Longitudinal Blood Transcriptomic Changes Predict Lung Function Decline in patients with Idiopathic Pulmonary Fibrosis. Longitudinal Blood Transcriptomic Changes Predict Lung Function Decline in patients with Idiopathic Pulmonary Fibrosis

Rationale: Molecular markers of disease progression in idiopathic pulmonary fibrosis are needed. Objective: Derive and validate a blood transcriptomic predictor of forced vital capacity (FVC) decline. Methods: A training cohort (n=74) of IPF patients was stratified according to the presence of progressive disease, defined as ≥10% relative decline in FVC over 12 months. Baseline to 4-month within-patient changes in gene expression were correlated with categorical FVC decline. Genes predictive of FVC decline were identified by two-group comparison with false discovery rate <5% followed by logistic LASSO regression and 10-Fold Cross-Validation for gene list prioritization. Independent validation cohorts with differing transcriptome assay platforms and blood transcriptome sampling times from UChicago (n=27), UPMC (n=35), and Imperial (n=24) underwent receiver operating characteristic with area under the curve (AUC) analyses for validation. Results: A longitudinally-derived FVC-gene predictor accurately discriminated most patients with stable and progressive IPF across four independent IPF cohorts with variable transcriptomic assay platforms and sampling times. The FVC-gene predictorand demonstrated sensitivity and specificity of 74.3% and 82.4% in the combined replication cohort. The likelihood ratio, LR+ and LR- were 4.11 and 0.32, respectively. TGF-beta was the highest-ranking canonical pathway by Gene Set Enrichment Analysis. An approach using longitudinal gene expression changes approach dramatically reduced within-group variation compared to cross-sectional expression for improved prediction modeling. Conclusions: This novel FVC-gene predictor developed from short-term longitudinal gene expression changes successfully discriminates most patients with high likelihood of one-year 10% FVC decline. This tool may better reflect disease activity and prove useful for predictive enrichment of clinical trial populations. Overall design: Study populations were collected from the University of Chicago Medical Center and was approved by the institutional review board (IRB#14163) and informed consent was provided by all study subjects. All patients with IPF met American Thoracic Society/European Respiratory Society (ATS/ERS) diagnosis criteria. Demographic information, clinical characteristics, and pulmonary function tests were collected from all patients with IPF. Spirometry testing, including forced vital capacity percent predicted (FVC% predicted), diffusion capacity for carbon monoxide percent predicted (DLCO % predicted) as well as lung volumes by plethysmography were obtained per ATS guidelines. The prognosis of IPF subjects was dichotomously categorized as FVC stable (FVC-S) or FVC decline (FVC-D) defined by < or ≥10% reduction in FVC% predicted from the baseline to over 2 years of follow-up. PBMC samples were analyzed.

研究依据：目前亟需特发性肺纤维化（idiopathic pulmonary fibrosis, IPF）疾病进展的分子标志物。
研究目标：推导并验证一种可预测用力肺活量（forced vital capacity, FVC）下降的血液转录组学预测模型。
方法：纳入74例IPF患者组成训练队列，根据是否存在疾病进展（定义为12个月内FVC相对下降≥10%）进行分层。将患者基线至4个月内的基因表达变化与分类变量FVC下降情况进行关联分析。通过组间比较（错误发现率<5%）、逻辑LASSO回归以及10折交叉验证（10-Fold Cross-Validation）筛选具有FVC下降预测价值的基因，实现基因列表优先级排序。
针对不同转录组检测平台、不同采血时间点的独立队列开展模型验证工作，分别为芝加哥大学（University of Chicago, UChicago）队列（n=27）、匹兹堡大学医学中心（University of Pittsburgh Medical Center, UPMC）队列（n=35）以及帝国理工学院（Imperial College London, Imperial）队列（n=24），采用受试者工作特征曲线（Receiver Operating Characteristic, ROC）及曲线下面积（area under the curve, AUC）分析完成验证。
结果：基于纵向分析得到的FVC-基因预测模型，可在4个采用不同转录组检测平台、不同采样时间点的独立IPF队列中，准确区分病情稳定与进展的患者。在合并验证队列中，该FVC-基因预测模型的灵敏度为74.3%，特异度为82.4%；似然比LR+与LR-分别为4.11与0.32。经基因集富集分析（Gene Set Enrichment Analysis, GSEA）显示，转化生长因子-β（transforming growth factor-beta, TGF-β）是排名最高的经典通路。与横断面基因表达分析相比，采用纵向基因表达变化的分析策略可显著降低组内变异，从而优化预测建模效果。
结论：本研究基于短期纵向基因表达变化构建的新型FVC-基因预测模型，可有效区分1年内FVC下降≥10%的高风险绝大多数患者。该工具可更好地反映疾病活动度，有望用于临床试验人群的预测性富集。
研究设计：研究对象招募自芝加哥大学医学中心，本研究已获得机构伦理委员会批准（伦理编号IRB#14163），所有研究对象均签署知情同意书。所有IPF患者均符合美国胸科学会/欧洲呼吸学会（American Thoracic Society/European Respiratory Society, ATS/ERS）的诊断标准。收集所有IPF患者的人口统计学信息、临床特征及肺功能检测数据。按照ATS指南开展肺功能检测，包括预测值百分比用力肺活量（FVC% predicted）、预测值百分比一氧化碳弥散量（diffusion capacity for carbon monoxide percent predicted, DLCO% predicted）以及体积描记法检测的肺容积。将IPF患者的预后二分类为FVC稳定组（FVC-S）与FVC下降组（FVC-D），定义为基线至2年随访期内FVC% predicted下降<10%或≥10%。对采集的外周血单个核细胞（peripheral blood mononuclear cell, PBMC）样本进行转录组分析。