Published Online: 5 September, 2018 | Supp Info: http://doi.org/10.1084/jem.20180300 Downloaded from jem.rupress.org on September 5, 2018 ARTICLE Rapid CLIP dissociation from MHC II promotes an unusual antigen presentation pathway in autoimmunity Yoshinaga Ito1,2, Orr Ashenberg3, Jason Pyrdol1, Adrienne M. Luoma1,2, Orit Rozenblatt‑Rosen3, Matan Hofree3, Elena Christian3, Lucas Ferrari de Andrade1,2, Rong En Tay1,2, Luc Teyton4, Aviv Regev3, Stephanie K. Dougan1,2, and Kai W. Wucherpfennig1,2 A number of autoimmunity-associated MHC class II proteins interact only weakly with the invariant chain–derived class II– associated invariant chain peptide (CLIP). CLIP dissociates rapidly from I-Ag7 even in the absence of DM, and this property is related to the type 1 diabetes–associated β57 polymorphism. We generated knock-in non-obese diabetic (NOD) mice with a single amino acid change in the CLIP segment of the invariant chain in order to moderately slow CLIP dissociation from I-Ag7. These knock-in mice had a significantly reduced incidence of spontaneous type 1 diabetes and diminished islet infiltration by CD4 T cells, in particular T cells specific for fusion peptides generated by covalent linkage of proteolytic fragments within β cell secretory granules. Rapid CLIP dissociation enhanced the presentation of such extracellular peptides, thus bypassing the conventional MHC class II antigen-processing pathway. Autoimmunity-associated MHC class II polymorphisms therefore not only modify binding of self-peptides, but also alter the biochemistry of peptide acquisition. Introduction The MHC locus plays a central role in susceptibility to many the P9 pocket (Brown et al., 1993; Scott et al., 1998). In contrast, human autoimmune diseases, including type 1 diabetes (T1D; the absence of a negative charge at β57 of DQ8, DQ2, and I-Ag7 Davies et al., 1994; Hu et al., 2015). In many of these diseases, results in a P9 pocket with a positive charge that has a strong the strongest association is observed with particular alleles of preference for negatively charged peptide side chains (Corper et MHC class II (MHC II) genes, providing strong evidence for a al., 2000; Lee et al., 2001; Kim et al., 2004). The major hypothesis critical role of antigen presentation to CD4 T cells. T1D is an ex- for the role of the β57 polymorphism in the pathogenesis of T1D cellent example for this general principle: susceptibility is most has been that it enables binding of pathogenic peptides (Todd et closely associated with certain alleles of the DQB1 gene, in par- al., 1987; Quartey-Papafio et al., 1995). As we will discuss here, ticular those encoding HLA-DQ8 (DQB1*03:02) and HLA-DQ2 the β57 polymorphism also has an impact on the affinity of the (DQB1*02:01; Todd et al., 1987; Concannon et al., 2009). The invariant chain–derived class II–associated invariant chain pep- DQB1*03:02 and DQB1*02:01 alleles share an important polymor- tide (CLIP), and may therefore also modulate the biochemistry phism: position 57 of the β chain encodes a nonaspartic residue of peptide binding. in T1D-associated alleles, but aspartic acid in most other DQB1 MHC II proteins associate with the invariant chain in the ER, alleles. This polymorphism is also relevant for the spontaneous and this complex is targeted to the endosomal compartment, mouse model of T1D in non-obese diabetic (NOD) mice because where the invariant chain is degraded, leaving CLIP in the bind- β57 of I-Ag7 is also a nonaspartic acid residue (serine; Acha-Orbea ing groove (Avva and Cresswell, 1994; Denzin and Cresswell, and McDevitt, 1987). Crystal structures of DQ8, DQ2, and I-Ag7 1995). Textbooks state that H2-DM (abbreviated as DM) induces have demonstrated that this polymorphic position has a major CLIP dissociation and thereby enables binding of peptides gener- impact on the charge of the P9 pocket of the peptide binding ated by proteolysis of exogenous antigens. However, the affinity groove (Corper et al., 2000; Lee et al., 2001; Kim et al., 2004). An of CLIP differs by four orders of magnitude among MHC II pro- aspartic acid at β57 forms a salt bridge with arginine 76 of the DQ teins because many polymorphic residues shape the specificity or I-A α chains, allowing binding of hydrophobic amino acids in of the peptide binding groove (Sette et al., 1995). We previously 1Department of Cancer Immunology and Virology, Dana‑Farber Cancer Institute, Boston, MA; 2Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA; 3Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA; 4Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA. Correspondence to Kai W. Wucherpfennig: kai _wucherpfennig@ dfci .harvard .edu; Stephanie K. Dougan: stephanie _dougan@ dfci .harvard .edu. © 2018 Ito et al. This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http:// www .rupress .org/ terms/ ). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https:// creativecommons .org/ licenses/ by ‑nc ‑sa/ 4 .0/ ). Rockefeller University Press https://doi.org/10.1084/jem.20180300 1 J. Exp. Med. 2018 demonstrated that the diabetes-associated I-Ag7 protein binds Results CLIP with very low affinity, allowing CLIP to rapidly dissociate Knock-in mice with a single amino acid substitution of CLIP in a DM-independent manner at an acidic pH characteristic for have a reduced incidence of T1D the endosomal peptide loading compartment (Hausmann et al., We generated knock-in mice with a single amino acid substitu- 1999). The low affinity of CLIP for I-Ag7 is related to the β57 poly- tion of the P9 anchor of CLIP. The methionine to alanine (ATG to morphism: the hydrophobic P9 anchor of CLIP (methionine) is GCT) substitution was designed to result in a moderate increase a poor fit for the positively charged P9 pocket, and substitution in CLIP affinity for I-Ag7 (Fig. 1, A and B; Hausmann et al., 1999). of the P9 anchor of CLIP to alanine or aspartic acid increases the Peptide binding studies demonstrated very little to no binding affinity of CLIP for I-Ag7. A number of MHC II proteins associated of WT CLIP to I-Ag7 at pH 5.2, which corresponds to the pH of the with human autoimmune diseases have been shown to have a endosomal peptide loading compartment. In contrast, binding low affinity for CLIP (Reed et al., 1997; Patil et al., 2001) . CLIP was clearly detected for I-Ag7 with a serine to aspartic acid mu- was also shown to bind with rather low affinity to HLA-DQ8, tation at position β57 (β S57D), indicating that the disease-asso- and peptide elution studies showed that HLA-DQ2 binds CLIP ciated β57 polymorphism impacts CLIP binding. A single amino in an unusual alternative register with relatively low affinity acid substitution at the P9 position of CLIP from methionine to (Fallang et al., 2008; Wiesner et al., 2008). Both HLA-DQ2 and alanine (M98A) resulted in a moderate increase of CLIP binding HLA-DQ8 also interact only weakly with DM (Fallang et al., 2008; to I-Ag7, while a high-affinity positive control peptide derived Zhou et al., 2016). Rapid CLIP dissociation may enable binding from albumin (Alb 560–574) showed strong binding to I-Ag7, as of peptides in compartments that lack DM and may also favor expected (Fig. 1 C). These results were consistent with previous g7 presentation of low-affinity peptides that are not edited by DM. peptide binding studies with I-A that demonstrated an IC50 of This hypothesis is consistent with data demonstrating that the >125 µM for WT CLIP, 15 µM for CLIP M98A, and 0.5 µM for CLIP bound repertoire of peptides has a lower average half-life for M98D at an acidic pH. Previous work had also demonstrated that I-Ag7 compared with other I-A proteins (Carrasco-Marin et al., CLIP binds to I-Ag7 at neutral pH, which is relevant for assembly 1996; Kropshofer et al., 1996). of I-Ag7 with invariant chain in the ER (Hausmann et al., 1999). These alterations in the biochemistry of peptide binding by The CLIP M98A mutation was introduced directly into the ge- I-Ag7 may have a significant impact on the pathogenesis of T1D nome of WT NOD mice by micro-injection of fertilized oocytes in NOD mice. There is increasing evidence for the importance with Cas9 mRNA, a guide RNA (gRNA) targeting the invariant of unique types of antigens that are released as proteolytic frag- chain gene (Cd74) and a single-stranded DNA oligonucleotide for ments by pancreatic β cells. One of the major identified antigens homology-directed repair of the double-strand break introduced is the insulin B9-23 peptide, which binds in at least two registers by Cas9. A small molecule inhibitor of nonhomologous end join- to I-Ag7 (Daniel et al., 1995; Mohan et al., 2011). Proinsulin under- ing was also coinjected, which was previously shown to reduce goes proteolytic processing in secretory granules of β cells, and off-target lesions and enhance the efficiency of homology-di- proteolytic fragments containing the insulin B9-23 epitope are rected repair (Maruyama et al., 2015). Furthermore, we used a present in these secretory granules (Mohan et al., 2010). Indeed, gRNA with a minimal length of 17 bases, which was shown to CD4 T cells specific for the insulin B12-20 peptide (a lower-affin- greatly diminish the frequency of off-target lesions (Fu et al., ity register) are only activated when APCs are incubated with the 2014).