Intestinal SEC16B modulates obesity by controlling dietary lipid absorption

ABSTRACTGenome-wide association studies (GWAS) have identified genetic variants in SEC16 homolog B (SEC16B) locus to be associated with obesity and body mass index (BMI) in various populations. SEC16B encodes a scaffold protein located at endoplasmic reticulum (ER) exit sites that is implicated to participate in the trafficking of COPII vesicles in mammalian cells. However, the function of SEC16B in vivo, especially in lipid metabolism, has not been investigated. Here we demonstrated that intestinal SEC16B is required for dietary lipid absorption in mice. We showed that Sec16b intestinal knockout (IKO) mice, especially female mice, were protected from HFD-induced obesity. Loss of SEC16B in intestine dramatically reduced postprandial serum triglyceride output upon intragastric lipid load or during overnight fasting and high-fat diet (HFD) refeeding. Further studies showed that intestinal SEC16B deficiency impaired apoB lipidation and chylomicron secretion. These results revealed that SEC16B plays important roles in dietary lipid absorption, which may shed light on the association between variants in SEC16B and obesity in human.

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A Variant Noncoding Region Regulates Prrx1 and Predisposes to Atrial Arrhythmias

Circulation Research ◽

10.1161/circresaha.121.319146 ◽

2021 ◽

Author(s):

Fernanda M Bosada ◽

Mathilde R Rivaud ◽

Jae-Sun Uhm ◽

Sander Verheule ◽

Karel van Duijvenboden ◽

...

Keyword(s):

Sodium Current ◽

Association Studies ◽

Noncoding Region ◽

Specific Gene ◽

Genome Wide Association Studies ◽

Enhancer Activity ◽

Atrial Cardiomyocytes ◽

The Impact ◽

Lineage Specific Gene

Rationale: Atrial Fibrillation (AF) is the most common cardiac arrhythmia diagnosed in clinical practice. Genome-wide association studies have identified AF-associated common variants across 100+ genomic loci, but the mechanism underlying the impact of these variant loci on AF susceptibility in vivo has remained largely undefined. One such variant region, highly associated with AF, is found at 1q24, close to PRRX1, encoding the Paired Related Homeobox 1 transcription factor. Objective: To identify the mechanistic link between the variant region at 1q24 and AF predisposition. Methods and Results: The mouse orthologue of the noncoding variant genomic region (R1A) at 1q24 was deleted using CRISPR genome editing. Among the genes sharing the topologically associated domain with the deleted R1A region (Kifap3, Prrx1, Fmo2, Prrc2c), only the broadly expressed gene Prrx1 was downregulated in mutants, and only in cardiomyocytes. Expression and epigenetic profiling revealed that a cardiomyocyte lineage-specific gene program (Mhrt, Myh6, Rbm20, Tnnt2, Ttn, Ckm) was upregulated in R1A-/- atrial cardiomyocytes, and that Mef2 binding motifs were significantly enriched at differentially accessible chromatin sites. Consistently, Prrx1 suppressed Mef2-activated enhancer activity in HL-1 cells. Mice heterozygous or homozygous for the R1A deletion were susceptible to atrial arrhythmia induction, had atrial conduction slowing and more irregular RR intervals. Isolated R1A-/- mouse left atrial cardiomyocytes showed lower action potential upstroke velocities and sodium current, as well as increased systolic and diastolic calcium concentrations compared to controls. Conclusions: The noncoding AF variant region at 1q24 modulates Prrx1 expression in cardiomyocytes. Cardiomyocyte-specific reduction of Prrx1 expression upon deletion of the noncoding region leads to a profound induction of a cardiac lineage-specific gene program and to propensity for AF. These data indicate that AF-associated variants in humans may exert AF predisposition through reduced PRRX1 expression in cardiomyocytes.

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Combined knockout of Lrrk2 and Rab29 does not result in behavioral abnormalities in vivo

10.1101/2020.05.13.093708 ◽

2020 ◽

Cited By ~ 2

Author(s):

Melissa Conti Mazza ◽

Victoria Nguyen ◽

Alexandra Beilina ◽

Jinhui Ding ◽

Mark R. Cookson

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Kinase Activity ◽

Association Studies ◽

Dopamine Neurons ◽

Substantia Nigra Pars Compacta ◽

Genome Wide Association Studies ◽

Double Knockout ◽

Knockout Mouse Model

AbstractCoding mutations in the LRRK2 gene, encoding for a large protein kinase, have been shown to cause familial Parkinson’s disease (PD). The immediate biological consequence of LRRK2 mutations is to increase kinase activity, leading to the suggestion that inhibition of this enzyme might be useful therapeutically to slow disease progression. Genome-wide association studies have identified the chromosomal loci around LRRK2 and one of its proposed substrates, RAB29, as contributors towards the lifetime risk of sporadic PD. Considering the evidence for interactions between LRRK2 and RAB29 on the genetic and protein levels, here we generated a double knockout mouse model and determined whether there are any consequences on brain function with aging. From a battery of motor and non-motor behavioral tests, we noted only that 18-24 month Rab29-/- and double (Lrrk2-/-/Rab29-/-) knockout mice had diminished locomotor behavior in open field compared to wildtype mice. However, no genotype differences were seen in number of substantia nigra pars compacta (SNc) dopamine neurons or in tyrosine hydroxylase levels in the SNc and striatum, which might reflect a PD-like pathology. These results suggest that depletion of both Lrrk2 and Rab29 is tolerated, at least in mice, and support that this pathway might be able to be safely targeted for therapeutics in humans.Significance statementGenetic variation in LRRK2 that result in elevated kinase activity can cause Parkinson’s disease (PD), suggesting LRRK2 inhibition as a therapeutic strategy. RAB29, a substrate of LRRK2, has also been associated with increased PD risk. Evidence exists for an interactive relationship between LRRK2 and RAB29. Mouse models lacking either LRRK2 or RAB29 do not show brain pathologies. We hypothesized that the loss of both targets would result in additive effects across in vivo and post-mortem assessments in aging mice. We found that loss of both LRRK2 and RAB29 did not result in significant behavioral deficits or dopamine neuron loss. This evidence suggests that chronic inhibition of this pathway should be tolerated clinically.

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Perspective of the GEMSTONE Consortium on Current and Future Approaches to Functional Validation for Skeletal Genetic Disease Using Cellular, Molecular and Animal-Modeling Techniques

Frontiers in Endocrinology ◽

10.3389/fendo.2021.731217 ◽

2021 ◽

Vol 12 ◽

Author(s):

Martina Rauner ◽

Ines Foessl ◽

Melissa M. Formosa ◽

Erika Kague ◽

Vid Prijatelj ◽

...

Keyword(s):

Resource Sharing ◽

Complex Traits ◽

Cellular Localization ◽

Target Genes ◽

Mission Statement ◽

Association Studies ◽

Repetitive Sequences ◽

Genome Wide Association Studies ◽

Causal Genes

The availability of large human datasets for genome-wide association studies (GWAS) and the advancement of sequencing technologies have boosted the identification of genetic variants in complex and rare diseases in the skeletal field. Yet, interpreting results from human association studies remains a challenge. To bridge the gap between genetic association and causality, a systematic functional investigation is necessary. Multiple unknowns exist for putative causal genes, including cellular localization of the molecular function. Intermediate traits (“endophenotypes”), e.g. molecular quantitative trait loci (molQTLs), are needed to identify mechanisms of underlying associations. Furthermore, index variants often reside in non-coding regions of the genome, therefore challenging for interpretation. Knowledge of non-coding variance (e.g. ncRNAs), repetitive sequences, and regulatory interactions between enhancers and their target genes is central for understanding causal genes in skeletal conditions. Animal models with deep skeletal phenotyping and cell culture models have already facilitated fine mapping of some association signals, elucidated gene mechanisms, and revealed disease-relevant biology. However, to accelerate research towards bridging the current gap between association and causality in skeletal diseases, alternative in vivo platforms need to be used and developed in parallel with the current -omics and traditional in vivo resources. Therefore, we argue that as a field we need to establish resource-sharing standards to collectively address complex research questions. These standards will promote data integration from various -omics technologies and functional dissection of human complex traits. In this mission statement, we review the current available resources and as a group propose a consensus to facilitate resource sharing using existing and future resources. Such coordination efforts will maximize the acquisition of knowledge from different approaches and thus reduce redundancy and duplication of resources. These measures will help to understand the pathogenesis of osteoporosis and other skeletal diseases towards defining new and more efficient therapeutic targets.

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Asthma-associated genetic variants induce IL33 differential expression through an enhancer-blocking regulatory region

Nature Communications ◽

10.1038/s41467-021-26347-z ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Ivy Aneas ◽

Donna C. Decker ◽

Chanie L. Howard ◽

Débora R. Sobreira ◽

Noboru J. Sakabe ◽

...

Keyword(s):

Association Studies ◽

Regulatory Region ◽

Airway Epithelial Cells ◽

Genome Wide Association Studies ◽

Airway Epithelial ◽

Allele Specific ◽

Enhancer Blocking ◽

Underlying Mechanisms

AbstractGenome-wide association studies (GWAS) have implicated the IL33 locus in asthma, but the underlying mechanisms remain unclear. Here, we identify a 5 kb region within the GWAS-defined segment that acts as an enhancer-blocking element in vivo and in vitro. Chromatin conformation capture showed that this 5 kb region loops to the IL33 promoter, potentially regulating its expression. We show that the asthma-associated single nucleotide polymorphism (SNP) rs1888909, located within the 5 kb region, is associated with IL33 gene expression in human airway epithelial cells and IL-33 protein expression in human plasma, potentially through differential binding of OCT-1 (POU2F1) to the asthma-risk allele. Our data demonstrate that asthma-associated variants at the IL33 locus mediate allele-specific regulatory activity and IL33 expression, providing a mechanism through which a regulatory SNP contributes to genetic risk of asthma.

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Abstract 49: Adipose-Specific Knockout of Trib1 Reduces Plasma Lipids and Diet-Induced Insulin Resistance, and Increases Circulating Adiponectin

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvb.37.suppl_1.49 ◽

2017 ◽

Vol 37 (suppl_1) ◽

Author(s):

Mikhaila A Smith ◽

Jian Cui ◽

Sumeet A Kheterpal ◽

Daniel J Rader ◽

Robert C Bauer

Keyword(s):

Body Mass ◽

Plasma Lipids ◽

Association Studies ◽

Genome Wide Association Studies ◽

Genetic Associations ◽

Tissue Mass ◽

Fed State ◽

Plasma Adiponectin ◽

Metabolic Role

Tribbles-1 (TRIB1) was recently identified through genome-wide association studies as a novel mediator of plasma lipids and coronary artery disease in humans. While subsequent in vivo mouse work confirmed a role for hepatic TRIB1 in these associations, little is known about metabolic roles for extra-hepatic Trib1. Interestingly, SNPs near the TRIB1 gene are significantly associated with circulating adiponectin levels in humans, suggesting a metabolic role for adipose TRIB1 . To further investigate this, we generated adipose-specific Trib1 KO mice (Trib1_ASKO) by crossing Trib1 cKO mice to transgenic Adiponectin-Cre mice. Chow-fed Trib1_ASKO mice exhibited no differences in adipose tissue mass and overall body mass as compared to control littermates (N=8/group). However, Trib1_ASKO mice had reduced total (-16.9%, p <0.01), HDL (-16.7%, p <0.01), and non-HDL cholesterol (-17.3%, p =0.068), as well as plasma triglycerides (-28.6%, p <0.001) as compared to WT mice. Trib1_ASKO mice also had increased plasma adiponectin levels, a finding more pronounced in female mice (+33.3%, p <0.001) than in males (+16.4%, p =0.072). Despite this increase, transcript levels of adipoQ were moderately decreased in Trib1_ASKO mice, suggesting a post-transcriptional mode of regulation. Transcript and protein levels of C/EBPα, the best described target of Trib1 and a key regulator of adipogenesis, remained unchanged. To further investigate the metabolic consequences of adipose-specific KO of Trib1 , WT and Trib1_ASKO mice were fed high-fat diet (HFD, 45% kCal fat) for 12 weeks to induce obesity. HFD-fed Trib1_ASKO mice had reduced fasting plasma glucose (-22.3%, p <0.05), insulin (-38.2%, p <0.05), and glucose tolerance (-19.8% AUC, p <0.05) compared to control mice. Body mass and fat mass of HFD-fed Trib1_ASKO mice remained unchanged from WT, and the reductions in plasma lipids and increase in plasma adiponectin persisted in the HFD-fed state. In summary, we present here the first in vivo validation of the human genetic association between TRIB1 and plasma adiponectin, and provide evidence suggesting that adipose TRIB1 contributes to the genetic associations observed in humans between TRIB1 and multiple metabolic parameters.

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The VNTR of the AS3MT gene is associated with brain activations during a memory span task and their training-induced plasticity

Psychological Medicine ◽

10.1017/s0033291720000720 ◽

2020 ◽

pp. 1-6 ◽

Cited By ~ 1

Author(s):

Wan Zhao ◽

Qiumei Zhang ◽

Xiongying Chen ◽

Yang Li ◽

Xiaohong Li ◽

...

Keyword(s):

Neural Plasticity ◽

Large Scale ◽

Memory Span ◽

Association Studies ◽

Variable Number Tandem Repeat ◽

Brain Activation ◽

Head Movements ◽

Span Task ◽

Genome Wide Association Studies

Abstract Background The Arsenic (+3 oxidation state) methyltransferase (AS3MT) gene has been identified as a top risk gene for schizophrenia in several large-scale genome-wide association studies. A variable number tandem repeat (VNTR) of this gene is the most significant expression quantitative trait locus, but its role in brain activity in vivo is still unknown. Methods We first performed a functional magnetic resonance imaging (fMRI) scan of 101 healthy subjects during a memory span task, trained all subjects on an adaptive memory span task for 1 month, and finally performed another fMRI scan after the training. After excluding subjects with excessive head movements for one or more scanning sessions, data from 93 subjects were included in the final analyses. Results The VNTR was significantly associated with both baseline brain activation and training-induced changes in multiple regions including the prefrontal cortex and the anterior and posterior cingulate cortex. Additionally, it was associated with baseline brain activation in the striatum and the parietal cortex. All these results were corrected based on the family-wise error rate method across the whole brain at the peak level. Conclusions This study sheds light on the role of AS3MT gene variants in neural plasticity related to memory span training.

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Quantitative Proteomics of Human Heart Samples Collected In Vivo Reveal the Remodeled Protein Landscape of Dilated Left Atrium Without Atrial Fibrillation

Molecular & Cellular Proteomics ◽

10.1074/mcp.ra119.001878 ◽

2020 ◽

Vol 19 (7) ◽

pp. 1132-1144

Author(s):

Nora Linscheid ◽

Pi Camilla Poulsen ◽

Ida Dalgaard Pedersen ◽

Emilie Gregers ◽

Jesper Hastrup Svendsen ◽

...

Keyword(s):

Atrial Fibrillation ◽

Mitral Valve ◽

Protein Expression ◽

High Resolution Mass Spectrometry ◽

Association Studies ◽

Genomic Research ◽

Genome Wide Association Studies ◽

History Of ◽

The Impact

Genetic and genomic research has greatly advanced our understanding of heart disease. Yet, comprehensive, in-depth, quantitative maps of protein expression in hearts of living humans are still lacking. Using samples obtained during valve replacement surgery in patients with mitral valve prolapse (MVP), we set out to define inter-chamber differences, the intersect of proteomic data with genetic or genomic datasets, and the impact of left atrial dilation on the proteome of patients with no history of atrial fibrillation (AF).We collected biopsies from right atria (RA), left atria (LA) and left ventricle (LV) of seven male patients with mitral valve regurgitation with dilated LA but no history of AF. Biopsy samples were analyzed by high-resolution mass spectrometry (MS), where peptides were pre-fractionated by reverse phase high-pressure liquid chromatography prior to MS measurement on a Q-Exactive-HF Orbitrap instrument. We identified 7,314 proteins based on 130,728 peptides. Results were confirmed in an independent set of biopsies collected from three additional individuals. Comparative analysis against data from post-mortem samples showed enhanced quantitative power and confidence level in samples collected from living hearts. Our analysis, combined with data from genome wide association studies suggested candidate gene associations to MVP, identified higher abundance in ventricle for proteins associated with cardiomyopathies and revealed the dilated LA proteome, demonstrating differential representation of molecules previously associated with AF, in non-AF hearts.This is the largest dataset of cardiac protein expression from human samples collected in vivo. It provides a comprehensive resource that allows insight into molecular fingerprints of MVP and facilitates novel inferences between genomic data and disease mechanisms. We propose that over-representation of proteins in ventricle is consequent not to redundancy but to functional need, and conclude that changes in abundance of proteins known to associate with AF are not sufficient for arrhythmogenesis.

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Identification of atrial fibrillation associated genes and functional non-coding variants

Nature Communications ◽

10.1038/s41467-019-12721-5 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 16

Author(s):

Antoinette F. van Ouwerkerk ◽

Fernanda M. Bosada ◽

Karel van Duijvenboden ◽

Matthew C. Hill ◽

Lindsey E. Montefiori ◽

...

Keyword(s):

Atrial Fibrillation ◽

Genetic Variants ◽

Target Gene ◽

Target Genes ◽

Association Studies ◽

Regulatory Region ◽

Regulatory Elements ◽

Genome Wide Association Studies ◽

Cx43 Expression

Abstract Disease-associated genetic variants that lie in non-coding regions found by genome-wide association studies are thought to alter the functionality of transcription regulatory elements and target gene expression. To uncover causal genetic variants, variant regulatory elements and their target genes, here we cross-reference human transcriptomic, epigenomic and chromatin conformation datasets. Of 104 genetic variant regions associated with atrial fibrillation candidate target genes are prioritized. We optimize EMERGE enhancer prediction and use accessible chromatin profiles of human atrial cardiomyocytes to more accurately predict cardiac regulatory elements and identify hundreds of sub-threshold variants that co-localize with regulatory elements. Removal of mouse homologues of atrial fibrillation-associated regions in vivo uncovers a distal regulatory region involved in Gja1 (Cx43) expression. Our analyses provide a shortlist of genes likely affected by atrial fibrillation-associated variants and provide variant regulatory elements in each region that link genetic variation and target gene regulation, helping to focus future investigations.

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Control of Hemoglobin Switching by BCL11A.

Blood ◽

10.1182/blood.v114.22.5.5 ◽

2009 ◽

Vol 114 (22) ◽

pp. 5-5

Author(s):

Jian Xu ◽

Vijay G. Sankaran ◽

Yuko Fujiwara ◽

Stuart H. Orkin

Keyword(s):

Gene Silencing ◽

Conflicts Of Interest ◽

Fetal Liver ◽

Association Studies ◽

Globin Gene ◽

Clinical Severity ◽

Genome Wide Association Studies ◽

Erythroid Cells ◽

B Locus

Abstract Abstract 5 All vertebrates switch expression of globin chains during development. In humans b-like globins switch from embryonic to fetal to adult, whereas in the mouse a single switch from embryonic to adult occurs. The switch from human fetal (g) to adult (b) expression is especially critical in the b-hemoglobin disorders, such as sickle cell anemia and the b-thalassemias. Delay of the switch or reactivation of the fetal gene in the adult stage greatly ameliorates clinical severity. Despite intensive molecular studies of the human b-globin cluster over more than two decades, the proteins regulating the switch, and the mechanisms controlling the process, have been largely elusive. Recently, genome-wide association studies identified genetic variation at a chromosome 2 locus that correlates with the level of HbF in different populations. The most highly associated single nucleotide polymorphisms (SNPs) reside in an intron of the BCL11A gene, which encodes a zinc-finger repressor protein. Previously we showed that shRNA-mediated ex vivo knockdown of BCL11A in cultured human CD34-derived erythroid precursors leads to robust HbF expression, consistent with a role for BCL11A in maintaining g-genes in a silenced state in adult cells. To address in vivo roles of BCL11A either in development or in globin gene silencing in an intact individual, we have employed stringent genetic tests of function in mice that carry a complete human b-globin gene cluster as a yeast artificial chromosome transgene (b-locus mice). Knockout of BCL11A in mice leads to failure to silence the endogenous b-like embryonic genes in adult erythroid cells of the fetal liver (>2500-fold derepression). The ratio of human g to b globin RNA in the fetal liver of BCL11A knockout mice is inverted compared to controls, such that g constitutes >90% of the b-like human expression at embryonic day (E)14.5 and >75% at E18.5. These quantitatively striking findings indicate that BCL11A controls developmental silencing of g-globin gene expression. To address by formal genetics the contribution of BCL11A to g silencing in adult animals we have employed conditional inactivation of BCL11A through hematopoietic- and erythroid-specific Cre-alleles. These experiments reveal that BCL11A is also required in vivo for g-gene silencing in adults. We observed that human g-globin expression is persistently derepressed >2000-fold (as compared to littermate controls) in bone marrow erythroblasts of 15-20 week old b-locus mice upon erythroid-specific deletion of BCL11A. Taken together, these findings establish BCL11A as the first genetically validated transcriptional regulator of both developmental control of globin switching and silencing of g-globin expression in adults. The recognition of these roles for BCL11A now permits focused mechanistic studies of the switch. In human erythroid cells, BCL11A physically interacts with at least two corepressor complexes, Mi-2/NuRD and LSD1/CoREST, as well as the erythroid transcription factor GATA-1 and the HMG-box protein SOX6. Rather than binding to the promoters of the g- or b-globin genes as do these latter factors, BCL11A protein occupies the upstream locus control and g-d-intergenic regions of the b-globin cluster (as determined by high resolution ChIP-Chip analysis), suggesting that BCL11A mediates long-range interactions and/or reconfigures the locus during different stages. An in-depth mechanistic understanding of globin switching offers the prospect for design of target-based activation of HbF in adult erythroid cells of patients with hemoglobin disorders. Disclosures: No relevant conflicts of interest to declare.

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The Oncogenic Functions of Nicotinic Acetylcholine Receptors

Journal of Oncology ◽

10.1155/2016/9650481 ◽

2016 ◽

Vol 2016 ◽

pp. 1-9 ◽

Cited By ~ 29

Author(s):

Yue Zhao

Keyword(s):

Nicotinic Acetylcholine Receptors ◽

Mammalian Cells ◽

Acetylcholine Receptors ◽

Association Studies ◽

Nicotine Addiction ◽

Signal Pathways ◽

Genome Wide Association Studies ◽

Nicotinic Acetylcholine ◽

Lung Cancers ◽

Numerous Cell

Nicotinic acetylcholine receptors (nAChRs) are ion channels that are expressed in the cell membrane of all mammalian cells, including cancer cells. Recent findings suggest that nAChRs not only mediate nicotine addiction in the brain but also contribute to the development and progression of cancers directly induced by nicotine and its derived carcinogenic nitrosamines whereas deregulation of the nAChRs is observed in many cancers, and genome-wide association studies (GWAS) indicate that SNPs nAChRs associate with risks of lung cancers and nicotine addiction. Emerging evidences suggest nAChRs are posited at the central regulatory loops of numerous cell growth and prosurvival signal pathways and also mediate the synthesis and release of stimulatory and inhibitory neurotransmitters induced by their agonists. Thus nAChRs mediated cell signaling plays an important role in stimulating the growth and angiogenic and neurogenic factors and mediating oncogenic signal transduction during cancer development in a cell type specific manner. In this review, we provide an integrated view of nAChRs signaling in cancer, heightening on the oncogenic properties of nAChRs that may be targeted for cancer treatment.

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