Abstract 4870: Mutational landscape and timing of resistant clone emergence in 104 Chinese pediatric patients with relapsed acute lymphoblastic leukemia
Authors: Li Benshang , Li Yongjin , Shen Shuhong , Zhu Xiaofan , Ma Xiaotu , Wang Ningling , Liu Yanling , Liu Yu , Zhang Hui , Lin Ting-Nien , Rusch Michael , Edmonson Michael , Easton John , Zhang Yingchi , Zhang Jingliao , Cheng Cheng , Tang Jingyan , Downing James R. , Pui Ching-Hon , Yang Jun J. , Zhang Jinghui 
Published: July 2017

Relapsed pediatric acute lympoblastic leukemia (ALL), occurring in 15-20% of cases, is one of the leading causes of cancer-related death in children, conferring a dismal survival rate of less than 40% primarily due to drug resistance. We performed whole-genome sequencing (WGS) and RNA-seq of matched diagnosis and relapse tumors as well as WGS of remission DNA from 104 pediatric ALL patients treated at Shanghai Children’s Medical Center (n=89), Institute of Hematology & Blood Disease Hospital in Tianjin (n=14) and the Second Hospital of Anhui Medical University (n=1) between 2003 and 2014. The median age at diagnosis was 6.29 (range, 0.23-16.05) years. Relapse occurred during chemotherapy in 85 patients and after completion of therapy in 19 patients.

Somatic mutation rate in ALL increased significantly from an average of 0.23 per Mb at diagnosis to 0.65 per Mb at relapse. We identified 34 potential driver genes at diagnosis and 45 at relapse based on significance of mutation recurrence and pathogenicity. The four most significant relapse-specific driver genes harbor known point mutations on purine metabolism genes NT5C2 (n=13) and PRPS1/PRPS2 (n=7), novel alterations affecting glucocorticoids receptor NR3C1 (n=13) and folylpolyglutamate synthetase FPGS (n=8). Functional characterization showed that all NR3C1 mutations resulted in significant loss of transcription activator function and subcellular mislocalization. Ectopic expression of mutant NR3C1 in ALL cell lines consistently led to prednisone resistance. Five driver genes (TP53, CREBBP, SMARCA4, WHSC1 and NIPBL) showed the highest increase (2-5 fold) of mutation frequency from diagnosis to relapse with mutations collectively present in 28% of relapsed ALL. Truncation mutations in DNA mismatch repair genes MLH1, MSH2, MSH6 and PMS2 occurred exclusively at relapse in four ALL with the highest mutation burden.

Targeted ultra-deep sequencing at 5,000X of 268 somatic alterations was performed on 214 serial bone-marrow samples collected during ALL therapy for 17 cases. The resulting mutant allele fraction (MAF) values showed high concordance with minimum residual disease (MRD) measured by flow cytometry, indicating suitability for quantifying leukemia burden. Temporal change of MAF in the serial samples also allows us to track clonal identity and emergence of drug-resistant clones during and after therapy. For example, one case had deep sequencing performed on 11 somatic lesions from 10 bone barrow samples collected during the 15 months between diagnosis and relapse. We found that a minor clone present in 0.5-1% of ALL blasts at diagnosis emerged five months prior to relapse, from which two new subclones arose harboring NT5C2 mutations L406&gt;SSF and D407&gt;DRD. Preliminary data generated from serial bone marrow samples provides the first insight into the use of somatic alterations for monitoring leukemia progress during relapse.

Citation Format: Benshang Li, Yongjin Li, Shuhong Shen, Xiaofan Zhu, Xiaotu Ma, Ningling Wang, Yanling Liu, Yu Liu, Hui Zhang, Ting-Nien Lin, Michael Rusch, Michael Edmonson, John Easton, Yingchi Zhang, Jingliao Zhang, Cheng Cheng, Jingyan Tang, James R. Downing, Ching-Hon Pui, Jun J. Yang, Jinghui Zhang. Mutational landscape and timing of resistant clone emergence in 104 Chinese pediatric patients with relapsed acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4870. doi:10.1158/1538-7445.AM2017-4870