An IFNG polymorphism is associated with interferon-beta response in Spanish MS patients

Pharmacogenetics: A strategy for personalized medicine for autoimmune diseases

For many years, a considerable number of patients with autoimmune diseases (ADs) have suffered from a lack of drug response and drug-related toxicity. Despite the emergence of new therapeutic options such as biological agents, patients continue to struggle with these problems. Unfortunately, new challenges, including the paradoxical effects of biological drugs, have complicated the situation. In recent decades, efforts have been made to predict drug response as well as drug-related side effects. Thanks to the many advances in genetics, evaluation of markers to predict drug response/toxicity before the initiation of treatment may be an avenue toward personalizing treatments. Implementing pharmacogenetics and pharmacogenomics in the clinic could improve clinical care; however, obstacles remain to effective personalized medicine for ADs. The present study attempted to clarify the concept of pharmacogenetics/pharmacogenomics for ADs. After an overview on the pathogenesis of the most common types of treatments, this paper focuses on pharmacogenetic studies related to the selected ADs. Bridging the gap between pharmacogenetics and personalized medicine is also discussed. Moreover, the advantages, disadvantages and recommendations related to making personalized medicine practical for ADs have been addressed.

Pharmacogenomics of Multiple Sclerosis: A Systematic Review

Background: Over the past two decades, various novel disease-modifying drugs for multiple sclerosis (MS) have been approved. However, there is high variability in the patient response to the available medications, which is hypothesized to be partly attributed to genetics. Objectives: To conduct a systematic review of the current literature on the pharmacogenomics of MS therapy. Methods: A systematic literature search was conducted using PubMed/MEDLINE database searching for articles investigating a role of genetic variation in response to disease-modifying MS treatments, published in the English language up to October 9th, 2018. PRISMA guidelines for systematic reviews were applied. Studies were included if they investigated response or nonresponse to MS treatment defined as relapse rate, by expanded disability status scale score or based on magnetic resonance imaging. The following data were extracted: first author's last name, year of publication, PMID number, sample size, ethnicity of patients, method, genes, and polymorphisms tested, outcome, significant associations with corresponding P-values and confidence intervals, response criteria, and duration of the follow-up period. Results: Overall, 48 articles published up to October 2018, evaluating response to interferon-beta, glatiramer acetate, mitoxantrone, and natalizumab, met our inclusion criteria and were included in this review. Among those, we identified 42 (87.5%) candidate gene studies and 6 (12.5%) genome-wide association studies. Existing pharmacogenomic evidence is mainly based on the results of individual studies, or on results of multiple studies, which often lack consistency. In recent years, hypothesis-free approaches identified novel candidate genes that remain to be validated. Various study designs, including the definition of clinical response, duration of the follow-up period, and methodology as well as moderate sample sizes, likely contributed to discordances between studies. However, some of the significant associations were identified in the same genes, or in the genes involved in the same biological pathways. Conclusions: At the moment, there is no available clinically actionable pharmacogenomic biomarker that would enable more personalized treatment of MS. More large-scale studies with uniform design are needed to identify novel and validate existing pharmacogenomics findings. Furthermore, studies investigating associations between rare variants and treatment response in MS patients, using next-generation sequencing technologies are warranted.

Pharmacogenetic Biomarkers to Predict Treatment Response in Multiple Sclerosis: Current and Future Perspectives

Disease-modifying therapies (DMTs) have significantly advanced the treatment of relapsing multiple sclerosis (MS), decreasing the frequency of relapses, disability, and magnetic resonance imaging lesion formation. However, patients' responses to and tolerability of DMTs vary considerably, creating an unmet need for biomarkers to identify likely responders and/or those who may have treatment-limiting adverse reactions. Most studies in MS have focused on the identification of pharmacogenetic markers, using either the candidate-gene approach, which requires prior knowledge of the genetic marker and its role in the target disease, or genome-wide association, which examines multiple genetic variants, typically single nucleotide polymorphisms (SNPs). Both approaches have implicated numerous alleles and SNPs in response to selected MS DMTs. None have been validated for use in clinical practice. This review covers pharmacogenetic markers in clinical practice in other diseases and then reviews the current status of MS DMT markers (interferon β, glatiramer acetate, and mitoxantrone). For a complex disease such as MS, multiple biomarkers may need to be evaluated simultaneously to identify potential responders. Efforts to identify relevant biomarkers are underway and will need to be expanded to all MS DMTs. These will require extensive validation in large patient groups before they can be used in clinical practice.

An integrated approach to design novel therapeutic interventions for demyelinating disorders

Therapeutic strategies are often based on two general principles: interference with the pathogenic process and repair of the damaged tissues. Recent studies, however, have suggested that several pathological conditions may result from the interplay between genetic susceptibility traits and environmental influences that, by modulating the epigenome, also affect disease onset and progression. Based on lessons from neural development, it is conceivable that new lines of preventive and possibly therapeutic intervention might be developed to modulate disease onset or decrease the severity of the symptoms. This review will discuss these concepts within the context of multiple sclerosis, the most common demyelinating disease of the central nervous system, and the leading cause of progressive neurological disability in young adults.

Allelic combinations of immune-response genes as possible composite markers of IFN-β efficacy in multiple sclerosis patients

Background: IFN-β is widely used as the first-line disease-modifying treatment for multiple sclerosis. However, 30–50% of multiple sclerosis patients do not respond to this therapy. Identification of genetic variants and their combinations that predict responsiveness to IFN-β could be useful for treatment prognosis. Materials & methods: The combinations of alleles of nine polymorphic loci in immune-response genes were analyzed in 253 Russian multiple sclerosis patients as possible determinants of clinically optimal IFN-β treatment response using APSampler software. Results: Carriage of TGFB1*-509C and CCR5*d was associated with favorable IFN-β response by itself. CCR5*d, IFNAR1*16725G, IFNG*874T and IFNB1*153T/T were the components of the combinations, associated with clinically optimal response to IFN-β. Carriage of composite markers (CCR5*d + IFNAR1*G + IFNB1*T/T) or (CCR5*d + IFNAR1*G + IFNG*T) is beneficial for IFN-β treatment efficacy. Discussion: The data obtained provides evidence of the cumulative effect of immune-response genes on IFN-β treatment efficacy. This joint contribution may reflect the additive effect of independent allelic variants and epistatic interactions between some of them.

Original submitted 2 July 2012; Revision submitted 21 September 2012

Single nucleotide polymorphisms in multiple sclerosis: disease susceptibility and treatment response biomarkers

Multiple sclerosis (MS) is a chronic inflammatory demyelinating and neurodegenerative disease of the central nervous system characterized by unpredictable and variable clinical course. Etiology of MS involves both genetic and environmental factors. New technologies identified genetic polymorphisms associated with MS susceptibility among which immunologically relevant genes are significantly overrepresented. Although individual genes contribute only a small part to MS susceptibility, they might be used as biomarkers, thus helping to identify accurate diagnosis, predict clinical disease course and response to therapy. This review focuses on recent progress in research on MS genetics with special emphasis on the possibility to use single nucleotide polymorphism of candidate genes as biomarkers of susceptibility to disease and response to therapy.

Pharmacogenomics in neurology: current state and future steps

In neurology, as in any other clinical specialty, there is a need to develop treatment strategies that allow stratification of therapies to optimize efficacy and minimize toxicity. Pharmacogenomics is one such method for therapy optimization: it aims to elucidate the relationship between human genome sequence variation and differential drug responses. Approaches have focused on candidate approaches investigating absorption-, distribution-, metabolism, and elimination (ADME)-related genes (pharmacokinetic pathways), and potential drug targets (pharmacodynamic pathways). To date, however, only few genetic variants have been incorporated into clinical algorithms. Unfortunately, a large number of studies have thrown up contradictory results due to a number of deficiencies, including small sample sizes, inadequate phenotyping, and genotyping strategies. Thus, there still exists an urgent need to establish biomarkers that could help to select for patients with an optimal benefit to risk relationship. Here we review recent advances, and limitations, in pharmacogenomics for agents used in neuroimmunology, neurodegenerative diseases, ischemic stroke, epilepsy, and primary headaches. Further work is still required in all of these areas, which really needs to progress on several fronts, including better standardized phenotyping, appropriate sample sizes through multicenter collaborations and judicious use of new technological advances such as genome-wide approaches, next generation sequencing and systems biology. In time, this is likely to lead to improvements in the benefit-harm balance of neurological therapies, cost efficiency, and identification of new drugs.

IL28B polymorphisms are not associated with the response to interferon-β in multiple sclerosis

Recent studies have revealed an association between interleukin 28B (IL28B) and response to IFN-alpha treatment in hepatitis C patients. Here we investigated the influence of IL28B polymorphisms in the response to interferon-beta (IFNβ) in multiple sclerosis (MS) patients. We genotyped two SNPs of the IL28B gene (rs8099917 and rs12979860) in 588 MS patients classified into responders (n=281) and non-responders (n=307) to IFNβ. Combined analysis of the study cohorts showed no significant associations between SNPs rs8099917 and rs12979860 and the response to treatment. These findings do not support a role of IL28B polymorphisms in the response to IFNβ in MS patients.

Single-nucleotide polymorphisms in response to interferon-beta therapy in multiple sclerosis

Interferon-beta (IFN-β) is one of the main first-line disease-modifying drugs indicated for the treatment of multiple sclerosis (MS). The drug exhibits only limited effectiveness, and does not produce clinical benefits in around 20%-50% of patients. The availability of biomarkers would be beneficial for identification of patients at high risk of treatment failure, before initiation of therapy. Over the last 5 years, the search for such biomarkers has intensified and various promising candidates have been uncovered. Here, we review the main attempts undertaken to identify polymorphic variants associated with response to IFN-β therapy in MS by means of candidate gene approaches and whole-genome association scans. Despite substantial progress made in the field, there is still a long way to go before biomarker discoveries can be incorporated into clinical practice to predict IFN-β-responder status in MS patients.

Influence of APOE gene polymorphisms on interferon-beta treatment response in multiple sclerosis

OBJECTIVE

Clinical trials with interferon beta in relapsing remitting multiple sclerosis (RRMS) have demonstrated a reduction in the relapse rate. Nevertheless, not all patients respond to this treatment, although there is no consensus regarding the definition of response to therapy. The reasons for this failure are not known but genetic factors probably influence this, as has been previously shown with Interleukin 10 or Interferon gamma polymorphisms. The role of apolipoprotein E (APOE) gene in MS has been investigated and does not appear to increase risk for MS or influence disease severity. Interestingly APOE variation influences response to cholinesterase inhibitor treatment in Alzheimer disease or to statins in hypercholesterolemia. This might have future implications for MS.

MATERIAL AND METHODS

We retrospectively reviewed 38 RRMS patients (32 females and 6 males) treated with interferon beta (INFbeta) over at least two years. Criteria for treatment were uniform accordingly to an "Advisory Committee for the Treatment of Multiple Sclerosis". We collected data variables including age, age of onset, clinical type or disease duration. Patients were classified, two years after the start of treatment, as responders and non-responders based upon clinical criteria available in the literature, which rely on the presence of relapses, increase of disability, or both. APOE genotype was determined from blood samples using validated polymerase chain reaction methods. Correlation between patient responding status with allele E2 or E4 was tested.

RESULTS

A total of 20 patients (52.6%) received subcutaneous INFbeta1b (Betaferón(®)), 13 (34.2%) INFbeta1a intramuscular (Avonex(®)), and 5 (13.2%) subcutaneous INFbeta1a (Rebif(®)). We found 2 patients (5.2%) heterozygous for the E2 allele and 9 (23.7%) for the E4 allele. No patient was homozygous for E2 or E4. Comparison of patients with and without E2 or E4 allele showed no significant differences in any of the ten therapy response variables assessed.

CONCLUSION

Findings of a recent meta-analysis have not supported a role for APOE in MS susceptibility or severity. We have not found, in our data, any influence of this gene in the RRMS response to INFbeta. However, larger series would be required to validate these results.

Glypican 5 is an interferon-beta response gene: a replication study

BACKGROUND

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system. Interferon-beta is the most usual therapy in relapsing-remiting MS. However, approximately 50% of the treated patients do not respond adequately. Very recently, a genome-wide association study on interferon-beta pharmacogenetics has described polymorphisms at several genes that are associated with response to this treatment. Our aim is to replicate the results obtained at the two loci most strongly implicated in the response to interferon-beta treatment, HAPLN1 and GPC5.

PATIENTS AND METHODS

We performed a case-control study, analyzing 199 patients with MS treated with interferon-beta for at least 2 years and at least two documented relapses over the 2 years, previous to treatment onset. Responders had neither relapses nor increase in expanded disability status scale (EDSS) over the 2-year follow-up period, whereas nonresponders had at least two relapses or an increase in EDSS of at least 1 point. We studied three single-nucleotide polymorphisms (SNPs) in the GPC5 locus and three SNPs in the HAPLN1 locus by TaqMan technology. Allelic frequencies between responders and nonresponders were compared by a chi-square test.

RESULTS

An association was found between GPC5 polymorphisms and the response to interferon-beta therapy in patients with MS, in agreement with earlier data (responder vs nonresponder patients: rs10492503, P = 0.0005). The other locus studied (HAPLN1) did not show association with treatment response to interferon-beta (all SNPs P > 0.05).

CONCLUSIONS

We confirm the association of polymorphisms within GPC5 with response to interferon-beta therapy in patients with MS.

United Europeans for development of pharmacogenomics in multiple sclerosis network

Multiple sclerosis (MS) is a chronic inflammatory, disabling disease of the CNS. A recent study has estimated the annual cost of MS in Europe at €12.5 billion. There is no definitive cure for the disease. Immunomodulatory therapies, such as IFN-β and glatiramer acetate, are only partially effective. Various new therapies in the final stages of clinical trials are being developed in the absence of efficacy biomarkers. Hence, there is a pressing need for identification of MS treatment response biomarkers. The focus of the multicenter research initiative United Europeans for the development of pharmacogenomics in MS (UEPHA*MS) is to promote and improve training opportunities in the novel supradisciplinary area of pharmacogenomics, biomarker research and systems biology applied to MS. UEPHA*MS is a Marie Curie Initial Training network funded by the 7th Framework Programme of the European Commission. The main scientific goals of this network are both to enhance our knowledge of the mechanisms determining response outcomes of existing immunomodulatory therapies and to identify novel therapeutic opportunities. UEPHA*MS is composed of 11 internationally recognized research teams from five countries with an assortment of expertise in complementary disciplines. The UEPHA*MS network will provide a coherent and internationally competitive platform for the training of young scientists based on multidisciplinary state-of-the-art laboratory-based and network-wide activities. This network will be instrumental in priming young scientists for Europe’s collective effort toward improved provision of healthcare based on personalized medicine.

Translation towards personalized medicine in Multiple Sclerosis

In recent years the realization that the concept 'one drug fits all' - does not work, created the need to shift gears from 'treating the disease' to 'treating the patient', and implementation of 'Personalized Medicine' where treatment is tailored to the individual. In chronic and progressive diseases, such as Multiple Sclerosis (MS), the need for tailored therapeutics is especially imperative, as the consequences of an ineffective medication might be irreversible dysfunction. In recent years accumulating evidence indicates that MS is not a single disease and that patients with different disease subtypes respond differently to a medication. Environment and genetics are among the factors that determine disease subtype and activity, and the patient's response to medication. Additional factors include demographic characteristics such as gender and age, as well as chrono-biological indicators. During the last few years, advances and availability of new technologies have brought genome-wide gene expression profiling studies to many medical fields, including MS. Genomic technologies have also stimulated pharmacogenetics studies, that aim to identify genetic factors that affect response to treatment. However, pharmacogenetics information is still immature to allow its translation to clinical practice in MS. Notably, one of the major limitations in obtaining reproducible data across MS pharmacogenetics studies has been the lack of a consensus as to the appropriate method for determining clinical response. In light of the rapid advances in technology and progress in applying individualized treatment strategies in other diseases, 'Personalized Medicine' for MS seems feasible within the coming years.

Pharmacogenomics of the response to IFN-β in multiple sclerosis: ramifications from the first genome-wide screen

Evaluation of: Byun E, Caillier SJ, Montalban X et al.: Genome-wide pharmacogenomic analysis of the response to interferon-β therapy in multiple sclerosis. Arch. Neurol. 65(3) 337–344 (2008). Specifically, IFN-β is the most widely used disease-modifying therapy for the treatment of multiple sclerosis. The main benefits of the therapy, fewer and less severe relapses as well as delayed disease progression, are seen in only approximately 50% of the patients. Genetic polymorphisms may constitute in-built determinants of individual differences in response to IFN-β. Prior attempts to identify such ‘predictors of response’ were hypothesis-driven in that they were based on preselection of candidate genes associated with Type I interferon pathways. In the present study, the authors performed the first ever nonbiased genome-wide association screen in an attempt to identify response-predictive SNPs. Using a robust four-stage completion strategy coupled to advanced SNP ranking/clustering algorithms, 18 significant SNPs were identified, many of which are located in genes that have never before been linked clearly to Type I interferon biology or therapeutic effects. While this study was not designed per se so as to validate earlier findings, genes arising from previous pharmacogenomic studies were generally not confirmed. This is due to major discrepancies between interstudy sets of used SNPs, but may also reflect differential strategies for ascertainment of response to IFN-β, or simply Type I/II errors. The 100-K SNP screen by Byun et al. hallmarks a new stage of pharmacogenomics research applied to multiple sclerosis treatments. Through the judicious implementation of DNA pooling on SNP microarrays, it vividly demonstrates that informative genome-wide pharmacogenomic screens can be performed at a fraction of the cost of individual microarray genotyping. Although, unquestionably, higher-density SNP screens and further replication studies are needed, this study is instrumental in bringing the concept of personalized medicine a (small) step closer to the multiple sclerosis patient. In addition, it has generated a flurry of novel information of likely importance in furthering our understanding of Type I interferon biology.

Environment-gene interaction in multiple sclerosis: human herpesvirus 6 and MHC2TA

Multiple sclerosis (MS) is an inflammatory disorder affecting the central nervous system, in which both genetic and environmental factors interact. Among these environmental contributors, herpesvirus has been proposed as an important etiologic factor. CIITA is a transcription factor controlling the expression of MHC class II genes, the main genetic determinants of MS susceptibility. This gene has been described as a target of the immunoevasive strategies, and it is therefore an attractive candidate gene to be at the genetic-viral crossroads. Two polymorphisms in MHC2TA gene (rs4,774G/C and rs3,087,456A/G) were studied in two groups: one in 22 multiple sclerosis patients with active human herpes virus 6 (HHV-6A) replication (HHV-6A-positive), and the other of 77 patients with no detectable HHV-6A active infection (HHV-6A-negative); a Spanish healthy control group (n = 520) was also included as external control. An association of the rs4,774C allele with the HHV-6A-positive group was found when compared with the HHV-6A-negative (47.7% vs 18.8%, p = 0.0001; odds ratio = 3.94) and also with the control group (47.7% vs 25.5%, p = 0.001, odds ratio = 2.67). No significant differences were observed between HHV-6A-negative subjects and healthy controls. Our data suggest that a strong gene-environment interaction occurs between HHV-6A active replication and MHC2TA rs4,774C or another polymorphism in tight linkage disequilibrium with it. Besides, this report indicates that when patients are grouped based upon a well-defined molecular event, complex diseases may reveal themselves as being constituted by distinct entities in which some genes may have a strong influence.