Project description:Genome-wide DNA methylation profiling of brain metastases from lung cancer, breast cancer, and melanoma samples. The Illumina Infinium 450K Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 methylation sites in formalin-fixed paraffin-embedded (FFPE) samples from brain metastases. Samples included 30 breast cancer brain metastases, 18 lung cancer brain metastases, 37 melanoma brain metastases, and 4 samples with brain metastases from patients with uncertain primary.
Project description:Lung metastases are detected in more than half of patients with metastatic tumors, yet it remains largely unknown why the lung environment is particularly permissive to metastases. Here, we describe that pulmonary aspartate promotes lung metastasis by rewiring the translatome of disseminating cancer cells. We found that both patients and mice with breast cancer have high concentrations of aspartate in their lung interstitial fluid. This extracellular aspartate activates the ionotropic N-methyl-D-aspartate (NMDA) receptor in cancer cells, which induces CREB-dependent mRNA expression of deoxyhypusine hydroxylase (DOHH). The latter is essential for hypusination, a posttranslational modification required for the activity of the non-classical translation initiation factor eIF5A. In turn, a translational program with TGF- signaling as a central hub promotes collagen remodeling in the disseminated breast cancer cells. We detect key aspects of this mechanism in lung metastases from patients with breast cancer. In summary, we discover that pulmonary aspartate increases with breast cancer and induces a signaling cascade that promote lung metastatic outgrowth.
Project description:Introduction: The incidence of brain metastases in cancer patients is increasing, with lung and breast cancer being the most common sources. Despite advancements in targeted therapies, the prognosis remains poor, highlighting the importance to investigate the underlying mechanisms in brain metastases. The aim of this study was to investigate the differences in the molecular mechanisms involved in brain metastasis of breast and lung cancers. In addition, we aimed to identify cancer lineage-specific druggable targets in the brain metastasis. Methods: To that aim, a cohort of 44 FFPE tissue samples, including 22 breast cancer and 22 lung adenocarcinoma (LUAD) and their matched-paired brain metastases were collected. Targeted gene expression profiles of primary tumors were compared to their matched-paired brain metastases samples using nCounter PanCancer IO 360™ Panel of NanoString technologies. Pathway analysis was performed using gene set analysis (GSA) and gene set enrichment analysis (GSEA). The validation was performed by using Immunohistochemistry (IHC) to confirm the expression of immune checkpoint inhibitors. Results: Our results revealed the significant upregulation of cancer-related genes in primary tumors compared to their matched-paired brain metastases (adj. p ≤ 0.05). We found that upregulated differentially expressed genes in breast cancer brain metastasis (BM-BC) and brain metastasis from lung adenocarcinoma (BM-LUAD) were associated with the metabolic stress pathway, particularly related to the glycolysis. Additionally, we found that the upregulated genes in BM-BC and BM-LUAD played roles in immune response regulation, tumor growth, and proliferation. Importantly, we identified high expression of the immune checkpoint VTCN1 in BM-BC, and VISTA, IDO1, NT5E, and HDAC3 in BM-LUAD. Validation using immunohistochemistry further supported these findings. Conclusion: In conclusion, the findings highlight the significance of using matched-paired samples to identify cancer lineage-specific therapies that may improve brain metastasis patients outcomes.
Project description:This is a genomic analysis of breast cancer metastasis using array based CGH and is part of a large study investigating the patterns and evolution of metastases from breast cancer using autopsy material accumulated over the last 50 years from a single institution. The samples used in the genomic profiling comprise the primary breast tumour and multiple matched metastases from each patient. The data demonstrate both the clonal nature of metastatic progression and the role of clonal evolution during progression. This study comprises six patients who died of metastatic breast cancer. For some patients the breast primary tumour and lymph node metastasis was obtained from previous surgical excision, otherwise material was obtained from a resulting autopsy. Each patient set of samples involves the primary breast tumour and multiple metastases, including from lung, liver, lymph node, adrenal gland, brain etc. DNA was extracted from formalin fixed paraffin embedded (FFPE) tissue blocks and analysed for DNA copy number alterations using an Agilent aCGH platform.
Project description:The lungs are a frequent target of metastatic breast cancer cells, but the underlying molecular mechanisms are unclear. All existing data were obtained either using statistical association between gene expression measurements found in primary tumors and clinical outcome, or using experimentally derived signatures from mouse tumor models. Here, we describe a distinct approach that consists to utilize tissue surgically resected from lung metastatic lesions and compare their gene expression profiles with those from non-pulmonary sites, all coming from breast cancer patients. We demonstrate that the gene expression profiles of organ-specific metastatic lesions can be used to predict lung metastasis in breast cancer. We identified a set of 21 lung metastasis-associated genes. Using a cohort of 72 lymph node-negative breast cancer patients, we developed a six-gene prognostic classifier that discriminated breast primary cancers with a significantly higher risk of lung metastasis. We then validated the predictive ability of the six-gene signature in 3 independent cohorts of breast cancers consisting of a total of 721 patients. Finally, we demonstrated that the signature improves risk stratification independently of known standard clinical parameters and a previously established lung metastasis signature based on an experimental breast cancer metastasis model. Experiment Overall Design: We used microarrays to identify lung metastasis-related genes in a series of 23 patients with breast cancer metastases. No replicate, no reference sample.
Project description:Metastasis is responsible for the majority of deaths in a variety of cancer types, including breast cancer. Although several factors or biomarkers have been identified to predict the outcome of patients with breast cancer, few studies have been conducted to identify metastasis-associated biomarkers. Quantitative iTRAQ proteomics analysis was used to detect differentially expressed proteins between lymph node metastases and their paired primary tumor tissues from 23 patients with metastatic breast cancer. Immunohistochemistry was performed to validate the expression of two upregulated (EpCAM, FADD) and two downregulated (NDRG1, αB-crystallin) proteins in 190 paraffin-embedded tissue samples. These four proteins were further analyzed for their correlation with clinicopathological features in 190 breast cancer patients. We identified 637 differentially regulated proteins (397 upregulated and 240 downregulated) in lymph node metastases compared with their paired primary tumor tissues. Furthermore, bioinformatics analysis using GEO profiling confirmed the difference in the expression of EpCAM between metastases and primary tumors tissues. Two upregulated (EpCAM, FADD) and two downregulated (NDRG1, αB-crystallin) proteins were associated with the progression of breast cancer. Obviously, EpCAM plays a role in the metastasis of breast cancer cells to the lymph node. We further identified αB-crystallin as an independent biomarker to predict lymph node metastasis and the outcome of breast cancer patients.
Project description:Next-Generation Sequencing was applied to investigate candidate breast cancer metastatic genes. PB targeted sequencing of primary tumours and metastases (3 lung metastases, 6 lung macro-metastases and 9 LM cell lines) allowed to identify Nfib as a candidate metastasis inducer.
Project description:Lung metastases are detected in more than half of patients with metastatic tumors. However, it remains largely unknown why the lung environment is a permissive niche for metastases. Here, we discover that pulmonary aspartate triggers a cellular signaling cascade in disseminated cancer cells resulting in a translational program that boosts lung metastasis. Specifically, we observe that patients and mice with breast cancer have high concentrations of aspartate in their lung interstitial fluid. This extracellular aspartate activates the ionotropic N-methyl-D-aspartate (NMDA) receptor in cancer cells, which induces CREB-dependent mRNA expression of deoxyhypusine hydroxylase (DOHH). The latter is essential for hypusination, a posttranslational modification required for the activity of the non-classical translation initiation factor eIF5A. In turn, a translational program with TGF-β signaling as a central hub promotes collagen remodeling in the disseminated breast cancer cells. We detect key aspects of this mechanism in lung metastases from patients with breast cancer. In summary, we discover that pulmonary aspartate increases with breast cancer and induces a signaling cascade promoting the growth of lung metastases.
Project description:Lung metastases are detected in more than half of patients with metastatic tumors. However, it remains largely unknown why the lung environment is a permissive niche for metastases. Here, we discover that pulmonary aspartate triggers a cellular signaling cascade in disseminated cancer cells resulting in a translational program that boosts lung metastasis. Specifically, we observe that patients and mice with breast cancer have high concentrations of aspartate in their lung interstitial fluid. This extracellular aspartate activates the ionotropic N-methyl-D-aspartate (NMDA) receptor in cancer cells, which induces CREB-dependent mRNA expression of deoxyhypusine hydroxylase (DOHH). The latter is essential for hypusination, a posttranslational modification required for the activity of the non-classical translation initiation factor eIF5A. In turn, a translational program with TGF-β signaling as a central hub promotes collagen remodeling in the disseminated breast cancer cells. We detect key aspects of this mechanism in lung metastases from patients with breast cancer. In summary, we discover that pulmonary aspartate increases with breast cancer and induces a signaling cascade promoting the growth of lung metastases.
Project description:Lung metastases are detected in more than half of patients with metastatic tumors. However, it remains largely unknown why the lung environment is a permissive niche for metastases. Here, we discover that pulmonary aspartate triggers a cellular signaling cascade in disseminated cancer cells resulting in a translational program that boosts lung metastasis. Specifically, we observe that patients and mice with breast cancer have high concentrations of aspartate in their lung interstitial fluid. This extracellular aspartate activates the ionotropic N-methyl-D-aspartate (NMDA) receptor in cancer cells, which induces CREB-dependent mRNA expression of deoxyhypusine hydroxylase (DOHH). The latter is essential for hypusination, a posttranslational modification required for the activity of the non-classical translation initiation factor eIF5A. In turn, a translational program with TGF-β signaling as a central hub promotes collagen remodeling in the disseminated breast cancer cells. We detect key aspects of this mechanism in lung metastases from patients with breast cancer. In summary, we discover that pulmonary aspartate increases with breast cancer and induces a signaling cascade promoting the growth of lung metastases.