Identification of non-cancer cells from cancer transcriptomic data

TY - JOUR

T1 - Identification of non-cancer cells from cancer transcriptomic data

AU - Bortolomeazzi, Michele

AU - Keddar, Mohamed Reda

AU - Ciccarelli, Francesca Donatella

AU - Benedetti, Lorena Gabriela

PY - 2019/10/22

Y1 - 2019/10/22

N2 - Interactions between cancer cells and non-cancer cells composing the tumour microenvironment play a primary role in determining cancer progression and shaping the response to therapy. The qualitative and quantitative characterisation of the different cell populations in the tumour microenvironment is therefore crucial to understand its role in cancer. In recent years, many experimental and computational approaches have been developed to identify the cell populations composing heterogeneous tissue samples, such as cancer. In this review, we describe the state-of-the-art approaches for the quantification of non-cancer cells from bulk and single-cell cancer transcriptomic data, with a focus on immune cells. We illustrate the main features of these approaches and highlight their applications for the analysis of the tumour microenvironment in solid cancers. We also discuss techniques that are complementary and alternative to RNA sequencing, particularly focusing on approaches that can provide spatial information on the distribution of the cells within the tumour in addition to their qualitative and quantitative measurements.

AB - Interactions between cancer cells and non-cancer cells composing the tumour microenvironment play a primary role in determining cancer progression and shaping the response to therapy. The qualitative and quantitative characterisation of the different cell populations in the tumour microenvironment is therefore crucial to understand its role in cancer. In recent years, many experimental and computational approaches have been developed to identify the cell populations composing heterogeneous tissue samples, such as cancer. In this review, we describe the state-of-the-art approaches for the quantification of non-cancer cells from bulk and single-cell cancer transcriptomic data, with a focus on immune cells. We illustrate the main features of these approaches and highlight their applications for the analysis of the tumour microenvironment in solid cancers. We also discuss techniques that are complementary and alternative to RNA sequencing, particularly focusing on approaches that can provide spatial information on the distribution of the cells within the tumour in addition to their qualitative and quantitative measurements.

KW - Tumour microenvironment RNA-seq Gene expression profiles Cell-specific signatures GSEA Deconvolution

M3 - Review article

SN - 1874-9399

JO - Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms

JF - Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms

M1 - 194445

ER -