Effects of Pathogenic Variations in the Human Rhodopsin Gene (hRHO) on the Predicted Accessibility for a Lead Candidate Ribozyme.
Effects of Pathogenic Variations in the Human Rhodopsin Gene (hRHO) on the Predicted Accessibility for a Lead Candidate Ribozyme.
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DOI：
10.1167/iovs.16-20877
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发表时间：
2017-07-01
影响因子：
4.4
通讯作者：
Sullivan JM
中科院分区：
文献类型：
--
作者：
Froebel BR;Trujillo AJ;Sullivan JM
基于锤头状核酶(HhRz)或RNA干扰(RNAi)的基因治疗常染色体显性疾病的非突变策略是基于这样的假设：在具有疾病表型的患者中，一种治疗方法可以等效地抑制所有/大部分多样化的突变mRNAs。然而，这一假设尚未得到正式检验。我们通过一项全面的生物信息学研究来解决这一问题，该研究旨在针对人视紫红质基因(HRHO)突变导致常染色体显性遗传性视网膜色素变性的患者，进行一项针对人视紫红质基因(HRHO)的单一先导hHRZ疗法(725GUC↓)的突变如何影响靶结构可及性的研究。以人类基因突变数据库和单核苷酸多态数据库为基础，对hRHO基因进行了错义、无义、插入、缺失、插入等共199个电子编码区突变。用MFold、SFold和OrigoWalk算法折叠每个mRNA，并接受一个名为RNA可及性多参数预测的生物信息学模型。将预测的每个突变体在广泛的局部区域和明确的铅核酶退火点上的可及性与野生型hRHO mRNA进行定量比较。725GUC↓站点的可访问性对某些突变很敏感。对于单核苷酸错义突变，突变距离hhRz退火点的距离增加了对预测可及性的影响，但一些距离较远的突变也会影响可及性。在这一特定背景下，不依赖突变的策略似乎是可行的，但某些突变可能通过影响目标退火点/区域的可及性而显著影响核酶或RNAi的有效性。在应用这种基因治疗策略时，必须考虑这种可能性。
The mutation-independent strategy for hammerhead ribozyme (hhRz) or RNA interference (RNAi)-based gene therapeutics to treat autosomal dominant diseases is predicated on the hypothesis that a single therapeutic would equivalently suppress all/most of the diverse mutant mRNAs in patients with the disease phenotype. However, the hypothesis has not been formally tested. We address this through a comprehensive bioinformatics study of how mutations affect target mRNA structure accessibility for a single lead hhRz therapeutic (725GUC↓), designed against human rod rhodopsin mRNA (hRHO), for patients with hRHO mutations that cause autosomal dominant retinitis pigmentosa. A total of 199 in silico coding region mutations (missense, nonsense, insert, deletion, indel) were made in hRHO mRNA based on Human Gene Mutation Database and Database of Single Nucleotide Polymorphisms. Each mRNA was folded with MFold, SFold, and OligoWalk algorithms and subjected to a bioinformatics model called multiparameter prediction of RNA accessibility. Predicted accessibility of each mutant over both a broad local region and the explicit lead ribozyme annealing site were compared quantitatively to wild-type hRHO mRNA. Accessibility of the 725GUC↓ site is sensitive to some mutations. For single nucleotide missense mutations, proximity of the mutation to the hhRz annealing site increases the impact on predicted accessibility, but some distant mutations also influence accessibility. A mutation-independent strategy appears viable in this specific context but certain mutations could significantly influence ribozyme or RNAi efficacy through impact on accessibility at the target annealing site/region. This possibility must be considered in applications of this gene therapy strategy.
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影响因子：
14.9
作者：
Ding, Y;Chan, CY;Lawrence, CE
通讯作者：
Lawrence, CE
影响因子：
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作者：
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作者：
MillingtonWard, S;ONeill, B;Farrar, GJ
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作者：
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通讯作者：
Turner, DH
影响因子：
3.5
作者：
RESTAGNO, G;MAGHTHEH, M;CARBONARA, A
通讯作者：
CARBONARA, A