like signature.ConclusionOur result suggested DS-ALL were highly heterogeneous. Though expression profiles of DS-ALL had similar to non-DS-ALL, frequencies of subtypes in DS-ALL were quite different from non-DS-ALL, that is, low incidence of ETV6-RUNX1 or HeH, and high incidence of Ph-like signatures. Because molecular targeting agents such as imatinib or ruxolitinib improve the prognosis of Ph-like ALL, these agents may be also promising for treatment of DS-ALL. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Comprehensive Sequencing Identifies High Frequency of Copy Number Changes in Korean Patients with Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) is a genetically complex and heterogeneous disease with a wide range of genetic variations thus identified. As genomic profiling and sequencing studies have revealed genetic basis of ALL, a number of genetic variations are gaining clinical significance in connection with risk stratification and targeted therapy. With the need for comprehensive high-throughput analysis, next-generation sequencing (NGS) has become a good candidate for clinical testing. We have designed a comprehensive NGS assay to detect somatic mutations, translocations, and copy number changes and have evaluated its clinical utility in patients with ALL. The panel reliably detected single nucleotide variations (SNV) and copy number analysis was exceptionally helpful in identifying geneic and chromosomal deletions and duplications.A total of 101 samples of 96 patients were tested. Those patients consist of 40 adults (median age 38, range 21-76) and 56 children (median age 6.5, range 0-17), and diagnoses include 76 B-ALLs and 20 T-ALLs. The most-frequently mutated gene was TP53 (7/96, 7.3%). Ras pathway were also frequently observed (21/96, 29%) in B-ALL and were associated with hyperdiploidy (P< 0.001). Mutations in PHF6, PTEN, FBXW7, JAK3 and WT1 were detected in patients with T-ALL, and all the variants were SNVs. PHF6 mutations were most common among T-ALL patients (7/20, 35%), followed by mutations in FBXW7 (5/20, 25%). Deletions outnumbered duplications, and the most frequently deleted was CDKN2A, followed by transcription factor genes including, IKZF1, PAX5, EBF1, and ETV6. IKZF1 deletion was more frequent in adults (P<0.005), and associated with BCR-ABL1 translocation (P<0.001). PAX5 deletion was also associated with BCR-ABL1 (P<0.001) and also observed in translocations representing Philadelphia-like ALL.Fifty patients were with chromosomal abnormality detected by NGS, and some of them showed normal cytogenetics with a conventional method. Hyperdiploidy and interstitial deletion or duplication can be more easily detected; 11 cases were reclassified as B-ALL with hyperdiploidy, and numerical abnormalities and other copy number changes were identified in seven and 20 patients, respectively. Among 31 gene fusions identified by RT-PCR or NGS RNA fusion panel, only 17 (54.8%) were detected by DNA-based NGS testing.Our NGS gene panel and bioinformatics tools showed excellent performance confirming the clinical utility in identification of important variants in patients with ALL. SNVs and CNVs could be identified simultaneously in a single assay, which could be an alternative or supplement for several conventional tests and simplify the testing processes. We found unexpectedly high proportion of CNVs in ALL, suggesting the need for intensive bioinformatics analysis for CNVs and careful interpretation. DisclosuresNo relevant conflicts of interest to declare.

Impact of IKZF1 Deletions and IKZF1 Plus in Pediatric Acute Lymphoblastic Leukemia Outcome

Introduction: Survival of children with acute lymphoblastic leukemia (ALL) has improved in the last decades, achieving approximately 80% in Argentina. However, relapses remain the most frequent adverse event and the identification of patients with higher risk need to be refined. Deletions in IKZF1(IKZF1del) in addition with deletion of CDKN2A, CDKN2B,PAX5 or PAR1 region define a new subgroup of patients (IKZF1plus) with higher relapse rate and poor survival.Objectives: To analyze the characteristics of patients with IKZF1del and IKZF1plus, assessing the impact of the copy number alterations in several genes on survival of pediatric ALL treated with ALLIC strategy.Methods: This is a retrospective analysis performed in the population of patients admitted from October 2009 to May 2018. Samples of 432 patients with diagnosis of ALL were collected and analyzed by MLPA P-335 (MRC-Holland) for copy number alterations of IKZF1, EBF1, JAK2, CDKN2A, CDKN2B, PAX5, ETV6, BTG1, RB1 genes and PAR1 region. IKZF1plus cases were defined as those with IKZF1del with at least one additional deletion in: PAX5, CDKN2A, CDKN2B, PAR1 region. Patients were treated with 2 consecutive ALLIC protocols, according to studies stratification. Patient characteristics were compared with chi-square and Wilcoxon-sum-rank-test. Survival probability was analyzed with Kaplan-Meier calculation and survival results compared with Log-rank-test.Results: IKZF1 was not deleted in 345 cases, IKZF1del was detected in 87 cases and 47 of them were defined as IKZF1plus. Statistically significant higher WBC, MRD+ positivity on day 15, day 33 and week 12, more BCR-ABL+ and high-risk group cases, null response and higher relapse rate were observed in the IKZF1del group (total) when comparing with IKZF1 not del, and also when comparing IKZF1plus vs IKZF1 not del + IKZF1del only. EFS (SE) and DFS (SE) probabilities were: 73 (4)% and 75 (3)% for IKZF1 not del, 66 (9)% and 70 (9)% for IKZF1del, and 20 (10)% and 21 (10)% for IKZF1plus, respectively (p<0.00001).DFS of the standard-risk group was not influenced by the presence of only 1 case of IKZF1del detected in this risk-group of patients. However, DFS of intermediate-risk patients was 41 (11)% for IKZF1plus while 70 (7)% and 73 (4)% were achieved for IKZF1del and IKZF1 not del respectively (p=0,0083). Therefore, high-risk patients with IKZF1plus achieved DFS of 12 (19)% vs 65 (7)% and 50 (21)% for IKZF not del and IKZF1del respectively (p=0.0085). DFS of patients with IKZF1del + CDKN2Adel was 30 (10)% and CDKN2A not deleted 67 (9)% (p=0.0433). DFS of patients with IKZF1del + CDKN2Bdel was 42 (12)% and 66 (9)% for CDKN2B not del. DFS of cases with IKZF1del in addition to deletion of ETV6, BTG1, EBF1 orJAK2 did not show statistically significant differences when comparing with IKZF1del + normal copy number of these genes. In addition, DFS of cases with RB1del was 36 (13)% while cases without RB1del showed 70 (3)% (p=0.0071).Conclusions: 1- Patients with IKZF1del and IKZF1plus disclosed biological features related to poor outcome. 2- IKZF1plus was associated with a poor outcome in intermediate and high-risk groups according to ALLIC stratification. 3- The addition of CDKN2Adel to IKZF1del influence the outcome. However, CDKN2Bdel did not show the same effect. 4- Copy number alterations of ETV6, BTG1, EBF1 or JAK2 did not demonstrate prognostic impact. 5- RB1 showed negative influence in survival. 6- Identification of patients with IKZF1plus at diagnosis could be very useful for improving risk-group stratification of pediatric ALL patients. DisclosuresNo relevant conflicts of interest to declare.

Inactivation of Stage-Specific B-Cell Commitment Genes Generates Distinct Molecular Subtypes of BCR-ABL1 Lymphoblastic Leukemia

Background Philadelphia-chromosome positive acute lymphoblastic leukemia (Ph+ ALL), the most common form of ALL in adults, is a highly aggressive blood malignancy defined by the BCR-ABL1 fusion. Although inhibitors targeting the BCR-ABL1 oncoprotein, such as imatinib, have significantly improved clinical response rates for this disease, a subset of patients are refractory to therapy or respond initially but relapse soon after. ABL1 kinase domain mutations partly explain differential responses in patients; however, for the majority of cases, a molecular basis that can reconcile this clinical observation is lacking.Methods Flow-sorted blasts from 53 primary samples, 49 de novo Ph+ ALL and 4 lymphoid blast crisis CML, were subjected to RNA sequencing (RNA-seq) and whole genome sequencing (WGS). Response rates were tracked using BCR-ABL1 transcript levels from patient blood.Results Hierarchical clustering of transcriptome data produced two molecular subgroups of Ph+ ALL. One subgroup, which we termed ‘Core-B’, upregulated key regulators of B-lymphoid differentiation including IL7R and MS4A1 (CD20). By contrast, the second subgroup upregulated an expression program related to hematopoietic stem cell (HSC) and myeloid differentiation, with upregulation of KIT, CD34, MPO, CSF3R, and GATA3. We termed this subgroup ‘Aberrant-Stem-Myeloid’ (ASM). These subgroups displayed a striking disparity in response rates to intensive chemotherapy with imatinib. Whereas ‘Core-B’ patients showed highly durable responses often lasting many years, ‘ASM’ patients frequently relapsed (4% vs 43% relapse; p=0.007). We used WGS analysis to investigate the genetic basis of these molecular subtypes. ‘Core-B’ Ph+ ALLs were enriched for deletions in PAX5, a B-cell specification gene, and CDKN2A/B, tumor suppressors. The ‘ASM’ subtype lacked these genetic alterations; instead, these leukemias were enriched for deletions in EBF1, an early B-cell lineage factor that represses T-lymphoid and myeloid lineages and is expressed before PAX5 in B-cell lineage differentiation. Accordingly, blasts from ‘ASM’ leukemias with EBF1 deletions showed decreased CD19 antigen expression and upregulation of myeloid antigens by clinical flow cytometry. Rare cases with concurrent EBF1 and PAX5 deletions showed expression features of both ‘ASM’ and ‘Core-B’ leukemias. Mutations observed in myeloid leukemias (TET2, RUNX1) were only present in the ‘ASM’ subtype. Loss of IKZF1, found in 77% of cases, also displayed distinct patterns between the two subgroups; deletions leading to the dominant negative isoform (Ik6) were enriched in the ‘Core-B’ subgroup (45% vs. 14%; p=0.019) while monosomy 7 and large deletions encompassing IKZF1 were enriched in the ‘ASM’ leukemias (41% vs. 10%; p=0.017). In 1 of 4 diagnosis/relapse patients analyzed, a molecular switch from ‘Core-B’ at diagnosis to ‘ASM’ at relapse was observed. The diagnostic ‘Core-B’ clone from this patient harbored a PAX5 mutation that was lost at relapse, whereas the relapsed ‘ASM’ clone harbored trisomy 21 and a RUNX1 mutation. Altogether, our data suggest that the ‘ASM’ leukemias emerge through dysregulation of genes earlier in lympho-myeloid specification compared to ‘Core-B’ leukemias.These findings led us to investigate if the ‘ASM’ subtype originates from an HSC and the ‘Core-B’ subtype originates from a B-cell progenitor. We first looked at the distribution of the long (p210) and short (p190) isoforms of BCR-ABL1 in the two subtypes. The p210 isoform, also the hallmark of CML, is speculated to arise in an HSC, and the p190 is thought to arise in a B-cell progenitor. Neither the p190 or p210 BCR-ABL1 isoform was enriched in either subgroup. We resolved highly purified HSC and progenitor subsets from CD34+CD19- cells, functionally evaluated by methylcellulose assays, and subjected them to a sensitive nested-PCR strategy. Cases from both the ‘ASM’ and ‘Core-B’ subtypes showed HSC/myeloid progenitor involvement regardless of the BCR-ABL1 isoform. This data suggest that the cell-of-origin does not play a role in establishing the molecular subtype of leukemia blasts.Conclusion There are two distinct molecular subtypes of Ph+ ALL that demonstrate differential responses to treatment and emerge from independent mutational routes. Moreover, the key genetic determinants that form the molecular subtype are secondary driver alterations that lie downstream of BCR-ABL1. DisclosuresNo relevant conflicts of interest to declare.

Abstract 3362: Mice with a “deletor” phenotype allow high resolution detection of lymphoid leukemia tumor suppressor genes

Abstract Mice that are homozygous for a deficiency allele of the DNA replication factor minichromosome maintenance protein 2 (designated Mcm2def) are born viable and are healthy for the first 2 months of life. Beginning at three months, these mice develop precursor T-cell lymphoblastic leukemia/lymphoma (pre-T LBL). Copy number aberration (CNA) analysis showed that these pre-T LBL samples had 8-14 small (100-1000 kb) interstitial deletions per sample. Remarkably, all mice had two or more deletions that encompassed genes known to be relevant for human pre-T LBL, including Pten, Cdkn1a, Tcf3, and Tcf12. Mice that express a NUP98-HOXD13 (NHD13) transgene develop a wide array of leukemias, most commonly myeloid, less commonly T-cell, and, rarely, B-lineage. To identify myeloid tumor suppressor genes, we crossed the NHD13 transgene onto the Mcm2def background. All Mcm2def:NHD13+ mice developed pre-T LBL by 3 months of age, reflecting the highly penetrant nature of the Mcm2def phenotype. None of the Mcm2def:NHD13+ mice developed myeloid leukemia. Surprisingly, approximately 30% of the Mcm2def:NHD13+ mice developed concurrent B-cell precursor acute lymphoblastic leukemia (BCP-ALL) and pre-T LBL. The thymus was typically infiltrated with pre-T LBL cells, whereas the bone marrow and spleen were infiltrated with BCP-ALL cells, characterized by clonal VDJ rearrangement and CD19 staining. Parenchymal organs (lung, kidney, liver) were variably infiltrated with pre-T LBL, BCP-ALL, or both. CNA analysis showed that the pre-T LBL were characterized by Pten, CDkn1a, Tcf3, and Tcf12 deletions, similar to the Mcm2def pre-T LBL, whereas the BCP-ALL were characterized by homozygous or heterozygous deletions of Pax5 and a 400 kb region encompassing Cebpb and Ptpn1. There were no shared deletions present in both BCP-ALL and pre-T LBL from the same mouse, indicating that the BCP-ALL and pre-T LBL arose independently, and not from a common precursor. The high frequency (5/7 samples) of acquired Pax5 deletions in the BCP-ALL samples serves to validate the model; whereas the finding of Cebpb/Ptpn1 deletions (5/7 samples) suggests an unanticipated role of either Cebpb or Ptpn1 in BCP-ALL. Citation Format: Mianmian Yin, Timour Baslan, Amy Freeland, Steven C. Pruitt, Peter D. Aplan. Mice with a “deletor” phenotype allow high resolution detection of lymphoid leukemia tumor suppressor genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3362.