Not Just a Sum? Identifying Different Types of Interplay between Constituents in Combined Interventions

Abstract

MotivationExperiments in which the effect of combined manipulations is compared with the effects of their pure constituents have received a great deal of attention. Examples include the study of combination therapies and the comparison of double and single knockout model organisms. Often the effect of the combined manipulation is not a mere addition of the effects of its constituents, with quite different forms of interplay between the constituents being possible. Yet, a well-formalized taxonomy of possible forms of interplay is lacking, let alone a statistical methodology to test for their presence in empirical data.ResultsStarting from a taxonomy of a broad range of forms of interplay between constituents of a combined manipulation, we propose a sound statistical hypothesis testing framework to test for the presence of each particular form of interplay. We illustrate the framework with analyses of public gene expression data on the combined treatment of dendritic cells with curdlan and GM-CSF and show that these lead to valuable insights into the mode of action of the constituent treatments and their combination.Availability and ImplementationR code implementing the statistical testing procedure for microarray gene expression data is available as supplementary material. The data are available from the Gene Expression Omnibus with accession number GSE32986.

Cellular and molecular synergy in AS01-adjuvanted vaccines results in an early IFNγ response promoting vaccine immunogenicity

“…To go beyond the simple pairwise comparison between immunostimulants, we used a statistical approach initially designed for the analysis of combination drugs. 15 This approach categorizes the potential contributive relationships that MPL and QS-21 provide in AS01 for each gene expressed (Fig. 2b , examples are shown in Supplementary Fig.…”

“…The rationale behind Adjuvant Systems and combination adjuvants is that combining two immunostimulants may trigger multiple immune pathways and improve the protective response to vaccination. 1 , 15 Yet, so far, most analyzes of combination adjuvants relied on visual comparisons between components in the absence of comprehensive statistical testing. 20 Here, we used a customized taxonomy and statistical framework to understand how MPL and QS-21 interact in AS01 at the transcriptional level.…”

“…The type of interplay for each DEG was identified in R using the algorithm described in ref. 15 Briefly, an empirical Bayes procedure (in limma R package) was used to estimate the contrasts that make up the different forms of interplay and to assess their significance. The significance of a particular form of interplay was subsequently obtained by applying an intersection-union hypothesis testing procedure to the proper combination of contrasts.…”

“…R code with an implementation of the procedure to identify different forms of interplay between AS01 components is included in the Supporting Information of ref. 15 …”