The genomic landscape of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21

Qingsong Gao, Sarra L. Ryan, Ilaria Iacobucci, Pankaj S Ghate, Ruth E Cranston, Claire J Schwab, Abdelrahman H Elsayed, Lei Shi, Stanley B Pounds, Shaohua Lei, Pradyumna Baviskar, Deqing Pei, Cheng Cheng, Matthew Bashton, Paul B Sinclair, David R. Bentley, Mark Ross, Zoya Kingsbury, Terena James, Kathryn G RobertsMeenakshi Devidas, Yiping Fan, Wenan Chen, Ti-Cheng Chang, Gang Wu, Andrew J. Carroll, Nyla A Heerema, Virginia Valentine, Marcus B Valentine, Wenjian Yang, Jun J. Yang, Anthony V Moorman, Christine J Harrison, Charles G. Mullighan*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)

Abstract

Intrachromosomal amplification of chromosome 21 defines a subtype of high-risk childhood acute lymphoblastic leukemia (iAMP21-ALL) characterized by copy number changes and complex rearrangements of chromosome 21. The genomic basis of iAMP21-ALL and the pathogenic role of the region of amplification of chromosome 21 to leukemogenesis remains incompletely understood. In this study, using integrated whole genome and transcriptome sequencing of 124 patients with iAMP21-ALL, including rare cases arising in the context of constitutional chromosomal aberrations, we identified subgroups of iAMP21-ALL based on the patterns of copy number alteration and structural variation. This large data set enabled formal delineation of a 7.8 Mb common region of amplification harboring 71 genes, 43 of which were differentially expressed compared with non-iAMP21–ALL ones, including multiple genes implicated in the pathogenesis of acute leukemia (CHAF1B, DYRK1A, ERG, HMGN1, and RUNX1). Using multimodal single-cell genomic profiling, including single-cell whole genome sequencing of 2 cases, we documented clonal heterogeneity and genomic evolution, demonstrating that the acquisition of the iAMP21 chromosome is an early event that may undergo progressive amplification during disease ontogeny. We show that UV-mutational signatures and high mutation load are characteristic secondary genetic features. Although the genomic alterations of chromosome 21 are variable, these integrated genomic analyses and demonstration of an extended common minimal region of amplification broaden the definition of iAMP21-ALL for more precise diagnosis using cytogenetic or genomic methods to inform clinical management.

Original languageEnglish
Pages (from-to)711-723
Number of pages13
JournalBlood
Volume142
Issue number8
Early online date22 May 2023
DOIs
Publication statusPublished - 24 Aug 2023

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