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

Oncotarget. 2017 Mar 21;8(12):19879-19893. doi: 10.18632/oncotarget.15190.


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.

Keywords: RNA sequencing; adjuvants; dendritic cells; immunotherapy; transcriptomics.

MeSH terms

  • Adjuvants, Immunologic / pharmacology
  • Antigens, CD1 / immunology
  • Antigens, CD1 / metabolism
  • Cells, Cultured
  • Cluster Analysis
  • Dendritic Cells / drug effects
  • Dendritic Cells / immunology*
  • Dendritic Cells / metabolism
  • Flow Cytometry
  • Gene Expression Profiling / methods
  • Gene Ontology
  • Glycoproteins / immunology
  • Glycoproteins / metabolism
  • Granulocyte-Macrophage Colony-Stimulating Factor / immunology
  • Granulocyte-Macrophage Colony-Stimulating Factor / pharmacology
  • Humans
  • Immunotherapy / methods*
  • Interferon Type I / biosynthesis
  • Interferon Type I / genetics
  • Interferon Type I / immunology
  • Oligodeoxyribonucleotides / immunology
  • Oligodeoxyribonucleotides / pharmacology
  • Protamines / immunology
  • Protamines / pharmacology
  • RNA / immunology
  • RNA / pharmacology
  • Sequence Analysis, RNA / methods*
  • Transcriptome / drug effects
  • Transcriptome / immunology
  • Vaccines / immunology*
  • Vaccines / therapeutic use
  • Viral Vaccines / immunology
  • Viral Vaccines / pharmacology


  • Adjuvants, Immunologic
  • Antigens, CD1
  • CD1C protein, human
  • CPG-oligonucleotide
  • FSME-IMMUN vaccine
  • Glycoproteins
  • Interferon Type I
  • Oligodeoxyribonucleotides
  • Protamines
  • Vaccines
  • Viral Vaccines
  • RNA
  • Granulocyte-Macrophage Colony-Stimulating Factor