Proteins Associated with Risk of Kidney Function Decline in the General Population

2021 ◽  
Vol 32 (9) ◽  
pp. 2291-2302
Author(s):  
Morgan E. Grams ◽  
Aditya Surapaneni ◽  
Jingsha Chen ◽  
Linda Zhou ◽  
Zhi Yu ◽  
...  
Keyword(s):  
Kidney Function ◽  
Plasma Proteins ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Proteomic Profiling ◽  
Content Type ◽  
Protein Levels ◽  
Time Periods ◽  
Egfr Decline

BackgroundProteomic profiling may allow identification of plasma proteins that associate with subsequent changesin kidney function, elucidating biologic processes underlying the development and progression of CKD.MethodsWe quantified the association between 4877 plasma proteins and a composite outcome of ESKD or decline in eGFR by ≥50% among 9406 participants in the Atherosclerosis Risk in Communities (ARIC) Study (visit 3; mean age, 60 years) who were followed for a median of 14.4 years. We performed separate analyses for these proteins in a subset of 4378 participants (visit 5), who were followed at a later time point, for a median of 4.4 years. For validation, we evaluated proteins with significant associations (false discovery rate <5%) in both time periods in 3249 participants in the Chronic Renal Insufficiency Cohort (CRIC) and 703 participants in the African American Study of Kidney Disease and Hypertension (AASK). We also compared the genetic determinants of protein levels with those from a meta-analysis genome-wide association study of eGFR.ResultsIn models adjusted for multiple covariates, including baseline eGFR and albuminuria, we identified 13 distinct proteins that were significantly associated with the composite end point in both time periods, including TNF receptor superfamily members 1A and 1B, trefoil factor 3, and β-trace protein. Of these proteins, 12 were also significantly associated in CRIC, and nine were significantly associated in AASK. Higher levels of each protein associated with higher risk of 50% eGFR decline or ESKD. We found genetic evidence for a causal role for one protein, lectin mannose-binding 2 protein (LMAN2).ConclusionsLarge-scale proteomic analysis identified both known and novel proteomic risk factors for eGFR decline.

scholarly journals Using a Two-Sample Mendelian Randomization Method in Assessing the Causal Relationships Between Human Blood Metabolites and Heart Failure

2021 ◽  
Vol 8 ◽  
Author(s):  
Zixian Wang ◽  
Shiyu Chen ◽  
Qian Zhu ◽  
Yonglin Wu ◽  
Guifeng Xu ◽  
...  
Keyword(s):  
Heart Failure ◽  
Human Blood ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Mendelian Randomization ◽  
Causal Effect ◽  
Meta Analysis ◽  
Sensitivity Analyses ◽  
Blood Metabolites ◽  
Causal Relationships

Background: Heart failure (HF) is the main cause of morbidity and mortality worldwide, and metabolic dysfunction is an important factor related to HF pathogenesis and development. However, the causal effect of blood metabolites on HF remains unclear.Objectives: Our chief aim is to investigate the causal relationships between human blood metabolites and HF risk.Methods: We used an unbiased two-sample Mendelian randomization (MR) approach to assess the causal relationships between 486 human blood metabolites and HF risk. Exposure information was obtained from Sample 1, which is the largest metabolome-based genome-wide association study (mGWAS) data containing 7,824 Europeans. Outcome information was obtained from Sample 2, which is based on the results of a large-scale GWAS meta-analysis of HF and contains 47,309 cases and 930,014 controls of Europeans. The inverse variance weighted (IVW) model was used as the primary two-sample MR analysis method and followed the sensitivity analyses, including heterogeneity test, horizontal pleiotropy test, and leave-one-out analysis.Results: We observed that 11 known metabolites were potentially related to the risk of HF after using the IVW method (P &lt; 0.05). After adding another four MR models and performing sensitivity analyses, we found a 1-SD increase in the xenobiotics 4-vinylphenol sulfate was associated with ~22% higher risk of HF (OR [95%CI], 1.22 [1.07–1.38]).Conclusions: We revealed that the 4-vinylphenol sulfate may nominally increase the risk of HF by 22% after using a two-sample MR approach. Our findings may provide novel insights into the pathogenesis underlying HF and novel strategies for HF prevention.

scholarly journals Proteomic Analysis of Trichoderma atroviride Reveals Independent Roles for Transcription Factors BLR-1 and BLR-2 in Light and Darkness

2011 ◽  
Vol 11 (1) ◽  
pp. 30-41 ◽  
Author(s):  
Alejandro Sánchez-Arreguín ◽  
Ana Silvia Pérez-Martínez ◽  
Alfredo Herrera-Estrella
Keyword(s):  
Transcription Factors ◽  
Blue Light ◽  
Light Pulse ◽  
Mechanical Damage ◽  
Pathogenic Fungi ◽  
Mrna Levels ◽  
Trichoderma Atroviride ◽  
Proteomic Profiling ◽  
Content Type ◽  
Protein Levels

ABSTRACT The genus Trichoderma is one of the most widely used biological control agents of plant-pathogenic fungi. The main mechanism for survival and dispersal of Trichoderma is through the production of asexual spores (conidia). The transition from filamentous growth to conidiation can be triggered by light, nutrient deprivation, and mechanical damage of the mycelium. We conducted proteomic profiling analyses of Trichoderma atroviride after a blue light pulse. The use of two-dimensional electrophoresis (2-DE) and mass spectrometry (MS) analysis allowed us to identify 72 proteins whose expression was affected by blue light. Functional category analysis showed that the various proteins are involved in metabolism, cell rescue, and protein synthesis. We determined the relationship between mRNA levels of selected genes 30 min after a light pulse and protein expression levels at different times after the pulse and found this correlation to be very weak. The correlation was highest when protein and mRNA levels were compared for the same time point. The transcription factors BLR-1 and BLR-2 are vital to the photoconidiation process; here we demonstrate that both BLR proteins are active in darkness and affect several elements at both the transcript and protein levels. Unexpectedly, in darkness, downregulation of proteins prevailed in the Δ blr-1 mutant, while upregulation of proteins predominated in the Δ blr-2 mutant. Our data demonstrate that the BLR proteins play roles individually and as a complex.

scholarly journals Common schizophrenia alleles are enriched in mutation-intolerant genes and maintained by background selection

2016 ◽  
Author(s):  
Antonio F Pardiñas ◽  
Peter Holmans ◽  
Andrew J Pocklington ◽  
Valentina Escott-Price ◽  
Stephan Ripke ◽  
...  
Keyword(s):  
Large Scale ◽  
Genome Wide Association Study ◽  
Rare Variants ◽  
Meta Analysis ◽  
Single Gene ◽  
Poor Quality ◽  
Background Selection ◽  
Loss Of Function ◽  
Risk Variants ◽  
Genomic Studies

Schizophrenia is a debilitating psychiatric condition often associated with poor quality of life and decreased life expectancy. Lack of progress in improving treatment outcomes has been attributed to limited knowledge of the underlying biology, although large-scale genomic studies have begun to provide such insight. We report the largest single cohort genome-wide association study of schizophrenia (11,260 cases and 24,542 controls) and through meta-analysis with existing data we identify 50 novel GWAS loci. Using gene-wide association statistics we implicate an additional set of 22 novel associations that map onto a single gene. We show for the first time that the common variant association signal is highly enriched among genes that are intolerant to loss of function mutations and that variants in these genes persist in the population despite the low fecundity associated with the disorder through the process of background selection. Associations point to novel areas of biology (e.g. metabotropic GABA-B signalling and acetyl cholinesterase), reinforce those implicated in earlier GWAS studies (e.g. calcium channel function), converge with earlier rare variants studies (e.g. NRXN1, GABAergic signalling), identify novel overlaps with autism (e.g. RBFOX1, FOXP1, FOXG1), and support early controversial candidate gene hypotheses (e.g. ERBB4 implicating neuregulin signalling). We also demonstrate the involvement of six independent central nervous system functional gene sets in schizophrenia pathophysiology. These findings provide novel insights into the biology and genetic architecture of schizophrenia, highlight the importance of mutation intolerant genes and suggest a mechanism by which common risk variants are maintained in the population.

Exploring evidence to develop a nomenclature for forensic accounting

2018 ◽  
Vol 30 (2) ◽  
pp. 135-154 ◽  
Author(s):  
Vida Botes ◽  
Ahmed Saadeh
Keyword(s):  
South Africa ◽  
New Zealand ◽  
Large Scale ◽  
Public Awareness ◽  
Meta Analysis ◽  
Future Research ◽  
Content Type ◽  
Forensic Accounting ◽  
Financial Scandals ◽  
Definition Of

Purpose Large-scale financial scandals in business have increased public awareness of fraud and the need for forensic accounting (FA) services. Despite a steadily growing body of knowledge of FA, Huber (2012) argued that the term FA is ill defined. This paper aims to support the development of a nomenclature for FA by gathering evidence on the prevalence of the term in the Southern Hemisphere. Hence the authors ask how, when, where and in which context the term FA appears. In analysing the evidence gathered, the authors also aim to identify changes to the use of the term. Finally, they intend to make suggestions for future development and research relating to the term to advance knowledge. The authors also aim to suggest a definition for the term FA. Design/methodology/approach To obtain evidence to support the development of an accepted definition for FA, a rigorous search of the literature is performed, using a structured review framework. Findings The findings of this paper demonstrate the prevalence of the term FA in publications in Australia, New Zealand and South Africa, but that limited publications from SA create opportunities for researchers from emerging economies to publish in the FA field. This meta-analysis shows among others a strong focus on the role of FA in fraud prevention and increased reliance on websites (in contrast to reliance on academic literature) for information on FA. This research identifies changes to the use of the term and concludes that the narrow definition of FA prevails. Delivering on the third objective of this paper, the authors provide insights into future developments in FA and find that a need exists to explore FA in a much wider context. Research limitations/implications The research is limited to Australia, New Zealand and South Africa. Limitations exist in that the authors focused particularly on high-quality journals and excluded other journals from our search. As they were specifically searching for the use of the term “forensic accounting”, they excluded any other term, e.g. fraud auditing, from the research. Future research may well expand the search terminology. Practical implications Without an established definition of the commonly used term forensic accounting, the general public will be confused about the services that can be expected from forensic accountants. To date, FA definitions have been formulated mostly intuitively; however, if FA is to grow as a field, an accepted definition needs to be formulated. Social implications FA offers a new area of growth in the accounting field. Clarification of exactly what is meant by the term has implications for future careers in the field of accounting. Originality/value To date, no study of this nature has been undertaken anywhere in the world.

scholarly journals Exome Array Analysis of Early-Onset Ischemic Stroke

Stroke ◽  
2020 ◽  
Vol 51 (11) ◽  
pp. 3356-3360
Author(s):  
Thomas Jaworek ◽  
Kathleen A. Ryan ◽  
Brady J. Gaynor ◽  
Patrick F. McArdle ◽  
Oscar C. Stine ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Early Onset ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Population Level ◽  
Small Vessel ◽  
Stroke Treatment ◽  
Functional Variants ◽  
Individual Snps

Background and Purpose: The genetic contribution to ischemic stroke may include rare- or low-frequency variants of high-penetrance and large-effect sizes. Analyses focusing on early-onset disease, an extreme-phenotype, and on the exome, the protein-coding portion of genes, may increase the likelihood of identifying such rare functional variants. To evaluate this hypothesis, we implemented a 2-stage discovery and replication design, and then addressed whether the identified variants also associated with older-onset disease. Methods: Discovery was performed in UMD-GEOS Study (University of Maryland-Genetics of Early-Onset Stroke), a biracial population-based study of first-ever ischemic stroke cases 15 to 49 years of age (n=723) and nonstroke controls (n=726). All participants had prior GWAS (Genome Wide Association Study) and underwent Illumina exome-chip genotyping. Logistic-regression was performed to test single-variant associations with all-ischemic stroke and TOAST (Trial of ORG 10172 in Acute Stroke Treatment) subtypes in Whites and Blacks. Population level results were combined using meta-analysis. Gene-based aggregation testing and meta-analysis were performed using seqMeta. Covariates included age and gender, and principal-components for population structure. Pathway analyses were performed across all nominally associated genes for each stroke outcome. Replication was attempted through lookups in a previously reported meta-analysis of early-onset stroke and a large-scale stroke genetics study consisting of primarily older-onset cases. Results: Gene burden tests identified a significant association with NAT10 in small-vessel stroke ( P =3.79×10 − 6 ). Pathway analysis of the top 517 genes ( P <0.05) from the gene-based analysis of small-vessel stroke identified several signaling and metabolism-related pathways related to neurotransmitter, neurodevelopmental notch-signaling, and lipid/glucose metabolism. While no individual SNPs reached chip-wide significance ( P <2.05×10 −7 ), several were near, including an intronic variant in LEXM (rs7549251; P =4.08×10 − 7 ) and an exonic variant in TRAPPC11 (rs67383011; P =5.19×10 − 6 ). Conclusions: Exome-based analysis in the setting of early-onset stroke is a promising strategy for identifying novel genetic risk variants, loci, and pathways.

scholarly journals TcI Isolates of Trypanosoma cruzi Exploit the Antioxidant Network for Enhanced Intracellular Survival in Macrophages and Virulence in Mice

2016 ◽  
Vol 84 (6) ◽  
pp. 1842-1856 ◽  
Author(s):  
María Paola Zago ◽  
Yashoda M. Hosakote ◽  
Sue-jie Koo ◽  
Monisha Dhiman ◽  
María Dolores Piñeyro ◽  
...  
Keyword(s):  
Trypanosoma Cruzi ◽  
Biological Behavior ◽  
Data Sets ◽  
Proteomic Profiling ◽  
Two Dimensional Gel Electrophoresis ◽  
Content Type ◽  
Transmission Cycle ◽  
Protein Levels ◽  
Flight Mass Spectrometry ◽  
And Control

Trypanosoma cruzispecies is categorized into six discrete typing units (TcI to TcVI) of which TcI is most abundantly noted in the sylvatic transmission cycle and considered the major cause of human disease. In our study, the TcI strains Colombiana (COL), SylvioX10/4 (SYL), and a cultured clone (TCC) exhibited different biological behavior in a murine model, ranging from high parasitemia and symptomatic cardiomyopathy (SYL), mild parasitemia and high tissue tropism (COL), to no pathogenicity (TCC). Proteomic profiling of the insect (epimastigote) and infective (trypomastigote) forms by two-dimensional gel electrophoresis/matrix-assisted laser desorption ionization–time of flight mass spectrometry, followed by functional annotation of the differential proteome data sets (≥2-fold change,P< 0.05), showed that several proteins involved in (i) cytoskeletal assembly and remodeling, essential for flagellar wave frequency and amplitude and forward motility of the parasite, and (ii) the parasite-specific antioxidant network were enhanced in COL and SYL (versus TCC) trypomastigotes. Western blotting confirmed the enhanced protein levels of cytosolic and mitochondrial tryparedoxin peroxidases and their substrate (tryparedoxin) and iron superoxide dismutase in COL and SYL (versus TCC) trypomastigotes. Further, COL and SYL (but not TCC) were resistant to exogenous treatment with stable oxidants (H2O2and peroxynitrite [ONOO−]) and dampened the intracellular superoxide and nitric oxide response in macrophages, and thus these isolates escaped from macrophages. Our findings suggest that protein expression conducive to increase in motility and control of macrophage-derived free radicals provides survival and persistence benefits to TcI isolates ofT. cruzi.

scholarly journals A Further Comment on ‘Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets’ by Lam et al.

2018 ◽  
Vol 21 (6) ◽  
pp. 538-545 ◽  
Author(s):  
W. D. Hill
Keyword(s):  
Cognitive Ability ◽  
Drug Targets ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Tissue Specific ◽  
Nootropic Drug ◽  
Genome Wide ◽  
Quality Control Metrics

Lam et al. (2018) respond to a commentary of their paper entitled ‘Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets’ Lam et al. (2017). While Lam et al. (2018) have now provided the recommended quality control metrics for their paper, problems remain. Specifically, Lam et al. (2018) do not dispute that the results of their multi-trait analysis of genome-wide association study (MTAG) analysis has produced a phenotype with a genetic correlation of one with three measures of education, but do claim the associations found are specific to the trait of cognitive ability. In this brief paper, it is empirically demonstrated that the phenotype derived by Lam et al. (2017) is more genetically similar to education than cognitive ability. In addition, it is shown that of the genome-wide significant loci identified by Lam et al. (2017) are loci that are associated with education rather than with cognitive ability.

scholarly journals Inflammatory Cytokines and Risk of Ischemic Stroke: A Mendelian Randomization Study

2022 ◽  
Vol 12 ◽  
Author(s):  
Yalan Li ◽  
Jun Lu ◽  
Jie Wang ◽  
Peizhi Deng ◽  
Changjiang Meng ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Inflammatory Cytokines ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Mendelian Randomization ◽  
Causal Effect ◽  
Meta Analysis ◽  
Outcome Data ◽  
Sensitivity Analyses ◽  
A Genome

Background: Observational studies have revealed the association between some inflammatory cytokines and the occurrence of ischemic stroke, but the causal relationships remain unclear.Methods: We conducted a two-sample Mendelian randomization (MR) analysis to assess the causal effects of thirty inflammatory cytokines and the risk of ischemic stroke. For exposure data, we collected genetic variants associated with inflammatory cytokines as instrumental variables (IVs) from a genome-wide association study (GWAS) meta-analysis from Finland (sample size up to 8,293). For the outcome data, we collected summary data of ischemic stroke from a large-scale GWAS meta-analysis involved 17 studies (34,217 cases and 406,111 controls). We further performed a series of sensitivity analyses as validation of primary MR results.Results: According to the primary MR estimations and further sensitivity analyses, we established one robust association after Bonferroni correction: the odds ratio (95% CI) per unit change in genetically increased IL-4 was 0.84 (0.89–0.95) for ischemic stroke. The chemokine MCP3 showed a nominally significant association with ischemic stroke risk (OR: 0.93, 95% CI: 0.88–0.99, unadjusted p &lt; 0.05). There was no evidence of a causal effect of other inflammatory cytokines and the risk of ischemic stroke.Conclusions: Our study suggested that genetically increased IL-4 levels showed a protective effect on the risk of ischemic stroke, which provides important new insights into the potential therapeutic target for preventing ischemic stroke.

scholarly journals Trans-ancestry genome-wide association study identifies novel genetic mechanisms in rheumatoid arthritis

2021 ◽  
Author(s):  
Kazuyoshi Ishigaki ◽  
Saori Sakaue ◽  
Chikashi Terao ◽  
Yang Luo ◽  
Kyuto Sonehara ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Association Study ◽  
Fine Mapping ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Genetic Research ◽  
Genome Wide Association ◽  
Polygenic Risk Score ◽  
Genome Wide

AbstractTrans-ancestry genetic research promises to improve power to detect genetic signals, fine-mapping resolution, and performances of polygenic risk score (PRS). We here present a large-scale genome-wide association study (GWAS) of rheumatoid arthritis (RA) which includes 276,020 samples of five ancestral groups. We conducted a trans-ancestry meta-analysis and identified 124 loci (P < 5 × 10-8), of which 34 were novel. Candidate genes at the novel loci suggested essential roles of the immune system (e.g., TNIP2 and TNFRSF11A) and joint tissues (e.g., WISP1) in RA etiology. Trans-ancestry fine mapping identified putatively causal variants with biological insights (e.g., LEF1). Moreover, PRS based on trans-ancestry GWAS outperformed PRS based on single-ancestry GWAS and had comparable performance between European and East Asian populations. Our study provides multiple insights into the etiology of RA and improves genetic predictability of RA.

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