Searching the Mouse Genome Informatics (MGI) Resources for Information on Mouse Biology from Genotype to Phenotype

Single-housing-induced islet epigenomic changes are related to polymorphisms in diabetic KK mice

A lack of social relationships is increasingly recognized as a type 2 diabetes (T2D) risk. To investigate the underlying mechanism, we used male KK mice, an inbred strain with spontaneous diabetes. Given the association between living alone and T2D risk in humans, we divided the non-diabetic mice into singly housed (KK-SH) and group-housed control mice. Around the onset of diabetes in KK-SH mice, we compared H3K27ac ChIP-Seq with RNA-Seq using pancreatic islets derived from each experimental group, revealing a positive correlation between single-housing-induced changes in H3K27ac and gene expression levels. In particular, single-housing-induced H3K27ac decreases revealed a significant association with islet cell functions and GWAS loci for T2D and related diseases, with significant enrichment of binding motifs for transcription factors representative of human diabetes. Although these H3K27ac regions were preferentially localized to a polymorphic genomic background, SNVs and indels did not cause sequence disruption of enriched transcription factor motifs in most of these elements. These results suggest alternative roles of genetic variants in environment-dependent epigenomic changes and provide insights into the complex mode of disease inheritance.

Strategies for dissecting the complexity of neurodevelopmental disorders

Neurodevelopmental disorders (NDDs) are associated with a wide range of clinical features, affecting multiple pathways involved in brain development and function. Recent advances in high-throughput sequencing have unveiled numerous genetic variants associated with NDDs, which further contribute to disease complexity and make it challenging to infer disease causation and underlying mechanisms. Herein, we review current strategies for dissecting the complexity of NDDs using model organisms, induced pluripotent stem cells, single-cell sequencing technologies, and massively parallel reporter assays. We further highlight single-cell CRISPR-based screening techniques that allow genomic investigation of cellular transcriptomes with high efficiency, accuracy, and throughput. Overall, we provide an integrated review of experimental approaches that can be applicable for investigating a broad range of complex disorders.

Genome-wide association analysis and Mendelian randomization proteomics identify drug targets for heart failure

We conduct a large-scale meta-analysis of heart failure genome-wide association studies (GWAS) consisting of over 90,000 heart failure cases and more than 1 million control individuals of European ancestry to uncover novel genetic determinants for heart failure. Using the GWAS results and blood protein quantitative loci, we perform Mendelian randomization and colocalization analyses on human proteins to provide putative causal evidence for the role of druggable proteins in the genesis of heart failure. We identify 39 genome-wide significant heart failure risk variants, of which 18 are previously unreported. Using a combination of Mendelian randomization proteomics and genetic cis-only colocalization analyses, we identify 10 additional putatively causal genes for heart failure. Findings from GWAS and Mendelian randomization-proteomics identify seven (CAMK2D, PRKD1, PRKD3, MAPK3, TNFSF12, APOC3 and NAE1) proteins as potential targets for interventions to be used in primary prevention of heart failure.

Determining the role of SGLT2 inhibition with Empagliflozin in the development of diabetic retinopathy

Diabetes mellitus is a chronic metabolic disease that occurs when the pancreas is not producing enough insulin or when the insulin that it does produce is not able to be used effectively in the body. This results in hyperglycemia and if the blood sugars are not controlled, then it can lead to serious damage of various body systems, especially the nerves and the blood vessels. Uncontrolled diabetes is a major cause of kidney failure, heart attacks, stroke and amputation. One of the most devastating complications for patients is diabetic retinopathy (DR) which represents the leading cause of preventable vision loss in people between 20 and 65 years of age. Sodium glucose transporter 2 (SGLT2) inhibitors have been shown to reduce the risk for cardiovascular and renal events, however literature highlighting their potential role to prevent DR is limited. We therefore used a relevant mouse model (Akimba) to explore the effects of the SGLT2 inhibitor, Empagliflozin (EMPA), on the development of diabetic retinal changes. Here we show that when given in the early stages of type 1 diabetes (T1D), EMPA reduced the weight loss usually associated with T1D, decreased diabetes-associated polydipsia, lowered fasting blood glucose levels, decreased kidney-to-body weight ratios and, most importantly in the current context, substantially reduced retinal abnormalities associated with DR. We show that EMPA reduces vascular leakage indicated by lower albumin staining in the vitreous humor and diminishes expression of the pathogenic factor VEGF in the retina. Additionally, EMPA significantly alters the retinal genetic signature. Our findings suggest that SGLT2 inhibition may be a useful therapeutic approach to prevent the development of DR and its severity if given early in the disease process.

Genome-wide pathogenesis interpretation using a heat diffusion-based systems genetics method and implications for gene function annotation

Background

Genetics is best dedicated to interpreting pathogenesis and revealing gene functions. The past decade has witnessed unprecedented progress in genetics, particularly in genome‐wide identification of disorder variants through Genome‐Wide Association Studies (GWAS) and Phenome‐Wide Association Studies (PheWAS). However, it is still a great challenge to use GWAS/PheWAS‐derived data to elucidate pathogenesis.

Methods

In this study, we used HotNet2, a heat diffusion‐based systems genetics algorithm, to calculate the networks for disease genes obtained from GWAS and PheWAS, with an attempt to get deeper insights into disease pathogenesis at a molecular level.

Results

Through HotNet2 calculation, significant networks for 202 (for GWAS) and 167 (for PheWAS) types of diseases were identified and evaluated, respectively. The GWAS‐derived disease networks exhibit a stronger biomedical relevance than PheWAS counterparts. Therefore, the GWAS‐derived networks were used for pathogenesis interpretation by integrating the accumulated biomedical information. As a result, the pathogenesis for 64 diseases was elucidated in terms of mutation‐caused abnormal transcriptional regulation, and 47 diseases were preliminarily interpreted in terms of mutation‐caused varied protein‐protein interactions. In addition, 3,802 genes (including 46 function‐unknown genes) were assigned with new functions by disease network information, some of which were validated through mice gene knockout experiments.

Conclusions

Systems genetics algorithm HotNet2 can efficiently establish genotype‐phenotype links at the level of biological networks. Compared with original GWAS/PheWAS results, HotNet2‐calculated disease‐gene associations have stronger biomedical significance, hence provide better interpretations for the pathogenesis of genome‐wide variants, and offer new insights into gene functions as well. These results are also helpful in drug development.

Review of Preferential Suspicious Genes in Microtia Patients Through Various Approaches

Recently, an increasing trend of the birth prevalence of anotia/microtia is observed in China, contributed by changes of social environment and lifestyle. There seems to be no major breakthroughs in exact pathogenesis of microtia, though the research results related to molecular genetics unceasingly appear. In this review, the authors focus on the results of various research methods which the authors regard as the preferential suspicious gene pool to facilitate the exploration of the pathogenic genes of microtia, knowing that the mechanism of microtia is very complicated. The advantages and limitations of these various approaches will also be systematically delineated. The authors believe that this review will give a deep insight in the genetic research of microtia and help plastic surgeons manage congenital microtia more effectively.

A core transcriptional signature of human microglia: Derivation and utility in describing region-dependent alterations associated with Alzheimer's disease

Growing recognition of the pivotal role microglia play in neurodegenerative and neuroinflammatory disorders has accentuated the need to characterize their function in health and disease. Studies in mouse have applied transcriptome-wide profiling of microglia to reveal key features of microglial ontogeny, functional profile, and phenotypic diversity. While similar, human microglia exhibit clear differences to their mouse counterparts, underlining the need to develop a better understanding of the human microglial profile. On examining published microglia gene signatures, limited consistency was observed between studies. Hence, we sought to derive a core microglia signature of the human central nervous system (CNS), through a comprehensive analysis of existing transcriptomic datasets. Nine datasets derived from cells and tissues, isolated from various regions of the CNS across numerous donors, were subjected independently to an unbiased correlation network analysis. From each dataset, a list of coexpressing genes corresponding to microglia was identified, with 249 genes highly conserved between them. This core signature included known microglial markers, and compared with other signatures provides a gene set specific to microglia in the context of the CNS. The utility of this signature was demonstrated by its use in detecting qualitative and quantitative region-specific alterations in aging and Alzheimer's disease. These analyses highlighted the reactive response of microglia in vulnerable brain regions such as the entorhinal cortex and hippocampus, additionally implicating pathways associated with disease progression. We believe this resource and the analyses described here, will support further investigations to the contribution of human microglia in CNS health and disease.