One of the things we wonder about a lot in biology is what is going on inside a cell. We have many ways to get at partial answers — Western blots, GFP fusions, transcriptional profiling, various proteomic techniques — and the number and power of these approaches is increasing. Here’s a new window on the internal state of a cell that makes use of a fundamental process of biology: the presentation of peptides by the class I MHC complex (Caron et al. 2011. The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation. Mol. Syst. Biol. 7 533-547, doi:10.1038msb.2011.68).
To understand what’s going on here you need to know a little about the amazing mechanisms that underlie an immune response. One of the problems the immune system has to solve is that viruses live inside cells, so in the early stages of a viral infection there may be little to see, and little for the immune system to respond to, in the extracellular environment. And so, conveniently, we have evolved a system to allow the immune system to look inside the cell. For historical reasons it’s called the Major Histocompatibility Complex class I, or MHC class I — it was discovered as a genetic locus that controlled the rejection of skin grafts in mice (hence histocompatibility), by George Snell. Basically what MHC class I molecules do is to go fishing inside the cell for peptides of a certain length, which are required to be from proteins that are made within the cell. These peptides are then captured in a “bear trap”-like structure at the top of the MHC molecule (which I have sketched here), transported to the cell surface, and offered up for recognition by T lymphocytes.
You don’t really need to know about the other parts of this system for the purposes of discussing this paper, but thanks to a mechanism called “tolerance”, briefly touched on here, T lymphocytes generally manage not to respond to peptides that come from proteins made by the host — that’s you. Instead, they focus on the foreign peptides, which are presumed to originate from viral proteins. The point to remember is this: the MHC itself isn’t selective for viral peptides, but brings a broad sampling of what’s inside the cell to the cell surface. It’s not an unbiased sample; peptides from some proteins are over-represented, others under-represented, and specific arrangements of amino acids are preferred for binding. But it offers a view of what’s going on inside the cell that is hard to get any other way. The question is, what is this view telling us? Caron et al. set out to answer this question by using a drug to manipulate the internal state of the cell, and looking with mass spec to see what happens to the peptides presented on MHC as a result.
The drug they used was rapamycin, which targets the creatively named “mammalian target of rapamycin” (mTOR), a serine/threonine kinase that sits at the nexus of a remarkable number of signaling pathways. Inputs to mTOR include growth factors, amino acids, and cellular energy; outputs include changes in translation, transcription, cellular metabolism, autophagy, energy homeostasis, and cell growth. If a method of detecting cell state changes is going to work on anything, it had better work on this. And it does. Of over 400 MHC-binding peptides that Caron et al. detected and identified at the cell surface, about half change in abundance in response to rapamycin treatment (and a few peptides appear that weren’t detectable before). When the authors looked at changes in transcription, the peptide changes and mRNA changes didn’t match: but when they looked at pathways, all the changes mapped to the same functional areas: proliferation, protein transport, DNA replication and transcription — all pathways that are controlled by mTOR. So transcriptional profiling is one window on what’s happening, and MHC-binding peptide profiling offers a second window that’s related but distinct.
Caron et al. dug a bit deeper into where the changes in peptide presentation are coming from, and came to the conclusion that, while changes in gene transcription do have an effect, changes in post-translational processing are considerably more important. In one case that they studied in detail, that of the mTOR-binding protein Rictor, the increase in the abundance of Rictor-derived peptides presented by the MHC seems to be due to an increase in mistakes in the process of translation — producing “defective ribosomal products” (DRiPs) that are rapidly degraded and may be preferentially presented. Again, these are changes that are hard to observe any other way.
Some of you may be wondering what the immune system itself makes of these changes. The easiest way to ask this is to look at whether the peptides that are undetectable in the absence of rapamycin, but appear in response to rapamycin treatment, are immunogenic. They can be — admittedly Caron et al. hit this question with a hammer by coating dendritic cells (the cells that are best at evoking immune responses) with synthetic peptide, then injecting the peptide-coated cells into mice. It’s unclear how important immune responses to peptide changes in response to signaling or drugs are likely to be, though there is good evidence that such changes can be important in the reaction of the immune system to cancer cells. In any case, whatever the effect on immunity, peptide presentation by the MHC now offers us a novel way to gain insight into changing network composition and behavior within the cell.
Caron E, Vincent K, Fortier MH, Laverdure JP, Bramoullé A, Hardy MP, Voisin G, Roux PP, Lemieux S, Thibault P, & Perreault C (2011). The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation. Molecular Systems Biology, 7 PMID: 21952136