Functional genomics identifies N-acetyllactosamine extension of complex N-glycans as a mechanism to evade lysis by natural killer cells
Xiaoxuan Zhuang,
James Woods,
Yanlong Ji,
Sebastian Scheich,
Fei Mo,
Sumati Rajagopalan,
Zana A. Coulibaly,
Matthias Voss,
Henning Urlaub,
Louis M. Staudt,
Kuan-Ting Pan,
Eric O. Long
Affiliations
Xiaoxuan Zhuang
Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Corresponding author
James Woods
Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
Yanlong Ji
Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
Sebastian Scheich
Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Fei Mo
National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
Sumati Rajagopalan
Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
Zana A. Coulibaly
Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Matthias Voss
Institute of Biochemistry, Kiel University, 24118 Kiel, Germany
Henning Urlaub
Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
Louis M. Staudt
Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Kuan-Ting Pan
Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
Eric O. Long
Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; Corresponding author
Summary: Natural killer (NK) cells are primary defenders against cancer precursors, but cancer cells can persist by evading immune surveillance. To investigate the genetic mechanisms underlying this evasion, we perform a genome-wide CRISPR screen using B lymphoblastoid cells. SPPL3, a peptidase that cleaves glycosyltransferases in the Golgi, emerges as a top hit facilitating evasion from NK cytotoxicity. SPPL3-deleted cells accumulate glycosyltransferases and complex N-glycans, disrupting not only binding of ligands to NK receptors but also binding of rituximab, a CD20 antibody approved for treating B cell cancers. Notably, inhibiting N-glycan maturation restores receptor binding and sensitivity to NK cells. A secondary CRISPR screen in SPPL3-deficient cells identifies B3GNT2, a transferase-mediating poly-LacNAc extension, as crucial for resistance. Mass spectrometry confirms enrichment of N-glycans bearing poly-LacNAc upon SPPL3 loss. Collectively, our study shows the essential role of SPPL3 and poly-LacNAc in cancer immune evasion, suggesting a promising target for cancer treatment.
