We propose the Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) method for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens. MAGeCK demonstrates better performance compared with existing methods, identifies both positively and negatively selected genes simultaneously, and reports robust results across different experimental conditions. Using public datasets, MAGeCK identified novel essential genes and pathways, including EGFR in vemurafenib-treated A375 cells harboring a BRAF mutation. MAGeCK also detected cell type-specific essential genes, including BCR and ABL1, in KBM7 cells bearing a BCR-ABL fusion, and IGF1R in HL-60 cells, which depends on the insulin signaling pathway for proliferation.

We propose a statistical algorithm MethylPurify that uses regions with bisulfite reads showing discordant methylation levels to infer tumor purity from tumor samples alone. MethylPurify can identify differentially methylated regions (DMRs) from individual tumor methylome samples, without genomic variation information or prior knowledge from other datasets. In simulations with mixed bisulfite reads from cancer and normal cell lines, MethylPurify correctly inferred tumor purity and identified over 96% of the DMRs. From patient data, MethylPurify gave satisfactory DMR calls from tumor methylome samples alone, and revealed potential missed DMRs by tumor to normal comparison due to tumor heterogeneity.

Introduction-The ability to maintain a homeostatic level of cell tension is essential for many physiological processes. Our group has recently reported that multicellularity is required for tensional homeostasis in endothelial cells. However, other studies have shown that isolated fibroblasts also maintain constant tension over short time scales without the need of cell-cell contacts. Therefore, in this study, our aim was to determine how different cell types regulate tension as isolated cells or in small clustered groupings and to investigate the role of cell-cell adhesion molecules, such as E-cadherin, in this system. Methods-Micropattern traction force microscopy was used to determine how bovine aortic endothelial cells, bovine vascular smooth muscle cells, mouse embryonic fibroblasts, and human gastric adenocarcinoma cells, with or without cell-cell interactions due to E-cadherin, maintain tensional homeostasis over time. Tension temporal fluctuations in single cells and cell clusters were evaluated. Results-We found that only endothelial cells require clustering for tensional homeostasis. The same was not verified in fibroblasts or vascular smooth muscle cells. Of relevance, in adenocarcinoma cells, we verified that tensional homeostasis was dependent on the competence of the adhesion molecule E-cadherin at both the single cells and multicellular levels. Conclusion-These findings indicate that cell-cell contacts may be critical for tensional homeostasis and, potentially, for barrier function of the endothelium. Furthermore, the cellcell adhesion molecule E-cadherin is an important regulator of tensional homeostasis, even in the absence of cadherin engagement with neighboring cells, which demonstrates its relevance not only as a structural molecule but also as a signaling moiety.

Background Tumour progression relies on the ability of cancer cells to penetrate and invade neighbouring tissues. E-cadherin loss is associated with increased cell invasion in gastric carcinoma, and germline mutations of the E-cadherin gene are causative of hereditary diffuse gastric cancer. Although E-cadherin dysfunction impacts cell–cell adhesion, cell dissemination also requires an imbalance of adhesion to the extracellular matrix (ECM). Methods To identify ECM components and receptors relevant for adhesion of E-cadherin dysfunctional cells, we implemented a novel ECM microarray platform coupled with molecular interaction networks. The functional role of putative candidates was determined by combining micropattern traction microscopy, protein modulation and in vivo approaches, as well as transcriptomic data of 262 gastric carcinoma samples, retrieved from the cancer genome atlas (TCGA). Results Here, we show that E-cadherin mutations induce an abnormal interplay of cells with specific components of the ECM, which encompasses increased traction forces and Integrin β1 activation. Integrin β1 synergizes with E-cadherin dysfunction, promoting cell scattering and invasion. The significance of the E-cadherin-Integrin β1 crosstalk was validated in Drosophila models and found to be consistent with evidence from human gastric carcinomas, where increased tumour grade and poor survival are associated with low E-cadherin and high Integrin β1 levels. Conclusions Integrin β1 is a key mediator of invasion in carcinomas with E-cadherin impairment and should be regarded as a biomarker of poor prognosis in gastric cancer.

Cell migration is identified as a highly orchestrated process. It is a fundamental and essential phenomenon underlying tissue morphogenesis, wound healing, and immune response. Under dysregulation, it contributes to cancer metastasis. Brain is considered to be the most complex organ in human body containing many types of neural cells with astrocytes playing crucial roles in monitoring both physiological and pathological functions. Astrocytoma originates from astrocytes and its most malignant type is glioblastoma multiforme (WHO Grade IV astrocytoma), which is capable to infiltrate widely into the neighboring brain tissues making a complete resection of tumors impossible. Very recently, we have reviewed the mechanisms for astrocytes in migration. Given the fact that astrocytoma shares many histological features with astrocytes, we therefore attempt to review the mechanisms for glioma cells in migration and compare them to normal astrocytes, hoping to obtain a better insight into the dysregulation of migratory mechanisms contributing to their metastasis in the brain.

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