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

Abstract

word count: 249 Figures: 7 Supplemental data: 1 supplemental methods and materials file Number of references: 45 Rogers et al. 2 Key points • Engineered IKZF1 perturbations result in a stem-cell like expression signature, enhanced engraftment in vivo, and multi-drug resistance • Loss of IKAROS may result in new vulnerabilities due to increased sensitivity to cytarabine and upregulation of JAK/STAT and mAb targets Rogers et al. 3 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 dynamics that can be directly linked to loss of IKAROS protein. IKZF1 knockout and heterozygous null cells displayed relative resistance to a number of commonly employed therapies for B-ALL including dexamethasone, vincristine, 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 IK6isoform tagged with GFP into the endogenous locus and observed a similar drug resistance profile with the exception of retained sensitivity to dexamethasone. Interestingly, IKZF1 knockout and IK6 knock-in cells both have significantly increased sensitivity to cytarabine, suggesting intensification of nucleoside analog therapy may be specifically effective for IKZF1-deleted B-ALL. 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.…”

Copy number alterations define outcome in Philadelphia chromosome-positive acute lymphoblastic leukemia

“…Helena Hohtari, 1 Niels Pallisgaard, 2 Matti Kankainen, 1,3,4,5 Pekka Ellonen, 6 Oscar Brück, 1 Timo Siitonen, 7 Marjaana Säily, 7 Marjatta Sinisalo, 8 Marja Pyörälä, 9 Maija Itälä-Remes, 10 Perttu Koskenvesa, 11 Erkki Elonen, 11 Satu Mustjoki 1,5,12 and Kimmo Porkka 1,5, 11…”

“…10 IKZF1 plus patients may be primary resistant at the progenitor/stem cell level to TKI-based therapies and more detailed mechanistic studies may give insight to effective treatment alternatives. 11 Retinoids, immunomodulatory drugs, crizotinib, and a combination of asciminib and ponatinib are currently being investigated and may provide an alternative also for the elderly patients and those non-eligible for intensive therapies. [12][13][14][15] To conclude, testing for CNA should be implemented in the routine diagnostics of Ph+ ALL.…”

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.…”