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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

Tandem duplications (TDs) of the UBTF gene have been recently described as a recurrent alteration in pediatric acute myeloid leukemia (AML). Here, by screening 1946 newly diagnosed adult AML, we found that UBTF-TDs occur in about 3% of patients aged 18–60 years, in a mutually exclusive pattern with other known AML subtype-defining alterations. The characteristics of 59 adults with UBTF-TD AML included young age (median 37 years), low bone marrow (BM) blast infiltration (median 25%), and high rates of WT1 mutations (61%), FLT3-ITDs (51%) and trisomy 8 (29%). BM morphology frequently demonstrates dysmyelopoiesis albeit modulated by the co-occurrence of FLT3-ITD. UBTF-TD patients have lower complete remission (CR) rates (57% after 1 course and 76% after 2 courses of intensive chemotherapy [ICT]) than UBTF-wild-type patients. In patients enrolled in the ALFA-0702 study (n = 614 patients including 21 with UBTF-TD AML), the 3-year disease-free survival (DFS) and overall survival of UBTF-TD patients were 42.9% (95%CI: 23.4–78.5%) and 57.1% (95%CI: 39.5–82.8%) and did not significantly differ from those of ELN 2022 intermediate/adverse risk patients. Finally, the study of paired diagnosis and relapsed/refractory AML samples suggests that WT1-mutated clones are frequently selected under ICT. This study supports the recognition of UBTF-TD AML as a new AML entity in adults.

Oncogenic alterations underlying B-cell acute lymphoblastic leukemia (B-ALL) in adults remain incompletely elucidated. To uncover novel oncogenic drivers, we performed RNA sequencing and whole-genome analyses in a large cohort of unresolved B-ALL. We identified a novel subtype characterized by a distinct gene expression signature and the unique association of 2 genomic microdeletions. The 17q21.31 microdeletion resulted in a UBTF::ATXN7L3 fusion transcript encoding a chimeric protein. The 13q12.2 deletion resulted in monoallelic ectopic expression of the homeobox transcription factor CDX2, located 138 kb in cis from the deletion. Using 4C-sequencing and CRISPR interference experiments, we elucidated the mechanism of CDX2 cis-deregulation, involving PAN3 enhancer hijacking. CDX2/UBTF ALL (n = 26) harbored a distinct pattern of additional alterations including 1q gain and CXCR4 activating mutations. Within adult patients with Ph− B-ALL enrolled in GRAALL trials, patients with CDX2/UBTF ALL (n = 17/723, 2.4%) were young (median age, 31 years) and dramatically enriched in females (male/female ratio, 0.2, P = .002). They commonly presented with a pro-B phenotype ALL and moderate blast cell infiltration. They had poor response to treatment including a higher risk of failure to first induction course (19% vs 3%, P = .017) and higher post-induction minimal residual disease (MRD) levels (MRD ≥ 10−4, 93% vs 46%, P < .001). This early resistance to treatment translated into a significantly higher cumulative incidence of relapse (75.0% vs 32.4%, P = .004) in univariate and multivariate analyses. In conclusion, we discovered a novel B-ALL entity defined by the unique combination of CDX2 cis-deregulation and UBTF::ATXN7L3 fusion, representing a high-risk disease in young adults.

Not available.

Intra-tumor heterogeneity portends poor outcome in many cancers. In AML, a higher number of drivers worsens prognosis. The Shannon Index is a robust metric of clonal heterogeneity that accounts for the number of clones, but also their relative abundance. We show that a Shannon Index can be estimated from bulk sequencing, which is correlated (ρ = 0.76) with clonal diversity from single-colony genotyping. In a discovery cohort of 292 patients with sequencing of 43 genes, a higher number of drivers (HR = 1.18, P = 0.028) and a lower Shannon Index (HR = 0.68, P = 0.048), the latter reflecting clonal dominance, are independently associated with worse OS independently of European LeukemiaNet 2017 risk. These findings are validated in an independent cohort of 1184 patients with 111-gene sequencing (number of drivers HR = 1.16, P = 1 × 10−5, Shannon Index HR = 0.81, P = 0.007). By re-interrogating paired diagnosis/relapse exomes from 50 cytogenetically normal AMLs, we find clonal dominance at diagnosis to be correlated with the gain of a significantly higher number of mutations at relapse (P = 6 × 10−6), hence with clonal sweeping. Our results suggest that clonal dominance at diagnosis is associated with the presence of a leukemic phenotype allowing rapid expansion of new clones and driving relapse after chemotherapy.

Germline DDX41 mutations are involved in familial myelodysplastic syndromes (MDSs) and acute myeloid leukemias (AMLs). We analyzed the prevalence and characteristics of DDX41-related myeloid malignancies in an unselected cohort of 1385 patients with MDS or AML. Using targeted next-generation sequencing, we identified 28 different germline DDX41 variants in 43 unrelated patients, which we classified as causal (n = 21) or unknown significance (n = 7) variants. We focused on the 33 patients having causal variants, representing 2.4% of our cohort. The median age was 69 years; most patients were men (79%). Only 9 patients (27%) had a family history of hematological malignancy, and 15 (46%) had a personal history of cytopenia years before MDS/AML diagnosis. Most patients had a normal karyotype (85%), and the most frequent somatic alteration was a second DDX41 mutation (79%). High-risk DDX41 MDS/AML patients treated with intensive chemotherapy (n = 9) or azacitidine (n = 11) had an overall response rate of 100% or 73%, respectively, with a median overall survival of 5.2 years. Our study highlights that germline DDX41 mutations are relatively common in adult MDS/AML, often without known family history, arguing for systematic screening. Salient features of DDX41-related myeloid malignancies include male preponderance, frequent preexisting cytopenia, additional somatic DDX41 mutation, and relatively good outcome.

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

Background IG/TR-based minimal residual disease (MRD) is a faithful marker of response to therapy and the strongest predictor of relapse in acute lymphoblastic leukemia (ALL). In adults with Philadelphia chromosome-positive (Ph+) ALL, MRD is commonly monitored by BCR-ABL1 transcript quantification, although its prognostic significance has not been compared to IG/TR MRD to date. Recently, it has been shown that BCR-ABL1 rearrangement may be found and persist in non-lymphoblastic cells in some patients. In the prospective GRAAPH-2014 trial, using a dual IG/TR and BCR-ABL1 MRD monitoring, we aimed to study the biological and clinical significance of persistent BCR-ABL1 clonal hematopoiesis (CH) in adults with de novo Ph+ ALL. Patients and Methods The study comprised 156 adults with de novo Ph+ ALL randomized in the GRAAPH-2014 trial. Bone marrow (BM) and peripheral blood (PB) follow-up (FU) samples were collected after each treatment cycle and before hematopoietic stem cell transplantation (HSCT). MRD monitoring was performed by quantification of both BCR-ABL1 transcripts and IG/TCR clonal rearrangements on all available samples and MRD quantification of genomic BCR-ABL1 breakpoint fusion was also performed for 37 patients. MRD results were considered discordant if more than one log10 difference or positivity/negativity discordance on the same FU sample was evidenced. Cell fractions from 14 peripheral blood mononuclear cells (PBMC) samples (T-cells, B-cells and monocytes) were FACS-sorted and evaluated for BCR-ABL1 expression. Achievement of major molecular response (MMR) defined as Results Quantification of BCR-ABL1 transcripts and IG/TR MRD levels on 876 samples from 156 patients (456 BM and 542 PB) identified 54 out of 142 (38%) evaluable patients with consistently discordant MRD results in at least 3 different timepoints, suggesting the persistence of non-lymphoblastic BCR-ABL1-positive cells in these patients and BCR-ABL1 CH. Possible bias related to variable BCR-ABL1 expression was ruled out by genomic BCR-ABL1 quantification on 263 FU samples (r s=0.89, p We then evaluated the clinical significance of BCR-ABL1 CH. Unexpectedly, CH+ patients had a significant lower cumulative incidence of relapse (CIR) (panel A, hazard ratio (HR) 0.37, 95% CI [0.15-0.90], p=0.03). However, this lower CIR did not translate into longer disease-free survival (DFS) (panel B, HR=0.85, 95% CI [0.44-1.63], p=0.63). Since an imbalance in alloSCT was observed between CH+ and CH- patients, we tested if the observed difference in CIR may be related to different alloSCT outcomes. When censoring patients at alloSCT, the difference in CIR was indeed no longer significant (subhazard ratio (SHR) 0.48, 95% CI [0.16-1.43], p=0.19). More interestingly, the benefit of alloSCT was restricted to CH- patients. Using alloSCT as a time-dependent variable, DFS was indeed improved by alloSCT in CH- (SHR 0.40, 95% CI [0.17-0.91], p=0.03, panel C) but not in CH+ patients (SHR 1.12, 95%CI [0.32-3.87], p=0.86, panel D) despite a non-significant interaction between CH status and alloSCT. Conclusion More than one third of adults with de novo Ph+ ALL displays persistent measurable BCR-ABL1 signal during therapy, likely related to BCR-ABL1 CH. Strikingly, this condition is not associated with a higher risk of relapse nor with poorer overall outcomes in the GRAAPH-2014 trial. Moreover, our results suggest that patients with BCR-ABL1 CH may not be good candidates for alloSCT. By contrast, IG/TR MRD may allow to identify patients with the higher risk of relapse. These results highlight the need for implementation of IG/TR MRD in adult Ph+ ALL to guide therapeutic decisions. Figure 1 Figure 1. Disclosures Rousselot: Incyte, Pfizer: Consultancy, Research Funding. Chalandon: Incyte, BMS, Pfizer, Abbie, MSD, Roche, Novartis, Amgen: Other: Advisory Board; Incyte: Speakers Bureau; Incyte, BMS, Pfizer, Abbie, MSD, Roche, Novartis, Gilead, Amgen, Jazz, Astra Zenec: Other: Travel EXpenses, Accomodation. Straetmans: Alexion: Membership on an entity's Board of Directors or advisory committees. Huguet: Novartis: Other: Advisor; Jazz Pharmaceuticals: Other: Advisor; Celgene: Other: Advisor; BMS: Other: Advisor; Amgen: Other: Advisor; Pfizer: Other: Advisor. Dombret: Amgen: Honoraria, Research Funding; Incyte: Honoraria, Research Funding; Jazz Pharmaceuticals: Honoraria, Research Funding; Novartis: Research Funding; Pfizer: Honoraria, Research Funding; Servier: Research Funding; Abbvie: Honoraria; BMS-Celgene: Honoraria; Daiichi Sankyo: Honoraria. Boissel: SANOFI: Honoraria; CELGENE: Honoraria; Servier: Consultancy, Honoraria; Amgen: Consultancy, Honoraria, Research Funding; PFIZER: Consultancy, Honoraria; Bristol-Myers Squibb: Honoraria, Research Funding; Incyte: Honoraria; Novartis: Consultancy, Honoraria, Research Funding; JAZZ Pharma: Honoraria, Research Funding.

Intra-tumor heterogeneity portends poor outcome in many cancers. In AML, a higher number of drivers worsens prognosis. The Shannon Index is a robust metric of clonal heterogeneity that accounts for the number of clones, but also their relative abundance. We show that a Shannon Index can be estimated from bulk sequencing, which is correlated (ρ = 0.76) with clonal diversity from single-colony genotyping. In a discovery cohort of 292 patients with sequencing of 43 genes, a higher number of drivers (HR = 1.18, P = 0.028) and a lower Shannon Index (HR = 0.68, P = 0.048), the latter reflecting clonal dominance, are independently associated with worse OS independently of European LeukemiaNet 2017 risk. These findings are validated in an independent cohort of 1184 patients with 111-gene sequencing (number of drivers HR = 1.16, P = 1 × 10

Non-del(5q) transfusion-dependent low/intermediate-1 myelodysplastic syndrome (MDS) patients achieve an erythroid response with lenalidomide in 25% of cases. Addition of an erythropoiesis-stimulating agent could improve response rate. The impact of recurrent somatic mutations identified in the diseased clone in response to lenalidomide and the drug's effects on clonal evolution remain unknown. We investigated recurrent mutations by next-generation sequencing in 94 non-del(5q) MDS patients randomized in the GFM-Len-Epo-08 clinical trial to lenalidomide or lenalidomide plus epoetin β. Clonal evolution was analyzed after 4 cycles of treatment in 42 cases and reanalyzed at later time points in 18 cases. The fate of clonal architecture of single CD34(+)CD38(-) hematopoietic stem cells was also determined in 5 cases. Mutation frequency was >10%: SF3B1 (74.5%), TET2 (45.7%), DNMT3A (20.2%), and ASXL1 (19.1%). Analysis of variant allele frequencies indicated a decrease of major mutations in 15 of 20 responders compared with 10 of 22 nonresponders after 4 cycles. The decrease in the variant allele frequency of major mutations was more significant in responders than in nonresponders (P < .001). Genotyping of single CD34(+)CD38(-) cell-derived colonies showed that the decrease in the size of dominant subclones could be associated with the rise of founding clones or of hematopoietic stem cells devoid of recurrent mutations. These effects remained transient, and disease escape was associated with the re-emergence of the dominant subclones. In conclusion, we show that, although the drug initially modulates the distribution of subclones, loss of treatment efficacy coincides with the re-expansion of the dominant subclone. This trial was registered at www.clinicaltrials.gov as #NCT01718379.

International audience; We report the case of a 31 year-old man diagnosed with an atypical acute leukemia difficult to characterize cytologically. The immunophenotyping identified a blastic population co-expressing myeloid, lymphoidBand lymphoid T markers suggesting the diagnosis of either a mixed phenotype acute leukemia (MPAL) or an early T-cell precursor acute lymphoblastic leukemia (ETP-ALL). Because of the poor prognosis linked to these leukemias, the patient benefited from chemotherapy targeting both myeloid and lymphoid components, followed by allogeneic hematopoietic stem cell transplantation. DNA-based techniques analyzing B and T-cell clonality identified partial rearrangements in immunoglobulin and TCR genes, allowing the monitoring of minimal residual disease. This observation highlights the difficulty to classify some atypical cases of acute leukemias. It emphasizes on the complementarity of cytomorphology, immunophenotyping by flow cytometry and molecular techniques in order to promptly characterize and treat these leukemias.

Bromodomain and Extra-Terminal inhibitors (BETi) such as OTX015 are active in Acute Myeloid Leukaemias (AML). Their activity on Leukemic Stem Cells (LSCs) is less documented. We interrogated the anti-LSC activity of OTX015 in a niche-like long-term culture in 26 primary AML samples and validated our findings in vivo. OTX015 impaired LSCs in AMLs harbouring Core Binding Factor or KMT2A gene fusions, NPM1 or chromatin/spliceosome genes mutations, but not in those with aneuploidy/TP53 mutations. In four patients, we dissected the transcriptomic footprint of Bet inhibition on LSCs versus blasts. Our results can instruct future clinical trials of BETi in AML.

Introduction Le syndrome de Sweet (SS) est caracterise par une accumulation de polynucleaires neutrophiles matures (PNN) dans le derme. Dix pour cent des patients ayant un SS ont une hemopathie myeloide (HM) sous-jacente, mais le lien physiopathologique entre ces deux maladies n’est pas elucide. L’objectif de cette etude etait de determiner si les PNN dermiques au cours des SS associes aux HM (SS-HM) etaient d’origine clonale. Materiel et methodes Nous avons mene une etude retrospective incluant tous les patients atteints d’un SS et d’une HM diagnostiques a l’Hopital Saint-Louis et a l’Hopital Saint-Antoine, Paris, France, entre 2005 et 2018. Le sequencage haut-debit (Next-Generation Sequencing, NGS) d’un panel de 80 genes impliques dans les hemopathies myeloides etait realise sur l’ADN extrait de prelevement medullaire ou sanguin (echantillons hematopoietiques) et de coupes de biopsies cutanees du SS incluses en paraffine. Resultats Dix patients ( Figure 1 ) ont ete analyses, dont 6 presentant une leucemie aigue myeloide, 2 un syndrome myelodysplasique (SMD), 1 un syndrome myeloproliferatif (SMP) et 1 un SMD/SMP. L’analyse par NGS des echantillons hematopoietiques a mis en evidence des mutations oncogeniques chez 9 des 10 patients (mediane 3 mutations par patient [1–10]). Les mutations les plus frequentes affectaient des genes codant pour des facteurs impliques dans l’epissage (SRSF2, PRPF8), dans la transcription (TP53, RUNX1) et le complexe cohesine (STAG2) et des regulateurs epigenetiques (TET2, DNMT3A). De maniere frappante, dans tous les cas, le clone majoritaire identifie dans l’echantillon hematopoietique etait egalement retrouve dans la biopsie cutanee. Discussion Il s’agit du premier travail etudiant le profil mutationnel de l’infiltrat neutrophilique dermique du SS et de la cellule myeloide tumorale dans une cohorte de SS-HM, et montrant un lien clonal entre le SS et l’HM. Ceci avait ete prealablement suggere par des etudes d’hybridation par fluorescence in situ. L’hypothese d’une contamination de la biopsie cutanee par les cellules circulantes etait ecartee devant les frequences alleliques importantes observees a l’analyse par NGS des biopsies cutanees. Chez 6 patients, le SS survenait apres introduction d’un traitement specifique de l’HM, dont 3 apres azacytidine ou inhibiteur de FLT3, traitements responsables de la differentiation terminale des cellules blastiques myeloides. Le SS survenait toutefois en l’absence de traitement inducteur chez 4 patients. Dans ces cas, des facteurs locaux immunologiques encore indetermines pourraient favoriser la maturation cellulaire. Conclusion Nous demontrons pour la premiere fois que les PNN matures infiltrant la peau au cours des SS-HM se sont differencies a partir du clone myeloide tumoral, que le SS soit induit par un traitement ou non.

Erythropoiesis stimulating agents (ESA) are generally first-line treatments of anemia in lower risk myelodysplastic syndrome (MDS), yielding response rates of 30 to 60%, median response duration of 20 to 24 months1,2 and a possible survival improvement compared to RBC transfusions alone.1–3 Main consensus prognostic factors of better response to ESA include low or int-1 IPSS, low RBC transfusion burden, and low serum EPO (sEPO).4 Other reported prognostic factors for response to ESA include marrow multilineage dysplasia, flow cytometry scoring,5 ERK and STAT5 phosphorylation in erythroblasts,6,7 and IPSS-R.8

Background: MDS and AML are mostly found in elderly patients. However, even in this population there is increasing evidence of predisposing genetic conditions, which have been underdiagnosed so far. Identifying inherited predisposition to myeloid disorders can be crucial especially in the context of hematopoietic stem cell transplantation (HSCT). Germline mutations in the DEAD/H-box helicase gene DDX41 have been identified in families with multiple cases of MDS or AML but also in sporadic cases. We aimed to analyze the prevalence and clinical features of DDX41-related myeloid malignancies within an unselected cohort of pts diagnosed with MDS or AML (MDS/AML). Methods Between March 2017 and June 2018, mutation screening was performed in 842 consecutive pts with a diagnosis of MDS/AML in a single center at Hôpital Saint-Louis, Paris. DNA was obtained from bone marrow or peripheral blood. Targeted sequencing of all exons of a panel of 80 genes recurrently mutated in myeloid malignancies was performed using custom capture-based library preparation (Agilent SureSelect) and Illumina sequencing. Sanger sequencing was performed on selected pts' cultured skin fibroblasts to check for the putative germline origin of the variants. Results We identified a DDX41 gene variant in 36 unrelated pts (4% of 842). We focused on the 32 pts having at least one DDX41 variant with a variant allele frequency (VAF) ranging from 40 to 60% highly suggestive of a germline origin, which was subsequently confirmed in all available cases (N=7). Sixteen variants were classified as pathogenic or likely pathogenic based on major predicted changes in protein sequence while the 16 others were missense variants of unknown significance (VUS), which scored deleterious in most algorithms (Figure 1A). An additional, likely somatic DDX41 mutation (VAF < 40%) was present in 18 of 32 pts (56%). Overall, 22 pts could be unambiguously considered as having a DDX41-related malignancy based on the presence of a major disturbing mutation and/or a second DDX41 mutation, while 10 pts had a single VUS. Twenty-six variants were newly described, including a recurrent one, G173R found in 5 pts, all having a second DDX41 mutation. Median age of the 32 patients was 70 years (35-88). Only 4 pts (12%) had a familial history of hematologic disorders. According to revised WHO classification, 4 (12.5%) had MDS-MLD, 8 MDS-EB (25%), 12 AML (37.5%), 6 MDS/MPN (18.7%), one 5q syndrome and one aplastic anemia. Strikingly, 15/32 (47%) pts had a history of cytopenia several years before blastic evolution and the 5 pts with G173R presented with hypoplastic MDS or initially isolated cytopenias, suggesting a specific functional effect of this mutation. Karyotype was normal in 16 pts (44%), complex in one, 12 pts had an isolated abnormality, and three had cytogenetic failure. Additional driver mutations were identified in most (27/32,84%) pts (Figure 1B), but we noticed that they were less frequent and at lower VAF in pts having both germline and somatic DDX41 mutations as compared to pts with a single variant (median 1.5 vs 3 mutations, median VAF 7% vs 29.5%, p Seven low-risk MDS pts were untreated, 7 received ESA and 5 (71%) responded. Ten high-risk MDS/AML pts received a hypomethylating agent and 8 (80%) achieved hematological response. Nine AML pts received intensive chemotherapy, with a complete response rate of 100% (7/7, 2 ongoing) and 5 of them had HSCT, all of them being alive with tolerable toxicity. Five pts died, median OS was 87 months, and 2-y OS was 89%. No difference on OS was observed between single and double-DDX41 mutated pts. Conclusions: DDX41 germline variant carriers represent a significant part of MDS/AML pts, the vast majority presenting without familial history. The predicted change in protein and/or the presence of a second somatic mutation strongly support the causality of the germline variant in most pts. By contrast with previous reports, pts frequently presented a phase of cytopenia before overt malignancy. Finally, outcome regarding response to treatment and OS in this DDX41-mutated cohort appeared relatively favorable. Figure 1. Figure 1. Disclosures Peffault De Latour: Pfizer Inc.: Consultancy, Honoraria, Research Funding; Alexion Pharmaceuticals, Inc.: Consultancy, Honoraria, Research Funding; Amgen Inc.: Research Funding; Novartis: Consultancy, Honoraria, Research Funding. Fenaux:Otsuka: Honoraria, Research Funding; Jazz: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; Celgene: Honoraria, Research Funding.

Context. AML is an oligoclonal disease. Intratumoral genetic heterogeneity (ITH) is pervasive in cancers and has often been linked to poor outcome. Except in patients (pts) with complex karyotypes (Bochtler, J Clin Oncol 2013), the clinical relevance of ITH remains unknown in AML. We assessed ITH in a real-life AML cohort. Methods. Since Nov 2015, all newly diagnosed AML pts at our institution were analyzed by targeted sequencing with a 60-gene myeloid panel at an average depth of 815X. Variant Allele Frequencies (VAF) were adjusted for copy number variation to estimate Cancer Cell Fractions (CCFs) and rank mutations by decreasing CCFs. Mutations were segregated into different clones when distant by >10% CCF. Ancestral (as opposed to secondary) mutations are defined as those belonging to the first clone (Figure). We could next derive for each pt the total number of clones and the ITH index, defined as the ratio of secondary to ancestral mutations (according to Turajlic, Cell 2018). Results. We studied 201 consecutive AML pts (median age 67 years, secondary AML 24%). The median number of mutations was 4 (range 0-12). Clonal heterogeneity (>1 clone) was found in 71% of pts with a median of 2 clones per pt (range 1-5). 140 pts received intensive chemotherapy (IC), 50 hypomethylating agents (HMA) and 11 best supportive care (BSC) only. Signaling (FLT3, NRAS, KRAS, KIT, JAK2, CBL, CSF3R, BRAF, NF1, PTPN11, RIT1, CALR and MPL, 60%), DNA methylation (DNTM3A, TET2, IDH1/2, 54%), NPM1 (29%), spliceosome (U2AF1, SRSF2, SF3B1, ZRSR2, PRPF8, 27.9%) and tumor suppressors (PHF6, TP53, WT1, 27.4%) were the most frequently mutated pathways. ELN 2017 risk category was favorable, intermediate, adverse and not evaluable in 35%, 27%, 35% and 3% of pts respectively. Increasing ITH was associated with a higher number of clones (p=0.001) and of mutations (p0.05. ITH was not different among ELN 2017 risk categories (p=0.15). ITH was independent of age, WBC count and type of AML (secondary vs de novo), all p>0.2. There was no significant difference in the number of mutations (p=0.12), clones (p=0.58) or ITH indexes (p=0.38) according to IC/HMA/BSC treatment strategies. We next performed a preliminary analysis of the prognostic impact of ITH in the 140 pts treated with IC (median age 58y), with a median follow-up of only 12.5 months. 117 (84%) pts achieved CR and 32 (23%) were transplanted in first CR. Median event-free survival (EFS) was 18.7 vs 8.0 months in pts with adv and non-adv ELN risk, respectively (p=0.016). In univariate analyses, DNA methylation (p=0.04) and spliceosome (p=0.007) mutations were the two pathways predicting adverse outcome. The number of mutations (p=0.6) or of clones (p=0.8) had no impact on EFS. Pts with fewer secondary than ancestral mutations (ITH Conclusion. Our results confirm that most AMLs are oligoclonal. Surprisingly, higher ITH is not related to older age or secondary AML. Our preliminary results suggest that lower ITH translates into shorter EFS in pts treated with IC. Longer follow-up and/or increased pt numbers are warranted to determine whether NGS-based assessments of clonal heterogeneity can improve AML risk stratification. Figure. Figure. Disclosures Fenaux: Otsuka: Honoraria, Research Funding; Jazz: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; Celgene: Honoraria, Research Funding.

The last three authors contributed equally to this work. Introduction: Allogeneic hematopoietic stem cell transplantation (HSCT) may improve long-term survival of patients with acute lymphoblastic leukemia (ALL) at high risk of relapse. However, ovarian failure is observed in 70 to 90% of patients who received myeloablative HSCT. Autotransplantation of cryopreserved ovarian cortex harvested before gonadotoxic treatments has been shown to re-establish the menstrual cycles and lead to the birth of healthy children (Donnez J. N Engl J Med, 2018). In patients treated for acute leukemia, concern has been expressed about the risk of leukemia recurrence after the ovarian autotransplantation due to the potential presence of residual leukemic cells in the ovarian tissue (Dolmans MM. Blood, 2010). To date, there were only few studies evaluating the presence of leukemic cells in cryopreserved ovarian tissue, and in most cases ovarian tissues were harvested at diagnosis of ALL or early after onset of chemotherapy. The present study prospectively investigated, in the context of fertility preservation, the presence of leukemic cells in cryopreserved ovarian samples harvested before allogeneic HSCT in patients in complete remission (CR) of ALL. Patients and Methods: From October 2015 to May 2018, all female patients with ALL who had a leukemia specific marker and underwent ovarian cryopreservation before allogeneic HSCT as part of preservation fertility program in 3 centers were included in the study. Consents were obtained from the guardians and/or age appropriate patients. The specific local ethical committees approved the study. Ovariectomy was performed after patients achieved CR, mostly in the weeks preceding HSCT. Ovarian cortex was separated into several fragments and cryopreserved as previously described (Poirot C. Human Reprod, 2002). When more than 14 cortical fragments were obtained, one was dedicated to molecular analysis, as well as the ovarian medulla. MRD quantification was performed by quantitative PCR of clonal rearrangements of immunoglobulin/T-cell receptor genes (Ig/TCR) or oncogenic fusion genes, according to EuroMRD and European Against Cancer (EAC) guidelines. MRD in ovarian samples were compared to MRD in bone marrow (BM) sample obtained at the same time point. Results: Fourteen patients were included in the study: 12 with B-cell precursor ALL, 1 with T-cell ALL and 1 with mixed phenotype acute leukemia. MRD marker was Ig/TCR rearrangement in 12 cases, M-BCR-ABL transcript in 1 case and genomic MLL-AF4 in 1 case. Median age at transplant was 18.2 years (range 1.1 - 35.2 years). Criteria for HSCT were poor early response to treatment (N=8), Philadelphia positive ALL (N=1), or previous relapse (N=5). With a median follow-up after HSCT of 8.1 months (range 0.8 - 29.8 months), all patients are disease-free. At the time of ovariectomy, 7/14 (50%) patients had undetectable MRD in ovarian samples, 6 had low positivity below 10-4 and one had positive MRD higher than 10-4. Unexpectedly of the 7 patients with positive ovarian MRD, 4 were undetectable in BM. One of the 7 patients with undetectable MRD in ovarian samples was positive in bone marrow. Concordant results were observed between the cortex and medulla samples in 10 of the 11 cases where both could be tested. Conclusions: To our knowledge, this series is the largest cohort evaluating MRD in ovarian samples from patients with ALL in complete remission after full chemotherapy regimen. We detected low levels of residual leukemic cells in ovarian tissues in half of the patients, some of them having no detectable MRD in BM at the time of ovariectomy, suggesting that leukemic cells could preferentially persist in ovary. Our results warrant further analyses of an extended cohort and longer post-transplant follow-up to better assess the potential presence of leukemic cells in ovarian samples and evaluate the impact of ovarian MRD status on post HSCT relapse. Still, autotransplantation of cryopreserved ovarian cortex could be discussed after allogeneic HSCT in patients with undetectable ovarian MRD. Table 1. MRD evaluation in bone marrow and ovarian samples. BM, bone marrow; BCP-ALL, B-cell precursor ALL; Ph-positive ALL, ALL with Philadelphia chromosome; NA: not available. Undetectable MRD means negative result obtained with a sensitivity of 10-4 or 10-5. BCR-ABL1 MRD results are expressed as the BCR-ABL1/ABL1 transcripts ratio. Disclosures No relevant conflicts of interest to declare.

Background Cutaneous leishmaniasis is caused by several Leishmania species that are associated with variable outcomes before and after therapy. Optimal treatment decision is based on an accurate identification of the infecting species but current methods to type Leishmania isolates are relatively complex and/or slow. Therefore, the initial treatment decision is generally presumptive, the infecting species being suspected on epidemiological and clinical grounds. A simple method to type cultured isolates would facilitate disease management. Methodology We analyzed MALDI-TOF spectra of promastigote pellets from 46 strains cultured in monophasic medium, including 20 short-term cultured isolates from French travelers (19 with CL, 1 with VL). As per routine procedure, clinical isolates were analyzed in parallel with Multilocus Sequence Typing (MLST) at the National Reference Center for Leishmania. Principal Findings Automatic dendrogram analysis generated a classification of isolates consistent with reference determination of species based on MLST or hsp70 sequencing. A minute analysis of spectra based on a very simple, database-independent analysis of spectra based on the algorithm showed that the mutually exclusive presence of two pairs of peaks discriminated isolates considered by reference methods to belong either to the Viannia or Leishmania subgenus, and that within each subgenus presence or absence of a few peaks allowed discrimination to species complexes level. Conclusions/Significance Analysis of cultured Leishmania isolates using mass spectrometry allows a rapid and simple classification to the species complex level consistent with reference methods, a potentially useful method to guide treatment decision in patients with cutaneous leishmaniasis., Author Summary Cutaneous leishmaniasis is a disease due to a small parasite called Leishmania. This parasite causes disfiguring skin lesions that last for months or years. There are many different subtypes of Leishmania, each giving rise to lesions of different severity and responding to therapies in its own way. Treating physicians must know as soon as possible which subtype of Leishmania is involved to propose the best treatment. Because it is impossible to differentiate the Leishmania subtypes microscopically, the identification of the culprit subtype currently requires complex and expensive typing methods, the results of which are generally obtained several weeks after the diagnosis. Here, we have evaluated the ability of a new method using mass spectrometry to differentiate Leishmania subtypes. Our results were consistent with those provided by reference typing methods and were obtained rapidly after the parasite had been cultured in vitro. This new method may help physicians know very soon which Leishmania subtype is involved thereby facilitating treatment choice.

Lenalidomide (Len) is the reference treatment of anemia in patients with del(5q) MDS with half of them being responders. An erythroid response is also achieved in ~25% of non del(5q) low-risk or int-1 MDS patients. The mechanisms of resistance are still unclear although the molecular target of Len, Cereblon, a receptor for several substrates including Ikaros, Aiolos and the casein kinase 1 in the E3 ubiquitin ligase Cul4A-DDB1-Roc1, had been identified. Biomarkers are needed to avoid inappropriate exposure to the risk of severe neutropenia or thrombocytopenia. In this study, we investigated biomarkers of response to Len treatment in a cohort of 132 non del(5q) MDS patients, non-responders to erythropoiesis-stimulating agent (ESA) and enrolled in the GFM-LenEpo 08 clinical trial (NCT01718379). Patients were randomized to Len 10mg/day (L-arm) or Len 10 mg/day plus Epoetin beta (60,000 units/w) (LE-arm) and evaluated after 4 cycles. The biological studies were conducted in 99/132 patients including 41 responders and 58 non responders. According to IWG2006, HI-E was significantly higher in LE-arm (52%) vs. L-arm (31%) (p=0.031). Extensive genotyping study of 29 genes (ASXL1, CBL, CSNK1A, DNMT3A, ETV6, EZH2, FLT3, IDH1, IDH2, IKZF1, IKZF3, JAK2, KIT, KRAS, MPL, NPM1, NRAS, PHF6, PTPN11, RIT1, RUNX1, SETBP1, SF3B1, SRSF2, TET2, TP53, U2AF1, WT1, ZRSR2) was conducted in the 99 patients by NGS or Sanger approaches. Found all along the coding sequence of the genes and with variable VAF, mutations in SF3B1 (73%), TET2 (46%), ASXL1 (20%) and DNMT3A (20%) genes did not influence the response in the L-arm or LE-arm. Previously identified in myeloma cells resistant to Len treatment, an IKZF1 mutation located in the exon 5 of the gene and affecting the binding domain of the protein has been reported during Len treatment in one patient with del(5q) MDS and was associated with a loss of efficacy of the Len treatment in vivo. In this cohort, we did not find any mutation in the exon 5 of IKZF1 or IKZF3 or in the exons 3 and 4 of CSNK1A which are described as affecting their domain of interaction with Cereblon. A A>G polymorphism in the 5’UTR region of CRBN gene (rs1672753) was significantly associated with HI-E in the whole cohort (41.5% in responders vs. 22.4% in non-responders; p=0.048). A gene expression profiling (GEP) study was conducted on BMMC of 50 at inclusion and 24 paired samples before and after 4 cycles of treatment. Using a Gene Set Enrichment Analysis (GSEA), the comparison of GEP in 24 paired samples linked the response in L-arm or LE-arm to a signature of 32 up-regulated genes exclusively involved in the immune response. A supervised GSEA analysis combined with a Pam R strategy of GEP before treatment identified a predictive signature of 36 up-regulated genes mainly involved in translation, epigenetic regulation of transcription, cell division and DNA repair. Slight variations of CRBN gene expression level were not correlated to the response. However, the resistance in L-arm and LE-arm was predicted by a low expression level of NPM1 (P In conclusion, resistance to Lenalidomide or Lenalidomide plus EPO seems not be associated with a particular mutational profile nor with mutations in recently identified Cereblon targets. By contrast, a low expression level of NPM1 associated with a A/A polymorphism of CRBN is highly predictive of a treatment failure by Lenalidomide or Lenalidomide plus EPO non del(5q) MDS patients. Disclosures Chesnais: celgene: Research Funding. Sardnal:Celgene: Research Funding. Passet:Celgene: Research Funding. Gauthier:Celgene: Research Funding. Kosmider:Celgene: Research Funding. Fontenay:Celgene: Research Funding.