Integrative Analyses Reveal Tstd1 as a Potential Modulator of HDL Cholesterol and Mitochondrial Function in Mice

High-density lipoprotein (HDL) cholesterol levels are closely associated with human health and diseases. To identify genes modulating plasma HDL levels, we integrated HDL measurements and multi-omics data collected from diverse mouse cohorts and combined a list of systems genetics methods, including quantitative trait loci (QTL) mapping analysis, mediation analysis, transcriptome-wide association analysis (TWAS), and correlation analysis. We confirmed a significant and conserved QTL for plasma HDL on chromosome 1 and identified that Tstd1 liver transcript correlates with plasma HDL in several independent mouse cohorts, suggesting Tstd1 may be a potential modulator of plasma HDL levels. Correlation analysis using over 70 transcriptomics datasets in humans and mice revealed consistent correlations between Tstd1 and genes known to be involved in cholesterol and HDL regulation. Consistent with strong enrichment in gene sets related to cholesterol and lipoproteins in the liver, mouse strains with high Tstd1 exhibited higher plasma levels of HDL, total cholesterol and other lipid markers. GeneBridge using large-scale expression datasets identified conserved and positive associations between TSTD1/Tstd1 and mitochondrial pathways, as well as cholesterol and lipid pathways in human, mouse and rat. In summary, we identified Tstd1 as a new modulator of plasma HDL and mitochondrial function through integrative systems analyses, and proposed a new mechanism of HDL modulation and a potential therapeutic target for relevant diseases. This study highlights the value of such integrative approaches in revealing molecular mechanisms of complex traits or diseases.

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Abstract 76: MicroRNA-144 Regulates Hepatic ABCA1 and Plasma HDL Following Activation of the Nuclear Receptor FXR

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvb.33.suppl_1.a76 ◽

2013 ◽

Vol 33 (suppl_1) ◽

Author(s):

Thomas Vallim ◽

Elizabeth Tarling ◽

Tammy Kim ◽

Mete Civelek ◽

Angel Baldan ◽

...

Keyword(s):

Lipid Metabolism ◽

Nuclear Receptor ◽

Molecular Mechanisms ◽

Lipoprotein Metabolism ◽

Density Lipoprotein ◽

Hdl Cholesterol ◽

Farnesoid X Receptor ◽

Abca1 Protein

Rationale The bile acid receptor Farnesoid-X-Receptor (FXR) regulates many aspects of lipid metabolism by various complex and not fully understood molecular mechanisms. We set out to investigate the molecular mechanisms for FXR-dependent regulation of lipid and lipoprotein metabolism. Objective To identify FXR-regulated microRNAs that were subsequently involved in regulating lipid metabolism. Methods and Results ATP binding cassette transporter A1 (ABCA1) is a major determinant of plasma High Density Lipoprotein (HDL)-cholesterol levels. Here we show that activation of the nuclear receptor FXR in vivo increases hepatic levels of miR-144, which in turn lower hepatic ABCA1 and plasma HDL levels. We identified two complementary sequences to miR-144 in the 3’ untranslated region (UTR) of ABCA1 mRNA that are necessary for miR-144-dependent regulation. Overexpression of miR-144 in vitro decreased both cellular ABCA1 protein and cholesterol efflux to lipid-poor apolipoprotein A-I (ApoA-I) protein, whilst overexpression in vivo reduced hepatic ABCA1 protein and plasma HDL- cholesterol. Conversely, silencing miR-144 in mice increased hepatic ABCA1 protein and HDL- cholesterol. In addition, we utilized tissue-specific FXR deficient mice to show that induction of miR-144 and FXR-dependent hypolipidemia requires hepatic, but not intestinal FXR. Finally, we identified functional FXR response elements (FXREs) upstream of the miR-144 locus, consistent with direct FXR regulation. Conclusion In conclusion, we have identified a pathway involving FXR, miR-144 and ABCA1 that together regulate plasma HDL cholesterol. This pathway may be therapeutically targeted in the future in order to increase HDL levels.

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Investigating tissue-relevant causal molecular mechanisms of complex traits using probabilistic TWAS analysis

10.1101/808295 ◽

2019 ◽

Cited By ~ 2

Author(s):

Yuhua Zhang ◽

Corbin Quick ◽

Ketian Yu ◽

Alvaro Barbeira ◽

Francesca Luca ◽

...

Keyword(s):

Gene Expression ◽

Complex Traits ◽

Large Scale ◽

Molecular Mechanisms ◽

Association Studies ◽

Complex Trait ◽

Causal Effects ◽

Biological Mechanisms ◽

Integrative Framework ◽

Eqtl Data

AbstractTranscriptome-wide association studies (TWAS), an integrative framework using expression quantitative trait loci (eQTLs) to construct proxies for gene expression, have emerged as a promising method to investigate the biological mechanisms underlying associations between genotypes and complex traits. However, challenges remain in interpreting TWAS results, especially regarding their causality implications. In this paper, we describe a new computational framework, probabilistic TWAS (PTWAS), to detect associations and investigate causal relationships between gene expression and complex traits. We use established concepts and principles from instrumental variables (IV) analysis to delineate and address the unique challenges that arise in TWAS. PTWAS utilizes probabilistic eQTL annotations derived from multi-variant Bayesian fine-mapping analysis conferring higher power to detect TWAS associations than existing methods. Additionally, PTWAS provides novel functionalities to evaluate the causal assumptions and estimate tissue- or cell-type specific causal effects of gene expression on complex traits. These features make PTWAS uniquely suited for in-depth investigations of the biological mechanisms that contribute to complex trait variation. Using eQTL data across 49 tissues from GTEx v8, we apply PTWAS to analyze 114 complex traits using GWAS summary statistics from several large-scale projects, including the UK Biobank. Our analysis reveals an abundance of genes with strong evidence of eQTL-mediated causal effects on complex traits and highlights the heterogeneity and tissue-relevance of these effects across complex traits. We distribute software and eQTL annotations to enable users performing rigorous TWAS analysis by leveraging the full potentials of the latest GTEx multi-tissue eQTL data.

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Abstract 325: HDL Binding Rates for MPO: An Index of Functionality?

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvb.32.suppl_1.a325 ◽

2012 ◽

Vol 32 (suppl_1) ◽

Author(s):

Linghong Kong ◽

Daisy Sahoo ◽

Mary Sorci-Thomas ◽

Hao Zhang ◽

Kirkwood A Pritchard

Keyword(s):

Metabolic Syndrome ◽

Large Scale ◽

Hypochlorous Acid ◽

Density Lipoprotein ◽

Hdl Cholesterol ◽

Time Frame ◽

Paraoxonase 1 ◽

Hdl Function ◽

Biophysical Interactions

Statement of Problem: Measurements of high density lipoprotein (HDL) function are reported to be more predictive for atheroprotection than measurements of HDL cholesterol. Unfortunately, bioassays of HDL function are complex, manual and time-consuming, making them impractical for routine clinical use. As such, well-standardized and easy-to-use assays of HDL function are desperately needed to make better informed clinical decisions. We are developing a panel of biolayer interferometry ( BLI ) assays on the Octet Red (forteBio, Inc) that measure HDL binding rates for biomolecules that regulate HDL function. Previously we showed that hypochlorous acid-modified HDL (ox-HDL) bound paraoxonase 1, myeloperoxidase (MPO) and cholesteryl ester transfer protein at faster rates than native HDL (n-HDL). Based on these data, we hypothesize that BLI assays of HDL binding rates might be useful for assessing functionality in vivo. Methods: To test this hypothesis, the biophysics of HDL interactions with MPO was examined in rodent models of metabolic syndrome and hypercholesterolemia and in patients with documented cardiovascular disease (CVD). Briefly, HDL was immunocaptured onto anti-apoA-I biosensors, incubated in a standardized solution of MPO and binding rates determined in ∼3.5 min/sample. Results: HDL from fructose-fed hamsters tended to bind MPO at faster rates than from chow-fed hamsters (300% of control p<0.07, n=6). HDL from hypercholesterolemic Ldlr -/- mice bound MPO at much faster rates than HDL from control mice (175% of control p<0.05, n=4). HDL from patients with CVD bound MPO at faster rates than HDL from control humans (280% of control p<0.004, n=6). Conclusions: HDL in hamsters with metabolic syndrome, mice with hypercholesterolemia and patients with CVD appears to bind MPO at faster rates than their corresponding controls. Automated BLI assays make it possible to complete large scale clinical studies in a reasonable time frame. Finally biophysical interactions of HDL with biomolecules such as MPO may be a useful approach for quantifying HDL functionality.

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Melatonin Inhibits Vascular Endothelial Cell Pyroptosis by Improving Mitochondrial Function via UQCRC1 Up-regulation and Demethylation

Biochemistry and Cell Biology ◽

10.1139/bcb-2020-0279 ◽

2020 ◽

Author(s):

Junfa Zeng ◽

Jun Tao ◽

Linzhen Xia ◽

Zhaolin Zeng ◽

Jiaojiao Chen ◽

...

Keyword(s):

Endothelial Cell ◽

Mitochondrial Function ◽

Molecular Mechanisms ◽

Core Protein ◽

Umbilical Vein ◽

Low Density Lipoprotein ◽

Vascular Endothelial Cell ◽

Density Lipoprotein ◽

Chronic Inflammatory Disease ◽

Umbilical Vein Endothelial Cells

Atherosclerosis (AS) is a chronic inflammatory disease that involves cell death and endothelial dysfunction. Melatonin is an endocrine hormone with anti-inflammatory and anti-AS effects. However, the underlying molecular mechanisms of melatonin anti-AS effect are still unknown. A previous study has shown that pyroptosis plays a detrimental role in AS development. Therefore, this study was designed to investigate the anti-pyroptotic effects and potential mechanisms of melatonin in the atherosclerotic endothelium. In this study, melatonin attenuated the expression of pyroptosis-related genes, including NLRP3, caspase-1 and IL-1β, in human umbilical vein endothelial cells treated with oxidised low-density lipoprotein. Furthermore, melatonin up-regulated ten-eleven translocation 2 (TET2) expression, inhibited ubiquinol-cytochrome c reductase core protein 1 (UQCRC1) methylation and reduced pyroptosis. The up-regulation of UQCRC1 via melatonin improved mitochondrial function, thereby inhibiting oxidative stress and endothelial cell pyroptosis. Collectively, our results indicated that melatonin prevented endothelial cell pyroptosis by up-regulating TET2 to inhibit UQCRC1 methylation and improve mitochondrial function.

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Genetic contributors to lipoprotein cholesterol levels in an intercross of 129S1/SvImJ and RIIIS/J inbred mice

Physiological Genomics ◽

10.1152/physiolgenomics.00168.2003 ◽

2004 ◽

Vol 17 (2) ◽

pp. 114-121 ◽

Cited By ~ 15

Author(s):

Malcolm A. Lyons ◽

Ron Korstanje ◽

Renhua Li ◽

Kenneth A. Walsh ◽

Gary A. Churchill ◽

...

Keyword(s):

Total Cholesterol ◽

Inbred Mice ◽

Density Lipoprotein ◽

Hdl Cholesterol ◽

Lipoprotein Cholesterol ◽

Mouse Strains ◽

High Cholesterol ◽

Significant Qtls ◽

Cholesterol Levels ◽

Trait Locus

To determine the genetic contribution to variation among lipoprotein cholesterol levels, we performed quantitative trait locus (QTL) analyses on an intercross between mouse strains RIIIS/J and 129S1/SvImJ. Male mice of the parental strains and the reciprocal F1 and F2 populations were fed a high-cholesterol, cholic acid-containing diet for 8–12 wk. At the end of the feeding period, plasma total, high-density lipoprotein (HDL), and non-HDL cholesterol were determined. For HDL cholesterol, we identified three significant QTLs on chromosomes (Chrs) 1 ( D1Mit507, 88 cM, 72–105 cM, 4.8 LOD), 9 ( D11Mit149, 14 cM, 10–25 cM, 9.4 LOD), and 12 ( D12Mit60, 20 cM, 0–50 cM, 5.0 LOD). These QTLs were considered identical to QTLs previously named Hdlq5, Hdlq17, and Hdlq18, respectively, in crosses sharing strain 129. For total cholesterol, we identified two significant QTLs on Chrs 1 and 9, which were named Chol10 ( D1Mit507, 88 cM, 10–105 cM, 3.9 LOD) and Chol11 ( D11Mit149, 14 cM, 0–30 cM, 4.4 LOD), respectively. In addition, for total cholesterol, we identified two suggestive QTLs on Chrs 12 (distal) and 17, which remain unnamed. For non-HDL cholesterol, we identified and named one new QTL on Chr 17, Nhdlq3 ( D17Mit221, 58 cM, 45–60 cM, 3.4 LOD). Nhdlq3 colocalized with orthologous human QTLs for lipoprotein phenotypes, and with Abcg5 and Abcg8. Overall, we detected eight QTLs for lipoprotein cholesterol concentrations on Chrs 1, 9, 12, and 17 (each two per chromosome), including a new QTL for non-HDL cholesterol, Nhdlq3, on Chr 17.

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Epistasis contributes to the genetic buffering of plasma HDL cholesterol in mice

Physiological Genomics ◽

10.1152/physiolgenomics.00044.2010 ◽

2010 ◽

Vol 42A (4) ◽

pp. 228-234 ◽

Cited By ~ 3

Author(s):

Renhua H. Li ◽

Gary A. Churchill

Keyword(s):

High Fat Diet ◽

Genetic Factors ◽

Inbred Mouse ◽

Plasma Concentrations ◽

Density Lipoprotein ◽

Hdl Cholesterol ◽

Mouse Strains ◽

High Fat ◽

Expression Of Genes ◽

Genetic Buffering

Stressful environmental factors, such as a high-fat diet, can induce responses in the expression of genes that act to maintain physiological homeostasis. We observed variation in plasma concentrations of high-density lipoprotein (HDL) cholesterol across inbred mouse strains in response to high dietary fat intake. Several strains, including C57BL/6J, have stable levels of plasma HDL independent of diet, whereas other strains, including DBA2/J, show marked changes in plasma HDL. To explore this phenomenon further, we used publicly available data from a C57BL/6J × DBA/2J intercross to identify genetic factors that associate with HDL under high-fat diet conditions. Our analysis identified an epistatic interaction that plays a role in the buffering of HDL levels in C57BL/6J mice, and we have identified Arl4d as a candidate gene that mediates this effect. Structural modeling further elucidates the interaction of genetic factors that contribute to the robustness of HDL in response to high-fat diet in the C57BL/6J strain.

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Multiplexed targeted resequencing identifies coding and regulatory variation underlying phenotypic extremes of HDL-cholesterol in humans

10.1101/235887 ◽

2017 ◽

Author(s):

Sumeet A. Khetarpal ◽

Paul L. Babb ◽

Wei Zhao ◽

William F. Hancock-Cerutti ◽

Christopher D. Brown ◽

...

Keyword(s):

Complex Traits ◽

Association Studies ◽

Score Test ◽

Density Lipoprotein ◽

Hdl Cholesterol ◽

Cost Effective ◽

Genome Wide Association Studies ◽

Common Variants ◽

Protein Coding ◽

Targeted Resequencing

AbstractGenome-wide association studies have uncovered common variants at many loci influencing human complex traits and diseases, such as high-density lipoprotein cholesterol (HDL-C). However, the contribution of the identified genes is difficult to ascertain from current efforts interrogating common variants with small effects. Thus, there is a pressing need for scalable, cost-effective strategies for uncovering causal variants, many of which may be rare and noncoding. Here, we used a multiplexed inversion probe (MIP) target capture approach to resequence both coding and regulatory regions at seven HDL-C associated loci in 797 individuals with extremely high HDL-C vs. 735 low-to-normal HDL-C controls. Our targets included protein-coding regions of GALNT2, APOA5, APOC3, SCARB1, CCDC92, ZNF664, CETP, and LIPG (>9 kb), and proximate noncoding regulatory features (>42 kb). Exome-wide genotyping in 1,114 of the 1,532 participants yielded a >90% genotyping concordance rate with MIP-identified variants in ~90% of participants. This approach rediscovered nearly all established GWAS associations in GALNT2, CETP, and LIPG loci with significant and concordant associations with HDL-C from our phenotypic-extremes design at 0.1% of the sample size of lipid GWAS studies. In addition, we identified a novel, rare, CETP noncoding variant enriched in the extreme high HDL-C group (P<0.01, Score Test). Our targeted resequencing of individuals at the HDL-C phenotypic extremes offers a novel, efficient, and cost-effective approach for identifying rare coding and noncoding variation differences in extreme phenotypes and supports the rationale for applying this methodology to uncover rare variation—particularly non-coding variation--underlying myriad complex traits.

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A Large-Scale Mutagenesis and Strain Characterization Project To Identify Genetic Variability in Mice: Resources Available from the Jackson Laboratory Program for Genomic Applications (JAX PGA).

Blood ◽

10.1182/blood.v104.11.1578.1578 ◽

2004 ◽

Vol 104 (11) ◽

pp. 1578-1578

Author(s):

Luanne L. Peters ◽

Orah S. Platt ◽

Karen L. Svenson ◽

Beverly J. Paigen ◽

Gary A. Churchill ◽

...

Keyword(s):

Genetic Variation ◽

Animal Models ◽

Hypothesis Testing ◽

Statistical Power ◽

Large Scale ◽

Inbred Strains ◽

Chromosome 1 ◽

Mouse Strains ◽

Strain Characterization ◽

Jackson Laboratory

Abstract Identifying the genes and gene products relevant to physiological systems and creating opportunities to elucidate their function are essential first steps in understanding the pathophysiology of disease. To dissect the genetic variation underlying hematopoietic, cardiovascular, lung, and sleep dysfunction, we established a Center for Mouse Models of Heart, Lung, Blood and Sleep (HLBS) Disorders at The Jackson Laboratory as part of the NHLBI Program for Genomic Applications (PGA). The major goal of the JAX PGA is to enable researchers to link both single-gene mutations and quantitative trait loci (QTL) to gene function and disease. To achieve this goal, we are generating new mutations in mice by chemical (ENU) mutagenesis, and characterizing the common inbred mouse strains to detect existing genetic variation. Here, we report an extensive body of hematologically relevant strain characterization data and the establishment of new animal models. All strain characterization data is deposited into the Mouse Phenome Database (MPD, http://www.jax.org/phenome), also accessible via the JAX PGA website (http://pga.jax.org). Data for up to 48 inbred strains are currently available and include complete blood counts and coagulation profiles (PT, aPTT, fibrinogen). These data allow investigators to identify the most appropriate strains for (a) physiological testing; (b) drug development; (c) progenitors in QTL crosses; (d) sensitized mutagenesis screens; and (e) direct hypothesis testing. For example, to maximize the potential for successful QTL identification, parental strains that differ substantially in the phenotype of interest, at least 2 standard deviations (SD), should be selected. We used our strain survey data to select parental strains for identification of QTL for baseline WBC count, an important risk factor for sickle cell disease severity. The strains C57BLKS/J and SM/J have WBC counts of 12.6 ± 1.6 and 3.3 ± 0.8 x 103/μL, respectively, a difference much greater the 2 SD, indicating a high statistical power. We identified a highly significant QTL (LOD = 7) on chromosome 1 in an initial genome wide scan of 279 F2 animals. Moreover, the availability of extensive phenotypic data across the inbred strains in conjunction with the availability of saturated sslp and SNP maps has allowed us to identify QTL in silico. As an example of the utility of the MPD in hypothesis testing, a modifier gene associated with decreased VWF levels is present in 5 of the 6 MPD strains showing the highest aPTT levels (see abstract by Johnsen et al). In total, 44 different phenotypic projects, each consisting of large datasets, can be freely accessed through the MPD. The JAX PGA mutagenesis effort in C57BL/6J mice has likewise yielded valuable resources. Nearly 100 new mutant strains are in various stages of development, including strains with phenotypes of interest to the hematology community (e. g., anemia, thrombocytopenia, leukopenia, leukocytosis). These animal models and all other JAX PGA resources (protocols, software, QTL locations) are freely available to the scientific community.

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Transcriptional changes and preservation of bone mass in hibernating black bears

Scientific Reports ◽

10.1038/s41598-021-87785-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Anna V. Goropashnaya ◽

Øivind Tøien ◽

Thiruvarangan Ramaraj ◽

Anitha Sundararajan ◽

Faye D. Schilkey ◽

...

Keyword(s):

Gene Expression ◽

Bone Mass ◽

Large Scale ◽

Molecular Mechanisms ◽

Tricarboxylic Acid Cycle ◽

Mammalian Species ◽

Osteoclast Differentiation ◽

Gene Set Enrichment Analysis ◽

Gene Sets ◽

Transcriptional Changes

AbstractPhysical inactivity leads to losses of bone mass and strength in most mammalian species. In contrast, hibernating bears show no bone loss over the prolonged periods (4–6 months) of immobility during winter, which suggests that they have adaptive mechanisms to preserve bone mass. To identify transcriptional changes that underlie molecular mechanisms preventing disuse osteoporosis, we conducted a large-scale gene expression screening in the trabecular bone and bone marrow, comparing hibernating and summer active bears through sequencing of the transcriptome. Gene set enrichment analysis showed a coordinated down-regulation of genes involved in bone resorption, osteoclast differentiation and signaling, and apoptosis during hibernation. These findings are consistent with previous histological findings and likely contribute to the preservation of bone during the immobility of hibernation. In contrast, no significant enrichment indicating directional changes in gene expression was detected in the gene sets of bone formation and osteoblast signaling in hibernating bears. Additionally, we revealed significant and coordinated transcriptional induction of gene sets involved in aerobic energy production including fatty acid beta oxidation, tricarboxylic acid cycle, oxidative phosphorylation, and mitochondrial metabolism. Mitochondrial oxidation was likely up-regulated by transcriptionally induced AMPK/PGC1α pathway, an upstream stimulator of mitochondrial function.

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A large-scale genome-wide enrichment analysis identifies new trait-associated genes, pathways and tissues across 31 human phenotypes*

10.1101/160770 ◽

2017 ◽

Cited By ~ 5

Author(s):

Xiang Zhu ◽

Matthew Stephens

Keyword(s):

Complex Traits ◽

Large Scale ◽

Late Onset ◽

Association Studies ◽

Low Density Lipoprotein ◽

Density Lipoprotein ◽

Enrichment Analysis ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Artery Disease

Genome-wide association studies (GWAS) aim to identify genetic factors that are associated with complex traits. Standard analyses test individual genetic variants, one at a time, for association with a trait. However, variant-level associations are hard to identify (because of small effects) and can be difficult to interpret biologically. “Enrichment analyses” help address both these problems by focusing on sets of biologically-related variants. Here we introduce a new model-based enrichment analysis method that requires only GWAS summary statistics, and has several advantages over existing methods. Applying this method to interrogate 3,913 biological pathways and 113 tissue-based gene sets in 31 human phenotypes identifies many previously-unreported enrichments. These include enrichments of the endochondral ossification pathway for adult height, the NFAT-dependent transcription pathway for rheumatoid arthritis, brain-related genes for coronary artery disease, and liver-related genes for late-onset Alzheimer’s disease. A key feature of our method is that inferred enrichments automatically help identify new trait-associated genes. For example, accounting for enrichment in lipid transport genes yields strong evidence for association between MTTP and low-density lipoprotein levels, whereas conventional analyses of the same data found no significant variants near this gene.

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