Identification of Chromosomal Regions Linked to Diabetic Nephropathy: A Meta-Analysis of Genome-Wide Linkage Scans

Genetic predisposition to nephropathy and associated cardiovascular disease in people with type 1 diabetes: role of the angiotensinI-converting enzyme (ACE), and beyond; a narrative review

Hypertension, cardiovascular disease and kidney failure are associated with persistent hyperglycaemia and the subsequent development of nephropathy in people with diabetes. Diabetic nephropathy is associated with widespread vascular disease affecting both the kidney and the heart from an early stage. However, the risk of diabetic nephropathy in people with type 1 diabetes is strongly genetically determined, as documented in familial transmission studies. The search for the underlying genes has been extensive, using specific hypotheses, sibling linkage studies and genome-wide association studies (GWAS). The role of the angiotensinI-converting enzyme/kininase II (ACE) gene and genetic variability in ACE levels as a susceptibility and prognostic factor for diabetic nephropathy has been well documented in people with type 1 diabetes. The ACE gene insertion/deletion polymorphism, which is associated with plasma and tissue ACE levels, has been the most studied genomic variant in diabetic nephropathy. Recently, this polymorphism has also been associated with longevity in people with type 1 diabetes. The ACE I/D polymorphism has also been associated with vascular, extra-renal complications including myocardial infarction and lower-limb amputation in this population. Other genes and loci have been identified in linkage studies and GWAS, such as the COL4A3 gene or a region on chromosome 3q with the adiponectin gene. Replication was not always attempted and was rarely achieved, even for GWAS. Overall, effect sizes remain modest and no major gene has been identified, despite the strength of the genetic effect in transmission studies. We searched bibliographic databases for studies reporting genomic variants associated with diabetic nephropathy and meta-analyses of such studies. We selected important relevant studies for further discussion in this narrative review. This brief review attempts to summarise the current knowledge on the genetics of diabetic nephropathy and associated cardiovascular disease in people with type 1 diabetes, and discusses some conceptual and methodological issues relevant to the interpretation of past studies and the design of future ones.

Serpin Family B Member 2 Polymorphisms in Patients with Diabetic Kidney Disease: An Association Study

Diabetic kidney disease (DKD) is a serious microvascular complication of type 2 diabetes mellitus (T2DM). Despite the numerous genetic loci that have been associated with the disease in T2DM, the genetic architecture of DKD remains unclear until today. In contrast to SERPINE1, the contribution of SERPINB2 has not been examined in DKD. Therefore, we conducted the first genetic association study of SERPINB2 to elucidate its role in DKD. In total, the study involved 197 patients with DKD, 155 patients with T2DM without microvascular complications (diabetic kidney disease, diabetic retinopathy, and diabetic neuropathy), and 246 healthy controls. The generalized odds ratio (ORG) was calculated to estimate the risk on DKD development. The present association study regarding SERPINB2 SNPs (rs4941230, rs3819335, rs13381217, rs6140) did not reveal any significant association between SERPINB2 variants and DKD. Additional studies in other populations are necessary to further investigate the role of this gene in the progression of diabetes mellitus and development of DKD.

Key Genetic Components of Fibrosis in Diabetic Nephropathy: An Updated Systematic Review and Meta-Analysis

Renal fibrosis (RF) constitutes the common end-point of all kinds of chronic kidney disease (CKD), regardless of the initial cause of disease. The aim of the present study was to identify the key players of fibrosis in the context of diabetic nephropathy (DN). A systematic review and meta-analysis of all available genetic association studies regarding the genes that are included in signaling pathways related to RF were performed. The evaluated studies were published in English and they were included in PubMed and the GWAS Catalog. After an extensive literature review and search of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, eight signaling pathways related to RF were selected and all available genetic association studies of these genes were meta-analyzed. ACE, AGT, EDN1, EPO, FLT4, GREM1, IL1B, IL6, IL10, IL12RB1, NOS3, TGFB1, IGF2/INS/TH cluster, and VEGFA were highlighted as the key genetic components driving the fibrosis process in DN. The present systematic review and meta-analysis indicate, as key players of fibrosis in DN, sixteen genes. However, the results should be interpreted with caution because the number of studies was relatively small.

Identification of Chromosomal Regions Linked to Autism-Spectrum Disorders: A Meta-Analysis of Genome-Wide Linkage Scans

Background: Autism spectrum disorder (ASD) is a clinically and genetically heterogeneous group of pervasive neurodevelopmental disorders with a strong hereditary component. Although, genome-wide linkage scans (GWLS) and association studies (GWAS) have previously identified hundreds of ASD risk gene loci, the results remain inconclusive. Method: We performed a heterogeneity-based genome search meta-analysis (HEGESMA) of 15 genome scans of autism and ASD. Results: For strictly defined autism, data were analyzed across six separate genome scans. Region 7q22-q34 reached statistical significance in both weighted and unweighted analyses, with evidence of significantly low between-scan heterogeneity. For ASDs (data from 12 separate scans), chromosomal regions 5p15.33-5p15.1 and 15q22.32-15q26.1 reached significance in both weighted and unweighted analyses but did not reach significance for either low or high heterogeneity. Region 1q23.2-1q31.1 was significant in unweighted analyses with low between-scan heterogeneity. Finally, region 8p21.1-8q13.2 reached significant linkage peak in all our meta-analyses. When we combined all available genome scans (15), the same results were produced. Conclusions: This meta-analysis suggests that these regions should be further investigated for autism susceptibility genes, with the caveat that autism spectrum disorders have different linkage signals across genome scans, possibly because of the high genetic heterogeneity of the disease.

Meta-Analysis and Bioinformatics Detection of Susceptibility Genes in Diabetic Nephropathy

The latest meta-analysis of genome-wide linkage studies (GWLS) identified nine cytogenetic locations suggestive of a linkage with diabetic nephropathy (DN) due to type 1 diabetes mellitus (T1DM) and seven locations due to type 2 diabetes mellitus (T2DM). In order to gain biological insight about the functional role of the genes located in these regions and to prioritize the most significant genetic loci for further research, we conducted a gene ontology analysis with an over representation test for the functional annotation of the protein coding genes. Protein analysis through evolutionary relationships (PANTHER) version 16.0 software and Cytoscape with the relevant plugins were used for the gene ontology analysis, and the overrepresentation test and STRING database were used for the construction of the protein network. The findings of the over-representation test highlight the contribution of immune related molecules like immunoglobulins, cytokines, and chemokines with regard to the most overrepresented protein classes, whereas the most enriched signaling pathways include the VEGF signaling pathway, the Cadherin pathway, the Wnt pathway, the angiogenesis pathway, the p38 MAPK pathway, and the EGF receptor signaling pathway. The common section of T1DM and T2DM results include the significant over representation of immune related molecules, and the Cadherin and Wnt signaling pathways that could constitute potential therapeutic targets for the treatment of DN, irrespective of the type of diabetes.

Serpin Family E Member 1 Tag Single-Nucleotide Polymorphisms in Patients with Diabetic Nephropathy: An Association Study and Meta-Analysis Using a Genetic Model-Free Approach

BACKGROUND

Many lines of evidence highlight the genetic contribution on the development of diabetic nephropathy (DN). One of the studied genes is SERPINE1 whose the role in the risk of developing DN remains questionable. In order to elucidate the contribution of SERPINE1 in DN progression in the context of type 2 diabetes mellitus (T2DM), we conducted an association study and meta-analysis of SERPINE1 genetic variants.

MATERIALS AND METHODS

A total of 190 patients with DN, 150 T2DM (type 2 diabetes mellitus) patients without DN and 238 healthy controls were recruited. We selected five tag single-nucleotide polymorphisms (SNPs) from the HapMap. The generalized odds ratio (ORG) was calculated to estimate the risk on DN development. Subgroup analyses based on ethnicity and type of diabetes were also performed.

RESULTS

Both the present association study regarding SERPINE1 SNPs (rs2227667, rs2070682, rs1050813, rs2227690, rs2227692) did not found any significant association between SERPINE1 variants and DN and the meta-analysis of variant 4G>5G (rs1799889) did not also reveal a significant association between 4G>5G variant and DN in main and subgroup analyses.

DISCUSSION

In conclusion, the present association study and meta-analysis provides strong evidence that SERPINE1 genetic variant 4G>5G is not implicated in the risk or development of DN in Caucasians. Further studies in other populations remain to further investigate the role of this variant in the course of DN.

Immune-Related Gene Polymorphisms and Pharmacogenetic Studies in Nephrology

A large subgroup of patients with chronic kidney disease still encounter serious adverse effects and lack of responsiveness to medications, possibly because of the interindividual genetic variability in genes involved in the metabolism and transport of the treatments used. As a consequence, several pharmacogenetic studies have been conducted in nephrology patients that examine the effect of genetic variants in response to treatment in kidney diseases. The present commentary focuses on immune-related genes (TNF [tumor necrosis factor], MIF [macrophage migration inhibitory factor], and IL-10 [interleukin 10]) or those genes that may regulate the response to immunosuppressive medications (ABCB1 [ATP binding cassette subfamily B member 1] and ITPA [inosine triphosphatase]) used in kidney diseases. These genes were selected from those showing significant results in a recent meta-analysis of pharmacogenetic studies of patients with chronic kidney disease. This commentary highlights that certain polymorphisms should be investigated in patients with kidney diseases, especially if they are to be administered immunosuppressive agents. In certain cases, flavonoids such as quercetin may be beneficial.

Replication of chromosomal loci involved in Parkinson's disease: A quantitative synthesis of GWAS

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The first quantitative synthesis of GWAS regarding Parkinson’s Disease.

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Fifteen Parkinson’s Disease GWASs with 191.397 available SNPs pooled.

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User friendly software (METRADISC-XL) implemented.

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Seven chromosomal regions (bins) were replicated as associated with the Parkinson’s Disease trait.

Introduction

Parkinson’s disease is a neurodegenerative disorder with a complex etiology coming from interactions between genetic and environmental factors. Research on Parkinson’s disease genetics has been an effortful struggle, while new technologies and novel study designs served as indispensable boosters. Until now, 90 loci and 20 disease-causing gene mutations have been identified. In this study we describe a novel non-parametric approach to GWAS meta-analysis and its application in PD genetics.

Methods

A literature search was conducted to identify Genome-Wide Association Studies (GWAS) regarding Parkinson’s disease. We applied predefined inclusion criteria and extracted the reported SNPs and their respective position and statistical significance. We divided all chromosomes in approximately equal genetic distance segments called bins and recorded the most significant SNP from each bin and each study and ranked them in terms of their p-value. Ranks from each bin were summed, averaged and added in a heterogeneity-based analysis using the METRADISC-XL software. Weighted and unweighted analysis was performed.

Results

Five-hundred and forty-three SNPs and their respective p-values from 15 studies were matched in their corresponding bins. The METRADISC-XL analysis resulted in 7 bins with a significant p-value. A bin on chromosome 4 where the SNCA gene is located found with genome-wide significant association with Parkinson’s Disease.

Conclusion

This is the first time a non-parametric method is applied in GWAS meta-analysis. The results add some insight on the overall understanding of Parkinson’s disease genetics and serve as a first step of further convergent analysis with Genome-wide linkage studies.

Cadherin and Wnt signaling pathways as key regulators in diabetic nephropathy

AIM

A recent meta-analysis of genome-wide linkage studies (GWLS) has identified multiple genetic regions suggestive of linkage with DN harboring hundreds of genes. Moving this number of genetic loci forward into biological insight is truly the next step. Here, we approach this challenge with a gene ontology (GO) analysis in order to yield biological and functional role to the genes, an over-representation test to find which GO terms are enriched in the gene list, pathway analysis, as well as protein network analysis.

METHOD

GO analysis was performed using protein analysis through evolutionary relationships (PANTHER) version 14.0 software and P-values less than 0.05 were considered statistically significant. GO analysis was followed by over-representation test for the identification of enriched terms. Statistical significance was calculated by Fisher's exact test and adjusted using the false discovery rate (FDR) for correction of multiple tests. Cytoscape with the relevant plugins was used for the construction of the protein network and clustering analysis.

RESULTS

The GO analysis assign multiple GO terms to the genes regarding the molecular function, the biological process and the cellular component, protein class and pathway analysis. The findings of the over-representation test highlight the contribution of cell adhesion regarding the biological process, integral components of plasma membrane regarding the cellular component, chemokines and cytokines with regard to protein class, while the pathway analysis emphasizes the contribution of Wnt and cadherin signaling pathways.

CONCLUSIONS

Our results suggest that a core feature of the pathogenesis of DN may be a disturbance in Wnt and cadherin signaling pathways, whereas the contribution of chemokines and cytokines need to be studied in additional studies.

Mechanisms Underlying the Comorbidity of Schizophrenia and Type 2 Diabetes Mellitus

The mortality rate of patients with schizophrenia is high, and life expectancy is shorter by 10 to 20 years. Metabolic abnormalities including type 2 diabetes mellitus (T2DM) are among the main reasons. The prevalence of T2DM in patients with schizophrenia may be epidemiologically frequent because antipsychotics induce weight gain as a side effect and the cognitive dysfunction of patients with schizophrenia relates to a disordered lifestyle, poor diet, and low socioeconomic status. Apart from these common risk factors and risk factors unique to schizophrenia, accumulating evidence suggests the existence of common susceptibility genes between schizophrenia and T2DM. Functional proteins translated from common genetic susceptibility genes are known to regulate neuronal development in the brain and insulin in the pancreas through several common cascades. In this review, we discuss common susceptibility genes, functional cascades, and the relationship between schizophrenia and T2DM. Many genetic and epidemiological studies have reliably associated the comorbidity of schizophrenia and T2DM, and it is probably safe to think that common cascades and mechanisms suspected from common genes' functions are related to the onset of both schizophrenia and T2DM. On the other hand, even when genetic analyses are performed on a relatively large number of comorbid patients, the results are sometimes inconsistent, and susceptibility genes may carry only a low or moderate risk. We anticipate future directions in this field.

The genetic map of diabetic nephropathy: evidence from a systematic review and meta-analysis of genetic association studies

Despite the extensive efforts of scientists, the genetic background of diabetic nephropathy (DN) has not yet been clarified. To elucidate the genetic variants that predispose to the development of DN, we conducted a systematic review and meta-analysis of all available genetic association studies (GAS) of DN. We searched in the Human Genome Epidemiology Navigator (HuGE Navigator) and PubMed for available GAS of DN. The threshold for meta-analysis was three studies per genetic variant. The association between genotype distribution and DN was examined using the generalized linear odds ratio (OR_G). For variants with available allele frequencies, the examined model was the allele contrast. The pooled OR was estimated using the DerSimonian and Laird random effects model. The publication bias was assessed with Egger’s test. We performed pathway analysis of significant genes with DAVID 6.7. Genetic data of 606 variants located in 228 genes were retrieved from 360 GASs and were synthesized with meta-analytic methods. ACACB, angiotensin I-converting enzyme (ACE), ADIPOQ, AGT, AGTR1, AKR1B1, APOC1, APOE, ATP1B2, ATP2A3, CARS, CCR5, CGNL1, Carnosine dipeptidase 1 (CNDP1), CYGB-PRCD, EDN1, Engulfment and cell motility 1 (ELMO1), ENPP1, EPO, FLT4, FTO, GLO1, HMGA2, IGF2/INS/TH cluster, interleukin 1B (IL1B), IL8, IL10, KCNQ1, KNG, LOC101927627, Methylenetetrahydrofolate reductase, nitric oxide synthase 3 (NOS3), SET domain containing seven, histone lysine methyltransferase (SETD7), Sirtuin 1 (SIRT1), SLC2A1, SLC2A2, SLC12A3, SLC19A3, TCF7L2, TGFB1, TIMP1, TTC39C, UNC13B, VEGFA, WTAPP1, WWC1 as well as XYLT1 and three intergenic polymorphisms showed significant association with DN. Pathway analysis revealed the overrepresentation of six signalling pathways. The significant findings provide further evidence for genetic factors implication in DN offering new perspectives in discovery of new therapies.

Designing a QTL Mapping Study for Implementation in the Realized Collaborative Cross Genetic Reference Population

The Collaborative Cross (CC) mouse resource is a next-generation mouse genetic reference population (GRP) designed for high-resolution mapping of quantitative trait loci (QTL) of large effect affecting complex traits during health and disease. The CC resource consists of a set of 72 recombinant inbred lines (RILs) generated by reciprocal crossing of five classical and three wild-derived mouse founder strains. Complex traits are controlled by variations within multiple genes and environmental factors, and their mutual interactions. These traits are observed at multiple levels of the animals' systems, including metabolism, body weight, immune profile, and susceptibility or resistance to the development and progress of infectious or chronic diseases. Herein, we present general guidelines for design of QTL mapping experiments using the CC resource-along with full step-by-step protocols and methods that were implemented in our lab for the phenotypic and genotypic characterization of the different CC lines-for mapping the genes underlying host response to infectious and chronic diseases. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: CC lines for whole body mass index (BMI) Basic Protocol 2: A detailed assessment of the power to detect effect sizes based on the number of lines used, and the number of replicates per line Basic Protocol 3: Obtaining power for QTL with given target effect by interpolating in Table 1 of Keele et al. (2019).