Everyone’s genetics have a fat story to tell

In the last couple of posts, we introduced a family from Edmonton that we believe was involved in the first large-scale genome sequencing attempt of presumed healthy individuals in Canada.

Last week we focused on the youngest members of the DNA sequenced family, the young married couple that represents the future of the family. This week we will continue this family’s story with the oldest member of the family to have their DNA decoded, the beloved grandma of the young husband, and the surviving matriarch of the clan. As the oldest generation in the family to participate in DNA testing, she stands atop the genetic pyramid as her blueprint information is disseminated through each successive generation.

Her genetic story is as fascinating as everyone else’s in the world.

As we previously mentioned in the last blog post, everyone in the family turned out to be DNA carriers of different diseases, including grandma. Grandma had a likely pathogenic mutation in the ACADVL gene, which codes for very long-chain acyl-CoA dehydrogenase. Yes, that is the confusing name of this particular molecular robot of great importance.

What is it?

This enzyme is involved in mitochondrial fatty acid oxidation. That probably sounds meaningless as well, but biologically it is super important so let’s break it down here. An enzyme is a molecular robot that creates something new or destroys something old inside the cells. Fatty acid oxidation, on the other hand, is another way of stating the process of using your fat to produce energy for the needs of your body. This process takes place in your muscle cells and liver, in tiny compartments inside your cells called mitochondria. Mitochondria are essentially engine rooms that produce molecules that act as a storage space of energy, called adenosine triphosphates, abbreviated as ATP. Energy is a very ambiguous word that is confusing because it is difficult to imagine it as something concrete. ATP is a concrete entity though, a compound used throughout the body for variety of molecular reactions. You drop it somewhere else, and part of it is used as an attachment to some other molecular entity. But with that addition it can completely change the properties of the other molecule to which that piece of ATP was attached. And by properties, we really mean the three-dimensional shape. In the atomic world, it is all about the right configuration of atoms into specific molecular shape. Three-dimensional shape governs everything in the molecular world because the shape determines the distribution of electromagnetic forces. And electromagnetic forces are the key to all of the interactions between atoms, really, the key to life itself. The use of ATP to chemically adorn other structures in your cells, in essence can act as an “on” and “off” switch. Thus, in this case, the storage of “energy” is the fact that ATP can be used elsewhere in the body to drive molecular reactions. It does not really pocket some ambiguous energy and move it around. It is like chocolate chip cookies that can be used to influence the outcomes of many foods.

To continue with the biology lesson, fat itself comes in different forms. Fat basically is a long chain of carbon molecules. It is energy storage because you can nip those carbons away and enter them into a conveyor belt like production line inside the mitochondria that will utilize the compound to drive the production of ATP. Carbohydrates (sugar molecules stringed together, yum!), and proteins can also enter this production line, and thus we all know that fats, sugars and proteins are your food for the body. But fats come in a variety of different lengths of these carbon chains, and that can affect how they are processed. Very long-chain acyl-CoA dehydrogenase is used in the breakdown of… very long-chain fats (or fatty acids as scientists like to politely call them).

Just to complete the mini bio-lesson, each carbon atom is attached to another carbon atom by a chemical bond. The chemical bond is nothing physical, there is no bridge holding these atoms together. It simply refers to the fact that these atoms happen to be strongly attracted to one another through their atomic elements to a point that they travel everywhere together side by side. Thank you electromagnetic interaction! Kind of like human couples that spend all of their time together.

Back to the real world.

Deficiency of very long-chain acyl-CoA dehydrogenase is an autosomal recessive condition, meaning that in order for a disease to be materialized, each of the genes inherited from one’s parents have to be mutated. We covered the concept of disease inheritance types, in the last article discussing the family genetics.

If only one of the two genes is mutated, the person is considered a carrier, and typically is not affected by the disease. In essence, the other good copy of the gene inherited from one of the parents rescues the deficiency of the broken gene that was inherited from the other parent.

But we discussed that in the last article dedicated to the carrier status, that DNA mutation carriers can sometimes exhibit some disease symptoms too.

And very long-chain acyl-CoA dehydrogenase deficiency carriers appear to be another excellent example of that! Although rare, data suggests that carriers of ACADVL mutations can develop disease complications. Whether that's due to the somehow affected enzyme activity that leads to disease, or to totally independent other factors that happen to just coincide with the genetic mutation profile is perhaps only a matter of speculation. So let's look at this condition in more detail.

If the very long-chain acyl-CoA dehydrogenase enzyme activity is not present, the body cannot break down fat for energy and must instead rely on glucose sugars. Unfortunately glucose in the body is available only in a limited supply, and once it is used up, the body tries to use fat. In the case of the long chain fats, if your ACADVL genes are mutated and non-functional, it will do so without success. This in turn will lead to low blood sugar (called hypoglycemia), and a harmful build up of long-chain fats in the body.

Like with so many diseases, the resulting condition can be quite variable, causing mild effects in some people and serious health problems in others, even leading to death. The variability of a health condition’s manifestation is referred to as disease penetrance, a concept we also covered in the last blog post. Even more confounding, symptoms of the condition caused by mutations in the ACADVL genes may start in infancy or not until adulthood, so we are talking about variable outcomes at variable ages of onset. For the sake of simplicity, let’s focus on the adult symptoms of very long-chain acyl-CoA dehydrogenase deficiency, which appears to be the most common type of the condition. Unlike the more severe forms observed in babies or children, the adult form is usually asymptomatic and the primary symptom is frequent periods of muscle weakness. Muscle fibers could even breakdown, especially during heavy exercise or after going without food for a long period of time, exhibited by muscle aches, overall weakness, cramps or a reddish-brown color of the urine. If such adults do not get treatment, they can develop kidney failure. Adults typically do not develop hypoglycemia or the metabolic crises which can be observed in babies or children with the condition, nor the heart problems that also can be seen in babies.

What is the treatment? It primarily involves a specifically adjusted diet and avoiding prolonged or heavy exercise! Imagine the type of bodily damage that could be avoided with something as simple as that!

So what if you are “just” a DNA carrier of very long-chain acyl-CoA dehydrogenase deficiency, and only one of the ACADVL genes is affected? Typically such individuals have a normal fat metabolism, with enough working enzyme present to take care of things. But there appears to be published evidence showing DNA carriers can sometimes be in trouble too. Authors of that paper describing a heterozygous mutation individual with clinical symptoms of the disease, propose that some mutations might “exhibit transdominant negative effect”. For the fat breakdown enzyme to function, or in other words, for the molecular robot to be assembled for work, the protein encoded by the gene has to interact with a copy of itself, forming a dimer. Since it is two of the same proteins, it is referred to as a homodimer. It is molecularly attracted to itself if you will. Only then can such assembly of two proteins be an active enzyme that will perform work. This type of building a congregation of the same protein units to develop a final functional mega structure is very common in biology. Homodimers as homotetramers are the most commonly observed, but sometimes it can take more than a dozen of same protein units before the final structure comes to life. In this case, the authors proposed the following effect: “A heterozygous mutation may produce an aberrant monomer, resulting in the production of noxious homodimers even [while] one of a pair is normal.” Such molecular predicaments are also commonly observed.

So the big question is, should grandma be worried or tested for anything?

Probably not, considering the rarity of an event and the age of the person where symptoms would be expected to be seen. But this appears like a potentially stealthy problem, so perhaps a better question would be, does the patient observe any of the symptoms associated with the condition? Is there a struggle after strenuous exercise? Considering her age, such symptoms might actually be normal now, so has this ever been observed in her younger years? Excessive cramps? Cola-coloured urine observed in the past? Perhaps the patient’s understanding of their history will act as the guiding parameter, judged by the test ordering doctor if the condition should be further screened for or not. This would make carrier status very personalized and potentially medically important beyond just the reproductive component.

This once again demonstrates the complexity of how our genetic blueprint could be governing our health, and the potential interpretation of it, even in seemingly presumed simple situations of DNA mutation carriers.

Lineage of DNA, lineage of faith

This was not the only gene mutation that grandma was a carrier of, however. She was also a carrier of the SEPN1 gene mutation that we already discussed in the last article as it was also present in her grandson. So you now know where that reproductive risk came from!

Let’s switch from grandma to her son, or the father of the young husband of our last missive.

This is also an interesting story because he was the carrier of the SEPN1 gene mutation he inherited from his mom, or our grandma of the story, and he passed on that same mutation to his son, our young husband. He did not inherit the ACADVL gene mutation that we just discussed in detail from his mom. Basically, there is 50% chance that a parent will pass on a given DNA fragment down to their offspring. We all have two copies of identical DNA information inherited from each of our parents, and we will pass on only one of the two copies down to our offspring, some that we inherited from our mom, some that we inherited from our dad, and it is mostly a random process, hence the 50% chance that a child will inherit any genetic mutation from a carrier parent. The other 50% chance is that a normal non-mutated version is inherited.

This example of the SEPN1 mutation inheritance also demonstrates how the potential for disease development can stealthily travel down the family line for generations until it is “suddenly” paired up with another carrier of the same gene mutation and then the unexpected appearance of a disease in a family that previously never had such a condition takes everyone by surprise. This is almost what might have happened to this family!

Because the father of our husband was also found to be a carrier of the HFE gene mutation that we covered in detail in previous blog post. You would think we already exhausted that topic. We did not!

It turns out that being a carrier of the HFE gene mutation might help explain one of his own symptoms: anemia! Chronic inflammation such as those caused by infections, arthritis, inflammatory bowel disease or some cancers, can result in anemia, independent of iron deficiency. It is called anemia of chronic disease. This type of anemia is caused by the over-activation of hepcidin, which is a hormone involved in controlling iron levels in the body. Hepcidin reduces the levels of circulating iron levels by stimulating the iron absorption by cells. This process can aid in fighting infection as microbes need iron to proliferate. This is fine in the short-term in order to fight infection, but in a long-term condition, it can remove the iron needed for the production of blood cells, resulting in anemia. And wouldn’t you know it, it turns out that the HFE gene product regulates hepcidin levels. This means that the HFE gene has both an immunologic function and an iron-regulating function.

When the blood iron levels gets high, the HFE protein signals for the production of hepcidin, which will reduce the blood iron levels. So perhaps paradoxically, the HFE gene mutation that the father has could lead to two simultaneous counteracting activities. It could lead to dysregulated iron levels in the blood, which is possible in HFE gene carriers as we discussed in the last post. This abnormal increased level in turn could promote too much hepcidin, which would promote anemia development. Alternatively, the HFE gene mutation might not be affecting iron levels at all, but directly overzealously enhance the hepcidin levels, especially if this was compounded by chronic inflammation. There might be some evidence for that.

Heterozygotes in the HFE gene, as seen in our father, have been shown to have increased levels of ferritin, the molecule that is directly involved during iron absorption by cells and which is actually regulated by the hepcidin hormone. It is a cascade effect, HFE regulates hepcidin, hepcidin regulates ferritin. It is like a bureaucratic line of management to either ensure quality control, or waste precious resources. However, these are marginal effects only, with one study of nearly 8000 Danish male blood donors showing 5% increased ferritin levels in HFE heterozygotes, as compared to no mutation in the gene. But could this effect be further compounded by a chronic inflammatory condition? Chronic inflammation can inhibit the proliferation of red blood cells precursors. Another symptom that the father has been diagnosed with was gout, which is a form of inflammatory arthritis. And guess what, gout appears to also promote increased ferritin levels. Perhaps it was just enough that with the already present HFE gene mutation, together they lead to enough iron being removed from the blood by ferritin to cause anemia.

Very counterintuitive for a carrier of an iron-overload disease. If that indeed is the case, and this potentially could be investigated through certain blood testing, then it could call for some potentially very simple interventions as suggested by the above article: reduction in red meat consumption and occasional blood donation! Although the latter is apparently not appropriate for those with a history of gout and anemia, but which type of anemia was not specified. Anemia has been identified as a risk factor for gout. The question here is, can the reverse be true as well? Could an attempt to reduce gout incidence result in lowered ferritin levels which in turn could reverse the symptoms of anemia?

As you can see, the science behind health symptoms and its association to genetics can be very complicated, and we are only speculating.

In terms of inheritance, since our father’s mom was not a carrier of this mutation, it indicates that he must have inherited it from his father (whose DNA sequence was not available for analysis), and he could have easily passed it on to our husband. There is a 50% chance that the husband could have inherited, but he did not! And that’s lucky because we already know that the husband’s wife is also a carrier of that same gene mutation. In fact, the same exact mutation! That means, if the husband had inherited it from his father, the young couple could have ended up being carriers of the same hereditary hemochromatosis disease, and potentially put their future children at risk! No one in the family is known to have had the condition previously, at least not in recent memory, and boom, suddenly the condition could be showing up seemingly out of nowhere! This is exactly what plagues many families when carriers accidentally combine their genetic glitches. This is also why marriage between closely-related individuals is particularly dangerous to the health of future offspring, due to an increased likelihood that the carriers of the same diseases will match their DNA mutations. This is why screening prior to children can have enormous advantages now, which has never been previously available on the scale that it is currently.

This takes care of the one contiguous genetic lineages of this family: the grandma passing on her biological program to the father who passed the DNA instructions onto husband. Let’s take a look at the other genetic lineage, and see what the genome of the mother of our young husband revealed.

The most common risk factor, the most common disease

Mom brought a very different condition as a carrier, so now we know that there was no risk of her and the father uniting a disease through their genetics in their offspring. When they elected to have children, they could have never known. She was a carrier of a very rare condition caused by mutations in the SLC34A3 gene, that result in hereditary hypophosphatemic rickets with hypercalcuria. Seriously, that is the name of the condition! The gene encodes a molecular structure that acts as a channel that transports atoms across cell membranes, specifically in kidneys. One of these atoms is a phosphate, like the ones we find in ATP. Messing with the activity of these channels results in serious problems. The list of potential problems is not what you want to be coming across: kidney stones, kidney dysfunction due to calcium deposits, rickets, softening of the bones, affected growth, frontal bossing, increased fractures, bone pain, muscle weakness and decreased muscle tone, difficulty walking, and difficulty standing.

Unfortunately, in the case of this condition, carriers are especially likely to also be affected, most commonly showing elevated calcium levels in the urine, which was observed even in the very first genetic description of the disease. Increased urine calcium levels are the most common risk factor for kidney stones, a symptom observed in about half of the adults with recurrent calcium stones. A recent study indeed showed that SLC34A3 mutation carriers also have an increased risk of renal calcification, which was shown to be 16% compared to 5.6% in the general population. This is especially more likely to occur in individuals with decreased serum phosphate, decreased kidney reabsorption of phosphate, and increased serum 1,25(OH)2 vitamin D. The authors concluded that “all affected individuals and their first-degree relatives should be examined for renal calcifications.” In that study, only the carriers of mutations in the SLC34A3 gene were analyzed that have previously been established to lead to the disease, and that included deletion very similar to the one that was observed in the mother (but hers is even bigger).

Perhaps this should be noted and assessed further for potential health complications, even as a carrier of the condition.

In addition, the mom also had an autosomal dominant mutation, meaning only one mutated copy of the two genes obtained from her parents has to be affected to result in a condition. However, in this case it was not a clear diagnosis but rather the mutation was labelled as of uncertain significance. But because the mutation was such that its result would not produce an entire complete protein, but only a portion of it, the mutation was flagged for the doctor’s attention. This was similar to what was seen with our young wife, but for the wife it was further justified by the presence of a clinical diagnosis potentially corresponding to the mutation. In the mother’s case, it also seems to be justified by her family history. But flagging variants of unknown significance is not usual, and the purpose of the report that the doctor receives is to minimize the delivery of such results. The recommendation in this case is to check the future status of this particular mutation once its clinical significance is better understood.

The mutation was in a FLG gene, which codes for filaggrin, an important component of the outer layers of the skin. With this in mind, it will not be surprising to hear that mutations in this gene can result in a skin disorder called atopic dermatitis, also known as atopic eczema and the FLG gene mutation is the most significant known risk factor for this condition. We are talking about dry itchy skin with red rashes, and the most common skin disease in the world. In the case of this individual, we know there is a significant family history of eczema and psoriasis among her siblings. Clearly, one of the parents passed on a mutation that affected a number of children, and since it is a dominant mutation, it will continue to do so with each successive generation as long as the mutation is passed on further.

FLG is a special type of a gene where a portion of it is composed of repeating units of the same DNA code over and over. Repeating units in the gene means there will be repeating units in the protein. Indeed, the gene actually first leads to the production of a massive structure called profilaggrin which is then cut up into filaggrin components that are used in the proper structural development of the skin. Filaggrin itself can also be further broken down to smaller units (amino acids which are the building blocks of proteins), that can help the skin retain moisture. Nothing in biology is simple!

Thus, the big question is whether the mother ever had episodes of eczema or skin occurrences earlier in life, and if so, then this genetic association can help confirm the cause of the condition in the family. It also points towards further potential habits such as the avoidance of skin irritants, although people who experience such serious skin issues appear to do so reflexively anyway.

But there might be another very important reason to carefully correlate the skin symptoms to this particular genetic mutation. There is now mounting evidence suggesting that compromised FLG gene function can increase the likelihood of developing different types of cancer, primarily through the enhanced possibility of viral infections. One study showed that FLG mutation carriers are twice as likely to experience human papilloma virus related cancers, in a Danish population. These cancers include cervix, vagina, vulva, penis, anus and head and neck. If you are wondering why, filaggrin proteins are also expressed in the oral cavity, cervix, endometrium, and vagina. The increased risk was noted for cervical cancers and all human papilloma virus related cancers grouped together.

The association between the FLG mutations and head and neck cancer was also observed in a Chinese population study. In addition, that study also showed that FLG gene mutations could be linked to gastric cancer development, both when the cancer was associated Epstein-Barr virus infection or not. However, these studies look at ethnic specific mutations.

In the context that the impact of this mutation is not actually understood, this leaves a difficult decision to be made as to whether preventive measures such as vaccines and screening should be implemented. The findings associated with the FLG gene mutation and an increased risk of cancers is also fairly new. Once again, perhaps the patient’s understanding of their own history reported to her doctor will be the determining factor of how to move forward.

One thing is certain, genetic testing opens a new level of complexity in terms of potential medical management, as we are talking about potentially catching conditions prior to their development; conditions that can have a highly variable presence of symptoms or that might not ever materialize at all! It leads to difficult decisions between being proactive to maintain the best quality of health, and over-diagnosing with the excessive use of already-limited healthcare resources to try to catch something that might never even exist. On the other hand, the same can be said of every time someone goes for a physical check up. It is a rudimentary screening process aimed at catching problems before they become much bigger to deal with. Most of the time the test itself will be an unnecessary cost. The best form of action will likely depend on each individual case, and likely many missteps will be encountered before genomic medicine becomes fully entrenched as a routine.

Probably the most important news is that the mother did not pass any of her mutations onto her son, if these mutations have some underlying impact on health that we yet do not know.

The summary of the medically relevant genetic mutations in the sequenced family is presented below as a form of a pedigree. We recommend that every family should chart their family history in detail. This will be valuable information to any treating doctor anyway. On top of that, it might be very important information once a family decides to start sequencing their genomes, whether for proactive reasons like our family did, or whether for diagnosing a specific disease that might remain a mystery by clinical diagnosis.

This story emphasises the fact that DNA sequencing to screen for medical conditions is not trivial and the results might not be easy to interpret in terms of management. In the case of our family, the genetic results might have pinpointed the origins of two conditions, a predisposition to ulcerative colitis and atopic dermatitis without further recourse in terms of treatment benefits. However, these are still significant findings as the observed mutations have previously not been linked to the development of these conditions. Perhaps in time we will also learn that it pinpointed the origin of the symptoms found in father as well. This episode also points to the fact that DNA carrier status can be far more complicated and can contribute to symptoms that otherwise would not be understood, especially as to the cause of their origin. Perhaps it can even offer some intervention if the science reviewed in this post checks out. Finally, it points to potential reproductive decisions. The husband dodged two potential issues. He did not inherit the HFE gene mutation from his father. If he did, both he and his wife would be carriers of the same condition, potentially exposing their child to the risk of disease development. The condition might not have been serious enough to warrant in- vitro fertilization, but it illustrates the point of how easily diseases can materialize out of nowhere. He also did not inherit the FLG gene mutation from his mother, which appears to act in a dominant fashion to cause skin problems on the mother’s side of family.

If you are interested in your own genome sequencing journey, Merogenomics can aid you in accessing quality DNA tests for the benefit of your treating doctor. When it comes to full genome sequencing, choose your test wisely, or let an expert select the right test for you. Once you do, the complicated but amazing world of genetic mysteries will await you.

Happy genome sequencing!

This article has been produced by Merogenomics Inc. and edited by Kerri Bryant. Reproduction and reuse of any portion of this content requires Merogenomics Inc. permission and source acknowledgment. It is your responsibility to obtain additional permissions from the third party owners that might be cited by Merogenomics Inc. Merogenomics Inc. disclaims any responsibility for any use you make of content owned by third parties without their permission.

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