Alex Beckett

All Publications

• CD47 expression is critical for CAR T-cell survival in vivo JOURNAL FOR IMMUNOTHERAPY OF CANCER Beckett, A. N., Chockley, P., Pruett-Miller, S. M., Nguyen, P., Vogel, P., Sheppard, H., Krenciute, G., Gottschalk, S., DeRenzo, C. 2023; 11 (3)

  Abstract

  CD47 is an attractive immunotherapeutic target because it is highly expressed on multiple solid tumors. However, CD47 is also expressed on T cells. Limited studies have evaluated CD47-chimeric antigen receptor (CAR) T cells, and the role of CD47 in CAR T-cell function remains largely unknown.Here, we describe the development of CD47-CAR T cells derived from a high affinity signal regulatory protein α variant CV1, which binds CD47. CV1-CAR T cells were generated from human peripheral blood mononuclear cells and evaluated in vitro and in vivo. The role of CD47 in CAR T-cell function was examined by knocking out CD47 in T cells followed by downstream functional analyses.While CV1-CAR T cells are specific and exhibit potent activity in vitro they lacked antitumor activity in xenograft models. Mechanistic studies revealed CV1-CAR T cells downregulate CD47 to overcome fratricide, but CD47 loss resulted in their failure to expand and persist in vivo. This effect was not limited to CV1-CAR T cells, since CD47 knockout CAR T cells targeting another solid tumor antigen exhibited the same in vivo fate. Further, CD47 knockout T cells were sensitive to macrophage-mediated phagocytosis.These findings highlight that CD47 expression is critical for CAR T-cell survival in vivo and is a 'sine qua non' for successful adoptive T-cell therapy.

  View details for DOI 10.1136/jitc-2022-005857

  View details for Web of Science ID 000955922200017

  View details for PubMedID 36918226

  View details for PubMedCentralID PMC10016274

• Disruption of NSD1 in head and neck cancer promotes favorable chemotherapeutic responses linked to hypomethylation. Molecular cancer therapeutics Bui, N., Huang, J. K., Bojorquez-Gomez, A., Licon, K., Sanchez, K. S., Tang, S. N., Beckett, A. N., Wang, T., Zhang, W., Shen, J. P., Kreisberg, J. F., Ideker, T. 2018

  Abstract

  Human papillomavirus (HPV) negative head and neck squamous cell carcinoma (HNSCC) represents a distinct classification of cancer with poor expected outcomes. Of the 11 genes recurrently mutated in HNSCC, we identify a singular and substantial survival advantage for mutations in the gene encoding Nuclear Set Domain Containing Protein 1 (NSD1), a histone methyltransferase altered in approximately 10% of patients. This effect, a 55% decrease in risk of death in NSD1-mutated versus non-mutated patients, can be validated in an independent cohort. NSD1 alterations are strongly associated with widespread genome hypomethylation in the same tumors, to a degree not observed for any other mutated gene. To address whether NSD1 plays a causal role in these associations, we use CRISPR-Cas9 to disrupt NSD1 in HNSCC cell lines and find that this leads to substantial CpG hypomethylation and sensitivity to cisplatin, a standard chemotherapy in head and neck cancer, with a 40 - 50% decrease in IC50. Such results are reinforced by a survey of 1,001 cancer cell lines, in which loss-of-function NSD1 mutations have an average 23% decrease in cisplatin IC50 compared to cell lines with wild type NSD1. This study identifies a favorable subtype of head and neck cancer linked to NSD1 mutation, hypomethylation and cisplatin sensitivity.

  View details for DOI 10.1158/1535-7163.MCT-17-0937

  View details for PubMedID 29636367

• Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nature methods Shen, J. P., Zhao, D., Sasik, R., Luebeck, J., Birmingham, A., Bojorquez-Gomez, A., Licon, K., Klepper, K., Pekin, D., Beckett, A. N., Sanchez, K. S., Thomas, A., Kuo, C. C., Du, D., Roguev, A., Lewis, N. E., Chang, A. N., Kreisberg, J. F., Krogan, N., Qi, L., Ideker, T., Mali, P. 2017; 14 (6): 573-576

  Abstract

  We developed a systematic approach to map human genetic networks by combinatorial CRISPR-Cas9 perturbations coupled to robust analysis of growth kinetics. We targeted all pairs of 73 cancer genes with dual guide RNAs in three cell lines, comprising 141,912 tests of interaction. Numerous therapeutically relevant interactions were identified, and these patterns replicated with combinatorial drugs at 75% precision. From these results, we anticipate that cellular context will be critical to synthetic-lethal therapies.

  View details for DOI 10.1038/nmeth.4225

  View details for PubMedID 28319113

  View details for PubMedCentralID PMC5449203