A non-synonymous SNP in SIRT6 predicts neurological severity in Friedreich ataxia

Friedreich ataxia (FRDA) is a recessive neurodegenerative disease characterized by progressive ataxia, dyscoordination, and loss of vision. The variable length of the pathogenic GAA triplet repeat expansion in the FXN gene in part explains Inter-individual variability in severity of disease. The GAA repeat expansion leads to epigenetic silencing of FXN; therefore, variability in properties of epigenetic effector proteins could also regulate the severity of FRDA. In an exploratory analysis, DNA from 88 FRDA patients was analyzed to determine if any of 5 non-synonymous SNPs in HDACs/ SIRTs predicted FRDA disease severity. Results suggested the need for a full analysis (569 FRDA patients) at the rs352493 locus in SIRT6 (S46N SNP). Disease features were compared between patients with the common N46 SIRT6 variant and the less common S46 variant. Biochemical properties of SIRT6 were compared between S46 and N46. Linear regression of the exploratory cohort suggested a SNP (rs352493) in SIRT6 predicted neurologic severity. In follow up analysis, the genotype of SIRT6 at the locus rs352493 predicted disease features of FRDA. Patients with the S46 SIRT6 variant performed better on measures of neurological and visual function over time when compared to the more common N46 SIRT6 variant. S46 SIRT6 did not alter expression or enzymatic activity of SIRT6 or FXN however, S46 patients showed whole transcriptome differences compared to N46 patients, indicative of compensatory mechanisms against whole transcriptome changes seen in FRDA. Overall design: rnaseq and chipseq assay for 4 Friedreich Ataxia patients, 2 of which have the N46 genotype, the other two have the S46 genotype

弗里德赖希共济失调（Friedreich ataxia, FRDA）是一种隐性神经退行性疾病，以进行性共济失调、运动协调障碍与视力丧失为主要临床特征。FXN基因中致病性GAA三核苷酸重复扩增的长度变异，可部分解释FRDA疾病严重程度的个体间差异。GAA重复扩增会导致FXN基因发生表观遗传沉默，因此表观遗传效应蛋白的特性变异也可能调控FRDA的疾病严重程度。
本研究的探索性分析中，对88名FRDA患者的DNA进行了检测，以明确HDACs/SIRTs家族的5个非同义单核苷酸多态性（Single Nucleotide Polymorphism, SNP）是否可预测FRDA的疾病严重程度。分析结果提示，需对569名FRDA患者的SIRT6基因rs352493位点（S46N SNP）开展完整分析。
研究对比了携带常见N46型SIRT6变异体与稀有S46型变异体的FRDA患者的疾病特征，并比较了S46型与N46型SIRT6的生化特性。探索性队列的线性回归分析显示，SIRT6基因中的rs352493位点单核苷酸多态性可预测神经系统疾病严重程度。后续分析进一步证实，SIRT6基因rs352493位点的基因型可预测FRDA的疾病特征。与更常见的N46型SIRT6变异体携带者相比，携带S46型SIRT6变异体的患者在长期随访中的神经及视觉功能评分更优。
S46型SIRT6并未改变SIRT6或FXN的表达水平与酶活性，但相较于N46型患者，S46型患者存在全转录组表达差异，提示其存在针对FRDA中全转录组改变的代偿机制。
实验整体设计：对4名弗里德赖希共济失调患者开展RNA测序（RNA-sequencing, RNA-seq）与染色质免疫共沉淀测序（Chromatin Immunoprecipitation sequencing, ChIP-seq），其中2名携带N46基因型，另外2名携带S46基因型。