Abstract：
OBJECTIVE: Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations to the CF transmembrane conductance regulator (CFTR). Symptoms and severity of the disease can be quite variable suggesting modifier genes play an important role.
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.
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.
摘要：
目的：囊性纤维化（CF）是由CF跨膜传导调节因子（CFTR）突变引起的常染色体隐性疾病。疾病的症状和严重程度可能变化很大，表明修饰基因起着重要作用。
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。
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。
