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Acute myeloid leukemia (AML) is characterized by complex molecular alterations and driver mutations. Elderly patients show increased frequencies of IDH mutations with high chemoresistance and relapse rates despite recent therapeutic advances. Besides being associated with global promoter hypermethylation, IDH1 mutation facilitated changes in 3D DNA-conformation by CTCF-anchor methylation and upregulated oncogene expression in glioma, correlating with poor prognosis. Here, we investigated the role of IDH1 p.R132H mutation in altering 3D DNA-architecture and subsequent oncogene activation in AML. Using public RNA-Seq data, we identified upregulation of tyrosine kinase PDGFRA in IDH1-mutant patients, correlating with poor prognosis. DNA methylation analysis identified CpG hypermethylation within a CTCF-anchor upstream of PDGFRA in IDH1-mutant patients. Increased PDGFRA expression, PDGFRA-CTCF methylation and decreased CTCF binding were confirmed in AML CRISPR cells with heterozygous IDH1 p.R132H mutation and upon exogenous 2-HG treatment. IDH1-mutant cells showed higher sensitivity to tyrosine kinase inhibitor dasatinib, which was supported by reduced blast count in a patient with refractory IDH1-mutant AML after dasatinib treatment. Our data illustrate that IDH1 p.R132H mutation leads to CTCF hypermethylation, disrupting DNA-looping and insulation of PDGFRA, resulting in PDGFRA upregulation in IDH1-mutant AML. Treatment with dasatinib may offer a novel treatment strategy for IDH1-mutant AML.

Targeted interventions and new risk stratification approaches for the improvement of outcomes in B cell precursor acute lymphoblastic leukemia (BCP-ALL) require an understanding of high-risk driver subtypes, their clinical phenotypes and actionable targets. Currently, over 20 BCP-ALL subtypes have been identified based on genomic driver alterations and corresponding gene expression signatures, in particular in pediatric ALL. This complex molecular landscape is so far only partially defined in adult BCP-ALL patients. To characterize driver subtypes and their clinical phenotypes we performed transcriptome sequencing (Illumina) on Ph-negative adult BCP-ALL patients (n=376) treated on subsequent pediatric inspired protocols of the German Acute Lymphoblastic Leukemia Study Group (GMALL). Using random forest analyses of a well-defined patient subset with available WES/gene panel and DNA-methylation data, we established a 300-gene classifier which together with fusion calling and hotspot mutation calling reliably allocated samples to driver subtypes. Subgroup allocation was feasible for n=267 / 308 Ph-negative patients (86.7%) with Ph-like ALL (27.7%) being the most frequently observed subtype followed by DUX4 (14.6%), KMT2A (10.1%), PAX5-plus (9.7%), ZNF384 (9.0%), Near haploid - High hyperdiploid (NH-HeH, 6.0%), Low haploid - Near triploid (LH-NT, 6.0%) and TCF3-PBX1 (5.6%). With frequencies below 5% were observed: PAX5-alt, MEF2D, BCL2/MYC, ETV6-RUNX1, CEBP family member fusions and TCF3-HLF. The age distribution of these driver subtypes varied across our cohort (median age: 37 years, range: 16 - 81; left panel). Adult patients harboring ETV6-RUNX1 fusions (n=4) were 25 years or younger. NH-HeH, PAX5-plus and DUX4 ALL were also observed predominantly in younger patients (median ages: 24, 24, 30 years respectively; p As expected, male patients were slightly more represented in the cohort (55% male). However, significant differences were observed in the sex-distribution of molecular subgroups with a predominance of male patients in Ph-like (65.4%; p=0.045) and NH-HeH (82.4% p=0.024) ALL, while female patients were more frequent in DUX4 (60%, p=0.046) or KMT2A (75.5%; p=0.031) ALL. These data implicate that sex-specific host factors favor the selection of ALL driver alterations in adult ALL patients. We measured MRD by qRT-PCR quantification of patient specific immune gene rearrangement markers in our GMALL central reference lab. Data on MRD status after consolidation I which is the most relevant time-point for identification of high-risk patients in the GMALL protocol, were available in 132 patients (aged 18-55 years; right panel). Ph-like and KMT2A patients showed an unfavorable response to intensive induction with Molecular CR achieved in 60.6% and 61.1% respectively. In ZNF384 ALL patients, only n=5/13 achieved Molecular CR, while n=4 each were MRD-positive or had MRD below the quantitative detection range, suggesting that ZNF384 ALL might be a novel high-risk subgroup in adult BCP-ALL. Gene set enrichment analyses showed comparable patterns of JAK/STAT activation in ZNF384 and Ph-like cases as possible functional underpinning of a shared poor-response phenotype. Actionable genomic alterations were identified in n=13/74 Ph-like patients (17.6%). Out of these, ABL-class fusions as targets of ABL-TKI were identified in n=14 patients (PDGFRB: n=5; ABL1: n=4; CSF1R n=2) and one patient harbored an ETV6-NTRK3 fusion amenable to specific inhibitors. Our data extent the in-depth characterization of BCP-ALL molecular landscape in adult patients. We observe that sex-specific host factors favor the selection of leukemogenic drivers (male predominance: Ph-like, NH-HeH, female predominance: DUX4, KMT2A). ZNF384 ALL seems to be associated with unfavorable therapy response in adults and shares JAK/STAT activation patterns with Ph-like ALL. Figure Disclosures Fiedler: Jazz Pharmaceuticals: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: travel accomodations; Novartis: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: support in medical writing; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: travel accomodations, support in medical writing, Research Funding; Daiichi Sankyo Oncology: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: travel accomodations; BerGenBio ASA: Research Funding; AbbVie: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: support in medical writing; BMS: Honoraria; Gilead: Honoraria; Ariad/Incyte: Membership on an entity's Board of Directors or advisory committees; Servier: Honoraria, Other; Morphosys: Membership on an entity's Board of Directors or advisory committees. Viardot:Novartis: Honoraria, Other: advisory board; Kite/Gilead: Honoraria, Other: advisory board; Roche: Honoraria, Other: advisory board; Amgen: Honoraria, Other: advisory board. Topp:Amgen, Boehringer Ingelheim, KITE, Regeneron, Roche: Research Funding; Amgen, KITE, Novartis, Regeneron, Roche: Consultancy. Goekbuget:Servier: Consultancy, Research Funding; Jazz: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Amgen: Consultancy, Research Funding; Pfizer: Consultancy, Research Funding; Erytech: Consultancy; Kite: Consultancy; Gilead: Consultancy. Brüggemann:Affimed: Research Funding; Incyte: Consultancy; Celgene: Consultancy; Amgen: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria; Roche: Consultancy; Regeneron: Research Funding.

Introduction: In T-ALL, in contrast to BCP-ALL, molecular subgroups are less well defined. Molecular subgroups are based on aberrant expression of oncogenes often resting upon structural aberrations (chromosomal translocation, copy number variations, point mutations). So far, comprehensive studies on molecular subgroups have been predominantly performed in pediatric patients. The clinical relevance of molecular characteristics is not taken into account for risk stratification and targeted therapeutic options for T-ALL patients are limited. Risk stratification is mainly based on immunophenotype and MRD response. Thus, in the German Multicenter Study Group for Adult ALL (GMALL) protocols early and mature T-ALL and molecular failure after first consolidation are high risk features. Whole RNA transcriptome sequencing (RNAseq) enables molecular subgroup allocation profiles with potential prognostic relevance. Herein, we investigated a large cohort of 161 adult T-ALL patients with RNAseq for molecular subgroups and their clinical implication. Patients and methods : RNAseq data (Illumina HiSeq 4000, 100 or 125 bp paired-end, average read count ~30 million reads/sample) were generated from 161 adult T-ALL patients from diagnostic bone marrow samples. For 84 of these T-ALL patients, we additionally investigated DNA methylation using Infinium 450k methylation bead arrays and mutation status using deep targeted DNA sequencing with a gene panel consisting of 206 genes (HiSeq 1500, 100 bp paired-end, average ~800 reads/bp). All patients were treated likewise within pediatric inspired protocols of the GMALL. Clinical follow up and outcome data were available for 129 patients aged between 18 and 55 years. Results: Based on oncogene expression, we could assign molecular subgroups to 160 out of the 161 T-ALL patients: HOXA: n=37 (23%), TLX1: n=37 (23%), TAL/LMO: n=33 (20%), LYL1/LMO2: n=31 (19%), TLX3: n=17 (11%) , NKX2-1: n=4 (2%), TAL2: n=1 (1%). Among others, gene fusion events incorporating TAL1 (n=16), HOXA (n=6), TLX1 (n=14), TLX3 (n=2) and NKX2 (n=2) were detected as underlying mechanisms. Age distribution revealed more TAL/LMO in the younger population (16-25 years: 35% versus >35 years: 3%; p=0.001) and more LYL1/LMO2 and HOXA in the older patients (16-25 years: 23% vs. >35 years: 40%; n.s.). DNA methylation analyses for 84 of the 161 patients support the molecular classification with four distinct subgroups demonstrating a homogenous methylation profile for the TLX1 driven subgroup (methylation cluster M3, n=30). In contrast, methylation cluster M2 (n=21) showed a hypomethylation in CpG islands and comprises the majority of TAL/LMO positive cases (19/21) including all samples with STIL-TAL1 fusions. M1 (n=25) and M4 (n=7) clusters comprised TLX3 (mainly cluster M1, 8/10), HOXA and LYL1/LMO2 cases. Mutation analysis showed a high rate of NOTCH1 (n=71%) mutations in the TLX1 subgroup and an increased rate of mutations in the JAK/STAT pathway (n=29%) and epigenetic regulators (n=50%) in HOXA and LYL1/LMO2 subgroups. Regarding clinical outcome, 126 out of 129 (98%) patients achieved a morphologically complete remission (CR), two patients failed CR, one patient died during induction therapy. Regarding MRD response, 12% of the investigated T-ALL patients showed a molecular failure after consolidation. Noteworthy, we found a molecular CR for 28/30 (93%) patients in the TLX1 subgroup, but only 11/19 (58%) respectively 2/6 (33%) in the HOXA and the LYL1/LMO2 subgroup. This finding results in exceptional five year-overall survival (5y-OS) of 93% in TLX1 patients. Together with the NKX2-1 subgroup (n=4, with 100% 5y-OS), these patients build a prognostically favourable risk group in the overall cohort (94% 5y-OS versus 76% in TAL-LMO patients versus 62% in all other subgroups, p=0.007). This result could not only be found in the overall cohort, but also within the already good risk subgroup of thymic T-ALL patients (93% vs. 75%, p=0.02). Conclusion: This is to our knowledge the largest cohort of adult T-ALL patients characterized by RNAseq on molecular level. Our findings point towards an age dependent distribution of molecular subgroups contributing to age-dependent outcome differences. Patients with TLX1 reveal a molecular subgroup with extraordinary good prognosis. Within thymic T-ALL, the subgroup of patients without TLX1 (~53%) has an inferior but still good prognosis. Disclosures Fiedler: Gilead: Other: support for meeting attendance; Jazz Pharmaceuticals: Honoraria, Other: support for meeting attendance; Abbvie: Membership on an entity's Board of Directors or advisory committees; Morphosys: Consultancy, Honoraria; Celgene: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Consultancy, Honoraria; ARIAD/Incyte: Consultancy, Honoraria; Amgen: Consultancy, Honoraria, Other: support for meeting attendance, Patents & Royalties, Research Funding; Daiichi Sankyo: Other: support for meeting attendance. Alakel:Pfizer: Consultancy. Schwartz:AMGEN: Other: personal fees and non-financial support; Novartis: Other: personal fees and non-financial support; Jazz Pharmaceuticals: Other: personal fees and non-financial support; Pfizer: Other: personal fees ; BTG Intl Inc: Other: personal fees ; Gilead Sciences: Other: personal fees and non-financial support ; MSD Sharp & Dohme: Other: personal fees ; Basilea: Other: non-financial suppor. Müller-Tidow:Pfizer: Research Funding, Speakers Bureau; Daiichi Sankyo: Research Funding; Janssen-Cilag GmbH: Speakers Bureau; BiolineRx: Research Funding. Brüggemann:Regeneron: Research Funding; Affimed: Research Funding; Amgen: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria; Incyte: Consultancy; Roche: Consultancy; Celgene: Consultancy. Goekbuget:Servier: Consultancy, Research Funding; Amgen: Consultancy, Research Funding; Pfizer: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Gilead: Consultancy; Erytech: Consultancy; Kite: Consultancy; Jazz: Consultancy, Research Funding.