Stem cell–like epigenetic signature predicts resistance to CD19 CAR T-cell therapy in ALL

A stem cell–like epigenetic signature is identified in pretreatment samples from young patients with acute lymphoblastic leukaemia (ALL) who are resistant to CD19 chimeric antigen receptor (CAR) T-cell therapy, with potential utility for refining patient selection for appropriate treatment.

Despite remarkable remission rates, CD19 CAR T-cell therapy may fail in some patients with relapsed/refractory ALL. [N Engl J Med 2014;371:1507-1517; Blood 2015;126:681; Lancet 2015;385:517-528; Blood 2017;129:3322-3331] “Although CD19 is a common marker for CAR T-cell therapy, leukaemia patients may develop resistance to the therapy regardless of CD19 expression. Thus, in this study, we explored CD19-independent factors associated with poor responses to CAR T-cell therapy, and tested the hypothesis that differences in leukaemia between nonresponders and responders are detectable prior to therapy,” the investigators noted. [Masih KE, et al, AACR 2022, abstract 3851]

Pretreatment bone marrow aspirates (BMAs) were collected from 14 young patients with B-cell ALL. Of these, seven patients were nonresponders, defined as not achieving and maintaining minimal residual disease negativity at day 63, while seven patients who achieved complete remission served as controls. Their epigenetic patterns were characterized with a multiomic approach that included array-based methylation and assay for transposase-accessible chromatin by sequencing (ATAC-seq).

Study results revealed distinct DNA methylation profiles of nonresponders and responders prior to therapy. In methylation array analysis, nonresponders showed 238 regions of increased DNA methylation, some of which were associated with embryonic and cancer stem cell–like phenotype (p=8.15x10^-25).

Similarly, in ATAC-seq, the accessible chromatin region in nonresponders’ leukaemia samples were associated with stem cell proliferation (normalized enrichment score [NES], 2.31; p<0.0001) and cell cycling (NES, 2.27, p<0.0001), revealing chromatin accessibility patterns with multilineage properties of common myeloid progenitors (p=0.047) and B-cell ALL (p=0.16). These findings were further supported by an increase in pretreatment expression of multilineage phenotypes, such as CD19, CD20, CD33 and CD34 (p=0.009).

“We saw subpopulations of [pretreatment ALL] cells expressing both lymphoid and myeloid markers, indicating that the epigenomes of some nonresponsive leukaemia cells contained hybrid phenotypes of ALL and acute myeloid leukaemia [AML],” the investigators pointed out.

“The data support that leukaemias [in nonresponders] are relatively plastic … and rapidly adapt to the evolutionary pressure of CD19 CAR T-cells,” they suggested.

This study also demonstrated reduced gene expression of antigen presentation and processing pathways in nonresponders vs responders (p=0.0001), suggesting that CD19-positive nonresponsive leukaemias may not effectively process additional immune targets.

“We identified a CD19-independent predictive signature that can be detected prior to CAR T-cell therapy,” the investigators concluded. “Screening of this phenotype [ie, stem cell properties with multilineage potential] may allow clinicians to not only identify leukaemia patients unlikely to respond to CAR T-cell therapy, but also provide alternative therapies to improve their outcomes.”