Canakinumab reverses overexpression of inflammatory response genes in tumour necrosis factor receptor-associated periodic syndrome

Rebecca Torene, Nanguneri Nirmala, Laura Obici, Marco Cattalini, Vincent Tormey, Roberta Caorsi, Sandrine Starck-Schwertz, Martin Letzkus, Nicole Hartmann, Ken Abrams, Helen Lachmann, Marco Gattorno, Rebecca Torene, Nanguneri Nirmala, Laura Obici, Marco Cattalini, Vincent Tormey, Roberta Caorsi, Sandrine Starck-Schwertz, Martin Letzkus, Nicole Hartmann, Ken Abrams, Helen Lachmann, Marco Gattorno

Abstract

Objective: To explore whether gene expression profiling can identify a molecular mechanism for the clinical benefit of canakinumab treatment in patents with tumour necrosis factor receptor-associated periodic syndrome (TRAPS).

Methods: Blood samples were collected from 20 patients with active TRAPS who received canakinumab 150 mg every 4 weeks for 4 months in an open-label proof-of-concept phase II study, and from 20 aged-matched healthy volunteers. Gene expression levels were evaluated in whole blood samples by microarray analysis for arrays passing quality control checks.

Results: Patients with TRAPS exhibited a gene expression signature in blood that differed from that in healthy volunteers. Upon treatment with canakinumab, many genes relevant to disease pathogenesis moved towards levels seen in the healthy volunteers. Canakinumab downregulated the TRAPS-causing gene (TNF super family receptor 1A (TNFRSF1A)), the drug-target gene (interleukin (IL)-1B) and other inflammation-related genes (eg, MAPK14). In addition, several inflammation-related pathways were evident among the differentially expressed genes. Canakinumab treatment reduced neutrophil counts, but the observed expression differences remained after correction for this.

Conclusions: These gene expression data support a model in which canakinumab produces clinical benefit in TRAPS by increasing neutrophil apoptosis and reducing pro-inflammatory signals resulting from the inhibition of IL-1β. Notably, treatment normalised the overexpression of TNFRSF1A, suggesting that canakinumab has a direct impact on the main pathogenic mechanism in TRAPS.

Trial registration number: NCT01242813.

Keywords: Cytokines; Fever Syndromes; Inflammation.

Conflict of interest statement

KA: employee of Novartis Pharmaceuticals. MC: received speaker fees and served as a consultant for Novartis and SOBI. MG: received speaker fees and served as a consultant for Novartis and SOBI, and has received unrestricted grants for the Eurofever Registry from Novartis and SOBI. NH: employee of Novartis Institutes for Biomedical Research. HL: received speaker fees and served as a consultant for Novartis and SOBI. ML: employee of Novartis Institutes for Biomedical Research. NN: employee of Novartis Institutes for Biomedical Research. LO: received speaker fees and served as a consultant for Novartis. SS-S: employee of Novartis Institutes for Biomedical Research. RT: employee of Novartis Institutes for Biomedical Research.

Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Figures

Figure 1
Figure 1
Pathway maps showing changes in gene expression for tumour necrosis factor receptor-associated periodic syndrome (TRAPS) patients compared with healthy volunteers and for patients with TRAPS with canakinumab treatment compared with baseline. (A) Immune response TLR signalling. (B) Immune response IL-1 signalling. (C) Apoptosis and survival: endoplasmic reticulum stress response. (D) Autophagy. Next to each differentially expressed gene, a small icon representing a thermometer can be seen. The thermometers marked as ‘1’ reflect transcriptional levels at baseline relative to healthy subjects, while the ones marked as ‘2’ reflect changes post-treatment. Downregulation is indicated by a blue thermometer, while upregulation is marked by a red thermometer, with the level of dysregulation proportional to the length of the colour in the thermometer. Transcripts with a fold change of 1.4 or better are shown in solid black boxes, while those with a fold change between 1.3 and 1.4 are shown in dashed black boxes. Even though many of the fold changes in the pathway maps are lower than 1.4, the directionality of the dysregulation is consistently opposite between patients with TRAPS at baseline versus healthy subjects and in postcanakinumab-treated patients versus precanakinumab-treated patients. This lends support to the interpretation that these transcriptional changes are disease and treatment induced, respectively. In some of the cases, the transcripts are seen to be upregulated in the post-treatment contrast, but there is no thermometer denoted for the disease versus healthy contrast. In many of these cases, the fold change is in the opposite direction, but the absolute value is

Figure 2

Heatmap of gene expression levels…

Figure 2

Heatmap of gene expression levels for tumour necrosis factor receptor-associated periodic syndrome (TRAPS)…

Figure 2
Heatmap of gene expression levels for tumour necrosis factor receptor-associated periodic syndrome (TRAPS) disease signature genes. Genes with a Benjamini-Hochberg corrected p≤0.05 and an absolute fold change ≥2 between untreated patients with TRAPS at baseline and healthy volunteers define the TRAPS disease signature genes. Each gene is normalised by Z-score across all samples shown. Note how expression levels at both day 15 and day 113 postcanakinumab treatment move towards those seen in healthy volunteers.

Figure 3

Heatmap of gene expression levels…

Figure 3

Heatmap of gene expression levels for canakinumab signature genes. Genes with a Benjamini-Hochberg…

Figure 3
Heatmap of gene expression levels for canakinumab signature genes. Genes with a Benjamini-Hochberg corrected p≤0.05 and an absolute fold change ≥2 between day 15 post-treatment and baseline in tumour necrosis factor receptor-associated periodic syndrome patients define the canakinumab signature genes. Each gene is normalised by Z-score across all samples shown. Note how expression levels at both day 15 and day 113 postcanakinumab treatment move towards those seen in healthy volunteers.

Figure 4

The disease-causing gene ( TNFRSF1A…

Figure 4

The disease-causing gene ( TNFRSF1A , panel A), drug-target gene ( IL-1B ,…

Figure 4
The disease-causing gene (TNFRSF1A, panel A), drug-target gene (IL-1B, panel B) and inflammation-related genes (MAPK14 and NFKB1, panels C and D, respectively) are upregulated in tumour necrosis factor receptor-associated periodic syndrome (TRAPS) patients and downregulated upon canakinumab treatment. Lines connect data points originating from the same patient. The figure titles within each panel contain both the Entrez gene IDs (numbers preceding ‘_at’) and the gene symbols. Note how these genes are upregulated at baseline in patients with TRAPS relative to healthy volunteers. Upon treatment at day 15, the expression levels of the genes are reduced to those observed in healthy volunteers and this reduction is maintained through day 113. The fold change between baseline and visit 6 is indicated at the top of each graph.
Figure 2
Figure 2
Heatmap of gene expression levels for tumour necrosis factor receptor-associated periodic syndrome (TRAPS) disease signature genes. Genes with a Benjamini-Hochberg corrected p≤0.05 and an absolute fold change ≥2 between untreated patients with TRAPS at baseline and healthy volunteers define the TRAPS disease signature genes. Each gene is normalised by Z-score across all samples shown. Note how expression levels at both day 15 and day 113 postcanakinumab treatment move towards those seen in healthy volunteers.
Figure 3
Figure 3
Heatmap of gene expression levels for canakinumab signature genes. Genes with a Benjamini-Hochberg corrected p≤0.05 and an absolute fold change ≥2 between day 15 post-treatment and baseline in tumour necrosis factor receptor-associated periodic syndrome patients define the canakinumab signature genes. Each gene is normalised by Z-score across all samples shown. Note how expression levels at both day 15 and day 113 postcanakinumab treatment move towards those seen in healthy volunteers.
Figure 4
Figure 4
The disease-causing gene (TNFRSF1A, panel A), drug-target gene (IL-1B, panel B) and inflammation-related genes (MAPK14 and NFKB1, panels C and D, respectively) are upregulated in tumour necrosis factor receptor-associated periodic syndrome (TRAPS) patients and downregulated upon canakinumab treatment. Lines connect data points originating from the same patient. The figure titles within each panel contain both the Entrez gene IDs (numbers preceding ‘_at’) and the gene symbols. Note how these genes are upregulated at baseline in patients with TRAPS relative to healthy volunteers. Upon treatment at day 15, the expression levels of the genes are reduced to those observed in healthy volunteers and this reduction is maintained through day 113. The fold change between baseline and visit 6 is indicated at the top of each graph.

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