The Genetic Shadow of the Black Death
The Black Death was a highly infectious and usually fatal disease caused by the bacterium Yersinia pestis. The pandemic which raged across Northern Africa, Europe and the Middle East between 1345 and 1350 killed as much as 50% of the population. So did this massive and sudden death toll shape the human population? Did the survivors have favourable genes which they then passed on to subsequent generations?
These questions were addressed by a large team of human geneticists mostly based at the University of Chicago, in a study recently published in the journal Nature. The team started by studying DNA extracted from 360 skeletons buried either just before, during, or just after the Black Death plague. Most were exhumed from three graveyards in east London, close to the Tower of London and St. Paul’s Cathedral, but some were from equivalent burials in Denmark.
Searching for gene variants which abruptly increased in frequency at the time of the Black Death, they ended up with 4 clear examples, of which the strongest was a particular variant of the ERAP2 gene. The frequency of this variant in those surviving the Black death was double that in the population prior to the pandemic. So it would appear that this variant favoured survival.
The protein encoded by the ERAP2 gene is known to have a role in the immune response. There are two common variants of ERAP2. The variant associated with survival produces a full length, stable protein. The other variant produces a shorter protein which tends to be rapidly degraded within the cell.
To examine a role for ERAP2 in the response to Yersinia pestis, the team isolated immune cells from living donors with the different ERAP2 gene variants and infected them with the bacterium. Those cells with the full length, stable protein were better at killing the bacterium.
But the full length ERAP2 protein is not all good news. It is known to be a risk factor for developing an autoimmune condition called Crohn’s disease. This is a persistent inflammatory disease of the bowels and intestines, and it affects around 2 people in every thousand in Europe and North America. So it looks as if the price paid for improved survival from the Black Death, was a propensity to develop autoimmune disease.
Overall this study highlights a number of significant points:-
- A pre-disposition to developing certain auto-immune conditions is likely to be an outcome of genes inherited from survivors of the Black Death.
- The rapid increase at the time of the Black Death in the prevalence of a gene variant associated with resistance of bacterial infection shows Darwin’s theory of natural selection at work in human evolution.
- For many genes, it is not a simple question ‘good gene’ variants and ‘bad gene’ variants. Rather there are gene variants which are favourable in some circumstances (such as during pandemics of bacterial disease), but unfavourable in others (propensity to develop autoimmune disease).
- A powerful immune response is not always what you want.
© CC Rider
27th Oct 2022
A Nobel Prize for the Genetics of Human Evolution.
Congratulations to Professor Svante Pääbo for winning the 2022 Nobel Prize in Physiology and Medicine for his ground-breaking work on the genetics of human evolution. The Swedish born scientist, now at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, is not exactly a stranger to this Prize. His father, the biochemist Sune Bergström, was awarded a share of this award in 1982.
Prof. Pääbo’s work is on the sequencing of ancient DNA fragments obtained from the fossilised bones of early hominids. Over several years up to 2010, his team was able to assemble a complete genome sequence of Neanderthals. This could then be compared to the genome sequence of modern man, Homo sapiens. Surprisingly, several portions of the sequence were common to both, establishing that Neanderthals and Homo sapiens had interbred on more than one occasion. Cleary we can only speculate as to the circumstances of this genetic interflow. It does however overturn the previously established view that as Homo sapiens migrated out of Africa it had progressively displaced Neanderthals from Europe and Asia as it colonised these regions. This new genetic evidence shows instead that these two early hominids, at least for a time, must have lived side by side.
Another big surprise to come out of Pääbo’s work, was that when his team sequenced the DNA they extracted from a hominid finger bone found in the Denisova Cave in southern Siberia, it was neither Neanderthal nor sapiens. In other words, they had discovered a previously unknown extinct hominid branch, which is has been called the Denisovans. Even now, few physical remains of Denisovans have been found, but there is evidence for them being in Tibet, and arguably elsewhere too.
There is further evidence of hominid interbreeding, between Neanderthals and Denisovans. Indeed Pääbo’s team, on analysing the DNA from one bone fragment showed it was from a woman, which they nicknamed Denny, who had a Denisovan Father and a Neanderthal mother.
Although Neanderthals and Denisovans became extinct, some of their genes survive in modern human populations. In people whose ancestry orginates in Europe and Asia, up to 6% of their genome is Neanderthal in origin. Pääbo and his team suggest this inheritance has consequences, by demonstrating that a small cluster of Neanderthal genes located on chromosome 3 is a risk factor for the development of severe Covid-19 infections. Some 16% of Europeans and 50% of south Asians carry at least one copy of the Neanderthal versions of these genes.
Denisovan genes contribute to modern populations in south east Asia including the aboriginal peoples of Oceania. The Denisovan variant of the gene EPAS1, which aids the body’s response to limited oxygen availability, is common in Tibetans. It is thought to be an adaption to living at high altitude.
These insights into the unexpectly complex origins of modern man provided by Prof. Pääbo’s study of genomes could never have been obtained by conventional archaeology or palaeontology. He has provided an accessible account of his research in his 2014 autobiographical book ‘Neanderthal Man: In Search of Lost Genomes’.
© CC Rider
12th Oct 2022
Did a tiny change in a single gene drive the evolution of modern humans?
For a period of perhaps 500,000 years modern humans lived alongside earlier hominids, in particular Neanderthals. But by some 50,000 years ago, the other hominids had disappeared leaving just us, Homo sapiens, to take over the planet.
Quite what happened here we will never know, but genome sequencing is providing some intriguing insights. The genomes of modern humans can now be compared with those obtained from archaeological bone fragments of early hominid remains. Amongst other findings, this shows rather surprisingly, that Homo sapiens interbred with their hominid cousins on multiple occasions across Europe and Asia. In fact Neanderthals contribute around 2% of the DNA of those modern human populations which arose outside Africa.
A high quality Neanderthal genome sequence was obtained from a fossilised toe bone excavated from a cave in Siberia. This showed only a modest set of changes from the genomes of modern humans. These changes would have affected the structures of just 85 of the many thousands of different proteins that humans produce.
Fossilised skeletons show that Neanderthals were shorter and stockier than we are. But evidence from the tools and art left behind suggest that early Homo sapiens were the more skilful and imaginative. The consensus is that despite being less physically powerful, they were the more cunning hunter-gathers, and so out-competed the Neanderthals.
Measurements of fossilised skulls show that the overall brain size of Neanderthals was the same as that of modern humans. These fossils leave no record of the brain structure, but the conjecture is that the neocortex is better developed in Homo sapiens. The neocortex is the brain region responsible for higher cognitive activities, involved in attention, thought, perception and memory.
Of the 85 genes found to differ between Neanderthals and modern humans, 5 are associated with the development of the neocortex. One these genes, active in the developing human neocortex, is called TKTL1. This was the subject of a recent paper in the journal Science, published by a team of researchers based in Dresden and Leipzig, Germany. The TKTL1 gene of Homo sapiens produces a protein over 550 amino acids long. A tiny change in the gene causes it to differ by just a single amino acid from the equivalent protein produced by the Neanderthal TKTL1 gene. Amongst their findings, the team showed that the introduction of the Homo sapiens TKTL1 gene into a simple cell culture system of developing human brain increased the number of cells destined to become nerve cells. By contrast, introduction of the Neanderthal version of the gene did not.
The authors propose that the tiny difference between the Neanderthal and modern human version of the TKTL1 may have driven the development of a more advanced human neocortex. Could small gene changes such as this have been responsible for ultimate dominance of Homo sapiens?
28th Sept 2022
Gene Editing for the Treatment of Sickle Cell Disease
The recently developed technique of gene editing now enables us to make targeted changes within single genes. Any such edits will be life-long alterations of an individual’s DNA, and so this approach must be used with great caution. Nonetheless we are starting to see the first applications of gene editing to treat inherited diseases arising from faulty genes.
Amongst the most widespread of such diseases are those affecting for the red blood cell protein, haemoglobin. The most common of these is sickle cell disease. Globally, each year some 300,000 people are born with this inherited disease and they will have to live with this painful disease which can have serious debilitating consequences.
The faulty gene causing sickle cell disease persists in various populations in spite its harmful effects because it offers some protection from malaria. Many countries, from the Mediterranean through the Middle East and into much of Africa and Asia, once had high levels malaria. So people whose families originated from these regions can carry this faulty gene.
In sickle cell disease, the haemoglobin produced is less stable than the normal form. When it is destabilised it distorts the red blood cells it is packed in to. These then change from their normal rounded structure into a flattened and curved shape, reminiscent of the blade of a sickle, hence the name of the disease.
When the circulatory system is stressed, for instance during periods of intense cold, the amount of red blood cell sickling increases, and the distorted red blood cells can jam together and block small blood vessels. This causes intense pain, and can result in damage to the tissue normally supplied with oxygen by the blood vessels involved. Sickle cell patients will suffer periodic episodes of this throughout their lives.
Haemoglobin is the major protein of red blood cells and is responsible for carrying oxygen from the lungs around the body, and it has been studied intensively. Over 60 years ago, a biochemist called Vernon Ingram found that sickle cell disease arises from just a single aminoacid change in one of the two protein chains which make up the major form of adult haemoglobin.
This scientific breakthrough has until now not provided much benefit for patients. Treatments have largely been limited to pain killers and drugs aimed at stabilising their haemoglobin. Although new treatments have been introduced, they tend to be limited and less than satisfactory. Most do not address the route cause of the disease.
The major form of haemoglobin is composed of two protein chains, α and β. The sickle cell gene mutation affects only the β, chain: the α chain remains completely normal. During gestation, the developing foetus mostly expresses a different form of haemoglobin, in which α is combined instead with a third type of chain, γ. This αγ combination binds oxygen slightly tighter than the adult αβ combination, so that oxygen is drawn from the mother’s blood into the foetal red blood cells, and then around the foetus’s growing body. Around birth, γ production is switched off and β starts to replace it. Since this replacement is never complete, a little αγ persists in the adult. This persistent αγ is known to protect sickle cell patients against the worst outcomes of the disease.
We now know that the switch from γ to β production involves a gene called BCL11A, and we also know how it works. Interfering with this switch, should result in less αβ haemoglobin being produced in the adult, and more αγ should persist. In the USA, trial treatments of sickle cell patients have used the precise technique of gene editing to inactivate a specific target site on the BCL11A gene. The results show the levels of αγ haemoglobin now produced is indeed raised, at the expense of the faulty αβ. Critically, in the few patients treated thus far, this effect has been sufficient to prevent further sickling attacks.
This outcome is not a true cure for sickle cell, as the fault in the β gene remains, but at last it is beginning to look as if this nasty disease can now be effectively treated. More trials of this gene editing therapy will be needed to judge whether it should be approved for routine use.
© CC Rider
1st March 2022
Building the Body – HOX Genes
We start off our existence as a single fertilised cell, which as a result of several rounds of cell division becomes a simple ball of cells. How do we get from this to the fully formed, complex body of first a baby, then a child, and finally a fully grown adult? How do we develop a complex body plan with many different organs, all of which need to be the correct size and in the right place? Consider for instance our skeleton which has over 200 bones, many of which fit together in complex articulated joints that must have correctly attached muscles, tendons and ligaments to permit controlled movements.
Many different genes play a role in governing this development, but one important family of closely related genes are the HOX genes. These particular genes were first discovered by geneticists studying the development of the humble fruit fly. Their attention was drawn by bizarre mutations affecting the body plan, for example a leg which should be attached to the middle of the body sprouted in place of an antenna at the front of the head.
HOX genes are also found in animals. Like all mammals, humans have a total of 39 HOX genes, and these are again important in the development of the body plan. They are grouped together in four separate clusters on different chromosomes. Each cluster is a linear array of between 9 and 11 HOX genes.
In general, similar genes with related functions tend to be scattered around the DNA of our chromosomes in an apparently random manner, so that you can tell very little about the function of a gene from its location on a chromosome. The HOX genes are a standout exception to this.
In mammals the primary axis of development runs along the length of the body trunk, down the spine from the skull to the pelvic girdle, and in most species a tail. Remarkably the HOX genes are lined up in their arrays in precisely the order in which they function in this axis. So the first genes in the array govern the development of the vertebrae of the neck, just under the skull. Next are those responsible for the chest region with their attached ribs, then those governing the abdominal region, and then those controlling attachment of the pelvis and so on. It is thought that as the developing spine elongates downwards from the head end, a developmental clock progressively switchesonthe next HOX gene in the arrays in turn.
But the spinal axis is not the only developmental axis. Each of our limbs, arms and legs, has a developmental axis extending out from the attachment to the torso at shoulder/pelvic girdle, through the upper limb to elbow/knee joint, then the lower limb, wrist/ankle and eventually to the 5 digits (fingers/toes). HOX genes acting in the same sequence control these limb axes too.
We now know that in the fully formed adult body HOX genes retain their controlling activities. They are important in maintaining the body tissue structures and functions, amongst other things regulating the turnover of individual cells and their replacement by new ones. As such, their activities appear to become disorganised when these processes go wrong, which is what happens in cancer. So what started around a century ago as the study of genes in fruit fly development, through identifying the genes involved, is now leading to new insights into the abnormal body processes which give rise to cancer.
© CC Rider
5th Jan 2022
Gene Therapy for Babies with Severe Spinal Muscular Atrophy
A 5-month old baby boy called Arthur, diagnosed with the devastating condition of spinal muscular atrophy, has become the first patient to be treated in the United Kingdom by the National Health Service with a new gene therapy.
Spinal muscular atrophy, SMA for short, affects around 1 in every 10,000 births and is the result of mutations in a gene called SMN1. It is an inherited disease and babies born with it have mutations in both of their copies of the SMN1 gene. The absence of a functional SMN1 gene means they cannot make the corresponding protein.
Their parents will be healthy carriers with one normal SMN1 gene and one mutant copy, and it is this mutant copy which they will both have passed on to their affected child. In the parents, the single normal copy of the gene means that they are able to make the SMN protein in their cells, so they are unaffected. Around 1 in 50 of the population have a single SMN1 gene mutation and will be unaware of it, unless they have children with someone who also has such a mutation. Even then, their children have only a 1 in 4 risk of suffering from SMA. So nearly all the SMN1 gene mutation carriers in the population will be quite unaware of the danger to their children lurking in their mutated version of this genes. There is unlikely to be any family history of this condition amongst their relatives.
The affected children, lacking a normal functional SMN1 gene, are unable to make the SMN protein. Its absence causes the motor nerve cells emerging from their spinal columns to begin to die. These are the cells which control the movement of muscles, and as they die the muscles become progressively unresponsive and weaker. Babies with the most serious form of SMA face a short and limited existence. These babies are unable to sit up, and lose the ability to move their limbs and heads. Eventually the muscles needed for breathing begin to fail, and very sadly these children are unlikely to survive until their 3rd birthdays.
In 2019, the US Food and Drug Administration approved a gene therapy developed by Novartis for use in babies with severe SMA. Other jurisdictions have now followed suite. This involves infusing the children with a harmless virus modified to carry a normal copy of the SMN1 gene. Once these viruses have entered the baby’s cells, the SMN protein can be made, and the motor nerve cells will cease dying. Nearly all of the children in the clinical trials of this gene therapy have shown benefits, being able to breathe unaided at 14 months of age, and with a half of them able to sit independently at 18 months. Some treated children have reported even better responses. At present is too soon to be able to report the long-term outcomes of this treatment.
Now that we have an effective, if highly expensive treatment, it is important to diagnose SMA children as early as possible. Usually they are diagnosed at around 3 months of age onwards, when they fail to achieve the normal developmental milestones in mobility, such as reaching to grasp objects. The issue here is that once an affected child has been born, motor nerve cells are being lost steadily, and they cannot be replaced. A number of countries already use a genetic test to screen all babies at birth for SMA, and the pressure is now on for this to be adopted more widely, so as to maximise the benefits of this new gene therapy.
2nd Jun 2021
A Mutated Gene Which Causes Cancer
The adult human body is estimated to contain a total of 37 trillion cells. We have all arisen from a single fertilised cell by many rounds of cell division, giving firstly 2, then 4, then 8, then 16 cells and so forth. Once we have reached adult size, cell division is then tightly regulated to maintain the correct number of cells at the appropriate anatomical site. Any remaining cell division is balanced to only replace worn out or damaged cells. In cancer this tight regulation goes awry.
Cancer arises from damage to our DNA which results in a particular cell type undergoing continuous and uncontrolled cell division. In this way an excess of unnecessary and unwanted cells accumulates in the body. Over the last 50 years or so, cancer research has revealed that it is mutation in certain specific genes which drives the development of cancers. These genes are called oncogenes.
One instance of such genes are the set of three which carry the instructions to make normal variants of a protein called Ras. The Ras proteins act as signalling switches within our cells. Cells from time to time receive activating signals from within the body. When these become strong and prolonged, they can trigger the cell to start dividing and to become highly active. Ras has a role in transmitting such signals from the outside of the cell to its central nucleus, in which all our genes are stored.
Normally Ras flickers on and off according to these signals, as its structure is switched rapidly between active and inactive states, rather like a controlling circuit within a complex electronic device. However there are certain tiny errors, or mutations, which can occur within the Ras genes. Some of these then cause the Ras proteins they produce to be permanently locked into the ‘on’ state. If this happens, the signalling circuit which Ras participates in is permanently active and the cell is driven to undergo cell division without ceasing, producing more and more overactive cells.
Ras mutations are found in around one quarter of all human cancers, although the proportion varies greatly from one cancer type to another. For instance some 90% of pancreatic cancers contain mutations in a Ras gene, whereas other cancers show very little. With modern gene sequencing techniques, it is straight forward to find out whether the cancer in an individual patient has the Ras mutations, or not.
Cancer researchers are now trying to find ways of switching off excess Ras signalling in those cancers containing these mutations, but the challenge of being able to do this effectively and safely has so far proved elusive.
Ras is just one of several well-established oncogenes which can cause cancer when they are mutated.
2nd Feb 2021
Genes and Severe Covid-19
The Covid-19 virus has varying effects on different people. Many people experience no noticeable symptoms and their infections will only be revealed should they undergo a Covid-19 test. Others may experience just moderate symptoms which pass in a few days. However the real problem lies within the group of individuals who develop life-threatening respiratory disease. This is highly distressing and can even prove fatal, especially in the elderly, or those with pre-existing heart or lung conditions. Why is there such a very broad spectrum of response to Covid-19 infection? One interesting possibility is that disease severity may depend on the amount of virus someone is infected with. But another possibility is that some people have a genetic pre-disposition to respond badly to Covid-19.
It is this last possibility which has been investigated by a large international research group led by Dr J K Baillie in Edinburgh. This team scanned the entire genomes of 2244 patients who are in UK intensive care wards with severe Covid-19. They then performed computer searches which compared the frequency of gene variants within this group to those occurring amongst a large control group in the extensive UK genome database. They next verified their findings on a further group of 2415 severe Covid-19 patients. This work enabled them to identify 4 genome regions with particular gene variants found more often in the severe Covid-19 groups. To this another gene was added which does not have a variant DNA sequence, but which is expressed at higher levels in the Covid-19 sufferers compared to the normal population.
By knowing the individual genes involved in these variations it is possible to group them into two classes. One of these classes is involved in the very early responses to virus infection. Because such responses will have come into play several days before a patient develops severe Covid-19, there is little prospect that medical interventions here will be of benefit.
However the second class of genes control inflammatory responses, and it is dangerous over-reaction of on-going inflammatory responses in the lung which is the problem in severe Covid-19. Here there is hope that the new research has identified a new target suitable for clinical treatment. One gene in this second class is called Tyk2 (pronounced as tyke two) and this encodes an enzyme which drives prolonged inflammatory responses. The Tyk2 gene variant identified in severe Covid-19 causes too much Tyk2 enzyme to be produced. Excitingly, there is already a drug called baricitinib which is used to inhibit Tyk2 in the treatment of rheumatoid arthritis, another disease of excessive inflammation, in this instance in the joints rather than the lungs. Since baricitinib is already in clinical use, we already have a full knowledge of its safety profile and suitable dosage levels. Now we just need a clinical trial in severe Covid-19 to find out whether baricitinib does actually save lives and might speed the recovery of a patient who is in a very ill state in intensive care. If it does, it will not only provide a huge benefit, but it will also become a great example of how advanced genetics can provide improvements in medical care.
14th Dec 2020
Tocilizumab – a new Covid-19 drug obtained through genetics
Last week, almost buried by the latest positive announcements on Covid-19 vaccines, was the good news of a successful drug trial. Tocilizumab, a drug used for the treatment of severe arthritis, has been shown to more than halve the death rate in hospitalised patients with severe Covid-19 pneumonia.
In severe Covid-19 infections, over-activity of the patient’s immune system presents a danger to their survival, so doctors have been looking for ways to damp down this excessive response. The anti-inflammatory steroid, dexamethasone, was the first drug shown to have positive effects in this way. Now tocilizumab, which has previously been used to reduce immune over-activity in rheumatoid arthritis has been proven to benefit patients with severe Covid-19.
Tocilizumab works in a completely different way from dexamethasone. It specifically targets and blocks a protein on a major activation pathway which normally acts to trigger immune reactions. By blocking this particular protein, immune activation is reduced. So what does this have to do with genetics?
Well firstly, like many proteins in the immune system, the targeted protein could only be identified by first finding its gene. Secondly, once this gene hunting was successful, genetic engineering within research laboratories was needed to study the properties of this protein, and to raise an antibody which would recognise it specifically.
Finally, this antibody was initially generated in a laboratory mouse, so it is a mouse-derived antibody. As a foreign antibody it will not work well once administered into patients. The patient’s immune system will start to neutralise and remove it. To avoid this, more genetic engineering is needed to snip out the small elements of the antibody which actually bind to the target and graft them into a human antibody backbone. Such an antibody is now mostly of human origin and is therefore referred to as a humanized antibody.
Increasingly some our new important and most powerful medicines are humanized antibodies, for use in the treatment of serious diseases including rheumatoid arthritis and cancer.
In the case of tocilizumab, it still needs licence approval for use in severe Covid-19 infection, but since there is much clinical experience of its use in rheumatoid arthritis, this should be a straight-forward process. We can therefore be confident that we now have a new brick in the wall of our defences against the coronavirus.
23rd Nov 2020
What is an RNA Vaccine?
Congratulations to Pfizer and BioNTech on the successful interim results of their RNA vaccine against Covid-19. It is an extraordinary achievement to have reached this stage within some 10 months, when normally developing a vaccine this far would take around 10 years. This new candidate vaccine is a novel type of vaccine, being an RNA vaccine. Such vaccines have only been possible in recent years, resulting from advances in genetics. But what is an RNA vaccine, and how do they work?
Most people will be aware that the genes of living organisms, including humans, exist as DNA, or to give it its full chemical name deoxyribonucleic acid. This formal name arises from the fact that its backbone is made up of the sugar, deoxyribose. This is derived from the more usual sugar ribose by removing an oxygen atom from it, hence deoxyribose.
When a gene becomes active, it is copied out as a strand of RNA, in full, ribonucleic acid. RNA is very similar to DNA, but its name is due to a key chemical difference. Its backbone is made from normal ribose, not deoxyribose. This RNA version of the gene then directs the production of multiple copies of the encoded protein.
Many viruses, including Covid-19, do not have DNA. Instead the few genes they possess are in the form of RNA. When such viruses infect a cell, they release their RNA, which then hijacks the cell into making lots of the different viral proteins from which new virus particles can be assembled.
An RNA vaccine mimics this process but in a limited way. An artificial RNA encoding just a single virus protein is produced. Upon injection, this artificial RNA enters some of the recipient’s cells where it makes just the single encoded protein. The process is inherently safe because the other Covid-19 genes are absent, so the other proteins the virus needs cannot be made. Instead the single Covi-19 protein appears on the surface of the recipient’s cells. There it will be detected by the recipient’s immune system as a ‘foreign’ i.e. non-human protein. An immune response will then be triggered. This means that should, at a later time, the recipient encounter Covid-19, they will be protected from it.
One point should be made clear. Just because this is a RNA vaccine, and RNA is closely related to DNA, it cannot alter our own DNA, and so will not change our genetic make-up. In time the vaccine will be eliminated from our cells.
There are a number of hurdles to be overcome before this new vaccine can be licensed, and since this is a new type of vaccine, the authorities regulating the use of medicines will be especially vigilant. Another issue is that since RNA is not very stable, the vaccine will have to be stored and transported at very cold temperatures (-70o C). This raises complications in delivering it to clinics for use.
Nonetheless this vaccine candidate gives some hope at the end of the long and dark Covid-19 tunnel.
12th Nov 2020
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