FPGS relapse-specific mutations in relapsed childhood acute lymphoblastic leukemia

Sung-Liang Yu,Jun J Yang,Hui Zhang,Jinghui Zhang,Bing-Ching Ho,Xiaotu Ma,Shiann-Tarng Jou,Kang Hsi Wu ,Kai Hsin Lin ,Yin Chen Hsu ,Shu Huey Chen ,Hui Hua Chang ,Chih Hsiang Yu ,Shih Chung Wang ,Ching Hon Pui ,Dong‐Tsamn Lin ,Shu Wha Lin ,Yu Ling Ni ,Meng Yao Lu ,Chia-Ching Chang,Yung Li Yang

doi:10.1038/s41598-020-69059-y

Abstract

Although the cure rate for childhood acute lymphoblastic leukemia (ALL) has exceeded 80% with contemporary therapy, relapsed ALL remains a leading cause of cancer-related death in children. Relapse-specific mutations can be identified by comprehensive genome sequencing and might have clinical significance. Applying whole-exome sequencing to eight triplicate samples, we identified in one patient relapse-specific mutations in the folylpolyglutamate synthetase (FPGS) gene, whose product catalyzes the addition of multiple glutamate residues (polyglutamation) to methotrexate upon their entry into the cells. To determine the prevalence of mutations of the FPGS mutations, and those of two important genes in the thiopurine pathway, NT5C2 and PRPS1, we studied 299 diagnostic and 73 relapsed samples in 372 patients. Three more FPGS mutants were identified in two patients, NT5C2 mutations in six patients, and PRPS1 mutants in two patients. One patient had both NT5C2 and PRPS1 mutants. None of these alterations were detected at diagnosis with a sequencing depth of 1000X, suggesting that treatment pressure led to increased prevalence of mutations during therapy. Functional characterization of the FPGS mutants showed that they directly resulted in decreased enzymatic activity, leading to significant reduction in methotrexate polyglutamation, and therefore likely contributed to drug resistance and relapse in these cases. Thus, besides genomic alterations in thiopurine metabolizing enzymes, the relapse-specific mutations of FPGS represent another critical mechanism of acquired antimetabolite drug resistance in relapsed childhood ALL.

Highlights

The cure rate for childhood acute lymphoblastic leukemia (ALL) has exceeded 80% with contemporary therapy, relapsed ALL remains a leading cause of cancer-related death in children
We identified two additional patients with three folylpolyglutamate synthetase (FPGS) mutants (R141H, V136F and K215_V218delinsSP, the last two mutants occurred in the same patient), as well as six patients with NT5C2 and two patients with PRPS1 mutants
Studies focusing on the relapsed childhood ALL samples have identified several pathways that are highly susceptible to mutation, including those involved in RAS signaling, JAK-STAT signaling, transcriptional factors of lymphoid development, nucleoside metabolism, epigenetics modification and cell cycle r egulation[13,14,30]

Summary

Introduction

The cure rate for childhood acute lymphoblastic leukemia (ALL) has exceeded 80% with contemporary therapy, relapsed ALL remains a leading cause of cancer-related death in children. Applying whole-exome sequencing to eight triplicate samples, we identified in one patient relapse-specific mutations in the folylpolyglutamate synthetase (FPGS) gene, whose product catalyzes the addition of multiple glutamate residues (polyglutamation) to methotrexate upon their entry into the cells. Thiopurines are enzymatically converted to with cytotoxic thioguanine nucleotides inside the cell, and acquired mutations in the purine salvage pathway genes have been associated with thiopurine resistance in relapsed ALL (NT5C2, PRPS1)[16,17,18]. In a study of whole-exome sequencing of eight matched diagnosis-remission-relapse triplicate ALL samples, we identified a case that acquired a novel point mutation of FPGS at relapse. In addition to mutant enzymes in the purine pathway, acquired relapse-specific mutations in genes participating in MTX metabolism pathway provide a biochemical mechanism of antimetabolite drug resistance in relapsed childhood ALL

Methods

Results

Conclusion