Transcriptional consequences of impaired immune cell responses induced by cystic fibrosis plasma characterized via dual RNA sequencing

BMC Medical Genomics

Hiam Abdala-Valencia¹  Ramana V. Davuluri¹  Manoj Kandpal¹  Marc A. Sala¹  Vittobai Rangaraj²  Hara Levy³  Justin E. Ideozu³  Xi Zhang³ 

[1] 0000 0001 2299 3507, grid.16753.36, Northwestern University Feinberg School of Medicine, 60611, Chicago, IL, USA;0000 0004 0388 2248, grid.413808.6, Division of Pulmonary Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, 60611, Chicago, IL, USA;0000 0004 0388 2248, grid.413808.6, Division of Pulmonary Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, 60611, Chicago, IL, USA;Human Molecular Genetics Program, Stanley Manne Children’s Research Institute, 60614, Chicago, IL, USA;0000 0001 2299 3507, grid.16753.36, Northwestern University Feinberg School of Medicine, 60611, Chicago, IL, USA;

关键词: Cystic fibrosis;    miRNA;    Immune response;    PBMCs;    RNA-Seq;   

DOI  :  10.1186/s12920-019-0529-0

来源: publisher

【 摘 要 】

BackgroundIn cystic fibrosis (CF), impaired immune cell responses, driven by the dysfunctional CF transmembrane conductance regulator (CFTR) gene, may determine the disease severity but clinical heterogeneity remains a major therapeutic challenge. The characterization of molecular mechanisms underlying impaired immune responses in CF may reveal novel targets with therapeutic potential. Therefore, we utilized simultaneous RNA sequencing targeted at identifying differentially expressed genes, transcripts, and miRNAs that characterize impaired immune responses triggered by CF and its phenotypes.MethodsPeripheral blood mononuclear cells (PBMCs) extracted from a healthy donor were stimulated with plasma from CF patients (n = 9) and healthy controls (n = 3). The PBMCs were cultured (1 × 105 cells/well) for 9 h at 37 ° C in 5% CO2. After culture, total RNA was extracted from each sample and used for simultaneous total RNA and miRNA sequencing.ResultsAnalysis of expression signatures from peripheral blood mononuclear cells induced by plasma of CF patients and healthy controls identified 151 genes, 154 individual transcripts, and 41 miRNAs differentially expressed in CF compared to HC while the expression signatures of 285 genes, 241 individual transcripts, and seven miRNAs differed due to CF phenotypes. Top immune pathways influenced by CF included agranulocyte adhesion, diapedesis signaling, and IL17 signaling, while those influenced by CF phenotypes included natural killer cell signaling and PI3K signaling in B lymphocytes. Upstream regulator analysis indicated dysregulation of CCL5, NF-κB and IL1A due to CF while dysregulation of TREM1 and TP53 regulators were associated with CF phenotype. Five miRNAs showed inverse expression patterns with three target genes relevant in CF-associated impaired immune pathways while two miRNAs showed inverse expression patterns with two target genes relevant to a dysregulated immune pathway associated with CF phenotypes.ConclusionsOur results indicate that miRNAs and individual transcript variants are relevant molecular targets contributing to impaired immune cell responses in CF.

【 授权许可】

CC BY