Mandal et al. used “structural surfaceomics” – a novel approach combining cross-linking mass spectrometry and glycoprotein surface capture – to discover cell surface proteins with cancer-specific conformations. 2390 peptides were identified on Nomo1 AML cells, and manual mapping/mAb analysis identified the activated integrin β2 integrin conformation as widely expressed on AML cells. Recombinant antibodies to the active conformation and corresponding scFV-CD28 CAR T cells were generated. The CAR T cells mediated cytotoxicity of AML cells in vitro, and in mice, had a favorable safety profile and showed efficacy against AML cells and patient-derived xenografts.
Contributed by Paula Hochman
ABSTRACT: Safely expanding indications for cellular therapies has been challenging given a lack of highly cancer-specific surface markers. Here we explore the hypothesis that tumor cells express cancer-specific surface protein conformations that are invisible to standard target discovery pipelines evaluating gene or protein expression, and these conformations can be identified and immunotherapeutically targeted. We term this strategy integrating cross-linking mass spectrometry with glycoprotein surface capture 'structural surfaceomics'. As a proof of principle, we apply this technology to acute myeloid leukemia (AML), a hematologic malignancy with dismal outcomes and no known optimal immunotherapy target. We identify the activated conformation of integrin β2 as a structurally defined, widely expressed AML-specific target. We develop and characterize recombinant antibodies to this protein conformation and show that chimeric antigen receptor T cells eliminate AML cells and patient-derived xenografts without notable toxicity toward normal hematopoietic cells. Our findings validate an AML conformation-specific target antigen and demonstrate a tool kit for applying these strategies more broadly.
Author Info: (1) Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. (2) Department of Laboratory Medicine, University of California San Francisco
Author Info: (1) Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. (2) Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. (3) Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA. (4) The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. School of Pharmacy, University of Waterloo, Kitchener, Ontario, Canada. (5) Institute for Systems Biology, Seattle, WA, USA. (6) Department of Pediatrics, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA. Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California San Francisco, San Francisco, CA, USA. (7) Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. (8) Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. (9) The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. (10) Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle, Germany. (11) Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. (12) Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. (13) UCSF/Gladstone Institute for Genomic Immunology, San Francisco, CA, USA. (14) Department of Pediatrics, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA. Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. (15) Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital-Texas Children's Hospital, Houston, TX, USA. (16) Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital-Texas Children's Hospital, Houston, TX, USA. (17) Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. (18) Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA. (19) Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. (20) Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. (21) Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. (22) Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. (23) Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. (24) Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. (25) Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. (26) Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA. (27) Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital-Texas Children's Hospital, Houston, TX, USA. (28) UCSF/Gladstone Institute for Genomic Immunology, San Francisco, CA, USA. Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA. (29) Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle, Germany. (30) Department of Pediatrics, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA. (31) Department of Pediatrics, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA. Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. (32) Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA. (33) Institute for Systems Biology, Seattle, WA, USA. (34) The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. School of Pharmacy, University of Waterloo, Kitchener, Ontario, Canada. (35) Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA. (36) Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. arun.wiita@ucsf.edu. Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. arun.wiita@ucsf.edu. Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA. arun.wiita@ucsf.edu. Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA. arun.wiita@ucsf.edu.
