Pediatric T-ALL type-1 and type-2 relapses develop along distinct pathways of clonal evolution

Paulina Richter-Pechańska, Joachim B. Kunz, Tobias Rausch, Büşra Erarslan-Uysal, Beat Bornhauser, Viktoras Frismantas, Yassen Assenov, Martin Zimmermann, Margit Happich, Caroline von Knebel-Doeberitz, Nils von Neuhoff, Rolf Köhler, Martin Stanulla, Martin Schrappe, Gunnar Cario, Gabriele Escherich, Renate Kirschner-Schwabe, Cornelia Eckert, Smadar Avigad, Stefan M. PfisterMartina U. Muckenthaler, Jean Pierre Bourquin, Jan O. Korbel*, Andreas E. Kulozik*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

The mechanisms underlying T-ALL relapse remain essentially unknown. Multilevel-omics in 38 matched pairs of initial and relapsed T-ALL revealed 18 (47%) type-1 (defined by being derived from the major ancestral clone) and 20 (53%) type-2 relapses (derived from a minor ancestral clone). In both types of relapse, we observed known and novel drivers of multidrug resistance including MDR1 and MVP, NT5C2 and JAK-STAT activators. Patients with type-1 relapses were specifically characterized by IL7R upregulation. In remarkable contrast, type-2 relapses demonstrated (1) enrichment of constitutional cancer predisposition gene mutations, (2) divergent genetic and epigenetic remodeling, and (3) enrichment of somatic hypermutator phenotypes, related to BLM, BUB1B/PMS2 and TP53 mutations. T-ALLs that later progressed to type-2 relapses exhibited a complex subclonal architecture, unexpectedly, already at the time of initial diagnosis. Deconvolution analysis of ATAC-Seq profiles showed that T-ALLs later developing into type-1 relapses resembled a predominant immature thymic T-cell population, whereas T-ALLs developing into type-2 relapses resembled a mixture of normal T-cell precursors. In sum, our analyses revealed fundamentally different mechanisms driving either type-1 or type-2 T-ALL relapse and indicate that differential capacities of disease evolution are already inherent to the molecular setup of the initial leukemia. [Figure not available: see fulltext.]

Original languageEnglish
Pages (from-to)1759-1768
Number of pages10
JournalLeukemia
Volume36
Issue number7
DOIs
StatePublished - Jul 2022
Externally publishedYes

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