An OMICS-based study of the role of C3dg in keratinocytes: RNA sequencing, antibody-chip array, and bioinformatics approaches

• Published in: International journal of biological macromolecules 2019-07, Vol.133, p.391-411
• Main Authors: Zhang, Li-Li, Kwak, Hyunchang, Yin, Shang-Jun, Lee, Bit-Na, Chang, Ye-Jin, Hahn, Myong-Joon, Yang, Jun-Mo, Lee, Jae-Rin, Park, Yong-Doo
• Format: Article
• Language: English
• Subjects: C3dg; Keratinocytes; Microarray
• ISSN: 0141-8130; 1879-0003
• DOI: 10.1016/j.ijbiomac.2019.04.039

Previously, we have identified the C3dg protein as an important player in the pathogenesis of atopic dermatitis (AD). In this study, we aimed to identify critical factors associated with C3dg in human keratinocytes based on high-throughput screening (HTS) approaches. We overexpressed C3dg in HaCaT human keratinocytes and conducted serial HTS studies, including RNA sequencing analysis integrated with antibody-chip arrays and implementation of bioinformatics algorithms (PPI mappings). Cumulatively, these approaches identified several novel C3dg-associated genes and proteins that are thought to be significantly involved in skin diseases including AD. These novel genes and proteins included LPA, PROZ, BLK, CLDN11, and FGF22, which are believed to play important roles in C3dg-associated skin functions in keratinocytes, as well as genes related to the two important pathways of systemic lupus erythematosus and Staphylococcus aureus infection. In particular, FGF22 is a unique gene that was detected and validated in all methods applied in this study. By integrating the datasets obtained from these HTS studies and utilizing the strengths of each method, we obtained new insights into the functional role of C3dg in keratinocytes. The approach used here contributes to clinical understanding of C3dg-associated applications and may also be applicable to treatment of AD.