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Low hypodiploidy defines a rare subtype of B-cell acute lymphoblastic leukemia (B-ALL) with a dismal outcome. To investigate the genomic basis of low-hypodiploid ALL (LH-ALL) in adults, we analyzed copy-number aberrations, loss of heterozygosity, mutations, and cytogenetics data in a prospective cohort of Philadelphia (Ph)-negative B-ALL patients (n = 591, ages 18–84 years), allowing us to identify 80 LH-ALL cases (14%). Genomic analysis was critical for evidencing low hypodiploidy in many cases missed by cytogenetics. The proportion of LH-ALL within Ph-negative B-ALL dramatically increased with age, from 3% in the youngest patients (under 40 years old) to 32% in the oldest (over 55 years old). Somatic TP53 biallelic inactivation was the hallmark of adult LH-ALL, present in virtually all cases (98%). Strikingly, we detected TP53 mutations in posttreatment remission samples in 34% of patients. Single-cell proteogenomics of diagnosis and remission bone marrow samples evidenced a preleukemic, multilineage, TP53-mutant clone, reminiscent of age-related clonal hematopoiesis.Significance:We show that low-hypodiploid ALL is a frequent entity within B-ALL in older adults, relying on somatic TP53 biallelic alteration. Our study unveils a link between aging and low-hypodiploid ALL, with TP53-mutant clonal hematopoiesis representing a preleukemic reservoir that can give rise to aneuploidy and B-ALL.See related commentary by Saiki and Ogawa, p. 102.This article is highlighted in the In This Issue feature, p. 101

Supplementary figure 1. Sequencing-based analysis of CNA and LOH in adult LH-ALL. Supplementary figure 2. Representation of mutations in the frequent targeted genes in adult LH-ALL. Supplementary figure 3. Longitudinal assessment of TP53-mutant cell fraction as determined by ddPCR along with clonal IG/TR-based MRD quantification in three patients with undetectable TP53 mutation at remission. Supplementary figure 4. Merged single-cell analysis of cell-surface markers by ADT-sequencing of remission samples from three LH-ALL patients. Supplementary figure 5. Individual single-cell analyses of cell-surface markers by ADT-sequencing of remission samples from three LH-ALL patients. Supplementary figure 6. Individual analyses of single-cell immunophenotyping and genotyping of remission samples from three LH-ALL patients. Supplementary figure 7. Evaluation of allelic dropout rate on heterozygous single nucleotide polymorphism (SNPs) in remission samples. Supplementary figure 8. Individual single-cell analysis of cell-surface markers by ADT-sequencing of diagnosis samples from three LH-ALL patients. Supplementary figure 9. Single-cell genotyping of heterozygous SNPs allowing LOH assessment in diagnosis samples from three LH-ALL patients. Supplementary Figure 10. Distribution of single-cell genotypes of two LH-ALL patients with persistent TP53 and JAK2 (EI_046) or DNMT3A (EI_035) mutations in remission samples.

Supplementary Table 1. Karyotypes of LH-ALL patients at diagnosis. Supplementary Table 2. Somatic variants detected in LH-ALL patients at diagnosis. Supplementary Table 3. ARCH related variants detected in LH-ALL patients at remission. Supplementary Table 4. Minimal residual disease values of remission samples used for mutation analysis. Supplementary Table 5. Somatic alterations in cell populations from diagnostic samples (BMMC) based on single-cell analyses. Supplementary Table 6. Somatic alterations in FACS-sorted cell populations from diagnostic samples. Supplementary Table 7. Panel of genes for targeted sequencing. Supplementary Table 8. Single cell DNA amplicons for genotyping and LOH analyses. Supplementary Table 9. Single cell DNA amplicons for B-ALL clono-specific IG/TR detection. Supplementary Table 10. ADT-seq panel and spike-in antibodies. Supplementary Table 11. Single cell sequencing metrics.

Low hypodiploidy defines a rare subtype of B-cell acute lymphoblastic leukemia (B-ALL) with a dismal outcome. To investigate the genomic basis of low-hypodiploid ALL (LH-ALL) in adults, we analyzed copy-number aberrations, loss of heterozygosity, mutations, and cytogenetics data in a prospective cohort of Philadelphia (Ph)-negative B-ALL patients (n = 591, ages 18–84 years), allowing us to identify 80 LH-ALL cases (14%). Genomic analysis was critical for evidencing low hypodiploidy in many cases missed by cytogenetics. The proportion of LH-ALL within Ph-negative B-ALL dramatically increased with age, from 3% in the youngest patients (under 40 years old) to 32% in the oldest (over 55 years old). Somatic TP53 biallelic inactivation was the hallmark of adult LH-ALL, present in virtually all cases (98%). Strikingly, we detected TP53 mutations in posttreatment remission samples in 34% of patients. Single-cell proteogenomics of diagnosis and remission bone marrow samples evidenced a preleukemic, multilineage, TP53-mutant clone, reminiscent of age-related clonal hematopoiesis.Significance:We show that low-hypodiploid ALL is a frequent entity within B-ALL in older adults, relying on somatic TP53 biallelic alteration. Our study unveils a link between aging and low-hypodiploid ALL, with TP53-mutant clonal hematopoiesis representing a preleukemic reservoir that can give rise to aneuploidy and B-ALL.See related commentary by Saiki and Ogawa, p. 102.This article is highlighted in the In This Issue feature, p. 101

BackgroundIKZF1 gene deletion is an indicator of poor prognosis in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL). The AEIOP/BFM group proposed that the prognostic strength of IKZF1 deletion could be remarkably improved by taking into account additional genetic deletions and reported that among patients with an IKZF1 deletion those with deletions in CDKN2A/2B, PAX5, or PAR1 in the absence of ERG deletion, grouped as IKZF1(plus), had the worst outcome. ProcedureBetween 1998 and 2008, 1636 patients under 18 years of age with previously untreated BCP-ALL were registered in the EORTC 58951 trial. Those with multiplex ligation-dependent probe amplification data were included in this analysis. Unadjusted and adjusted Cox model was used to investigate the additional prognostic value of IKZF1(plus). ResultsAmong 1200 patients included in the analysis, 1039 (87%) had no IKZF1 deletion (IKZF1(WT)), 87 (7%) had an IKZF1 deletion but not IKZF1(plus) (IKZF1(del)) and 74 (6%) had IKZF1(plus). In the unadjusted analysis, both patients with IKZF1(del) (hazard ratio [HR] = 2.10, 95% confidence interval [CI]: 1.34-3.31) and IKZF1(plus) (HR = 3.07, 95% CI: 2.01-4.67) had a shorter event-free survival compared with IKZF1(WT). However, although the IKZF1(plus) status was associated with patients' characteristics indicating poor prognosis, the difference between IKZF1(plus) and IKZF1(del) was not statistically significant (HR = 1.46, 95% CI: 0.83-2.57, p = .19). The results of the adjusted analysis were similar to the unadjusted analysis. ConclusionsIn patients with BCP-ALL from the EORTC 58951 trial, the improvement of the prognostic importance of IKZF1 by considering IKZF1(plus) was not statistically significant.

International audience

International audience; Background During the 2005-2014 period, the GRAALL conducted the GRAALL-2005 trial in patients (pts) with Philadelphia chromosome (Ph)-negative ALL aged 18-59y. In this trial, all pts received a pediatric-inspired chemotherapy, whatever their age. Post-hoc analysis revealed an unacceptable TRM in pts aged 45-59y (Huguet et al. J Clin Oncol 2018; 36:2514-23). Allogeneic hematopoietic stem cell transplantation (HSCT) was offered in first complete remission (CR) to most CR pts, defined at high-risk (HR) by at least one baseline clinical or biological HR factor (CNS involvement, complex karyotype [≥5 abns.], low hypodiploidy/near triploidy, poor early blast clearance, late CR, as well as WBC ≥ 30x109/L, lack of CD10 expression, KMT2A rearrangement or TCF3::PBX1 fusion for B-cell precursor [BCP] ALL). Minimal residual disease (MRD) response was not considered for HSCT indication at that time.In the next GRAALL-2014 trial conducted in a similar population, we introduced two major changes in the treatment strategy. First, chemotherapy intensity (steroids, anthracycline and L-asparaginase) was reduced in pts aged 45-59y to decrease excessive TRM. Secondly, the indication for HSCT was modified, relying on IG/TR MRD response only (post-induction MRD ≥10-3 and/or post-consolidation MRD ≥10-4) while not on any former baseline HR criterion. Here, we compare the outcomes of the two trials, focusing on the impact of these two major evolutions.Patients & Methods A total of 743 pts treated in the GRAALL-2014 trial between 2015 and 2020 were compared to the 787 pts from the historical GRAALL-2005 trial, in terms of CR and induction death rates, rate of HSCT in CR1, cumulative incidence of TRM (CITRM) and relapse (CIR), relapse-free (RFS) and overall (OS) survival. It should be noted that two nested Phase 2 trials were introduced by amendment during the GRAALL-2014 course (in 2017 and 2018, respectively), aiming to evaluate post-remission addition of nelarabine and blinatumomab in 87 T-ALL and 94 BCP-ALL selected pts, respectively.Results Main patient characteristics, including age, gender, BCP/T-ALL, WBC, and historical baseline HR features, did not significantly differ between the two trial cohorts, even if CNS disease at diagnosis was more frequent in the 2014 cohort (12 vs 7%, p= 0.001).Outcome comparisons are shown in Table 1. Overall, the induction death rate was significantly reduced in the GRAALL-2014 (3 vs 6%, p= 0.005). As expected, this was only observed in pts aged 44-59y (3 vs 11%, p= 0.001), in whom dose-intensity reduction also translated into a higher need for second induction course (9 vs 5%, p= 0.05) eventually resulting in a higher CR rate (92 vs 86%, p= 0.05). Due to the newly introduced MRD-based stratification, the rate of pts with HSCT indication was markedly reduced (30 vs 65%, p

Case Presentation An 80-year-old-woman was referred for evaluation of chest pain that appeared after providing care at home for her sick husband, which included helping him to get up and move about. The pain was initially triggered by lifting heavy objects but then became constant, without exacerbating or relieving factors. The pain was located in the left hemithorax and was not associated with shortness of breath or cough. Because the patient did not feel any better after a month, her general practitioner ordered a radiograph, which revealed a suspicious pulmonary nodule in the left upper lobe. She was a lifelong nonsmoker and denied any drug abuse. She had not been professionally exposed to lung carcinogens. She had a medical history of type 2 diabetes, ischemic cardiomyopathy, and renal artery stenosis. Her father died of lung cancer. She resided in Lille, France, and did not report any recent travel.

IDH1 and IDH2 mutations (IDH1/2Mut) 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 IDH1/2Mut 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), IDH1/2Mut. Mutational patterns of IDH1/2Mut in T-ALL present some specific features compared to AML. Whereas IDH2R140Q mutation was frequent in T-ALL (25 of 51 mutations), the IDH2R172 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. IDH2Mut 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.

TO THE EDITOR: B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a rare aggressive malignancy in adults. BCP-ALL is frequently characterized by recurrent chromosomal translocations that deregulate proto-oncogenes or result in fusion genes encoding chimeric oncoproteins.[1][1] Gene

The KMT2A gene encodes a lysine-specific methyltransferase which is essential in epigenetic regulation during early development and hematopoiesis. KMT2A, also known as MLL (mixed-lineage leukemia),...

TO THE EDITOR: T-cell acute lymphoblastic leukemia (T-ALL) and T-cell lymphoblastic lymphoma (T-LBL) are aggressive neoplasms that result from the proliferation of T-lymphoid progenitors blocked at thymic stages of differentiation. They account for 15% and 25% of pediatric and adult ALLs, respectively. T-ALL/T-LBL are associated with a wide range of acquired genetic abnormalities that contribute to developmental arrest and abnormal proliferation. Although intensive treatment protocols have markedly improved the outcomes of children with T-ALL, cure rates remain below 60% for adults and 85% for children. The prognosis is particularly poor in relapsing patients, highlighting an urgent need for risk stratification factors at diagnosis.[...]

ETV6 is a target of recurrent aberrations in sporadic and familial acute lymphoblastic leukemia (ALL). Here, we report on a new pedigree with a germline ETV6 mutation in which the index patient and his father developed high hyperdiploid (HeH) ALL and polycythemia vera at age 13 and 51, respectively. The index patient achieved durable complete remission without transplantation but had persistent moderate thrombocytopenia without bleeding tendency. To determine the prevalence of ETV6 alterations in HeH-ALL, we screened 81 unrelated subjects with HeH-ALL by single nucleotide polymorphism array and high-throughput sequencing for the ETV6 gene. Overall, ETV6 microdeletions and mutations were identified in 9% of cases, all of which were somatic and considered as secondary events. Apart from the index patient, no germline ETV6 aberration was identified. Finally, we reviewed the literature for ETV6 germline aberrations and predispositions to ALL.

Acute lymphoblastic leukemias (ALL) are characterized by a large number of genetic abnormalities of prognostic and theranostic interest. Their detection requires the use of several conventional and molecular cytogenetic techniques in order to establish the most exhaustive genetic profile: conventional karyotype, FISH, SNP-Array and RT-MLPA for detection of fusion transcripts. Optical genome mapping technique is based on analysis of ultra-high molecular weight DNA (UHMW: 150 kbp-2.5 Mbp). It allows an automatic, high resolution, genome-wide detection of structural anomalies, including balanced translocations and copy number anomalies, making this technology a promising tool in ALL. However, very few data are available in ALL so far. Our objective was to compare optical mapping (Bionano Genomics) to standard techniques performed routinely (combination of karyotype, FISH, SNP-array and RT-MLPA) in 10 selected B or T-ALL patients carrying at least one major genetic abnormality including t(10;14) TLX1-TRA, t(9;22) BCR-ABL1 (e1a2 and e14a2 transcripts), t(10;11) MLLT10-PICALM, t(11;19) KMT2A-MLLT1, typical hyperdiploid profile, iAMP21, SET-NUP214 fusion, various deletions involving CDKN2A/CDKN2B, IKZF1, PAX5, PTEN, ERG and FBXW7. Abnormalities on SNP-array were retained when allele fraction was > 10% and larger than 1Mbp or > 20 kbp and involving one of the 186 genes defined as potentially relevant in leukemogenesis. A total of 79 anomalies meeting these criteria in SNP-array, and/or found by other standard techniques were identified (45 deletions, 16 whole chromosome gains, 10 duplications or partial gains, and 8 translocations). Bone marrow DMSO pellets from the 10 patients, all treated at the CHU Amiens-Picardie, were used for this study. The UHMW DNA extraction technique provided molecules with an average N50 (≥ 150 kbp) of 286 kbp, and an average coverage of 339x. Direct imaging of the DNA molecules was performed on the Bionano Saphyr system and structural variants were automatically detected using the Rare Variant Pipeline. Abnormalities analysis was blindly performed by two independent operators on the Bionano Access software (v 1.5.2.), one cytogeneticist with no training in optical mapping (operator 1) and the other optical mapping technician without training in cytogenetics (operator 2). Among the 79 relevant anomalies, 72 (91.1%) were found by operator 1 and 71 (89.9%) by operator 2. All (8/8) translocations, 43/45 (95.6%) of deletions, 8/10 (80%) of gains were found by both operators whereas 13/16 (81.25%) and 12/16 (75%) of chromosomal gains were found by operator 1 and 2 respectively. Concerning the 8 discrepancies between optical mapping and standard techniques, 4 of them were filtering issues. Three were low allelic frequency large gains clearly visible in raw data but rejected by software's CNV filters, totally, or partially for a trisomy 3 that caused the discrepancy between the two observers. The fourth was a deletion of VPREB1 gene, erroneously eliminated by operators because included in recurrent deletion zones of IGL locus. The 4 others discrepancies were non detected anomalies. Two of them were copy number variations in Xp22.33 (pseudoautosomal region), a non-covered area with the optical mapping technology, one of which was a P2RY8-CRLF2 fusion. Another sub-clonal gain (trisomy 21) found by karyotype and FISH (quantified at 7% of all nuclei) but not by SNP-array, was missed, even in raw data. The last was a near-tetraploid subclone, found only on karyotype, that might be strictly tetraploid and by definition undetectable by quantitative techniques. Interestingly, new anomalies, not detected by standard techniques, were revealed, including a translocation t(11;14)(p13;q11.2) LMO2-TRA, a translocation with inversion t(7;8)(q34;q24.1) TRB-MYC and a translocation t(14;20)(q32.33;q13.13) IGH-CEBPB. At last, in 3 cases, unidentified complex rearrangements by cytogenetics could be resolved using optical mapping. Thus, optical mapping represents an innovative, time and cost effective alternative to the different cytogenetic techniques currently performed routinely for ALL genetic characterization. It enables identification of complex cytogenetic events, including those currently inaccessible to standard techniques such as chromotripsis or certain complex translocations. Disclosures Lee: Bionano Genomics, San Diego: Current Employment. Ferret:Bionano Genomics: Research Funding.

Protein tyrosine phosphatase nonreceptor type 2 (PTPN2) is a phosphatase known to be a tumor suppressor gene in T-cell acute lymphoblastic leukemia (T-ALL). Because the full clinicobiologic characteristics of PTPN2 loss remain poorly reported, we aimed to provide a comprehensive analysis of PTPN2 deletions within a cohort of 430 patients, including 216 adults and 214 children treated according to the GRAALL03/05 (#NCT00222027 and #NCT00327678) and the FRALLE2000 protocols, respectively. We used multiplex ligation-dependent probe amplification to identify an 8% incidence of PTPN2 deletion, which was comparable in adult (9%) and pediatric (6%) populations. PTPN2 deletions were significantly associated with an αβ lineage and TLX1 deregulation. Analysis of the mutational genotype of adult T-ALL revealed a positive correlation between PTPN2 deletions and gain-of-function alterations in the IL7R/JAK-STAT signaling pathway as well as PHF6 and WT1 mutations. Of note, PTPN2 and PTEN (phosphatase and tensin homolog) deletions were mutually exclusive. Regarding treatment response, PTPN2-deleted T-ALLs were associated with a higher glucocorticoid response and a trend for improved survival in children, but not in adults, with a 5-year cumulative incidence of relapse of 8% for PTPN2-deleted pediatric cases vs 26% (P = .177).

We report a case of myeloproliferative neoplasm (MPN) with an atypical t(9;22;15)(p24;q11;q21) translocation, leading to a BCR-JAK2 fusion, associated with a trisomy of chromosome 8 in clonal evolution at karyotype. Patient's evolution was marked by an aggressive clinical course with rapid progression to blast phase within the first year after diagnosis. Examination of matched chronic phase and blast crisis samples by SNP-array karyotyping identified secondary acquired cryptic genetic events at the time of lymphoblastic transformation, including biallelic IKZF1 alteration and EBF1 and CDKN2A/B codeletions. This case is the first report describing acquisition of secondary genetic events leading to acute lymphoblastic progression in a rare MPN with BCR-JAK2 fusion.

Introduction. Cases series of patients with FIP1L1-PDGFRA (F/P)-associated chronic eosinophilic leukemia (F/P+ CEL) are scarce and of small sample-size. Low-dose imatinib mesylate (IM) is highly effective in this setting. Although successful treatment discontinuation has been reported, approximately 40% of the patients subsequently relapse. To date, no predictor of relapse after IM discontinuation has yet been evidenced. Methods. We conducted a French multicentric retrospective of patients diagnosed with F/P+ CEL between 2003-2019. Weight loss was defined as a 10% weight loss over the course of the disease's history. Complete (CHR) and partial (PHR) hematological responses were defined as a normalization of the absolute eosinophil count (AEC) and as a reduction in peripheral blood eosinophilia by at least 50% from baseline, respectively. Relapses were defined as the recurrence of eosinophilia, with or without evidence of F/P-gene transcript, but without any other explanation. Complete molecular response (CMR) was defined as a negative RT-PCR and/or RQ-PCR assay for F/P rearrangement. A backward stepwise logistic regression model was used to identify factors associated with relapse after IM discontinuation. Results. One hundred and fifty F/P+ CEL patients (145 males; mean (SD) age at diagnosis: 49 (+/-12 years) were included, among which 26 (17%) did not report any symptom. The main involved organs were the spleen (n=65, 43%), skin (n=47, 31%), heart (n=27, 18%), lungs (n=36, 24%), central nervous system (n=14, 9%), and bones/joints (n=8, 5%). Four (2,6%) patients showed features of vasculitis, involving the skin (n=2) and the CNS (n=2). The mean peak AEC was 10.3 G/L (+/-6 G/l). Besides eosinophilia, the most frequent associated complete blood count (CBC) abnormalities were thrombocytopenia (n=43, 28%), anemia (n=37, 24%), hyperleukocytosis (n=33, 22%) and monocytosis (n=25, 16%). Forty-seven (31%) patients had normal CBC besides eosinophilia. Bone marrow karyotype was normal in 91% (when tested, n=94). Serum vitamin B12 and tryptase (mean: 2386 (+/-1435) pmol/L and 34 (+/-20) µg/L) levels were elevated in 74 (94%) and 44 (79%) of patients respectively, whereas CRP and IgE levels were elevated in 31 (26%) and 12 (14%) each. None of the 37 (25%) patients that received first-line glucocorticoid therapy achieved CHR. All but 3 patients received IM (daily starting dose: 100 (n= 102; 72%), 200 (n=13; 9%) or 400 mg (n=20; 14%)), of whom 100% and 99% achieved CHR and CMR (when tested: n=84), respectively. The mean follow-up (FU) was 80 (+/- 56) months, with overall survival at 1, 5 and 10 years of 99%, 95% and 84% (reaching 100%, 98% and 89% in the 147 IMB-treated patients) respectively. Overall, 8 (5%) patients died during FU, including untreated patients with acute myeloblastic leukemia transformation (n=2) and a single patient with massive cerebral infarction. Eight patients relapsed during IM tapering, all of which were successfully treated when higher doses of IM were resumed. After a median [IQR] of 44 [27-72] months of IM treatment, 46 (32%) patients eventually discontinued IM, amongst whom 19 (41%) relapsed after a median of 10[4-23] months (42% of relapses defined by PCR). In multivariate analysis, weight loss (HR: 5,02 95%CI[1,9 - 28,04]; p =0,004), the time between onset of eosinophilia and IM initiation (HR 1,02 [1,00 - 1,03]; 0,01) and duration of IM treatment prior to discontinuation (HR: 0,97 [0,95-0,99]; p=0,01) were independent factors of relapse (Table 1). Conclusion. This large cohort further confirms that F/P+ CEL almost exclusively affects male patients, with spleen, skin, heart and lung involvements being the most frequent. While glucocorticoids never lead to the normalization of CBC parameters, IM is highly effective and treated patients carry an excellent prognosis. After IM discontinuation, although 60% of patients maintain CHR overtime, 40% subsequently relapse, with weight loss, time between onset of eosinophilia and IM initiation and duration of IM treatment prior to discontinuation being significant but moderate independent factors of relapse. Disclosures Nicolini: Incyte Biosciences: Honoraria, Research Funding, Speakers Bureau; Novartis: Research Funding, Speakers Bureau; Sun Pharma Ltd: Consultancy. Tavitian:Novartis: Membership on an entity's Board of Directors or advisory committees. Huguet:Novartis: Honoraria; BMS: Honoraria; Pfizer: Honoraria; Incyte Biosciences: Honoraria; Amgen: Honoraria; Servier: Honoraria; Jazz Pharmaceuticals: Honoraria. Jardin:Servier: Honoraria; janssen: Honoraria; celgene: Honoraria; roche: Honoraria; amgen: Honoraria.

Risk stratification in childhood T-cell acute lymphoblastic leukemia (T-ALL) is mainly based on minimal residual disease (MRD) quantification. Whether oncogenetic mutation profiles can improve the discrimination of MRD-defined risk categories was unknown. Two hundred and twenty FRALLE2000T-treated patients were tested retrospectively for NOTCH1/FBXW7/RAS and PTEN alterations. Patients with NOTCH1/FBXW7 (N/F) mutations and RAS/PTEN (R/P) germ line (GL) were classified as oncogenetic low risk (gLoR; n = 111), whereas those with N/F GL and R/P GL mutations or N/F and R/P mutations were classified as high risk (gHiR; n = 109). Day 35 MRD status was available for 191 patients. Five-year cumulative incidence of relapse (CIR) and disease-free survival were 36% and 60% for gHiR patients and 11% and 89% for gLoR patients, respectively. Importantly, among the 60% of patients with MRD

Differential impact of drugs on the outcome of ETV6-RUNX1 positive childhood B-cell precursor acute lymphoblastic leukaemia: results of the EORTC CLG 58881 and 58951 trials

International audience; Minimal residual disease (MRD) is known to be an independent prognostic factor in patients with acute lymphoblastic leukemia (ALL). High-throughput sequencing (HTS) is currently used in routine practice for the diagnosis and follow-up of patients with hematological neoplasms. In this retrospective study, we examined the role of immunoglobulin/T-cell receptor-based MRD in patients with ALL by HTS analysis of immunoglobulin H and/or T-cell receptor gamma chain loci in bone marrow samples from 11 patients with ALL, at diagnosis and during follow-up. We assessed the clinical feasibility of using combined HTS and bioinformatics analysis with interactive visualization using Vidjil software. We discuss the advantages and drawbacks of HTS for monitoring MRD. HTS gives a more complete insight of the leukemic population than conventional real-time quantitative PCR (qPCR), and allows identification of new emerging clones at each time point of the monitoring. Thus, HTS monitoring of Ig/TCR based MRD is expected to improve the management of patients with ALL.

Objectives Until recently, diagnostic laboratories that wanted to report on the international scale had limited options: they had to align their BCR–ABL1 quantification methods through a sample exchange with a reference laboratory to derive a conversion factor. However, commercial methods calibrated on the World Health Organization genetic reference panel are now available. We report results from a study designed to assess the comparability of the two alignment strategies. Design and methods Sixty follow-up samples from chronic myeloid leukemia patients were included. Two commercial methods calibrated on the genetic reference panel were compared to two conversion factor methods routinely used at Saint-Louis Hospital, Paris, and at Lille University Hospital. Results were matched against concordance criteria (i.e., obtaining at least two of the three following landmarks: 50, 75 and 90% of the patient samples within a 2-fold, 3-fold and 5-fold range, respectively). Results Out of the 60 samples, more than 32 were available for comparison. Compared to the conversion factor method, the two commercial methods were within a 2-fold, 3-fold and 5-fold range for 53 and 59%, 89 and 88%, 100 and 97%, respectively of the samples analyzed at Saint-Louis. At Lille, results were 45 and 85%, 76 and 97%, 100 and 100%, respectively. Agreements between methods were observed in the four comparisons performed. Conclusion Our data show that the two commercial methods selected are concordant with the conversion factor methods. This study brings the proof of principle that alignment on the international scale using the genetic reference panel is compatible with the patient sample exchange procedure. We believe that these results are particularly important for diagnostic laboratories wishing to adopt commercial methods.

Systemic EBV+ T-cell lymphoproliferative disease of childhood is a recent entity described in the 2008 World Health Organisation tumours of haematopoietic system and lymphoid tissues as a clonal T-cell EBV+ systemic proliferation. It occurs after acute or chronic active EBV infection. We report the case of a caucasian, immunocompetent 12-year-old girl, with no particular history, who presented with hemophagocytic lymphohistiocytosis in the aftermath of an infectious mononucleosis. Main symptoms were multiple organ failure, hepatosplenomegaly and pancytopenia. Histopathology of peripheral lymph node and bone marrow revealed a T-cell, CD8+, EBV+ lymphoproliferation. An elevated viral load was detected in blood by PCR. The patient died within 3 weeks. Since most of the cases have been reported in Asia and South America, few cases still have been described in Europe. Unlike B-cell lymphoproliferation in immunocompromised individuals, T-cell EBV+ lymphoproliferation occurs in immunocompetent patients and seems to be the consequence of a proliferative disorder of EBV-infected T-cells, attributed to a cytotoxic T-cell response deficiency. These T-cell proliferations are more frequently immunoreactive for CD8 than CD4. A key feature of the diagnosis might be EBV viral load.

Key Clinical Message Intrachromosomal amplification of chromosome 21 (iAMP21) defines a distinct cytogenetic subgroup of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) with poor prognosis that should be investigated in routine practice. Single-nucleotide polymorphism (SNP)-array provides a useful method to detect such cases showing a highly characteristic profile.

Mutation of the MYD88 gene has recently been identified in activated B-cell-like diffuse cell lymphoma and enhanced Janus kinase/signal transducer and activator of transcription (JAK-STAT) and nuclear factor κB (NF-κB) signaling pathways. A whole exome-sequencing study of Waldenstrom macroglobulinemia (WM) suggested a high frequency of MYD88 L265P mutation in WM. The genetic background is not fully deciphered in WM, although the role of NF-κB and JAK-STAT has been demonstrated. We analyzed MYD88 mutation in exon 5 and characterized the clinical significance of this genetic alteration in 67 WM patients. Clinical features; immunophenotypic markers; and conventional cytogenetic, fluorescence in situ hybridization, and single nucleotide polymorphism array data were analyzed. MYD88 L265P mutation was acquired in 79% of patients. Overall, we have identified alteration of the MYD88 locus in 91% of WM patients, including 12% with gain on chromosome 3 at the 3p22 locus that included the MYD88 gene. Patients with absence of MYD88 mutation were WM characterized with a female predominance, a splenomegaly, gain of chromosome 3, and CD27 expression. Importantly, inhibition of MYD88 signaling induced cytotoxicity and inhibited cell growth of cell lines issued from patients with WM. In conclusion, these results confirm a high frequency of MYD88 L265P mutation in WM. The discovery of MYD88 L265P mutation may contribute to a better understanding of the physiopathogeny of WM.

Le sequencage de nouvelle generation (NGS) represente un veritable saut technologique. Si les premieres applications ont surtout ete axees sur le sequencage de genome entier dans le but d’identifier de nouvelles mutations geniques, il fait aujourd’hui son apparition dans les laboratoires hospitaliers avec essentiellement des approches de resequencage cible. En oncohematologie, les applications hospitalieres sont en cours de transfert avec de nombreux avantages mais egalement certaines contraintes. L’objectif de cette revue est de faire un etat des lieux du NGS dans notre discipline en ce debut d’annee 2013.

Age-related EBV-associated lymphoproliferative disorders form a new clinicopathological group. Until recently, this group was associated with diffuse large B-cell lymphoma (DLBCL), characterised by an aggressive clinical presentation and a poor prognosis. Recent findings in Western Caucasian patients, however, suggest that this entity covers a wide spectrum of diseases, ranging from reactive follicular hyperplasia (HR) to DLBCL. We report the case of an 85-year-old Caucasian man showing lymphadenopathy and numerous hypodense lesions of the liver. Examination of a lymph node revealed follicular hyperplasia with EBV expression confined to germinal centres. The patient was treated with Rituximab and subsequently, the lesions of the liver were explored. They showed extensive necrosis and a polymorphic large B-cell population with strong EBV expression. This is the first report to describe age-related EBV-associated follicular hyperplasia at one site coexisting with DLBCL at another. This case warrants undertaking further investigations each time a diagnosis of age-related EBV-HR is associated with extranodal lesions.

DNA copy number analysis has been instrumental for the identification of genetic alterations in B-cell precursor acute lymphoblastic leukemia. Notably, some of these genetic defects have been associated with poor treatment outcome and might be relevant for future risk stratification. In this study, we characterized recurrent deletions of CD200 and BTLA genes, mediated by recombination-activating genes, and used breakpoint-specific polymerase chain reaction assay to screen a cohort of 1154 cases of B-cell precursor acute lymphoblastic leukemia uniformly treated according to the EORTC-CLG 58951 protocol. CD200/BTLA deletions were identified in 56 of the patients (4.8%) and were associated with an inferior 8-year event free survival in this treatment protocol [70.2% ± 1.2% for patients with deletions versus 83.5% ± 6.4% for non-deleted cases (hazard ratio 2.02; 95% confidence interval 1.23-3.32; P=0.005)]. Genetically, CD200/BTLA deletions were strongly associated with ETV6-RUNX1-positive leukemias (P

Risk-adjusted treatment stratification in T-cell acute lymphoblastic leukemias (T-ALLs) is currently based only on early response to chemotherapy. We investigated the prognostic implication of hyperactivation of NOTCH pathway resulting from mutations of NOTCH1 or FBXW7 in children with T-ALL enrolled in EORTC-CLG trials. Overall, 80 out of 134 (60%) patients were NOTCH+ (NOTCH1 and/or FBXW7 mutated). Although clinical presentations were not significantly associated with NOTCH status, NOTCH+ patients showed a better early response to chemotherapy as compared with NOTCH- patients, according to the rate of poor pre-phase 'responders' (25% versus 44%; P=0.02) and the incidence of high minimal residual disease (MRD) levels (11% (7/62) versus 32% (10/31); P=0.01) at completion of induction. However, the outcome of NOTCH+ patients was similar to that of NOTCH- patients, with a 5-year event-free survival (EFS) of 73% and 70% (P=0.82), and 5-year overall survival of 82% and 79% (P=0.62), respectively. In patients with high MRD levels, the 5-year EFS rate was 0% (NOTCH+) versus 42% (NOTCH-), whereas in those with low MRD levels, the outcome was similar: 76% (NOTCH+) versus 78% (NOTCH-). The incidence of isolated central nervous system (CNS) relapses was relatively high in NOTCH1+ patients (8.3%), which could be related to a higher propensity of NOTCH+ leukemic blasts to target the CNS.

In a case with secondary myelofibrosis occurring after essential thrombocythemia, cytogenetic analysis revealed an isolated translocation t(X;17)(q27;q22) in all cells. We found that a bacterial artificial chromosome (BAC) encompassing the breakpoint on chromosome 17 long arm contained only one gene, NOG. We therefore investigated the occurrence of this rare breakpoint in myeloproliferative disorders (MPDs). We identified three more patients with a 17q abnormality in MPDs: myelofibrosis with myeloid metaplasia (MMM); chronic myeloid leukemia positive for t(9;22)(q34;q11) with additional t(4;17)(p15;q22) at diagnosis; and myelofibrosis complicating polycythemia vera. All three cases exhibited a split of BACs containing NOG. The protein encoded by NOG, noggin, acts as an antagonist to bone morphogenetic secreted protein 2 and 4 (BMP2 and BMP4). A comparative analysis of gene expression on Agilent 22K oligonucleotide microarrays in purified CD34+ cells from the blood of MMM patients showed significant downregulation of BMPR2, BMPR1B, BMP2, and BMP8; upregulation of BMP3 and BMP10; and a trend to lower expression of NOG. Thus, given that expression and release of BMPs are important in the induction of osteosclerosis and angiogenic activity, the observed BMP deregulations could be triggered by potential NOG genetic alterations in the four cases here described, and may contribute to the myelofibrotic process characterized by bone marrow stromal reaction including collagen fibrosis, osteosclerosis, and angiogenesis.

International audience; High-throughput sequencing (HTS) is considered a technical revolution that has improved our knowledge of lymphoid and autoimmune diseases, changing our approach to leukaemia both at diagnosis and during follow-up. As part of an immunoglobulin/T cell receptor-based minimal residual disease (MRD) assessment of acute lymphoblastic leukaemia patients, we assessed the performance and feasibility of the replacement of the first steps of the approach based on DNA isolation and Sanger sequencing, using a HTS protocol combined with bioinformatics analysis and visualization using the Vidjil software. We prospectively analysed the diagnostic and relapse samples of 34 paediatric patients, thus identifying 125 leukaemic clones with recombinations on multiple loci (TRG, TRD, IGH and IGK), including Dd2/Dd3 and Intron/KDE rearrangements. Sequencing failures were halved (14% vs. 34%, P = 0.0007), enabling more patients to be monitored. Furthermore, more markers per patient could be monitored, reducing the probability of false negative MRD results. The whole analysis, from sample receipt to clinical validation, was shorter than our current diagnostic protocol, with equal resources. V(D)J recombination was successfully assigned by the software, even for unusual recombinations. This study emphasizes the progress that HTS with adapted bioinformatics tools can bring to the diagnosis of leukaemia patients.

International audience; Relapse after transplantation is a major cause of treatment failure in paediatric acute lymphoblastic leukaemia (ALL). Here, we report the findings of a prospective national study designed to investigate the feasibility of immune intervention in children in first or subsequent remission following myeloablative conditioning. This study included 133 children who received a transplant for ALL between 2005 and 2008. Minimal Residual Disease (MRD) based on T cell receptor/immunoglobulin gene rearrangements was measured on days -30, 30, 90 and 150 post-transplantation. Ciclosporin treatment was rapidly discontinued and donor lymphocyte infusions (DLI) were programmed for patients with a pre- or post-transplant MRD status ≥10(-3) . Only nine patients received DLI. Pre- and post-transplant MRD status, and the duration of ciclosporin were independently associated with 5-year overall survival (OS), which was 62·07% for the whole cohort. OS was substantially higher in patients cleared of MRD than in those with persistent MRD (52·3% vs. 14·3%, respectively). Only pre-transplant MRD status (Hazard Ratio 2·57, P = 0·04) and duration of ciclosporin treatment (P < 0·001) were independently associated with relapse. The kinetics of chimerism were not useful for predicting relapse, whereas MRD monitoring up to 90 d post-transplantation was a valuable prognostic tool to guide therapeutic intervention.

Myelofibrosis with myeloid metaplasia (MMM) is a rare myeloproliferative disorder which associates clonal proliferation of multi-potent hematologic progenitors and reactive fibrosis [1]. The karyot...

Thymomas are low-grade epithelial cancers of the thymus whose prevalence varies between 0.1/100,000 and 0.4/100,000. Familial occurrence of thymoma is very rare. We studied a family bearing the constitutional chromosome translocation t(14;20)(q24;p12), 3 of whose members had a thymoma. In this family, among 27 patients, 11 had the translocation: 3 had thymoma and 4 others had 5 different autoimmune diseases: type 1 diabetes mellitus, Graves' disease, pernicious anemia, primitive Sjögren disease, and autoimmune pancytopenia. FISH studies allowed us to be more specific about the translocation breakpoints. The 14q24 breakpoint was in intron 5 of RAD51L1, and the 20p12 breakpoint was 100 kb telomeric to BMP2. RAD51L1 is a tumor-suppressor gene belonging to the RAD51 family, already implicated in many tumors (uterine leiomyomas, pseudo-Meigs syndromes, pulmonary chondroid hamartomas) and involved in recombinational repair of DNA double-strand breaks. BMP2 belongs to the TGFbeta superfamily, and the BMP2-BMP4 genes are involved in thymocyte differentiation by blocking progression from CD4-CD8- to CD4+CD8+ while maintaining a sufficient pool of immature precursors. Dysregulation of RAD51L1 and/or BMP2 may explain this familial occurrence of thymomas and autoimmune diseases. Using QRT-PCR, we studied the expression of BMP2 in 20 sporadic thymomas and found various levels of expression that may be associated with autoimmune diseases.

Despite the favorable prognosis of patients with acute myeloid leukemia (AML) with t(8;21)(q22;q22) translocation, relapses still occur in about 30% of the cases but no initial factors can strongly predict the risk of relapse. Several recent studies suggest that monitoring minimal residual disease (MRD) may identify patients at risk of relapse. We prospectively monitored AML1-ETO rearrangement by real-time quantitative PCR (RQ-PCR) in 21 patients uniformly treated in our center. Blood (PB) and bone marrow (BM) samples were collected during and after therapy. At diagnosis, levels of AML1-ETO transcript showed large variations and there was a trend for a higher relapse rate in patients with high pretreatment expression levels (P=0.065). After induction therapy, absolute transcript levels (below 10(-3), compared to Kasumi cell line), or a greater than 3 log decrease by comparison to diagnosis levels, were significant predictors of the absence of relapse (P=0.02 and P=0.02, respectively). MRD levels after consolidation therapy were also significant indicators of relapse (P=10(-5)). Comparison of BM and PB samples showed similar sensitivity for detecting AML1-ETO transcript. In conclusion, RQ-PCR appears to be an early predictive factor of the relapse risk in AML with t(8;21). PB samples can be used adequately to evaluate the level of MRD by this technique.