An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis

Anti-TNF agents have been in the first line of treatment of various inflammatory diseases such as Rheumatoid Arthritis and Crohn’s Disease, with a number of different biologics being currently in use. A detailed analysis of their effect at transcriptome level has nevertheless been lacking. We herein present a concise analysis of an extended transcriptomics profiling of four different anti-TNF biologics upon treatment of the established hTNFTg (Tg197) mouse model of spontaneous inflammatory polyarthritis. We implement a series of computational analyses that include clustering of differentially expressed genes, functional analysis and random forest classification. Taking advantage of our detailed sample structure, we devise metrics of treatment efficiency that take into account changes in gene expression compared to both the healthy and the diseased state. Our results suggest considerable variability in the capacity of different biologics to modulate gene expression that can be attributed to treatment-specific functional pathways and differential preferences to restore over- or under-expressed genes. Early intervention appears to manage inflammation in a more efficient way but is accompanied by increased effects on a number of genes that are seemingly unrelated to the disease. Administration at an early stage is also lacking in capacity to restore healthy expression levels of under-expressed genes. We record quantifiable differences among anti-TNF biologics in their efficiency to modulate over-expressed genes related to immune and inflammatory pathways. More importantly, we find a subset of the tested substances to have quantitative advantages in addressing deregulation of under-expressed genes involved in pathways related to known RA comorbidities. Our study shows the potential of transcriptomic analyses to identify comprehensive and distinct treatment-specific gene signatures combining disease-related and unrelated genes and proposes a generalized framework for the assessment of drug efficacy, the search of biosimilars and the evaluation of the efficacy of TNF small molecule inhibitors.

A number of anti-TNF drugs are being used in the treatment of inflammatory autoimmune diseases, such as Rheumatoid Arthritis and Crohn’s Disease. Despite their wide use there has been, to date, no detailed analysis of their effect on the affected tissues at a transcriptome level. In this work we applied four different anti-TNF drugs on an established mouse model of inflammatory polyarthritis and collected a large number of independent biological replicates from the synovial tissue of healthy, diseased and treated animals. We then applied a series of bioinformatics analyses in order to define the sets of genes, biological pathways and functions that are affected in the diseased animals and modulated by each of the different treatments. Our dataset allowed us to focus on previously overlooked aspects of gene regulation. We found that the majority of differentially expressed genes in disease are under-expressed and that they are also associated with functions related to Rheumatoid Arthritis comorbidities such as cardiovascular disease. We were also able to define gene and pathway subsets that are not changed in the disease but are, nonetheless, altered under various treatments and to use these subsets in drug classification and assessment. Through the application of machine learning approaches we created quantitative efficiency profiles for the tested drugs, which showed some to be more efficiently addressing changes in the inflammatory pathways, while others being quantitatively superior in restoring gene expression changes associated to disease comorbidities. We thus, propose a concise computational pipeline that may be used in the assessment of drug efficacy and biosimilarity and which may form the basis of evaluation protocols for small molecule TNF inhibitors.

Certolizumab Pegol: A Review in Inflammatory Autoimmune Diseases

Certolizumab pegol (Cimzia^®) is a subcutaneously administered polyethylene glycolylated (PEGylated) antigen-binding fragment of a recombinant human monoclonal antibody that selectively neutralizes TNFα. The drug is indicated for a variety of inflammatory autoimmune diseases, including Crohn's disease (CD), rheumatoid arthritis (RA), psoriatic arthritis (PsA) and axial spondyloarthritis (axSpA), based on its benefit in these settings in well-designed clinical trials. In these studies, certolizumab pegol (as first- or subsequent-line therapy) reduced the severity of CD when used as an induction or maintenance therapy, and improved the signs/symptoms and slowed the radiographic progression of RA (with or without concomitant methotrexate), PsA and axSpA. Certolizumab pegol is generally well tolerated, with upper respiratory tract infections, rash and urinary tract infections being among the most frequent adverse reactions. Thus, certolizumab pegol is an effective option for the management of these autoimmune diseases.

[TNF inhibitors]

As of January 2016, 5 originator TNF inhibitors (infliximab, etanercept, adalimumab, golimumab and certolizumab pegol) and an infliximab biosimilar are available for rheumatoid arthritis (RA) in Japan. The efficacy and effectiveness of TNF inhibitors improve with concomitant methotrexate even for the least immunogenic agent. The Japan College of Rheumatology guideline for TNF inhibitor use in RA has been updated in March 2015, including recent evidences of effectiveness and safety partly from the postmarketing surveillance data in Japan. During the remission induction phase, maintenance of drug trough level above effective blood concentration is paramount, while the tapering and withdrawal of TNF inhibitors may be considered after achieving sustained remission.

Intravenous Versus Subcutaneous Anti-TNF-Alpha Agents for Crohn's Disease: A Comparison of Effectiveness and Safety

BACKGROUND

In recent years, there have been a number of pharmacological innovations for Crohn's disease (CD), a difficult-to-treat condition, including new treatment philosophies (e.g., top-down therapy) and new therapeutic options in terms of the agent and the route of administration. Three anti-tumor necrosis factor (anti-TNF-alpha) agents are available for use among CD patients in the United States: infliximab, an intravenous agent, and adalimumab and certolizumab pegol, 2 newer subcutaneous products. Infliximab is considered the "gold standard" because it has the longest clinical experience, and adalimumab and certolizumab pegol have each gained significant market share.

OBJECTIVE

To examine differences in effectiveness and safety between currently available intravenous and subcutaneous anti-TNF-alpha agents used to treat patients with CD.

METHODS

Data for this retrospective, administrative claims analysis were obtained from pharmacy and medical claims from major U.S. health plans geographically dispersed across 14 states during 2007-2011. Patients had at least 1 ICD-9-CM diagnosis for CD, 6 months pre-index eligibility, and initiated anti-TNF-alpha therapy on the index date. Patients in each cohort were propensity score matched on pre-index demographics, clinical characteristics, and baseline health care use. During the post-index period, age-sex adjusted incidence rate ratios (IRRs) of CD-related symptoms, infections, cancers, and hepatic-related conditions were compared using Cox (PH) models.

RESULTS

The matched cohorts included 515 patients in each group, with an average age of 39 years. Median follow-up was 17.5 months in the intravenous cohort and 17.7 months in the subcutaneous cohort. In terms of effectiveness outcomes, age-sex adjusted IRRs for the subcutaneous group, with the intravenous cohort as a reference, were as follows: 0.61 (95% CI = 0.32-1.18, P = 0.14) for anal fissures; 0.97 (95% CI = 0.72-1.30, P = 0.85) for abscess; 1.08 (95% CI = 0.79-1.04, P = 0.64) for fistulas; 1.12 (95% CI = 0.83-1.54, P = 0.45) for gastrointestinal hemorrhage; and 1.22 (95% CI = 0.93-1.59, P = 0.14) for a combined measure of obstruction, occlusion, stenosis, and stricture of intestine. In terms of safety outcomes, age-sex adjusted IRRs for the subcutaneous group were as follows: 0.85 (95% CI = 0.62-1.16, P = 0.30) for infections; 1.16 (95% CI = 0.71-1.89, P = 0.55) for cancers; and 1.23 (95% CI = 0.79-1.92, P = 0.35) for hepatic-related conditions.

CONCLUSIONS

After adjusting for baseline characteristics, effectiveness and safety outcomes appear to be comparable between intravenous and subcutaneous anti-TNF-alpha agents in patients with CD. With similar outcomes, other considerations such as convenience of administration and patient preference may play a more prominent role in choice of agent. Health care providers and health payers should inform CD patients about the range of options available when selecting an anti-TNF-alpha agent.