Pharmacogenomics and its implications for autoimmune disease

Frequency of pharmacogenomic variants affecting safety and efficacy of immunomodulators and biologics in a South Asian population from Sri Lanka

BACKGROUND

Immunomodulators are important for management of autoimmune diseases and hematological malignancies. Significant inter-individual variation in drug response/reactions exists due to genetic polymorphisms. We describe frequency of identified genetic polymorphisms among Sri Lankans.

METHODS

Sri Lankan data were obtained from an anonymized database of 670 participants. Data on variants and global distribution of Minor Allele frequency (MAF) of other populations (South Asian, Ashkenazi-Jewish, East-Asian, European-Finnish, European-non-Finnish, Latino-American, African/African-American) were obtained from pharmGKB online database.

RESULTS

SLC19A1 (rs1051266) variant had a MAF (95% CI) of 63.3% (60.7-65.9). Other common variants included FCGR3A (rs396991), MTHFR (rs1801133), ITPA (rs1127354), CYP2C9*3 (rs1057910) and NUD15*3 (rs116855232), with MAFs of 35.3% (32.7-37.9), 12.2% (10.4-13.9), 10.9% (9.2-12.6), 9.8% (8.2-11.4), 8.3% (6.8-9.8) respectively. Less commonly present variants included CYP2C9*2 (rs1799853) (2.5%[1.7-3.4]), TPMT*3C (rs1142345) (1.9%[1.1-2.6]), TPMT*3B (rs1800460) (0.2%[0-0.5]), CYP3A5*6 (rs10264272) (0.2%[0-0.4]) and CYP3A4*18 (rs28371759) (0.1%[0-0.2]). The SLC19A1 (rs1051266), NUD15*3 (rs116855232), CYP2C9*3 (rs1057910), FCGR3A (rs396991), and ITPA (rs1127354) showed significantly higher frequencies in Sri Lankans compared to many other populations, exceptions include FCGR3A in Ashkenazi-Jewish and ITPA in East-Asians. Conversely, MTHFR (rs1801133), TPMT*3B (rs1800460), and CYP2C9*2 (rs1799853) were significantly less prevalent among Sri Lankans than in  many other populations. Sri Lankans exhibited lower prevalence of TPMT*3C (rs1142345) compared to European-non-Finnish, Latino-Americans, and African/African-Americans; CYP3A4*18 (rs28371759) compared to East-Asians; and CYP3A5*6 (rs10264272) compared to African/African-Americans and Latino-Americans.

CONCLUSION

Sri Lankans exhibit higher frequencies in variants reducing methotrexate efficacy (SLC19A1), increasing azathioprine myelotoxicity (NUDT15), and lower frequencies in variants linked to increased azathioprine toxicity (TPMT*3B, TPMT*3C), reduced tacrolimus efficacy (CYP3A4*18), and methotrexate toxicity risk (MTHFR). Beneficial variants enhancing rituximab efficacy (FCGR3A) are more prevalent, while those reducing tacrolimus dosage (CYP3A5*6) are less common. This highlights need for targeted medication strategies to improve treatment outcomes.

The Circassians and the Chechens in Jordan: results of a decade of epidemiological and genetic studies

Circassians and Chechens in Jordan, both with Caucasian ancestry, are genetically isolated due to high rate of endogamous marriages. Recent interest in these populations has led to studies on their genetic similarities, differences, and epidemiological differences in various diseases. Research has explored their predisposition to conditions like diabetes, hypertension, and cancer. Moreover, pharmacogenetic (PGx) studies have also investigated medication response variations within these populations, and forensic studies have further contributed to understanding these populations. In this review article, we first discuss the background of these minority groups. We then show the results of a principle component analysis (PCA) to investigate the genetic relationships between Circassian and Chechen populations living in Jordan. We here present a summary of the findings from the 10 years of research conducted on them. The review article provides a comprehensive summary of research findings that are truly valuable for understanding the unique genetic characteristics, diseases' prevalence, and medication responses among Circassians and Chechens living in Jordan. We believe that gaining deeper comprehension of the root causes of various diseases and developing effective treatment methods that benefit the society as a whole are imperative to engaging a wide range of ethnic groups in genetic research.

Exploring pharmacogenetic variants for predicting response to anti-TNF therapy in autoimmune diseases: a meta-analysis

Aim: The aim of this study is to explore how SNPs may affect the response to anti-TNF-α therapy in the major autoimmune diseases, such as psoriasis, rheumatoid arthritis, inflammatory bowel diseases and Spondyloarthritis. Methodology: We conducted a systematic overview on the field, by assessing all studies that examined the association between polymorphisms and response to anti-TNF-α therapy in participants of European descent. Results: In total, six independent SNPs located in FCGR2A, FCGR3A, TNF-α and TNFRSF1B genes were significantly associated with response to TNF-α blockers, found mainly in disease-subgroup analyses. Conclusion: No common pharmacogenetic variant was identified for all autoimmune diseases under study, suggesting the requirement of more studies in the field in order to capture such predictive variants that will aid treatment selection.

Hepatitis C and interferon induced thyroiditis

Autoimmune thyroid diseases (AITDs) are complex diseases that develop as a result of interactions between genetic, epigenetic, and environmental factors. Significant progress has been made in our understanding of the genetic and environmental triggers contributing to AITD. The major environmental triggers of AITD include iodine, smoking, medications, pregnancy, and possibly stress. In this review we will focus on two well-documented environmental triggers of AITD, hepatitis C virus (HCV) infection and interferon alpha (IFNa) therapy. Chronic HCV infection has been shown to be associated with increased incidence of clinical and subclinical autoimmune thyroiditis (i.e. the presence of thyroid antibodies in euthyroid subjects). Moreover, IFNa therapy of chronic HCV infection is associated with subclinical or clinical thyroiditis in up to 40% of cases which can be autoimmune, or non-autoimmune thyroiditis. In some cases interferon induced thyroiditis (IIT) in chronic HCV patients may result in severe symptomatology necessitating discontinuation of therapy. While the epidemiology and clinical presentation of HCV and interferon induced thyroiditis have been well characterized, the mechanisms causing these conditions are still poorly understood.

Adverse drug reactions in older people

Adverse drug reactions (ADR) pose significant health-related problems for the older person. Many studies from around the world report a significant incidence of ADR in general and in elderly people in particular, resulting in an increase in drug-related morbidity and mortality. Older people appear to be particularly at risk of experiencing an ADR due to a range of factors, which include polypharmacy, altered drug pharmacokinetic profiles and pharmacodynamic responses, drug interactions and cognitive problems that increase the risk in this patient group. Certain drug classes, such as hypoglycaemic agents and cardiovascular active medicines, have been identified as common causes of ADR. Many studies suggest that the majority of ADR are preventable, so that several different approaches have been tried in an attempt to limit this problem, such as the use of computerized systems to communicate routine issues of patient care, interventions made by pharmacists, spontaneous reporting and continuous education of health care professionals. Whilst all have been shown to reduce drug-related events, identifying individuals at high risk of developing ADR at the point of prescribing by using a risk stratification model could improve the identification and prevention of ADR. This article discusses the clinical impact of ADR in older people and the relative merits of the various approaches tested to date before suggesting areas that require further research.

Gene expression profiling: classification of mice with left ventricle systolic dysfunction using microarray analysis

OBJECTIVE

We tested the hypothesis that a set of differentially expressed genes could be used to classify mice according to cardiovascular phenotype after prolonged catecholamine stress.

DESIGN

Prospective, randomized study.

SETTING

University-based research laboratory.

SUBJECTS

One hundred seventy-three male mice were studied: wild-type (WT) C57, WT FVB, WT B6129SF2/J, and beta2 adrenergic receptor knockout.

INTERVENTIONS

Mice of each genotype were randomly assigned to 14-day infusions of isoproterenol (120 microg/g/day) or no treatment. Approximately half of the animals underwent left ventricle pressure volume loop analysis. The remaining animals were killed for extraction of messenger RNA from whole heart preparations for microarray analysis.

MEASUREMENTS AND MAIN RESULTS

We observed that WT FVB and beta2 adrenergic receptor knockout mice developed systolic dysfunction in response to continuous catecholamine infusion, whereas WT C57 mice developed diastolic dysfunction. Using these mice as the derivation cohort, we identified a set of 83 genes whose differential expression correlated with left ventricle systolic dysfunction. The gene set was then used to accurately classify mice from a separate group (WT B6129SF2/J) into the cohort that developed left ventricle systolic dysfunction after catecholamine stress.

CONCLUSIONS

The differential expression pattern of 83 genes can be used to accurately classify mice according to physiological phenotype after catecholamine stress.

Incidence and nature of infectious disease in patients treated with anti-TNF agents

Tumor necrosis factor alpha (TNF-alpha) inhibitors offer a targeted therapeutic strategy that contrasts with the nonspecific immunosuppressive agents traditionally used to treat most inflammatory diseases. These biologic agents have had a significant impact in ameliorating the signs and symptoms of inflammatory rheumatoid disease and improving patient function. From the onset of clinical trials, a central concern of cytokine blockade has been a potential increase in susceptibility to infections. Not surprisingly, a variety of infections have been reported in association with the use of TNF-alpha inhibitor agents. In particular, there is evidence suggesting an increased rate of granulomatous infections in patients treated with monoclonal TNF-alpha inhibitors. This review provides the incidence and nature of infections in patients treated with TNF-alpha inhibitor agents and reminds the clinician of the required vigilance in monitoring patients.

Researchers' perceptions of the ethical implications of pharmacogenomics research with children

BACKGROUND

This paper presents the results of an exploratory qualitative study that assesses Canadian pediatric researchers' perceptions of a pre-selected group of ethical issues raised by pharmacogenomics research with children.

METHODS

As a pilot study, we conducted semi-structured telephone interviews with Canadian pediatric pharmacogenomic researchers. The interviews were guided by the following themes: (1) benefits and risks of inclusion, (2) the consent/assent process, and (3) the return of research results.

RESULTS

Issues about assent, consent, risks and benefits, as well as the communication of results were addressed by the respondents. Some issues, such as the unique vulnerability of children, the long term privacy concerns associated with biobanking, additional core elements that need to be discussed and included in the consent/assent forms, as well as the challenges of communicating research results in a pediatric research were not explicitly identified by the respondents.

CONCLUSION

Further consideration should be given to address the ethical challenges of including children in pharmacogenomics research. This exploratory study indicates that further guidance is needed if children are to be protected and yet benefit from such research.

Etiopathogenesis of primary biliary cirrhosis

Primary biliary cirrhosis (PBC) is an autoimmune disease of the liver characterized by progressive bile duct destruction eventually leading to cirrhosis and liver failure. The serological hallmark of the disease is the presence of circulating antimitochondrial antibodies (AMA). These reflect the presence of autoreactive T and B cells to the culprit antigens, the E2 subunits of mitochondrial 2-oxo-acid dehydrogenase enzymes, chiefly pyruvate dehydrogenase (PDC-E2). The disease results from a combination of genetic and environmental risk factors. Genetic predisposition is indicated by the higher familial incidence of the disease particularly among siblings and the high concordance rate among monozygotic twins. Environmental triggering events appear crucial to disrupt a pre-existing unstable immune tolerance of genetic origin allowing, after a long latency, the emergence of clinical disease. Initiating mimotopes of the vulnerable epitope of the PDC-E2 autoantigen can be derived from microbes that utilize the PDC enzyme or, alternatively, environmental xenobiotics/chemical compounds that modify the structure of native proteins to make them immunogenic. A further alternative as a source of antigen is PDC-E2 derived from apoptotic cells. In the effector phase the biliary ductular cell, by reason of its proclivity to express the antigen PDC-E2 in the course of apoptosis, undergoes a multilineage immune attack comprised of CD4⁺ and CD8⁺ T cells and antibody. In this article, we critically review the available evidence on etiopathogenesis of PBC and present interpretations of complex data, new developments and theories, and nominate directions for future research.

APS--more systemic disease than SLE

The antiphospholipid syndrome is a systemic autoimmune disease that can have serious consequences for patients. Importantly, there is a wide range of clinical presentations. In this issue we have attempted to provide an overview of these features and place it in the context of autoimmunity.

Inflammation and oxidative stress in obstructive sleep apnea syndrome

Similar to obesity, with which it is closely associated, obstructive sleep apnea syndrome (OSAS) is rapidly becoming a worldwide epidemic. Current knowledge of its pathogenesis has been significantly enriched by numerous experimental studies that have demonstrated an important role of oxidative stress and inflammation. Furthermore, new and exciting data strongly connect these two components in the perpetuation of the condition via the overexpression of nuclear factor kappaB. Experimental data support the hypothesis that nutrition might represent a promising future approach with antioxidants currently being good candidates for the modulation of cardiovascular sequelae, although weight reduction and controlled positive airway pressure remain the only established treatments for OSAS. We discuss herein the recent literature that illustrates these new paradigms and speculate on possible implications and future scenarios.

Biomarkers, self-antigens and the immunological homunculus

The notion of the immunological homunculus arose from the observations (1) that the healthy adaptive immune system is inclined to respond (T cell reactivity and autoantibodies) to particular sets of body molecules (self-antigens) and (2) that autoimmune diseases are characterized by sets of autoimmune reactivity to some of the very same self-antigens recognized by healthy subjects - with an obvious difference in outcome. I termed this natural autoimmune structuring of the immune system, the immunological homunculus - the immune system's representation of the body. What might be the selective advantage of an immune system expressing patterns of built-in autoimmunity to particular sets of self-molecules? To better characterize the homunculus, we have used informatic tools to study patterns of antibodies to many hundreds of self-molecules arrayed on glass slides - an antigen chip of our design. Results using the antigen chip suggest that the particular self-reactivities comprising the homunculus could serve as a set of biomarkers that help the immune system initiate and regulate the inflammatory processes that maintain the body.