Project description:Whole genome bisulphite sequencing of 2 human breast cancer cell lines representing a breast primary tumor and a matched lymph node metastasis. Sequencing of bisulfite converted DNA of cancer cell line samples.
Project description:To identify the mRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) involved in the pathogenesis of breast cancer, we performed the whole transcriptome sequencing. The whole transcriptome sequencing was performed with three breast cancer tissues with or without lymph node metastasis in each group, respectively. The results showed that 728 mRNAs, 131 lncRNAs, and 144 circRNAs were differentially expressed in lymph node metastasis group and no lymph node metastasis group (fold change≥2, p<0.05). These data indicate that dysregulation of mRNAs, lncRNAs, and circRNAs may contribute to breast cancer progression.
Project description:Breast cancer brain metastasis has been recognized as one of the central issues in breast cancer research. Elucidation of the process and pathway that mediate this step is expected to provide important clues for a better understanding of breast cancer metastasis. Increasing evidence suggests that the aberrant glycosylation patterns greatly contribute to the cell invasion and cancer metastasis. Herein, we combined next generation RNA sequencing with liquid chromatograph-tandem mass spectrometry based proteomic and N-glycomic analysis from five breast cancer cell lines and one brain cancer cell line to investigate the possible mechanism of breast cancer brain metastasis. 24763 genes were identified including 14551 differentially expressed genes across six cell lines while proteomic analysis allowed the quantitation of 1096 differentially expressed proteins with approximately 83.8% proteins’ regulation matching their gene expression change. The genes/proteins associated with cell movement were highlighted in the breast cancer brain metastasis. Integrin signaling pathway and the up-regulation of α-integrin (ITGA2, ITGA3) associated with the brain metastatic process was shown through Ingenuity Pathway Analysis (IPA). Overall 91 glycosylation genes were selected from transcriptomic data and all exhibited differential expression. 12 glycogenes showed unique expression in 231BR. The regulation of these genes could result in an activation prediction of sialylation function in 231BR by ingenuity pathway analysis. In agreement with the changes of glycogenes, 60 N-glycans out of 63 identified exhibited differential expression among cell lines. The correlation of glycogenes and glycans revealed the importance of sialylation and sialylated glycans in breast cancer brain metastasis. Highly sialylated glycans, which were up-regulated in brain seeking cell line 231BR, probably contributes to brain metastasis.
Project description:SRC-1 (NCOA1) is a steroid receptor coactivator that has been associated with various aspects of the progression of breast cancer disease such as tamoxifen resistance, metastasis, cell proliferation and invasiveness. In a tamoxifen resistant breast cancer cell line (LY2), SRC-1 has been found to interact with the developmental transcription factor HoxC11. ChIP-sequencing of HoxC11 in LY2 cells shows where the transcription factor binds throughout the genome. LY2 cells were treated with either tamoxifen or vehicle and immunoprecipitated with anti-Hoxc11
Project description:This study investigates the role of Biglycan (BGN) in promoting epithelial migration during mammary gland development and breast cancer metastasis. Using in vitro and in vivo models, including a 3D organoid migration assay and single-cell RNA sequencing, we demonstrate that BGN enhances the interaction between WNT3A and FZD6, activating the WNT signaling pathway. This activation promotes epithelial cell migration and breast cancer metastasis. The findings provide new insights into breast cancer metastasis mechanisms and identify BGN as a potential therapeutic target.
Project description:The progression of cancer to metastatic disease is a major cause of death. We identified miR-708 being transcriptionally repressed by polycomb repressor complex (PRC2)-induced H3-K27 trimethylation in metastatic breast cancer. miR-708 targets the endoplasmic reticulum protein neuronatin (Nnat) to decrease intracellular calcium (Ca2+) level, resulting in reduction of activation of ERK and FAK, decreased cell migration, and impaired metastases. Functional complementation experiments with Nnat-3’UTR mutant, which is refractory to suppression by miR-708, rescued cell migration and metastasis defects. In breast cancer patients, miR-708 expression was decreased in lymph node and distal metastases, suggesting a metastasis-suppressive role. Our findings uncover a mechanistic role for miR-708 in metastasis and provide a rationale for developing miR-708 as a therapeutic agent against metastatic breast cancer. Sequencing miRNAs from Human breast cancer cells: MCF10A, MCF7, MDA-MB-231, MDA-MB-LM2
Project description:Whole genome bisulphite sequencing of 2 human breast cancer cell lines representing a breast primary tumor and a matched lymph node metastasis.
Project description:Clusters of circulating tumor cells (CTC-clusters) are present in the blood of patients with cancer but their contribution to metastasis is not well defined. Here, we first use mouse models to demonstrate that breast cancer cells injected intravascularly as clusters are more prone to survive and colonize the lungs than single cells. Primary mammary tumors comprised of tagged cells give rise to oligoclonal CTC-clusters, with 50-fold increased metastatic potential, compared with single CTCs. Using intravital imaging and in vivo flow cytometry, CTC-clusters are visualized in the tumor circulation, and they demonstrate rapid clearance in peripheral vessels. In patients with breast cancer, presence of CTC-clusters is correlated with decreased progression-free survival. RNA sequencing identifies the cell junction protein plakoglobin as most differentially expressed between clusters and single human breast CTCs. Expression of plakoglobin is required for efficient CTC-cluster formation and breast cancer metastasis in mice, while its expression is associated with diminished metastasis-free survival in breast cancer patients. Together, these observations suggest that plakoglobin-enriched primary tumor cells break off into the vasculature as CTC-clusters, with greatly enhanced metastasis propensity. RNA-seq from 29 samples (15 pools of single CTCs and 14 CTC-clusters) isolated from 10 breast cancer patients
Project description:Breast cancer is the leading type of cancer in women. Breast cancer brain metastasis is considered as an essential issue in breast cancer patients. Membrane proteins play important roles in breast cancer brain metastasis that contributes to the cell adhesion and penetration of blood-brain barrier. To achieve a deeper insight of the mechanism of breast cancer brain metastasis, liquid chromatography tandem mass spectrometry (LC-MS/MS) was performed to analyze the enriched membrane proteomes from six different breast cancer cell lines. Quantitative proteomic data of all cell lines were compared with MDA-MB-231BR which has the specific brain metastasis capacity. 1239 proteins were identified and 990 were quantified with more than 70% of membrane proteins in all cell lines. Each cell line can be separated apart from others in PCA. Ingenuity pathway analysis (IPA) supported the high brain metastatic ability of 231BR and suggested importance of the up-regulation of integrin proteins and down-regulation of EPHA in brain metastasis. 28 proteins were observed unique expression alteration in 231BR. The up-regulation of NPM1, hnRNP Q, hnRNP K and eIF3l and the down-regulation of TUBB4B and TUBB were observed to be associated with the brain metastasis cell line and may contributes to the breast cancer brain metastasis.
Project description:Brain metastatic disease occurs in 10-30% of metastatic breast cancer cases. The incidence of brain metastases is increasing with median overall survival < 2 years for patients. In order to better characterize oncogenic pathway activity pertinent to breast cancer brain metastasis, exome capture RNA sequencing was carried out on patient matched primary breast with brain metastatic tumor samples for 45 cases of breast cancer brain metastasis (N= 90 samples). Here, exome capture RNA sequencing data is deposited as sequencing batch corrected log2 transformed trimmed M of means (TMM) normalized counts per million (CPM) (log2(TMM-CPM +1) gene expression values (n=16,714 protein coding genes; N=90 tumor samples).