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

doi:10.1016/j.xpro.2022.101910

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

STAR Protoc. 2022 Dec 16;3(4):101910. doi: 10.1016/j.xpro.2022.101910. Epub 2022 Dec 8.

Affiliations

¹ 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. Electronic address: shirawg@broadinstitute.org.
² Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³ Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
⁴ Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Virology, Harvard Medical School, Boston, MA, USA.
⁵ 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.
⁶ 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.

Abstract

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.

Keywords: Immunology; Mass Spectrometry; Microbiology.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Histocompatibility Antigens Class I*
Humans
Mass Spectrometry
Peptides / chemistry
Viruses*

Substances

Histocompatibility Antigens Class I
Peptides

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

Authors

Affiliations

Abstract

Publication types

MeSH terms

Substances

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