The omics based study for the role of superoxide dismutase 2 (SOD2) in keratinocytes: RNA sequencing, antibody-chip array and bioinformatics approaches

In this study, we aimed to identify critical factors associated with superoxide dismutase 2 (SOD2) in human keratinocytes through gene and protein expression profiling approaches. After recombinant SOD2 was exogenously added to culture media, we conducted serial OMICS studies, which included RNA sequencing analysis, integrated antibody-chip arrays, and the implementation of bioinformatics algorithms, in order to reveal genes and proteins that are possibly associated with SOD2 in keratinocytes. These approaches identified several novel genes and proteins in keratinocytes that are associated with exogenous SOD2. These novel genes included DCT, which was up-regulated, and CD38, GPR151, HCK, KIT, and AFP, which were down-regulated. Among them, CD38 and KIT were also predicted as hub proteins in PPI mappings. By integrating the datasets obtained from these complementary high-throughput OMICS studies and utilizing the strengths of each method, we obtained new insights into the functional role of externally added SOD2 in skin cells and into several critical genes that are thought to play important roles in SOD2-associated skin function. The approach used here could help contribute to our clinical understanding of SOD2-associated applications and may be broadly applicable to a wider range of diseases. AbbreviationsSOD2

superoxide dismutase 2

DAVID

the database for annotation, visualization and integrated discovery

KEGG

Kyoto Encyclopedia of Genes and Genomes

PPI

protein–protein interactions

HTS

High-throughput screening

superoxide dismutase 2

the database for annotation, visualization and integrated discovery

Kyoto Encyclopedia of Genes and Genomes

protein–protein interactions

High-throughput screening

Communicated by Ramaswamy H. Sarma