Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Combining Human Genetics of Multiple Sclerosis with Oxidative Stress Phenotype for Drug Repositioning.

ABSTRACT: In multiple sclerosis (MS), oxidative stress (OS) is implicated in the neurodegenerative processes that occur from the beginning of the disease. Unchecked OS initiates a vicious circle caused by its crosstalk with inflammation, leading to demyelination, axonal damage and neuronal loss. The failure of MS antioxidant therapies relying on the use of endogenous and natural compounds drives the application of novel approaches to assess target relevance to the disease prior to preclinical testing of new drug candidates. To identify drugs that can act as regulators of intracellular oxidative homeostasis, we applied an in silico approach that links genome-wide MS associations and molecular quantitative trait loci (QTLs) to proteins of the OS pathway. We found 10 drugs with both central nervous system and oral bioavailability, targeting five out of the 21 top-scoring hits, including arginine methyltransferase (CARM1), which was first linked to MS. In particular, the direction of brain expression QTLs for CARM1 and protein kinase MAPK1 enabled us to select BIIB021 and PEITC drugs with the required target modulation. Our study highlights OS-related molecules regulated by functional MS variants that could be targeted by existing drugs as a supplement to the approved disease-modifying treatments.

SUBMITTER: Olla S

PROVIDER: S-EPMC8705550 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Combining Human Disease Genetics and Mouse Model Phenotypes towards Drug Repositioning for Parkinson's disease.

Project description:Parkinson's disease (PD) is a severe neurodegenerative disorder without effective treatments. Here, we present a novel drug repositioning approach to predict new drugs for PD leveraging both disease genetics and large amounts of mouse model phenotypes. First, we identified PD-specific mouse phenotypes using well-studied human disease genes. Then we searched all FDA-approved drugs for candidates that share similar mouse phenotype profiles with PD. We demonstrated the validity of our approach using drugs that have been approved for PD: 10 approved PD drugs were ranked within top 10% among 1197 candidates. In predicting novel PD drugs, our approach achieved a mean average precision of 0.24, which is significantly higher (p<e-11) than 0.16 for a state-of-art drug discovery approach based on mouse phenotype data. Comparison of gene expression profiles between PD and top-ranked drug candidates indicates that quetiapine has the potential to treat PD.

| S-EPMC4765695 | biostudies-literature

Enhancing the Promise of Drug Repositioning through Genetics.

Project description:The development of new drugs has become challenging as the necessary investments in time and money have increased while drug approval rates have decreased. A potential solution to this problem is drug repositioning which aims to use existing drugs to treat conditions for which they were not originally intended. One approach that may enhance the likelihood of success is to reposition drugs against a target that has a genetic basis. The multitude of genome-wide association studies (GWASs) conducted in recent years represents a large potential pool of novel targets for drug repositioning. Although trait-associated variants identified from GWAS still need to be causally linked to a target gene, recently developed functional genomic techniques, databases, and workflows are helping to remove this bottleneck. The pre-clinical validation of repositioning against these targets also needs to be carefully performed to ensure that findings are not confounded by off-target effects or limitations of the techniques used. Nevertheless, the approaches described in this review have the potential to provide a faster, cheaper and more certain route to clinical approval.

| S-EPMC5724196 | biostudies-literature

Progress in multiple sclerosis genetics.

Project description:A genetic component in the susceptibility to multiple sclerosis (MS) has long been known, and the first and major genetic risk factor, the HLA region, was identified in the 1970's. However, only with the advent of genome-wide association studies in the past five years did the list of risk factors for MS grow from 1 to over 50. In this review, we summarize the search for MS risk genes and the latest results. Comparison with data from other autoimmune and neurological diseases and from animal models indicates parallels and differences between diseases. We discuss how these translate into an improved understanding of disease mechanisms, and address current challenges such as genotype-phenotype correlations, functional mechanisms of risk variants and the missing heritability.

| S-EPMC3492804 | biostudies-literature

Lipopolysaccharide Binding Protein and Oxidative Stress in a Multiple Sclerosis Model.

Project description:Recent findings in experimental autoimmune encephalomyelitis (EAE) suggest that altering certain bacterial populations present in the gut may lead to a proinflammatory condition, that could result in the development of multiple sclerosis (MS). Also, Reactive Oxygen Species seem to be involved in the course of MS. In this study, it has been aimed to relate all these variables starting from an analysis of the lipopolysaccharide (LPS) and LPS-binding protein (LBP) with the determination of parameters related to oxidative stress in the blood, brain and spinal cord. For this purpose, samples obtained from EAE rats and relapsing-remitting (RRMS) MS patients were used. In addition, EAE rats were treated with Natalizumab, N-acetyl-cysteine and dimethyl fumarate. Natalizumab was also employed in RRMS. The results of this study revealed an improvement in the clinical symptoms of the EAE and MS with the treatments, as well as a reduction in the oxidative stress parameters and in LBP. Correlations between the clinical variables of the disease, i.e. oxidative damage and LBP, were established. Although the conclusions of this research are indeed relevant, further investigation would be necessary to establish the intrinsic mechanisms of the MS-oxidative stress-microbiota relationship.

| S-EPMC5233624 | biostudies-literature

Oxidative Stress Marker Aberrations in Multiple Sclerosis: A Meta-Analysis Study.

Project description:Oxidative stress has been suggested to play a key role in multiple sclerosis (MS), but clinical data on oxidative stress markers in MS patients were inconsistent. This study sought to quantitatively summarize the data of oxidative stress markers in the blood and cerebrospinal fluid (CSF) of patients with MS in the literature. We conducted a systematic search of PubMed and Web of Science and included studies if they provided data on the concentrations of oxidative stress markers in the peripheral blood and CSF of MS patients and healthy control (HC) subjects. The systematic search resulted in the inclusion of 31 studies with 2,001 MS patients and 2,212 HC subjects for meta-analysis. Random-effects meta-analysis demonstrated that patients with MS had significantly increased concentrations of blood oxidative stress markers compared with HC subjects for malondialdehyde (MDA; Hedges' g, 2.252; 95% CI, 1.080 to 3.424; p < 0.001) and lipid hydroperoxide by tert-butyl hydroperoxide-initiated chemiluminescence (CL-LOOH; Hedges' g, 0.383; 95% CI, 0.065 to 0.702; p = 0.018). In contrast, concentrations of albumin (Hedges' g, -1.036; CI, -1.679 to -0.394; p = 0.002) were significantly decreased in MS patients when compared with those in HC subjects. However, the other analyzed blood oxidative stress markers did not show significant differences between cases and controls. Furthermore, this meta-analysis showed significant association between CSF MDA and MS (Hedges' g, 3.275; 95% CI, 0.859 to 5.691; p = 0.008). Taken together, our results revealed increased blood and CSF MDA and decreased blood albumin levels in patients with MS, strengthening the clinical evidence of increased oxidative stress in MS.

| S-EPMC7479227 | biostudies-literature

Connecting genetics and gene expression data for target prioritisation and drug repositioning.

Project description:Developing new drugs continues to be a highly inefficient and costly business. By repurposing an existing compound for a different indication, drug repositioning offers an attractive alternative to traditional drug discovery. Most of these approaches work by matching transcriptional disease signatures to anti-correlated gene expression profiles of drug perturbations. Genome-wide association studies (GWASs) are of great interest to researchers in the pharmaceutical industry because drug programmes with supporting genetic evidence are more likely to successfully progress through the drug discovery pipeline. Here, we present a systematic approach to generate drug repositioning hypothesis based on disease genetics by mining public repositories of GWAS data and drug transcriptomic profiles. We find that genes genetically associated with a certain disease are more likely to be differentially expressed in the same disease (p-value?=?1.54e-17 and AUC?=?0.75) and that, in existing drug - disease combinations, genes significantly up- or down-regulated after drug treatment are enriched for genes genetically associated with that disease (p-value?=?1.1e-79 and AUC?=?0.64). Finally, we use this framework to generate and rank novel GWAS-driven drug repositioning predictions.

| S-EPMC5984374 | biostudies-literature

Genetics of oxidative stress in obesity.

Project description:Obesity is a multifactorial disease characterized by the excessive accumulation of fat in adipose tissue and peripheral organs. Its derived metabolic complications are mediated by the associated oxidative stress, inflammation and hypoxia. Oxidative stress is due to the excessive production of reactive oxygen species or diminished antioxidant defenses. Genetic variants, such as single nucleotide polymorphisms in antioxidant defense system genes, could alter the efficacy of these enzymes and, ultimately, the risk of obesity; thus, studies investigating the role of genetic variations in genes related to oxidative stress could be useful for better understanding the etiology of obesity and its metabolic complications. The lack of existing literature reviews in this field encouraged us to gather the findings from studies focusing on the impact of single nucleotide polymorphisms in antioxidant enzymes, oxidative stress-producing systems and transcription factor genes concerning their association with obesity risk and its phenotypes. In the future, the characterization of these single nucleotide polymorphisms (SNPs) in obese patients could contribute to the development of controlled antioxidant therapies potentially beneficial for the treatment of obesity-derived metabolic complications.

| S-EPMC3958901 | biostudies-literature

Disease phenotype prediction in multiple sclerosis

Project description:Progressive multiple sclerosis (PMS) is currently diagnosed retrospectively. Here, we work towards a set of biomarkers that could assist in early diagnosis of PMS. A selection of cerebrospinal fluid metabolites (n=15) was shown to differentiate between PMS and its preceding phenotype in an independent cohort (AUC=0.93). Complementing the classifier with conformal prediction showed that highly confident predictions could be made, and that three out of eight patients developing PMS within three years of sample collection were predicted as PMS at that time point. Finally, this methodology was applied to PMS patients part of a clinical trial for intrathecal treatment with rituximab. The methodology showed that 68% of the patients decreased their similarity to the PMS phenotype one year after treatment. In conclusion, the inclusion of confidence predictors contributes with more information compared to traditional machine learning, and this information is relevant for disease monitoring. Cohort 1 assays are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS1464' rel='noopener noreferrer' target='_blank'>MTBLS1464</a>.Cohort 2 assays are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS558' rel='noopener noreferrer' target='_blank'>MTBLS558</a>.

2023-05-31 | MTBLS1464 | MetaboLights

Multiple Sclerosis between Genetics and Infections: Human Endogenous Retroviruses in Monocytes and Macrophages.

Project description:The etiology of multiple sclerosis (MS) is still unknown, but there is strong evidence that genetic predisposition associated with environmental factors can trigger the disease. An estimated 30 million years ago, exogenous retroviruses are thought to have integrated themselves into human germ line cells, becoming part of human DNA and being transmitted over generations. Usually such human endogenous retroviruses (HERVs) are silenced or expressed at low levels, but in some pathological conditions, such as MS, their expression is higher than that in the healthy population. Three HERV families have been associated with MS: HERV-H, HERV-K, and HERV-W. The envelope protein of MS-associated retrovirus (MSRV) from the HERV-W family currently has the strongest evidence as a potential trigger for MS. In addition to expression in peripheral immune cells, MSRV is expressed in monocytes and microglia in central nervous system lesions of people with MS and, through the activation of toll-like receptor 4, it has been shown to drive the production of proinflammatory cytokines, reduction of myelin protein expression, and death of oligodendrocyte precursors. In conclusion, the association between HERVs and MS is well documented and a pathological role for MSRV in MS is plausible. Further studies are required to determine whether the presence of these HERVs is a cause or an effect of immune dysregulation in MS.

| S-EPMC4689809 | biostudies-literature

The genetics of multiple sclerosis in Latin America.

Project description:BACKGROUND:In today's globalised world, the heterogeneity of diseases such as multiple sclerosis has been studied since it has been suggested that ethnic differences, in conjunction with geographical and environmental factors, influence its incidence and prevalence. AIM:Based on this, an attempt has been made to identify the genetic factors that may confer risk or protection, not only for developing multiple sclerosis but also for determining the course of its evolution. RESULTS:In Latin America we have some data about this, which have been replicated in different populations in the entire region, with very different results compared with other regions, which could explain not only the different frequencies in some populations, such as Caucasians, but also the course of the disease and the response to actual treatments. However, in addition to these findings, other associated epigenetic mechanisms have also been found in our populations, such as levels of vitamin D, parasitic diseases, and indigenous populations. Therefore, the study of epigenetics plays a crucial role in understanding the physiopathology of multiple sclerosis. It must be studied in each population, especially in Latin America, due to its broad heterogeneity. CONCLUSION:It is very important to understand not only the genetic and external factors with these very specific effects in multiple sclerosis patients, but also the way they interact and are able to explain the frequency and some specific phenotypes of the disease in our populations besides the posibility to be a very specific treatment target.

| S-EPMC5617105 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data