Association of aberrantASNSimprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL

Abstract

Karyotype is an important prognostic factor in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL), but the underlying pharmacogenomics remains unknown. Asparaginase is an integral component in current chemotherapy for childhood BCP-ALL. Asparaginase therapy depletes serum asparagine. Normal hematopoietic cells can produce asparagine by asparagine synthetase (ASNS) activity, while ALL cells are unable to synthesize adequate amounts of asparagine. The ASNS gene has a typical CpG island in its promoter. Thus, methylation of the ASNS CpG island could be one of the epigenetic mechanisms for ASNS gene silencing in BCP-ALL. To gain deep insights into the pharmacogenomics of asparaginase therapy, we investigated the association of ASNS methylation status with asparaginase sensitivity. ASNS CpG island is largely unmethylated in normal hematopoietic cells but is allele-specifically methylated in BCP-ALL cells. The ASNS gene is located at 7q21, an evolutionally conserved imprinted gene cluster. ASNS methylation in childhood BCP-ALL is associated with an aberrant methylation of the imprinted gene cluster at 7q21. Aberrant methylation of mouse Asns and a syntenic imprinted gene cluster is also confirmed in leukemic spleen samples from ETV6-RUNX1 knock-in mice. In three childhood BCP-ALL cohorts, ASNS is highly methylated in BCP-ALL with favorable karyotypes but is mostly unmethylated in BCP-ALL with poor prognostic karyotypes. Higher ASNS methylation is associated with higher l-asparaginase sensitivity in BCP-ALL through lower ASNS gene and protein expression levels. These observations demonstrate that silencing of the ASNS gene due to aberrant imprinting is a pharmacogenetic mechanism for the leukemia-specific activity of asparaginase therapy in BCP-ALL.

Association of allele-specific methylation of the ASNS gene with asparaginase sensitivity and prognosis in T-ALL

“…CG dinucleotides using NGS technology, as we previously reported 17 . The methylation status in each of the 23 CG dinucleotides showed an almost similar pattern in each cell line (Figure 1A).…”

“…These our previous observations of BCP-ALL suggested that the ASNS gene in T-ALL cells may also be methylated in an allele-specific manner as a result of aberrant imprinting of the 7q21 imprinted gene cluster, but it remains to be elucidated. Moreover, ASNS methylation status in childhood BCP-ALL was highly associated with cytogenetic abnormalities; highly methylated status was associated with favorable karyotypes, while unmethylated status was associated with poor prognostic karyotypes 17 . In childhood T-ALL, the recently identified SPI1 fusion (TCF7-SPI1 and STMN1-SPI1 fusions) is the first cytogenetic abnormality associated with poor prognosis 20 .…”

“…Allele-specific methylation is a hallmark of genomic imprinting, and the ASNS gene is located adjacent to the 7q21 imprinted gene clusters 18,19 . Of note, in BCP-ALL, the methylation status of the ASNS gene was associated with an aberrant methylation of the 7q21 imprinted gene cluster 17 . These our previous observations of BCP-ALL suggested that the ASNS gene in T-ALL cells may also be methylated in an allele-specific manner as a result of aberrant imprinting of the 7q21 imprinted gene cluster, but it remains to be elucidated.…”

Insights on Metabolic Reprogramming and Its Therapeutic Potential in Acute Leukemia

“…Specifically, ALL blasts, differently from ALL cell lines, express very low levels of ASNS and correlation between its expression and sensitivity to ASNase was not informative [108]. Recently, methylation of CpG islands in ASNS gene has been demonstrated as one of the epigenetic mechanisms responsible for ASNS gene silencing in B-ALL; higher ASNS methylation is described to be associated with higher ASNase sensitivity through lower ASNS transcript and protein levels [109]. In T-ALL, T-cell leukemia homeobox protein 1-positive (TLX1+) patients express low levels of ASNS when compared with TLX3+ and TLX-negative patients, due to epigenetic silencing of ASNS by both DNA methylation and a decrease of active histone marks; in addition, promoter methylation of the ASNS gene correlated with ASNase sensitivity in both T-ALL cell lines and patient-derived xenografts [110].…”

Novel Approaches Outside the Setting of Immunotherapy for the Treatment of Multiple Myeloma: The Case of Melflufen, Venetoclax, and Selinexor

“…Regarding the combination of venetoclax plus pomalidomide, in the ongoing multicenter, randomized, open-label phase 3 study CANOVA (NCT03539744), RRMM patients with t(11;14) will be randomized 1:1 to venetoclax or pomalidomide plus dexamethasone ( 40 ). The treatment will continue until PD, unacceptable toxicity, or withdrawal from the study.…”