Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect

Abstract

Leukemic relapse remains a major barrier to successful allogeneic hematopoietic stem cell transplantation (allo-HSCT) for aggressive hematologic malignancies. The basis for relapse of advanced lymphoid malignancies remains incompletely understood and may involve escape from the graft-versus-leukemia (GvL) effect. We hypothesized that for patients with chronic lymphocytic leukemia (CLL) treated with allo-HSCT, leukemic cell–intrinsic features influence transplant outcomes by directing the evolutionary trajectories of CLL cells. Integrated genetic, transcriptomic, and epigenetic analyses of CLL cells from 10 patients revealed that the clinical kinetics of post-HSCT relapse are shaped by distinct molecular dynamics. Early relapses after allo-HSCT exhibited notable genetic stability; single CLL cell transcriptional analysis demonstrated a cellular heterogeneity that was static over time. In contrast, CLL cells relapsing late after allo-HSCT displayed notable genetic evolution and evidence of neoantigen depletion, consistent with marked single-cell transcriptional shifts that were unique to each patient. We observed a greater rate of epigenetic change for late relapses not seen in early relapses or relapses after chemotherapy alone, suggesting that the selection pressures of the GvL bottleneck are unlike those imposed by chemotherapy. No selective advantage for human leukocyte antigen (HLA) loss was observed, even when present in pretransplant subpopulations. Gain of stem cell modules was a common signature associated with leukemia relapse regardless of posttransplant relapse kinetics. These data elucidate the biological pathways that underlie GvL resistance and posttransplant relapse.

Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy

“…Future studies should also address the mechanism of DLIinduced T PEX -like cell expansion and whether molecular therapies can recapitulate this effect. The critical roles likely played by leukemia cells and alloreactivity should also be better understood given their known influence on GvL escape (Bachireddy et al, 2020). In addition, while these T cell-exhausted subsets have now been observed in multiple clinical settings, which aspects of their underlying molecular machinery and distinct regulatory circuits remain specific to the leukemic or GvL setting and which generally extend to other cancers and human diseases should be explored.…”

“…For cryopreserved BMMCs from patient 5283 with CLL, samples were processed as previously described for subsequent inDrop sequencing (Bachireddy et al, 2020). Briefly, dead cells were removed via an OptiPrep selection protocol, and viable cells were then subjected to immunomagnetic selection (MACS CD19 MicroBeads; Miltenyi Biotec) using MS columns to isolate C19 + and CD19 -, which were then mixed at a 1:1 ratio at a total concentration of 1.15 3 10 5 cells/mL in a 15% OptiPrep solution in PBS and kept on ice until time of encapsulation.…”

“…For BMMC samples from patient 5283, cell encapsulation and subsequent library preparation were performed as previously described (Bachireddy et al, 2020). Briefly, cells were encapsulated with RT/lysis mix and barcoded hydrogen beads (BHBs; from 1CellBio) and maintained at 4 C in their respective syringes throughout using refrigerated copper coiling.…”

“…We identified T cells with maximum likelihood of mapping to either MC1 or MC2 metacusters and labeled them as T PEX -like and similarly T cells mapped to either MC3 or MC4 metaclusters as T EX -like. Analysis of CLL inDrop Raw count data were initially processed using the dropEst software suite as previously described (Bachireddy et al, 2020;Petukhov et al, 2018). Count matrices from bone marrow inDrop datasets for the patient with CLL were first filtered by library size, with a total of 12,254 T cells (3112, 5487, 3655 T cells from F1, F2, F3 samples respectively) remaining cells over 3 time points, which included 0 (pre-DLI), and 6 and 128 months post-DLI (Figure 3F and S7D).…”

Clonal Evolution of High-Risk Chronic Lymphocytic Leukemia: A Contemporary Perspective

“…Allogeneic HSCT exemplifies the power of harnessing antitumor immunity for cancer treatment, but relapses nevertheless occur. Recently, Bachireddy and colleagues investigated the evolutionary dynamics underlying resistance to graft-versus-leukemia (GvL) effect, uncovering mechanisms that may have potential broader relevance for CLL immunotherapy ( 151 ). Through longitudinal analysis integrating genetic, transcriptomic and epigenetic analyses, Bachireddy et al.…”