Moving beyond DNA: A brief history of epigenetics

Posted February 18, 2016 in Episona Blog by Mike Karsian

The search for new therapies for Friedreich's Ataxia based on epigenetics is more and more relevant , but, what does epigenetics mean?. In this post we can find a brief informative explanation in layman words about epigenetics, and the chronology of discoveries in which current knowledge is based.

Targeted RNA or BDNF gene transfer protects against frataxin deficiency

Ian Fyfe, Research Highlight: Nature Reviews Neurology (2016), doi:10.1038/nrneurol.2016.19, Published online 26 February 2016

In two recently published studies, the pathological consequences of this FXN mutation have been successfully counteracted in in vitro and in vivo models with the use of different approaches, each with therapeutical potential.

-In the first study, David Corey and colleagues introduced synthetic anti‑GAA duplex RNA molecules into patient-derived cells that had the FXN mutation, this increased expression of frataxin by up to sixfold. They believe that their findings are a starting point for the development of RNA-based drugs, and are looking to take the next step.

-The second study, led by Javier Diaz-Nido, did not involve targeting the FXN gene, but aimed to block the apoptosis. Neurotrophic factors are potent suppressors of neuronal apoptosis, they were able to protect neurons from death triggered by frataxin gene silencing”. Now, they plan to test whether there is a synergy between two gene therapy strategies: one based on frataxin gene replacement and the other based on neurotrophic factor gene delivery

ORIGINAL ARTICLES:
-Katsu-Jiménez, Y. et al. Gene transfer of brain derived neurotrophic factor (BDNF) prevents neurodegeneration triggered by frataxin deficiency. Mol. Ther.
-Li, L. et al. Activating frataxin expression by repeat-targeted nucleic acids. Nat. Comm.

Genotoxicity in Mice Following AAV Gene Delivery: A Safety Concern for Human Gene Therapy?

Randy J Chandler, Matthew C LaFave, Gaurav K Varshney, Shawn M Burgess and Charles P Venditti; (Nature) Molecular Therapy 24, 198-201 (February 2016) | doi:10.1038/mt.2016.17


Given the lack of therapies for the many diseases that rAAV gene therapy promises to treat, such as lethal inborn errors of metabolism, the risk of toxicity imposed by rAAV exposure will need to be balanced against the significant benefits offered by effective gene therapy, which for some patients could be lifesaving.

Although the lack of natural pathogenicity and the capacity for effective gene delivery coupled with stable, long-term gene expression have supported the advancement of rAAV as an optimal vector for human clinical trials, recent studies in mice have challenged the belief that rAAV is an innocuous gene therapy vector.

MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression

Paugh SW, Coss DR, Bao J, Laudermilk LT, Grace CR, Ferreira AM, M. Brett Waddell, Granger Ridout, Deanna Naeve, Michael Leuze, Philip F. LoCascio, John C. Panetta, Mark R. Wilkinson, Ching-Hon Pui, Clayton W. Naeve, Edward C. Uberbacher, Erik J. Bonten, William E. Evans (2016); PLoS Comput Biol 12(2): e1004744. doi:10.1371/journal.pcbi.1004744

OPEN ACCESS

Friedreichs ataxia, the most common form of ataxia in humans, is caused by the expansion of a (GAA)n repeat in intron 1 of the Frataxin gene, which in turn results in transcriptional silencing, presumably because of the triplex-forming potential of the (GAA)n repeat. This suggests that, not only may the formation of DNA triplexes be a well-conserved and essential mechanism to regulate gene transcription, but that stable or prolonged triplex formation may have undesirable consequences.

Friedreich ataxia is not only a GAA repeats expansion disorder: implications for molecular testing and counselling

Dorota Hoffman-Zacharska , Tomasz Mazurczak, Tomasz Zajkowski, Renata Tataj, Paulina Górka-Skoczylas, Katarzyna Połatyńska, Łukasz Kępczyński, Mariusz Stasiołek, Jerzy Bal; Journal of Applied Genetics
pp 1-7 DOI:10.1007/s13353-015-0331-4 First online: 23 February 2016

Routine FRDA molecular diagnostics is focused on (GAA)n expansion analysis. Additional tests are considered only in cases of heterozygous expansion carriers and an atypical clinical picture. Analyses of the parent’s carrier status, together with diagnostic tests, are performed in rare cases.

Combined Cerebellar Proton MR Spectroscopy and DWI Study of Patients with Friedreich’s Ataxia

Laura Ludovica Gramegna, Caterina Tonon , David Neil Manners, Antonella Pini, Rita Rinaldi, Stefano Zanigni, Claudio Bianchini, Stefania Evangelisti, Filippo Fortuna, Valerio Carelli, Claudia Testa, Raffaele Lodi; The Cerebellum pp 1-7, First online: 20 February 2016 DOI: 10.1007/s12311-016-0767-z

The correlation between NAA/Cr and the severity of disability suggests that this biochemical in vivo MR parameter might be a useful biomarker to evaluate therapeutic interventions.

CNS Drug Delivery: Beyond the Spinal Cord

Recently the intrathecal administration has been proposed as part of a hopeful therapy for FA (Intrathecal delivery of frataxin mRNA encapsulated in lipid nanoparticles to dorsal root ganglia as a potential therapeutic for Friedreich’s ataxia). This paper shows (in laboratory animals) the feasibility of the use of intrathecal administration to reach efficiently the dorsal root ganglia.

This presentation explains the current state of the art in other neurological diseases in which it is required reach the CNS.

Mission: Improve outcomes for epileptic patients who don’t respond to conventional treatments by administering reformulated, micro-doses of anti-epileptic drugs directly to the brain.

Retrotope Advances RT001 in Clinical Trials to Treat Friedreich's ataxia

(Ref: Marketwired) February 22nd, 2016

LOS ALTOS, CA--(Marketwired) - Retrotope, a privately held clinical stage pharmaceutical company, today announced the successful completion of the first dose cohort and the opening of patient enrollment for the highest dose cohort in its ongoing 28-day study of orally dosed RT001 in Friedreich's ataxia (FA) patients. RT001 was well tolerated and no serious adverse events or dose limiting toxicities were observed.

Long-term effect of epoetin alfa on clinical and biochemical markers in friedreich ataxia

Saccà, F., Puorro, G., Marsili, A., Antenora, A., Pane, C., Casali, C., Marcotulli, C., Defazio, G., Liuzzi, D., Tatillo, C., Cambriglia, D. M., Schiano di Cola, G., Giuliani, L., Guardasole, V., Salzano, A., Ruvolo, A., De Rosa, A., Cittadini, A., De Michele, G. and Filla, A. (2016), Long-term effect of epoetin alfa on clinical and biochemical markers in friedreich ataxia. Mov. Disord.. doi: 10.1002/mds.26552

Although results are not in favor of an effect of epoetin alfa in Friedreich ataxia, this is the largest trial testing its effect. It is still possible that epoetin alfa may show some symptomatic effect on upper-limb performance. This study provides class I evidence that erythropoietin does not ameliorate VO2 max in patients with Friedreich ataxia.

Reversal of epigenetic promoter silencing in Friedreich ataxia by a class I histone deacetylase inhibitor

Yogesh K. Chutake, Christina C. Lam, Whitney N. Costello, Michael P. Anderson and Sanjay I. Bidichandani; Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw107 First published online: February 20, 2016

OPEN

We conclude that repeat-mediated epigenetic promoter silencing in FRDA is mediated by class I HDACs, and it is reversible via treatment with specific inhibitors. It is noteworthy that the correction of both the structural and functional defects of the FXN promoter in FRDA, albeit partial, occurs in its natural genomic context, i.e. while in continued physical proximity to the cis-acting expanded GAA-TR sequence. These features bode well for the development of class I HDAC inhibitors as a rational therapeutic modality for FRDA.

UNC gene therapy spinout Bamboo Therapeutics raises $49.5M Series A

Startups, Biotech, By Meghana Keshavan http://medcitynews.com.

The startup’s developing gene therapies for rare neurologic diseases, which include Giant axonal neuropathy (GAN), Canavan disease, Friedreich’s ataxia as well as Duchenne muscular dystrophy. Bamboo’s most advanced program is its therapeutic for GAN, which is currently in Phase 1/2 trials. CBS News ran a piece on Bamboo’s approach to GAN in October.

Agilis Biotherapeutics and Waisman Biomanufacturing Enter Into Exclusive Manufacturing Agreement for Friedreich’s Ataxia Gene Therapy

February 18, 2016,  CAMBRIDGE, Mass. & MADISON, Wis.--(BUSINESS WIRE)--Agilis Biotherapeutics, LLC (Agilis), a biotechnology company advancing innovative gene therapies for rare genetic diseases that affect the central nervous system (CNS), and Waisman Biomanufacturing, a non-profit gene and cell therapy development and manufacturing group located at the UW-Madison Waisman Center, (Waisman) announced today that the companies have entered into an exclusive partnership agreement for the production of Agilis’ novel gene therapy product, AGIL-FA, for the treatment of Friedreich’s ataxia (FA).

Intrathecal delivery of frataxin mRNA encapsulated in lipid nanoparticles to dorsal root ganglia as a potential therapeutic for Friedreich’s ataxia

Joseph F. Nabhan, Kristy M. Wood, Varada P. Rao, Jeffrey Morin, Surya Bhamidipaty, Timothy P. LaBranche, Renea L. Gooch, Fazli Bozal, Christine E. Bulawa & Braydon C. Guild; Nature, Scientific Reports 6, Article number: 20019 (2016) doi:10.1038/srep20019

OPEN

When FXN LNPs were delivered by intrathecal administration, we detected recombinant human FXN protein in DRG. These observations provide the first demonstration that RTT can be used for the delivery of therapeutic mRNA to DRG.
Remarkably, greater than 50% mFXN protein derived from LNPs was detected seven days after intravenous administration of FXN LNPs, suggesting that the half-life of mFXN in vivo exceeds one week.

Understanding the Role of Mitochondrial Pathophysiology in Friedreich's Ataxia

Rosella Abeti, Michael H. Parkinson, Iain P. Hargreaves, Mark A. Pook, Andrey Y. Abramov, Paola Giunti, Biophysical Journal, Volume 110, Issue 3, Supplement 1, 16 February 2016, Page 474a, ISSN 0006-3495, doi:10.1016/j.bpj.2015.11.2534.

By using functional microscopy and biochemical techniques we were able to demonstrate that mitochondria are deregulated in neurons from the FRDA mouse models.

Scientists find potential treatment for Friedreich’s ataxia

UT Southwestern, Newsroom. DALLAS – Feb. 16, 2016 – Researchers at UT Southwestern Medical Center have identified synthetic RNA and DNA that reverses the protein deficiency causing Friedreich’s ataxia, a neurological disease for which there is currently no cure.

Astrocyte Resilience to Oxidative Stress Induced by Insulin-like Growth Factor I (IGF-I) Involves Preserved AKT (Protein Kinase B) Activity

David Dávila, Silvia Fernández and Ignacio Torres-Alemán; The Journal of Biological Chemistry, 291, 2510-2523. doi: 10.1074/jbc.M115.695478

These results point out the importance of AKT activation for astrocyte survival during oxidative stress and reinforce the idea that modulation of astrocytes by IGF-I forms part of the brain responses to oxidative damage.

Energy metabolism in neuronal/glial induction and iPSC-based modeling of brain disorders

Barbara Mlody, Carmen Lorenz, Gizem Inak, Alessandro Prigione; Seminars in Cell & Developmental Biology, Available online 11 February 2016, ISSN 1084-9521, doi: 10.1016/j.semcdb.2016.02.018.

Neurons derived from FRDAiPSCs recapitulated the characteristic features of the disease terms of GAA expansion as well as FRDA instability. Importantly, impaired mitochondrial function could be observed in derived neuronal cells, including decreased mitochondrial membrane potential and progressive mitochondrial degeneration. Hence, the iPSC system may represent a promising tool for advancing the understanding of the mechanisms of action and brain targeting of mitochondrial disorders due to both nuclear and mitochondrial mutations.

Usefulness of plasma high sensitive troponin t and Nt-proBNP in the diagnosis of cardiopathy in Friedreich ataxia,

Lise Legrand, Carole Maupain, Marie Lorraine Monin, Alina Tataru, Alexandra Durr, Françoise Pousset, Richard Isnard; Archives of Cardiovascular Diseases Supplements, Volume 8, Issue 1, January 2016, Page 25, ISSN 1878-6480, doi: 10.1016/S1878-6480(16)30075-1.

Plasma High sensitive troponin is a diagnostic marker of hypertrophic cardiomyopathy in Friedreich ataxia’s patients, whereas plasma Nt-proBNP is associated with cardiac events and could be a prognostic marker in these patients.

Human Frataxin Folds Via an Intermediate State. Role of the C-Terminal Region

Santiago E. Faraj, Rodolfo M. González-Lebrero, Ernesto A. Roman & Javier Santos; (Nature) Scientific Reports 6, Article number: 20782 (2016) doi:10.1038/srep20782

OPEN

The aim of this study is to investigate the folding reaction of human frataxin, whose deficiency causes the neurodegenerative disease Friedreich’s Ataxia (FRDA). The characterization of different conformational states would provide knowledge about how frataxin can be stabilized without altering its functionality.

Ferroptosis: process and function

Y Xie, W Hou, X Song, Y Yu1, J Huang, X Sun, R Kang and D Tang; Cell Death and Differentiation (2016) 23, 369–379; doi:10.1038/cdd.2015.158; published online 22 January 2016

OPEN

Ferroptosis is a recently recognized form of regulated cell death. It is characterized morphologically by the presence of smaller than normal mitochondria with condensed mitochondrial membrane densities, reduction or vanishing of mitochondria crista, and outer mitochondrial membrane rupture.

Gene transfer of brain derived neurotrophic factor (BDNF) prevents neurodegeneration triggered by frataxin deficiency

Y Katsu-Jiménez, F Loria, JC Corona, and J Diaz-Nido; Molecular Therapy accepted article preview 5 February 2016; doi: 10.1038/mt.2016.32

Co-injection of a herpesviral vector encoding for BDNF efficiently prevents both the development of cerebellar neuropathology and the ataxic phenotype. These data demonstrate the potential therapeutic usefulness of neurotrophins like BDNF to protect frataxin-deficient neurons from degeneration.

This work was supported by grants of the Spanish National Research Plan (SAF 2012-38042) and the Autonomous Government of Madrid (S2010/BMD-2331). Research at the authors laboratory is also supported by Friedreich Ataxia Research Alliance (FARA), Ataxia UK, FARA Ireland, Spanish FEDAES, GENEFA, Babel Family, Italian ASIA and Swedich BotaFA.

Activating frataxin expression by repeat-targeted nucleic acids

Liande Li, Masayuki Matsui & David R. Corey; Nature Communications 7, Article number: 10606 doi:10.1038/ncomms10606

Iintroducing anti-GAA duplex RNAs or single-stranded locked nucleic acids into patient-derived cells increases FXN protein expression to levels similar to analogous wild-type cells. Synthetic nucleic acids that target GAA repeats can be lead compounds for restoring curative FXN levels.

Pluripotent stem cells in disease modelling and drug discovery

Yishai Avior, Ido Sagi & Nissim Benvenisty; Nature Reviews Molecular Cell Biology (2016) doi:10.1038/nrm.2015.27 Published online 28 January 2016

The ability to model human diseases using cultured PSCs has revolutionized the ways in which we study monogenic, complex and epigenetic disorders, as well as early- and late-onset diseases. Despite the promising future of PSC-based therapies, there are still substantial hurdles between its potential and its fulfilment. In the future, we expect to have repositories of PSCs that will enable the modelling of practically any genetic disease.
 Examples of drug screening in Friedreich's ataxia using patient-derived induced pluripotent stem cell models: Forskolin and RG2833

Menlo Park biotech buys French company, Annapurna Therapeutics

Silicon Valley Bussiness Journal, Feb 1, 2016, Cromwell Schubarth, TechFlash Editor Silicon Valley Business Journal

Avalanche Biotechnologies has agreed to acquire Paris-based Annapurna Therapeutics in a $105.6 million deal that expands its gene therapy pipeline. The Menlo Park company led by Paul Cleveland said the deal will combine his company's four gene therapy programs for ophthalmic diseases with Annapurna’s gene therapies for Alpha1-antitrypsin (A1AT) deficiency, cardiomyopathy associated with Friedreich’s ataxia, hereditary angioedema, and severe allergies.



Related news (January 5,2016): Annapurna Therapeutics (formerly AAVLife SAS) to Collaborate with Weill Cornell Medicine on Gene-Therapy Portfolio

Investigación Médica: Houston, tenemos un problema

Medical Research: Houston, we have a problem...

Cth2 Protein Mediates Early Adaptation of Yeast Cells to Oxidative Stress Conditions

Castells-Roca L, Pijuan J, Ferrezuelo F, Bellí G, Herrero E (2016). PLoS ONE 11(1): e0148204. doi:10.1371/journal.pone.0148204

Open Access

Cellular responses to environmental stresses involve changes in RNA transcript levels, through the modulation of the kinetics of transcription and decay rates of individual mRNA molecules.