scholarly journals Modifiers of CAG/CTG Repeat Instability: Insights from Mammalian Models

2021 ◽  
Vol 10 (1) ◽  
pp. 123-148
Author(s):  
Vanessa C. Wheeler ◽  
Vincent Dion
Keyword(s):  
Age Of Onset ◽  
Association Studies ◽  
Repeat Expansion ◽  
Model Systems ◽  
Genome Wide Association Studies ◽  
Repeat Instability ◽  
Pathway Crosstalk ◽  
Genomic Locations ◽  
Exciting Area ◽  
Ctg Repeat

At fifteen different genomic locations, the expansion of a CAG/CTG repeat causes a neurodegenerative or neuromuscular disease, the most common being Huntington’s disease and myotonic dystrophy type 1. These disorders are characterized by germline and somatic instability of the causative CAG/CTG repeat mutations. Repeat lengthening, or expansion, in the germline leads to an earlier age of onset or more severe symptoms in the next generation. In somatic cells, repeat expansion is thought to precipitate the rate of disease. The mechanisms underlying repeat instability are not well understood. Here we review the mammalian model systems that have been used to study CAG/CTG repeat instability, and the modifiers identified in these systems. Mouse models have demonstrated prominent roles for proteins in the mismatch repair pathway as critical drivers of CAG/CTG instability, which is also suggested by recent genome-wide association studies in humans. We draw attention to a network of connections between modifiers identified across several systems that might indicate pathway crosstalk in the context of repeat instability, and which could provide hypotheses for further validation or discovery. Overall, the data indicate that repeat dynamics might be modulated by altering the levels of DNA metabolic proteins, their regulation, their interaction with chromatin, or by direct perturbation of the repeat tract. Applying novel methodologies and technologies to this exciting area of research will be needed to gain deeper mechanistic insight that can be harnessed for therapies aimed at preventing repeat expansion or promoting repeat contraction.

scholarly journals Sept8/SEPTIN8 involvement in cellular structure and kidney damage is identified by genetic mapping and a novel human tubule hypoxic model

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gregory R. Keele ◽  
Jeremy W. Prokop ◽  
Hong He ◽  
Katie Holl ◽  
John Littrell ◽  
...  
Keyword(s):  
Complex Traits ◽  
Genetic Model ◽  
Association Studies ◽  
Model Systems ◽  
Linear Mixed Effect Model ◽  
Genome Wide Association Studies ◽  
Tubulointerstitial Injury ◽  
Heritable Variation ◽  
Mixed Effect

AbstractChronic kidney disease (CKD), which can ultimately progress to kidney failure, is influenced by genetics and the environment. Genes identified in human genome wide association studies (GWAS) explain only a small proportion of the heritable variation and lack functional validation, indicating the need for additional model systems. Outbred heterogeneous stock (HS) rats have been used for genetic fine-mapping of complex traits, but have not previously been used for CKD traits. We performed GWAS for urinary protein excretion (UPE) and CKD related serum biochemistries in 245 male HS rats. Quantitative trait loci (QTL) were identified using a linear mixed effect model that tested for association with imputed genotypes. Candidate genes were identified using bioinformatics tools and targeted RNAseq followed by testing in a novel in vitro model of human tubule, hypoxia-induced damage. We identified two QTL for UPE and five for serum biochemistries. Protein modeling identified a missense variant within Septin 8 (Sept8) as a candidate for UPE. Sept8/SEPTIN8 expression increased in HS rats with elevated UPE and tubulointerstitial injury and in the in vitro hypoxia model. SEPTIN8 is detected within proximal tubule cells in human kidney samples and localizes with acetyl-alpha tubulin in the culture system. After hypoxia, SEPTIN8 staining becomes diffuse and appears to relocalize with actin. These data suggest a role of SEPTIN8 in cellular organization and structure in response to environmental stress. This study demonstrates that integration of a rat genetic model with an environmentally induced tubule damage system identifies Sept8/SEPTIN8 and informs novel aspects of the complex gene by environmental interactions contributing to CKD risk.

scholarly journals Genetic Variability in Molecular Pathways Implicated in Alzheimer's Disease: A Comprehensive Review

2021 ◽  
Vol 13 ◽  
Author(s):  
David Vogrinc ◽  
Katja Goričar ◽  
Vita Dolžan
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Age Of Onset ◽  
Association Studies ◽  
The Elderly ◽  
Gene Clustering ◽  
Molecular Pathways ◽  
Genome Wide Association Studies ◽  
Cellular Processes ◽  
Increased Risk

Alzheimer's disease (AD) is a complex neurodegenerative disease, affecting a significant part of the population. The majority of AD cases occur in the elderly with a typical age of onset of the disease above 65 years. AD presents a major burden for the healthcare system and since population is rapidly aging, the burden of the disease will increase in the future. However, no effective drug treatment for a full-blown disease has been developed to date. The genetic background of AD is extensively studied; numerous genome-wide association studies (GWAS) identified significant genes associated with increased risk of AD development. This review summarizes more than 100 risk loci. Many of them may serve as biomarkers of AD progression, even in the preclinical stage of the disease. Furthermore, we used GWAS data to identify key pathways of AD pathogenesis: cellular processes, metabolic processes, biological regulation, localization, transport, regulation of cellular processes, and neurological system processes. Gene clustering into molecular pathways can provide background for identification of novel molecular targets and may support the development of tailored and personalized treatment of AD.

Gene Co-Expression Network Analysis Implicates microRNA Processing in Parkinson’s Disease Pathogenesis

2018 ◽  
Vol 18 (4) ◽  
pp. 191-199 ◽  
Author(s):  
Jason A. Chen
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Network Analysis ◽  
Statistical Power ◽  
Association Studies ◽  
Model Systems ◽  
Specific Cell ◽  
Genome Wide Association Studies ◽  
Microrna Processing ◽  
Highly Correlated

Background: Recent advances in genetics have provided insights into important inherited causes of Parkinson’s disease (PD), but the underlying biological mechanisms are still incompletely understood. Gene expression studies have pointed toward the dysregulation of neuroinflammation, mitochondrial function, and protein degradation pathways. Objective: We aimed to identify groups of dysregulated genes in PD. Methods: In order to increase statistical power and control for potential confounders, we re-analyzed transcriptomic data from PD patients and model systems, integrating additional genomic data using a systems biology approach. Using weighted gene co-expression network analysis, we partitioned genes into co-expressed modules. Results: One co-expression module, M13, had an expression trajectory that was highly correlated with PD, was not characterized by any specific cell type markers, and was enriched in PD genes identified by genome-wide association studies. Genes within M13 seemed to be related to global microRNA biogenesis, and DICER1 and AGO3 were highly connected within the module. The NUCKS1 gene, previously identified as part of the PARK16 locus, was also a hub gene within M13. Conclusion: These results suggest that microRNA processing and function may play a role in the pathogenesis of PD, and thus may represent a useful target for future drug development.

scholarly journals Alzheimer’s Disease risk modifier genes do not impact tau aggregate uptake, seeding or maintenance in cell models

2019 ◽  
Author(s):  
Sourav Kolay ◽  
Marc I. Diamond
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Gene Knockout ◽  
Association Studies ◽  
Modifier Genes ◽  
Model Systems ◽  
Genome Wide Association Studies ◽  
Tau Pathology ◽  
Risk Modifier ◽  
Tau Aggregate

ABSTRACTAlzheimer’s disease (AD) afflicts millions of people worldwide, and is caused by accumulated amyloid beta and tau pathology. Progression of tau pathology in AD may utilize prion mechanisms of propagation in which pathological tau aggregates released from one cell are taken up by neighboring or connected cells and act as templates for their own replication, a process termed “seeding.” In cultured cells we have modeled various aspects of pathological tau propagation, including uptake of aggregates, induced (naked) seeding by exogenous aggregates, seeding caused by Lipofectamine-mediated delivery to the cell interior, and chronic maintenance of aggregates in cells through mother-to-daughter transmission. The factors that regulate these processes are not well understood, and we hypothesized that AD risk modifier genes might play a role. We identified 22 genes strongly linked to AD via meta-analysis of genome-wide association studies (GWAS). We used CRISPR/Cas-9 to individually knock out each in gene in HEK293T cells, and verified disruption using genomic sequencing. We then tested the effect of gene knockout in tau aggregate uptake, naked and Lipofectamine-mediated seeding, and aggregate maintenance in cultured cell lines. GWAS gene knockouts had no effect on these models of tau pathology. With obvious caveats due to the model systems used, these results imply that these 22 AD risk modifier genes do not directly modulate tau uptake, seeding, or aggregate maintenance.

What Genetics Tells us About the Causes and Mechanisms of Parkinson's Disease

2011 ◽  
Vol 91 (4) ◽  
pp. 1161-1218 ◽  
Author(s):  
Olga Corti ◽  
Suzanne Lesage ◽  
Alexis Brice
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Late Onset ◽  
Association Studies ◽  
Lewy Bodies ◽  
Mendelian Inheritance ◽  
Model Systems ◽  
Motor Disorder ◽  
Genome Wide Association Studies ◽  
New Genes

Parkinson's disease (PD) is a common motor disorder of mysterious etiology. It is due to the progressive degeneration of the dopaminergic neurons of the substantia nigra and is accompanied by the appearance of intraneuronal inclusions enriched in α-synuclein, the Lewy bodies. It is becoming increasingly clear that genetic factors contribute to its complex pathogenesis. Over the past decade, the genetic basis of rare PD forms with Mendelian inheritance, representing no more than 10% of the cases, has been investigated. More than 16 loci and 11 associated genes have been identified so far; genome-wide association studies have provided convincing evidence that polymorphic variants in these genes contribute to sporadic PD. The knowledge acquired of the functions of their protein products has revealed pathways of neurodegeneration that may be shared between inherited and sporadic PD. An impressive set of data in different model systems strongly suggest that mitochondrial dysfunction plays a central role in clinically similar, early-onset autosomal recessive PD forms caused by parkin and PINK1, and possibly DJ-1 gene mutations. In contrast, α-synuclein accumulation in Lewy bodies defines a spectrum of disorders ranging from typical late-onset PD to PD dementia and including sporadic and autosomal dominant PD forms due to mutations in SCNA and LRRK2. However, the pathological role of Lewy bodies remains uncertain, as they may or may not be present in PD forms with one and the same LRRK2 mutation. Impairment of autophagy-based protein/organelle degradation pathways is emerging as a possible unifying but still fragile pathogenic scenario in PD. Strengthening these discoveries and finding other convergence points by identifying new genes responsible for Mendelian forms of PD and exploring their functions and relationships are the main challenges of the next decade. It is also the way to follow to open new promising avenues of neuroprotective treatment for this devastating disorder.

Identifying Novel Psoriatic Disease Drug Targets Using a Genetics-Based Priority Index Pipeline

2021 ◽  
pp. 247553032110260
Author(s):  
Audrey Bui ◽  
Jared Liu ◽  
Julie Hong ◽  
Edward Hadeler ◽  
Megan Mosca ◽  
...  
Keyword(s):  
Psoriatic Arthritis ◽  
Drug Targets ◽  
Association Studies ◽  
Therapeutic Targets ◽  
Genome Wide Association Studies ◽  
Priority Index ◽  
Psoriatic Disease ◽  
Genome Wide ◽  
Pathway Crosstalk ◽  
Potential Drug Targets

Background: Despite numerous genome-wide association studies conducted in psoriasis and psoriatic arthritis, only a small fraction of the identified genes has been therapeutically targeted. Objective: We sought to identify and analyze potential therapeutic targets for psoriasis and psoriatic arthritis (PsA) using the priority index (Pi), a genetics-dependent drug target prioritization approach. Methods: Significant genetic variants from GWAS for psoriasis, PsA, and combined psoriatic disease were annotated and run through the Pi pipeline. Potential drug targets were identified based on genomic predictors, annotation predictors, pathway enrichment, and pathway crosstalk. Results: Several gene targets were identified for psoriasis and PsA that demonstrated biological associations to their respective diseases. Some are currently being explored as potential therapeutic targets (i.e. ICAM1, NF-kB, REV3 L, ADRA1B for psoriasis; CCL11 for PsA); others have not yet been investigated (i.e. LNPEP, LCE3 for psoriasis; UBLCP1 for PsA). Additionally, many nodal points of potential intervention were identified as promising therapeutic targets. Of these, some are currently being studied such as TYK2 for psoriasis, and others have yet to be explored (i.e. PPP2CA, YAP1, PI3 K, AKT, FOXO1, RELA, CSF2, IFNGR1, IFNGR2 for psoriasis; GNAQ, PLCB1, GNAI2 for PsA). Conclusion: Through Pi, we identified data-driven candidate therapeutic gene targets and pathways for psoriasis and PsA. Given the sparse PsA specific genetic studies and PsA specific drug targets, this analysis could prove to be particularly valuable in the pipeline for novel psoriatic therapies.

scholarly journals Pairwise effects between lipid GWAS genes modulate lipid plasma levels and cellular uptake

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Magdalena Zimoń ◽  
Yunfeng Huang ◽  
Anthi Trasta ◽  
Aliaksandr Halavatyi ◽  
Jimmy Z. Liu ◽  
...  
Keyword(s):  
Complex Traits ◽  
Human Genetics ◽  
Association Studies ◽  
Large Population ◽  
Plasma Lipid ◽  
Model Systems ◽  
Lipid Lowering ◽  
Genome Wide Association Studies ◽  
Lipid Levels ◽  
Gene Pairs

AbstractComplex traits are characterized by multiple genes and variants acting simultaneously on a phenotype. However, studying the contribution of individual pairs of genes to complex traits has been challenging since human genetics necessitates very large population sizes, while findings from model systems do not always translate to humans. Here, we combine genetics with combinatorial RNAi (coRNAi) to systematically test for pairwise additive effects (AEs) and genetic interactions (GIs) between 30 lipid genome-wide association studies (GWAS) genes. Gene-based burden tests from 240,970 exomes show that in carriers with truncating mutations in both, APOB and either PCSK9 or LPL (“human double knock-outs”) plasma lipid levels change additively. Genetics and coRNAi identify overlapping AEs for 12 additional gene pairs. Overlapping GIs are observed for TOMM40/APOE with SORT1 and NCAN. Our study identifies distinct gene pairs that modulate plasma and cellular lipid levels primarily via AEs and nominates putative drug target pairs for improved lipid-lowering combination therapies.

scholarly journals Accounting for age-of-onset and family history improves power in genome-wide association studies

2021 ◽  
Author(s):  
Emil M Pedersen ◽  
Esben Agerbo ◽  
Oleguer Plana-Ripoll ◽  
Jakob Grove ◽  
Julie W. Dreier ◽  
...  
Keyword(s):  
Family History ◽  
Age Of Onset ◽  
Threshold Model ◽  
Association Studies ◽  
Case Control ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Large Power ◽  
Standard Case ◽  
Genome Wide

AbstractGenome-wide association studies (GWAS) have revolutionized human genetics, allowing researchers to identify thousands of disease-related genes and possible drug targets. However, case-control status does not account for the fact that not all controls may have lived through their period of risk for the disorder of interest. This can be quantified by examining the age-of-onset distribution and the age of the controls or the age-of-onset for cases. The age-of-onset distribution may also depend on information such as sex and birth year. In addition, family history is not routinely included in the assessment of control status. Here we present LT-FH++, an extension of the liability threshold model conditioned on family history (LT-FH), that jointly accounts for age-of-onset and sex, as well as family history. Using simulations, we show that, when family history and the age-of-onset distribution are available, the proposed approach yields large power gains over both LT-FH and genome-wide association study by proxy (GWAX). We applied our method to four psychiatric disorders available in the iPSYCH data, and to mortality in the UK Biobank, finding 20 genome-wide significant associations with LT-FH++, compared to 10 for LT-FH and 8 for a standard case-control GWAS. As more genetic data with linked electronic health records become available to researchers, we expect methods that account for additional health information, such as LT-FH++, to become even more beneficial.

Activation of Vascular Cells by Microparticles and Other Danger Signals Via the CD36 Scavenger Receptor

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. SCI-12-SCI-12
Author(s):  
Roy L. Silverstein
Keyword(s):  
Signaling Pathways ◽  
Vessel Wall ◽  
Association Studies ◽  
Oxidant Stress ◽  
Scavenger Receptor ◽  
Model Systems ◽  
Foam Cell Formation ◽  
Genome Wide Association Studies ◽  
Antioxidant Genes ◽  
Danger Signals

Abstract SCI-12 Clinically significant thrombotic events are common complications of many systemic diseases associated with chronic inflammation, including atherosclerosis, diabetes mellitus, cancer, and chronic autoimmune rheumatologic disorders. Many of these potentially life-threatening thrombi occur in the arterial circulation and likely relate to inappropriate platelet activation and/or vessel wall injury. CD36 is a type B scavenger receptor expressed on platelets, monocytes, microvascular endothelial cells (MVEC), and vascular smooth muscle cells (VSMC) that recognizes and responds to endogenous and exogenous “danger signals” including advanced glycated proteins (AGE), microbial cell wall components, and oxidized phospholipids that are found on the surface of oxidized LDL (oxLDL) and cell-derived microparticles (MP). Mouse FeCl3 thrombosis model systems revealed that genetic deletion of cd36 rescued the prothrombotic phenotypes associated with hyperlipidemia, oxidant stress, or diabetes/hyperglycemia. Interestingly, compared to wild type mice, fewer MP were incorporated into thrombi formed in cd36 null mice after FeCl3-induced vascular injury. Cd36 deficiency also provides partial protection from atherosclerosis in experimental mouse models. On a cellular level, the prothrombotic, pro-atherogenic, and anti-angiogenic activities of CD36 relate to ligand-dependent alterations of platelet, macrophage, and vessel wall cellular functions. For example, CD36 binding to MP, AGE, or oxLDL “sensitizes” platelets to activation by low doses of agonists, such as ADP. In macrophages, CD36 interactions with oxLDL leads to lipid internalization, foam cell formation, and inhibition of migration. In the vessel wall CD36 promotes VSMC oxidant stress and MVEC apoptosis. Mechanistically, CD36 transmits intracellular signals in response to ligand engagement that involve recruitment of specific Src family kinases to its short cytoplasmic tail, with subsequent activation of specific MAP kinase pathways and Vav family guanine nucleotide exchange factors. These signaling pathways remain incompletely understood, but impact many important cellular processes, including cytoskeletal dynamics, cell polarity, transcription of antioxidant genes controlled by the transcription factor Nrf2, and activation of NADPH oxidases. Specific components of CD36 signaling pathways depend on the cellular context and in some cases involve engagement of co-receptors, including integrins, TLRs, and tetraspanins. Recent targeted genome-wide association studies suggest that cd36 polymorphisms associate with CD36 expression levels on platelets and monocytes as well as with risk of thrombotic, metabolic, and atherosclerotic disorders. Targeting CD36 may therefore provide novel approaches to many important human vascular diseases. Disclosures: No relevant conflicts of interest to declare.

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