Cystic Fibrosis: Systems Biology Analysis from Homozygous p.Phe508del Variant Patients’ Samples Reveals Perturbations in Tissue-Specific Pathways

Table 1

Literature review and data collection for the predicted HBS-DEGs in the context of CF pathogenesis. Only those studies were considered that explored gene expression data.

Symbol	Gene name	Network	Expression	CF-related	Tissue
APP	Amyloid beta precursor protein	Bronchial	Down	—	—
C3AR1	Complement C3a receptor 1	Bronchial	Up	Yes	Lung [62]
CCL4	C–C motif chemokine ligand 4	Bronchial	Up	Yes	Lung [63], Tear fluid [64]
CD53	CD53 molecule	Bronchial	Up	Yes	Nasal (airway inflammation) [65], Lung [66]
CDC16	Cell division cycle 16	Bronchial	Down	Yes	Blood neutrophils [67]
CLU	Clusterin	Bronchial	Down	Yes	Lung (airway secretions) [68]
CXCR4	C–X–C motif chemokine receptor 4	Bronchial	Up	Yes	Lung [69]
FCER1G	Fc fragment of IgE receptor Ig	Bronchial	Up	Yes	Lung [66, 70], Pancreas [71], Intestine [72]
FGR	FGR protooncogene, Src family tyrosine kinase	Bronchial	Up	Yes	Kidney [73]
FPR1	Formyl peptide receptor 1	Bronchial	Up	—	—
IL1B	Interleukin 1 beta	Bronchial	Up	Yes	Airway mucopurulent secretions [74, 75]
NFKBIA	NFKB inhibitor alpha	Bronchial	Up	Yes	Bronchial gland cells [76], Lung [77]
PLA2G4B	Phospholipase A2 group IVB	Bronchial	Down	Yes	Lung [78]
PLAU	Plasminogen activator, urokinase	Bronchial	Up	Yes	Airway epithelia [79]
PLAUR	Plasminogen activator, urokinase receptor	Bronchial	Up	Yes	Airway epithelia [79]
PTAFR	Platelet activating factor receptor	Bronchial	Up	—	—
S100A12	S100 calcium-binding protein A12	Bronchial	Up	Yes	Lung sputum [80–82]
SAA1	Serum amyloid A1	Bronchial	Up	Yes	Lung fibroblasts [83], Lung [62, 78], Blood [84]
TNFRSF1B	TNF receptor superfamily member 1B	Bronchial	Up	—	—
UBC	Ubiquitin C	Bronchial	Down	—	—
ACTB	Actin beta	Rectal	Up	Yes	Lung [13, 85]
TUBB4B	Tubulin beta 4B class IVb	Rectal	Up	Yes	Airway epithelia [86], ciliated cells [86]
YWHAZ	Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta	Rectal	Up	—	—