beadarray: R classes and methods for Illumina bead-based data. NPJ Breast Cancer 4, 5 (2018).ĭunning, M. Associations between genomic stratification of breast cancer and centrally reviewed tumour pathology in the METABRIC cohort. Tubular carcinoma of the breast: further evidence to support its excellent prognosis. Stromal elements act to restrain, rather than support, pancreatic ductal adenocarcinoma. Depletion of carcinoma-associated fibroblasts and fibrosis induces immunosuppression and accelerates pancreas cancer with reduced survival. Resistance to checkpoint blockade therapy through inactivation of antigen presentation. Hypoxia, DNA repair and genetic instability. Mechanisms of hypoxia-mediated immune escape in cancer. Enhancer mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Gene expression profiling in breast cancer: classification, prognostication, and prediction. Patterns of immune infiltration in breast cancer and their clinical implications: a gene-expression-based retrospective study. Association between CD8 + T-cell infiltration and breast cancer survival in 12 439 patients. Multiplexed epitope-based tissue imaging for discovery and healthcare applications. Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy. A new genome-driven integrated classification of breast cancer and its implications. Tumour hypoxia promotes tolerance and angiogenesis via CCL28 and T reg cells. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Studies of the HER-2/neu proto-oncogene in human breast and ovarian cancer.
Define cytometry drivers#
An integrated approach to uncover drivers of cancer. histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data. Molecular heterogeneity of breast carcinomas and the cancer stem cell hypothesis. MicroRNAs reprogram normal fibroblasts into cancer-associated fibroblasts in ovarian cancer. Fibroblast heterogeneity and immunosuppressive environment in human breast cancer. Expression of CD68 in non-myeloid cell types. Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups. Segmenting and tracking multiple dividing targets using ilastik.
Define cytometry software#
CellProfiler: image analysis software for identifying and quantifying cell phenotypes. A map of human type 1 diabetes progression by imaging mass cytometry. Simultaneous multiplexed imaging of mRNA and proteins with subcellular resolution in breast cancer tissue samples by mass cytometry.
The shaping and functional consequences of the microRNA landscape in breast cancer. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. A single-cell atlas of the tumor and immune ecosystem of human breast cancer. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes. Emerging landscape of oncogenic signatures across human cancers. Genome-driven integrated classification of breast cancer validated in over 7,500 samples. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Molecular portraits of human breast tumours. In summary, systematic analysis of single-cell phenotypic and spatial correlates of genomic alterations in cancer revealed how genomes shape both the composition and architecture of breast tumor ecosystems and will enable greater understanding of the phenotypic impact of genomic alterations. Several features of tumor ecosystems, including cellular neighborhoods, were linked to prognosis, illustrating their clinical relevance. Epithelial luminal cell phenotypes separated into those predominantly impacted by mutations and those affected by copy number aberrations. Distinct combinations of cell phenotypes and cell–cell interactions were associated with genomic subtypes of breast cancer. Single-cell analysis revealed cell phenotypes spanning epithelial, stromal and immune types. To investigate these relationships, we used imaging mass cytometry to quantify the expression of 37 proteins with subcellular spatial resolution in 483 tumors from the METABRIC cohort. Genomic alterations shape cell phenotypes and the structure of tumor ecosystems in poorly defined ways.
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