HLA-I immunopeptidome profiling of human cells infected with high-containment enveloped viruses

Shira Weingarten-Gabbay; Leah R. Pearlman; Da-Yuan Chen; Susan Klaeger; Hannah B. Taylor; Nicole L. Welch; Derin B. Keskin; Steven A. Carr; Jennifer G. Abelin; Mohsan Saeed; Pardis C. Sabeti

STAR Protocols (Dec 2022)

HLA-I immunopeptidome profiling of human cells infected with high-containment enveloped viruses

Shira Weingarten-Gabbay,
Leah R. Pearlman,
Da-Yuan Chen,
Susan Klaeger,
Hannah B. Taylor,
Nicole L. Welch,
Derin B. Keskin,
Steven A. Carr,
Jennifer G. Abelin,
Mohsan Saeed,
Pardis C. Sabeti

Affiliations

Shira Weingarten-Gabbay: Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA; Corresponding author
Leah R. Pearlman: Broad Institute of MIT and Harvard, Cambridge, MA, USA
Da-Yuan Chen: Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
Susan Klaeger: Broad Institute of MIT and Harvard, Cambridge, MA, USA
Hannah B. Taylor: Broad Institute of MIT and Harvard, Cambridge, MA, USA
Nicole L. Welch: Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Virology, Harvard Medical School, Boston, MA, USA
Derin B. Keskin: Broad Institute of MIT and Harvard, Cambridge, MA, USA; Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
Steven A. Carr: Broad Institute of MIT and Harvard, Cambridge, MA, USA
Jennifer G. Abelin: Broad Institute of MIT and Harvard, Cambridge, MA, USA
Mohsan Saeed: Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
Pardis C. Sabeti: Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA; Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA

Journal volume & issue: Vol. 3, no. 4
p. 101910

Abstract

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Summary: Immunopeptidome profiling of infected cells is a powerful technique for detecting viral peptides that are naturally processed and loaded onto class I human leukocyte antigens (HLAs-I). Here, we provide a protocol for preparing samples for immunopeptidome profiling that can inactivate enveloped viruses while still preserving the integrity of the HLA-I complex. We detail steps for lysate preparation of infected cells followed by HLA-I immunoprecipitation and virus inactivation. We further describe peptide purification for mass spectrometry outside a high-containment facility.For complete details on the use and execution of this protocol, please refer to Weingarten-Gabbay et al. (2021).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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