Three stories from the world of medical genetics

Sofia Dolotovskaya, N+1 

We have already talked about the fact that with the help of personal genomics you can find out about our origin, and talked about personal experience of genetic testing. Another huge area of application of personal genomics is the study of the genetics of various medical and physiological features: from a tendency to baldness and obesity to a predisposition to serious diseases. In the broadest sense of the word, all this can be called medical genetics, and it will be discussed today.

To begin with, let's look at how scientists establish links between genetics and physiological characteristics of the body. The main way to study such relationships is genome–wide association search, or GWAS (Genome-Wide Association Studies). The purpose of GWAS is to find a statistical association between genetic traits – for example, different variants of the same gene – and phenotypic traits – for example, diseases or type of constitution. To search for such associations, the genomes of two groups of people are compared: carriers of the studied trait and the control group. All these people are genotyped using microchips that identify millions of known single-nucleotide polymorphisms. If it turns out that some variant of polymorphism is more common in people with the disease, then this variant is considered "associated" with this disease - or rather, with an increased risk of this disease.

The search for associations does not necessarily have to be genome-wide: there are also studies focusing on just one or several parts of the genome. However, the principle is always the same: to determine the risk coefficient, which shows how much more often a particular polymorphism occurs in people with the disease than in people without it. It is with such coefficients that companies engaged in direct-to-consumer genomics work (that is, offering genome analysis to ordinary people, not scientists). Consumers are genotyped according to polymorphisms for which associations with signs and diseases have already been established (usually several hundred polymorphisms are included in genetic testing), and they are informed how likely they are to have these signs higher or lower than the population as a whole.

The problem, however, is that a person has very few signs and diseases that are inherited according to simple Mendelian laws – that is, they demonstrate an obvious correlation of the mutation with the disease. These include monogenic diseases defined by a "breakdown" in one gene. This is, for example, phenylketonuria – a violation of the metabolism of the amino acid phenylalanine – or hemophilia, known to everyone from school textbooks. To diagnose such diseases or determine the fact of carriage, it is enough to check for the presence of a mutation in a particular gene (and this, of course, is also included in genetic testing). However, most of the signs are complex, that is, they are determined by the work of many genes, which also interact with each other and with external factors in every way.

Therefore, the most difficult thing is the interpretation of the received data. Are the detected polymorphisms related to the mechanism of the disease? Starting from what values can the risk coefficient be considered statistically reliable? If you make the confidence threshold too high, you can lose genetic variants with a weak but real effect. If you make it too low, then everything will be associated with everything. And finally, what should the patient and his doctor do with such information: is the risk of developing the disease worth the risks associated with its prevention (for example, with the removal of the breast)? And if the disease is incurable – is it worth knowing about the risk of its occurrence at all?

Medical genetics deals with all these issues – it is a huge area of knowledge where traditional medicine, molecular biology, bioinformatics, and bioethics intersect. Of course, it is impossible to tell about it in any detail in one text. But we can recall several stories about unusual genes and polymorphisms that distinguish us from each other and affect our lives.

In an article published in The New York Times and caused a huge resonance, the actress told about her decision: she was found to have a mutation in the BRCA1 gene, which greatly increases the risk of breast cancer and ovarian cancer. In Jolie's case, doctors estimated these risks as 87 percent for breast cancer and 50 percent for ovarian cancer. The actress' story led to the "Angelina Jolie effect" http://www.vechnayamolodost.ru/pages/pages/premasdslhore7a.html : In the UK alone, the number of women who signed up for genetic testing increased 2.5 times in June-July 2013. Later, in 2015, Jolie had an operation to remove her ovaries.

What are these genes – BRCA? They got their name from the English "breast cancer susceptibility gene" (susceptibility to breast cancer), and there are only two of them: BRCA1 and BRCA2. These are tumor suppressor genes: in a normal (not mutated) state, such genes regulate the cell cycle, preventing uncontrolled cell growth. If, as a result of mutations, the activity of these genes is reduced or blocked, cells can go down the path of malignant growth – that is, form a tumor.

Hundreds of mutations are known in the BRCA1 and BRCA2 genes, and not all of them are dangerous, and some are simply not yet studied. Mutations in BRCA genes are not the only cause of breast cancer: they are detected in only 5-10 percent of women with breast cancer and 10-15 percent of women with ovarian cancer. However, in women who have inherited "dangerous" mutations, the risk of breast cancer and ovarian cancer increases many times: about 5 and 10-30 times, respectively. Approximately – because the risk depends on the type of mutation and varies for different ethnic groups. Mutations in the BRCA genes also increase, although not so much, the risk of other malignant tumors – for example, cervical and pancreatic cancer in the case of BRCA1 and stomach and gallbladder cancer in the case of BRCA2. Men with harmful mutations in the BRCA genes also have a much higher risk of breast cancer. However, since the incidence of this cancer in men is very low, the absolute risk of a tumor in men with mutations eventually turns out to be equal or even lower than in women without mutations.

Despite the fact that men do not fall into the risk group, it must be understood that any person can be the carrier of a dangerous mutation, and a child with a 50 percent probability inherits it from a parent of any gender. Therefore, doctors recommend that women who have a history of breast/ovarian cancer not only on the maternal side, but also on the paternal side, undergo genetic testing for BRCA gene mutations. Testing is also advised for Ashkenazi Jews, whose mutations in the BRCA genes are much more common than in other ethnic groups. Well, what to do if testing for dangerous mutations showed positive results is up to everyone to decide. Of course, after consulting with a geneticist.

The reason is the inability to digest lactose, the main carbohydrate of milk. In people with lactose intolerance, a glass of fresh milk can cause intestinal colic, bloating, diarrhea and even vomiting. And all this is due to a small molecule of lactose, which, unchanged, cannot penetrate into the intestinal cells and therefore accumulates in its lumen. As a result, the body osmotically loses water, and bacteria that can digest lactose begin to multiply in the intestine. Toxins and gases released by bacteria cause bloating and other unpleasant symptoms.

How, then, do babies cope with milk? And why do some adults drink as much milk as they want (the vast majority of them in Europe), while others can't even afford ice cream? The fact is that in infants, as well as in some adults, the enzyme lactase is synthesized in the intestine, which splits the lactose molecule into two components: glucose and galactose. And these simple sugars are already easily absorbed by our body. 

In most mammals, lactase is synthesized only in childhood, when the baby feeds on mother's milk. After that, the synthesis is turned off, because there is no lactose anywhere except milk, and adult animals do not drink milk. That is why, by the way, giving milk to hedgehogs caught in the forest is not a good idea. The hedgehog will not refuse milk, but it will not bring him any benefit. The same applies to cats, although some of them are able to digest small amounts of lactose (by the way, scientists don't really understand why yet). In most people, lactase also ceases to be synthesized with age. This happens in five or seven years. But then where do people who are able to drink milk come from?

It turns out that in some people, lactase synthesis continues throughout life. This is due to a mutation in the regulatory region of the lactase gene. This point mutation (that is, the replacement of one nucleotide by another) makes the regulatory region more attractive to the protein, which, by binding to it, triggers the reading of the gene – the synthesis of lactase. The ability to digest lactose in adulthood is a dominant trait: people who are heterozygous for the resistance gene synthesize half as much lactase as homozygotes, but this is enough to successfully digest milk.

All Europeans who are able to drink milk owe this to one mutation, which, according to geneticists, originated in Europe about 7 thousand years ago and from there penetrated east to India. In Africa, the ability to drink milk is determined by other, independently originated nucleotide substitutions, of which geneticists count at least three. That is, the ability to drink milk independently arose in different parts of the world at least four times. At the same time, once it arose, lactose resistance spread with amazing speed: in some East African ethnic groups, it became almost ubiquitous in just 3 thousand years. This suggests that this trait was subjected to a very strong positive selection. What was the evolutionary advantage of being able to drink milk?

This question is especially interesting because, as archaeologists have found out, they were able to make cheese in Europe and Asia Minor about 10 thousand years ago. This became known thanks to the finds of clay pots with holes that were used as a sieve for straining fermented milk. What does lactose have to do with it? And despite the fact that during lactic acid fermentation, Lactobacillus bacteria digest lactose, releasing lactic acid. Cottage cheese, which is obtained as a result of such fermentation, no longer contains a dangerous substance and even people who do not have resistance mutations can eat it. That is, a person learned to get rid of lactose in dairy products himself – much earlier than genetics caught up with technology.

Recently, scientists have finally come close to answering the question of what gave people the ability to drink milk. If you look at the map of the prevalence of lactose resistance in Europe, you can see that from the southeast to the northwest, the number of people able to drink milk is increasing. Farming was also spreading along the same vector in Europe, and with it dairy farming. In Asia Minor, the first rounds were domesticated already 10 thousand years ago, dairy farming reached the Balkans 8 thousand years ago, and Scandinavia and Britain reached 2 thousand years later. Comparing the data of population genetics and archeology, scientists have shown that lactose resistance spread as a result of the settlement of new territories: in a fast-growing moving population, the frequency of beneficial mutation is becoming higher where this population is moving, and not where it came from. Therefore, in the Scandinavian countries, where farming has reached the latest, the prevalence of lactose resistance is 90-95 percent.

Today, the first place in the ability to digest milk belongs to the Netherlands, where 99 percent of the population cope with it. Denmark is lagging behind the Netherlands quite a bit. In Russia, about 70-80 percent of people have lactose resistance. The situation is very bad in Southeast Asia: only 2-5 percent of people can digest milk there. And finally, no one can drink milk among American Indians.

Their number is only about 20 thousand people, and until the 1950s they had almost no contact with the outside world and did not know money. Nevertheless, this isolated people is directly related to genotyping. We will find out what it is just below.

Fore became known thanks to the epidemic of Kuru disease, which was discovered by Australian colonialists in the early 1950s and reached its peak in the 1960s, claiming more than 1,000 lives. Kuru is an incurable neurological disease, the name of which in the Fore language means "tremor", since its main symptoms are tremor and jerky movements of the head. Kuru is also often called a "laughing disease" in connection with the pathological bouts of laughter that patients suffer from. Other symptoms of kuru include impaired coordination and depression. At the last stage, ulcers appear, the patient cannot speak and does not respond to external stimuli. The clinical stage of kuru lasts about a year and ends with death.

Kuru belongs to the class of transmissible spongiform encephalopathies. All of them are characterized by progressive degradation of brain neurons, which leads to severe disorders of motor and mental activity. Such encephalopathy is called "spongiform" because there are many holes in the cerebral cortex that make the brain look like a sponge, and "transmissible" because it can be infected by contact with infectious agents.

Agents in this case are extremely interesting things. These are neither bacteria nor viruses, but prions (from the English protein – protein and infection – infection) are proteins with an abnormal tertiary structure that, when in contact with homologous normal proteins, cause them to turn into prions (something like a zombie apocalypse, but in the world of proteins). Accumulating in cells, prions form protein aggregates that cause damage and ultimately tissue death. Interestingly, prion aggregates are extremely stable and do not lend themselves to denaturation, so it is very difficult to destroy them or at least restrain their reproduction. To date, all prion diseases remain incurable and lead to death. The most famous of them are Creutzfeldt–Jakob disease and fatal familial insomnia.

All prions are formed from the PrP protein, a common membrane protein that is encoded by the PRNP gene. The PrP protein is synthesized mainly in the cells of the nervous system, but in low concentrations it is found in many other tissues. Its functions are not yet exactly known. The normal isoform of this protein is called PrPC, and the abnormal infectious one is called PrPSc. The transformation of a normal PrPC protein into an abnormal prion protein PrPSc can occur in three ways: as a result of infection (for example, when eating infected food), by hereditary means (when receiving a mutant copy of the gene from one of the parents) or spontaneously (as a result of somatic mutation or spontaneous change in the conformation of a normal protein).

In the case of the Kurus, the disease spread among the Fore people through ritual cannibalism. The brains and internal organs of those who died from kuru were considered a valuable source of energy. Despite the fact that fore usually did not eat people who died of diseases, they considered kuru not a disease, but rather a mental illness caused by damage or a curse. At the same time, Kuru disease was 8-9 times more common among women and children than among men: it was believed that eating human flesh makes men weaker in fights. After the Australian colonial authorities banned cannibalism in Papua New Guinea, the Kuru epidemic gradually came to naught. But even at the beginning of the 21st century, individual cases of the disease were noted, because the incubation period of the kuru can last up to 50 years.

So what does genotyping have to do with it? And despite the fact that in 2009, American scientists showed that some people can eat the brains of infected chickens without any health risk (Mead et al., A Novel Protective Prion Protein Variant that Colocalizes with Kuru Exposure http://www.nejm.org/doi/full/10.1056/NEJMoa0809716 // N Engl J Med 2009). It turned out that one of the variants of the prion protein PRNP gene is associated with resistance to chicken and other prion diseases. This genotype is found in those areas of Papua New Guinea where Kuru disease was most common and is not found either in Kuru patients or in populations not familiar with this disease. That is, the appearance of this variant of PRNP is an excellent example of recent selection in the human population. And people with such a genotype can eat as many brains as they want.

There are many more similar stories to tell. One of the many polymorphism databases, SNPedia http://snpedia.com/index.php/SNPedia , currently contains more than 75 thousand polymorphisms associated with diseases and physiological characteristics of the body. Such databases are continuously replenished with new data on associations. So, even having the results of one genotyping, you can learn something new about yourself literally every day.

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29.10.2015