New tool enables scientists to interpret 'dark matter' DNA

Gladstone Institutes. "New tool enables scientists to interpret 'dark matter' DNA: Breakthrough technology opens the door to identifying new drug targets that could treat many genetic diseases." ScienceDaily. ScienceDaily, 4 April 2016. .

Scientists at the Gladstone Institutes have invented a new way to read and interpret the human genome. The computational method, called TargetFinder, can predict where non-coding DNA--the DNA that does not code for proteins--interacts with genes. This technology helps researchers connect mutations in the so-called genomic "dark matter" with the genes they affect, potentially revealing new therapeutic targets for genetic disorders.

"Our ability to predict the gene targets of enhancers so accurately enables us to link mutations in enhancers to the genes they target," said Pollard. "Having that link is the first step towards using these connections to treat diseases."

Intracellular Delivery of Proteins with Cell-Penetrating Peptides for Therapeutic Uses in Human Disease

Ana Dinca, Wei-Ming Chien and Michael T. Chin. Int. J. Mol. Sci. 2016, 17(2), 263; doi:10.3390/ijms17020263

Review
OPEN ACCESS

Cell-penetrating peptides (CPPs), a group of small peptides capable of promoting transport of molecular cargo across the plasma membrane, have become important tools in promoting the cellular uptake of exogenously delivered proteins. Although the molecular mechanisms of uptake are not firmly established, CPPs have been empirically shown to promote uptake of various molecules, including large proteins over 100 kiloDaltons (kDa).

Genome-editing Technologies for Gene and Cell Therapy

Morgan L Maeder and Charles A Gersbach, Molecular Therapy (2016); 24 3, 430–446. doi:10.1038/mt.2016.10

OPEN ACCES (Creative Commons CC-BY license)

Common DNA targeting platforms for genome editing.

Gene therapy has historically been defined as the addition of new genes to human cells. However, the recent advent of genome-editing technologies has enabled a new paradigm in which the sequence of the human genome can be precisely manipulated to achieve a therapeutic effect. This includes the correction of mutations that cause disease, the addition of therapeutic genes to specific sites in the genome, and the removal of deleterious genes or genome sequences. This review presents the mechanisms of different genome-editing strategies and describes each of the common nuclease-based platforms, including zinc finger nucleases, transcription activator-like effector nucleases (TALENs), meganucleases, and the CRISPR/Cas9 system. We then summarize the progress made in applying genome editing to various areas of gene and cell therapy, including antiviral strategies, immunotherapies, and the treatment of monogenic hereditary disorders.

New developments and controversies in iron metabolism and iron chelation therapy.

Christina N Kontoghiorghe and George J Kontoghiorghes, World J Methodol. 2016 March 26; 6(1): 1–19. Published online 2016 March 26. doi: 10.5662/wjm.v6.i1.1

Open-Access

"Similar issues in relation to chelating drug development were raised with the journal Annals of Neurology regarding the use of (Ferriprox) in Friedreich ataxia patients where the lack of crucial diagnostic and therapeutic outcome procedures in relation to focal iron levels and lack of iron balance studies were questioned. The need for personalised medicine was also raised since there is wide variation in the severity of the disease and level of focal iron deposits in the heart and brain of Friedreich ataxia patients. In this case the editors of the journal referred to “expensive studies to track iron scores” and “the company developing the drug spends millions of dollars”. It should be noted that the original proposal for the use of (Ferriprox) in Friedreich ataxia patients was suggested many years ago and  was developed following academic initiatives.

The introduction of Deferiprone (Ferriprox) for the treatment of non iron loaded patients by targeting focal toxic iron deposits, e.g., in Friedreich ataxia and toxic labile iron, e.g., in diabetic and non-diabetic glomerular disease is a reflection of the antioxidant and safety potential of this drug. The safety of (Ferriprox) in many categories of non iron loaded diseases has also been confirmed in clinical trials involving patients with the anaemia of chronic disease, renal dialysis, infections, Parkinson’s and other neurodegenerative diseases, etc. As in many other cases of drug development the introduction prospects of Ferriprox in these diseases is based on commercial and not ethical criteria.

Clinical Experience With Deferiprone Treatment for Friedreich Ataxia.

Elincx-Benizri S, Glik A, Merkel D, Arad M, Freimark D, Kozlova E, Cabantchik I, Hassin-Baer S. J Child Neurol. March 29, 2016, doi: 10.1177/0883073816636087

The authors conclude that combined therapy of a low dose of deferiprone with idebenone is relatively safe, might improve neurological function, and seems to improve heart hypertrophy, warranting further studies.

Assessment and management of cavus foot deformity

J. Grice, H. Willmott, H. Taylor, Orthopaedics and Trauma, Available online 8 March 2016, ISSN 1877-1327, doi:10.1016/j.mporth.2016.02.001.

Careful examination should be performed and underlying neurological conditions sought. We outline an á la carte approach to surgical management, in which deformity of the ankle and hindfoot is addressed before moving on to assessment and correction of the mid- and forefoot.

Iron Homeostasis in Health and Disease

Raffaella Gozzelino, and Paolo Arosio; Review: Int. J. Mol. Sci. 2016, 17(1), 130; doi:10.3390/ijms17010130

OPEN ACESS

 It is established the involvement of this metal in Friedrich’s ataxia, a disease characterized by progressive degeneration of sensory neurons in the dorsal root ganglia caused by a mutation in the frataxin gene. Frataxin plays an essential role in delivering Fe to mitochondrial pathways involved in ISC biogenesis and when its functionality is reduced below a critical threshold, Fe accumulates in mitochondria. Reduced mitochondrial functioning and impaired electron transport chain results in Fe-mediated ROS, which was shown to positively correlate with the severity of Friedrich’s ataxia.

Genome Editing of Structural Variations: Modeling and Gene Correction

Chul-Yong Park, Jin Jea Sung, Dong-Wook Kim, Trends in Biotechnology, Available online 23 March 2016, ISSN 0167-7799, doi:10.1016/j.tibtech.2016.02.011.

Although in vivo gene correction using genetic scissor technology (Meganucleases, ZFNs, TALENs and CRISPR/Cas9) may be available and desirable in the future, effective and cell-specific delivery systems should be developed. These technologies promise to expand our understanding of the mechanism of SVs and our ability to treat SV-related diseases.

For Friedreich's ataxia (FRDA), regions containing GAA repeats from frataxin(FXN) intron 1 were removed by expressing ZFNs targeting 334bp and 896bp upstream of GAA repeats in FRDA fibroblasts and lymphoblasts. The FRDA phenotype was reversed, with increased frataxin expression, when corrected FRDA fibroblasts were converted to iPSCs and differentiated into neurons (Li, Y. et al. (2015)).

Translatability: What does it mean in drug discovery?

Matthew Tudor, Jeffery Hermes, Jing Li (Screening & Protein Science, Merck Research Laboratories,USA), Drug Discovery Today, Available online 26 March 2016, ISSN 1359-6446, doi:10.1016/j.drudis.2016.03.010.

We can develop multiple disease-relevant in vitro and in vivo models as a means of further validation of the initial target hypothesis, and pursue decisive experiments that will enable early no-go calls to be made on targets. However, such surrogate assays can reach the wrong conclusion because they will have imperfect predictivity of the results of a well-designed Phase II clinical trial. Disease relevant assays can serve as ‘gate-keepers’ to inform the probability of the translatability but always have to be interpreted as suggestive rather than definitive.

Friedreich’s ataxia (FA), an autosomal-recessive disease, is caused by a trinucleotide GAA repeat expansion which leads to the reduction of FXN protein expression. The protein function is not entirely understood. Attempts to correct putative FXN mutation sequelae by reversing mitochondrial dysfunction, such as by using ion chelators and antioxidants, are broadly reported. Such symptomatic intervention can be viewed as spreading of bets in addition to direct FXN protein intervention, but the odds are clearly against such nonspecific approaches because of the unknown FXN biology. The more certain bet is on what human genetics is telling us: that restoration of FXN protein levels would be effective. To that end, efforts to improve the rate of transcriptional read-through or splicing would be expected to have higher chances of significantly impacting the clinical state.

Mitochondrial iron overload: causes and consequences

Tracey A Rouault, Current Opinion in Genetics & Development, Volume 38, June 2016, Pages 31-37, ISSN 0959-437X, http://dx.doi.org/10.1016/j.gde.2016.02.004.

The mystery of mitochondrial iron overload diseases — how is mitochondrial iron homeostasis regulated? Despite the fact that much is now known about how mitochondrial Fe-S clusters are assembled and transferred, several major mysteries remain about how mitochondria regulate iron homeostasis in the mitochondrial matrix.The challenge ahead is to identify the full roster of transporters involved in mitochondrial iron homeostasis and to try to identify a regulatory ‘overlord’ that regulates a nuclear transcriptional response to perceived iron deficiency.