Implication of sestrin3 in epilepsy and its comorbidities

Abstract Epilepsy is a serious neurological disorder affecting about 1% of the population worldwide. Epilepsy may arise as a result of acquired brain injury, or as a consequence of genetic predisposition. To date, genome-wide association studies and exome sequencing approaches have provided limited insights into the mechanisms of acquired brain injury. We have previously reported a pro-epileptic gene network, which is conserved across species, encoding inflammatory processes and positively regulated by sestrin 3 (SESN3). In this study, we investigated the phenotype of SESN3 knock-out rats in terms of susceptibility to seizures and observed a significant delay in status epilepticus onset in SESN3 knock-out compared to control rats. This finding confirms previous in vitro and in vivo evidence indicating that SESN3 may favor occurrence and/or severity of seizures. We also analyzed the phenotype of SESN3 knock-out rats for common comorbidities of epilepsy, i.e. anxiety, depression, and cognitive impairment. SESN3 knock-out rats proved less anxious compared to control rats in a selection of behavioral tests. Taken together, the present results suggest that SESN3 may regulate mechanisms involved in the pathogenesis of epilepsy and its comorbidities.

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Humanized TREM2 mice reveal microglia-intrinsic and -extrinsic effects of R47H polymorphism

Journal of Experimental Medicine ◽

10.1084/jem.20171529 ◽

2018 ◽

Vol 215 (3) ◽

pp. 745-760 ◽

Cited By ~ 86

Author(s):

Wilbur M. Song ◽

Satoru Joshita ◽

Yingyue Zhou ◽

Tyler K. Ulland ◽

Susan Gilfillan ◽

...

Keyword(s):

Late Onset ◽

Association Studies ◽

Amyloid Β ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Soluble Trem2 ◽

The Common ◽

Late Onset Dementia

Alzheimer’s disease (AD) is a neurodegenerative disease that causes late-onset dementia. The R47H variant of the microglial receptor TREM2 triples AD risk in genome-wide association studies. In mouse AD models, TREM2-deficient microglia fail to proliferate and cluster around the amyloid-β plaques characteristic of AD. In vitro, the common variant (CV) of TREM2 binds anionic lipids, whereas R47H mutation impairs binding. However, in vivo, the identity of TREM2 ligands and effect of the R47H variant remain unknown. We generated transgenic mice expressing human CV or R47H TREM2 and lacking endogenous TREM2 in the 5XFAD AD model. Only the CV transgene restored amyloid-β–induced microgliosis and microglial activation, indicating that R47H impairs TREM2 function in vivo. Remarkably, soluble TREM2 was found on neurons and plaques in CV- but not R47H-expressing 5XFAD brains, although in vitro CV and R47H were shed similarly via Adam17 proteolytic activity. These results demonstrate that TREM2 interacts with neurons and plaques duing amyloid-β accumulation and R47H impairs this interaction.

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PICALM modulates autophagy activity and tau accumulation

Nature Communications ◽

10.1038/ncomms5998 ◽

2014 ◽

Vol 5 (1) ◽

Cited By ~ 123

Author(s):

Kevin Moreau ◽

Angeleen Fleming ◽

Sara Imarisio ◽

Ana Lopez Ramirez ◽

Jacob L. Mercer ◽

...

Keyword(s):

Genetic Risk ◽

Association Studies ◽

Genome Wide Association Studies ◽

Transgenic Models ◽

Autophagosome Formation ◽

Genome Wide ◽

Autophagy Pathway ◽

Autophagy Activity

Abstract Genome-wide association studies have identified several loci associated with Alzheimer’s disease (AD), including proteins involved in endocytic trafficking such as PICALM/CALM (phosphatidylinositol binding clathrin assembly protein). It is unclear how these loci may contribute to AD pathology. Here we show that CALM modulates autophagy and alters clearance of tau, a protein which is a known autophagy substrate and which is causatively linked to AD, both in vitro and in vivo. Furthermore, altered CALM expression exacerbates tau-mediated toxicity in zebrafish transgenic models. CALM influences autophagy by regulating the endocytosis of SNAREs, such as VAMP2, VAMP3 and VAMP8, which have diverse effects on different stages of the autophagy pathway, from autophagosome formation to autophagosome degradation. This study suggests that the AD genetic risk factor CALM modulates autophagy, and this may affect disease in a number of ways including modulation of tau turnover.

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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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Genetic Analysis of Osteoblast Activity Identifies Zbtb40 as a Regulator of Osteoblast Activity and Bone Mass

10.1101/828525 ◽

2019 ◽

Author(s):

Madison L. Doolittle ◽

Gina M Calabrese ◽

Larry D. Mesner ◽

Dana A. Godfrey ◽

Robert D. Maynard ◽

...

Keyword(s):

Bone Formation ◽

Genetic Basis ◽

Association Studies ◽

Genome Wide Association Studies ◽

Loss Of Function ◽

Mineral Density ◽

Osteoblast Activity ◽

Genome Wide ◽

Increased Risk

ABSTRACTOsteoporosis is a genetic disease characterized by progressive reductions in bone mineral density (BMD) leading to an increased risk of fracture. Over the last decade, genome-wide association studies (GWASs) have identified over 1000 associations for BMD. However, as a phenotype BMD is challenging as bone is a multicellular tissue affected by both local and systemic physiology. Here, we focused on a single component of BMD, osteoblast-mediated bone formation in mice, and identified associations influencing osteoblast activity on mouse Chromosomes (Chrs) 1, 4, and 17. The locus on Chr. 4 was in an intergenic region between Wnt4 and Zbtb40, homologous to a locus for BMD in humans. We tested both Wnt4 and Zbtb40 for a role in osteoblast activity and BMD. Knockdown of Zbtb40, but not Wnt4, in osteoblasts drastically reduced mineralization. Additionally, loss-of-function mouse models for both genes exhibited reduced BMD. Our results highlight that investigating the genetic basis of in vitro osteoblast mineralization can be used to identify genes impacting bone formation and BMD.

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An integrated platform to systematically identify causal variants and genes for polygenic human traits

10.1101/813618 ◽

2019 ◽

Cited By ~ 3

Author(s):

Damien J. Downes ◽

Ron Schwessinger ◽

Stephanie J. Hill ◽

Lea Nussbaum ◽

Caroline Scott ◽

...

Keyword(s):

Genetic Variants ◽

Association Studies ◽

Significant Proportion ◽

Genome Wide Association Studies ◽

Effector Genes ◽

Genome Wide ◽

Common Genetic Variants ◽

Integrated Platform ◽

Causal Variants

ABSTRACTGenome-wide association studies (GWAS) have identified over 150,000 links between common genetic variants and human traits or complex diseases. Over 80% of these associations map to polymorphisms in non-coding DNA. Therefore, the challenge is to identify disease-causing variants, the genes they affect, and the cells in which these effects occur. We have developed a platform using ATAC-seq, DNaseI footprints, NG Capture-C and machine learning to address this challenge. Applying this approach to red blood cell traits identifies a significant proportion of known causative variants and their effector genes, which we show can be validated by direct in vivo modelling.

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Complex polymorphisms in endocytosis genes suggest alpha-cyclodextrin as a treatment for breast cancer

10.1101/152405 ◽

2017 ◽

Author(s):

Knut M. Wittkowski ◽

Christina Dadurian ◽

Martin P. Seybold ◽

Han Sang Kim ◽

Ayuko Hoshino ◽

...

Keyword(s):

Breast Cancer ◽

Animal Studies ◽

Association Studies ◽

Treatment Options ◽

Cell Cycle Control ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

Estrogen Receptor Positive

AbstractMost breast cancer deaths are caused by metastasis and treatment options beyond radiation and cytotoxic drugs, which have severe side effects, and hormonal treatments, which are or become ineffective for many patients, are urgently needed. This study reanalyzed existing data from three genome-wide association studies (GWAS) using a novel computational biostatistics approach (muGWAS), which had been validated in studies of 600–2000 subjects in epilepsy and autism. MuGWAS jointly analyzes several neighboring single nucleotide polymorphisms while incorporating knowledge about genetics of heritable diseases into the statistical method and about GWAS into the rules for determining adaptive genome-wide significance.Results from three independent GWAS of 1000–2000 subjects each, which were made available under the National Institute of Health’s “Up For A Challenge” (U4C) project, not only confirmed cell-cycle control and receptor/AKT signaling, but, for the first time in breast cancer GWAS, also consistently identified many genes involved in endo-/exocytosis (EEC), most of which had already been observed in functional and expression studies of breast cancer. In particular, the findings include genes that translocate (ATP8A1, ATP8B1, ANO4, ABCA1) and metabolize (AGPAT3, AGPAT4, DGKQ, LPPR1) phospholipids entering the phosphatidylinositol cycle, which controls EEC. These novel findings suggest scavenging phospholipids via alpha-cyclodextrins (αCD) as a novel intervention to control local spread of cancer, packaging of exosomes (which prepare distant microenvironment for organ-specific metastases), and endocytosis of β1 integrins (which are required for spread of metastatic phenotype and mesenchymal migration of tumor cells).Beta-cyclodextrins (βCD) have already been shown to be effective inin vitroand animal studies of breast cancer, but exhibits cholesterol-related ototoxicity. The smaller αCDs also scavenges phospholipids, but cannot fit cholesterol. Anin-vitrostudy presented here confirms hydroxypropyl (HP)-αCD to be twice as effective as HPβCD against migration of human cells of both receptor negative and estrogen-receptor positive breast cancer.If the previous successful animal studies with βCDs are replicated with the safer and more effective αCDs, clinical trials of adjuvant treatment with αCDs are warranted. Ultimately, all breast cancer are expected to benefit from treatment with HPαCD, but women with triplenegative breast cancer (TNBC) will benefit most, because they have fewer treatment options and their cancer advances more aggressively.

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How to discover a metabolic pathway? An update on gene identification in aliphatic glucosinolate biosynthesis, regulation and transport

Biological Chemistry ◽

10.1515/hsz-2013-0286 ◽

2014 ◽

Vol 395 (5) ◽

pp. 529-543 ◽

Cited By ~ 26

Author(s):

Lea Møller Jensen ◽

Barbara Ann Halkier ◽

Meike Burow

Keyword(s):

Association Studies ◽

Phylogenetic Analyses ◽

Lessons Learned ◽

Genome Wide Association ◽

Gene Identification ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Aliphatic Glucosinolates ◽

Biosynthesis Regulation

Abstract Identification of enzymes, regulators and transporters involved in different metabolic processes is the foundation to understand how organisms function. There are, however, many difficulties in identifying candidate genes as well as in proving their in vivo roles. In this review, we describe different approaches utilized in Arabidopsis thaliana to identify gene candidates and experiments required to prove the function of a given candidate. For example, we use the production of methionine-derived aliphatic glucosinolates that represent major defence compounds in A. thaliana. Nearly all biosynthetic genes, as well as the first sets of regulators and transporters, have been identified. An array of approaches, i.e. classical mapping, quantitative trait loci (QTL) mapping, eQTL mapping, co-expression, genome wide association studies (GWAS), mutant screens and phylogenetic analyses, has been exploited to increase the number of identified genes. Here we summarize the lessons learned from the different approaches used over the years with the aim to help designing and combining new approaches in the future.

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“Zebrafishing” for Novel Genes Relevant to the Glomerular Filtration Barrier

BioMed Research International ◽

10.1155/2013/658270 ◽

2013 ◽

Vol 2013 ◽

pp. 1-12 ◽

Cited By ~ 29

Author(s):

Nils Hanke ◽

Lynne Staggs ◽

Patricia Schroder ◽

Jennifer Litteral ◽

Susanne Fleig ◽

...

Keyword(s):

Glomerular Filtration ◽

Barrier Function ◽

Association Studies ◽

Genome Wide Association Studies ◽

Glomerular Filtration Barrier ◽

Novel Genes ◽

Zebrafish Model ◽

Filtration Barrier

Data for genes relevant to glomerular filtration barrier function or proteinuria is continually increasing in an era of microarrays, genome-wide association studies, and quantitative trait locus analysis. Researchers are limited by published literature searches to select the most relevant genes to investigate. High-throughput cell cultures and otherin vitrosystems ultimately need to demonstrate proof in anin vivomodel. Generating mammalian models for the genes of interest is costly and time intensive, and yields only a small number of test subjects. These models also have many pitfalls such as possible embryonic mortality and failure to generate phenotypes or generate nonkidney specific phenotypes. Here we describe anin vivozebrafish model as a simple vertebrate screening system to identify genes relevant to glomerular filtration barrier function. Using our technology, we are able to screen entirely novel genes in 4–6 weeks in hundreds of live test subjects at a fraction of the cost of a mammalian model. Our system produces consistent and reliable evidence for gene relevance in glomerular kidney disease; the results then provide merit for further analysis in mammalian models.

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Contributions of Function-Altering Variants in Genes Implicated in Pubertal Timing and Body Mass for Self-Limited Delayed Puberty

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/jc.2017-02147 ◽

2017 ◽

Vol 103 (2) ◽

pp. 649-659 ◽

Cited By ~ 10

Author(s):

Sasha R Howard ◽

Leonardo Guasti ◽

Ariel Poliandri ◽

Alessia David ◽

Claudia P Cabrera ◽

...

Keyword(s):

Body Mass ◽

Rare Variants ◽

Association Studies ◽

Delayed Puberty ◽

Age At Menarche ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Whole Exome ◽

Timing Of Puberty

Abstract Context Self-limited delayed puberty (DP) is often associated with a delay in physical maturation, but although highly heritable the causal genetic factors remain elusive. Genome-wide association studies of the timing of puberty have identified multiple loci for age at menarche in females and voice break in males, particularly in pathways controlling energy balance. Objective/Main Outcome Measures We sought to assess the contribution of rare variants in such genes to the phenotype of familial DP. Design/Patients We performed whole-exome sequencing in 67 pedigrees (125 individuals with DP and 35 unaffected controls) from our unique cohort of familial self-limited DP. Using a whole-exome sequencing filtering pipeline one candidate gene [fat mass and obesity–associated gene (FTO)] was identified. In silico, in vitro, and mouse model studies were performed to investigate the pathogenicity of FTO variants and timing of puberty in FTO+/− mice. Results We identified potentially pathogenic, rare variants in genes in linkage disequilibrium with genome-wide association studies of age at menarche loci in 283 genes. Of these, five genes were implicated in the control of body mass. After filtering for segregation with trait, one candidate, FTO, was retained. Two FTO variants, found in 14 affected individuals from three families, were also associated with leanness in these patients with DP. One variant (p.Leu44Val) demonstrated altered demethylation activity of the mutant protein in vitro. Fto+/− mice displayed a significantly delayed timing of pubertal onset (P < 0.05). Conclusions Mutations in genes implicated in body mass and timing of puberty in the general population may contribute to the pathogenesis of self-limited DP.

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Alzheimer's disease-associated P460L mutation in ephrin receptor type A1 (EphA1) leads to dysregulated Rho-GTPase signaling

10.1101/2021.06.17.448790 ◽

2021 ◽

Author(s):

Yoon Kim ◽

Gorka Lasso ◽

Hardik Patel ◽

Badri Vardarajan ◽

Ismael Santa-Maria ◽

...

Keyword(s):

Rho Gtpase ◽

Late Onset ◽

Association Studies ◽

Genome Wide Association Studies ◽

Genome Wide ◽

The Brain ◽

Receptor Tyrosine Kinase Family

Recently, late onset AD (LOAD) genome-wide association studies identified EphA1, a member of receptor tyrosine kinase family (RTK) as a disease associated loci. In the follow-up study where 3 independent LOAD cohorts were performed, a P460L coding mutation in EphA1 loci showed a significant association with LOAD. However, the role of EphA1 and P460L mutant EphA1 in AD is not fully understood. We have characterized this mutation biophysically and biochemically. Our structural in silico model and in vitro biochemical analysis demonstrate that EphA1-P460L mutation makes the receptor constitutively active suggesting a gain-of-toxic function leading to chronic EphA1 signaling in the brain. Moreover, we report that the EphA1 P460L variant triggers Rho-GTPase signaling dysregulation that could potentially contribute to spine morphology abnormalities and synaptic dysfunction observed in AD pathology.

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