A Molecular Signature Response Classifier to Predict Inadequate Response to Tumor Necrosis Factor-α Inhibitors: The NETWORK-004 Prospective Observational Study

Abstract

Introduction: Timely matching of patients to beneficial targeted therapy is an unmet need in rheumatoid arthritis (RA). A molecular signature response classifier (MSRC) that predicts which patients with RA are unlikely to respond to tumor necrosis factor-α inhibitor (TNFi) therapy would have wide clinical utility.

Methods: The protein-protein interaction map specific to the rheumatoid arthritis pathophysiology and gene expression data in blood patient samples was used to discover a molecular signature of non-response to TNFi therapy. Inadequate response predictions were validated in blood samples from the CERTAIN cohort and a multicenter blinded prospective observational clinical study (NETWORK-004) among 391 targeted therapy-naïve and 113 TNFi-exposed patient samples. The primary endpoint evaluated the ability of the MSRC to identify patients who inadequately responded to TNFi therapy at 6 months according to ACR50. Additional endpoints evaluated the prediction of inadequate response at 3 and 6 months by ACR70, DAS28-CRP, and CDAI.

Results: The 23-feature molecular signature considers pathways upstream and downstream of TNFα involvement in RA pathophysiology. Predictive performance was consistent between the CERTAIN cohort and NETWORK-004 study. The NETWORK-004 study met primary and secondary endpoints. A molecular signature of non-response was detected in 45% of targeted therapy-naïve patients. The MSRC had an area under the curve (AUC) of 0.64 and patients were unlikely to adequately respond to TNFi therapy according to ACR50 at 6 months with an odds ratio of 4.1 (95% confidence interval 2.0-8.3, p value 0.0001). Odds ratios (3.4-8.8) were significant (p value < 0.01) for additional endpoints at 3 and 6 months, with AUC values up to 0.74. Among TNFi-exposed patients, the MSRC had an AUC of up to 0.83 and was associated with significant odds ratios of 3.3-26.6 by ACR, DAS28-CRP, and CDAI metrics.

Conclusion: The MSRC stratifies patients according to likelihood of inadequate response to TNFi therapy and provides patient-specific data to guide therapy choice in RA for targeted therapy-naïve and TNFi-exposed patients.

Keywords: Drug response prediction; Gene expression; Precision medicine; Prospective observational study; Rheumatoid arthritis; TNF inhibitor.

Fig. 1

Response biomarkers are in the same network vicinity of the human interactome as the RA disease module. Proteins encoded by transcripts predictive of response were mapped onto the human interactome. Proteins are shown in circles and pairwise physical protein–protein interactions are indicated as lines. The RA disease module is composed of seed and DIAMOnD genes (teal). The proteins encoded by 11 transcript features (diamonds) were either part or significantly connected to the RA disease module (p value < 0.05)

Fig. 2

Cross-validation of the MSRC among 245 patients from the CERTAIN study. a Receiver operating characteristic curve for stratification of patients based on CDAI, DAS28-CRP, ACR70, and ACR50 clinical outcomes. b Comparison of model scores for patients with or without a detected molecular signature of non-response. Boxes and intersecting line depict interquartile range and median, respectively. Bisecting colored lines indicate change in mean. Ratio of the occurrence rates for ≤ remission, ≤ LDA, ≥ moderate or ≥ high disease activity per c CDAI and d DAS28-CRP among patients for whom a molecular signature of non-response was or was not detected. Bars indicate a greater proportion of patients with a molecular signature when above 1.0 or without a detected molecular signature when below 1.0

Fig. 3

Validation of the MSRC to identify patients naïve to targeted therapies who are unlikely to respond to TNFi therapy. Receiver operating characteristic curve for stratification of patients based on CDAI, DAS28-CRP, ACR70, and ACR50 clinical outcomes at a 3 months and b 6 months. Comparison of model scores at c 3 months and d 6 months for patients with or without a detected molecular signature of non-response. Boxes and intersecting line depict interquartile range and median, respectively. Bisecting colored lines indicate change in mean. Ratio of the occurrence rates for ≤ remission, ≤ LDA, ≥ moderate or ≥ high disease activity per e CDAI and f DAS28-CRP among patients for whom a molecular signature of non-response was or was not detected. Bars indicate a greater proportion of patients with a molecular signature when above 1.0 or without a detected molecular signature when below 1.0

Fig. 4

Validation of the MSRC to identify TNFi-exposed patients who are unlikely to respond to TNFi therapy. a Receiver operating characteristic curve for stratification of patients who are receiving a TNFi therapy based on achievement of CDAI remission or DAS28-CRP remission 3 months after test results. b Comparison of model scores for patients with or without a detected molecular signature of non-response. Boxes and intersecting line depict interquartile range and median, respectively. Bisecting colored lines indicate change in mean

Fig. 5

Biology of inadequate response to TNFi therapies. The MSRC includes transcripts that encode proteins involved in many aspects of RA pathophysiology: innate immune response, cytokine biosynthesis, T and B cell homeostasis, bone homeostasis, the unfolded protein response, autophagy, apoptosis, and pro-inflammatory signaling. Detailed text and additional references can be found in the Supplemental Discussion