Genomic features of CAR T treatment failure in patients with lymphoma

CD19-directed chimeric antigen receptor (CAR-19)-reprogrammed autologous T-cells are innovative immunotherapies for heavily pretreated patients with diffuse large B-cell lymphoma (DLBCL); however, across CAR-19 products, ~60% of patients fail to achieve complete tumor eradication and prolonged remission. Inflammatory markers and clinical factors are associated with impaired responses, but tumor-intrinsic resistance drivers are largely undefined.

Here, we summarize the key genomic features underlying anti-CD19 CAR T-cell treatment failure in patients with lymphoma based on the recent article published by Jain, et al., in Blood in 2022.¹

Methods

Whole-genome sequencing (WGS) analysis was performed on samples from patients with relapsed or refractory (R/R) DLBCL who had received treatment with CAR-19 T cells (R/R lymphoma cohort, n = 49). To increase the statistical power, WGS data from untreated DLBCL cases from the Pan-Cancer Analysis of Whole Genomes (PCAWG) were also added to the comparative analysis (PCAWG cohort, n = 50).

Results

• Follow up and clinical outcomes of 47 out of 49 LBCL patients were included in the progression-free survival (PFS) and overall survival (OS) analysis (excluded cases: relapse-only sample with transitory complete remission [n = 1] and early therapy-related death [n = 1] not evaluable for PFS).
• Demographics, disease characteristics, and responses to CAR-19 for all patients are summarized in Table 1.
• The median follow-up was 17.3 months.
• Median OS and PFS for the entire cohort were 11.6 months and 8 months, respectively.
• The progression-free response was observed in 36.7% of patients.

Table 1. Patient baseline characteristics*

Treatment resistance

Overall, markers of genomic complexity (APOBEC and chromothripsis) and specific genomic alterations (RHOA) were associated with resistance to CAR-19 immunotherapy for aggressive B-cell lymphomas. Further details on the genomic complexity and specific genome alterations are summarized below.

Mutational signature gene association

Twelve single base substitution (SBS) mutational signatures were involved in the R/R lymphoma cohort.

• Presence of APOBEC (SBS2 and SBS13) signatures was associated with significantly worse PFS, with 12/13 (92%) patients progressing (all patients, p = 0.0023; considering only de novo DLBCL [n = 40], p = 0.045).
• Among additional mutational signatures tested, SBS18 was associated with post-CAR-19 progression in 9/11 (81%) patients (all patients, p = 0.0396; considering only de novo DLBCL [n = 40], p = 0.045).
• This SBS signature reflects genomic damage from oxygen-radical stress.

Deletion of 3p21.31 (RHOA) association

• TP53 deletion was the most frequent in 49 R/R patients and mono-allelic or biallelic loss of TP53 was highly prevalent (59.2%; p = 0.76) but did not predict the poor outcome.
• Focal deletions of 3P21.31 containing RHOA were found to be significantly enriched in the R/R patient’s cohort and independently predicted poor outcomes (p = 0.0013).
• Loss of RHOA was also associated with poor OS (p = 0.023).

Structural variants

WGS identified four main complex structural variants and complex events:

• Double minutes (n = 6)
• Chromothripsis (n = 23)
• Chromoplexy (n = 18)
• Templated insertion (n = 11)

Only chromothripsis showed worse PFS (p = 0.026) after CAR-19 treatment, with 18/22 (81.8%) cases (R/R DLBCL) experiencing early progression; however, this was not associated with OS. All de novo DLBCL with double minutes rapidly progressed and died after CAR-19 (p = 0.017 for PFS; p = 0.0011 for OS).

Conclusion

Despite unprecedented overall response rates to CAR-19 in heavily pretreated patients with DLBCL, a significant number of patients often fail to achieve survival outcomes. Genomic complexity and alterations appear to promote an immunosuppressive tumor microenvironment, limiting CAR-19 efficacy. The results discussed here are the foundation of further functional studies that can establish mechanistically how complex lymphoma genomes promote an environment hostile to CAR T cells and possibly other emerging immunotherapies.