The majority of cancer studies are conducted with the two-dimensional (2D) culture method, which does not reflect tumor in vivo structure. The 3D culture method can form free bundles of cancer cells and spheroid, which mimics the tumor microenvironment in vivo. However, the molecules and signaling pathways between the 2D and 3D culture methods are still unknown. In this study, we aim to identify the key molecules and signaling pathways by analyzing the RNA-seq data. The GSE190296 was created by the BGISEQ-500 (Homo sapiens). The KEGG and GO analyses indicated sulfur compound metabolic process and regulation of leukocyte mediated immunity are the major differences between 2D and 3D renal cancer cell cultures. Moreover, we figured out several interactive genes including MYC, EGF, VEGFA, STAT3, NOTCH1, CAT, CCND1, HSPA8, DLG4, and HSPA5. Our study may provide new knowledge on the differences between 2D and 3D cancer cell cultures.

Colorectal cancer is a major cause of cancer deaths in the US. DNA damage is considered to be a novel target for the treatment of colorectal cancer. However, the molecular mechanisms and functions are still unclear. In this study, we aim to identify the significant molecules and signaling by analyzing the RNA-seq data. The GSE189366 was created by the BGISEQ-500 (Homo sapiens). The KEGG and GO analyses indicated the p53 signaling pathway and Hippo signaling pathway are major affected processes in colorectal cancer by DNA damage. Furthermore, we identified ten key interactive molecules including CDK1, STAT3, MDM2, CCNB1, CCNA2, CDKN1A, PCNA, AURKA, PLK1, and CDC6. Our study may provide potential drug targets for colorectal cancer.