Analysis of multiple gene co-expression networks to discover interactions favoring CFTR biogenesis and [DELA]F508-CFTR rescue

• Published in: BMC medical genomics 2021-10, Vol.14 (1)
• Main Authors: Strub, Matthew D, Gao, Long, Tan, Kai, McCray, Paul B
• Format: Article
• Language: English
• Subjects: Causes of; Cystic fibrosis; Gene expression; Genetic aspects; Health aspects; Interactomes; Medical research; Medicine, Experimental; Membrane proteins; Protein biosynthesis
• ISSN: 1755-8794; 1755-8794
• DOI: 10.1186/s12920-021-01106-7

We previously reported that expression of a miR-138 mimic or knockdown of SIN3A in primary cultures of cystic fibrosis (CF) airway epithelia increased [DELA]F508-CFTR mRNA and protein levels, and partially restored CFTR-dependent chloride transport. Global mRNA transcript profiling in [DELA]F508-CFBE cells treated with miR-138 mimic or SIN3A siRNA identified two genes, SYVN1 and NEDD8, whose inhibition significantly increased [DELA]F508-CFTR trafficking, maturation, and function. Little is known regarding the dynamic changes in the CFTR gene network during such rescue events. We hypothesized that analysis of condition-specific gene networks from transcriptomic data characterizing [DELA]F508-CFTR rescue could help identify dynamic gene modules associated with CFTR biogenesis. We applied a computational method, termed M-module, to analyze multiple gene networks, each of which exhibited differential activity compared to a baseline condition. In doing so, we identified both unique and shared gene pathways across multiple differential networks. To construct differential networks, gene expression data from CFBE cells were divided into three groups: (1) siRNA inhibition of NEDD8 and SYVN1; (2) miR-138 mimic and SIN3A siRNA; and (3) temperature (27 [degrees]C for 24 h, 40 [degrees]C for 24 h, and 27 [degrees]C for 24 h followed by 40 [degrees]C for 24 h). Interrogation of individual networks (e.g., NEDD8/SYVN1 network), combinations of two networks (e.g., NEDD8/SYVN1 + temperature networks), and all three networks yielded sets of 1-modules, 2-modules, and 3-modules, respectively. Gene ontology analysis revealed significant enrichment of dynamic modules in pathways including translation, protein metabolic/catabolic processes, protein complex assembly, and endocytosis. Candidate CFTR effectors identified in the analysis included CHURC1, GZF1, and RPL15, and siRNA-mediated knockdown of these genes partially restored CFTR-dependent transepithelial chloride current to [DELA]F508-CFBE cells. The ability of the M-module to identify dynamic modules involved in [DELA]F508 rescue provides a novel approach for studying CFTR biogenesis and identifying candidate suppressors of [DELA]F508.