Potential value of differential expression of CDC42 gene in adult and umbilical cord blood reticulocytes

Abstract

Objective To explore critical regulatory genes in the hemoglobin switch process by analyzing transcriptomic data from the GSE6236, GSE17639 and GSE35102 datasets. Methods The mRNA expression profiles of the three datasets were downloaded from the GEO database and gene annotation was performed using the AnnoProbe package.The remove-BatchEffect function of the Limma package was used to remove batch effects. Weighted gene co-expression network analysis (WGCNA) was used to explore the most relevant modular genes in reticulocytes. The receiver operating characteristic curve (ROC) was used to assess the value of differential genes in differentiating between cord blood and adult peripheral blood reticulocytes. The GSE35102 dataset was used to validate changes in differential gene expression during hemoglobin transformation. Finally, real-time quantitative PCR was used to verify differential gene expression in cord blood and adult peripheral blood reticulocytes. Results Twelve genes showed differential expression in reticulocytes from cord blood and adult peripheral blood ( |logFC|≥1.5, P<0.05). WGCNA found that genes in the blue module were most strongly associated with reticulocytes (R2 =0.76,P<0.001). Of the five genes that overlapped between the two, only CDC42 showed differential expression in the combined dataset (t =3.776, P<0.001) and was able to better differentiate between reticulocytes in cord blood and adult peripheral blood. The expression of CDC42 varied significantly during the hemoglobin transformation process (Z = -2.908, P<0.01), and was significantly lower in adult reticulocytes compared to reticulocytes from cord blood (t =7.824, P <0.001). Conclusion The CDC42 gene is involved in the hemoglobin switching of reticulocytes and could be a potential therapeutic target for sickle cell disease.

Keywords

• reticulocytes
• transcriptome
• wgcna
• cdc42
• sickle cell disease