So we have the first prize of the 2019 Nobel season, Medicine/Physiology for William Kaelin Jr. (Dana-Farber), Peter Ratcliffe (Oxford), and Gregg Semenza (Johns Hopkins), for their work in cellular adaptation to oxygen levels. This was not one of the outcomes that was in the top of the betting range, but it sure wasn’t in the bottom, either, since these same researchers shared the Lasker Prize in basic medical research for these discoveries in 2016. It’s a worthy discovery and a worthy award, and it makes for a story that touches a lot of other important topics.

Semenza was the discoverer of the hypoxia-inducible factor (HIF) proteins. It was already apparent from the work of several other groups over a century of work that oxygen levels led to changes in things such as red blood cell production, and as genetic explanations came to the fore, it became clear that this was due to altered gene transcription. Most obviously, these were changes in the upregulation of EPO (erythropoetin, the protein that stimulates RBC formation. But how did cells know that oxygen levels were low, and how was this coupled to gene regulation and protein expression? Semenza’s work (and Ratcliffe’s at Oxford) tracked down the (rather long) stretch of the EPO gene that was involved in its complex regulatory regime, and narrowed down to a 50-base pair region that bound a particular transcription factor protein under low oxygen levels. This was HIF, and it became clear once it had been identified that it was part of a general cellular response (and wasn’t just part of EPO production, which happens mostly in the kidney). HIF itself turned out to be a tight complex of two other proteins, one of which (now called HIF1-alpha) is the oxygen-sensitive part of the machinery. (As it has turned out, erythropoiesis is controlled more by a related HIF protein called HIF2-alpha via the EPAS2 gene, but that’s another story that came out of this work).

That leads one, as biology answers do, to ask another question and wonder how HIF1-alpha itself is regulated. A number of groups showed that it apparently wasn’t so much a protein expression-driven process as one that depending on how HIF1-alpha was degraded once it was out there in the cells. Under normal oxygen levels it gets regularly cleared out, but low oxygen levels suppress this and allow it to build up to functional levels. Kaelin and his group had been studying a tumor suppressor gene called VHL, and their work and others began to point toward it being tangled up with HIF function somehow (which is not something you’d have predicted from just looking at either field). Moreover, VHL also was showing interactions with and similarities to proteins that were known to be involved in ubiquitination pathways (a common means of tagging proteins for degradation), and sure enough, the story came together.

Ratcliffe’s group showed that VHL was a key part of HIF degradation, as part of a ubiquitin-ligase complex that marked HIF for clearance by the proteasome. And his lab and Kaelin’s both demonstrated how this was hooked up to oxygen levels: particular proline residues in HIF1-alpha were hydroxylated by prolyl-4-hydroxylase enzymes, which have iron in their catalytic active side and are dependent on oxygen (the very O atoms that get transferred onto the prolines as hydroxy groups). And the hydroxylated form of HIF has a different conformation that allows it to be recognized by VHL: low oxygen levels shut down the hydroxylase enzyme, which stops hydroxylating HIF, which allows it to stop getting recognized by VHL and thus subsequently degraded, which allows its levels to build up to where it can go to the nucleus and bind to the promoter for the EPO gene, which sets off new gene expression. This also allows you to see how tumor biology ties into the HIF story, since solid tumors are almost invariably low in oxygen due to their density and fast metabolism – disrupting their adaptation to these conditions could make them more sensitive to all sorts of other therapy.

The system described above is exactly how the gears and pulleys and chains tend to be hooked together in the cell, but remember that all the components of this system are doing other things the whole time as well: HIF proteins aren’t the only things hydroxylated by that prolyl-4-hydroxylase, VHL recognizes other proteins for degradation, HIF1-alpha binds to many more DNA sites than just the promoter for EPO, and so on. You can draw these pathways out as a single long chain across the page, but the interactions go up and down that page to other proteins and pathways entirely (and likely enough, if you wanted a full picture, would need to come up out of that page and point to three-and four-dimensional interaction networks beyond those, some of which are looped back into the other ones, and on and on. . .) These connections lead to still more ideas and hypotheses, of course – for example, VHL and its role in protein degradation have made it a subject of great interest in the targeted protein degradation field, which is heading off into totally different areas).

The “Advanced Information” section for today’s award (which is excellently done, as usual) will send you down some of those pathways in the HIF and VHL systems, and also provides many references for the papers that announced these various discoveries. The connection to cancer has already been mentioned, and there are also HIF implications for immune function, inflammation, wound healing, and many other processes. This work has naturally identified a number of points where one could imagine pharmaceutical intervention as well, and a great deal of work has gone into those over the last ten to twenty years. But then, a great deal of work has gone into this whole field: low oxygen levels were first shown to increase red blood cell levels in the 1880s! If you want to see how science builds on itself, tracking this story through the decades is a fine example indeed. Congratulations to today’s laureates!