RNA sequencing to predict response to TNF-α inhibitors reveals possible mechanism for nonresponse in smokers

BACKGROUND

Several studies have employed microarray-based profiling to predict response to tumor necrosis factor-alpha inhibitors (TNFi) in rheumatoid arthritis (RA); yet efforts to validate these targets have failed to show predictive abilities acceptable for clinical practice.

METHODS

The eighty most extreme responders and nonresponders to TNFi therapy were selected from the observational BiOCURA cohort. RNA sequencing was performed on mRNA from peripheral blood mononuclear cells (PBMCs) collected before initiation of treatment. The expression of pathways as well as individual gene transcripts between responders and nonresponders was investigated. Promising targets were technically replicated and validated in n = 40 new patients using qPCR assays.

RESULTS

Before therapy initiation, nonresponders had lower expression of pathways related to interferon and cytokine signaling, while also showing higher levels of two genes, GPR15 and SEMA6B (p = 0.02). The two targets could be validated, however, additional analyses revealed that GPR15 and SEMA6B did not independently predict response, but were rather dose-dependent markers of smoking (p < 0.0001).

CONCLUSIONS

The study did not identify new transcripts ready to use in clinical practice, yet GPR15 and SEMA6B were recognized as candidate explanatory markers for the reduced treatment success in RA smokers.

Necessity of TNF-alpha inhibitor discontinuation in rheumatoid arthritis is predicted by smoking and number of previously used biological DMARDs

OBJECTIVES

Despite the success of TNF-alpha inhibitor (TNFi) treatment in rheumatoid arthritis (RA), a substantial number of patients necessitate discontinuation. Prediction thereof would be clinically relevant and guide the decision whether to start TNFi treatment.

METHODS

Data were used from the observational BiOCURA cohort, in which patients initiating biological treatment were enrolled and followed up for one year. In the model development cohort (n=192), a model predicting TNFi discontinuation was built using Cox-regression with backward selection (p<0.05). The parameters of the model were tested again in a model refinement cohort (n=60), for significance (p<0.05) and consistency of effect. In addition, we performed a systematic review to put our study results into perspective.

RESULTS

Of the 252 patients who initiated TNFi treatment, 103 (41%) had to discontinue treatment. Discontinuation was predicted at baseline by female gender, current smoking, high visual analogue scale of general health, and higher number of previously used biological disease-modifying anti-rheumatic drugs (bDMARDs). At refinement, smoking status and number of previously used bDMARDs remained with re-estimated hazard ratios (HRs) in the total cohort of 1.74 (95%-CI 1.15-2.63, p<0.01) and 1.40 (95%-CI 1.1-1.68, p<0.01), respectively. Using these two predictors, we developed a simple score predicting discontinuation (PPV=72.3%). From literature, predictors were pack years of smoking, number of previously used bDMARDs, lack of any concomitant DMARD therapy and in particular lack of concomitant methotrexate (MTX).

CONCLUSIONS

TNFi discontinuation is predicted by current smoking and number of previously used bDMARDs, as well as by pack years of smoking and lack of any concomitant DMARD/MTX therapy.

Polymorphisms in the multidrug-resistance 1 gene related to glucocorticoid response in rheumatoid arthritis treatment

A substantial proportion of rheumatoid arthritis (RA)-patients experience an insufficient response to glucocorticoids, an important therapeutic agent in RA. The multidrug-resistance 1 (MDR1) gene product P-glycoprotein (P-gp) is an efflux pump that actively transports substrates, such as glucocorticoids, out of the cell. We investigated if the variation in response might be explained by single-nucleotide polymorphisms (SNPs) in the MDR1 gene. RA-patients treated with intravenous methylprednisolone pulses (n = 18) or oral prednisone/prednisolone (n = 22) were included in a prospective cohort, and clinical response was measured after 5 and 30 days, respectively. The C1236T, G2677A/T, and C3435T SNPs were determined, and the functionality of P-gp was assessed by flow cytometry (Rhodamine efflux assay). Carriage of the G2677A/T SNP was significantly associated with response (OR = 6.18, p = 0.035), the other SNPs showed trends. Stratified for received treatment, the effect was only present in methylprednisolone treated patients. Mutant allele carriage significantly decreased functionality of P-gp in B cells, though had a smaller impact in other PBMC subtypes. Carriage of a MDR1 SNP was related to a response to methylprednisolone in this study, which his suggests that RA-patients carrying wild-type alleles might benefit from P-gp inhibition or administration of glucocorticoid analogues that are non-P-gp substrates.

Differences between serum polar lipid profiles of male and female rheumatoid arthritis patients in response to glucocorticoid treatment

Objective

As there are pharmacological differences between males and females, and glucocorticoid (GC) treatment is associated with increased cardiovascular mortality rate in rheumatoid arthritis (RA) patients, it is important to study serum polar lipid profiles of male and female patients in response to GC therapy. Gender differences may require an adjustment to the treatment strategy for a selection of patients.

Methods

Serum samples from 281 RA patients were analysed using a targeted lipidomics platform. The differences in GC use and gender on polar lipid profiles were cross sectionally examined by multiple linear regressions, while correcting for confounding factors.

Results

Differences in polar lipids between GC users and non-GC users in females and males were merely restricted to lysophospholipids (lysophosphatidylcholines and lysophosphatidylethanolamines). Lysophospholipids in female patients treated with GCs were significantly higher than female patients not treated with GCs (p = 6.0 E−6), whereas no significant difference was observed in male GC users versus non-users (p = 0.397).

Conclusion

The lysophospholipid profiles in response to GCs were significantly different between male and female RA patients, which may have implications for the cardiovascular risk of GC treatment.

Electronic supplementary material

The online version of this article (doi:10.1007/s10787-016-0284-1) contains supplementary material, which is available to authorized users.

Exploring the Inflammatory Metabolomic Profile to Predict Response to TNF-α Inhibitors in Rheumatoid Arthritis

In clinical practice, approximately one-third of patients with rheumatoid arthritis (RA) respond insufficiently to TNF-α inhibitors (TNFis). The aim of the study was to explore the use of a metabolomics to identify predictors for the outcome of TNFi therapy, and study the metabolomic fingerprint in active RA irrespective of patients’ response. In the metabolomic profiling, lipids, oxylipins, and amines were measured in serum samples of RA patients from the observational BiOCURA cohort, before start of biological treatment. Multivariable logistic regression models were established to identify predictors for good- and non-response in patients receiving TNFi (n = 124). The added value of metabolites over prediction using clinical parameters only was determined by comparing the area under receiver operating characteristic curve (AUC-ROC), sensitivity, specificity, positive- and negative predictive value and by the net reclassification index (NRI). The models were further validated by 10-fold cross validation and tested on the complete TNFi treatment cohort including moderate responders. Additionally, metabolites were identified that cross-sectionally associated with the RA disease activity score based on a 28-joint count (DAS28), erythrocyte sedimentation rate (ESR) or C-reactive protein (CRP). Out of 139 metabolites, the best-performing predictors were sn1-LPC(18:3-ω3/ω6), sn1-LPC(15:0), ethanolamine, and lysine. The model that combined the selected metabolites with clinical parameters showed a significant larger AUC-ROC than that of the model containing only clinical parameters (p = 0.01). The combined model was able to discriminate good- and non-responders with good accuracy and to reclassify non-responders with an improvement of 30% (total NRI = 0.23) and showed a prediction error of 0.27. For the complete TNFi cohort, the NRI was 0.22. In addition, 88 metabolites were associated with DAS28, ESR or CRP (p<0.05). Our study established an accurate prediction model for response to TNFi therapy, containing metabolites and clinical parameters. Associations between metabolites and disease activity may help elucidate additional pathologic mechanisms behind RA.

Can baseline serum microRNAs predict response to TNF-alpha inhibitors in rheumatoid arthritis?

BACKGROUND

In rheumatoid arthritis, prediction of response to TNF-alpha inhibitor (TNFi) treatment would be of clinical value. This study aims to discover miRNAs that predict response and aims to replicate results of two previous studies addressing this topic.

METHODS

From the observational BiOCURA cohort, 40 adalimumab- (ADA) and 40 etanercept- (ETN) treated patients were selected to enter the discovery cohort and baseline serum profiling on 758 miRNAs was performed. The added value of univariately selected miRNAs (p < 0.05) over clinical parameters in prediction of response was determined by means of the area under the receiver operating characteristic curve (AUC-ROC). Validation was performed by TaqMan single qPCR assays in 40 new patients.

RESULTS

Expression of miR-99a and miR-143 predicted response to ADA, and miR-23a and miR-197 predicted response to ETN. The addition of miRNAs increased the AUC-ROC of a model containing only clinical parameters for ADA (0.75 to 0.97) and ETN (0.68 to 0.78). In validation, none of the selected miRNAs significantly predicted response. miR-23a was the only overlapping miRNA compared to the two previous studies, however inversely related with response in one of these studies. The reasons for the inability to replicate previously proposed miRNAs predicting response to TNFi and replicate those from the discovery cohort were investigated and discussed.

CONCLUSIONS

To date, no miRNA consistently predicting response to TNFi therapy in RA has been identified. Future studies on this topic should meet a minimum of standards in design that are addressed in this study, in order to increase the reproducibility.

Personalized biological treatment for rheumatoid arthritis: a systematic review with a focus on clinical applicability

OBJECTIVES

To review studies that address prediction of response to biologic treatment in RA and to explore the clinical utility of the studied (bio)markers.

METHODS

A search for relevant articles was performed in PubMed, Embase and Cochrane databases. Studies that presented predictive values or in which these could be calculated were selected. The added value was determined by the added value on prior probability for each (bio)marker. Only an increase/decrease in chance of response ⩾15% was considered clinically relevant, whereas in oncology values >25% are common.

RESULTS

Of the 57 eligible studies, 14 (bio)markers were studied in more than one cohort and an overview of the added predictive value of each marker is presented. Of the replicated predictors, none consistently showed an increase/decrease in probability of response ⩾15%. However, positivity of RF and ACPA in case of rituximab and the presence of the TNF-α promoter 308 GG genotype for TNF inhibitor therapy were consistently predictive, yet low in added predictive value. Besides these, 65 (bio)markers studied once showed remarkably high (but not validated) predictive values.

CONCLUSION

We were unable to address clinically useful baseline (bio)markers for use in individually tailored treatment. Some predictors are consistently predictive, yet low in added predictive value, while several others are promising but await replication. The challenge now is to design studies to validate all explored and promising findings individually and in combination to make these (bio)markers relevant to clinical practice.

Contribution of the subjective components of the disease activity score to the response to biologic treatment in rheumatoid arthritis

OBJECTIVE

A significant proportion of patients with rheumatoid arthritis do not respond adequately to biologic treatment. We hypothesized that lack of response to (biologic) disease-modifying antirheumatic drugs (DMARDs) is high in patients in whom the subjective, patient-reported component of the Disease Activity Score 28 (DAS28) is high at baseline. The primary aim of our present study was to investigate the contribution of the more subjective versus the objective components of the DAS28 to response to biologic agents in RA patients, as well as the changes in this contribution over time. The secondary aim was to examine whether the value of this subjective contribution at baseline affects the response to treatment.

METHODS

The DAS28-P (the subjective components of the DAS28 relative to the total DAS28) was calculated. Patients were derived from the computer-assisted Management in Early Rheumatoid Arthritis Trial-II and the Biologicals and Outcome Compared and Predicted in Utrecht Region in Rheumatoid Arthritis Study. Ordinal logistic regression analyses were performed.

RESULTS

The DAS28-P score at baseline was not associated with the level of response according to European League Against Rheumatism criteria at 3 months. Overall, a significant reduction in the DAS28-P score was observed 3 months after start of treatment, showing a greater reduction of the combined subjective components in good responders.

CONCLUSION

The results reject the hypothesis that the lack of response to biologic DMARDs is especially high in patients in whom the patient-reported component of the DAS28 is high at baseline; these subjective components are not linked to treatment response.

Serious infections in systemic lupus erythematosus with a focus on pneumococcal infections

Background

Infections are important denominators of morbidity and mortality in patients with systemic lupus erythematosus (SLE). Pneumococcus pneumoniae has been identified as a relatively frequent cause of serious infections in SLE and vaccination against this pathogen is possible. We analysed the incidence of serious infections in a cohort of SLE patients, focussing on Streptococcus pneumoniae.

Methods

We retrospectively screened the medical records of all SLE patients who were regularly seen in the outpatient clinic of our department between January 2010 and December 2012. We registered all infections that necessitated admission to the hospital (serious infection) and compared relevant clinical and laboratory parameters and immunomodulating/immunosuppressive treatment in patients with and without serious infections.

Results

In the total cohort of 260 patients, there were 132 episodes of serious infection in 70 patients, with a median follow-up per patient of 11.4 years (range 0 to 50.2 years). S. pneumoniae accounted for 11/132 (8.3%) serious infection episodes and eight of 11 episodes were invasive. With a follow-up of 3970.6 years for the total cohort, this leads to an incidence of 201/100.000 patient-years. In the multivariate analysis neither clinical parameters nor use of immunosuppressive drugs correlated with occurrence of serious infections.

Conclusions

Compared to the incidence of invasive pneumococcal infections in the Dutch population (15.6/100.000 patient years), the incidence in SLE patients is 13 times higher. This, in combination with the absence of a relation to use of immunosuppressive drugs, is a strong argument to recommend vaccination against S. pneumoniae in all SLE patients.