The Effects of Knockdown of CD24 and CD44 on Proteomics and N-glycomics in Colon Cancer

Abstract

Clusters of differentiation (CDs) are glycoproteins which are expressed on the surface of different cells in the body. They are involved in the communication between cells and the induction of intracellular signalling. Among them, CD24 is correlated with tumorigenesis and tumour progression, while CD44 is closely associated with cancer cell metastasis and chemotherapy resistance. Both CD24 and CD44 are commonly used as markers for many cancer types and their overexpression is frequently associated with a poor prognosis. Despite the critical roles of CD24 and CD44 in cancer progression, little is known about proteome and glycome alterations derived from their knockdowns. To address this point, analysis by bottom-up proteomics and N-glycomics of colorectal cancer tissue under stable knockdowns of CD24 and CD44 were performed in this work. By the proteomic approach a number of proteins associated with cancer development, including cancer cell differentiation, migration, invasion and metastasis were identified. Some of the proteins can be used as indicators for evaluating treatment against CD24 or CD44. The regulation of some proteins was not coincided with references due to the certain compensatory changes that occurred. Further work focused on differentially abundant proteins (DAPs) and differentially abundant N-glycans which may provide valuable insights into the physiological and pathophysiological roles of CD24 and CD44 in colorectal cancer (CRC). Extracellular-matrix-organization and reactome-biological-oxidations were the main pathways involved in the development of CRC after knockdowns of CD24 and CD44, respectively. In addition, the differentially regulated N-glycans with N-acetylneuraminic acid (Neu5Ac) or N-glycolylneuraminic acid (Neu5Gc), especially Neu5Gc1Neu5Ac2HexNAc4Hex6Fuc2Red-HexNAc1, have a significant abundance on CRC after knockdowns of CD24 and CD44. After comparison of both knockdowns against a wild type to generate lists of regulated proteins and N-glycans, these resulting lists were compared as well. While there is an overlap in the results of differentially regulated proteins and N-glycans for CD24kd and CD44kd, the number of regulated proteins and N-glycans exclusive for the CD24 or CD44 knockdown condition was higher. In summary, the results generated in this work extend the knowledge of the molecular changes associated with CD24 and CD44 in cancer by analysing the respective knockdowns in colorectal cancer samples.