Cargando…

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

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 samples using simulated, flow cytometry, and immunohistochemistry data. quanTIseq analysis of 8000 tumor samples revealed that cyt...

Descripción completa

Detalles Bibliográficos
Autores principales: Finotello, Francesca, Mayer, Clemens, Plattner, Christina, Laschober, Gerhard, Rieder, Dietmar, Hackl, Hubert, Krogsdam, Anne, Loncova, Zuzana, Posch, Wilfried, Wilflingseder, Doris, Sopper, Sieghart, Ijsselsteijn, Marieke, Brouwer, Thomas P., Johnson, Douglas, Xu, Yaomin, Wang, Yu, Sanders, Melinda E., Estrada, Monica V., Ericsson-Gonzalez, Paula, Charoentong, Pornpimol, Balko, Justin, de Miranda, Noel Filipe da Cunha Carvahlo, Trajanoski, Zlatko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6534875/
https://www.ncbi.nlm.nih.gov/pubmed/31126321
http://dx.doi.org/10.1186/s13073-019-0638-6
Descripción
Sumario: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 samples using simulated, flow cytometry, and immunohistochemistry data. quanTIseq analysis of 8000 tumor samples revealed that cytotoxic T cell infiltration is more strongly associated with the activation of the CXCR3/CXCL9 axis than with mutational load and that deconvolution-based cell scores have prognostic value in several solid cancers. Finally, we used quanTIseq to show how kinase inhibitors modulate the immune contexture and to reveal immune-cell types that underlie differential patients’ responses to checkpoint blockers. Availability: quanTIseq is available at http://icbi.at/quantiseq. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13073-019-0638-6) contains supplementary material, which is available to authorized users.