Most relapses of acute lymphoblastic leukemia (ALL) occur in patients with a medium risk (MR) for relapse on the Associazione Italiana di Ematologia e Oncologia Pediatrica and Berlin-Frankfurt-Münster (AIEOP-BFM) ALL protocol, based on persistence of minimal residual disease (MRD). New insights into biological features that are associated with MRD are needed. Here, we identify the glycosylphosphatidylinositol-anchored cell surface protein vanin-2 (VNN2; GPI-80) by charting the cell surface proteome of MRD very high-risk (HR) B-cell precursor (BCP) ALL using a chemoproteomics strategy. The correlation between VNN2 transcript and surface protein expression enabled a retrospective analysis (ALL-BFM 2000; N = 770 cases) using quantitative polymerase chain reaction to confirm the association of VNN2 with MRD and independent prediction of worse outcome. Using flow cytometry, we detected VNN2 expression in 2 waves, in human adult bone marrow stem and progenitor cells and in the mature myeloid compartment, in line with proposed roles for fetal hematopoietic stem cells and inflammation. Prospective validation by flow cytometry in the ongoing clinical trial (AIEOP-BFM 2009) identified 10% (103/1069) of VNN2+ BCP ALL patients at first diagnosis, primarily in the MRD MR (48/103, 47%) and HR (37/103, 36%) groups, across various cytogenetic subtypes. We also detected frequent mutations in epigenetic regulators in VNN2+ ALLs, including histone H3 methyltransferases MLL2, SETD2, and EZH2 and demethylase KDM6A. Inactivation of the VNN2 gene did not impair leukemia repopulation capacity in xenografts. Taken together, VNN2 marks a cellular state of increased resistance to chemotherapy that warrants further investigations. Therefore, this marker should be included in diagnostic flow cytometry panels.

Alacris Theranostics Berlin Germany

Department of Health Sciences and Technology and Institute for Molecular Systems Biology ETH Zurich Zurich Switzerland

Department of Hematology University Hospital Schleswig Holstein Kiel Germany

Department of Oncology University Children's Hospital Zurich and Children's Research Center Zurich Switzerland

Department of Pediatric Hematology and Oncology Charles University Hospital Motol Prague Czech Republic

Department of Pediatrics University Medical Center Schleswig Holstein Campus Kiel Kiel Germany

Department of Stem Cell Transplantation University Children's Hospital Zurich Zurich Switzerland; and

Department of Vertebrate Genomics Max Planck Institute for Molecular Genetics Berlin Germany

Department of Women's and Children's Health University of Padova Padova Italy

Italian Institute for Genomic Medicine Turin Italy

M Tettamanti Research Center University of Milano Bicocca Monza Italy

Pediatric Hematology and Oncology Charité University Hospital Berlin Germany

Pediatric Hematology and Oncology Hannover Medical School Hannover Germany

St Anna Children's Hospital and Children's Cancer Research Institute Vienna Austria

Erratum v

Blood Adv. 2022 Apr 26;6(8):2700. doi: 10.1182/bloodadvances.2021005366. PubMed

Zobrazit více v PubMed

Gu Z, Churchman ML, Roberts KG, et al. PAX5-driven subtypes of B-progenitor acute lymphoblastic leukemia. Nat Genet. 2019;51(2):296-307. PubMed PMC

Flohr T, Schrauder A, Cazzaniga G, et al; International BFM Study Group (I-BFM-SG) . Minimal residual disease-directed risk stratification using real-time quantitative PCR analysis of immunoglobulin and T-cell receptor gene rearrangements in the international multicenter trial AIEOP-BFM ALL 2000 for childhood acute lymphoblastic leukemia. Leukemia. 2008;22(4):771-782. PubMed

Moorman AV, Enshaei A, Schwab C, et al. A novel integrated cytogenetic and genomic classification refines risk stratification in pediatric acute lymphoblastic leukemia. Blood. 2014;124(9):1434-1444. PubMed

O’Connor D, Enshaei A, Bartram J, et al. Genotype-Specific minimal residual disease interpretation improves stratification in pediatric acute lymphoblastic leukemia. J Clin Oncol. 2018;36(1):34-43. PubMed PMC

Fischer U, Forster M, Rinaldi A, et al. Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options. Nat Genet. 2015;47(9):1020-1029. PubMed PMC

Holmfeldt L, Wei L, Diaz-Flores E, et al. The genomic landscape of hypodiploid acute lymphoblastic leukemia. Nat Genet. 2013;45(3):242-252. PubMed PMC

Mullighan CG, Goorha S, Radtke I, et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature. 2007;446(7137):758-764. PubMed

Stanulla M, Dagdan E, Zaliova M, et al; International BFM Study Group . IKZF1plus defines a new minimal residual disease-dependent very-poor prognostic profile in pediatric B-cell precursor acute lymphoblastic leukemia. J Clin Oncol. 2018;36(12):1240-1249. PubMed

Roberts KG, Li Y, Payne-Turner D, et al. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med. 2014;371(11):1005-1015. PubMed PMC

Hussein SMI, Puri MC, Tonge PD, et al. Genome-wide characterization of the routes to pluripotency [published correction appears in Nature. 2015;523(7562):626]. Nature. 2014;516(7530):198-206. PubMed

Hofmann A, Gerrits B, Schmidt A, et al. Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells. Blood. 2010;116(13):e26-e34. PubMed

Mirkowska P, Hofmann A, Sedek L, et al. Leukemia surfaceome analysis reveals new disease-associated features. Blood. 2013;121(25):e149-e159. PubMed

Granjeaud S, Naquet P, Galland F. An ESTs description of the new vanin gene family conserved from fly to human. Immunogenetics. 1999;49(11-12):964-972. PubMed

Kaskow BJ, Proffitt JM, Blangero J, Moses EK, Abraham LJ. Diverse biological activities of the vascular non-inflammatory molecules - the vanin pantetheinases [published correction appears in Biochem Biophys Res Commun. 2012;422(4):786]. Biochem Biophys Res Commun. 2012;417(2):653-658. PubMed PMC

Nitto T, Onodera K. Linkage between coenzyme a metabolism and inflammation: roles of pantetheinase. J Pharmacol Sci. 2013;123(1):1-8. PubMed

Aurrand-Lions M, Galland F, Bazin H, Zakharyev VM, Imhof BA, Naquet P. Vanin-1, a novel GPI-linked perivascular molecule involved in thymus homing. Immunity. 1996;5(5):391-405. PubMed

Yoshitake H, Takeda Y, Nitto T, Sendo F, Araki Y. GPI-80, a beta2 integrin associated glycosylphosphatidylinositol-anchored protein, concentrates on pseudopodia without association with beta2 integrin during neutrophil migration. Immunobiology. 2003;208(4):391-399. PubMed

Prashad SL, Calvanese V, Yao CY, et al. GPI-80 defines self-renewal ability in hematopoietic stem cells during human development. Cell Stem Cell. 2015;16(1):80-87. PubMed PMC

Matsuoka Y, Sumide K, Kawamura H, Nakatsuka R, Fujioka T, Sonoda Y. GPI-80 expression highly purifies human cord blood-derived primitive CD34-negative hematopoietic stem cells. Blood. 2016;128(18):2258-2260. PubMed

Cario G, Zimmermann M, Romey R, et al. Presence of the P2RY8-CRLF2 rearrangement is associated with a poor prognosis in non-high-risk precursor B-cell acute lymphoblastic leukemia in children treated according to the ALL-BFM 2000 protocol. Blood. 2010;115(26):5393-5397. PubMed

Schrappe M. Minimal residual disease: optimal methods, timing, and clinical relevance for an individual patient. Hematology Am Soc Hematol Educ Prog. 2012;2012:137-142. PubMed

Attarbaschi A, Mann G, Panzer-Grümayer R, et al. Minimal residual disease values discriminate between low and high relapse risk in children with B-cell precursor acute lymphoblastic leukemia and an intrachromosomal amplification of chromosome 21: the Austrian and German acute lymphoblastic leukemia Berlin-Frankfurt-Munster (ALL-BFM) trials. J Clin Oncol. 2008;26(18):3046-3050. PubMed

Dworzak MN, Buldini B, Gaipa G, et al; International-BFM-FLOW-network . AIEOP-BFM consensus guidelines 2016 for flow cytometric immunophenotyping of pediatric acute lymphoblastic leukemia. Cytometry B Clin Cytom. 2018;94(1):82-93. PubMed

Kalbfleisch JD, Prentice RL. The Statistical Analysis of Failure Time Data. New York, NY: John Wiley & Sons, Inc.; 1980.

Schrappe M, Hunger SP, Pui CH, et al. Outcomes after induction failure in childhood acute lymphoblastic leukemia. N Engl J Med. 2012;366(15):1371-1381. PubMed PMC

Eckert C, von Stackelberg A, Seeger K, et al. Minimal residual disease after induction is the strongest predictor of prognosis in intermediate risk relapsed acute lymphoblastic leukaemia - long-term results of trial ALL-REZ BFM P95/96. Eur J Cancer. 2013;49(6):1346-1355. PubMed

Rhein P, Mitlohner R, Basso G, et al. CD11b is a therapy resistance- and minimal residual disease-specific marker in precursor B-cell acute lymphoblastic leukemia. Blood. 2010;115(18):3763-3771. PubMed

Conter V, Bartram CR, Valsecchi MG, et al. Molecular response to treatment redefines all prognostic factors in children and adolescents with B-cell precursor acute lymphoblastic leukemia: results in 3184 patients of the AIEOP-BFM ALL 2000 study. Blood. 2010;115(16):3206-3214. PubMed

Hunger SP, Ohyashiki K, Toyama K, Cleary ML. Hlf, a novel hepatic bZIP protein, shows altered DNA-binding properties following fusion to E2A in t(17;19) acute lymphoblastic leukemia. Genes Dev. 1992;6(9):1608-1620. PubMed

Inukai T, Hirose K, Inaba T, et al. Hypercalcemia in childhood acute lymphoblastic leukemia: frequent implication of parathyroid hormone-related peptide and E2A-HLF from translocation 17;19. Leukemia. 2007;21(2):288-296. PubMed

Frismantas V, Dobay MP, Rinaldi A, et al. Ex vivo drug response profiling detects recurrent sensitivity patterns in drug-resistant acute lymphoblastic leukemia. Blood. 2017;129(11):e26-e37. PubMed PMC

Mullighan CG, Su X, Zhang J, et al; Children’s Oncology Group . Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N Engl J Med. 2009;360(5):470-480. PubMed PMC

Yasuda T, Tsuzuki S, Kawazu M, et al. Recurrent DUX4 fusions in B cell acute lymphoblastic leukemia of adolescents and young adults [published correction appears in Nat Genet. 2016;48(12):1591]. Nat Genet. 2016;48(5):569-574. PubMed

Roberts KG, Morin RD, Zhang J, et al. Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell. 2012;22(2):153-166. PubMed PMC

Mar BG, Bullinger LB, McLean KM, et al. Mutations in epigenetic regulators including SETD2 are gained during relapse in paediatric acute lymphoblastic leukaemia. Nat Commun. 2014;5(1):3469. PubMed PMC

Vora A, Goulden N, Wade R, et al. Treatment reduction for children and young adults with low-risk acute lymphoblastic leukaemia defined by minimal residual disease (UKALL 2003): a randomised controlled trial. Lancet Oncol. 2013;14(3):199-209. PubMed

Popov AM, Verzhbitskaya Ty, Fechina LG, Shestopalov AV, Plyasunova SA. Acute leukemias: immunophenotypic differences between blast cells and their nonneoplastic analogues in bone marrow. Clin Oncohematol. 2016;9(3):302-313.

Bastian L, Schroeder MP, Eckert C, et al. PAX5 biallelic genomic alterations define a novel subgroup of B-cell precursor acute lymphoblastic leukemia. Leukemia. 2019;33(8):1895-1909. PubMed

Ntziachristos P, Tsirigos A, Van Vlierberghe P, et al. Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia. Nat Med. 2012;18(2):298-301. PubMed PMC

Schäfer V, Ernst J, Rinke J, et al. EZH2 mutations and promoter hypermethylation in childhood acute lymphoblastic leukemia. J Cancer Res Clin Oncol. 2016;142(7):1641-1650. PubMed PMC

Chase A, Cross NC. Aberrations of EZH2 in cancer. Clinical Cancer Res. 2011;17(9):2613-2618. PubMed

Nikoloski G, Langemeijer SM, Kuiper RP, et al. Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes. Nat Genet. 2010;42(8):665-667. PubMed

Saygin C, Hirsch C, Przychodzen B, et al. Mutations in DNMT3A, U2AF1, and EZH2 identify intermediate-risk acute myeloid leukemia patients with poor outcome after CR1. Blood Cancer J. 2018;8(1):4. PubMed PMC

Ortega-Molina A, Boss IW, Canela A, et al. The histone lysine methyltransferase KMT2D sustains a gene expression program that represses B cell lymphoma development. Nat Med. 2015;21(10):1199-1208. PubMed PMC

Mar BG, Kahn J, Zon RL, et al. SETD2 heterozygous loss in leukemia leads to chemotherapy resistance through attenuation of the DNA damage response. Blood. 2015;130(24):2631-2641. PubMed PMC

Ntziachristos P, Tsirigos A, Welstead GG, et al. Contrasting roles of histone 3 lysine 27 demethylases in acute lymphoblastic leukaemia. Nature. 2014;514(7523):513-517. PubMed PMC

Wang L, Shilatifard A. UTX mutations in human cancer. Cancer Cell. 2019;35(2):168-176. PubMed PMC

Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139-140. PubMed PMC

Herwig R, Hardt C, Lienhard M, Kamburov A. Analyzing and interpreting genome data at the network level with ConsensusPathDB. Nat Protoc. 2016;11(10):1889-1907. PubMed

Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005;102(43):15545-15550. PubMed PMC