TP53 deficiency induces a low-adhesion transcriptomic signature correlating with accelerated CAR-T cell exhaustion in B-ALL.

BACKGROUND

Chimeric antigen receptor T-cell (CAR-T) therapy is a potent treatment for relapsed/refractory B-cell acute lymphoblastic leukemia (R/R B-ALL). However, patients harboring TP53 alterations experience disproportionately high relapse rates, and the underlying tumor-intrinsic mechanisms driving this resistance remain poorly understood.

METHODS

We engineered isogenic TP53-wildtype and TP53-knockout NALM-6 B-ALL cell models using CRISPR/Cas9. The specific impact of p53 loss on CD19 CAR-T cell cytotoxicity, proliferation, and exhaustion was evaluated using in vitro co-culture assays. Associated molecular alterations and adaptive responses were profiled via RNA-sequencing (RNA-seq).

RESULTS

In in vitro assays, TP53-deficient B-ALL cells exhibited intrinsic resistance to CAR-T-mediated killing. Co-culturing with these TP53-null targets reduced CAR-T cell expansion, suppressed effector cytokine secretion, and accelerated a T-cell exhaustion phenotype, indicated by the co-expression of PD-1, TIM-3, and LAG-3. Transcriptomic profiling revealed that TP53 deficiency induces a low-adhesion signature, characterized by the coordinated downregulation of core extracellular matrix (ECM) and cell adhesion genes, including ITGB1 and LAMA5. This transcriptional profile suggests a structural remodeling that potentially deprives CAR-T cells of the mechanical anchoring requisite for establishing a stable immunological synapse (IS). Furthermore, TP53-deficient cells failed to activate immunogenic signaling pathways, such as IL-2/STAT5, under immune pressure.

CONCLUSIONS

Our in vitro findings indicate that TP53 deficiency in B-ALL cells downregulates adhesion networks and impairs immunogenic signaling, which correlates with accelerated CAR-T cell exhaustion. These transcriptomic and cellular observations suggest a potential link between TP53-mediated adhesion loss and CAR-T resistance, warranting further in vivo validation and biophysical investigations.