Inhibition of the FOXO1 transcription factor (TF) in CAR T cells reduced expansion, downregulated memory markers, and induced an exhaustion gene signature. Conversely, overexpression of FOXO1, but not the related TF TCF1, induced a surface memory phenotype and a naive-like, non-exhausted gene signature, leading to significant tumor control in humanized mouse models of leukemia and osteosarcoma. A “regulon” of genes modulated by FOXO1 was found to be enriched in CAR T cell products of responding CLL patients, while the regulon and FOXO1 epigenetic signature were enhanced in B-ALL patients with durable CAR T cell persistence.
Contributed by Morgan Janes
ABSTRACT: A major limitation of chimeric antigen receptor (CAR) T cell therapies is the poor persistence of these cells in vivo(1). The expression of memory-associated genes in CAR T cells is linked to their long-term persistence in patients and clinical efficacy(2-6), suggesting that memory programs may underpin durable CAR T cell function. Here we show that the transcription factor FOXO1 is responsible for promoting memory and restraining exhaustion in human CAR T cells. Pharmacological inhibition or gene editing of endogenous FOXO1 diminished the expression of memory-associated genes, promoted an exhaustion-like phenotype and impaired the antitumour activity of CAR T cells. Overexpression of FOXO1 induced a gene-expression program consistent with T cell memory and increased chromatin accessibility at FOXO1-binding motifs. CAR T cells that overexpressed FOXO1 retained their function, memory potential and metabolic fitness in settings of chronic stimulation, and exhibited enhanced persistence and tumour control in vivo. By contrast, overexpression of TCF1 (encoded by TCF7) did not enforce canonical memory programs or enhance the potency of CAR T cells. Notably, FOXO1 activity correlated with positive clinical outcomes of patients treated with CAR T cells or tumour-infiltrating lymphocytes, underscoring the clinical relevance of FOXO1 in cancer immunotherapy. Our results show that overexpressing FOXO1 can increase the antitumour activity of human CAR T cells, and highlight memory reprogramming as a broadly applicable approach for optimizing therapeutic T cell states.
Author Info: (1) Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. (2) Department of Pediatrics, Perelman School of Medicine,
Author Info: (1) Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. (2) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (3) Department of Pathology, Stanford University, Stanford, CA, USA. Department of Bioengineering, Stanford University, Stanford, CA, USA. Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. (4) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (5) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (6) Department of Pathology, Stanford University, Stanford, CA, USA. Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. Department of Genetics, Stanford University, Stanford, CA, USA. Genentech, South San Francisco, CA, USA. (7) Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. (8) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (9) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (10) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (11) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (12) Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (13) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (14) Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. (15) Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. (16) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (17) Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. (18) Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. (19) Department of Genetics, Stanford University, Stanford, CA, USA. (20) Department of Pathology, Stanford University, Stanford, CA, USA. Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. (21) Department of Pathology, Stanford University, Stanford, CA, USA. Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. (22) Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (23) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (24) Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (25) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA. Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (26) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA. Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (27) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA. Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (28) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA. (29) Department of Pathology, Stanford University, Stanford, CA, USA. Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. (30) Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. (31) Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. (32) Department of Pathology, Stanford University, Stanford, CA, USA. Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. (33) Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. cmackall@stanford.edu. Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. cmackall@stanford.edu. Department of Pediatrics, Stanford University, Stanford, CA, USA. cmackall@stanford.edu. Department of Medicine, Stanford University, Stanford, CA, USA. cmackall@stanford.edu. (34) Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. weberew@chop.edu. Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. weberew@chop.edu. Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. weberew@chop.edu. Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA. weberew@chop.edu. Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. weberew@chop.edu. Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. weberew@chop.edu.
