Quantitative Proteomics Reveals Knockdown of CD44 Promotes Proliferation and Migration in Claudin-Low MDA-MB-231 and Hs 578T Breast Cancer Cell Lines

CD44 is a transmembrane glycoprotein that can regulate the oncogenic
process. This is known to be a marker of the claudin-low subtype of
breast cancer, as well as a cancer stem cell marker. However, its
functional regulatory roles are poorly understood in claudin-low breast
cancer. To gain comprehensive insight into the function of CD44, we
performed an in-depth tandem mass tag-based proteomic analysis of
two claudin-low breast cancer cell lines (MDA-MB-231 and Hs 578T)
transfected with CD44 siRNA. As a result, we observed that 2736 proteins
were upregulated and 2172 proteins were downregulated in CD44-knockdown
MDA-MB-231 cells. For Hs 578T CD44-knockdown cells, 412 proteins were
upregulated and 443 were downregulated. Gene ontology and network
analyses demonstrated that the suppression of this marker mediates
significant functional alterations related to oncogenic cellular processes,
including proliferation, metabolism, adhesion, and gene expression
regulation. A functional study confirmed that CD44 knockdown inhibited
proliferation by regulating the expression of genes related to cell
cycle, translation, and transcription. Moreover, this promoted the
expression of multiple cell adhesion-associated proteins and attenuated
cancer cell migration. Finally, our proteomic study defines the landscape
of the CD44-regulated proteome of claudin-low breast cancer cells,
revealing changes that mediate cell proliferation and migration. Our
proteomics data set has been deposited to the ProteomeXchange Consortium
via the PRIDE repository with the data set identifier PXD015171.