Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci

Cystic Fibrosis (CF) exhibits morbidity in several organs, including progressive lung disease in all patients and intestinal obstruction at birth (meconium ileus) in ~15%. Individuals with the same causal CFTR mutations show variable disease presentation which is partly attributed to modifier genes. With >6,500 participants from the International CF Gene Modifier Consortium, genome-wide association investigation identified a new modifier locus for meconium ileus encompassing ATP12A on chromosome 13 (min p = 3.83x10-10); replicated loci encompassing SLC6A14 on chromosome X and SLC26A9 on chromosome 1, (min p-16, 2.81x10−11, respectively); and replicated a suggestive locus on chromosome 7 near PRSS1 (min p = 2.55x10-7). PRSS1 is exclusively expressed in the exocrine pancreas and was previously associated with non-CF pancreatitis with functional characterization demonstrating impact on PRSS1 gene expression. We thus asked whether the other meconium ileus modifier loci impact gene expression and in which organ. We developed and applied a colocalization framework called the Simple Sum (SS) that integrates regulatory and genetic association information, and also contrasts colocalization evidence across tissues or genes. The associated modifier loci colocalized with expression quantitative trait loci (eQTLs) for ATP12A (p = 3.35x10-8), SLC6A14 (p = 1.12x10-10) and SLC26A9 (p = 4.48x10-5) in the pancreas, even though meconium ileus manifests in the intestine. The meconium ileus susceptibility locus on chromosome X appeared shifted in location from a previously identified locus for CF lung disease severity. Using the SS we integrated the lung disease association locus with eQTLs from nasal epithelia of 63 CF participants and demonstrated evidence of colocalization with airway-specific regulation of SLC6A14 (p = 2.3x10-4). Cystic Fibrosis is realizing the promise of personalized medicine, and identification of the contributing organ and understanding of tissue specificity for a gene modifier is essential for the next phase of personalizing therapeutic strategies.

囊性纤维化（Cystic Fibrosis, CF）可累及多个器官并引发病变：所有患者均会出现进行性肺部疾病，约15%的患儿出生时即发生胎粪性肠梗阻（meconium ileus）。携带相同致病性CFTR基因突变的患者，其疾病表型存在差异，这一现象部分可由修饰基因解释。
依托国际CF基因修饰联盟（International CF Gene Modifier Consortium）的逾6500名受试者，研究团队通过全基因组关联研究（genome-wide association investigation），发现了13号染色体上包含ATP12A的全新胎粪性肠梗阻修饰基因座（最小P值为3.83×10⁻¹⁰）；验证了X染色体上包含SLC6A14、1号染色体上包含SLC26A9的已报道基因座（二者最小P值分别为1.6×10⁻¹⁶与2.81×10⁻¹¹）；并重复验证了7号染色体上PRSS1附近的提示性基因座（最小P值为2.55×10⁻⁷）。
PRSS1仅在外分泌胰腺（exocrine pancreas）中表达，既往研究已将其与非囊性纤维化胰腺炎（non-CF pancreatitis）相关联，功能表征实验证实该基因可影响PRSS1的基因表达。为此，本研究旨在探究其余胎粪性肠梗阻修饰基因座是否会影响基因表达，以及具体作用于何种器官。
研究团队开发并应用了一种名为简和法（Simple Sum, SS）的共定位分析框架，该框架可整合调控遗传学与遗传关联信息，同时可对比不同组织或基因间的共定位证据。上述关联的修饰基因座与胰腺中的ATP12A、SLC6A14、SLC26A9的表达数量性状基因座（expression quantitative trait loci, eQTLs）存在共定位现象（P值分别为3.35×10⁻⁸、1.12×10⁻¹⁰和4.48×10⁻⁵），尽管胎粪性肠梗阻的病变部位为肠道。
X染色体上的胎粪性肠梗阻易感基因座，其位置似乎与既往发现的CF肺部疾病严重程度相关基因座存在偏移。研究团队利用简和法，将肺部疾病关联基因座与63名CF患者鼻上皮（nasal epithelia）的eQTL数据进行整合，证实其与SLC6A14的气道特异性调控存在共定位证据（P=2.3×10⁻⁴）。
囊性纤维化领域正逐步实现精准医学（personalized medicine）的愿景，明确受累器官并阐明基因修饰的组织特异性，对于下一阶段的个性化治疗策略开发至关重要。