METHODS: Exome sequencing was performed on six individuals carrying homozygous deltaF508 for CFTR genotype but present with rapidly progressing CF (RPCF). Data was analyzed using an unbiased genome-wide genetic burden test against 3076 controls. Single cell RNA sequencing data from LungMAP was utilized to evaluate unique and co-expression of candidate genes, and structural modeling to evaluate the deleterious effects of identified candidate variants.
RESULTS: We have identified solute carrier family 26 member 9 (SLC26A9) as a modifier gene to be associated with RPCF. Two rare missense SLC26A9 variants were discovered in three of six individuals deemed to have RPCF: c.229G > A; p.G77S (present in two patients), and c.1885C > T; p.P629S. Co-expression of SLC26A9 and CFTR mRNA is limited across different lung cell types, with the highest level of co-expression seen in human (6.3 %) and mouse (9.0 %) alveolar type 2 (AT2) cells. Structural modeling suggests deleterious effects of these mutations as they are in critical protein domains which might affect the anion transport capability of SLC26A9.
CONCLUSIONS: The enrichment of rare and potentially deleterious SLC26A9 mutations in patients with RPCF suggests SLC26A9 may act as an alternative anion transporter in CF and is a modifier gene associated with this lung phenotype.
方法:对6个携带CFTR基因型纯合deltaF508但存在快速进展CF(RPCF)的个体进行外显子组测序。使用针对3076个对照的无偏全基因组遗传负荷测试来分析数据。来自LungMAP的单细胞RNA测序数据用于评估候选基因的独特和共表达,和结构建模,以评估所确定的候选变体的有害影响。
结果:我们已经确定溶质载体家族26成员9(SLC26A9)是与RPCF相关的修饰基因在被认为具有RPCF的六个个体中的三个中发现了两个罕见的错义SLC26A9变体:c.229G>A;p.G77S(存在于两名患者中),和c.1885C>T;p.P629S.SLC26A9和CFTRmRNA的共表达在不同的肺细胞类型中是有限的,在人(6.3%)和小鼠(9.0%)肺泡2型(AT2)细胞中观察到最高水平的共表达。结构建模表明这些突变的有害作用,因为它们在关键蛋白质结构域中,可能会影响SLC26A9的阴离子转运能力。
结论:RPCF患者中罕见且潜在有害的SLC26A9突变的富集表明SLC26A9可能作为CF中的替代阴离子转运蛋白,并且是与该肺表型相关的修饰基因。