TY - JOUR
T1 - Immune-related pan-cancer gene expression signatures of patient survival revealed by NanoString-based analyses
AU - D'Angelo, Alberto
AU - Kilili, Huseyin
AU - Chapman, Robert
AU - Generali, Daniele
AU - Tinhofer, Ingeborg
AU - Luminari, Stefano
AU - Donati, Benedetta
AU - Ciarrocchi, Alessia
AU - Giannini, Riccardo
AU - Moretto, Roberto
AU - Cremolini, Chiara
AU - Pietrantonio, Filippo
AU - Sobhani, Navid
AU - Bonazza, Debora
AU - Prins, Robert
AU - Song, Seung Geun
AU - Jeon, Yoon Kyung
AU - Pisignano, Giuseppina
AU - Cinelli, Mattia
AU - Bagby, Stefan
AU - Urrutia, Araxi O
N1 - Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
PY - 2023/1/17
Y1 - 2023/1/17
N2 - The immune system plays a central role in the onset and progression of cancer. A better understanding of transcriptional changes in immune cell-related genes associated with cancer progression, and their significance in disease prognosis, is therefore needed. NanoString-based targeted gene expression profiling has advantages for deployment in a clinical setting over RNA-seq technologies. We analysed NanoString PanCancer Immune Profiling panel gene expression data encompassing 770 genes, and overall survival data, from multiple previous studies covering 10 different cancer types, including solid and blood malignancies, across 515 patients. This analysis revealed an immune gene signature comprising 39 genes that were upregulated in those patients with shorter overall survival; of these 39 genes, three (MAGEC2, SSX1 and ULBP2) were common to both solid and blood malignancies. Most of the genes identified have previously been reported as relevant in one or more cancer types. Using Cibersort, we investigated immune cell levels within individual cancer types and across groups of cancers, as well as in shorter and longer overall survival groups. Patients with shorter survival had a higher proportion of M2 macrophages and γδ T cells. Patients with longer overall survival had a higher proportion of CD8+ T cells, CD4+ T memory cells, NK cells and, unexpectedly, T regulatory cells. Using a transcriptomics platform with certain advantages for deployment in a clinical setting, our multi-cancer meta-analysis of immune gene expression and overall survival data has identified a specific transcriptional profile associated with poor overall survival.
AB - The immune system plays a central role in the onset and progression of cancer. A better understanding of transcriptional changes in immune cell-related genes associated with cancer progression, and their significance in disease prognosis, is therefore needed. NanoString-based targeted gene expression profiling has advantages for deployment in a clinical setting over RNA-seq technologies. We analysed NanoString PanCancer Immune Profiling panel gene expression data encompassing 770 genes, and overall survival data, from multiple previous studies covering 10 different cancer types, including solid and blood malignancies, across 515 patients. This analysis revealed an immune gene signature comprising 39 genes that were upregulated in those patients with shorter overall survival; of these 39 genes, three (MAGEC2, SSX1 and ULBP2) were common to both solid and blood malignancies. Most of the genes identified have previously been reported as relevant in one or more cancer types. Using Cibersort, we investigated immune cell levels within individual cancer types and across groups of cancers, as well as in shorter and longer overall survival groups. Patients with shorter survival had a higher proportion of M2 macrophages and γδ T cells. Patients with longer overall survival had a higher proportion of CD8+ T cells, CD4+ T memory cells, NK cells and, unexpectedly, T regulatory cells. Using a transcriptomics platform with certain advantages for deployment in a clinical setting, our multi-cancer meta-analysis of immune gene expression and overall survival data has identified a specific transcriptional profile associated with poor overall survival.
UR - http://www.scopus.com/inward/record.url?scp=85146401923&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0280364
DO - 10.1371/journal.pone.0280364
M3 - Article
C2 - 36649303
SN - 1932-6203
VL - 18
JO - PLoS ONE
JF - PLoS ONE
IS - 1
M1 - e0280364
ER -