Transcriptome Analysis of Triple-Negative HCC1937 and MDA-MB-231 Breast Cancer Cells Treated with Kalanchoe pinnata Revealed the Regulation of Migration and Invasion via the Downregulation of the Genes JAK2, ROCK1 and ROCK2

Triple-negative breast cancer (TNBC) is a type of breast cancer with high mortality due to aggressive tumor behavior and limited treatment options. Natural products have been studied for their potential as alternatives to combine with cancer drugs to improve treatment efficacy. Plant phytoconstituents can regulate cellular processes such as proliferation, differentiation, invasion, angiogenesis, and migration. Kalanchoe pinnata has been used in traditional medicine; it contains flavonoids, phenols, alkaloids, glycosides, bufadienolides, and tannins, among others. In the present investigation, we evaluated the effects of aqueous extract and the underlying molecular mechanisms in two breast cancer cell lines, HCC1937 and MDA-MB-231, with a focus on cellular migration. The cytotoxic activity results revealed that HCC1937 cells are more sensitive to aqueous extracts than are MDA-MB-231 cells. Compared with that of 48 h-treated MDA-MB-231 cells, cell migration was affected in HCC1937 cells after 24 h of treatment. The extract had greater anti-invasion effects on HCC1937 cells (37.7%, p < 0.01) than on MDA-MB-231 cells (47%, p < 0.05). An RNA-seq assay revealed 1850 differentially expressed genes (DEGs) in HCC1937 cells versus 1534 in MDA-MB-231 cells. WebGestalt analysis revealed the downregulation of genes involved in cell–cell adhesion, ruffle organization, and cell–substrate junctions, with more downregulated genes in HCC1937 cells. The downregulated genes analyzed with KOBAS-i were associated with MAPK signaling, focal adhesion, PI3K-Akt signaling, regulation of the actin cytoskeleton, and the ECM-receptor interaction pathway. In addition, IPA network analysis revealed that the RHO GTPase cycle, RHOA signaling, JAK/STAT signaling, actin cytoskeleton signaling and Integrin signaling pathways were inhibited. The data from the docking study indicated the binding potential of quercetin-3-O-arabinoside, kaempferol, quercetin, and apigenin with the JAK2, ROCK1, ROCK2, and PIK3CA proteins. Thus, our results demonstrate that K. pinnata inhibits the proliferation and invasion of TNBC cells by targeting genes involved in these important processes; thus, K. pinnata has the potential to be used in combination with chemotherapeutic drugs for cancer treatment.