## Archive for May, 2016

### Hepatitis C

May 29, 2016

I once previously wrote something about hepatitis C in this blog which was directed to the mathematical modelling aspects. Here I want to write about the disease itself. This has been stimulated by talks I heard at a meeting of the Mainzer Medizinische Gesellschaft. The speakers were Ralf Bartenschlager from Heidelberg and and Stefan Zeuzem from Frankfurt. The first speaker is a molecular biologist who has made important contributions to the understanding of the structure and life cycle of the virus. For this work he got the 2015 Robert Koch prize together with Charles Rice from the Rockefeller University. The second speaker is a clinician.

Hepatitis C is transmitted by blood to blood contact. According to Zeuzem the main cause of the spread of this disease in developed countries is intravenous drug use. Before there was a test for the disease it was also spread via blood transfusions. (At one time the risk of infection with hepatitis due to a blood transfusion was 30%. This was mainly hepatitis B and by the time of discovery of hepatitis C, when the risk from hepatitis B had essentially been eliminated, it had dropped to 5%.) He also mentioned that there is a very high rate of infection in certain parts of Egypt due to the use of unsterilized needles in the treatment of other diseases. Someone asked how the disease could have survived before there were injections. He did not give a definitive answer but he did mention that while heterosexual contacts generally carry little risk of infection with this virus homosexual contacts between men do carry a significant risk. The disease typically becomes chronic and has few if any symptoms for many years. It does have dramatic long-term effects, namely cirrhosis and cancer of the liver. He showed statistics illustrating how public health policies have influenced the spread of the disease in different countries. The development in France has been much more favourable (with less cases) than in Germany, apparently due to a publicity campaign as a result of political motives with no direct relevance to the disease. The development in the UK has been much less favourable than it has even in Germany due an almost complete lack of publicity on the theme for a long time. The estimated number of people infected in Germany is 500000. The global number is estimated as 170 million.

There has been a dramatic improvement in the treatment of hepatitis C in the past couple of years and this was the central theme of the talks. A few years ago the situation was as follows. Drugs (a combination of ribavirin and interferon $\alpha$) could be used to eliminate the virus in a significant percentage of patients, particularly for some of the sub-types of the virus. The treatment lasted about a year and was accompanied by side effects that were so severe that there was a serious risk of patients breaking it off. Now the treatment only lasts a few weeks, it cures at least 95% of the patients and in many situations 99% of them. The side effects of the new treatments are moderate. There is just one problem remaining: the drugs for the best available treatment are sold for extremely high prices. The order of magnitude is 100000 euros for a treatment. Zeuzem explained various aspects of the dynamics which has led to these prices and the circumstances under which they might be reduced in the future. In general this gave a rather depressing picture of the politics of health care relating to the approval and prescription of new drugs.

Let me get back to the scientific aspects of the theme, as explained by Bartenschlager. A obvious question to ask is: if hepatitis C can essentially be cured why does HIV remain essentially incurable despite the huge amount of effort and money spent on trying to find a treatment? The simple answer seems to be that HIV can hide while HCV cannot. Both these viruses have an RNA genome. Since the copying of RNA is relatively imprecise they both have a high mutation rate. This leads to a high potential for the development of drug resistance. This problem has nevertheless been overcome for HCV. Virus particles are continually being destroyed by the immune system and for the population to survive new virus particles must be produced in huge numbers. This is done by the liver cells. This heavy burden kills the liver cells after a while but the liver is capable of regenerating, i.e, replacing these cells. The liver has an impressive capability to survive this attack but every system has its limits and eventually, after twenty or thirty years, the long-term effects already mentioned develop. An essential difference between HIV and HCV is that the RNA of HCV can be directly read by ribosomes to produce viral proteins. By contrast, the RNA of HIV is used as a template to produce DNA by the enzyme reverse transcriptase and this DNA is integrated into the DNA of the cell. This integrated DNA (known as the provirus) may remain inactive, not leading to production of protein. As long as this is the case the virus is invisible to the immune system. This is one way the virus can hide. Moreover the cell can divide producing new cells also containing the provirus. There is also another problem. The main target of HIV are the T-helper cells. However the virus can also infect other cells such as macrophages or dendritic cells and the behaviour of the virus in these other cells is different from that in T-helper cells. It is natural that a treatment should be optimized for what happens in the typical host cell and this may be much less effective in the other cell types. This means that the other cells may serve as a reservoir for the virus in situations where the population is under heavy pressure from the immune system or drug treatment. This is a second sense in which the virus can hide.

Some of the recent drugs used to treat HCV are based on ideas developed for the treatment of HIV. For instance a drug of this kind may inhibit certain of the enzymes required for the reproduction of the virus. There is one highly effective drug in the case of HCV which works in a different way. The hepatitis C virus produces one protein which has no enzymatic activity and it is at first sight hard to see what use this could be for the virus. What it in fact does is to act as a kind of docking station which organizes proteins belonging to the cell into a factory for virus production.

The hepatitis C virus is a valuable example which illustrates the relations between various aspects of medical progress: improvement in scientific understanding, exploitation of that information for drug design, political problems encountered in getting an effective drug to the patients who need it. Despite the negative features which have been mentioned it is the subject of a remarkable success story.

### Flying to Copenhagen without a carpet

May 11, 2016

This semester I have a sabbatical and I am profiting from it by travelling more than I usually do. At the moment I am visiting the group of Carsten Wiuf and Elisenda Feliu at the University of Copenhagen for two weeks. The visit here also gives me the opportunity to discuss with people at the Niels Bohr Institute. Note that the authors of the paper I quoted in the post on NF$\kappa$B were at the NBI when they wrote it and in particular Mogens Jensen is still there now. I gave a talk on some of my work on the Calvin cycle at NBI today. Afterwards I talked to Mogens and one of his collaborators and found out that he is still very active in modelling this system.

I was thinking about my previous visits to Copenhagen and, in particular, that the first one was on a flying carpet. The background to this is that when I was seven years old I wrote a story in school with the title ‘The Magic Carpet’. I do not have the text any more but I know it appeared in the School Magazine that year. In my own version there was also a picture which I will say more about later. But first something about the story, of which I was the hero. I bought the carpet in Peshawar and used it to visit places in the world I was interested in. For some reason I no longer know I had a great wish at that time to visit Copenhagen. Perhaps it was due to coming into contact with stories of Hans Christian Andersen. In any case it is clear that having the chance this was one of the first places I visited using the magic carpet. The picture which I drew showed something closer to home. There I can be seen sitting on the carpet, wearing the blue jersey which was my favourite at that time, while the carpet bent upwards so as to just pass over the tip of the spire of St. Magnus Cathedral in Kirkwall. In the story it was also related that one of the effects of my journey was a newspaper article reporting a case of ‘mass hallucination’. I think my teachers were impressed at my using this phrase at my age. They might have been less impressed if they had known my source for this, which was a Bugs Bunny cartoon.

During my next visit to Copenhagen in 2008 (here I am not counting changing planes there on the way to Stockholm, which I did a few times) I was at a conference at the Niels Bohr Institute in my old research field of mathematical relativity and I gave a talk in that area. Little did I think I would return there years later and talk about something completely different. I remember that there was a photo in the main lecture room where many of the founders of quantum mechanics are sitting in the first row. From my own point of view I am happy that another person who can be seen there is Max Delbrück, a shining example of a switch from physics to biology. My next visit to Copenhagen was for the conference which I wrote about in a previous post. It was at the University. Since that a lot has happened with chemical reaction network theory and with my understanding of it. The lecture course I gave means that some of the points I mentioned in my post at that time are things I have since come to understand in some depth. I look forward to working on projects in that area with people here in the coming days.

### NFκB

May 1, 2016

NF$\kappa$B is a transcription factor, i.e. a protein which can bind to DNA and cause a particular gene to be read more or less often. This means that more or less of a certain protein is produced and this changes the behaviour of the cell. The full name of this transcription factor is ‘nuclear factor, $\kappa$-light chain enhancer of B cells’. The term ‘nuclear factor’ is clear. The substance is a transcription factor and to bind to DNA it has to enter the nucleus. NF$\kappa$B is found in a wide variety of different cells and its association with B cells is purely historical. It was found in the lab of David Baltimore during studies of the way in which B cells are activated. It remains to explain the $\kappa$. B cells produce antibodies each of which consists of two symmetrical halves. Each half consists of a light and a heavy chain. The light chain comes in two variants called $\kappa$ and $\lambda$. The choice which of these a cell uses seems to be fairly random. The work in the Baltimore lab had found out that NF$\kappa$B could skew the ratio. I found a video by Baltimore from 2001 about NF$\kappa$B. This is probably quite out of date by now but it contained one thing which I found interesting. Under certain circumstances it can happen that a constant stimulus causing activation of NF$\kappa$B leads to oscillations in the concentration. In the video the speaker mentions ‘odd oscillations’ and comments ‘but that’s for mathematicians to enjoy themselves’. It seems that he did not believe these oscillations to be biologically important. There are reasons to believe that they might be important and I will try to explain why. At the very least it will allow me to enjoy myself.

Let me explain the usual story about how NF$\kappa$B is activated. There are lots of animated videos on Youtube illustrating this but I prefer a description in words. Normally NF$\kappa$B is found in the cytosol bound to an inhibitor I$\kappa$B. Under certain circumstances a complex of proteins called IKK forms. The last K stands for kinase and IKK phosphorylates I$\kappa$B. This causes I$\kappa$B to be ubiquinated and thus marked for degradation (cf. the discussion of ubiquitin here). When it has been destroyed NF$\kappa$B is liberated, moves to the nucleus and binds to DNA. What are the circumstances mentioned above? There are many alternatives. For instance TNF$\alpha$ binds to its receptor, or something stimulates a toll-like receptor. The details are not important here. What is important is that there are many different signals which can lead to the activation of NF$\kappa$B. What genes does NF$\kappa$B bind to when it is activated? Here again there are many possibilities. Thus there is a kind of bow tie configuration where there are many inputs and many outputs which are connected to a single channel of communication. So how is it possible to arrange that when one input is applied, e.g. TNF$\alpha$ the right genes are switched on while another input activates other genes through the same mediator NF$\kappa$B? One possibility is cross-talk, i.e. that this signalling pathway interacts with others. If this cannot account for all the specificity then the remaining possibility is that information is encoded in the signal passing through NF$\kappa$B itself. For example, one stimulus could produce a constant response while another causes an oscillatory one. Or two stimuli could cause oscillatory responses with different frequencies. Evidently the presence of oscillations in the concentration of NF$\kappa$B presents an opportunity for encoding more information than would otherwise be possible. To what extent this really happens is something where I do not have an overview at the moment. I want to learn more. In any case, oscillations have been observed in the NF$\kappa$B system. The primary thing which has been observed to oscillate is the concentration of NF$\kappa$B in the nucleus. This oscillation is a consequence of the movement of the protein between the cytosol and the nucleus. There are various mathematical models for describing these oscillations. As usual in modelling phenomena in cell biology there are models which are very big and complicated. I find it particularly interesting when some of the observations can be explained by a simple model. This is the case for NF$\kappa$B where a three-dimensional model and an explanation of its relations to the more complicated models can be found in a paper by Krishna, Jensen and Sneppen (PNAS 103, 10840). In the three-dimensional model the unknowns are the concentrations of NF$\kappa$B in the nucleus, I$\kappa$B in the cytoplasm and mRNA coding for I$\kappa$B. The oscillations in normal cells are damped but sustained oscillations can be seen in mutated cells or corresponding models.

What is the function of NF$\kappa$B? The short answer is that it has many. On a broad level of description it plays a central role in the phenomenon of inflammation. In particular it leads to production of the cytokine IL-17 which in turn, among other things, stimulates the production of anti-microbial peptides. When these things are absent it leads to a serious immunodeficiency. In one variant of this there is a mutation in the gene coding for NEMO, which is one of the proteins making up IKK. A complete absence of NEMO is fatal before birth but people with a less severe mutation in the gene do occur. There are symptoms due to things which took place during the development of the embryo and also immunological problems, such as the inability to deal with certain bacteria. The gene for NEMO is on the X chromosome so that this disease is usually limited to boys. More details can be found in the book of Geha and Notarangelo mentioned in  a previous post.