Pathways of MHC I cross-presentation of exogenous antigens

Abstract

Phagocytes, particularly dendritic cells (DCs), generate peptide-major histocompatibility complex (MHC) I complexes from antigens they have collected from cells in tissues and report this information to CD8 T cells in a process called cross-presentation. This process allows CD8 T cells to detect, respond and eliminate abnormal cells, such as cancers or cells infected with viruses or intracellular microbes. In some settings, cross-presentation can help tolerize CD8 T cells to self-antigens. One of the principal ways that DCs acquire tissue antigens is by ingesting this material through phagocytosis. The resulting phagosomes are key hubs in the cross-presentation (XPT) process and in fact experimentally conferring the ability to phagocytize antigens can be sufficient to allow non-professional antigen presenting cells (APCs) to cross-present. Once in phagosomes, exogenous antigens can be cross-presented (XPTed) through three distinct pathways. There is a vacuolar pathway in which peptides are generated and then bind to MHC I molecules within the confines of the vacuole. Ingested exogenous antigens can also be exported from phagosomes to the cytosol upon vesicular rupture and/or possibly transport. Once in the cytosol, the antigen is degraded by the proteasome and the resulting oligopeptides can be transported to MHC I molecule in the endoplasmic reticulum (ER) (a phagosome-to-cytosol (P2C) pathway) or in phagosomes (a phagosome-to-cytosol-to-phagosome (P2C2P) pathway). Here we review how phagosomes acquire the necessary molecular components that support these three mechanisms and the contribution of these pathways. We describe what is known as well as the gaps in our understanding of these processes.

Keywords: Antigen presentation; Cross-presentation; MHC I; Phagosome.

Fig. 1.

Overview of the Classical MHC I and MHC II Antigen Presentation Pathways. MHC I Presentation. 1) Endogenous proteins are conjugated with ubiquitin. 2) Poly-ubiquitinated proteins are targeted for degradation by proteasomes. 3) The proteasome hydrolyzes the endogenous proteins into oligopeptide fragments. 4) Some of the peptides are transported into the ER by TAP. 5) In the ER, the aminopeptidase, ERAP1 further trims N-extended peptides to mature epitopes (typically 8–9 amino acids long). Peptides of the right length and sequence bind to the empty MHC I molecules that have been retained and stabilized in the ER by the peptide-loading complex (PLC). The PLC is made up of the proteins: calreticulin, tapasin and ERp57. 6–8) The resulting peptide:MHC I complexes dissociate from the PLC and are transported to the cell surface for presentation. MHC II Presentation. 1) In the ER, MHC II molecules assemble and associate with the invariant chain/CD74, which blocks peptide-binding. 2) Sorting sequences on the invariant chain directs the transport of MHC II molecules into endosomes/phagosomes. 3) In these vacuoles, the invariant chain is proteolytically cleaved from the MHC II molecules leaving only the CLIP region bound in the peptide-binding groove. 4) Exogenous antigens are internalized into endosomes and phagosomes. 5) Cathepsins and other proteases hydrolyze antigens in the endosomes/phagosomes into peptides. 6) In order for these peptides to bind to the MHC II molecule, HLA-DM catalyzes the removal of CLIP from the peptide binding groove and its replacement with high affinity peptides. 7,8) The resulting MHC II-peptide complexes are then transported to the cell surface for presentation. (Created with BioRender.com)

Fig. 2.

The Phagosome to Cytosol (P2C) Pathway of Cross Presentation. 1) Exogenous antigen is taken up by an antigen presenting cell through phagocytosis. 2) Nox2 in the phagosome produces ROS, and in DCs, the resulting elevation in pH reduces destruction of antigen by limiting its hydrolysis. 3) The largely intact antigen exits the phagosome into the cytosol potentially through an ERAD-like mechanism, possibly involving Sec61 (black dashed arrow), or through phagosomal rupture, the latter of which may be enhanced by ROS damage to the vacuole’s membrane. Subsequent steps 4–9 are similar to Fig. 1 A. 4) In the cytosol, the antigen is degraded by the proteasome into peptide fragments. 5) Some of the peptide fragments enters the ER through the TAP transporter. 6) Long peptides are trimmed by ERAP1, and then peptides of the right size and sequence bind to MHC I molecules. 7–9) The peptide-MHC I complexes are released from the ER and transported to the cell surface for presentation. Dashed lines indicate steps that are not absolutely certain. (Created with BioRender.com)

Fig. 3.

The Phagosome to Cytosol to Phagosome (P2C2P) Pathway of Cross Presentation. 1) Phagocytosis of an exogenous antigen by an antigen presenting cell. 2) Similar to Fig. 2, the antigen exits the phagosome into the cytosol potentially through phagosomal rupture and/or an ERAD-like mechanism. 3) The antigen is hydrolyzed by the proteasome into peptide fragments. 4) Some of the peptide fragments go back into the phagosome through the TAP transporter. 5) In the phagosome, long peptides are trimmed by the aminopeptidase IRAP and possibly ERAP1. 6) (A) MHC I molecules are delivered to the phagosome from the cell surface, potentially through an endosomal recycling compartment (ERC) increased by TLR signaling, or (B) from the ER, (C) possibly associated with the PLC. Rab39a helps deliver empty MHC I complexes from the ER. Peptides of the right size and sequence then bind to MHC I molecules. It is not clear whether imported peptide-occupied MHC I molecules can exchange peptides in phagosomes. 7) Once the peptide:MHC I complex is formed in the phagosome, it exits and is transported to the cell surface via mechanisms potentially involving the GTPases, Arf6, Rab11 and Rab22. Dashed lines indicate steps that are not absolutely certain. (Created with BioRender.com)

Fig. 4.

The Vacuolar Pathway of Cross Presentation. 1) Exogenous antigen is internalized through phagocytosis. 2) The antigen is cleaved by intraphagosomal proteases, such as Cathepsin S, into peptides and these are potentially further trimmed by the aminopeptidases, IRAP and ERAP1. 3A-C). The peptides of the right size and sequence are bound by MHC I molecules in the phagosome (the potential sources of intraphagosomal MHC I molecules (dashed red arrows) are the same as discussed in Fig. 3). 4,5) Once peptides are loaded onto MHC molecules, the peptide-MHC I complexes will exit the phagosome and are transported for display on the cell surface of the antigen presenting cell as described in Fig. 3. Dashed lines indicate steps that are not absolutely certain. (Created with BioRender.com)