Friedreich’s Ataxia


By: Suban Farah as part of the Neurodegenerative Disorders group


Neurodegeneration (or neurodegenerative disorders) is the umbrella term for the types of conditions that are representative of proFriedreich'S_Ataxia-1.jpggressive damage of nerve tissue in the brain, in which some bodily functions gradually deteriorate. Friedreich’s Ataxia (FA), named after German physicist Nikolaus Friedreich, is one of the specific conditions classified as a neurodegenerative disorder. It is characterized by progressive loss of nerve tissue in the spinal cord that results in weakened muscle coordination.[1] FA is a rare disease with early onset but, with a prevalence rate of roughly 1 in 50,000, it is also known to be the most common inherited ataxia.[2] This disorder is caused by an abnormal expansion of GAA·TTC repeats in the frataxin (FXN) gene.[1]
Although gait abnormality is the first symptom to appear in individuals, other associated symptoms of FA include dysarthria, hearing and vision impairment, scoliosis, diabetes, and heart disease.[2] Similar to many other neurodegenerative diseases, there is currently no cure for FA. However, some of the symptoms and associated complications of FA can be treated to help individuals improve the quality and duration of their life. Thus, individuals with FA may benefit from treatment such as speech therapy, physical therapy, and pharmacotherapy.[2]
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3.1 Genetic Component:


3.1.1 Inheritance Pattern

Friedreich’s Ataxia has an autosomal recessive inheritance pattern.[1] Thus, for an individual to be affected there must be a mutation in both copies of the FXN gene in each cell. Each parent of an individual with FA carries at least one copy of the mutated gene; however, as a carrier, they generally would not display any signs and symptoms of the condition.

3.1.2 Cause of Friedreich's Ataxia

FA is caused by a mutation in the FXN gene. This gene is made up of seven exons covering roughly 80 kb of DNA[3]. It is mapped on chromosome 9q13 and codes for a protein called frataxin.[3] Similar to other neurodegenerative diseases, such as Huntington’s, a trinucleotide expansion is responsible for causing this condition. In the first intron of the FXN gene (which is ~11 kb long), there are a number of GAA·TTC repeats located in the middle of an Alu sequence[3,4]. Normal individuals have up to 36 repeats; however, individuals with FA have an abnormal triplet expansion, where repeats often range anywhere from 70 to upwards of a 1000. The severity of this condition is correlated with the number of GAA·TTC repeats found in the FXN gene.[5]
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As well, there is an inverse relationship between the number of repeats and FXN gene production, wherein the expanded triplet repeats cause a deficit in the amount FXN mRNA, thus, resulting in decreased levels of frataxin. As a result of abnormal triplet expansion, FXN mRNA production is 4%-29%[6]of typical levels. Frataxin is essential for maintaining proper mitochondrial function, which is, consequently, important for muscle and nerve cells. It is highly expressed in the granular layer of the cerebellum, the dorsal root ganglia, as well as muscles and the heart.[7]




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Figure 1. Diagram showing triplex formation leading to a pause at the promoter distal end of the structure

3.1.3 Ways Triplet Expansion Can Affect Gene Expression


3.1.3a Triplet Repeats Can Intrinsically Block Transcription Elongation


Past experiments have examined only isolated, uninterrupted GAA·TTC repeats – excluding other frataxin gene sequences to ensure there would be no other confounding factors. Accordingly, by using T7 RNA polymerase, researchers wanted to determine whether, in fact, levels of transcript vary depending on the length of triplet repeats in the template strand. Thus, they observed that gradually increasing the number of repeats, the amount of RNA produced decreased.[8] Hence, proving that there is an inverse relationship between GAA·TTC length and the production of FXN mRNA.
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In addition, GAA·TTC repeats can result in an uncommon, yet stable, DNA structure that impedes transcription.[8] Since the triplet repeats are purine-pyrimidine polymers (R-Y), they can assume different structural forms, such as triplexes (R-R-Y or Y-R-Y) -- 'called sticky DNA'.[8,9] In this same study, it was also found that the formation of triplexes in vitrocould cause RNA polymerase to pause and become sequestered in the distal end of the triplet tract (Figure 1).(8,10) As a result, blocking transcription elongation and reducing cellular frataxin levels.

3.1.3b Aberrant Splicing


Since the triplet expansion is located in the first intron, research has been conducted to figure out how the abnormal repeats lead to reduced frataxin production if they normally should be spliced out. Interestingly, Baralle et al. (2008) observed that the deficit of FXN mRNA in FA is a result of atypical mRNA splicing, wherein intron 1 is retained.[3] In their experiment hybrid minigenes (pEDA) were used to examine the effect of GAA and TTC repeats on transcription and pre-mRNA processing. GAA or TTC repeats (n=100) were cloned in various intronic positions along the pEDA construct, then the resulting minigenes were transfected into COS-7 cells. The effects observed with the insertion of the GAA repeats differed from that of the corresponding TTC minigene. An important difference was that GAA repeats induced retention of upstream and downstream introns and the exclusion of exons.[3] Thus, facilitating an aberrant splicing mechanism.
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Splicing differences between FA affected and unaffected transcripts

In an attempt to examine this mechanism some more, they observed that expanded GAA repeats actually a block in the turnover of an upstream intermediate (iUP). As a result, iUP accumulates and is not processed into mature mRNA. The researchers behind this study hypothesized that the accumulation of this intermediate can be attributed to the binding of splicing factors (such as PABPN1, hnRNPA1, hnRNPA2, and many from the serine/arginine [SR] protein family) to GAA repeats. Consequently, preventing their typical assembly at the splice junctions, thus, leading to degradation and a lower abundance of mature mRNA. Although this is a major discovery for FA research, the splicing abnormalities in the frataxin minigene were found to be context and position dependent.[3]


3.1.3c Chromatin Involvement in Gene Silencing

Brain cells and lymphoblasts from FA affected patients all show a similar pattern – an FXN mRNA deficit. The area flanking the repeat on FA alleles is associated with decreased acetylation or a great deal of DNA methylation compared to genes of unaffected individuals.[11] This region is also enriched for histone modifications that are characteristic of transcriptionally repressed genes. It has been found that the methylation protection of 3 CpG residues, typically seen upstream of the GAA repeat on unaffected alleles, is also lost. One of these residues, residue 13, is within an enhancer box site that is important for promoter activity in reporter assays in mouse myoblast cells.[12]
Usually, without expanded GAA repeats, intron 1 binds proteins that positively affect FXN transcription. This binding creates natural ‘methylation footprints’ by protecting the binding sites from DNA methylation. The access of these proteins to DNA is hindered when more compact chromatin are formed on the FXN gene due to expanded triplet repeats. This notion is supported by the disappearance of ‘methylation footprints’ in FA affected alleles. Hence, reduction in transcription initiation can stem from the lack of binding of these transcription factors that normally protects those CpG residues from methylation – the loss of the normal ‘methylation footprint'.[12]
As well, in FA affected cells, a direct relationship between the extent of DNA methylation and the number of triplet repeats has been discovered.(13) This is logical since FA severity is related to repeat length; therefore, a relationship between disease severity and DNA methylation should also exists. Since chromatin compaction is associated with high levels of H3K9Me2 (Histone 3 at lysine 9), in a relatively recent experiment, the first intron was examined in four FA patients for the presence of this histone modification. Results illustrated that, indeed, these individuals exhibited high levels of H3K9Me2 and had only 10–30% of the FXN mRNA seen in unaffected individuals.[1] Therefore, this demonstrates that chromatin changes may be accountable for causing Friedreich’s ataxia.

3.1.4 Effects of Transcription Factors on mRNA Levels

Li et al. (2010) have found that a decreased level of frataxin gene transcription is most likely a result of reduced accessibility to the promoter by transcription factors.[14] Prior to their study, specific transcription factors influencing FXN gene expression were not known. However, in conducting their research, they identified two regulatory factors, SRF and TFAP2, which bind to the FXN promoter region.[14]
To investigate whether these two transcription factors are involved in frataxin expression, SRF and TFAP2 were over-expressed in either lymphoblasts from a FA affected individual or a healthy individual. Interestingly, they observed that an over-expression of these transcription factors in FA lymphoblasts significantly increased levels of frataxin mRNA compared to that of the healthy control individual, in which there were no significant effects. Thus, these results suggest that SRF and TFAP2 can play a role in regulating frataxin expression. Furthermore, this research is important because these findings can help in the identification of new treatment techniques for FA, which can aid in slowing disease progression.[14]


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3.2 Treatment


3.2.1 Idebenone

Idebenone is a powerful antioxidant drug that was first introduced into markets in 1986. It is a synthetic short-chain benzoquinone that is similar in structure to coenzyme Q. It is used to alleviate some of the symptoms associated with FA.[14] It has been shown to be effective in decreasing the level of oxidants that are believed to hinder neurological function and cause heart problems in patients with Friedreich's ataxia.[2]

3.2.2 Histone Deacetylase Inhibitors

Histone deacetylase (HDAC) inhibitors have been found to reverse gene silencing in patients affected by Friedreich’s ataxia.[15] Previous experiments have demonstrated that GAA·TTC expansions can induce a number of changes in chromatin structure; thus, HDAC inhibitors are used to counter histone acetylation in order to reduce gene silencing, thereby promoting
frataxin expression.[16] Although HDAC inhibitors were successful in increasing frataxin in FA affected lymphocytes, they may have a few limitations. For instance, scientists are still unaware of whether the effect of these inhibitors is replicable in neurons and cardiac myocytes that are also affected in FA patients. As well, it is still unknown if HDAC inhibitors have any affects on the transcription of other genes. Therefore, further research must still be done before this form of treatment is deemed a ‘holy grail’ treatment for FA patients.



See Also:




References

  1. Kumari, D., Biacsi, E.R., & Usdin, K. Repeat expansion affects both transcription initiation and elongation in Friedreich ataxia cells. The Journal of Biological Chemistry. 286. 4209–4215 (2011)
  2. Tsou, A.Y., Friedman, L.S., Wilson, R.B., & Lynch, D.R. Pharmacotherapy for Friedreich ataxia. CNS Drugs. 23(3), 213-223 (2009)
  3. Baralle, M., Pastor, T., Bussani, E., & Pagani, F. Influence of Friedreich ataxia GAA noncoding repeat expansions on pre-mRNA processing.The American Society of Human Genetics. 83. 77-88 (2008)
  4. Clark, R.M., Dalgliesh, G.L., Endres, D., Gomez, M., Taylor, J., Bidichandani, S.I. Expansion of GAA triplet repeats in the human genome: Unique origin of the FRDA mutation at the center of an Alu. Genomics. 83. 373-383 (2004)
  5. Schmucker, S., & Puccio, H. Understanding the molecular mechanisms of Friedreich’s ataxia to develop therapeutic approaches. Hum. Mol. Genet. 19(1), R103-R110 (2010)
  6. Campuzano, V. et al. Frataxin is reduced in Friedreich ataxia patients and is associated with mitochondrial membranes. Hum Mol Genet. 6. 1771-1780 (1997)
  7. Rotig, A. et al. Aconitase and mitochondrial iron-sulphur protein deficiency in Friedreich ataxia. Nat Genet. 17. 215-217 (1997)
  8. Grabczyk, E., Usdin, K. The GAA*TTC triplet repeat expanded in Friedreich's ataxia impedes transcription elongation by T7 RNA polymerase in a length and supercoil dependent manner. Nucleic Acids Res. 28. 2815-2822 (2000)
  9. Jain, A., Rajeswari, M.R., Ahmed, F. Formation and thermodynamic stability of intermolecular (R*R*Y) DNA triplex in GAA/TTC repeats associated with Freidreich's ataxia. J Biomol Struct Dyn. 19. 691-699 (2002)
  10. Grabczyk, E., Mancuso, M., Sammarco, M.C. A persistent RNA.DNA hybrid formed by transcription of the Friedreich ataxia triplet repeat in live bacteria, and by T7 RNAP in vitro. Nucleic Acids Res. 35. 5351-5359 (2007)
  11. Greene, E., Mahishi, L., Entezam, A., Kumari, D., Usdin, K. Repeat-induced epigenetic changes in intron 1 of the frataxin gene and its consequences in Friedreich ataxia. Nucleic Acids Res. 35. 3383-3390 (2007)
  12. Castaldo, I. et al. DNA methylation in intron 1 of the frataxin gene is related to GAA repeat length and age of onset in Friedreich ataxia patients. J Med Genet. 45. 808-812 (2008)
  13. Li, K., Singh, A., Crooks, D.R., Dai, X., Cong, Z., Pan, L., Ha, D., Rouault, T.A. Expression of human frataxin is regulated by transcription factors SRF and TFAP2. PLoS One. 5. e12286 (2010)
  14. Tonon, C., Lodi, R. Idebenone in Friedreich’s ataxia. Expert Opin. Pharmacother. 9(13). 2327-2337 (2008)
  15. Festenstein, R. Breaking the silence in Friedreich's ataxia. Nat Chem Biol.2. 512 - 513 (2006)
  16. Herman, D., Jenssen, K., Burnett, R., Soragni, E., Perlman, S.L., Gottesfeld, J.M. Histone deacetylase inhibitors reverse gene silencing in Friedreich's ataxia. Nat Chem Biol, 2. 551-558 (2006)