In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases

A systems biology approach for discovering the cellular and molecular aspects of psychogenic non-epileptic seizure

Objectives

Psychogenic non-epileptic seizure (PNES) is the most common non-epileptic disorder in patients referring to epilepsy centers. Contrary to common beliefs about the disease's harmlessness, the death rate of PNES patients is similar to drug-resistant epilepsy. Meanwhile, the molecular pathomechanism of PNES is unknown with very limited related research. Thus, the aim of this in silico study was to find different proteins and hormones associated with PNES via a systems biology approach.

Methods

Different bioinformatics databases and literature review were used to find proteins associated with PNES. The protein-hormone interaction network of PNES was constructed to discover its most influential compartments. The pathways associated with PNES pathomechanism were found by enrichment analysis of the identified proteins. Besides, the relationship between PNES-related molecules and psychiatric diseases was discovered, and the brain regions that could express altered levels of blood proteins were discovered.

Results

Eight genes and three hormones were found associated with PNES through the review process. Proopiomelanocortin (POMC), neuropeptide Y (NPY), cortisol, norepinephrine, and brain-derived neurotrophic factor (BDNF) were identified to have a high impact on the disease pathogenesis network. Moreover, activation of Janus kinase-signaling transducer and activator of transcription (JAK-STAT) and JAK, as well as signaling of growth hormone receptor, phosphatidylinositol 3-kinase /protein kinase B (PI3K/AKT), and neurotrophin were found associated with PNES molecular mechanism. Several psychiatric diseases such as depression, schizophrenia, and alcohol-related disorders were shown to be associated with PNES predominantly through signaling molecules.

Significance

This study was the first to gather the biochemicals associated with PNES. Multiple components and pathways and several psychiatric diseases associated with PNES, and some brain regions that could be altered during PNES were suggested, which should be confirmed in further studies. Altogether, these findings could be used in future molecular research on PNES patients.

Prognostic factors for the development of systemic lupus erythematosus in patients with immune thrombocytopenia

BACKGROUND

Patients with immune thrombocytopenia (ITP) have a risk of developing systemic lupus erythematosus (SLE). We sought to examine the clinical characteristics of patients with primary ITP who later developed SLE and identified the risk factors for the development of SLE.

METHODS

We retrospectively examined patients who were diagnosed with primary ITP at a tertiary hospital between August 2001 and November 2019. We compared the clinical characteristics according to the development of SLE. Logistic regression analysis was performed to identify the factors associated with the development of SLE.

RESULTS

Of 130 patients with primary ITP, 10 (7.7%) were later diagnosed with SLE during follow-up (median, 30 months [IQR, 15.5-105]). The presence of skin bleeding, organ bleeding, lymphocytopenia, anemia, and antinuclear antibody (ANA) positivity (≥ 1:160) were more common among patients who later developed SLE than did those who did not develop SLE. Multivariate analysis showed that young age (< 40 years; odds ratio [OR], 6.307 [95% confidence interval (CI), 1.114-34.908]; P = 0.035), organ bleeding (OR, 13.672 [95% CI, 2.437-76.689]; P = 0.003), and ANA positivity (1:160; OR, 6.638 [95% CI, 1.399-31.504]; P = 0.017) were significantly associated with the development of SLE.

CONCLUSIONS

Young age (< 40 years), organ bleeding, and ANA positivity (≥ 1:160) were risk factors for the development of SLE in patients with primary ITP. Close follow-up is needed to detect the development of SLE in patients with ITP and the abovementioned risk factors.

Systemic lupus erythematosus-complicating immune thrombocytopenia: From pathogenesis to treatment

Immune thrombocytopenia (ITP) is a common hematological manifestation of systemic lupus erythematosus (SLE). The heterogeneity of its clinical characteristics and therapeutic responses reflects a complex pathogenesis. A better understanding of its pathophysiological mechanisms and employing an optimal treatment regimen is therefore important to improve the response rate and prognosis, and avoid unwanted outcomes. Besides glucocorticoids, traditional immunosuppressants (i.e. cyclosporine, mycophenolate mofetil) and intravenous immunoglobulins, new therapies are emerging and promising for the treatment of intractable SLE-ITP, such as thrombopoietin receptor agonists (TPO-RAs), platelet desialylation inhibitors(i.e. oseltamivir), B-cell targeting therapy(i.e. rituximab, belimumab), neonatal Fc receptor(FcRn) inhibitor, spleen tyrosine kinase(Syk) inhibitor and Bruton tyrosine kinase(BTK) inhibitor et al., although more rigorous randomized controlled trials are needed to substantiate their efficacy. In this review, we update our current knowledge on the pathogenesis and treatment of SLE-ITP.

Vaccination in pediatric acquired inflammatory immune-mediated neuromuscular disorders

AIM

To analyse literature data on vaccine related induction, worsening of the disease and disease reccurrences as well as vaccine safety and efficacy among pediatric patients with acquired inflammatory immune-mediated neuromuscular disorders (NMD).

METHODS

Medline, Pub Med and Scopus database search from 1975 to 2020 focused on pediatric age was conducted including peer reviews, meta analyses and epidemiological studies on vaccination and Guillain-Barré syndrome (GBS), Bell's palsy, optic neuritis (ON), myasthenia gravis (MG), chronic inflammatory demyelinating polyneuropathy (CIDP) and immune-mediated inflammatory myopathy (IM).

RESULTS AND CONCLUSION

s: There are no strong evidence supporting relationship between vaccination with different pediatric vaccines and development of first episodes or reccurrences of GBS, Bell's palsy, optic neuritis (ON), juvenile MG, CIDP, and IM. The vaccination and revaccination with inactivated vaccines is considered safe in children with medical history of GBS, Bell's palsy, ON, MG and IM. Caution when immunization against influenza, quadrivalent conjugated meningococcal vaccine (MCV4) and pneumococcal disease and avoiding tetanus toxoid immunization in CIDP patients is suggested. Patients with immune mediated acquired NMD should be vaccinated with live vaccines before the initiation of immunosupressive treatment. Immunosuppressed patients with low protective antibody titers should be considered for revaccination.

Causality assessment of adverse events following immunization: the problem of multifactorial pathology

The analysis of Adverse Events Following Immunization (AEFI) is important in a balanced epidemiological evaluation of vaccines and in the issues related to national vaccine injury compensation programs. If manufacturing defects or vaccine storage and delivering errors are excluded, the majority of adverse reactions to vaccines occur as excessive or biased inflammatory and immune responses. These unwanted phenomena, occasionally severe, are associated with many different endogenous and exogenous factors, which often interact in complex ways. The confirmation or denial of the causal link between an AEFI and vaccination is determined pursuant to WHO guidelines, which propose a four-step analysis and algorithmic diagramming. The evaluation process from the onset considers all possible "other causes" that can explain the AEFI and thus exclude the role of the vaccine. Subsequently, even if there was biological plausibility and temporal compatibility for a causal association between the vaccine and the AEFI, the guidelines ask to look for any possible evidence that the vaccine could not have caused that event. Such an algorithmic method presents some concerns that are discussed here, in the light of the multifactorial nature of the inflammatory and immune pathologies induced by vaccines, including emerging knowledge of genetic susceptibility to adverse effects. It is proposed that the causality assessment could exclude a consistent association of the adverse event with the vaccine only when the presumed "other cause" is independent of an interaction with the vaccine. Furthermore, the scientific literature should be viewed not as an exclusion criterion but as a comprehensive analysis of all the evidence for or against the role of the vaccine in causing an adverse reaction. These issues are discussed in relation to the laws that, in some countries, regulate the mandatory vaccinations and the compensation for those who have suffered serious adverse effects.

Causality assessment of adverse events following immunization: the problem of multifactorial pathology

The analysis of Adverse Events Following Immunization (AEFI) is important in a balanced epidemiological evaluation of vaccines and in the issues related to vaccine injury compensation programs. The majority of adverse reactions to vaccines occur as excessive or biased inflammatory and immune responses. These unwanted phenomena, occasionally severe, are associated with many different endogenous and exogenous factors, which often interact in complex ways. The confirmation or denial of the causal link between an AEFI and vaccination is determined pursuant to WHO guidelines, which propose a four-step analysis and algorithmic diagramming. The evaluation process from the onset considers all possible "other causes" that might explain the AEFI and thus exclude the role of the vaccine. Subsequently, even if there was biological plausibility and temporal compatibility for a causal association between the vaccine and the AEFI, the guidelines ask to look for any possible evidence that the vaccine could not have caused that event. Such an algorithmic method presents several concerns that are discussed here, in the light of the multifactorial nature of the inflammatory and immune pathologies induced by vaccines, including emerging knowledge of genetic susceptibility to adverse effects. It is proposed that the causality assessment could exclude a consistent association of the adverse event with the vaccine only when the presumed "other cause" is independent of an interaction with the vaccine. Furthermore, the scientific literature should be viewed not as an exclusion criterion but as a comprehensive analysis of all the evidence for or against the role of the vaccine in causing an adverse reaction. Given these inadequacies in the evaluation of multifactorial diseases, the WHO guidelines need to be reevaluated and revised. These issues are discussed in relation to the laws that, in some countries, regulate the mandatory vaccinations and the compensation for those who have suffered serious adverse effects.

Guillain-Barré syndrome and influenza vaccines: current evidence

OBJECTIVE

Guillain-Barré Syndrome (GBS) as a consequence of influenza vaccination is a relevant topic, yet to be clarified, which raises concern both amongst health care personnel and the general population. Every study and pharmacovigilance system point to need of further research and the importance of continuous monitoring of safety regarding influenza vaccines. The aim of the present study is to investigate the publication of new data since the realisation of our meta-analysis of GBS and influenza vaccines (published in 2015).

METHODS

A systematic revision of PubMed, Embase, and Web of Knowledge (WOS) databases has been carried out. These report observational studies assessing GBS risk after the administration of influenza vaccines from May 2014 up to July 20th, 2017.

RESULTS

The research yielded 107 articles. Only three studies met established inclusion criteria and referred to an estimation GBS risk after some influenza vaccine. Two studies investigated GBS risk by the pandemic A/H1N1 vaccine, while only one looked into season vaccines.

CONCLUSIONS

The present systematic review, conducted after the publication of our previous meta-analysis, seems to confirm its previous results. Therefore, GBS should be considered an infrequent adverse effect of influenza vaccination, which should not negatively influence its acceptance. Unfortunately, very few of the systematically surveyed studies meeting inclusion criteria. This fact sharply contrasts with the current consensus as to the need of continuously monitoring the safety of influenza vaccines.

Gulf War Illness: Unifying Hypothesis for a Continuing Health Problem

An estimated 25%⁻32% of veterans of the 1991 Gulf War continue to experience multiple unexplained health problems known as Gulf War Illness (GWI). GWI encompasses chronic pain, musculoskeletal weakness, headache, fatigue, cognitive deficits, alterations in mood, and numerous multi-system complaints. Most potential exposures implicated in GWI were not well documented but included varying levels of several neurotoxicants as well as the anticholinergic drug pyridostigmine bromide (PB), which was routinely taken as prophylaxis against the nerve agent soman. While some veterans also took chloroquine as an antimalarial agent, the literature suggests an association between receipt of multiple vaccinations prior to or during the conflict (perhaps combined with other exposures), and GWI. In-theater exposures may account for any single individual veteran's ill health but many veterans of the same era who were not deployed overseas also suffer the same or similar symptoms. The features of GWI also overlap with those of fibromyalgia, chronic fatigue syndrome and multiple chemical sensitivity, in all of which liver dysfunction has been documented, suggesting a unifying hypothesis. It is proposed that multiple vaccinations, with concurrent or subsequent exposure to PB or additional chemical insults of a liver-damaging nature, plausibly explain the pathogenesis and the observed chronicity of GWI. The suggested mechanism for GWI is thus a chemically-induced impaired liver function, with the spillage of stored vitamin A compounds ("retinoids") into the circulation in toxic concentrations, resulting in an endogenous chronic form of hypervitaminosis A. Implications of the hypothesis are briefly reviewed.

[Autoimmune/inflammatory syndrome induced by adjuvants]

The development of autoimmune/inflammatory syndrome induced by adjuvants (ASIA) is associated with the hyperergic reaction of the human immune system. The development of autoimmune inflammation is preceded by contact with internal or external trigger factors (adjuvants) of immune disorders. ASIA is associated with an individual genetic predisposition that is probably associated with the carriage of HLA-DRB1*01 or HLA-DRB4. The paper presents five possible options for the impact of adjuvants in the pathogenesis of autoimmune disorders. It gives diagnostic criteria for the syndrome, as well as its clinical, laboratory and morphological manifestations. Emphasis is laid on the importance of morphological changes in the diagnosis of autoimmune disorders. The spectrum of morphological changes in ASIA is extensive. The tissues show signs of immune inflammation, such as lymphohistiocytic infiltration, granulomatous inflammation, and scleroderma-like changes. The characteristic feature is the regression of clinical, laboratory, and morphological manifestations after adjuvant removal.

The ASIA syndrome: basic concepts

The autoimmune/inflammatory syndrome induced by adjuvants (ASIA), also known as Shoenfeld’s syndrome, encompasses several autoimmune conditions/phenomena that are induced following the exposure to substances with adjuvant activity. The disease spectrum is heterogeneous in respect to clinical presentation as well as severity of the clinical manifestations. Adjuvants are included in vaccination formulations for their immunogenic properties. Despite being generally well tolerated, safe and effective, some genetically predisposed individuals can develop generalized non-specific constitutional symptoms, autoantibody production, new onset, or worsening of disease presentation. In this review, we focus on the current knowledge presented in the literature on ASIA syndrome, increasing physician awareness about the basic concepts of ASIA syndrome and highlight the devastating amount of data accumulated in the last few years concerning the relationship between various adjuvants and autoimmunity.

Autoimmune/inflammatory syndrome induced by adjuvants (Shoenfeld’s syndrome) – An update

Autoimmune/inflammatory syndrome induced by adjuvants (ASIA) has been widely described in many studies conducted thus far. The syndrome incorporates five immune-mediated conditions, all associated with previous exposure to various agents such as vaccines, silicone implants and several others. The emergence of ASIA syndrome is associated with individual genetic predisposition, for instance those carrying HLA-DRB1*01 or HLA-DRB4 and results from exposure to external or endogenous factors triggering autoimmunity. Such factors have been demonstrated as able to induce autoimmunity in both animal models and humans via a variety of proposed mechanisms. In recent years, physicians have become more aware of the existence of ASIA syndrome and the relationship between adjuvants exposure and autoimmunity and more cases are being reported. Accordingly, we have created a registry that includes at present more than 300 ASIA syndrome cases that have been reported by different physicians worldwide, describing various autoimmune conditions induced by diverse adjuvants.

In this review, we have summarized the updated literature on ASIA syndrome and the knowledge accumulated since 2013 in order to elucidate the association between the exposure to various adjuvant agents and its possible clinical manifestations. Furthermore, we especially referred to the relationship between ASIA syndrome and systemic lupus erythematosus (SLE) and antiphospholipid syndrome (APS).

Temporal Association of Certain Neuropsychiatric Disorders Following Vaccination of Children and Adolescents: A Pilot Case-Control Study

BACKGROUND

Although the association of the measles, mumps, and rubella vaccine with autism spectrum disorder has been convincingly disproven, the onset of certain brain-related autoimmune and inflammatory disorders has been found to be temporally associated with the antecedent administration of various vaccines. This study examines whether antecedent vaccinations are associated with increased incidence of obsessive-compulsive disorder (OCD), anorexia nervosa (AN), anxiety disorder, chronic tic disorder, attention deficit hyperactivity disorder, major depressive disorder, and bipolar disorder in a national sample of privately insured children.

METHODS

Using claims data, we compared the prior year's occurrence of vaccinations in children and adolescents aged 6-15 years with the above neuropsychiatric disorders that were newly diagnosed between January 2002 and December 2007, as well as two control conditions, broken bones and open wounds. Subjects were matched with controls according to age, gender, geographical area, and seasonality. Conditional logistic regression models were used to determine the association of prior vaccinations with each condition.

RESULTS

Subjects with newly diagnosed AN were more likely than controls to have had any vaccination in the previous 3 months [hazard ratio (HR) 1.80, 95% confidence interval 1.21-2.68]. Influenza vaccinations during the prior 3, 6, and 12 months were also associated with incident diagnoses of AN, OCD, and an anxiety disorder. Several other associations were also significant with HRs greater than 1.40 (hepatitis A with OCD and AN; hepatitis B with AN; and meningitis with AN and chronic tic disorder).

CONCLUSION

This pilot epidemiologic analysis implies that the onset of some neuropsychiatric disorders may be temporally related to prior vaccinations in a subset of individuals. These findings warrant further investigation, but do not prove a causal role of antecedent infections or vaccinations in the pathoetiology of these conditions. Given the modest magnitude of these findings in contrast to the clear public health benefits of the timely administration of vaccines in preventing mortality and morbidity in childhood infectious diseases, we encourage families to maintain vaccination schedules according to CDC guidelines.

A novel method for estimating transgender status using electronic medical records

PURPOSE

We describe a novel algorithm for identifying transgender people and determining their male-to-female (MTF) or female-to-male (FTM) identity in electronic medical records of an integrated health system.

METHODS

A computer program scanned Kaiser Permanente Georgia electronic medical records from January 2006 through December 2014 for relevant diagnostic codes, and presence of specific keywords (e.g., "transgender" or "transsexual") in clinical notes. Eligibility was verified by review of de-identified text strings containing targeted keywords, and if needed, by an additional in-depth review of records. Once transgender status was confirmed, FTM or MTF identity was assessed using a second program and another round of text string reviews.

RESULTS

Of 813,737 members, 271 were identified as possibly transgender: 137 through keywords only, 25 through diagnostic codes only, and 109 through both codes and keywords. Of these individuals, 185 (68%, 95% confidence interval [CI]: 62%-74%) were confirmed as definitely transgender. The proportions (95% CIs) of definite transgender status among persons identified via keywords, diagnostic codes, and both were 45% (37%-54%), 56% (35%-75%), and 100% (96%-100%). Of the 185 definitely transgender people, 99 (54%, 95% CI: 46%-61%) were MTF, 84 (45%, 95% CI: 38%-53%) were FTM. For two persons, gender identity remained unknown. Prevalence of transgender people (per 100,000 members) was 4.4 (95% CI: 2.6-7.4) in 2006 and 38.7 (95% CI: 32.4-46.2) in 2014.

CONCLUSIONS

The proposed method of identifying candidates for transgender health studies is low cost and relatively efficient. It can be applied in other similar health care systems.

A novel method for estimating transgender status using electronic medical records

PURPOSE

We describe a novel algorithm for identifying transgender people and determining their male-to-female (MTF) or female-to-male (FTM) identity in electronic medical records of an integrated health system.

METHODS

A computer program scanned Kaiser Permanente Georgia electronic medical records from January 2006 through December 2014 for relevant diagnostic codes, and presence of specific keywords (e.g., "transgender" or "transsexual") in clinical notes. Eligibility was verified by review of de-identified text strings containing targeted keywords, and if needed, by an additional in-depth review of records. Once transgender status was confirmed, FTM or MTF identity was assessed using a second program and another round of text string reviews.

RESULTS

Of 813,737 members, 271 were identified as possibly transgender: 137 through keywords only, 25 through diagnostic codes only, and 109 through both codes and keywords. Of these individuals, 185 (68%, 95% confidence interval [CI]: 62%-74%) were confirmed as definitely transgender. The proportions (95% CIs) of definite transgender status among persons identified via keywords, diagnostic codes, and both were 45% (37%-54%), 56% (35%-75%), and 100% (96%-100%). Of the 185 definitely transgender people, 99 (54%, 95% CI: 46%-61%) were MTF, 84 (45%, 95% CI: 38%-53%) were FTM. For two persons, gender identity remained unknown. Prevalence of transgender people (per 100,000 members) was 4.4 (95% CI: 2.6-7.4) in 2006 and 38.7 (95% CI: 32.4-46.2) in 2014.

CONCLUSIONS

The proposed method of identifying candidates for transgender health studies is low cost and relatively efficient. It can be applied in other similar health care systems.

T cell epitope redundancy: cross-conservation of the TCR face between pathogens and self and its implications for vaccines and autoimmunity

T cells are extensively trained on 'self' in the thymus and then move to the periphery, where they seek out and destroy infections and regulate immune response to self-antigens. T cell receptors (TCRs) on T cells' surface recognize T cell epitopes, short linear strings of amino acids presented by antigen-presenting cells. Some of these epitopes activate T effectors, while others activate regulatory T cells. It was recently discovered that T cell epitopes that are highly conserved on their TCR face with human genome sequences are often associated with T cells that regulate immune response. These TCR-cross-conserved or 'redundant epitopes' are more common in proteins found in pathogens that have co-evolved with humans than in other non-commensal pathogens. Epitope redundancy might be the link between pathogens and autoimmune disease. This article reviews recently published data and addresses epitope redundancy, the "elephant in the room" for vaccine developers and T cell immunologists.

Overall conceptual framework for studying the genetics of autoimmune diseases following vaccination: a regulatory perspective

The US Vaccine Adverse Event Reporting System contains case reports of autoimmune diseases (ADs) occurring following vaccinations. ADs are rare and occur in unvaccinated people, making the potential association between vaccines and ADs challenging to evaluate. Developing mechanistic pathways that link genes, immune mediators, vaccine components and ADs would be helpful for hypothesis generation, enhancing theories of biologic plausibility and grouping rare autoimmune adverse events to increase the ability to detect and evaluate safety signals. Here, we propose a conceptual framework for investigating the genetics of ADs as safety signals following vaccination, potentially contributing to the identification of relevant biomarkers. We also discuss a study design that incorporates genetic information into postmarket clinical evaluation of autoimmune adverse events following vaccination.

Peptide motif analysis predicts alphaviruses as triggers for rheumatoid arthritis

Rheumatoid arthritis (RA) develops in response to both genetic and environmental factors. The strongest genetic determinant is HLA-DR, where polymorphisms within the P4 and P6 binding pockets confer elevated risk. However, low disease concordance across monozygotic twin pairs underscores the importance of an environmental factor, probably infectious. The goal of this investigation was to predict the microorganism most likely to interact with HLA-DR to trigger RA under the molecular mimicry hypothesis. A set of 185 structural proteins from viruses or intracellular bacteria was scanned for regions of sequence homology with a collagen peptide that binds preferentially to DR4; candidates were then evaluated against a motif required for T cell cross-reactivity. The plausibility of the predicted agent was evaluated by comparison of microbial prevalence patterns to epidemiological characteristics of RA. Peptides from alphavirus capsid proteins provided the closest fit. Variations in the P6 position suggest that the HLA binding preference may vary by species, with Ross River virus, Chikungunya virus, and Mayaro virus peptides binding preferentially to DR4, and peptides from Sindbis/Ockelbo virus showing stronger affinity to DR1. The predicted HLA preference is supported by epidemiological studies of post-infection chronic arthralgia. Parallels between the cytokine profiles of RA and chronic alphavirus infection are discussed.