Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
Department of Surgery, College of Medicine, Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA.
J Cyst Fibros. 2021 Mar;20(2):356-363. doi: 10.1016/j.jcf.2020.12.018. Epub 2021 Jan 23.
CF patients demonstrate clinical heterogeneity and much remains unknown about how to risk stratify individuals for disease progression. The most common cystic fibrosis mutation, F508del, is a protein folding mutation that has been shown in vitro to negatively affect proteostasis and CFTR transcription. Since CFTR is expressed in the nasal epithelium, we hypothesized that by using unbiased transcriptomics we could gain clinically relevant insights about differential gene expression and heterogeneity in CF patients as well as assess proteostatic dysfunction in the nasal epithelium.
Using nasal curettage and RNA-seq we assessed differential gene expression in F508del homozygotes compared to healthy volunteers. Gene set enrichment analysis was performed using a list of known chaperones. Pilot and validation cohorts were studied.
PCA analysis and gene expression heatmaps exhibited greater heterogeneity among CF than healthy volunteers. Differentially expressed genes were enriched for the downregulation of ciliary/microtubular genes and the upregulation of inflammatory/immune response genes in F508del homozygotes compared to healthy volunteers. Gene set analysis identified negative enrichment for chaperone genes and decreased CFTR transcription in the F508del homozygotes. We also found preliminary evidence for the recently identified ionocyte in the nasal specimens.
CF patients homozygous for F508del demonstrate heterogeneous gene expression profiles, proteostatic dysregulation, and reduced CFTR transcription. Larger studies are needed to determine whether nasal epithelial gene transcription profiles can be leveraged for insights into disease heterogeneity.
CF 患者表现出临床异质性，对于如何对个体进行疾病进展风险分层，仍有许多未知。最常见的囊性纤维化突变 F508del 是一种蛋白折叠突变，已在体外证明其对蛋白质稳态和 CFTR 转录具有负面影响。由于 CFTR 在鼻上皮细胞中表达，我们假设通过使用无偏转录组学，我们可以获得有关 CF 患者差异基因表达和异质性的临床相关见解，并评估鼻上皮细胞的蛋白质稳态功能障碍。
使用鼻刮除术和 RNA-seq，我们评估了 F508del 纯合子与健康志愿者相比的差异基因表达。使用已知伴侣蛋白列表进行了基因集富集分析。研究了试点和验证队列。
PCA 分析和基因表达热图显示 CF 患者比健康志愿者具有更大的异质性。与健康志愿者相比，F508del 纯合子中差异表达的基因富集了纤毛/微管基因的下调和炎症/免疫反应基因的上调。基因集分析发现伴侣蛋白基因呈负富集，CFTR 转录减少。我们还在鼻标本中发现了最近发现的离子细胞的初步证据。
F508del 纯合子 CF 患者表现出异质的基因表达谱、蛋白质稳态失调和 CFTR 转录减少。需要更大的研究来确定鼻上皮细胞基因转录谱是否可以用于深入了解疾病异质性。
