Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219-3130, USA.
Am J Respir Crit Care Med. 2011 Jun 1;183(11):1499-509. doi: 10.1164/rccm.201006-0912OC. Epub 2011 Feb 4.
Because acute lung injury is a sporadic disease produced by heterogeneous precipitating factors, previous genetic analyses are mainly limited to candidate gene case-control studies.
To develop a genome-wide strategy in which single nucleotide polymorphism associations are assessed for functional consequences to survival during acute lung injury in mice.
To identify genes associated with acute lung injury, 40 inbred strains were exposed to acrolein and haplotype association mapping, microarray, and DNA-protein binding were assessed.
The mean survival time varied among mouse strains with polar strains differing approximately 2.5-fold. Associations were identified on chromosomes 1, 2, 4, 11, and 12. Seven genes (Acvr1, Cacnb4, Ccdc148, Galnt13, Rfwd2, Rpap2, and Tgfbr3) had single nucleotide polymorphism (SNP) associations within the gene. Because SNP associations may encompass "blocks" of associated variants, functional assessment was performed in 91 genes within ± 1 Mbp of each SNP association. Using 10% or greater allelic frequency and 10% or greater phenotype explained as threshold criteria, 16 genes were assessed by microarray and reverse real-time polymerase chain reaction. Microarray revealed several enriched pathways including transforming growth factor-β signaling. Transcripts for Acvr1, Arhgap15, Cacybp, Rfwd2, and Tgfbr3 differed between the strains with exposure and contained SNPs that could eliminate putative transcriptional factor recognition sites. Ccdc148, Fancl, and Tnn had sequence differences that could produce an amino acid substitution. Mycn and Mgat4a had a promoter SNP or 3'untranslated region SNPs, respectively. Several genes were related and encoded receptors (ACVR1, TGFBR3), transcription factors (MYCN, possibly CCDC148), and ubiquitin-proteasome (RFWD2, FANCL, CACYBP) proteins that can modulate cell signaling. An Acvr1 SNP eliminated a putative ELK1 binding site and diminished DNA-protein binding.
Assessment of genetic associations can be strengthened using a genetic/genomic approach. This approach identified several candidate genes, including Acvr1, associated with increased susceptibility to acute lung injury in mice.
由于急性肺损伤是由异质诱发因素引起的散发性疾病，先前的遗传分析主要局限于候选基因病例对照研究。
开发一种全基因组策略，评估单核苷酸多态性与急性肺损伤小鼠生存的功能相关性。
为了鉴定与急性肺损伤相关的基因，对 40 个近交系进行丙烯醛暴露，并进行单倍型关联图谱分析、微阵列分析和 DNA-蛋白质结合分析。
不同品系的平均生存时间差异很大，两极品系相差约 2.5 倍。在染色体 1、2、4、11 和 12 上发现了关联。7 个基因（Acvr1、Cacnb4、Ccdc148、Galnt13、Rfwd2、Rpap2 和 Tgfbr3）在基因内具有单核苷酸多态性（SNP）关联。由于 SNP 关联可能包含相关变异的“块”，因此在每个 SNP 关联的±1 Mbp 内对 91 个基因进行了功能评估。使用等位基因频率大于等于 10%且表型解释大于等于 10%作为阈值标准，通过微阵列和逆转录实时聚合酶链反应评估了 16 个基因。微阵列显示了几个富集的途径，包括转化生长因子-β信号通路。暴露后不同品系的 Acvr1、Arhgap15、Cacybp、Rfwd2 和 Tgfbr3 的转录本不同，并且含有可能消除潜在转录因子识别位点的 SNP。Ccdc148、Fancl 和 Tnn 具有可能导致氨基酸取代的序列差异。Mycn 和 Mgat4a 分别具有启动子 SNP 或 3'非翻译区 SNP。几个基因是相关的，编码受体（ACVR1、TGFBR3）、转录因子（MYCN，可能是 CCDC148）和泛素-蛋白酶体（RFWD2、FANCL、CACYBP）蛋白，这些蛋白可以调节细胞信号。Acvr1 SNP 消除了一个潜在的 ELK1 结合位点，并减少了 DNA-蛋白质结合。
使用遗传/基因组方法可以加强遗传关联的评估。该方法鉴定了几个候选基因，包括 Acvr1，它与小鼠急性肺损伤的易感性增加有关。
