Single-cell ATAC-seq maps the comprehensive and dynamic chromatin accessibility landscape of CAR-T cell dysfunction.

Area of Science:

• Immunology
• Cancer Biology
• Epigenetics

Background:

• Chimeric antigen receptor T cell (CAR-T) therapy shows promise for hematopoietic malignancies but faces challenges like relapse and poor persistence due to CAR-T cell exhaustion.
• The underlying mechanisms of CAR-T cell exhaustion and strategies to mitigate it remain largely unknown, hindering therapeutic efficacy.

Purpose of the Study:

• To elucidate the epigenetic mechanisms driving CAR-T cell exhaustion during tumor cell stimulation.
• To identify key regulatory factors involved in CAR-T cell exhaustion.
• To explore therapeutic strategies targeting these factors to enhance CAR-T cell function.

Main Methods:

• Single-cell ATAC-seq (scATAC-seq) was employed to map the dynamic chromatin accessibility landscape of CAR-T cells upon tumor cell co-culture.
• Analysis of differential chromatin accessibility and transcription factor (TF) motif accessibility identified regulatory networks.
• scATAC-seq was performed on patient-derived CAR-T cells to validate findings.

Main Results:

• CAR-T cells exhibited rapid differentiation and increased exhaustion after in vitro co-culture with tumor cells.
• Distinct TF networks were identified, coordinating CAR-T cell exhaustion.
• BATF and IRF4 were identified as pivotal regulators of CAR-T cell exhaustion in both experimental and patient-derived CAR-T cells.
• Knockdown of BATF or IRF4 enhanced CAR-T cell killing ability, reduced exhaustion, and prolonged in vivo persistence.

Conclusions:

• This study uncovers the epigenetic regulatory mechanisms underlying CAR-T cell exhaustion.
• BATF and IRF4 are critical regulators of CAR-T cell exhaustion.
• Targeting BATF and IRF4 presents a promising strategy for engineering improved CAR-T cell therapies with enhanced clinical benefits.