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.

CD44，作为一种跨膜糖蛋白，在调控肿瘤发生过程中发挥着关键作用。该蛋白已知为 Claudin-low 亚型乳腺癌的标志物，同时也是肿瘤干细胞标志物。然而，在 Claudin-low 乳腺癌中，其功能调控作用尚不明确。为了全面深入地探究 CD44 的功能，我们对两种 Claudin-low 乳腺癌细胞系（MDA-MB-231 和 Hs 578T）进行了基于串联质谱标签的蛋白质组学分析，这些细胞系已被转染 CD44 siRNA。结果显示，在 CD44 敲低后的 MDA-MB-231 细胞中，上调了 2736 种蛋白质，下调了 2172 种蛋白质。对于 Hs 578T CD44 敲低细胞，上调了 412 种蛋白质，下调了 443 种蛋白质。基因本体和网络分析表明，该标志物的抑制介导了与肿瘤细胞发生过程相关的显著功能改变，包括增殖、代谢、粘附和基因表达调控。功能研究证实，CD44 敲低通过调节与细胞周期、翻译和转录相关的基因表达来抑制增殖。此外，这还促进了多种与细胞粘附相关的蛋白的表达，并减弱了癌细胞的迁移。最终，我们的蛋白质组学研究描绘了 Claudin-low 乳腺癌细胞中 CD44 调控的蛋白质组图谱，揭示了介导细胞增殖和迁移的变化。我们的蛋白质组学数据集已通过 PRIDE 存储库提交至 ProteomeXchange 联盟，数据集标识符为 PXD015171。