Amyotrophic lateral sclerosis

 My name is Antony Rizk and I am a senior at UIUC studying MCB and Kinesiology. I have a deep interest in genetics and as a result for this course in IB 364 I had to choose a disease to study and find a gene that is stongly associated with it. So, that landed me with Amyotrophic Lateral sclerosis (ALS) and a gene that is strongly related to this disease which is Superoxide dismutase 1. I have shadowed with a neurosurgeon before and I myself want to be an orthopedic surgeon, so I was interested in really understanding this disease as I have an extra interest in a disorder that affects the nervous and musculoskeletal system.

ALS was often referred to as Lou Gherrigs disease after the famous baseball player died from it two years after being diagnosed. It is a neurodegenerative diseases that affects the motor neurons in the spinal cord, nerves and brain. To this day the average rate of diagnosis is about 5 per 100,000 people which makes it a relatively rare disease, but still does affect a large number of people. The interesting thing about SOD1 is that it is found in almost every cell of the body and its primary role is to neutralize free radicals which are anyways generated as a normal part of human metabolism. So, mutations in this gene can affect how the body deals with free radicals and specifically if free radicals are left to roam, they can damage many different parts of the body.

There are many ways to study disease onset and progression. In terms of relation to a disease regarding a gene that codes for a protein, there are multiple techniques that can be used to determine both expression and differences between control/wild type variants and disease variants. Furthermore, the study of genetics can go beyond just pre-transcriptional variations but also through epigenetic changes which are post transcriptional modifications that can be inherited and or altered based on the environment. This is particularly what makes the study of genetics so interesting because on top of how each of us differ genetically from each other based on the sheer amount of information present within each of our cells, the concept of how our genes will react with the environment and thus manifest physically is something that there is still so much to be discovered on for both ALS and other diseases.  

In terms of genomics, there have been many variants of SOD1 genes observed in human and animal models that are tied to ALS or ALS like symptoms, despite the differences in SOD1 structure across species. Some variants are more so associated with ALS, but this does not mean the body is wrong in making these variants. The body itself does not code for disease on its own and certain variants may confer benefits in other areas as Matt Ridley author of Genome: the autobiography of a species in 23 chapters would argue. Genomics are a powerful tool to use to identify genetic factors for a disease, epigenetic modifications to genes associated with disease, creating precise drugs, and overall understanding disease mechanics to help prevent onset or worsening of the disease. These can be done through many genomic methods and techniques such as Whole genome sequencing (WGS), Whole exon sequencing (WES), Genome wide association studies (GWAS), epigenomics, proteomics, and many more. Throughout this blog we will  be looking at the use of all these genomic techniques and how they are used for the study of ALS and its association with SOD1. We will also discuss information on screening, prevention, and treatment. Everything will be broken up into sections for ease of information usage and organization. 

Structure and Role of SOD1

SOD1 is composed of 154 amino acids in length and has a mass of 15,936 Da. The gene that codes for superoxide dismutase 1 (SOD1) is localized on chromosome 21.  The main role it plays in the body is destroying free radicals within the body as a normal part of both aerobic and anaerobic metabolism. It acts as a homodimer to convert naturally occurring but very harmful superoxide radicals into oxygen and hydrogen peroxide. It also has been found to have a peptide that displays antibacterial, anti fungal, and anti-MRSA activity. So, when these free radicals are left unchecked as would be the function in a mutant version of SOD1, the free radicals would damage certain parts of the body and thus the progression of ALS is left leading to also sorts of neurological defects that eventually becomes paralysis across all the limbs and leads to the eventual death of the patient. Furthermore, it has been found that people with ALS have altered immune function and that having a pre diagnosed auto immune condition can lead to an increased likelihood of being diagnosed with ALS. Based on genomic data for the localization of SOD1 which itself is an intracellular protein, it was found mainly in the  nucleoplasm, plasma membrane & cytosol. Of all the portions in the brain, it is most expressed in the pons which is a portion of the brain stem. This makes sense as to why ALS affects motor function since if this area of the brain is affected, it would greatly affect movement of a person. This information was utilized through a genomic technique of immunofluorescence which is when an antigen is used to tag specific tissues and thus find the localization of certain proteins within cells. A common piece of genetic knowledge is that every single cell of the body contains all the same information as in all the DNA present in the body is encoded into each cell, but different cells just express different genes within each part of the coded DNA to differentiate into different tissues in the body. So, when it comes to SOD1, it is localized within the  nucleoplasm, plasma membrane & cytosol of the cell, but in terms of where on the body it is most concentrated in, it is mainly found in the liver and kidneys. This is interesting considering that dysfunction of this protein is mainly attributed to ALS which mainly presents with neurological symptoms. However we have to consider the context of this where the liver and kidneys are the main sites for detoxifying the body and thus antioxidant activity within these two areas would be high and are most likely coupled with many other proteins as well, whereas the nerves of the body may be more sensitive and thus more susceptible to damage. Overall, SOD1 has a very important role in the body which is why it is the main protein of concern when it comes to ALS based on how common it was found to be among people who suffer with ALS.  Here is a protein image of ALS obtained from the protein data bank.

SOD1 phylogeny

SOD1 is relatively conserved among most species, yet there are a few differences. Considering that it is found in many species much simpler than humans, it highlights the importance of this gene overtime and how why it is relatively conserved among species. For example based on this multiple alignment technique from the NCBI using Constraint-based Multiple Alignment Tool it showed how relatively conserved SOD1 is among many different species as seen here

Furthermore, we can see based on this phylogeny tree how how SOD1 diverged overtime with the closest relative being the ORangutan to humans. However, they live long lives and cannot easily be used for experiments so rodents are the next closest to humans on this phylogeny tree. They reproduce quickyl and their sequences for SOD1 are still relatively similar to humans, although human SOD1 put into rats has been found to elicit symptoms close to that of ALS. Furthermore, ALS like disease in other animals have been observed with mutations in SOD1 also associated with disease onset such as in dogs.

Mutations and Epigenetic associated with SOD1

There are two genetic variations that have been linked to ALS. One has been a repeated expansion in the C9orf72 gene and the other being a missense mutation which is when a different amino acid is coded than the original amino acid at a certain position in the SOD1 gene. There are multiple different missense SOD1 mutations at different locations that have been found to lead to similar progression of ALS of which can be found at the protein data bank where the different structures can be viewed. In terms of epigenetic changes regarding SOD1 there have not been many conclusive studies found on this, but considering that less than 10 percent of cases of ALS are familial and over 90 percent are sporadic, then ALS would be more likely to have environmental and/or epigenetic modifications associated with it. However, when it came to the environment a cohort study done by Korner et al. in 2019 assessed many environmental/lifestyle factors to see if they correlated with ALS such as physical activity, diet, smoking status, residential environment, and potential toxin exposure before symptom onset and throughout the course of the disease. The study did not find any conclusive or statistically significant data on lifestyle factors that can contribute to ALS. So, when it came to epigenetic modifications regarding ALS a twin study found that pairs of twins with ALS were classified as epigenetically older, and all ALS patients commonly had differences between them and normal pairs in CPG islands that involve GABA signaling, and other important neurobiological functions like glutamate metabolism. Glutamate is also an important component of glutathione which is the one of the bodies main antioxidants, so this could make sense as free radical damage is tied to being "biologically older". Therefore, free radical damage may cause advanced aging and possible different methylation patterns in different genes which are associated with ALS. This is important because it provides insight that certain genes are being either up or down regulated and if scientists can figure out what epigenetic changes are taking place, it can lead to better treatment outcomes for ALS patients.

Screening, Prevention, and Treatment

There is no direct test for ALS, but it is mainly  based around the symptoms present with testing for upper and lower motor neuron degeneration based on muscle weakness in the areas these control, as long as other neurological diseases are ruled out. Genetic tests can be used, but the interesting thing is that SOD1 mutations are not definitive in leading to ALS. Therefore, it is a combination of factors that would eventually lead for someone to be diagnosed with ALS. ALS also affects those over 40 and the risk of being diagnosed with ALS being very rare before 40 and increasing exponentially from 40 onwards. In terms of prevention for ALS, there is sadly nothing that has been found to be effective. Often people only find out they have ALS because they start presenting with symptoms and get tested by a professional. Furthermore, once symptom onset begins, patient death usually occurs within 2-5 years. However, there are emerging treatments for ALS that are not cures but help slow disease progression. A recent analysis done by  Tzeplaeff et al., in 2023 found that The main deficiencies/compromised systems in ALS are Oxidative stress, excitotoxicity, mitochondrial and proteasomal dysfunctions, RNA metabolism, altered synaptic function, disturbed axonal transport, and neuroinflammation. So through genomic techniques used to study disease mechanisms, drugs such as the antioxidant Edaravone which deals with the oxidative stress associated with ALS often associated with a compromised SOD1 gene can serve as an effective treatment in slowing disease progression.

Conclusion and Questions for the Future

In Conclusion, ALS still has no treatments, although the rate of diagnosis is relatively the same. I believe there are still some questions that are left to be answered and directions to be looked at for possible forms of prevention. For example, certain nutrients are found to play an important role in neurological health such as cholesterol for maintaing myelin sheaths, Omega 3 fatty acids, B vitamins such as thiamin, and minerals such as magnesium. Furthermore, the minerals copper and zinc are important for sod1 functioning as they are both part of the protein complex and thus maintaining dietary status of both of these may play an important role in possible protection from ALS. Considering the number of cases related to nutritional deficiencies and the rise of diseases preventable through nutritional means, it is worth considering to look at possible alterations or mutations in copper and zinc metabolism in individuals as another means to assess risk for ALS. Overall, there are many avenues of thought for ALS and more research is needed to help treat ALS once and for all. Thank you very much for reading my blog and I hope you have been well informed on ALS!