Methotrexate (MTX), a folate antagonist which blocks de novo nucleotide biosynthesis and DNA replication, is an anchor drug in acute lymphoblastic leukemia (ALL) treatment. However, drug resistance is a primary hindrance to curative chemotherapy in leukemia and its molecular mechanisms remain poorly understood. We have recently shown that impaired folylpolyglutamate synthetase (FPGS) splicing possibly contributes to the loss of FPGS activity in MTX-resistant leukemia cell line models and adult leukemia patients. However, no information is available on the possible splicing alterations in FPGS in pediatric ALL. Here, using a comprehensive PCR-based screen we discovered and characterized a spectrum of FPGS splicing alterations including exon skipping and intron retention, all of which proved to frequently emerge in both pediatric and adult leukemia patient specimens. Furthermore, an FPGS activity assay revealed that these splicing alterations resulted in loss of FPGS function. Strikingly, pulse-exposure of leukemia cells to antifolates and other chemotherapeutics markedly enhanced the prevalence of several FPGS splicing alterations in antifolate-resistant cells, but not in their parental antifolate-sensitive counterparts. These novel findings suggest that an assortment of deleterious FPGS splicing alterations may constitute a mechanism of antifolate resistance in childhood ALL. Our findings have important implications for the rational overcoming of drug resistance in individual leukemia patients.Despite the high cure rates that are currently achieved, approximately 20% of pediatric acute lymphoblastic leukemia (ALL) patients experience a relapse and face poor prognosis. 1,2 Drug resistance in leukemia continues to be a major obstacle to targeted combination therapy. Although various molecular mechanisms have been classified in model systems, the major mechanisms for clinical drug resistance remain largely unknown. 3 One of the key components of contemporary treatment of ALL is the folate antagonist methotrexate (MTX). Folates play a crucial role as one-carbon donors in multiple biosynthetic pathways including de novo synthesis of purines and thymidylate, amino acid metabolism, mitochondrial protein synthesis and DNA methylation. 4,5 Antifolates including MTX are potent inhibitors of several folate-dependent enzymes engaged in nucleotide biosynthesis, thereby inhibiting DNA replication and leading to cell death. 6 The cytotoxic activity of various antifolates is largely dependent on the activity of folylpolyglutamate synthetase (FPGS). The latter enzyme catalyzes the addition of multiple glutamate residues (i.e., polyglutamylation) to both folates and antifolates upon their entry into the cell. 7 This unique metabolic conversion dramatically enhances the intracellular retention of antifolates including MTX as the polyglutamate forms of antifolates are no longer substrates of various efflux transporters. 8 Polyglutamylation also decreases the Ki of MTX and other antifolates like pemetrexed to their target enzymes in...