Molecular Profiling Identifies CD49d and CD79b as Predictive Markers for Acquired Acalabrutinib Resistance in Patients With Chronic Lymphocytic Leukemia

Contemporary studies of Bruton tyrosine kinase inhibitor (BTKi) resistance focus on mutations in the B-cell receptor (BCR) pathway, but alternative mechanisms of resistance remain undefined. Here, we sought to identify novel predictive markers of acquired resistance to acalabrutinib, a second-generation BTKi, in patients with chronic lymphocytic leukemia (CLL). Clinical samples from 41 patients with relapsed/refractory or treatment-naive CLL receiving acalabrutinib as part of a clinical trial (NCT02029443) were divided into two groups: those who continued to respond to treatment (NP, n = 23) and those who developed progressive disease on acalabrutinib therapy (PD, n = 18). Peripheral blood mononuclear cells (PBMCs) from the two groups of patients were profiled at baseline (BL) and at a second timepoint (T2) by RNA-seq and flow cytometry. Our findings show a correlation between acquired resistance to acalabrutinib and upregulation of integrin alpha-4 (ITGA4; CD49d), the BCR surface receptor CD79B, and oncogenes such as MYC, LAG3, and MCL1 in CLL cells. High surface expression of CD49d and CD79b prior to acalabrutinib therapy was associated with increased risk of disease progression on acalabrutinib in patients with CLL. When stratified by pretreatment CD49d surface expression, the CD49d^hi group (defined as ≥ 30% CD49d+ cells at baseline) showed reduced acalabrutinib-induced lymphocytosis and higher levels of tumor proliferation markers such as CD38 and Ki-67 compared with the CD49d^lo group (defined as < 30% CD49d+ cells at baseline). In summary, CD49d and CD79b are useful predictive markers for CLL progression on acalabrutinib. Trial Registration: ClinicalTrials.gov identifier: NCT02029443.