A novel stem cell epigenome biomarker for primary non-response to CD19 CAR T cells in pediatric ALL

In the American Association for Cancer Research (AACR) Annual Meeting 2022, Dr. Katherine Masih from the National Cancer Institute and Seattle Children’s Hospital, the United States, discussed the identification of a novel stem cell epigenome with multi-lineage potential (SCE-MLP) that is linked to primary non-response to CD19 chimeric antigen receptor (CAR) T-cell therapy among pediatric patients with acute lymphoblastic leukemia (ALL).1

Treatment of children with relapsed/refractory ALL has been transformed with the use and approval of CD19 CARs, which induce remission in up to 80% of B-cell ALL (B-ALL) patients.1 Unfortunately, its durable response rate is up to 50% with a relapse of CD19-negative disease detected in 25% of initial responders. Therefore, a pre-treatment biomarker is needed to prioritize CD19 CAR treatment for responders and prevent futile therapy.1

So far, most research focused on relapse after initial response and identified the antigen-dependent disease as the most common reason.1 Initially, most patients are primary sensitive (PS), having a minimal residual disease (MRD) with CD19 CAR expansion, while some patients are primary non-responders (PNRs), having progressive CD19-positive disease with CD19-CAR expansion.1 This occurs in 10%-20% of patients, highlighting the insufficient eligibility assessment to predict all PNRs. Some studies have identified dysfunctional T-cells which are used to produce CD19 CARs or decreased death receptor expression in genome-wide cell line screening as the potential sources of PNR.1

A study aimed to identify what made patients non-responsive to CD19 CAR T-cell therapy was conducted, and hypothesized that PNRs have distinct leukemias compared with responders with differences that can be detected before treatment.1 A total of 14 pediatric/young adult patients with B-ALL were treated with CD19 CAR T cells and stratified based on their response as PNRs or PS.1 Their bone marrow aspirate (BMA) was pretreated and analyzed with genomics and transcriptomics.1 No significant difference in CD19 ribonucleic acid (RNA) expression was seen by using the bulk RNA sequencing, thus ruling out the possibility of pre-existing alterations among patients.1 A methylation signature was identified to predict PNR to CD19 CAR, particularly hypermethylation at promoter genes in embryonic stem cells (ESCs).1

An independent cohort of 124 acute leukemia patients was analyzed to detect methylation patterns and showed regions of hypermethylation shared with mixed phenotype acute leukemia (MPAL).1 Hypermethylated genes appeared to be bound by PRC2 and its cofactors in ESCs.1 Moreover, an increase in chromatin accessibility in ESCs was detected in PNR compared with PS.1 To determine the transcription factors (TFs) involved in PNR, a differential motif enrichment was done and showed no significant difference in RUNX1, a master TF in B-ALL, and a significant difference in ERG (ETSI), which drive myeloid and lymphoid leukemias, leading to poor outcomes.1 Among the participating patients, no significant difference in common lymphoid progenitors was seen, but increased accessibility in regions associated with hematopoietic stem cells in myeloid and lymphoid progenitors.1 Furthermore, PNR leukemias demonstrated a decreased expression of antigen presentation and processing pathways compared with PS leukemias, leading to a decreased immunogenicity.1

Hence, these data identified SCE-MLP as a novel candidate biomarker for antigen-independent PNR to CD19 CAR T-cell therapy.1 It is characterized by 238 differentially methylated regions that are detectable before therapy, and is associated with stem cell phenotype and inherent plasticity, maintenance of B-ALL phenotype, while harboring myeloid and stem cell characteristics, as well as decreased antigen presentation and processing.1

In conclusion, SCE-MLP is a novel marker of PNR to CD19 CAR in childhood ALL, and can be detected prior to therapy for improvement in patient selection and eligibility for CD19 CAR therapy based on the response.1 Future trials may include multispecific CARs to target antigens expressed in the PNR subpopulations.1

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