Genetic Strategies to Understand Human Diabetic Nephropathy: In Silico Strategies for Molecular Data—Association Studies

2019 ◽  
pp. 241-275
Author(s):  
Marisa Canadas-Garre ◽  
Laura J. Smyth ◽  
Kerry Anderson ◽  
Katie Kerr ◽  
Amy Jayne McKnight
Keyword(s):  
Diabetic Nephropathy ◽  
In Silico ◽  
Association Studies ◽  
Data Association ◽  
Molecular Data ◽  
Genetic Strategies

scholarly journals UTMOST, a single and cross-tissue TWAS (Transcriptome Wide Association Study), reveals new ASD (Autism Spectrum Disorder) associated genes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Cristina Rodriguez-Fontenla ◽  
Angel Carracedo
Keyword(s):  
In Silico ◽  
Association Studies ◽  
Meta Analysis ◽  
Neurodevelopmental Disorder ◽  
Gastrointestinal Symptoms ◽  
Tissue Expression ◽  
Autism Spectrum ◽  
Biological Characterization ◽  
Large Size ◽  
Body Tissues

AbstractAutism spectrum disorders (ASD) is a complex neurodevelopmental disorder that may significantly impact on the affected individual’s life. Common variation (SNPs) could explain about 50% of ASD heritability. Despite this fact and the large size of the last GWAS meta-analysis, it is believed that hundreds of risk genes in ASD have yet to be discovered. New tools, such as TWAS (Transcriptome Wide Association Studies) which integrate tissue expression and genetic data, are a great approach to identify new ASD susceptibility genes. The main goal of this study is to use UTMOST with the publicly available summary statistics from the largest ASD GWAS meta-analysis as genetic input. In addition, an in silico biological characterization for the novel associated loci was performed. Our results have shown the association of 4 genes at the brain level (CIPC, PINX1, NKX2-2, and PTPRE) and have highlighted the association of NKX2-2, MANBA, ERI1, and MITF at the gastrointestinal level. The gastrointestinal associations are quite relevant given the well-established but unexplored relationship between ASD and gastrointestinal symptoms. Cross-tissue analysis has shown the association of NKX2-2 and BLK. UTMOST-associated genes together with their in silico biological characterization seems to point to different biological mechanisms underlying ASD etiology. Thus, it would not be restricted to brain tissue and it will involve the participation of other body tissues such as the gastrointestinal.

scholarly journals Molecular Modeling of Differentially Phosphorylated Serine 10 and Acetylated lysine 9/14 of Histone H3 Regulates their Interactions with 14-3-3ζ, MSK1, and MKP1

2013 ◽  
Vol 7 ◽  
pp. BBI.S12449 ◽  
Author(s):  
Ajit K. Sharma ◽  
Abhilasha Mansukh ◽  
Ashok Varma ◽  
Nikhil Gadewal ◽  
Sanjay Gupta
Keyword(s):  
Molecular Modeling ◽  
Protein Kinase ◽  
Chromatin Structure ◽  
In Silico ◽  
Association Studies ◽  
Regulatory Proteins ◽  
Mitogen Activated Protein Kinase ◽  
Site Specific ◽  
Mitogen Activated Protein ◽  
Neighboring Site

Histone modifications occur in precise patterns, with several modifications known to affect the binding of proteins. These interactions affect the chromatin structure, gene regulation, and cell cycle events. The dual modifications on the H3 tail, serine10 phosphorylation, and lysine14 acetylation (H3Ser10PLys14Ac) are reported to be crucial for interaction with 14-3-3ζ. However, the mechanism by which H3Ser10P along with neighboring site-specific acetylation(s) is targeted by its regulatory proteins, including kinase and phosphatase, is not fully understood. We carried out molecular modeling studies to understand the interaction of 14-3-3ζ, and its regulatory proteins, mitogen-activated protein kinase phosphatase-1 (MKP1), and mitogen- and stress-activated protein kinase-1 (MSK1) with phosphorylated H3Ser10 alone or in combination with acetylated H3Lys9 and Lys14. In silico molecular association studies suggested that acetylated Lys14 and phosphorylated Ser10 of H3 shows the highest binding affinity towards 14-3-3ζ. In addition, acetylation of H3Lys9 along with Ser10PLys14Ac favors the interaction of the phosphatase, MKP1, for dephosphorylation of H3Ser10P. Further, MAP kinase, MSK1 phosphorylates the unmodified H3Ser10 containing N-terminal tail with maximum affinity compared to the N-terminal tail with H3Lys9AcLys14Ac. The data clearly suggest that opposing enzymatic activity of MSK1 and MKP1 corroborates with non-acetylated and acetylated, H3Lys9Lys14, respectively. Our in silico data highlights that site-specific phosphorylation (H3Ser10P) and acetylation (H3Lys9 and H3Lys14) of H3 are essential for the interaction with their regulatory proteins (MKP1, MSK1, and 14-3-3ζ) and plays a major role in the regulation of chromatin structure.

Genetic Strategies to Understand Human Diabetic Nephropathy: Wet-Lab Approaches

2019 ◽  
pp. 205-240
Author(s):  
Laura J. Smyth ◽  
Katie Kerr ◽  
Seamus Duffy ◽  
Jill Kilner ◽  
Amy Jayne McKnight
Keyword(s):  
Diabetic Nephropathy ◽  
Wet Lab ◽  
Genetic Strategies

scholarly journals Evidence for GRN as part of a neuroinflammatory mechanism connecting common neurodegenerative diseases

2020 ◽  
Author(s):  
Mike A. Nalls ◽  
Cornelis Blauwendraat ◽  
Lana Sargent ◽  
Dan Vitale ◽  
Hampton Leonard ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Neurodegenerative Diseases ◽  
Genetic Risk ◽  
Association Studies ◽  
Molecular Data ◽  
Genome Wide Association Studies ◽  
Data Types ◽  
Genome Wide ◽  
Trait Locus ◽  
Lateral Sclerosis

SUMMARYBackgroundPrevious research using genome wide association studies (GWAS) has identified variants that may contribute to lifetime risk of multiple neurodegenerative diseases. However, whether there are common mechanisms that link neurodegenerative diseases is uncertain. Here, we focus on one gene, GRN, encoding progranulin, and the potential mechanistic interplay between genetic risk, gene expression in the brain and inflammation across multiple common neurodegenerative diseases.MethodsWe utilized GWAS, expression quantitative trait locus (eQTL) mapping and Bayesian colocalization analyses to evaluate potential causal and mechanistic inferences. We integrate various molecular data types from public resources to infer disease connectivity and shared mechanisms using a data driven process.FindingseQTL analyses combined with GWAS identified significant functional associations between increasing genetic risk in the GRN region and decreased expression of the gene in Parkinson’s, Alzheimer’s and amyotrophic lateral sclerosis. Additionally, colocalization analyses show a connection between blood based inflammatory biomarkers relating to platelets and GRN expression in the frontal cortex.InterpretationGRN expression mediates neuroinflammation function related to general neurodegeneration. This analysis suggests shared mechanisms for Parkinson’s, Alzheimer’s and amyotrophic lateral sclerosis.FundingNational Institute on Aging, National Institute of Neurological Disorders and Stroke, and the Michael J. Fox Foundation.

scholarly journals High Elmo1 expression aggravates and low Elmo1 expression prevents diabetic nephropathy

2016 ◽  
Vol 113 (8) ◽  
pp. 2218-2222 ◽  
Author(s):  
Catherine K. Hathaway ◽  
Albert S. Chang ◽  
Ruriko Grant ◽  
Hyung-Suk Kim ◽  
Victoria J. Madden ◽  
...  
Keyword(s):  
Diabetic Nephropathy ◽  
Transforming Growth Factor ◽  
Association Studies ◽  
Lipid Peroxides ◽  
Transforming Growth Factor Β1 ◽  
Genome Wide Association Studies ◽  
Diabetic Mice ◽  
Stage Renal Disease ◽  
End Stage

Human genome-wide association studies have demonstrated that polymorphisms in the engulfment and cell motility protein 1 gene (ELMO1) are strongly associated with susceptibility to diabetic nephropathy. However, proof of causation is lacking. To test whether modest changes in its expression alter the severity of the renal phenotype in diabetic mice, we have generated mice that are type 1 diabetic because they have the Ins2Akita gene, and also have genetically graded expression of Elmo1 in all tissues ranging in five steps from ∼30% to ∼200% normal. We here show that the Elmo1 hypermorphs have albuminuria, glomerulosclerosis, and changes in the ultrastructure of the glomerular basement membrane that increase in severity in parallel with the expression of Elmo 1. Progressive changes in renal mRNA expression of transforming growth factor β1 (TGFβ1), endothelin-1, and NAD(P)H oxidase 4 also occur in parallel with Elmo1, as do the plasma levels of cystatin C, lipid peroxides, and TGFβ1, and erythrocyte levels of reduced glutathione. In contrast, Akita type 1 diabetic mice with below-normal Elmo1 expression have reduced expression of these various factors and less severe diabetic complications. Remarkably, the reduced Elmo1 expression in the 30% hypomorphs almost abolishes the pathological features of diabetic nephropathy, although it does not affect the hyperglycemia caused by the Akita mutation. Thus, ELMO1 plays an important role in the development of type 1 diabetic nephropathy, and its inhibition could be a promising option for slowing or preventing progression of the condition to end-stage renal disease.

Nephroprotective effect of Combretum micranthum G. Don in nicotinamide-streptozotocin induced diabetic nephropathy in rats: In-vivo and in-silico experiments

2020 ◽  
Vol 261 ◽  
pp. 113133
Author(s):  
Mabozou Kpemissi ◽  
Adrian-Valentin Potârniche ◽  
Povi Lawson-Evi ◽  
Kossi Metowogo ◽  
Mamatchi Melila ◽  
...  
Keyword(s):  
Diabetic Nephropathy ◽  
In Silico ◽  
Combretum Micranthum ◽  
Nephroprotective Effect

scholarly journals A systematic review and meta-analysis of genetic association studies for the role of inflammation and the immune system in diabetic nephropathy

2017 ◽  
Vol 10 (3) ◽  
pp. 293-300 ◽  
Author(s):  
Maria Tziastoudi ◽  
Ioannis Stefanidis ◽  
Georgios M. Hadjigeorgiou ◽  
Konstantinos Stravodimos ◽  
Elias Zintzaras
Keyword(s):  
Systematic Review ◽  
Diabetic Nephropathy ◽  
Immune System ◽  
Genetic Association ◽  
Association Studies ◽  
Meta Analysis ◽  
Genetic Association Studies

scholarly journals DOP54 Integrated network analysis using patient-specific single-nucleotide polymorphism profiles uncovers new pathways involved in ulcerative colitis pathogenesis

2020 ◽  
Vol 14 (Supplement_1) ◽  
pp. S092-S092
Author(s):  
D Modos ◽  
J Brooks ◽  
P Sudhakar ◽  
B Verstockt ◽  
B Alexander-Dann ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Network Analysis ◽  
Tight Junctions ◽  
In Silico ◽  
Target Genes ◽  
Association Studies ◽  
Patient Specific ◽  
Genome Wide Association Studies ◽  
Single Nucleotide ◽  
Network Propagation

Abstract Background Genome-wide association studies have deciphered the single nucleotide polymorphisms (SNPs) which are responsible for ulcerative colitis (UC) susceptibility. However, to understand how these SNPs are involved in UC, additional methods are necessary. One such approach is in silico network propagation modelling, which can discover how the effects of SNPs in UC can affect the whole cell. A complementary approach is weighted gene co-expression network analysis (WGCNA), where co-regulated genes are identified using transcriptomic data. Integrating these two methods can shed light on how SNPs are affecting the transcriptome of UC patients. Methods We used immunochip profiles of 941 UC patients and focussed on UC-associated SNPs altering regulatory regions. Based on these regions, we identified affected genes. To understand how their corresponding proteins rewire transcriptional regulation, we predicted the path between these proteins and relevant transcription factors (TF) using the OmniPath signalling network (http://omnipathdb.org). From the TFs, we propagated the signal further to target genes using TFlink (https://tflink.net) and GTRD (http://gtrd.biouml.org). To evaluate the predicted network propagation signal, we conducted WGCNA with transcriptomics data from 46 matching patients’ (GEO ID: GSE48959). To interpret the results, we used Gene Ontology Biological Process annotations of the target genes, and we compared the function and regulation of affected genes and the determined WGCNA modules. Results We found 9 predominant signalling pathways, some already known from other studies to be involved in UC pathogenesis, including NFkB signalling, chemokine signalling, Notch pathway, JAK/STAT signalling. Downstream of these pathways we identified potential key TFs regulate the UC phenotype, for example NFKB1, GATA3, GTF2I. The targets of these TFs were enriched in the WGCNA modules of the patients. The WGCNA modules and the transcriptionally affected genes had enriched processes including cell migration, TGF-β signalling, exocytosis, adaptive T- and B-cell-specific immune responses and tight junctions. We also found myogenetic development specific TFs affected transcriptionally such as MyoD, MEF2A, MEF2D. We are currently validating these results through patient-specific biopsies. Conclusion In silico methods bring us closer to understanding UC pathogenesis. Our results suggest that in a well-defined set of patients, weakened tight junctions and insufficient immune response can lead to dysfunctional epithelial barrier, resulting in poor wound healing in UC. We hope the developed workflow will provide novel diagnostic and therapeutic options in UC.

Deciphering diabetic nephropathy: progress using genetic strategies

2000 ◽  
Vol 9 (2) ◽  
pp. 99-106 ◽  
Author(s):  
Sharon G. Adler ◽  
Madeleine Pahl ◽  
Michael F. Seldin
Keyword(s):  
Diabetic Nephropathy ◽  
Genetic Strategies
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