From Renoir to Epigenomics. How we are using the marks on cells’ DNA to study autoimmunity

Luncheon of the boating party
Luncheon of the boating party is an oil on canvas painting by Pierre-Auguste Renoir. It was painted in 1881 and is now at The Phillips Collection in Washington, DC. Image obtained from flickr (CC BY license).

Simple answers to complex questionsAuthorship: Eddie Cano-Gámez.


Autoimmunity from Bosch to Renoir

The painting is called Luncheon of the Boating Party. In it a group of friends are having lunch. At one end of the table a young woman gesticulates while talking to her little dog. There is another woman drinking from a glass and yet another one stares into space, caught in her own thoughts. It is a fine summer afternoon and somehow, despite the immobility of the characters, one can hear the distinctive clattering of glasses and ice cubes. When Pierre-Auguste Renoir painted this scene in 1881, his abilities as an artist were no doubt at their best: he was to become one of the most iconic exponents of French impressionism. Back then, few would’ve thought that only 10 years later Renoir’s arms would be wrapped in bandages and that a personal assistant would need to hand him his paint brushes. Renoir, as many others before and after, became a victim of a condition poorly understood at the time: rheumatoid arthritis.

Renoir is not the only example of arthritis in art or in history. The Portrait of a Youth painted by Sandro Botticelli as early as 1480 could in fact depict a man with juvenile arthritis. And it is possible that even earlier Hieronymus Bosch picked arthritic individuals as some of the subjects for his Procession of the Cripples. Bosch lived 300 years before Renoir, and Renoir 150 years before us. Yet, despite the medical advances of our times, there is still no cure for rheumatoid arthritis. The medications that exist focus only on making quality of life better. Why is this the case? Is finding a cure for rheumatoid arthritis really such a difficult task? And if so, where does the difficulty come from? To understand this, we need to plunge into the depths of autoimmune disease.

portrait of a young man
Portrait of a young man by Sandro Botticelli (1483). Now at the National Gallery of Art (Washington, DC). Image obtained from flickr (CC BY license)

Rheumatoid arthritis is only one of tens of conditions classified as autoimmune diseases. Some others include multiple sclerosis (a brain condition), inflammatory bowel disease (an autoinflammatory condition of the intestines) and lupus (an incredibly complex condition, famously popularised by the TV series House MD). If taken as a group, these diseases affect between 3% and 10% of the population. But, perhaps counterintuitively, it is not the joints, the brain or the intestines which are directly affected in these diseases, but rather something less obvious. What all of these disorders share is a faulty immune system. Under normal circumstances, the immune system attacks pathogens which try to infect us. In autoimmune disease, however, it destroys healthy organs like the brain or the components of the joints. Why this happens has been an outstanding question in the field of immunology for decades and different hypotheses have been proposed to explain it. Perhaps the most widely known is the idea that some bacteria have evolved to “look like humans”. If we zoom into these pathogens very closely (at the level of individual molecules on their surface), these bacteria would look incredibly similar to human tissues. This can confuse the immune system, which can not tell them apart from our own organs. This explanation, called molecular mimicry, appears in several textbooks. But molecular mimicry cannot explain every disease. Sometimes there is something else which triggers autoimmunity: it could be something we ate (like gluten in individuals predisposed to celiac disease) or something we were exposed to. Sometimes there is no evident cause at all. Perhaps the most sincere thing to say would be that we do not really understand.

Setting the scene

There is, however, one  very curious fact about autoimmune diseases which could help us understand them: these conditions tend to cluster in families. In such families, it is common to find several members who all suffer from arthritis, or who show different types of immune disease. This intriguing fact immediately suggests that there must be something that predisposes people to diseases, something passed from generation to generation, something hidden in the letters of human DNA. But what exactly is this something? This is the very question which has fuelled the last 15 years of research.

To answer this, geneticists devised a simple approach. They first set out to find all possible individuals suffering from autoimmune disease and recruited as many Renoirs and Portraits of young men as possible. Once recruited, geneticists took cells from these individuals and read their DNA. The idea was straightforward: to compare their DNA with that of healthy people. In this way, whichever sections of the DNA predisposed people to, say, arthritis could be identified. And indeed, they were found. Thanks to these studies (called genome-wide association studies or GWAS) today we have mapped hundreds of differences between healthy and sick individuals. Most of these come in the form of tiny changes to the sequence of DNA (often no bigger than a single letter). We call these genetic variants. The next step was, in principle, extremely simple: to study those genetic variants and find out what exactly they were doing. But there was a problem: this task turned out to be extremely difficult.

To fully understand what makes this a difficult problem, we have to explore human DNA in more detail. For the purpose of this blog, let’s imagine DNA not as a molecule, but as a book. In fact, let’s imagine DNA isn’t simply any book, but a copy of The Bald Soprano, the absurdist play by Eugène Ionesco (La cantatrice chauve in the original French). Let us read the first lines of The Bald Soprano:

THE BALD SOPRANO

THE CHARACTERS: Mr. Smith, Mrs. Smith, Mr. Martin, Mrs. Martin, Mary, The Maid, The Fire Chief.

SCENE: A middle-class English interior, with English armchairs. An English evening. Mr. Smith, an Englishman, seated in his English armchair and wearing English slippers, is smoking his English pipe and reading an English newspaper, near an English fire. He is wearing English spectacles and a small gray English mustache. Beside him, in another English armchair, Mrs. Smith, an Englishwoman, is darning some English socks. A long moment of English silence. The English clock strikes 17 English strokes.

MRS. SMITH : There, it’s nine o’clock. We’ve drunk the soup, and eaten the fish and chips, and the English salad. The children have drunk English water. We’ve eaten well this evening. That’s because we live in the suburbs of London and because our name is Smith.

MR. SMITH: [continues to read, clicks his tongue.]

Let’s now stop for a moment and analyse our imaginary DNA fragment. The opening begins: “The characters: Mr. Smith, Mrs. Smith…” It is perfectly clear that nobody is meant to read this sentence aloud. Then why did Ionesco wrote it? This line tells the producer of the play how many characters she should hire. The second line is even more puzzling: “Scene: A middle-class English interior, with English arm-chairs…” Again, it is obvious that nobody need recite this aloud (though it does makes a funny reading). It is an indication for the people in charge of designing the costumes and props which will appear on stage. It isn’t until the third paragraph that we find something which ought to be read: “Mrs Smith: There, it’s nine o’clock…“. But even here, the line opens with two words (Mrs Smith) which should not be read aloud: they are meant to indicate who will be in charge of reading the line. Obviously, The Bald Soprano is not meant to be read but to be performed on stage. It is its performing nature which begs for this long list of indications to set the scene, the characters and even the tone of voice.

Chauve_Noctambule
Photograph from a representation of The Bald Soprano (1968). Image obtained from Wikimedia Commons.

DNA is no different: it is also meant to be performed (though, in this case, not by actresses but by cells). In fact, only 2% of human DNA is directly readable in the way “There, it’s nine o’clock” is. We call this DNA coding and it contains genes. The remaining 98%  (which people used to call junk DNA) is not meant to be read. It is non-coding, and it does not contain genes. Some of it is structural (i.e. it acts like scaffolding in chromosomes), while some of it contains long lists of indications that specify which cell should read each gene, under which circumstances, and at which level. We call this DNA regulatory. Because these indications are not written in standard “genetic code”, we are as of today, unable to decipher them (perhaps not surprisingly, since we are not the performers which were originally meant to read them).

Now we are in a position to understand why it is so difficult to understand autoimmune disease. The vast majority of genetic variants linked to arthritis or other autoimmunities are in non-coding DNA. Since we cannot read non-coding DNA, we do not know what these sections mean. For example: which cell is using this DNA? (which in the Ionesco analogy would mean which actress is reading these lines?). It is difficult to know, since the immune system is formed of tons of different cells (T cells, B cells, macrophages, dendritic cells, neutrophils and a long list of other creatures) and the possibilities are endless. Moreover, we do not know what the function of this non-coding DNA is at all. Does it regulate the level of gene expression (equivalent to how loudly or quietly a line should be read) or does it regulate the context in which genes are active (equivalent to the moment of the play in which a line is read)? Once we answer these questions for one genetic variant, we will need to do it again and again for the hundreds of variants linked to disease. Hence the complexity of the problem. How could we ever hope to find a cure for arthritis if we can’t understand any of this information?

In a recently published study, we proposed an alternative approach. Let’s go back to the Ionesco example. If human DNA really was a copy of The Bald Soprano, and if it were to be performed, what would happen? Perhaps the actress interpreting Mrs Smith would have her own copy of the play. Not only that: she would need to learn it by heart, which means she would flip the pages over and over again, folding the corners of the most difficult paragraphs and highlighting her favourite passages. DNA is no different. Each cell has its own copy, and this copy is covered with the marks and highlights that the cell has added to read it more easily. We call this collection of marks the epigenome, and the field dedicated to study them epigenetics. What if we could read the copies of The Bald Soprano owned by different cells and compare their personal marks? Perhaps that could help us read the non-coding genome.

Notes in book margins
Epigenetic marks might act like footnotes and marks in books, rapidly indicating where a passage is located and how to read it. This example captures the thoughts of a reader of Shakespeare’s Hamlet. Image obtained from flickr (CC BY license)

Break a leg!

And that is how we set out to prepare our performance. We first recruited our actresses, our cells. To do so, we obtained T cells and monocytes from a handful of healthy people (we focused on T cells and monocytes because a large body of research suggests they hold the key to autoimmunity). Next we asked them to play their respective roles: in the lab, we tricked these cells into believing that they were seeing a pathogen or some other type of immune threat. Once cells reacted, we recorded their behaviour by looking at the marks they added to their copies of the DNA. We focused on one particular mark, a type of chemical modification which works as a bookmark, physically separating the sections of DNA which are frequently read or used.

Finally, we cross compared the notes of different performers. We asked which lines were highlighted by each cell, zooming specifically into the DNA sections linked to , say, arthritis. We wanted to understand which cells were constantly using these sections of the DNA. Could any of them be reading an abnormally high number of “arthritis” passages? This is equivalent to finding out which actress is playing the villain of a play by only looking at the highlights on her copy. Each cell was assigned a score according to how likely it was to be “the villain”. In more scientific terms, these are measurements of how often a cell reads or uses the DNA regions associated with disease (a measurement we call enrichment). We did this using genetic variants linked to different autoimmune diseases.

Our observations confirmed our suspicions: we found that T cells are extremely important in autoimmunity. But not just any T cells. Our evidence points to memory T cells in particular (a more experienced type of T cell) . It is very likely that something is going wrong in the T cells of people with autoimmune diseases. But not only that: because we read their DNA at different points in time, we also have a pretty good idea of when T cells start malfunctioning. This seems to happen very early (perhaps only a few hours) after they start responding to a threat. T cells fail to do their job, so to speak, during the first act of the play. Perhaps here, like in classic Greek tragedies, all the events which slowly unfold and come to haunt us in the final scene have their origin at the very beginning of the first act (think for example of the oracle in Oedipus Rex).

But what does this mean to people suffering from autoimmunities? Can this information be used in any way to cure future Renoirs? The answer is perhaps, but definitely not immediately. Our work gives one clear message: that we should be studying in more detail what T cells do when they start responding. Which part of this process is defective in autoimmunity? And how can we correct it? The solution to this problem lies very far ahead, but we are slowly moving towards it.


Eddie is a PhD student in genetics at the Wellcome Sanger Institute and The University of Cambridge. For any concerns, suggestions or comments regarding this blog, please contact the author at ecg@sanger.ac.uk

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