作者
Shunsuke Kimura,Lindsey E. Montefiori,Ilaria Iacobucci,Yaqi Zhao,Qingsong Gao,Elisabeth M Paietta,Claudia Haferlach,A Douglas Laird,Paul E Mead,Zhaohui Gu,Wendy Stock,Mark R. Litzow,Jacob M Rowe,Selina M Luger,Stephen Kelly,Georgina L Ryland,Breon M Schmidt,Paul G Ekert,Alicia Oshlack,Sean M. Grimmond,Jacqueline Rehn,James Breen,David T Yeung,Deborah L. White,Ibrahim Aldoss,Elias J Jabbour,Ching-Hon Pui,Manja Meggendorfer,Wencke Walter,Wolfgang Kern,Torsten Haferlach,Samuel W Brady,Jinghui Zhang,Kathryn G. Roberts,Piers Blombery,Charles G. Mullighan
摘要
Transcriptome sequencing has identified multiple subtypes of B-progenitor acute lymphoblastic leukemia (B-ALL) of prognostic significance, but a minority of cases lack a known genetic driver. Here, we used integrated whole genome (WGS) and transcriptome sequencing (RNA-seq), enhancer mapping and chromatin topology analysis to identify previously unrecognized genomic drivers in B-ALL. 3,221 newly diagnosed and 177 relapsed B-ALL cases with tumor RNA-seq were studied. WGS was performed to detect mutations, structural variants, and copy number alterations. Integrated analysis of histone 3 lysine 27 acetylation and chromatin looping was performed using HiChIP. We identified a subset of 17 newly diagnosed and 5 relapsed B-ALL cases with a distinct gene expression profile and two universal and unique genomic alterations resulting from aberrant RAG activation: a focal deletion downstream of PAN3 at 13q12.2 resulting in CDX2 deregulation by the PAN3 enhancer, and a focal deletion of exons 18-21 of UBTF at 17q21.31 resulting in a chimeric fusion, UBTF::ATXN7L3. A subset of cases also had rearrangement and increased expression of the PAX5 gene, which is otherwise uncommon in B-ALL. Patients were more commonly female and young adult with median age 35 (12-70). The immunophenotype was characterized by CD10 negativity and IgM positivity. Among 16 patients with known clinical response, 9 (56.3%) had high-risk features including relapse (n = 4) or minimal residual disease >1% at the end of remission induction (n = 5). CDX2-deregulated, UBTF::ATXN7L3 rearranged -B-ALL is a high risk subtype of leukemia in young adults for which novel therapeutic approaches are required.