Validity of clinical associations of biomarkers in translational research studies: the case of systemic autoimmune diseases

An Update on Antiphospholipid Syndrome

PURPOSE OF REVIEW

To review the recent available evidence on epidemiology, pathogenesis, clinical phenotypes, and management of antiphospholipid syndrome (APS) and summarize potential future research perspectives.

RECENT FINDINGS

Accumulating evidence has further expanded our understanding of the disease, including new data about the incidence and prevalence of APS, novel pathways supporting the role of thrombo-inflammation in APS including platelet, monocyte and endothelial cell activation, pro-inflammatory cytokine and chemokine production, complement activation, neutrophil extracellular trap release, and type I interferon gene expression that could yield to new potential treatment targets, better identification of criteria and non-criteria clinical phenotypes, antiphospholipid antibody profiles and their associations with clinical outcomes, prognostic tools, and treatment strategies based on recent evidence-based recommendations for patients with thrombotic and obstetric APS, with or without systemic lupus erythematosus. Ongoing research efforts and international collaborations enhance our knowledge of this rare and often devastating syndrome and help improve patient care and health outcomes.

Does seronegative obstetric APS exist? "pro" and "cons"

Antiphospholipid Syndrome (APS) is the commonest treatable cause of recurrent miscarriage and pharmacological treatment of pregnant patients with antiphospholipid antibodies (aPL) should aim at preventing obstetric complications and maternal thrombotic events. Conventional treatment for patients with an established diagnosis of obstetric APS (OAPS), generally resulting in over 70-80% successful pregnancies. Since seropositive (SP)-APS and seronegative (SN)-APS patients had shown similar clinical profiles, patients with SN- OAPS, as well as SP-OAPS, should receive combined treatment in order to improve the pregnancy prognosis; indeed, current standard of care increased good pregnancy outcome in SN-APS, with similar effect to confirmed APS. The above data suggest that there are patients with the clinical manifestations of OAPS but persistently negative to conventional aPL that need to be identified to ensure adequate therapy and therefore a better prognosis. The clinical utility of non-criteria aPL in the diagnosis of SN-APS is still a matter of debate. In the last decade more and more studies have reported the presence of patients suffering from SN-APS in which non-conventional ("non-criteria") aPL might be present or antibodies may be detected using methodological approaches different from the traditional assays. To improve test standardization large prospective, multicenter, and multinational studies are needed. Therefore, when assessing a patient with clinical manifestations consistent with OAPS but aPL negative using the conventional available assays, the clinician should consider the possibility that the patient is affected with SN-APS.

Mixing omics: combining genetics and metabolomics to study rheumatic diseases

Metabolomics is an exciting field in systems biology that provides a direct readout of the biochemical activities taking place within an individual at a particular point in time. Metabolite levels are influenced by many factors, including disease status, environment, medications, diet and, importantly, genetics. Thanks to their dynamic nature, metabolites are useful for diagnosis and prognosis, as well as for predicting and monitoring the efficacy of treatments. At the same time, the strong links between an individual's metabolic and genetic profiles enable the investigation of pathways that underlie changes in metabolite levels. Thus, for the field of metabolomics to yield its full potential, researchers need to take into account the genetic factors underlying the production of metabolites, and the potential role of these metabolites in disease processes. In this Review, the methodological aspects related to metabolomic profiling and any potential links between metabolomics and the genetics of some of the most common rheumatic diseases are described. Links between metabolomics, genetics and emerging fields such as the gut microbiome and proteomics are also discussed.

Regulatory Forum Opinion Piece*: Veterinary Pathologists in Translational Pharmacology and Biomarker Integration in Drug Discovery and Development

This article highlights emerging roles for veterinary pathologists outside of traditional functions and in line with the translational research (TR) approach. Veterinary pathologists offer unique and valuable expertise toward addressing particular TR and associated translational pharmacology questions, identifying gaps and risks in biomarker and pathology strategies, and advancing TR team decision making. Veterinary pathologists' attributes that are integral to the TR approach include (i) well-developed understanding of comparative physiology, pathology, and disease; (ii) extensive experience in interpretation and integration of complex data sets on whole-body responses and utilizing this for deciphering pathogenesis and translating events between laboratory species and man; (iii) proficiency in recognizing differences in disease end points among individuals, animal species and strains, and assessing correlations between these differences and other investigative (including biomarker) findings; and (iv) strong background in a wide spectrum of research technologies that can address pathomechanistic questions and biomarker needs. Some of the more evident roles in which veterinary pathologists can offer their greatest contributions to address questions and strategies of TR and biomarker integration will be emphasized.

[Therapeutic strategies for systemic lupus erythematosus]

Therapeutic strategy means the definition of a long-term target, which should be reached by a chosen management. As for rheumatoid arthritis, the treat to target initiative recommends remission as the target for systemic lupus erythematosus (SLE) but the command variables of remission are not yet defined. The basis of a therapeutic strategy is first the analysis of those factors that may influence the achievement of the objectives: SLE disease activity, the differentiation of damage, organ manifestations, comorbidities, genetics, sex, age of onset and considering the pathophysiological basis are some of these factors. The next step is the analysis of the available substances and concepts that allow the target to be reached. Finally, rules for management (e.g. guidelines) are needed that enrich the possibility to reach the target and improve the prognosis of patients suffering from SLE.

Modular transcriptional repertoire analyses of adults with systemic lupus erythematosus reveal distinct type I and type II interferon signatures

OBJECTIVE

The role of interferon-α (IFNα) in the pathogenesis of systemic lupus erythematosus (SLE) is strongly supported by gene expression studies. The aim of this study was to improve characterization of the blood IFN signature in adult SLE patients.

METHODS

Consecutive patients were enrolled and followed up prospectively. Microarray data were generated using Illumina BeadChips. A modular transcriptional repertoire was used as a framework for the analysis.

RESULTS

Our repertoire of 260 modules, which consisted of coclustered gene sets, included 3 IFN-annotated modules (M1.2, M3.4, and M5.12) that were strongly up-regulated in SLE patients. A modular IFN signature was observed in 54 of 62 patients (87%) or 131 of all 157 samples (83%). The IFN signature was more complex than expected, with each module displaying a distinct activation threshold (M1.2 < M3.4 < M5.12), thus providing a modular score by which to stratify SLE patients based on the presence of 0, 1, 2, or 3 active IFN modules. A similar gradient in modular IFN signature was observed within patients with clinically quiescent disease, for whom moderate/strong modular scores (2 or 3 active IFN modules) were associated with higher anti-double-stranded DNA titers and lower lymphocyte counts than those in patients with absent/mild modular scores (0 or 1 active IFN modules). Longitudinal analyses revealed both stable (M1.2) and variable (M3.4 and M5.12) components of modular IFN signature over time in single patients. Interestingly, mining of other data sets suggested that M3.4 and M5.12 could also be driven by IFNβ and IFNγ.

CONCLUSION

Modular repertoire analysis reveals complex IFN signatures in SLE, which are not restricted to the previous IFNα signature, but which also involve IFNβ and IFNγ.

Advances in systems biology approaches for autoimmune diseases

Because autoimmune diseases (AIDs) result from a complex combination of genetic and epigenetic factors, as well as an altered immune response to endogenous or exogenous antigens, systems biology approaches have been widely applied. The use of multi-omics approaches, including blood transcriptomics, genomics, epigenetics, proteomics, and metabolomics, not only allow for the discovery of a number of biomarkers but also will provide new directions for further translational AIDs applications. Systems biology approaches rely on high-throughput techniques with data analysis platforms that leverage the assessment of genes, proteins, metabolites, and network analysis of complex biologic or pathways implicated in specific AID conditions. To facilitate the discovery of validated and qualified biomarkers, better-coordinated multi-omics approaches and standardized translational research, in combination with the skills of biologists, clinicians, engineers, and bioinformaticians, are required.

Socioeconomic status. The relationship with health and autoimmune diseases

Socioeconomic status (SES) is a hierarchical social classification associated with different outcomes in health and disease. The most important factors influencing SES are income, educational level, occupational class, social class, and ancestry. These factors are closely related to each other as they present certain dependent interactions. Since there is a need to improve the understanding of the concept of SES and the ways it affects health and disease, we review herein the tools currently available to evaluate SES and its relationship with health and autoimmune diseases.

Validation of new biomarkers in systemic autoimmune diseases

Biomarkers have an important influence on the clinical decision-making processes involved in diagnosis, assessment of disease activity, allocation of treatment, and determining prognosis. The clinical usefulness of a biomarker is dependant on demonstration of its validity. Ideally, biomarkers should provide information not available from currently available tests and should be tested as they would be used in clinical practice; however, potential biomarkers could be affected by many different clinical or patient variables-such as disease activity, therapeutic intervention, or the presence of comorbidities--and validation studies might not include all the design features that are required to ensure that the biomarker is a true measure of the clinical process it is intended to reflect. In this Review, we appraise studies that have been conducted to validate six promising new biomarkers for diagnosis, disease activity assessment, or prognosis in patients with systemic autoimmune diseases. We discuss the validity of these six biomarkers with particular reference to the features of the studies that lend weight to or distract from their findings. The intent of this discussion is to draw attention to elements of validation study design that should be considered when evaluating the robustness of a biomarker, which differ according to the marker's intended use.