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1.
Nat Commun ; 10(1): 2983, 2019 07 05.
Article in English | MEDLINE | ID: mdl-31278301

ABSTRACT

Ttriple-negative breast cancer (TNBC) is an aggressive and highly metastatic breast cancer subtype. Enhanced TNBC cell motility is a prerequisite of TNBC cell dissemination. Here, we apply an imaging-based RNAi phenotypic cell migration screen using two highly motile TNBC cell lines (Hs578T and MDA-MB-231) to provide a repository of signaling determinants that functionally drive TNBC cell motility. We have screened ~4,200 target genes individually and discovered 133 and 113 migratory modulators of Hs578T and MDA-MB-231, respectively, which are linked to signaling networks predictive for breast cancer progression. The splicing factors PRPF4B and BUD31 and the transcription factor BPTF are essential for cancer cell migration, amplified in human primary breast tumors and associated with metastasis-free survival. Depletion of PRPF4B, BUD31 and BPTF causes primarily down regulation of genes involved in focal adhesion and ECM-interaction pathways. PRPF4B is essential for TNBC metastasis formation in vivo, making PRPF4B a candidate for further drug development.


Subject(s)
Cell Movement/genetics , Gene Expression Regulation, Neoplastic , Protein Serine-Threonine Kinases/metabolism , Ribonucleoprotein, U4-U6 Small Nuclear/metabolism , Triple Negative Breast Neoplasms/pathology , Antigens, Nuclear/genetics , Antigens, Nuclear/metabolism , Cell Line, Tumor , Cohort Studies , Datasets as Topic , Disease-Free Survival , Extracellular Matrix/metabolism , Female , Focal Adhesions/genetics , Humans , Intravital Microscopy , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/metabolism , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Protein Serine-Threonine Kinases/genetics , RNA Interference , RNA Splicing/genetics , RNA, Small Interfering/metabolism , Ribonucleoprotein, U4-U6 Small Nuclear/genetics , Signal Transduction/genetics , Survival Analysis , Transcription Factors/genetics , Transcription Factors/metabolism , Triple Negative Breast Neoplasms/genetics , Triple Negative Breast Neoplasms/mortality
2.
Sci Rep ; 9(1): 10989, 2019 07 29.
Article in English | MEDLINE | ID: mdl-31358840

ABSTRACT

The efficacy of prospective cancer treatments is routinely estimated by in vitro cell-line proliferation screens. However, it is unclear whether tumor aggressiveness and patient survival are influenced more by the proliferative or the migratory properties of cancer cells. To address this question, we experimentally measured proliferation and migration phenotypes across more than 40 breast cancer cell-lines. Based on the latter, we built and validated individual predictors of breast cancer proliferation and migration levels from the cells' transcriptomics. We then apply these predictors to estimate the proliferation and migration levels of more than 1000 TCGA breast cancer tumors. Reassuringly, both estimates increase with tumor's aggressiveness, as qualified by its stage, grade, and subtype. However, predicted tumor migration levels are significantly more strongly associated with patient survival than the proliferation levels. We confirmed these findings by conducting siRNA knock-down experiments on the highly migratory MDA-MB-231 cell lines and deriving gene knock-down based proliferation and migration signatures. We show that cytoskeletal drugs might be more beneficial in patients with high predicted migration levels. Taken together, these results testify to the importance of migration levels in determining patient survival.


Subject(s)
Breast Neoplasms/pathology , Cell Movement , Cell Proliferation , Transcriptome , Breast Neoplasms/diagnosis , Breast Neoplasms/genetics , Cell Line, Tumor , Female , Gene Expression Regulation, Neoplastic , Humans , Neoplasm Invasiveness/diagnosis , Neoplasm Invasiveness/genetics , Neoplasm Invasiveness/pathology , Prognosis , Survival Analysis
3.
PLoS One ; 9(10): e109688, 2014.
Article in English | MEDLINE | ID: mdl-25289886

ABSTRACT

In many situations, 3D cell cultures mimic the natural organization of tissues more closely than 2D cultures. Conventional methods for phenotyping such 3D cultures use either single or multiple simple parameters based on morphology and fluorescence staining intensity. However, due to their simplicity many details are not taken into account which limits system-level study of phenotype characteristics. Here, we have developed a new image analysis platform to automatically profile 3D cell phenotypes with 598 parameters including morphology, topology, and texture parameters such as wavelet and image moments. As proof of concept, we analyzed mouse breast cancer cells (4T1 cells) in a 384-well plate format following exposure to a diverse set of compounds at different concentrations. The result showed concentration dependent phenotypic trajectories for different biologically active compounds that could be used to classify compounds based on their biological target. To demonstrate the wider applicability of our method, we analyzed the phenotypes of a collection of 44 human breast cancer cell lines cultured in 3D and showed that our method correctly distinguished basal-A, basal-B, luminal and ERBB2+ cell lines in a supervised nearest neighbor classification method.


Subject(s)
Antineoplastic Agents/pharmacology , Epithelial Cells/drug effects , Image Processing, Computer-Assisted/statistics & numerical data , Phenotype , Animals , Cell Culture Techniques , Cell Line, Tumor , Drug Delivery Systems , Epithelial Cells/metabolism , Epithelial Cells/pathology , Female , Humans , Image Processing, Computer-Assisted/methods , Imaging, Three-Dimensional , Mammary Glands, Animal/drug effects , Mammary Glands, Animal/metabolism , Mammary Glands, Animal/pathology , Mammary Glands, Human/drug effects , Mammary Glands, Human/metabolism , Mammary Glands, Human/pathology , Mice
4.
Mol Syst Biol ; 10: 744, 2014 Aug 01.
Article in English | MEDLINE | ID: mdl-25086087

ABSTRACT

Over the last decade, the field of cancer metabolism has mainly focused on studying the role of tumorigenic metabolic rewiring in supporting cancer proliferation. Here, we perform the first genome-scale computational study of the metabolic underpinnings of cancer migration. We build genome-scale metabolic models of the NCI-60 cell lines that capture the Warburg effect (aerobic glycolysis) typically occurring in cancer cells. The extent of the Warburg effect in each of these cell line models is quantified by the ratio of glycolytic to oxidative ATP flux (AFR), which is found to be highly positively associated with cancer cell migration. We hence predicted that targeting genes that mitigate the Warburg effect by reducing the AFR may specifically inhibit cancer migration. By testing the anti-migratory effects of silencing such 17 top predicted genes in four breast and lung cancer cell lines, we find that up to 13 of these novel predictions significantly attenuate cell migration either in all or one cell line only, while having almost no effect on cell proliferation. Furthermore, in accordance with the predictions, a significant reduction is observed in the ratio between experimentally measured ECAR and OCR levels following these perturbations. Inhibiting anti-migratory targets is a promising future avenue in treating cancer since it may decrease cytotoxic-related side effects that plague current anti-proliferative treatments. Furthermore, it may reduce cytotoxic-related clonal selection of more aggressive cancer cells and the likelihood of emerging resistance.


Subject(s)
Breast Neoplasms/metabolism , Cell Movement , Computational Biology/methods , Glycolysis , Lung Neoplasms/metabolism , Cell Line, Tumor , Cell Proliferation , Gene Silencing , Humans , Lactic Acid/metabolism , Models, Biological , RNA, Small Interfering/genetics
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