背景:结节病是一种异质性肉芽肿性疾病,没有准确的疾病进展生物标志物。因此,我们分析并整合了DNA甲基化,mRNA,和microRNAs来鉴定与结节病和疾病进展相关的分子变化,这些变化可能阐明疾病的潜在机制和潜在的生物标志物。
方法:使用来自64例结节病受试者和16例健康对照的支气管肺泡灌洗细胞。在IlluminaHuman甲基化EPIC阵列上对DNA甲基化进行了分析,通过RNA测序的mRNA,和miRNA通过小RNA测序。线性模型适合测试结节病诊断和进展表型的效果,调整年龄,性别,吸烟,和数据的主要组成部分。我们使用每个数据集中的特征子集构建了一个有监督的多组模型。
结果:我们确定了1,459个CpG,64个mRNA,与对照组相比,与结节病相关的5种miRNA和与疾病进展相关的4种mRNA。我们的整合模型强调了PI3K/AKT1途径的突出性,这在T细胞和mTOR功能中很重要。新的免疫相关基因和miRNA,包括LYST,RGS14,SLFN12L,和hsa-miR-199b-5p,区分结节病与对照组。我们的整合模型还证明了IL20RB的差异表达/甲基化,ABCC11、SFSWAP、AGBL4,miR-146a-3p,和miR-378b在非进行性结节病和进行性结节病之间。
结论:利用DNA甲基化,转录组,结节病BAL细胞中的miRNA测序,我们发现了与疾病相关的广泛的分子变化,许多参与免疫反应。这些分子可以作为诊断/预后生物标志物和/或药物靶标。尽管未来的测试需要确认。
BACKGROUND: Sarcoidosis is a heterogeneous granulomatous disease with no accurate biomarkers of disease progression. Therefore, we profiled and integrated the DNA methylome, mRNAs, and microRNAs to identify molecular changes associated with sarcoidosis and disease progression that might illuminate underlying mechanisms of disease and potential biomarkers.
METHODS: Bronchoalveolar lavage cells from 64 sarcoidosis subjects and 16 healthy controls were used. DNA methylation was profiled on Illumina HumanMethylationEPIC arrays, mRNA by RNA-sequencing, and miRNAs by small RNA-sequencing. Linear models were fit to test for effect of sarcoidosis diagnosis and progression phenotype, adjusting for age, sex, smoking, and principal components of the data. We built a supervised multi-omics model using a subset of features from each dataset.
RESULTS: We identified 1,459 CpGs, 64 mRNAs, and five miRNAs associated with sarcoidosis versus controls and four mRNAs associated with disease progression. Our integrated model emphasized the prominence of the PI3K/AKT1 pathway, which is important in T cell and mTOR function. Novel immune related genes and miRNAs including LYST, RGS14, SLFN12L, and hsa-miR-199b-5p, distinguished sarcoidosis from controls. Our integrated model also demonstrated differential expression/methylation of IL20RB, ABCC11, SFSWAP, AGBL4, miR-146a-3p, and miR-378b between non-progressive and progressive sarcoidosis.
CONCLUSIONS: Leveraging the DNA methylome, transcriptome, and miRNA-sequencing in sarcoidosis BAL cells, we detected widespread molecular changes associated with disease, many which are involved in immune response. These molecules may serve as diagnostic/prognostic biomarkers and/or drug targets, although future testing is required for confirmation.