Modeling IKZF1 lesions in B-ALL reveals distinct chemosensitivity patterns and potential therapeutic vulnerabilities

Abstract

IKAROS family zinc finger 1 (IKZF1) alterations represent a diverse group of genetic lesions that are associated with an increased risk of relapse in B-lymphoblastic leukemia (B-ALL). Due to the heterogeneity of concomitant lesions, it remains unclear how IKZF1 abnormalities directly affect cell function and therapy resistance and whether their consideration as a prognostic indicator is valuable in improving outcome. We used CRISPR/Cas9 to engineer multiple panels of isogeneic lymphoid leukemia cell lines with a spectrum of IKZF1 lesions in order to measure changes in chemosensitivity, gene expression, cell cycle, and in vivo engraftment that can be linked to loss of IKAROS protein. IKZF1 knockout and heterozygous null cells displayed relative resistance to a number of common therapies for B-ALL including dexamethasone, asparaginase, and daunorubicin. Transcription profiling revealed a stem/myeloid cell-like phenotype and JAK/STAT upregulation after IKAROS loss. We also used a CRISPR homology-directed repair (HDR) strategy to knock-in the dominant-negative IK6 isoform into the endogenous locus and observed a similar drug resistance profile with the exception of retained dexamethasone sensitivity. Interestingly, IKZF1 knockout and IK6 knock-in cells both have significantly increased sensitivity to cytarabine, likely owing to marked downregulation of SAMHD1 after IKZF1 knockout. Both types of IKZF1 lesions decreased survival time of xenograft mice, with higher numbers of circulating blasts and increased organ infiltration. Given these findings, exact specification of IKZF1 status in patients may be a beneficial addition to risk stratification and could inform therapy.

Next‐generation sequencing‐based analysis to assess the pattern of relapse in patients with Philadelphia‐positive acute lymphoblastic leukemia

“…To drive B-lymphoid development, Ikaros has been reported to repress hematopoietic stem-cell-specific gene expression programs during early lineage specification [37,38]. Additionally, IKZF1 deletion in B-ALL shows a more stem cell-like signature in gene expression profiling than the wild-type IKZF1, and the expression of a stem cell program has been associated with drug resistance and poor outcomes in other types of leukemia [39][40][41]. The relapse pattern of our study suggests a role for IKZF1 in mediating drug resistance and relapse.…”

IKZF1 Alterations and Therapeutic Targeting in B-Cell Acute Lymphoblastic Leukemia

“…Novel approaches to addressing IKZF1 deletions, partial or whole-gene, and their associated poor outcome in certain B-ALL subtypes, may center around overcoming the described chemotherapy resistance associated with these alterations. IKZF1 loss is associated with the stem cell gene expression signature and may thus render cells more quiescent [91]. IKZF1 loss has been associated with dexamethasone resistance in some studies, and this may be related to the degree of IKZF1 loss [91][92][93][94].…”

“…IKZF1 loss is associated with the stem cell gene expression signature and may thus render cells more quiescent [91]. IKZF1 loss has been associated with dexamethasone resistance in some studies, and this may be related to the degree of IKZF1 loss [91][92][93][94]. In NALM6 cells, IKZF1 knockout was associated with relative resistance to daunorubicin and asparaginase, while the Tanoue cell line with IKZF1 knockout showed relative resistance to vincristine and asparaginase [91].…”

Prognostic significance of copy number variation in B-cell acute lymphoblastic leukemia

“…Increasing evidence indicated that IKZF1 deletions mediate cellular drug resistance and relapse. For example, Rogers et.al ( 52 ) established that the IKZF1 deletion was resistant to dexamethasone, asparaginase, and daunorubicin by upregulating the JAK/STAT pathway. In addition, the IKZF1 deletion affects sensitivity to cytarabine by downregulating the SAMHD1 pathway ( 52 ); STEEGHS et.…”

“…For example, Rogers et.al ( 52 ) established that the IKZF1 deletion was resistant to dexamethasone, asparaginase, and daunorubicin by upregulating the JAK/STAT pathway. In addition, the IKZF1 deletion affects sensitivity to cytarabine by downregulating the SAMHD1 pathway ( 52 ); STEEGHS et. al ( 14 ) suggested that the loss of IKZF1 caused prednisolone resistance by elevating intracellular ATP and glucose levels, whereas drug sensitivity was recovered by inhibition of glycolysis.…”