Objective To screen genes differentially expressed between dermal papilla cells from occipital and vertex scalp of patients with androgenic alopecia (AGA) through a 3D culture system.Methods Dermal papilla cells isolated from the occipital scalp tissue of patients with AGA were cultured in a 2D system for several days.Then,the third-passage dermal papilla cells were subjected to a 3D culture with the presence of dihydrotestosterone (DHT) for 72 hours (experimental group).The dermal papilla cells isolated from the vertex scalp tissue of patients with AGA,which were cultured in a 3D system with dimethyl sulfoxide,but not DHT,served as the control group.Subsequently,total RNA was extracted from the cells and reversely transcribed into cDNA followed by labeling with Cy3 and hybridization to a NimbleGen microarray.Gene ontology (GO) and pathway analysis was carried out to screen differentially expressed genes between the experimental and control group.Real time PCR was conducted to validate the results of microarray analysis.Results As the genome-wide expression profile analysis showed,there were 622 genes differentially expressed between the experimental group and control group,of which,359 were up-regulated and 263 were down-regulated in the experimental group compared with the control group.The above results were corffirmed by real time PCR.GO analysis revealed that the up-regulated genes,such as the CHEK1 and Tobl genes,were mainly involved in the inhibition of cell proliferation and promotion of cell apoptosis,while the down-regulated genes,such as the BAMBI,EFNA3,Dlx3 and UCGC genes,were associated with the acceleration of cell proliferation as well as the growth and development of epidermis.Pathway analysis showed that cell circle-controlling molecules were the most abundant molecules.Conclusions Numerous signalling molecules and pathways are involved in the development of AGA,which are mainly responsible for the modulation of cell circle,proliferation and apoptosis.