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(2024-08-31 14:29):
#paper https://doi.org/10.15326/jcopdf.2023.0399
Chen, J., Xu, Z., Sun, L., Yu, K., Hersh, C. P., Boueiz, A., ... Batmanghelich, K. (2023). Deep learning integration of chest computed tomography and gene expression identifies novel aspects of COPD. Chronic Obstructive Pulmonary Diseases: Journal of the COPD Foundation, 10(4), 355-368. 这篇论文通过深度学习的方法，联合分析了慢性阻塞性肺病（COPD）患者的胸部CT扫描图像和血液RNA测序数据，以探索肺部结构变化与血液转录组模式之间的新型关系。研究识别出了两种图像-表达轴（IEAs），分别与肺气肿和气道疾病相关，揭示了它们与COPD的不同临床测量和健康预后的关联。此外，研究还通过生物信息学分析，确定了与这两种IEAs相关的生物学通路。这项研究为理解COPD的异质性提供了新的视角，并可能有助于开发针对性的治疗方法。
Chronic obstructive pulmonary diseases (Miami, Fla.),
2023-Oct-26.
DOI: 10.15326/jcopdf.2023.0399
PMID: 37413999
PMCID:PMC10699487
Abstract:
Rationale: Chronic obstructive pulmonary disease (COPD) is characterized by pathologic changes in the airways, lung parenchyma, and persistent inflammation, but the links between lung structural changes and blood transcriptome patterns …
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Rationale: Chronic obstructive pulmonary disease (COPD) is characterized by pathologic changes in the airways, lung parenchyma, and persistent inflammation, but the links between lung structural changes and blood transcriptome patterns have not been fully described.Objections: The objective of this study was to identify novel relationships between lung structural changes measured by chest computed tomography (CT) and blood transcriptome patterns measured by blood RNA sequencing (RNA-seq).Methods: CT scan images and blood RNA-seq gene expression from 1223 participants in the COPD Genetic Epidemiology (COPDGene®) study were jointly analyzed using deep learning to identify shared aspects of inflammation and lung structural changes that we labeled image-expression axes (IEAs). We related IEAs to COPD-related measurements and prospective health outcomes through regression and Cox proportional hazards models and tested them for biological pathway enrichment.Results: We identified 2 distinct IEAs: IEAemph which captures an emphysema-predominant process with a strong positive correlation to CT emphysema and a negative correlation to forced expiratory volume in 1 second and body mass index (BMI); and IEAairway which captures an airway-predominant process with a positive correlation to BMI and airway wall thickness and a negative correlation to emphysema. Pathway enrichment analysis identified 29 and 13 pathways significantly associated with IEAemph and IEAairway, respectively (adjusted p<0.001).Conclusions: Integration of CT scans and blood RNA-seq data identified 2 IEAs that capture distinct inflammatory processes associated with emphysema and airway-predominant COPD.
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