Alexander Eric Doan

All Publications

• FOXO1 is a master regulator of memory programming in CAR T cells. Nature Doan, A. E., Mueller, K. P., Chen, A. Y., Rouin, G. T., Chen, Y., Daniel, B., Lattin, J., Markovska, M., Mozarsky, B., Arias-Umana, J., Hapke, R., Jung, I. Y., Wang, A., Xu, P., Klysz, D., Zuern, G., Bashti, M., Quinn, P. J., Miao, Z., Sandor, K., Zhang, W., Chen, G. M., Ryu, F., Logun, M., Hall, J., Tan, K., Grupp, S. A., McClory, S. E., Lareau, C. A., Fraietta, J. A., Sotillo, E., Satpathy, A. T., Mackall, C. L., Weber, E. W. 2024

  Abstract

  A major limitation of chimeric antigen receptor (CAR) T cell therapies is the poor persistence of these cells in vivo1. The expression of memory-associated genes in CAR T cells is linked to their long-term persistence in patients and clinical efficacy2-6, 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.

  View details for DOI 10.1038/s41586-024-07300-8

  View details for PubMedID 38600391

  View details for PubMedCentralID 8900215

• The replication enhancer crtS depends on transcription factor Lrp for modulating binding of initiator RctB to ori2 of Vibrio cholerae. Nucleic acids research Doan, A., Chatterjee, S., Kothapalli, R., Khan, Z., Sen, S., Kedei, N., Jha, J. K., Chattoraj, D. K., Ramachandran, R. 2024; 52 (2): 708-723

  Abstract

  Replication of Vibrio cholerae chromosome 2 (Chr2) initiates when the Chr1 locus, crtS (Chr2 replication triggering site) duplicates. The site binds the Chr2 initiator, RctB, and the binding increases when crtS is complexed with the transcription factor, Lrp. How Lrp increases the RctB binding and how RctB is subsequently activated for initiation by the crtS-Lrp complex remain unclear. Here we show that Lrp bends crtS DNA and possibly contacts RctB, acts that commonly promote DNA-protein interactions. To understand how the crtS-Lrp complex enhances replication, we isolated Tn-insertion and point mutants of RctB, selecting for retention of initiator activity without crtS. Nearly all mutants (42/44) still responded to crtS for enhancing replication, exclusively in an Lrp-dependent manner. The results suggest that the Lrp-crtS controls either an essential function or more than one function of RctB. Indeed, crtS modulates two kinds of RctB binding to the origin of Chr2, ori2, both of which we find to be Lrp-dependent. Some point mutants of RctB that are optimally modulated for ori2 binding without crtS still remained responsive to crtS and Lrp for replication enhancement. We infer that crtS-Lrp functions as a unit, which has an overarching role, beyond controlling initiator binding to ori2.

  View details for DOI 10.1093/nar/gkad1111

  View details for PubMedID 38000366

  View details for PubMedCentralID PMC10810183

• FOXO1 is a master regulator of CAR T memory programming. Research square Doan, A., Mueller, K. P., Chen, A., Rouin, G. T., Daniel, B., Lattin, J., Chen, Y., Mozarsky, B., Markovska, M., Arias-Umana, J., Hapke, R., Jung, I., Xu, P., Klysz, D., Bashti, M., Quinn, P. J., Sandor, K., Zhang, W., Hall, J., Lareau, C., Grupp, S. A., Fraietta, J. A., Sotillo, E., Satpathy, A. T., Mackall, C. L., Weber, E. W. 2023

  Abstract

  Poor CAR T persistence limits CAR T cell therapies for B cell malignancies and solid tumors1,2. The expression of memory-associated genes such as TCF7 (protein name TCF1) is linked to response and long-term persistence in patients3-7, thereby implicating memory programs in therapeutic efficacy. Here, we demonstrate that the pioneer transcription factor, FOXO1, is responsible for promoting memory programs and restraining exhaustion in human CAR T cells. Pharmacologic inhibition or gene editing of endogenous FOXO1 in human CAR T cells diminished the expression of memory-associated genes, promoted an exhaustion-like phenotype, and impaired antitumor activity in vitro and in vivo. FOXO1 overexpression induced a gene expression program consistent with T cell memory and increased chromatin accessibility at FOXO1 binding motifs. FOXO1-overexpressing cells retained function, memory potential, and metabolic fitness during settings of chronic stimulation and exhibited enhanced persistence and antitumor activity in vivo. In contrast, TCF1 overexpression failed to enforce canonical memory programs or enhance CAR T cell potency. Importantly, endogenous FOXO1 activity correlated with CAR T and TIL responses in patients, underscoring its clinical relevance in cancer immunotherapy. Our results demonstrate that memory reprogramming through FOXO1 can enhance the persistence and potency of human CAR T cells and highlights the utility of pioneer factors, which bind condensed chromatin and induce local epigenetic remodeling, for optimizing therapeutic T cell states.

  View details for DOI 10.21203/rs.3.rs-2802998/v1

  View details for PubMedID 37986944

  View details for PubMedCentralID PMC10659532

• daf-16/FoxO promotes gluconeogenesis and trehalose synthesis during starvation to support survival ELIFE Hibshman, J. D., Doan, A. E., Moore, B. T., Kaplan, R. W., Hung, A., Webster, A. K., Bhatt, D. P., Chitrakar, R., Hirschey, M. D., Baugh, L. 2017; 6

  Abstract

  daf-16/FoxO is required to survive starvation in Caenorhabditis elegans, but how daf-16IFoxO promotes starvation resistance is unclear. We show that daf-16/FoxO restructures carbohydrate metabolism by driving carbon flux through the glyoxylate shunt and gluconeogenesis and into synthesis of trehalose, a disaccharide of glucose. Trehalose is a well-known stress protectant, capable of preserving membrane organization and protein structure during abiotic stress. Metabolomic, genetic, and pharmacological analyses confirm increased trehalose synthesis and further show that trehalose not only supports survival as a stress protectant but also serves as a glycolytic input. Furthermore, we provide evidence that metabolic cycling between trehalose and glucose is necessary for this dual function of trehalose. This work demonstrates that daf-16/FoxO promotes starvation resistance by shifting carbon metabolism to drive trehalose synthesis, which in turn supports survival by providing an energy source and acting as a stress protectant.

  View details for DOI 10.7554/eLife.30057

  View details for Web of Science ID 000413726200001

  View details for PubMedID 29063832

  View details for PubMedCentralID PMC5655125