CD49d Expression Identifies a Biologically Distinct Subtype of Chronic Lymphocytic Leukemia with Inferior Progression Free Survival on BTK Inhibitor Therapy (2022)

Background: Acalabrutinib, a highly selective Bruton tyrosine kinase inhibitor (BTKi), is effective and well tolerated for patients with chronic lymphocytic leukemia (CLL). During treatment with BTKis, transient lymphocytosis is observed due to the efflux of CLL cells from lymphoid organs. CD49d, the alpha chain of the CD49d/CD29 integrin very late antigen-4 (VLA-4), is a key mediator in CLL microenvironmental interactions. High CD49d expression has been associated with inferior response to ibrutinib (Tissino, 2018). Here, we investigated the role of CD49d in response to acalabrutinib in 48 patients with CLL enrolled in a single-center, phase 2 study (NCT02337829). Methods: Patients were divided into CD49d positive (CD49d+, n = 27, 56%) and CD49d negative (CD49dneg, n = 21, 44%) groups based on the established 30% cutoff, as assessed by flow cytometry. CD49d activation was measured as VLA-4 receptor occupancy (RO), as described (Tissino, 2018). Time to progression was estimated using the Kaplan-Meier method. RNA sequencing (RNA-seq) of CD19+ selected CLL cells from CD49d+ (n = 10) and CD49dneg (n = 10) subsets was performed at baseline and 6 months on acalabrutinib. Results: After the first month on acalabrutinib, the median increase in absolute lymphocyte count (ALC) for CD49d+ CLL was 6.4% vs. 50.4% for CD49dneg (P = .02). However, the increase in ALC on day 3 of 42% and 48%, respectively, was comparable (P = .8). A subset of patients showed bimodal CD49d (bimCD49d) expression, with concomitant presence of CD49d positive and negative subpopulations. In these cases, the fraction of CD49d+ CLL cells increased significantly on day 3 (P = .002), but decreased at 6 months (P = .004), suggesting that CD49d+ cells may be better able to remain tissue bound on chronic therapy or reenter lymphoid tissues at higher rates than CD49dneg cells. While constitutive VLA-4 activation was reduced in patients on acalabrutinib, BCR and CXCR4 stimulation still increased VLA-4 RO on CLL cells even after 6 months of treatment. PI3K, in addition to BTK signaling, is implicated in inside-out activation of VLA-4. In vitro, addition of the PI3K inhibitor duvelisib to acalabrutinib-treated CLL cells completely blocked BCR- but not CXCR4- induced VLA-4 activation. The overall response rate of the study was 95.8% (Sun, 2020). Sixteen patients progressed at a median of 42.5 months, 3 with transformation. Time to progression for patients with CD49d+ and CD49dneg CLL (applying 30% cutoff) did not differ (P = .4). However, at 72 months 50% of the combined CD49d+ and bimCD49d patients (n = 37) were estimated progression-free vs 90% of patients with a homogeneous CD49dneg CLL population (n = 11, P = .02). Of 13 patients progressing with CLL, 12 (92%) were CD49d+ or bimodal CD49d and 11 (85%) had BTK and/or PLCG2 mutations. To dissect the impact of CD49d expression on CLL pathobiology and the response to acalabrutinib, we compared transcriptomes of CD49d+ and CD49dneg subsets by RNA-seq. A distinct gene expression profile separated the groups by principal component analysis. Using gene set enrichment analysis, CD49d+ CLL showed constitutively more immunoreceptor, NF-kappa B, and cytokine/JAK-STAT signaling, as well as enhanced cell survival, adhesion and migration capacity compared to CD49dneg CLL (FDR <.25). After 6 months on acalabrutinib, all 20 patients achieved a clinical response and all samples showed downregulation of B-cell receptor and NF-kappa B target genes, as expected for BTKi therapy. Interestingly, on acalabrutinib, CD49d+ samples not only maintained a higher level of activation compared to CD49dneg CLL, but differences in the degree of cytokine (IL-6, IL-10) and STAT3 signaling became more prominent. Conclusion. CD49d+ and CD49dneg CLL cells are rapidly mobilized out of lymph nodes at the start of acalabrutinib therapy, but CD49d+ cells appear able to reenter or persist in lymphoid tissues better than CD49dneg cells. Bimodal CD49dneg and CD49d+ cases share an increased risk of disease progression, with most patients having detectable BTK or PLCG2 mutations at the time of progression. The transcriptional program of CD49d+ CLL reflects upregulation of survival and activation pathways that may increase tolerance to BTKi therapy and set the stage for clonal evolution. Thus, CD49d/VLA-4 emerges as a microenvironmental factor that contributes to BTKi resistance and a possible therapeutic target to improve on BTKi therapy.