Novel Targets Identified By in Vitro Screening of Patient Samples with Adult Acute Lymphoblastic Leukemia

Introduction: Acute lymphoblastic leukemia (ALL) is considered a success story in pediatrics, with cure rates greater than 85%. In contrast, the estimated cure rate for adolescent and young adult (AYA) patients is estimated at 60% and is just 20-40% for adults. This is thought to be secondary to chemotherapy associated toxicities for older patients as well as different disease biology. In the AYA population, more patients carry the chemo-resistant Ph-like phenotype, with an estimated incidence of up to 27%. However, the genetic profile of adult ALL has not been well described. In addition, although the ABL specific kinase inhibitors and JAK inhibitors are predicted to be active in Ph-like ALL, there are no reports on functional drug sensitivity data in AYA or adult ALL. Our group has been collecting functional data on both newly diagnosed and relapsed AYA and adult patients since 2010; in this study we summarize the functional data obtained during this time. Materials and Methods: All clinical samples were obtained with informed consent and approval of the institutional review board at OHSU. Data obtained on both newly diagnosed and relapsed patients obtained from Jan 2010 to present was reviewed. At the time of diagnosis or at relapse, mononuclear cells were isolated from bone marrow aspirates of patients and exposed to a library of 130 small molecule inhibitors at varying concentrations. After 72 hours, cell viability was assessed via an MTS based assay and drug efficacy was assessed based on the IC₅₀ of of each panel drug against each patient sample. The calculated IC₅₀ for each drug was compared to the median IC₅₀ of over 1000 patient samples and was deemed hypersensitive if the IC50 value was below the 20^th percentile. A pathway was considered to be actively targeted if patients had more than one inhibitor targeting that pathway identified as hypersensitive, or a single drug was considered valid if it was hypersensitive in replicate testing.

Results: We identified a total of 42 adults with either B-cell or T-cell ALL who had analyzable data; those with Ph+ ALL were excluded. Of these, 28 had B cell ALL including the MLL rearrangement and 14 had T cell ALL. For the B cell ALL group, 17 had data obtained at diagnosis and 11 at relapse. 75% of patients had at least one active inhibitor identified, with the range being from 2-25 inhibitors per patient targeting from 1-5 different pathways per patient. We found that 35% of patient samples were sensitive to a JAK inhibitor, an ABL inhibitor or both. In addition, we found overlapping sensitivities with 43% of patient samples sensitive to PI3K/AKT/mTOR inhibitors, 43% of samples were sensitive to IGF1R inhibitors, 49% were sensitive to PDGFR/VEGFR inhibitors, 18% were sensitive to p38MAPK inhibitors and 11% each were sensitive to CSF1R or FLT3 inhibitors. Of note, all of the FLT3 inhibitor sensitivities were within the MLL-rearranged subgroup. Among the T-ALL group, 10 had data obtained at diagnosis and 4 at relapse. 52% of the samples had at least one inhibitor identified, with the range being from 1-20 inhibitors targeting from 1-4 pathways per patient. Drugs targeting the following pathways were identified: JAK family (57.1%), ERBBB family (57.1%), SYK (28.5%), and HDAC, MDM2 and aurora kinase (14.3% each).

Discussion: This study provides the evidence that there are multiple novel potentially targetable pathways present in AYA and adult patients with ALL. Given the poor outcomes in this group of patients, further exploration of these potentially targetable pathways is warranted.