Use of Chromosomal Microarray Analysis (CMA) to Identify Targetable Mutations in Acute Lymphoblastic Leukemia
Authors: McNeer Jennifer , Raca Gordana , Gurbuxani Sandeep , Mayfield Jodi , Stock Wendy 
Published: October 2019

Abstract
Background: The success in treatment of B acute lymphoblastic leukemia (B-ALL) is partially attributable to careful risk stratification of patients, based largely on biology of disease and disease response to therapy. Recently, gene expression profiling and subsequent high-throughput sequencing of B-ALL has resulted in the identification of a novel high-risk subset of patients with an activated kinase signature similar to patients with Philadelphia chromosome (Ph)-positive ALL, which is currently known as Ph-like ALL (Mullighan et al Nature 2007, Den Boer et al Lancet Oncol 2009). Identification of patients with Ph-like ALL using standard diagnostic techniques will be of great clinical importance since the activated kinases present in these leukemias may be therapeutically targeted. Here we report two patients with B-ALL who had residual disease after induction, neither of whom had a classic high-risk karyotype. Using chromosomal microarray analysis (CMA) we identified targetable kinase mutations in each patient that resulted in a change in therapy and eradication of minimal residual disease (MRD).
Patient 1: An 11 year old female presented with fever, malaise, and decreased appetite. The initial WBC count was 28.2 K/µL with 65% blasts, hemoglobin was 5.9 gm/dL, and platelets were 46 K/µL. Flow cytometry confirmed B-ALL. Cytogenetic analysis revealed the following karyotype: 46,XX,add(5)(q13.3),add(6)(q13)[13]/46,XX[5].
She was started on four-drug induction chemotherapy, but at the end of induction, there were 90% blasts in the marrow, consistent with induction failure. Using CMA, multiple regions of copy number loss were detected, one of which was a microdeletion at 5q32-q33.3 with breakpoints located in the EBF1 and PDGFRB genes. Fluorescence in situ hybridization (FISH) analysis confirmed the presence of a PDGFRB rearrangement. The deletion likely resulted in the EBF1-PDGFRB fusion, previously described in rare cases of high-risk B-ALL.
Based on previous reports that hematologic malignancies with PDGFRB fusions respond to the addition of a tyrosine kinase inhibitor (TKI) to therapy, imatinib was added to the chemotherapy backbone, and then dasatinib for broader tyrosine kinase inhibition. At the end of 8 weeks of this consolidation treatment there was no morphologic or immunophenotypic evidence of residual leukemia.
Patient 2: A 28 year old male presented with abdominal pain, fatigue, and weight loss. The initial WBC was 210.7 K/µL with 94% blasts, hemoglobin was 8.8 gm/dL, and platelets were 43 K/µL. Flow cytometry confirmed B-ALL, and cytogenetic analysis showed one abnormal clone: 45,X,-Y,del(9)(p13p24)[11].
The patient received a four-drug induction, and at the end of induction therapy, MRD was present at a level of 4%. After 8 weeks of consolidation chemotherapy, MRD remained at a level of 1.3%.
Several aberrations were detected by CMA, including a 360 kb copy number gain within the 9q34.12-34.13 segment of the long arm of chromosome 9. It involved the chromosome segment between the NUP214 and ABL1 genes, likely resulting in formation of a NUP214-ABL1 fusion gene and upregulation of the ABL1 kinase activity. Dasatinib was added to the chemotherapy regimen, and eight weeks later the marrow had no evidence of MRD.
Discussion: We successfully employed CMA to identify 2 patients with B-ALL and a targetable fusion gene. Until now, CMA has been used to identify submicroscopic genetic lesions in ALL, often in genes that drive leukemogenesis. It has not yet been used for identification of patients with Ph-like ALL. Based on these two index cases, we have now begun prospectively to analyze leukemic blasts of patients with B-ALL who do not have classically prognostic cytogenetics using CMA and a panel of selected FISH probes. Using this approach, we have been able to identify Ph-like genetic lesions, and we plan to utilize this information to tailor therapy with early introduction of an appropriate TKI in order to achieve MRD-negative remissions.
Figure 1 Figure Legend: CMA results for patients 1 and 2. Top panel: Array plot showing the 8.6Mb 5q32-q33.3 deletion (red bar) in patient 1, that fuses exon 11 of the EBF1 gene with exon 15 of PDGFRB. Bottom panel: The 360kb duplication at 9q34 (blue bar) in patient 2, with the breakpoints within the ABL1 gene and the NUP214 gene, resulting in the NUP214-ABL1 fusion. Figure 1. Figure Legend: CMA results for patients 1 and 2. Top panel: Array plot showing the 8.6Mb 5q32-q33.3 deletion (red bar) in patient 1, that fuses exon 11 of the EBF1 gene with exon 15 of PDGFRB. Bottom panel: The 360kb duplication at 9q34 (blue bar) in patient 2, with the breakpoints within the ABL1 gene and the NUP214 gene, resulting in the NUP214-ABL1 fusion.

Disclosures
Off Label Use: Use of tyrosine kinase inhibitors as adjunct therapy in Ph-like B-ALL.