Anne E. Kwitek

Various states of cardiomyocyte (CM) polyploidy have been associated with cardiac injury responses, including regeneration and heart failure. However, our understanding of the comprehensive mechanisms governing CM ploidy and its relationship with heart physiology is limited. To address this issue and uncover genetic regulators, we surveyed CM ploidy across a new genetic resource known as the Hybrid Rat Diversity Panel (HRDP) and found significant variation in ploidy phenotypes across the panel. Using select rat strains with divergent displays of CM ploidy, we found that CM hyperpolyploidization (≥8 N) positively correlates with various physiological parameters, namely left ventricular dilation and reduced ejection fraction. Genome-wide association mapping identified several loci significantly associated with frequency of hyperpolyploid CMs. Investigation of genes harboring damaging protein coding variants within these loci identified enrichment of cytoarchitectural genes, of which the ACTIN-binding protein, Shroom3 , was found to be strongly and specifically expressed in CMs and harbors 7 damaging protein coding variants. CM-specific deletion of Shroom3 resulted in increased hyperpolyploidization and left ventricular dilation with reduced ejection fraction. Furthermore, functional characterization of single-nucleotide variants resulting in amino acid changes within SHROOM3 confirmed two protein coding variants that disrupted SHROOM3–ACTIN interaction and led to altered expression of genes involved in DNA replication. This study elucidates the genetic determinants of CM ploidy phenotypes and solidifies a correlative relationship between CM ploidy and left ventricular function. Importantly, CM intrinsic expression of at least one gene mapped in this study, Shroom3 , is confirmed to regulate CM hyperpolyploidization and cardiac function.

Syncytiotrophoblast stress contributes to the pathogenesis of preeclampsia, but many of the underlying causes remain undetermined. Previous work has implicated the loss of placental HDAC9-mediated Rgs2 transcription in the disorder. Extending these findings, we report that HDAC9 and RGS2 were abundant and localized primarily to syncytiotrophoblast cells of the control placenta. Expression of both targets was attenuated in these cells during preeclampsia and thus may be an underappreciated source of syncytiotrophoblast stress, warranting further investigation.

BACKGROUND: Hypertension or elevated blood pressure (BP) is a worldwide clinical challenge and the leading primary risk factor for kidney dysfunctions, heart failure, and cerebrovascular disease. The kidney is a central regulator of BP by maintaining sodium-water balance. Multiple genome-wide association studies revealed that BP is a heritable quantitative trait, modulated by several genetic, epigenetic, and environmental factors. The SNPs identified in genome-wide association studies predominantly (>95%) reside within noncoding genomic regions, making it difficult to understand how they regulate BP. Given the central role of the kidney in regulating BP, we hypothesized that chromatin-accessible regions in renal tissue would be enriched for BP-associated single nucleotide polymorphisms. METHODS: We manually dissected 2 important kidney segments that maintain the sodium-water balance: proximal tubules and medullary thick ascending limbs from the human and rat kidneys. To delineate their chromatin and transcriptomic profiles, we performed the assay for transposase-accessible chromatin and RNA sequencing, respectively. RESULTS: The chromatin accessibility maps revealed the shared and unique cis -regulatory elements that modulate the chromatin accessibility in proximal tubule and medullary thick ascending limbs of humans and rats. We developed a visualization tool to compare the cross-species epigenomic maps to identify potential regulatory targets for hypertension pathogenesis. We also identified a significant enrichment of BP-associated single nucleotide polymorphisms (1064 for human proximal tubule and 1172 for human medullary thick ascending limbs) within accessible chromatin regions of both segments, including rs1173771 and rs1421811 at the NPR3 locus and rs1800470 at the TGFb1 locus. CONCLUSIONS: Collectively, this study lays a foundation for interrogating how intergenic single nucleotide polymorphisms may regulate polygenic traits such as BP.

Rat models have been a major model for studying complex disease mechanisms, behavioral phenotypes, environmental factors, and for drug development and discovery. Inbred rat strains control for genetic background and allow for repeated, reproducible, cellular and whole animal phenotyping. The Hybrid Rat Diversity Panel (HRDP) was designed to be a powerful panel of inbred rats with genomic, physiological, and behavioral data to serve as a resource for systems genetics. The HRDP consists of 96–98 inbred rat strains aimed to maximize power to detect specific genetic loci associated with complex traits while maximizing the genetic diversity among strains. The panel consists of 32–34 genetically diverse inbred strains and two panels of recombinant inbred panels. To establish the HRDP program, embryo resuscitation and breeding were done to establish colonies for distribution. Whole genome sequencing was performed to achieve 30X coverage. Genomic, phenotype, and strain information is available through the Hybrid Rat Diversity Panel Portal at the Rat Genome Database (http://rgd.mcw.edu).

The Rat Genome Database (RGD) is a multispecies knowledgebase which integrates genetic, multiomic, phenotypic, and disease data across 10 mammalian species. To support cross-species, multiomics studies and to enhance and expand on data manually extracted from the biomedical literature by the RGD team of expert curators, RGD imports and integrates data from multiple sources. These include major databases and a substantial number of domain-specific resources, as well as direct submissions by individual researchers. The incorporation of these diverse datatypes is handled by a growing list of automated import, export, data processing, and quality control pipelines. This article outlines the development over time of a standardized infrastructure for automated RGD pipelines with a summary of key design decisions and a focus on lessons learned.

Gene pathways and gene-regulatory networks are used to describe the causal relationship between genes, based on biological experiments. However, many genes are still to be studied to define novel pathways. To address this, a gene-clustering algorithm has been used to group correlated genes together, based on the similarity of their gene expression level. The existing methods cluster genes based on only one type of omics data, which ignores the information from other types. A large sample size is required to achieve an accurate clustering structure for thousands of genes, which can be challenging due to the cost of multi-omics data. Meta-analysis has been used to aggregate the data from multiple studies and improve the analysis results. We propose a computationally efficient meta-analytic gene-clustering algorithm that combines multi-omics datasets from multiple studies, using the fixed effects linear models and a modified weighted correlation network analysis framework. The simulation study shows that the proposed method outperforms existing single omic-based clustering approaches when multi-omics data and/or multiple studies are available. A real data example demonstrates that our meta-analytic method outperforms single-study based methods.

Objective: Food insecurity (FI) is associated with poor metabolic health. It is assumed that energy intake and diet quality underlie this association. We tested the hypothesis that dietary factors (quantity and quality) mediate the association of FI with excess weight, waist circumference and glycemic control [glycohemoglobin (A1C)]. Methods: A mediation analysis was performed on data from the National Health And Nutrition Examination Survey using FI as an independent variable; body mass index (BMI), waist circumference, and A1C as metabolic outcome variables and total energy intake, macronutrients, and diet quality measured by the Healthy Eating Index-2015 (HEI-2015) as potential mediators. Results: Despite a greater prevalence of obesity in participants experiencing FI, daily reported energy intake was similar in food-secure and -insecure subjects. In adjusted analyses of the overall cohort, none of the examined dietary factors mediated associations between FI and metabolic outcomes. In race-stratified analyses, total sugar consumption was a partial mediator of BMI in non-Hispanic Whites, while diet quality measures (HEI-2015 total score and added sugar subscore) were partial mediators of waist circumference and BMI, respectively, for those in the “other” ethnic group. Conclusion: Dietary factors are not the main factors underlying the association of FI with metabolic health. Future studies should investigate whether other social determinants of health commonly present in the context of FI play a role in this association.

In mice, three distinct isoforms of Agouti-related peptide are encoded via distinct first exons. In the arcuate nucleus of the hypothalamus, Krüppel-like factor 4 stimulates transcription of the dominant isoform in lean mice, but this mechanism is altered during diet-induced obesity.

Syncytiotrophoblast stress is theorized to drive development of preeclampsia, but its molecular causes and consequences remain largely undefined. Multiple hormones implicated in preeclampsia signal via the Gαq cascade, leading to the hypothesis that excess Gαq signaling within the syncytiotrophoblast may contribute. First, we present data supporting increased Gαq signaling and antioxidant responses within villous and syncytiotrophoblast samples of human preeclamptic placenta. Second, Gαq was activated in mouse placenta using Cre-lox and DREADD methodologies. Syncytiotrophoblast-restricted Gαq activation caused hypertension, kidney damage, proteinuria, elevated circulating proinflammatory factors, decreased placental vascularization, diminished spiral artery diameter, and augmented responses to mitochondrial-derived superoxide. Administration of the mitochondrial-targeted antioxidant Mitoquinone attenuated maternal proteinuria, lowered circulating inflammatory and anti-angiogenic mediators, and maintained placental vascularization. These data demonstrate a causal relationship between syncytiotrophoblast stress and the development of preeclampsia and identify elevated Gαq signaling and mitochondrial reactive oxygen species as a cause of this stress.

Metabolic diseases are a host of complex conditions, including obesity, diabetes mellitus, and metabolic syndrome. Endocrine control systems (eg, adrenals, thyroid, gonads) are causally linked to metabolic health outcomes. N/NIH Heterogeneous Stock (HS) rats are a genetically heterogeneous outbred population developed for genetic studies of complex traits. Genetic mapping studies in adult HS rats identified loci associated with cardiometabolic risks, such as glucose intolerance, insulin resistance, and increased body mass index. This study determined underappreciated metabolic health traits and the associated endocrine glands within available substrains of the HS rat founders. We hypothesize that the genetic diversity of the HS rat founder strains causes a range of endocrine health conditions contributing to the diversity of cardiometabolic disease risks. ACI/EurMcwi, BN/NHsdMcwi, BUF/MnaMcwi, F344/StmMcwi, M520/NRrrcMcwi, and WKY/NCrl rats of both sexes were studied from birth until 13 weeks of age. Birth weight was recorded, body weight was measured weekly, metabolic characteristics were assessed, and blood and tissues were collected. Our data show wide variation in endocrine traits and metabolic health states in ACI, BN, BUF, F344, M520, and WKY rat strains. This is the first report to compare birth weight, resting metabolic rate, endocrine gland weight, hypothalamic–pituitary–thyroid axis hormones, and brown adipose tissue weight in these rat strains. Importantly, this work unveils new potential for the HS rat population to model early life adversity and adrenal and thyroid pathophysiology. The HS population likely inherited risk alleles for these strain-specific traits, making the HS rat a powerful model to investigate interventions on endocrine and metabolic health.