title: Harnessing RNA sequencing for global, unbiased evaluation of two new adjuvants for dendritic-cell immunotherapy.
abstract: 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.
authors.affiliation: Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
authors.forename: Till S M
authors.initials: TSM
authors.lastname: Mathan
authors.affiliation: Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
authors.forename: Johannes
authors.initials: J
authors.lastname: Textor
authors.affiliation: Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.|Department of Oncology and Pathology, Karolinska University Hospital Solna, Karolinska Institute, Stockholm, Sweden.
authors.forename: Annette E
authors.initials: AE
authors.lastname: Sköld
authors.affiliation: Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
authors.forename: Inge
authors.initials: I
authors.lastname: Reinieren-Beeren
authors.affiliation: Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
authors.forename: Tom
authors.initials: T
authors.lastname: van Oorschot
authors.affiliation: Miltenyi Biotec GmbH, Bergisch Gladbach, Germany.
authors.forename: Mareke
authors.initials: M
authors.lastname: Brüning
authors.affiliation: Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
authors.forename: Carl G
authors.initials: CG
authors.lastname: Figdor
authors.affiliation: Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.|Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.
authors.forename: Sonja I
authors.initials: SI
authors.lastname: Buschow
authors.affiliation: Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
authors.forename: Ghaith
authors.initials: G
authors.lastname: Bakdash
authors.affiliation: Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.|Department of Medical Oncology, Radboud University Medical Centre, Nijmegen, The Netherlands.
authors.forename: I Jolanda M
authors.initials: IJM
authors.lastname: de Vries
mesh_terms: D000276:Adjuvants, Immunologic / Q000494:pharmacology; D018949:Antigens, CD1 / Q000276:immunology / Q000378:metabolism; D002478:Cells, Cultured; D016000:Cluster Analysis; D003713:Dendritic Cells / Q000187:drug effects / Q000276:immunology* / Q000378:metabolism; D005434:Flow Cytometry; D020869:Gene Expression Profiling / Q000379:methods; D063990:Gene Ontology; D006023:Glycoproteins / Q000276:immunology / Q000378:metabolism; D016178:Granulocyte-Macrophage Colony-Stimulating Factor / Q000276:immunology / Q000494:pharmacology; D006801:Humans; D007167:Immunotherapy / Q000379:methods*; D007370:Interferon Type I / Q000096:biosynthesis / Q000235:genetics / Q000276:immunology; D009838:Oligodeoxyribonucleotides / Q000276:immunology / Q000494:pharmacology; D011479:Protamines / Q000276:immunology / Q000494:pharmacology; D012313:RNA / Q000276:immunology / Q000494:pharmacology; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000187:drug effects / Q000276:immunology; D014612:Vaccines / Q000276:immunology* / Q000627:therapeutic use; D014765:Viral Vaccines / Q000276:immunology / Q000494:pharmacology
chemical_list: D000276:Adjuvants, Immunologic; D018949:Antigens, CD1; C437944:CD1C protein, human; C408982:CPG-oligonucleotide; C547297:FSME-IMMUN vaccine; D006023:Glycoproteins; D007370:Interferon Type I; D009838:Oligodeoxyribonucleotides; D011479:Protamines; D014612:Vaccines; D014765:Viral Vaccines; D012313:RNA; D016178:Granulocyte-Macrophage Colony-Stimulating Factor
keywords: RNA sequencing; adjuvants; dendritic cells; immunotherapy; transcriptomics