Research Papers:

Harnessing RNA sequencing for global, unbiased evaluation of two new adjuvants for dendritic-cell immunotherapy

Till S.M. Mathan, Johannes Textor, Annette E. Sköld, Inge Reinieren-Beeren, Tom van Oorschot, Mareke Brüning, Carl G. Figdor, Sonja I. Buschow, Ghaith Bakdash and I. Jolanda M. de Vries _

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Oncotarget. 2017; 8:19879-19893. https://doi.org/10.18632/oncotarget.15190

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Till S.M. Mathan1, Johannes Textor1, Annette E. Sköld1,2, Inge Reinieren-Beeren1, Tom van Oorschot1, Mareke Brüning3, Carl G. Figdor1, Sonja I. Buschow1,4,*, Ghaith Bakdash1,*, I. Jolanda M. de Vries1,5

1Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands

2Department of Oncology and Pathology, Karolinska University Hospital Solna, Karolinska Institute, Stockholm, Sweden

3Miltenyi Biotec GmbH, Bergisch Gladbach, Germany

4Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands

5Department of Medical Oncology, Radboud University Medical Centre, Nijmegen, The Netherlands

*Authors contributed equally

Correspondence to:

I. Jolanda M. de Vries, email: [email protected]

Keywords: dendritic cells, immunotherapy, RNA sequencing, adjuvants, protamine-RNA, transcriptomics

Received: September 09, 2016    Accepted: December 05, 2016    Published: February 08, 2017


Effective stimulation of immune cells is crucial for the success of cancer immunotherapies. Current approaches to evaluate the efficiency of stimuli are mainly defined by known flow cytometry-based cell activation or cell maturation markers. This method however does not give a complete overview of the achieved activation state and may leave important side effects unnoticed. Here, we used an unbiased RNA sequencing (RNA-seq)-based approach to compare the capacity of four clinical-grade dendritic cell (DC) activation stimuli used to prepare DC-vaccines composed of various types of DC subsets; the already clinically applied GM-CSF and Frühsommer meningoencephalitis (FSME) prophylactic vaccine and the novel clinical grade adjuvants protamine-RNA complexes (pRNA) and CpG-P. We found that GM-CSF and pRNA had similar effects on their target cells, whereas pRNA and CpG-P induced stronger type I interferon (IFN) expression than FSME. In general, the pathways most affected by all stimuli were related to immune activity and cell migration. GM-CSF stimulation, however, also induced a significant increase of genes related to nonsense-mediated decay, indicating a possible deleterious effect of this stimulus. Taken together, the two novel stimuli appear to be promising alternatives. Our study demonstrates how RNA-seq based investigation of changes in a large number of genes and gene groups can be exploited for fast and unbiased, global evaluation of clinical-grade stimuli, as opposed to the general limited evaluation of a pre-specified set of genes, by which one might miss important biological effects that are detrimental for vaccine efficacy.

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