<p>supplementary data Figure S1. Gene expression signatures define distinct molecular groups of T-ALL. Figure S2. Global flow chart of the patients Figure S3. Comparison of outcomes between LALA94 patients with central lab onco-genetic study performed (dotted line) and patients without (full line). Figure S4. Epigenetic histone marks. Figure S5. Kaplan-Meier graph for OS is shown for TAL1+ patients treated on LALA-94 vs. GRAALL-2003/2005 trials. Figure S6. TAL1 expression normalised to GAPDH by RTQ-PCR in 8 PDX treated with L-asparaginase (Rf. Figure 4H). Figure S7. (A) Correlation analysis between ASNS expression and ASNS promoter methylation ratio. (B) ASNS transcriptional expression normalized to GAPDH in T-ALL, in normal Bone Marrow (BM) (100%, 50%, 10% and 1%) and in normal Peripheral Blood Cells (PBL) (100%, 50%, 10% and 1. (C) comparison of ASNS transcriptional expression in non-sorted diagnostic sample, blast and non-blast sorted cells in two patients with a hypermethylated ASNS promoter (UPNT-573 and UPNT-498) and high ASNS expression (T3 tertile) (left) and, in primary samples and PDX (Primary Derived Xenograft) using a human specific Taqman system for two hypermethylated cases (UPNT-485 and UPNT-419) and two hypomethylated cases (UPNT-615 and UPNT-241) (right). (D) Correlation analysis between ASNS expression and ASNS promoter methylation ratio in purified blasts cells (PDX n=8 )and sorted primary samples (n=3). (E) Correlation analysis between ASNS expression (RNA-seq) and ASNS promoter methylation ratio in a series of 13 T-ALL cell lines (LOUCY, DND41, RPMI8402, HPB-ALL, ALL-SIL, TALL1, MOLT3, PEER, SUPT1, PF382, MOLT3, MOLT16, JURKAT). Table S1. Clinico-biological characteristics of patients included in the LALA94 trial according to their inclusion in the present study. Table S2. GRAALL03, 05 and LALA94 trials overview and drug administration schedule. Table S3. SiRNA sequences Table S4. Probes sequences for ASNS MS-MLPA analysis Table S5. DNA Global Methylation study Table S6. Characteristics of TLX1+, TLX3+ and TLX neg patients Table S7. Clinico-biological characteristics of T1 (lower ASNS methylation tertile) and T2+T3 (higher methylation tertiles) adult T-ALL. Table S8. Univariate and multivariate analysis for EFS and OS</p>
Abstract IDH1 and IDH2 mutations (IDH1/2 Mut ) are recognized as recurrent genetic alterations in acute myeloid leukemia (AML) and associated with both clinical impact and therapeutic opportunity due to the recent development of specific IDH1/2 Mut inhibitors. In T-cell acute lymphoblastic leukemia (T-ALL), their incidence and prognostic implications remain poorly reported. Our targeted next-generation sequencing approach allowed comprehensive assessment of genotype across the entire IDH1 and IDH2 locus in 1085 consecutive unselected and newly diagnosed patients with T-ALL and identified 4% of, virtually exclusive (47 of 49 patients), IDH1/2 Mut . Mutational patterns of IDH1/2 Mut in T-ALL present some specific features compared to AML. Whereas IDH2 R140Q mutation was frequent in T-ALL (25 of 51 mutations), the IDH2 R172 AML hotspot was absent. IDH2 mutations were associated with older age, an immature phenotype, more frequent RAS gain-of-function mutations and epigenetic regulator loss-of-function alterations ( DNMT3A and TET2 ). IDH2 mutations, contrary to IDH1 mutations, appeared to be an independent prognostic factor in multivariate analysis with the NOTCH1/FBXW7/RAS/PTEN classifier. IDH2 Mut were significantly associated with a high cumulative incidence of relapse and very dismal outcome, suggesting that IDH2 -mutated T-ALL cases should be identified at diagnosis in order to benefit from therapeutic intensification and/or specific IDH2 inhibitors.
