scholarly journals Protein-Based Immunome Wide Association Studies (PIWAS) for the Discovery of Significant Disease-Associated Antigens

2021 ◽  
Vol 12 ◽  
Author(s):  
Winston A. Haynes ◽  
Kathy Kamath ◽  
Rebecca Waitz ◽  
Patrick S. Daugherty ◽  
John C. Shon
Keyword(s):  
Lupus Erythematosus ◽  
Statistical Power ◽  
Association Studies ◽  
Synthetic Data ◽  
Peptide Arrays ◽  
Protein Antigens ◽  
Bacterial Display ◽  
Candidate Protein ◽  
Next Generation Sequencing Ngs ◽  
Significant Disease

Identification of the antigens associated with antibodies is vital to understanding immune responses in the context of infection, autoimmunity, and cancer. Discovering antigens at a proteome scale could enable broader identification of antigens that are responsible for generating an immune response or driving a disease state. Although targeted tests for known antigens can be straightforward, discovering antigens at a proteome scale using protein and peptide arrays is time consuming and expensive. We leverage Serum Epitope Repertoire Analysis (SERA), an assay based on a random bacterial display peptide library coupled with next generation sequencing (NGS), to power the development of Protein-based Immunome Wide Association Study (PIWAS). PIWAS uses proteome-based signals to discover candidate antibody-antigen epitopes that are significantly elevated in a subset of cases compared to controls. After demonstrating statistical power relative to the magnitude and prevalence of effect in synthetic data, we apply PIWAS to systemic lupus erythematosus (SLE, n=31) and observe known autoantigens, Smith and Ribosomal protein P, within the 22 highest scoring candidate protein antigens across the entire human proteome. We validate the magnitude and location of the SLE specific signal against the Smith family of proteins using a cohort of patients who are positive by predicate anti-Sm tests. To test the generalizability of the method in an additional autoimmune disease, we identified and validated autoantigenic signals to SSB, CENPA, and keratin proteins in a cohort of individuals with Sjogren’s syndrome (n=91). Collectively, these results suggest that PIWAS provides a powerful new tool to discover disease-associated serological antigens within any known proteome.

scholarly journals Protein-based Immunome Wide Association Studies (PIWAS) for the discovery of significant disease-associated antigens

2020 ◽  
Author(s):  
Winston A. Haynes ◽  
Kathy Kamath ◽  
Patrick S. Daugherty ◽  
John C. Shon
Keyword(s):  
Antibody Response ◽  
Lupus Erythematosus ◽  
Statistical Power ◽  
Association Studies ◽  
Synthetic Data ◽  
Peptide Arrays ◽  
Protein Antigens ◽  
Major Step ◽  
Bacterial Display ◽  
Ribosomal P

AbstractIdentification of the antigens associated with antibodies is vital to understanding immune responses in the context of infection, autoimmunity, and cancer. Discovering antigens at a proteome scale could enable broader identification of antigens that are responsible for generating an immune response or driving a disease state. Although targeted tests for known antigens can be straightforward, discovering antigens at a proteome scale using protein and peptide arrays is time consuming and expensive. We leverage Serum Epitope Repertoire Analysis (SERA), an assay based on a random bacterial display peptide library coupled with NGS, to power the development of Protein-based Immunome Wide Association Study (PIWAS). PIWAS uses proteome-based signals to discover candidate antibody-antigen epitopes that are significantly elevated in a subset of cases compared to controls. After demonstrating statistical power relative to the magnitude and prevalence of effect in synthetic data, we apply PIWAS to systemic lupus erythematosus (SLE, n=31) and observe known autoantigens, Smith and Ribosomal P, within the 22 highest scoring candidate protein antigens across the entire human proteome. We validate the magnitude and location of the SLE specific signal against the Smith family of proteins using a cohort of patients who are positive by predicate anti-Sm tests. Collectively, these results suggest that PIWAS provides a powerful new tool to discover disease-associated serological antigens within any known proteome.Author SummaryInfection, autoimmunity, and cancer frequently induce an antibody response in patients with disease. Identifying the protein antigens that are involved in the antibody response can aid in the development of diagnostics, biomarkers, and therapeutics. To enable high-throughput antigen discovery, we present PIWAS, which leverages the SERA technology to identify antigens at a proteome- and cohort-scale. We demonstrate the ability of PIWAS to identify known autoantigens in SLE. PIWAS represents a major step forward in the ability to discover protein antigens at a proteome scale.

scholarly journals Estimating the effective sample size in association studies of quantitative traits

2021 ◽  
Author(s):  
Andrey Ziyatdinov ◽  
Jihye Kim ◽  
Dmitry Prokopenko ◽  
Florian Privé ◽  
Fabien Laporte ◽  
...  
Keyword(s):  
Statistical Power ◽  
Quantitative Traits ◽  
Mixed Model ◽  
Association Studies ◽  
Effective Sample Size ◽  
Environment Interaction ◽  
Uk Biobank ◽  
Gene Environment Interaction ◽  
Gene Environment ◽  
The Uk

Abstract The effective sample size (ESS) is a metric used to summarize in a single term the amount of correlation in a sample. It is of particular interest when predicting the statistical power of genome-wide association studies (GWAS) based on linear mixed models. Here, we introduce an analytical form of the ESS for mixed-model GWAS of quantitative traits and relate it to empirical estimators recently proposed. Using our framework, we derived approximations of the ESS for analyses of related and unrelated samples and for both marginal genetic and gene-environment interaction tests. We conducted simulations to validate our approximations and to provide a quantitative perspective on the statistical power of various scenarios, including power loss due to family relatedness and power gains due to conditioning on the polygenic signal. Our analyses also demonstrate that the power of gene-environment interaction GWAS in related individuals strongly depends on the family structure and exposure distribution. Finally, we performed a series of mixed-model GWAS on data from the UK Biobank and confirmed the simulation results. We notably found that the expected power drop due to family relatedness in the UK Biobank is negligible.

scholarly journals THU0017 ATTEMPTS TO LINK EXONIC GENE POLYMORPHISMS TO SYSTEMIC LUPUS ERYTHEMATOSUS (SLE)-ASSOCIATED PROTEIN MODIFIED FUNCTIONALITY: A STRUCTURAL BIOLOGY APPROACH

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 221.1-222
Author(s):  
E. Eliopoulos ◽  
G. Goulielmos ◽  
M. Matalliotakis ◽  
D. Vlachakis ◽  
T. Niewold ◽  
...  
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Protein Structure ◽  
Molecular Modeling ◽  
Nucleic Acid ◽  
Molecular Mechanics ◽  
Lupus Erythematosus ◽  
Gene Polymorphisms ◽  
Association Studies ◽  
Systemic Lupus ◽  
Molecular Graphics

Background:Gene association studies and genome wide association studies (GWAS) have played a primary role in depicting genetic contributions to systemic lupus erythematosus (SLE) development, while accommodating the exonic polymorphisms on the protein structure level, when available, enhances our understanding of protein function modification or depletion. Linking human genetics with therapeutic targets requires the biological function of the causal gene and variant to be known.Objectives:To investigate recently identified SLE-associated functional gene polymorphisms, such asPARP1,ITGAM, TNFAIP3, NCF1, PON1, IFIH1, SH2B3andTYK2[1-4] by correlation to protein structure and function.Methods:Three-dimensional (3D) homology modeling and molecular mechanics/dynamics studies were applied for the localization of the polymorphisms under study on the respective proteins. The mutants were constructed using molecular modeling with the program Maestro (Schrodinger, LLC), which was also used to analyze the conformational changes caused by the mutation. All figures depicting 3D models were created using the molecular graphics program PyMOL V.2.2 [5].Results:Modeling revealed that rs1136410 SNP encodes the less common polymorphism Val762Ala onPARP1that reduces enzymatic activity of Poly(ADP-ribose) polymerase 1 (Figure 1),ITGAMpolymorphism rs1143679 (Arg77His) on Integrin alpha M, component of the macrophage-1 antigen complex affects protein surface recognition,TNFAIP3rs2230926 polymorphism encodes Cys instead of Phe at residue 127 of the ubiquitin editing A20 protein, while rs201802880 polymorphism of the neutrophil cytosolic factor 1 (NCF1) gene modifies the function of the cytosolic subunit of neutrophil NADPH oxidase with the mutation Arg90His.PON1is involved in the oxidative stress process that cause tissue damage observed in SLE and anti-phospholipid syndrome (APS). ThePON1Gln192Arg mutation (rs662 SNP) affects shape and recognition of the ligand recognition site as part of the evolutionary process, whileIFIH1(rs35667974) helicase C domain1 mutant I923V is located on an essential RNA beta loop interacting directly with the nucleic acid (Figure 2). Finally, the rs3184504 SNP ofSH2B3gene generates mutant Arg262Trp on SH2 adapter protein 3, acting as a signaling pathway involved in autoimmune disorders, while inTYK2 gene, one of the Janus kinases, the rs35018800 producing mutant Ala928Val modifies the ADP binding site.Figure 1.Details of the Val762 interaction where V762A mutation occurs in PARP1protein.Figure 2.Nucleic acid interacting IFIH1 helicase beta-loop where I923V mutation occurs (in purple).Conclusion:Based on several examples, we have tried to define a rational link from SLE-associated gene polymorphisms to structure and to modified function, including metagenomic analysis of SNPs, protein crystallography, protein molecular modeling, molecular mechanics and dynamics. Locating, shaping and understanding the target protein interaction interface plays a decisive role in most cases and provides clues for further pharmacological or medical actions [6].References:[1]Hur JW et al (2006). Rheumatology 45:711-7[2]Maiti AK et al (2014). Hum Mol Genet 23:4161-76[3]Shimane K et al (2010). Arthritis Rheum. 62:574-9[4]Linge P et al (2019). Ann Rheum Dis. 2019 Nov 8. pii: annrheumdis-2019-215820[5]Schrödinger LLC: The PyMOL Molecular Graphics System 2016 version 2.2. Available from: pymol.org/2/support.html[6]Plenge RM et al (2013). Nat Rev Drug Discov 12:581–94Disclosure of Interests:None declared

scholarly journals 2dFDR: a new approach to confounder adjustment substantially increases detection power in omics association studies

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Sangyoon Yi ◽  
Xianyang Zhang ◽  
Lu Yang ◽  
Jinyan Huang ◽  
Yuanhang Liu ◽  
...  
Keyword(s):  
Multiple Testing ◽  
Statistical Power ◽  
Association Studies ◽  
Control Procedure ◽  
Multiple Testing Correction ◽  
New Approach ◽  
False Discovery ◽  
Traditional Procedure ◽  
Extensive Evaluation ◽  
Confounder Adjustment

AbstractOne challenge facing omics association studies is the loss of statistical power when adjusting for confounders and multiple testing. The traditional statistical procedure involves fitting a confounder-adjusted regression model for each omics feature, followed by multiple testing correction. Here we show that the traditional procedure is not optimal and present a new approach, 2dFDR, a two-dimensional false discovery rate control procedure, for powerful confounder adjustment in multiple testing. Through extensive evaluation, we demonstrate that 2dFDR is more powerful than the traditional procedure, and in the presence of strong confounding and weak signals, the power improvement could be more than 100%.

scholarly journals Common genetic variants with fetal effects on birth weight are enriched for proximity to genes implicated in rare developmental disorders

2021 ◽  
Author(s):  
Robin N Beaumont ◽  
Isabelle K Mayne ◽  
Rachel M Freathy ◽  
Caroline F Wright
Keyword(s):  
Birth Weight ◽  
Statistical Power ◽  
Developmental Disorders ◽  
Association Studies ◽  
Later Life ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Common Genetic Variants ◽  
Causal Genes

Abstract Birth weight is an important factor in newborn survival; both low and high birth weights are associated with adverse later-life health outcomes. Genome-wide association studies (GWAS) have identified 190 loci associated with maternal or fetal effects on birth weight. Knowledge of the underlying causal genes is crucial to understand how these loci influence birth weight and the links between infant and adult morbidity. Numerous monogenic developmental syndromes are associated with birth weights at the extreme ends of the distribution. Genes implicated in those syndromes may provide valuable information to prioritize candidate genes at the GWAS loci. We examined the proximity of genes implicated in developmental disorders (DDs) to birth weight GWAS loci using simulations to test whether they fall disproportionately close to the GWAS loci. We found birth weight GWAS single nucleotide polymorphisms (SNPs) fall closer to such genes than expected both when the DD gene is the nearest gene to the birth weight SNP and also when examining all genes within 258 kb of the SNP. This enrichment was driven by genes causing monogenic DDs with dominant modes of inheritance. We found examples of SNPs in the intron of one gene marking plausible effects via different nearby genes, highlighting the closest gene to the SNP not necessarily being the functionally relevant gene. This is the first application of this approach to birth weight, which has helped identify GWAS loci likely to have direct fetal effects on birth weight, which could not previously be classified as fetal or maternal owing to insufficient statistical power.

scholarly journals AB0013 ASSOCIATION BETWEEN STAT4 POLYMORPHISM AND MANIFESTATIONS OF SLE

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 1041.1-1041
Author(s):  
V. Agarwal ◽  
S. Kakati ◽  
P. Debbaruah
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Lupus Erythematosus ◽  
Indian Population ◽  
Association Studies ◽  
Statistical Significance ◽  
Elevated Serum ◽  
Systemic Lupus ◽  
Cutaneous Manifestations ◽  
Genotype Group ◽  
Dsdna Antibody

Background:SNP rs7574865, located within the third intron of STAT4 gene at chromosome 2, has been associated with susceptibility to SLE among different ethnic groups.1,2 Interestingly, we recently have documented an association between this gene and susceptibility to systemic lupus erythematosus (SLE) in Indian population.3Objectives:To determine whether the STAT4 (rs7574865) SNP is associated with clinical and immunological manifestations in SLE.Methods:The study was carried out on 100 unrelated SLE (SLICC criteria 2012) patients from North-East India. Genotyping of STAT4 rs7574865 SNP was done using Taqman probe and Real-Time Polymerase chain reaction. An association study was performed between the alleles and genotypes of STAT4 rs7574865 with the clinical and immunological manifestations included in the SLE SLICC classification criteria. For all analysis, the statistical significance was fixed at 5% level of significance (p < 0.05).Results:The mean duration of illness was 2.69±2.55 years. Cases and Controls remained in Hardy-Weinberg equilibrium.The occurrence of Photosensitivity and hyperpigmentation was significantly higher in TT genotype group (97.22% and 77.77%, respectively) with p <0.001 in each case.SLE patients with nephritis (Albuminuria >500mg/24 hours) and elevated serum creatinine were both significantly higher in TT genotype group as compared to GT and GG (p< 0.001 and p=0.001 respectively).The Anti-dsDNA antibody was significantly associated with TT genotype (p <0.001).Conclusion:Our study provides evidence regarding the association between STAT4 rs7574865 gene polymorphism is risk factor for cutaneous manifestations, Lupus nephritis and Anti ds-DNA positivity in SLE. So, our findings reinforce the need for further association studies including prospective studies with larger subjects in order to replicate such findings.References:[1]Graham RR, Ph D, Hom G, Ph D, Behrens TW, Bakker PIW De, et al. and the Risk of Rheumatoid Arthritis and Systemic Lupus Erythematosus. N Engl J Med. 2007;357(10):977–86.[2]Yuan H, Feng JB, Pan HF, Qiu LX, Li LH, Zhang N, et al. A meta-analysis of the association of STAT4 polymorphism with systemic lupus erythematosus. Mod Rheumatol. 2010;20(3):257–62.[3]Gupta V, Kumar S, Pratap A, Singh R, Kumari R, Kumar S, et al. Association of ITGAM, TNFSF4, TNFAIP3 and STAT4 gene polymorphisms with risk of systemic lupus erythematosus in a North Indian population. Lupus. 2018;27(12):1973–9.Disclosure of Interests:None declared

scholarly journals New Horizons in the Genetic Etiology of Systemic Lupus Erythematosus and Lupus-Like Disease: Monogenic Lupus and Beyond

2020 ◽  
Vol 9 (3) ◽  
pp. 712 ◽  
Author(s):  
Erkan Demirkaya ◽  
Sezgin Sahin ◽  
Micol Romano ◽  
Qing Zhou ◽  
Ivona Aksentijevich
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Lupus Erythematosus ◽  
Current Knowledge ◽  
Association Studies ◽  
Severe Disease ◽  
Genetic Diagnosis ◽  
Genome Wide Association Studies ◽  
Systemic Lupus ◽  
Degree Relative ◽  
Adult Age

Systemic lupus erythematosus (SLE) is a clinically and genetically heterogeneous autoimmune disease. The etiology of lupus and the contribution of genetic, environmental, infectious and hormonal factors to this phenotype have yet to be elucidated. The most straightforward approach to unravel the molecular pathogenesis of lupus may rely on studies of patients who present with early-onset severe phenotypes. Typically, they have at least one of the following clinical features: childhood onset of severe disease (<5 years), parental consanguinity, and presence of family history for autoimmune diseases in a first-degree relative. These patients account for a small proportion of patients with lupus but they inform considerable knowledge about cellular pathways contributing to this inflammatory phenotype. In recent years with the aid of new sequencing technologies, novel or rare pathogenic variants have been reported in over 30 genes predisposing to SLE and SLE-like diseases. Future studies will likely discover many more genes with private variants associated to lupus-like phenotypes. In addition, genome-wide association studies (GWAS) have identified a number of common alleles (SNPs), which increase the risk of developing lupus in adult age. Discovery of a possible shared immune pathway in SLE patients, either with rare or common variants, can provide important clues to better understand this complex disorder, it’s prognosis and can help guide new therapeutic approaches. The aim of this review is to summarize the current knowledge of the clinical presentation, genetic diagnosis and mechanisms of disease in patents with lupus and lupus-related phenotypes.

scholarly journals Host Genetics and Gut Microbiome: Perspectives for Multiple Sclerosis

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1181
Author(s):  
Alessandro Maglione ◽  
Miriam Zuccalà ◽  
Martina Tosi ◽  
Marinella Clerico ◽  
Simona Rolla
Keyword(s):  
Multiple Sclerosis ◽  
Environmental Factors ◽  
Lupus Erythematosus ◽  
Gut Microbiome ◽  
Complex Disease ◽  
Current Knowledge ◽  
Association Studies ◽  
Future Research ◽  
Genome Wide Association Studies ◽  
Host Genetics

As a complex disease, Multiple Sclerosis (MS)’s etiology is determined by both genetic and environmental factors. In the last decade, the gut microbiome has emerged as an important environmental factor, but its interaction with host genetics is still unknown. In this review, we focus on these dual aspects of MS pathogenesis: we describe the current knowledge on genetic factors related to MS, based on genome-wide association studies, and then illustrate the interactions between the immune system, gut microbiome and central nervous system in MS, summarizing the evidence available from Experimental Autoimmune Encephalomyelitis mouse models and studies in patients. Finally, as the understanding of influence of host genetics on the gut microbiome composition in MS is in its infancy, we explore this issue based on the evidence currently available from other autoimmune diseases that share with MS the interplay of genetic with environmental factors (Inflammatory Bowel Disease, Rheumatoid Arthritis and Systemic Lupus Erythematosus), and discuss avenues for future research.

scholarly journals FRI0453 COMPARATIVE GENE PROFILE IN MONOCYTES FROM CHILDHOOD- AND ADULT-ONSET SYSTEMIC LUPUS ERYTHEMATOSUS: CLUES TO DIFFERENT SYSTEMIC INVOLVEMENT

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 823.2-824
Author(s):  
I. C. Aranda-Valera ◽  
A. M. Patiño-Trives ◽  
R. M. Rosa ◽  
M. A. Aguirre ◽  
P. S. Laura ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Endothelial Dysfunction ◽  
Lupus Erythematosus ◽  
Association Studies ◽  
Atherogenic Index ◽  
Molecular Profile ◽  
Research Support ◽  
Systemic Involvement ◽  
Dsdna Antibodies ◽  
And Oxidative Stress

Background:Objectives:1. This study, developed within the Innovative Medicines Initiative Joint Undertaking project PRECISESADS framework, aimed at identify specific inflammatory and oxidative stress determinants involved in the enhanced CV-risk present in SLE patients and to analyze the relevance of the sustained positivity for anti-dsDNA on the establishment of their atherothrombotic status.Methods:One hundred and twenty-four SLE consecutive patients (not including patients with associated antiphospholipid syndrome), belonging to the PRECISESADS project, were evaluated for the presence of CVD and its association with positivity for anti-dsDNA antibodies. A second cohort of 62 SLE patients was included, of which endothelial dysfunction, lipid profile, the presence of atheroma plaques (identified by a pathologic increase in the carotid intimae media thickness -CIMT-), and the frequencies of anti-dsDNA positivity for 7 years, were evaluated. Serum inflammatory and oxidative stress biomolecules, and NETosis-derived bioproducts were further evaluated by multiplex assay and specific commercial kits, respectively. Besides, miRNnomes were identified using next-generation sequencing. Clinical significance of the biomolecules analyzed was explored by correlation/association studies with immunological and CV-risk features.Results:A significant relationship among the incidence of CVD (i.e. thrombosis or cardiac involvement) and the positivity for anti-dsDNA antibodies was recognized in the first SLE cohort. Accordingly, in the second SLE cohort, significantly impaired micro-vascular endothelial function (identified by reduction of hyperemia post-occlusion area), increased atherogenic index and pathologic increase in the CIMT were assessed in patients positive for anti-dsDNA in relation to anti-dsDNA negative patients. Around a 65% of SLE patients displayed a sustained positivity for anti-dsDNA antibodies for more than 7 years. These patients showed a distinctive and specific molecular profile compared with patients that had remained negative for anti-dsDNA, including increased inflammatory profile (IL1B, IL2, IL6, IL17, EOTAXIN, FGF, GMCSF, IFNγ, IP10, RANTES, TNF), enhanced oxidative status (lipoperoxides), and higher NETosis (nucleosomes, elastase). Levels of those biomolecules were closely interconnected and associated to their regulatory miRNAs, which accordingly exhibited differential expression in SLE anti-dsDNA(+)vsanti-dsDNA(-) patients. Finally, the frequency for positivity of anti-dsDNA significantly correlated both with markers of endothelial dysfunction and with the presence of atheroma plaques in SLE patients, pointing at the direct involvement of anti-dsDNA-Abs in the development of these processes.Conclusion:1. Positivity for anti-dsDNA antibodies confers a specific inflammatory/oxidative profile linked to an enhanced CV-risk in SLE patients. 2. Moreover, the sustained positivity for anti-dsDNA antibodies fosters the establishment of an atherothrombotic status in these autoimmune patients.Acknowledgments:Supported by the EU/EFPIA –IMI-JU PRECISESADS (n° 115565) and ISCIII (PI18/0837 and RIER RD16/0012/0015), Co-funded with FEDER.Disclosure of Interests:Inmaculada Concepcion Aranda-Valera: None declared, Alejandra M. Patiño-Trives: None declared, Roldán Molina Rosa: None declared, Maria A Aguirre: None declared, Pérez Sánchez Laura: None declared, Carlos Pérez Sánchez: None declared, María Luque-Tévar: None declared, Iván Arias de la Rosa: None declared, Maria del Carmen Abalos-Aguilera: None declared, Desiree Ruíz-Vilchez: None declared, Mario Espinosa: None declared, Nuria Barbarroja Puerto Grant/research support from: ROCHE and Pfizer., Speakers bureau: ROCHE and Celgene., Eduardo Collantes-Estévez Grant/research support from: ROCHE and Pfizer., Speakers bureau: ROCHE, Lilly, Bristol and Celgene., Chary Lopez-Pedrera Grant/research support from: ROCHE and Pfizer.

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