UNLABELLED: Genomic characterization of pediatric patients with acute myeloid leukemia (AML) has led to the discovery of somatic mutations with prognostic implications. Although gene-expression profiling can differentiate subsets of pediatric AML, its clinical utility in risk stratification remains limited. Here, we evaluate gene expression, pathogenic somatic mutations, and outcome in a cohort of 435 pediatric patients with a spectrum of pediatric myeloid-related acute leukemias for biological subtype discovery. This analysis revealed 63 patients with varying immunophenotypes that span a T-lineage and myeloid continuum designated as acute myeloid/T-lymphoblastic leukemia (AMTL). Within AMTL, two patient subgroups distinguished by FLT3-ITD and PRC2 mutations have different outcomes, demonstrating the impact of mutational composition on survival. Across the cohort, variability in outcomes of patients within isomutational subsets is influenced by transcriptional identity and the presence of a stem cell-like gene-expression signature. Integration of gene expression and somatic mutations leads to improved risk stratification. SIGNIFICANCE: Immunophenotype and somatic mutations play a significant role in treatment approach and risk stratification of acute leukemia. We conducted an integrated genomic analysis of pediatric myeloid malignancies and found that a combination of genetic and transcriptional readouts was superior to immunophenotype and genomic mutations in identifying biological subtypes and predicting outcomes. This article is highlighted in the In This Issue feature, p. 549.

Department of Biostatistics St Jude Children's Research Hospital Memphis Tennessee

Department of Cell Biology Erasmus Medical Center Rotterdam the Netherlands

Department of Computational Biology St Jude Children's Research Hospital Memphis Tennessee

Department of Internal Medicine Hematology and Oncology Center of Molecular Biology and Gene Therapy Masaryk University Hospital Brno Czech Republic

Department of Oncology St Jude Children's Research Hospital Memphis Tennessee

Department of Pathology St Jude Children's Research Hospital Memphis Tennessee

Department of Pediatric Hematology and Oncology Aghia Sophia Children's Hospital Athens Greece

Department of Pediatric Hematology Oncology IRCCS Ospedale Pediatrico Bambino Gesù Sapienza University of Rome Rome Italy

Department of Pediatric Oncology Hematology Erasmus Medical Center Sophia Children's Hospital Rotterdam the Netherlands

Department of Pediatrics Stanford University School of Medicine Stanford California

Department of Pharmacotherapy and Translational Research College of Pharmacy University of Florida Gainesville Florida

Department of Women's and Children's Health Hematology Oncology Clinic and Lab University of Padova IRP Padova Italy

Division of Pharmaceutics College of Pharmacy and Comprehensive Cancer Center The Ohio State University Columbus Ohio

Pediatric Translational Medicine Institute Shanghai Children's Medical Center Shanghai Jiao Tong University School of Medicine Shanghai China

Comment In

Blood Cancer Discov. 2(6):549. PubMed

See more in PubMed

Bennett JM, Catovsky D, Daniel MT, Flandrin G, Galton DA, Gralnick HR, et al. Proposed revised criteria for the classification of acute myeloid leukemia. A report of the French-American-British Cooperative Group. Ann Intern Med 1985;103:620–5. PubMed

Arber DA, Orazi A, Hasserjian R, Thiele J, Borowitz MJ, Le Beau MM, et al. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood 2016;127:2391–405. PubMed

Zwaan CM, Kolb EA, Reinhardt D, Abrahamsson J, Adachi S, Aplenc R, et al. Collaborative efforts driving progress in pediatric acute myeloid leukemia. J Clin Oncol 2015;33:2949–62. PubMed PMC

de Rooij JD, Branstetter C, Ma J, Li Y, Walsh MP, Cheng J, et al. Pediatric non-Down syndrome acute megakaryoblastic leukemia is characterized by distinct genomic subsets with varying outcomes. Nat Genet 2017;49:451–6. PubMed PMC

Bolouri H, Farrar JE, Triche T, Jr, Ries RE, Lim EL, Alonzo TA, et al. The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions. Nat Med 2018;24:103–12. PubMed PMC

Liu Y, Li C, Shen S, Chen X, Szlachta K, Edmonson MN, et al. Discovery of regulatory noncoding variants in individual cancer genomes by using cis-X. Nat Genet 2020;52:811–8. PubMed PMC

Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, Payne-Turner D, et al. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature 2012;481:157–63. PubMed PMC

Liu Y, Easton J, Shao Y, Maciaszek J, Wang Z, Wilkinson MR, et al. The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia. Nat Genet 2017;49:1211–8. PubMed PMC

Alexander TB, Gu Z, Iacobucci I, Dickerson K, Choi JK, Xu B, et al. The genetic basis and cell of origin of mixed phenotype acute leukaemia. Nature 2018;562:373–9. PubMed PMC

Gutierrez A, Kentsis A.Acute myeloid/T-lymphoblastic leukaemia (AMTL): a distinct category of acute leukaemias with common pathogenesis in need of improved therapy. Br J Haematol 2018;180:919–24. PubMed PMC

Shiozawa Y, Malcovati L, Galli A, Sato-Otsubo A, Kataoka K, Sato Y, et al. Aberrant splicing and defective mRNA production induced by somatic spliceosome mutations in myelodysplasia. Nat Commun 2018;9:3649. PubMed PMC

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003;13:2498–504. PubMed PMC

Faber ZJ, Chen X, Gedman AL, Boggs K, Cheng J, Ma J, et al. The genomic landscape of core-binding factor acute myeloid leukemias. Nat Genet 2016;48:1551–6. PubMed PMC

Gollner S, Oellerich T, Agrawal-Singh S, Schenk T, Klein HU, Rohde C, et al. Loss of the histone methyltransferase EZH2 induces resistance to multiple drugs in acute myeloid leukemia. Nat Med 2017;23:69–78. PubMed PMC

Aries IM, Bodaar K, Karim SA, Chonghaile TN, Hinze L, Burns MA, et al. PRC2 loss induces chemoresistance by repressing apoptosis in T cell acute lymphoblastic leukemia. J Exp Med 2018;215:3094–114. PubMed PMC

Hollink IH, van den Heuvel-Eibrink MM, Zimmermann M, Balgobind BV, Arentsen-Peters ST, Alders M, et al. Clinical relevance of Wilms tumor 1 gene mutations in childhood acute myeloid leukemia. Blood 2009;113:5951–60. PubMed

Pellin D, Loperfido M, Baricordi C, Wolock SL, Montepeloso A, Weinberg OK, et al. A comprehensive single cell transcriptional landscape of human hematopoietic progenitors. Nat Commun 2019;10:2395. PubMed PMC

Ng SW, Mitchell A, Kennedy JA, Chen WC, McLeod J, Ibrahimova N, et al. A 17-gene stemness score for rapid determination of risk in acute leukaemia. Nature 2016;540:433–7. PubMed

Elsayed AH, Rafiee R, Cao X, Raimondi S, Downing JR, Ribeiro R, et al. A six-gene leukemic stem cell score identifies high risk pediatric acute myeloid leukemia. Leukemia 2020;34:735–45. PubMed PMC

Valk PJ, Verhaak RG, Beijen MA, Erpelinck CA, Barjesteh van Waalwijk van Doorn-Khosrovani S, Boer JM, et al. Prognostically useful gene-expression profiles in acute myeloid leukemia. N Engl J Med 2004;350:1617–28. PubMed

Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND, et al. Genomic classification and prognosis in acute myeloid leukemia. N Engl J Med 2016;374:2209–21. PubMed PMC

Bullinger L, Dohner K, Bair E, Frohling S, Schlenk RF, Tibshirani R, et al. Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N Engl J Med 2004;350:1605–16. PubMed

Ross ME, Mahfouz R, Onciu M, Liu HC, Zhou X, Song G, et al. Gene expression profiling of pediatric acute myelogenous leukemia. Blood 2004;104:3679–87. PubMed

Montefiori LE, Bendig S, Gu Z, Chen X, Polonen P, Ma X, et al. Enhancer hijacking drives oncogenic BCL11B expression in lineage ambiguous stem cell leukemia. Cancer Discov 2021. Jun 8 [Epub ahead of print]. PubMed PMC

Di Giacomo D, La Starza R, Gorello P, Pellanera F, Kalender Atak Z, De Keersmaecker K, et al. 14q32 rearrangements deregulating BCL11B mark a distinct subgroup of T and myeloid immature acute leukemia. Blood 2021;138:773–84. PubMed PMC

Riemke P, Czeh M, Fischer J, Walter C, Ghani S, Zepper M, et al. Myeloid leukemia with transdifferentiation plasticity developing from T-cell progenitors. EMBO J 2016;35:2399–416. PubMed PMC

Rasche M, Steidel E, Kondryn D, Von Neuhoff N, Sramkova L, Creutzig U, et al. Impact of a risk-adapted treatment approach in pediatric AML: a report of the AML-BFM registry 2012. Blood 2019;134 (Supplement_1):293.

Alexander TB, Wang L, Inaba H, Triplett BM, Pounds S, Ribeiro RC, et al. Decreased relapsed rate and treatment-related mortality contribute to improved outcomes for pediatric acute myeloid leukemia in successive clinical trials. Cancer 2017;123:3791–8. PubMed PMC

Rusch M, Nakitandwe J, Shurtleff S, Newman S, Zhang Z, Edmonson MN, et al. Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome. Nat Commun 2018;9:3962. PubMed PMC

Van Allen EM, Robinson D, Morrissey C, Pritchard C, Imamovic A, Carter S, et al. A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: implications for precision cancer medicine. Oncotarget 2016;7:52888–99. PubMed PMC

Uzilov AV, Ding W, Fink MY, Antipin Y, Brohl AS, Davis C, et al. Development and clinical application of an integrative genomic approach to personalized cancer therapy. Genome Med 2016;8:62. PubMed PMC

Bonnet D, Dick JE.Human acute myeloid leukemia is organized as a hierarchy that originates from a primitive hematopoietic cell. Nat Med 1997;3:730–7. PubMed

McLeod C, Gout AM, Zhou X, Thrasher A, Rahbarinia D, Brady SW, et al. St. Jude Cloud—a pediatric cancer genomic data sharing ecosystem. Cancer Discov 2021;11:1082–99. PubMed PMC

Anders S, Pyl PT, Huber W.HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics 2015;31:166–9. PubMed PMC

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 2015;43:e47. PubMed PMC

Leek JT, Johnson WE, Parker HS, Fertig EJ, Jaffe AE, Zhang Y, Storey JD, Torres LC.sva: Surrogate Variable Analysis. R package version 3.40.0. 2021. Available from: https://bioconductor.org/packages/release/bioc/html/sva.html.

Van der Maaten LJP HG.Visualizing data using t-SNE. J Mach Learn Res 2008;9:2579–605.

Goeman JJ, van de Geer SA, de Kort F, van Houwelingen HC.A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 2004;20:93–9. PubMed

Balgobind BV, Van den Heuvel-Eibrink MM, De Menezes RX, Reinhardt D, Hollink IH, Arentsen-Peters ST,, et al. Evaluation of gene expression signatures predictive of cytogenetic and molecular subtypes of pediatric acute myeloid leukemia. Haematologica 2011;96:221–30. PubMed PMC

Buelow DR, Pounds SB, Wang YD, Shi L, Li Y, Finkelstein D, et al. Uncovering the genomic landscape in newly diagnosed and relapsed pediatric cytogenetically normal FLT3-ITD AML. Clin Transl Sci 2019;12:641–7. PubMed PMC

Ho PA, Alonzo TA, Gerbing RB, Pollard J, Stirewalt DL, Hurwitz C, et al. Prevalence and prognostic implications of CEBPA mutations in pediatric acute myeloid leukemia (AML): a report from the Children's Oncology Group. Blood 2009;113:6558–66. PubMed PMC

Rubnitz JE, Lacayo NJ, Inaba H, Heym K, Ribeiro RC, Taub J, et al. Clofarabine can replace anthracyclines and etoposide in remission induction therapy for childhood acute myeloid leukemia: the AML08 multicenter, randomized phase III trial. J Clin Oncol 2019;37:2072–81. PubMed PMC

Tosi S, Kamel YM, Owoka T, Federico C, Truong TH, Saccone S.Paediatric acute myeloid leukaemia with the t(7;12)(q36;p13) rearrangement: a review of the biological and clinical management aspects. Biomark Res 2015;3:21. PubMed PMC

Noort S, Zimmermann M, Reinhardt D, Cuccuini W, Pigazzi M, Smith J, et al. Prognostic impact of t(16;21)(p11;q22) and t(16;21)(q24;q22) in pediatric AML: a retrospective study by the I-BFM study group. Blood 2018;132:1584–92. PubMed PMC

Gruber TA, Gedman AL, Zhang J, Koss CS, Marada S, Ta HQ, et al. An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia. Cancer Cell 2012;22:683–97. PubMed PMC

Hollink IHIM, van den Heuvel-Eibrink MM, Arentsen-Peters STCJM, Pratcorona M, Abbas S, Kuipers JE, et al. NUP98/NSD1 characterizes a novel poor prognostic group in acute myeloid leukemia with a distinct HOX gene expression pattern. Blood 2011;118:3645–56. PubMed

de Rooij JD, Hollink IH, Arentsen-Peters ST, van Galen JF, Beverloo HB, Baruchel A, et al. NUP98/JARID1A is a novel recurrent abnormality in pediatric acute megakaryoblastic leukemia with a distinct HOX gene expression pattern. Leukemia 2013;27:2280–8. PubMed

Bisio V, Zampini M, Tregnago C, Manara E, Salsi V, Di Meglio A, et al. NUP98-fusion transcripts characterize different biological entities within acute myeloid leukemia: a report from the AIEOP-AML group. Leukemia 2017;31:974–7. PubMed

Hollink IH, Zwaan CM, Zimmermann M, Arentsen-Peters TC, Pieters R, Cloos J, et al. Favorable prognostic impact of NPM1 gene mutations in childhood acute myeloid leukemia, with emphasis on cytogenetically normal AML. Leukemia 2009;23:262–70. PubMed

Brown P, McIntyre E, Rau R, Meshinchi S, Lacayo N, Dahl G, et al. The incidence and clinical significance of nucleophosmin mutations in childhood AML. Blood 2007;110:979–85. PubMed PMC

Sandahl JD, Coenen EA, Forestier E, Harbott J, Johansson B, Kerndrup G, et al. t(6;9)(p22;q34)/DEK-NUP214-rearranged pediatric myeloid leukemia: an international study of 62 patients. Haematologica 2014;99:865–72. PubMed PMC

Taketani T, Taki T, Sako M, Ishii T, Yamaguchi S, Hayashi Y.MNX1-ETV6 fusion gene in an acute megakaryoblastic leukemia and expression of the MNX1 gene in leukemia and normal B cell lines. Cancer Genet Cytogenet 2008;186:115–9. PubMed

Analysis of rare driving events in pediatric acute myeloid leukemia