Baseline Peripheral Blood Mononuclear Cell Transcriptomics Before Ustekinumab Treatment Is Linked With Crohn's Disease Clinical Response at 1 Year

Abstract

Introduction: Ustekinumab, a monoclonal antibody to the p40 subunit of interleukin (IL)-12 and IL-23, is used for Crohn's disease (CD), and the documented clinical remission rate after 1 year was observed in approximately 50% of patients. We aimed to identify predictors for a clinical response using peripheral blood obtained from patients with CD just before ustekinumab treatment initiation.

Methods: RNA extraction from peripheral blood mononuclear cells was followed by mRNA paired-end sequencing. Differential gene expression was performed using DESeq2.

Results: We processed samples from 36 adults with CD (13 men, 36%) obtained at baseline before starting ustekinumab treatment. Twenty-two of 36 (61%) were defined as responders and 14/36 (39%) as nonresponders after 1 year based on Physician Global Assessment. Differential gene expression between responders (n = 22) and nonresponders (n = 14) did not show a gene expression signature that passed false discovery rate (FDR) correction. However, the analyses identified 68 genes, including CXCL1/2/3, which were induced in nonresponders vs responders with P < 0.05 and fold change above 1.5. Functional annotation enrichments of these 68 genes using ToppGene indicated enrichment for cytokine activity (FDR = 1.98E-05), CXCR chemokine receptor binding (FDR = 2.11E-05), IL-10 signaling (FDR = 5.03E-07), genes encoding secreted soluble factors (FDR = 1.73E-05), and myeloid dendritic cells (FDR = 1.80E-08).

Discussion: No substantial differences were found in peripheral blood mononuclear cell transcriptomics between responders and nonresponders. However, among the nonresponders, we noted an increased inflammatory response enriched for pathways linked with cytokine activity and chemokine receptor binding and innate myeloid signature. A larger cohort is required to validate and further explore these findings.

Figure 1.

Unsupervised clustering of Crohn's disease peripheral blood mononuclear cell transcriptomics before ustekinumab treatment colored by response after 1 year. (a) Principal component analysis (PCA) using the 12,773 genes that passed expression filtering. Values off PC1 (b) and PC2 (c) stratified by response at 1 year showing a trend in the difference between responders and nonresponders (Mann-Whitney P = 0.07).

Figure 2.

Variation in the expression of the 85 genes linked to ustekinumab response was not linked to disease location. Principal components 1 (PC) that summarized the greatest variation (37.89% of the overall variation) values were extracted. The Crohn’s disease responders significantly different from nonresponders along PC1 values (P < 0.007, a), while no significant difference was noted when samples were stratified by disease location (L1, L2, L3 in b). (c) Large fraction of the 84 genes were still significantly differentially expressed when the comparison between responders and nonresponders was performed only within the Crohn's disease group with only ileal involvement (L1).

Figure 3.

Nonresponders show upregulation of genes enriched for chemokines and myeloid cells. Functional annotation enrichments of the 68 genes induced in peripheral blood mononuclear cell of nonresponders vs responders using ToppGene/ToppCluster and is visualized using Cytoscape.