Tumor microenvironment: barrier or opportunity towards effective cancer therapy
Tumor microenvironment (TME) is a specialized ecosystem of host components, designed
by tumor cells for successful development and metastasis of tumor. With the advent of 3D …
by tumor cells for successful development and metastasis of tumor. With the advent of 3D …
The continuum of cancer immunosurveillance: prognostic, predictive, and mechanistic signatures
J Galon, HK Angell, D Bedognetti, FM Marincola - Immunity, 2013 - cell.com
Numerous analyses of large patient cohorts identified specific patterns of immune activation
associated with patient survival. We established these as the immune contexture …
associated with patient survival. We established these as the immune contexture …
[HTML][HTML] Cholesterol and matrisome pathways dysregulated in astrocytes and microglia
The impact of apolipoprotein E ε4 (APOE4), the strongest genetic risk factor for Alzheimer's
disease (AD), on human brain cellular function remains unclear. Here, we investigated the …
disease (AD), on human brain cellular function remains unclear. Here, we investigated the …
Determining cell type abundance and expression from bulk tissues with digital cytometry
Single-cell RNA-sequencing has emerged as a powerful technique for characterizing
cellular heterogeneity, but it is currently impractical on large sample cohorts and cannot be …
cellular heterogeneity, but it is currently impractical on large sample cohorts and cannot be …
Profiling cell type abundance and expression in bulk tissues with CIBERSORTx
CB Steen, CL Liu, AA Alizadeh… - Stem Cell Transcriptional …, 2020 - Springer
CIBERSORTx is a suite of machine learning tools for the assessment of cellular abundance
and cell type-specific gene expression patterns from bulk tissue transcriptome profiles. With …
and cell type-specific gene expression patterns from bulk tissue transcriptome profiles. With …
Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data
F Finotello, C Mayer, C Plattner, G Laschober… - Genome medicine, 2019 - Springer
We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from
bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor …
bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor …
A single-cell transcriptomic map of the human and mouse pancreas reveals inter-and intra-cell population structure
Although the function of the mammalian pancreas hinges on complex interactions of distinct
cell types, gene expression profiles have primarily been described with bulk mixtures. Here …
cell types, gene expression profiles have primarily been described with bulk mixtures. Here …
Accurate estimation of cell composition in bulk expression through robust integration of single-cell information
We present Bisque, a tool for estimating cell type proportions in bulk expression. Bisque
implements a regression-based approach that utilizes single-cell RNA-seq (scRNA-seq) or …
implements a regression-based approach that utilizes single-cell RNA-seq (scRNA-seq) or …
Robust enumeration of cell subsets from tissue expression profiles
We introduce CIBERSORT, a method for characterizing cell composition of complex tissues
from their gene expression profiles. When applied to enumeration of hematopoietic subsets …
from their gene expression profiles. When applied to enumeration of hematopoietic subsets …
Systematic pan-cancer analysis of tumour purity
The tumour microenvironment is the non-cancerous cells present in and around a tumour,
including mainly immune cells, but also fibroblasts and cells that comprise supporting blood …
including mainly immune cells, but also fibroblasts and cells that comprise supporting blood …